Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold211
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1275876
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 151255 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:887587 original size:22 final size:22
Alignment explanation
Indices: 887559--887602 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
887549 GCTTTTTGGG
887559 GTTTTTTTTTTTTTTGTTTTTT
1 GTTTTTTTTTTTTTTGTTTTTT
887581 GTTTTTTTTTTTTTTGTTTTTT
1 GTTTTTTTTTTTTTTGTTTTTT
887603 TTTGGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (22 bp):
GTTTTTTTTTTTTTTGTTTTTT
Found at i:887612 original size:22 final size:22
Alignment explanation
Indices: 887565--887614 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
887555 TGGGGTTTTT
**
887565 TTTTTTTTTGTTTTTTGTTTTT
1 TTTTTTTTTGTTTTTTGTTTGC
887587 TTTTTTTTTGTTTTTT-TTTGGC
1 TTTTTTTTTGTTTTTTGTTT-GC
887609 TTTTTT
1 TTTTTT
887615 ATTTTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (22 bp):
TTTTTTTTTGTTTTTTGTTTGC
Found at i:887612 original size:25 final size:24
Alignment explanation
Indices: 887560--887629 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
887550 CTTTTTGGGG
* **
887560 TTTTTTTTTTTTTTGTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTGGC
887584 TTTTTTTTTTTTGTTTTTTTTTGGC
1 TTTTTTTTTTTT-TTTTTTTTTGGC
* **
887609 TTTTTTATTTTCATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
887630 ATGGTTAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 20 0.51
25 19 0.49
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.87
Consensus pattern (24 bp):
TTTTTTTTTTTTTTTTTTTTTGGC
Found at i:887614 original size:1 final size:1
Alignment explanation
Indices: 887560--887605 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
887550 CTTTTTGGGG
* * *
887560 TTTTTTTTTTTTTTGTTTTTTGTTTTTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
887606 GGCTTTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:896446 original size:2 final size:2
Alignment explanation
Indices: 896439--896483 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
896429 TTACTTATTT
* * * *
896439 TC TC TC TC TT TC TC TC TG TC TG TC TG TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
896481 TC T
1 TC T
896484 TGTATATTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.40, G:0.07, T:0.53
Consensus pattern (2 bp):
TC
Found at i:897425 original size:2 final size:2
Alignment explanation
Indices: 897418--897445 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
897408 NNNNNNNNNN
897418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
897446 AGGACGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:899417 original size:12 final size:12
Alignment explanation
Indices: 899390--899430 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
899380 GTCGAAAGCT
*
899390 AATCGGATGTGAA
1 AATCTGATG-GAA
899403 AATCTGATGGAA
1 AATCTGATGGAA
*
899415 AATCTGATAGAA
1 AATCTGATGGAA
899427 AATC
1 AATC
899431 GTATCGTCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (12 bp):
AATCTGATGGAA
Found at i:899541 original size:12 final size:12
Alignment explanation
Indices: 899524--899550 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
899514 ACCCTGTTCC
899524 GTCCGTCCGTCT
1 GTCCGTCCGTCT
899536 GTCCGTCCGTCT
1 GTCCGTCCGTCT
899548 GTC
1 GTC
899551 ACGTTTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.26, T:0.33
Consensus pattern (12 bp):
GTCCGTCCGTCT
Found at i:900320 original size:162 final size:164
Alignment explanation
Indices: 900115--900434 Score: 491
Period size: 164 Copynumber: 2.0 Consensus size: 164
900105 ATATATTTGC
*
900115 AGTAAGGTTTTAAAAATTTAAATTTCATCCAGGTAGTCAAATAGTAGCAGAAAATTGACATTTAT
1 AGTAAGGTTTTAAAAATTTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACATTTAT
* *
900180 CACTCCAAA-A-AAACATAGATCCGAGAACTCCTCTTAAAATTTAATGGATAGACACATCATACC
66 CACTCCAAATATAAACATAGATCCGAGAACCCCTCTTAAAATTAAATGGATAGACACATCATACC
* *
900243 TTGGGATATGATAGGGATTTTTCTATAGATGTGT
131 TTGGGATATGATAGGGACTGTTCTATAGATGTGT
** * * *
900277 AGTAAGGTTTTAAAAATTTTTATTTCGTTCAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTAT
1 AGTAAGGTTTTAAAAATTTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACATTTAT
* * ** *
900342 CACTCCAAATATAATCATAGATCCTAGAACCCCTCTTATGATTAAATGGATAGACACATCATATC
66 CACTCCAAATATAAACATAGATCCGAGAACCCCTCTTAAAATTAAATGGATAGACACATCATACC
900407 TTGGGATATGATAGGGACTGTTCTATAG
131 TTGGGATATGATAGGGACTGTTCTATAG
900435 TGCATTGTAG
Statistics
Matches: 141, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
162 68 0.48
163 1 0.01
164 72 0.51
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (164 bp):
AGTAAGGTTTTAAAAATTTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACATTTAT
CACTCCAAATATAAACATAGATCCGAGAACCCCTCTTAAAATTAAATGGATAGACACATCATACC
TTGGGATATGATAGGGACTGTTCTATAGATGTGT
Found at i:900456 original size:162 final size:162
Alignment explanation
Indices: 900115--900467 Score: 480
Period size: 162 Copynumber: 2.2 Consensus size: 162
900105 ATATATTTGC
*
900115 AGTAAGGTTTTAAAAATTTAAATTTCATCCAGGTAGTCAAATAGTAGCAGAAAATTGACATTTAT
1 AGTAAGGTTTTAAAAATTTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACATTTAT
* *
900180 CACTCCAAAAAAACATAGATCCGAGAACTCCTCTTAAAATTTAATGGATAGACACATCATACCTT
66 CACTCCAAAAAAACATAGATCCGAGAACCCCTCTTAAAATTAAATGGATAGACACATCATACCTT
* * **
900245 GGGATATGATAGGGATTTTTCTATAGATGTGT
131 GGGATATGATAGGGACTGTTCTATAGATGCAT
** * * *
900277 AGTAAGGTTTTAAAAATTTTTATTTCGTTCAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTAT
1 AGTAAGGTTTTAAAAATTTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACATTTAT
* * ** *
900342 CACTCCAAATATAATCATAGATCCTAGAACCCCTCTTATGATTAAATGGATAGACACATCATATC
66 CACTCCAAA-A-AAACATAGATCCGAGAACCCCTCTTAAAATTAAATGGATAGACACATCATACC
900407 TTGGGATATGATAGGGACTGTTCTATAG-TGCAT
129 TTGGGATATGATAGGGACTGTTCTATAGATGCAT
* *
900440 TGT-A-GTTTTGAAAAA-TTAAATTTAATCC
1 AGTAAGGTTTT-AAAAATTTAAATTTCATCC
900468 CGAGGCCCAT
Statistics
Matches: 165, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
161 13 0.08
162 74 0.45
163 6 0.04
164 72 0.44
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (162 bp):
AGTAAGGTTTTAAAAATTTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACATTTAT
CACTCCAAAAAAACATAGATCCGAGAACCCCTCTTAAAATTAAATGGATAGACACATCATACCTT
GGGATATGATAGGGACTGTTCTATAGATGCAT
Found at i:905423 original size:21 final size:21
Alignment explanation
Indices: 905399--905441 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
905389 TAATTAGATA
*
905399 TTGAATCTTGAATTTCGAATC
1 TTGAATCTCGAATTTCGAATC
*
905420 TTGAATCTCGTATTTCGAATC
1 TTGAATCTCGAATTTCGAATC
905441 T
1 T
905442 CGTATTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (21 bp):
TTGAATCTCGAATTTCGAATC
Found at i:905439 original size:14 final size:14
Alignment explanation
Indices: 905422--905467 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
905412 TTCGAATCTT
905422 GAATCTCGTATTTC
1 GAATCTCGTATTTC
*
905436 GAATCTCGTATTTT
1 GAATCTCGTATTTC
*
905450 GAATCTCGTATCTC
1 GAATCTCGTATTTC
905464 GAAT
1 GAAT
905468 GACCCTTCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (14 bp):
GAATCTCGTATTTC
Found at i:907488 original size:23 final size:23
Alignment explanation
Indices: 907458--907503 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
907448 TTTTCATTTT
*
907458 GAAAATTTATAGAGGTAAATCCA
1 GAAAATTTAGAGAGGTAAATCCA
907481 GAAAATTTAGAGAGGTAAATCCA
1 GAAAATTTAGAGAGGTAAATCCA
907504 TGTATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (23 bp):
GAAAATTTAGAGAGGTAAATCCA
Found at i:907812 original size:42 final size:42
Alignment explanation
Indices: 907753--907895 Score: 169
Period size: 42 Copynumber: 3.1 Consensus size: 42
907743 GTCGTAAGCC
907753 TTTTCAAAGTCTAGAAATAGTTGTATACCGTTTTAATTATTA
1 TTTTCAAAGTCTAGAAATAGTTGTATACCGTTTTAATTATTA
*
907795 TTTTCACAGTCTAGAAATAGTCTAGAAATAATAGTATACCGTTTTAATTATTA
1 TTTTCAAAGTCTAG-AA-A---TAG---T--T-GTATACCGTTTTAATTATTA
*
907848 TTTTCAAAGTCTAGAAATAGTAGTATACCGTTTTAATTATTA
1 TTTTCAAAGTCTAGAAATAGTTGTATACCGTTTTAATTATTA
907890 TTTTCA
1 TTTTCA
907896 CAAATTGCAA
Statistics
Matches: 87, Mismatches: 3, Indels: 22
0.78 0.03 0.20
Matches are distributed among these distances:
42 39 0.45
43 2 0.02
44 1 0.01
45 1 0.01
47 3 0.03
48 3 0.03
50 1 0.01
51 1 0.01
52 3 0.03
53 33 0.38
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.43
Consensus pattern (42 bp):
TTTTCAAAGTCTAGAAATAGTTGTATACCGTTTTAATTATTA
Found at i:907840 original size:53 final size:53
Alignment explanation
Indices: 907760--907868 Score: 191
Period size: 53 Copynumber: 2.1 Consensus size: 53
907750 GCCTTTTCAA
* * *
907760 AGTCTAGAAATAGTTGTATACCGTTTTAATTATTATTTTCACAGTCTAGAAAT
1 AGTCTAGAAATAATAGTATACCGTTTTAATTATTATTTTCAAAGTCTAGAAAT
907813 AGTCTAGAAATAATAGTATACCGTTTTAATTATTATTTTCAAAGTCTAGAAAT
1 AGTCTAGAAATAATAGTATACCGTTTTAATTATTATTTTCAAAGTCTAGAAAT
907866 AGT
1 AGT
907869 AGTATACCGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (53 bp):
AGTCTAGAAATAATAGTATACCGTTTTAATTATTATTTTCAAAGTCTAGAAAT
Found at i:914250 original size:21 final size:21
Alignment explanation
Indices: 914191--914274 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
914181 ATTTTTCAAT
*
914191 TAATTATGTCGACATGCAAGA
1 TAATTATGTCAACATGCAAGA
* * *
914212 TAAATATGTTGAA-TTGCAAGA
1 TAATTATG-TCAACATGCAAGA
* *
914233 TAGTTATGTCAACATGCAACA
1 TAATTATGTCAACATGCAAGA
* **
914254 TAACTATGTTGACATGCAAGA
1 TAATTATGTCAACATGCAAGA
914275 AAACTACAAT
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.06
21 42 0.89
22 2 0.04
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (21 bp):
TAATTATGTCAACATGCAAGA
Found at i:914262 original size:42 final size:42
Alignment explanation
Indices: 914194--914274 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
914184 TTTCAATTAA
* *
914194 TTATGTCGACATGCAAGATAAATATGTTGA-ATTGCAAGATAG
1 TTATGTCAACATGCAACATAAATATGTTGACA-TGCAAGATAG
*
914236 TTATGTCAACATGCAACATAACTATGTTGACATGCAAGA
1 TTATGTCAACATGCAACATAAATATGTTGACATGCAAGA
914275 AAACTACAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (42 bp):
TTATGTCAACATGCAACATAAATATGTTGACATGCAAGATAG
Found at i:914382 original size:21 final size:21
Alignment explanation
Indices: 914358--914429 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
914348 CTTCCTACCG
*
914358 ATGTCAACATCCAACTTCTTT
1 ATGTCAACATGCAACTTCTTT
*
914379 ATGTTAACATGCAACTTCTTT
1 ATGTCAACATGCAACTTCTTT
* *
914400 ATGTCGACATGCAACTT-ATT
1 ATGTCAACATGCAACTTCTTT
*
914420 ATGTCGACAT
1 ATGTCAACAT
914430 TTTAGTTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 12 0.26
21 34 0.74
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (21 bp):
ATGTCAACATGCAACTTCTTT
Found at i:914482 original size:21 final size:20
Alignment explanation
Indices: 914457--914538 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 20
914447 GCAAGATAAA
914457 TATGTTGACATGCAACATAT
1 TATGTTGACATGCAACATAT
*
914477 TCATGTCGACATGCAA-ATTAGT
1 T-ATGTTGACATGCAACA-TA-T
* *
914499 TATGTTGACATACAACTTA-
1 TATGTTGACATGCAACATAT
*
914518 TAAGTTG-CATGTCAACATAT
1 TATGTTGACATG-CAACATAT
914538 T
1 T
914539 CATCTCGCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 3 0.06
19 12 0.24
20 3 0.06
21 29 0.59
22 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (20 bp):
TATGTTGACATGCAACATAT
Found at i:914548 original size:21 final size:21
Alignment explanation
Indices: 914524--914599 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
914514 CTTATAAGTT
914524 GCATGTCAACATATTCATCTC
1 GCATGTCAACATATTCATCTC
* *
914545 GCATGT-ATACATAACTAAGT-T-
1 GCATGTCA-ACAT-ATTCA-TCTC
914566 GCATGTCAACATATTCATCTC
1 GCATGTCAACATATTCATCTC
* *
914587 GTATATCAACATA
1 GCATGTCAACATA
914600 AAAAAGTTGC
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 1 0.02
20 5 0.12
21 31 0.72
22 5 0.12
23 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (21 bp):
GCATGTCAACATATTCATCTC
Found at i:914568 original size:42 final size:42
Alignment explanation
Indices: 914517--914613 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
914507 CATACAACTT
*
914517 ATAAGTTGCATGTCAACATATTCATCTCGCATGT-ATACATAA
1 ATAAGTTGCATGTCAACATATTCATCTCGCATATCA-ACATAA
* *
914559 CTAAGTTGCATGTCAACATATTCATCTCGTATATCAACATAA
1 ATAAGTTGCATGTCAACATATTCATCTCGCATATCAACATAA
*
914601 AAAAGTTGCATGT
1 ATAAGTTGCATGT
914614 TGACATAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
42 48 0.98
43 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (42 bp):
ATAAGTTGCATGTCAACATATTCATCTCGCATATCAACATAA
Found at i:914641 original size:42 final size:42
Alignment explanation
Indices: 914595--914729 Score: 155
Period size: 42 Copynumber: 3.2 Consensus size: 42
914585 TCGTATATCA
914595 ACATAAAAAAGTTGCATGTTGACATAAATAAGTTGCATGTCG
1 ACATAAAAAAGTTGCATGTTGACATAAATAAGTTGCATGTCG
* **
914637 ACATAAATAAGTTGCATGTTGACATAAATAAGTTTTATGTC-
1 ACATAAAAAAGTTGCATGTTGACATAAATAAGTTGCATGTCG
*** ** * * *
914678 AGCATATTTATCTTGCATGTTAACGTAAATTAGTTGCATGTCG
1 A-CATAAAAAAGTTGCATGTTGACATAAATAAGTTGCATGTCG
914721 ACATAAAAA
1 ACATAAAAA
914730 GATACCATCT
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 74 0.97
43 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (42 bp):
ACATAAAAAAGTTGCATGTTGACATAAATAAGTTGCATGTCG
Found at i:914676 original size:21 final size:21
Alignment explanation
Indices: 914595--914670 Score: 134
Period size: 21 Copynumber: 3.6 Consensus size: 21
914585 TCGTATATCA
*
914595 ACATAAAAAAGTTGCATGTTG
1 ACATAAATAAGTTGCATGTTG
*
914616 ACATAAATAAGTTGCATGTCG
1 ACATAAATAAGTTGCATGTTG
914637 ACATAAATAAGTTGCATGTTG
1 ACATAAATAAGTTGCATGTTG
914658 ACATAAATAAGTT
1 ACATAAATAAGTT
914671 TTATGTCAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (21 bp):
ACATAAATAAGTTGCATGTTG
Found at i:914683 original size:21 final size:21
Alignment explanation
Indices: 914595--914727 Score: 133
Period size: 21 Copynumber: 6.3 Consensus size: 21
914585 TCGTATATCA
* *
914595 ACATAAAAAAGTTGCATGTTG
1 ACATAAATAAGTTGCATGTCG
914616 ACATAAATAAGTTGCATGTCG
1 ACATAAATAAGTTGCATGTCG
*
914637 ACATAAATAAGTTGCATGTTG
1 ACATAAATAAGTTGCATGTCG
**
914658 ACATAAATAAGTTTTATGTC-
1 ACATAAATAAGTTGCATGTCG
** ** **
914678 AGCATATTTATCTTGCATGTTA
1 A-CATAAATAAGTTGCATGTCG
* *
914700 ACGTAAATTAGTTGCATGTCG
1 ACATAAATAAGTTGCATGTCG
914721 ACATAAA
1 ACATAAA
914728 AAGATACCAT
Statistics
Matches: 88, Mismatches: 22, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
20 1 0.01
21 86 0.98
22 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (21 bp):
ACATAAATAAGTTGCATGTCG
Found at i:914819 original size:21 final size:21
Alignment explanation
Indices: 914788--914866 Score: 122
Period size: 21 Copynumber: 3.8 Consensus size: 21
914778 ATCTGATTCC
*
914788 AATTTTCTTGCATGTCAACAT
1 AATTATCTTGCATGTCAACAT
* *
914809 AATTATGTTGCATGTTAACAT
1 AATTATCTTGCATGTCAACAT
914830 AATTATCTTGCATGTCAACAT
1 AATTATCTTGCATGTCAACAT
*
914851 ATTTATCTTGCATGTC
1 AATTATCTTGCATGTC
914867 GACTTATCTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.43
Consensus pattern (21 bp):
AATTATCTTGCATGTCAACAT
Found at i:915884 original size:13 final size:13
Alignment explanation
Indices: 915866--915894 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
915856 ACACATTATA
915866 ATTCTCACTAAGC
1 ATTCTCACTAAGC
915879 ATTCTCACTAAGC
1 ATTCTCACTAAGC
915892 ATT
1 ATT
915895 TCAGAGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (13 bp):
ATTCTCACTAAGC
Found at i:919993 original size:45 final size:44
Alignment explanation
Indices: 919904--919994 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 44
919894 ATAATTTTTT
*
919904 TTACAATATGAAATGAATTATCCGTCTTACCGTCGGGGGGCTGA
1 TTACAATATGAAATGAATTATCCGTCTTACCGTCGGGGGCCTGA
*
919948 TNTACAATATGAAATGAATTATCCGTCTTACCGTCGGGTGCCTGA
1 T-TACAATATGAAATGAATTATCCGTCTTACCGTCGGGGGCCTGA
919993 TT
1 TT
919995 TCCTCTTGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 2 0.05
45 42 0.95
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (44 bp):
TTACAATATGAAATGAATTATCCGTCTTACCGTCGGGGGCCTGA
Found at i:921857 original size:45 final size:45
Alignment explanation
Indices: 921639--921836 Score: 342
Period size: 45 Copynumber: 4.4 Consensus size: 45
921629 AAATTCAATA
* * *
921639 CTGTCCCGTCCATCTCTTACACTGTCCTATCCTTTACACCCTGTT
1 CTGTGCCGTCCATTTCTTACACTGTCATATCCTTTACACCCTGTT
921684 CTGTGCCGTCCATTTCTTACACTGTCATATCCTTTACACCCTGTT
1 CTGTGCCGTCCATTTCTTACACTGTCATATCCTTTACACCCTGTT
*
921729 CTGTGCCGTCCATTTCTTACACTCTCATATCCTTTACACCCTGTT
1 CTGTGCCGTCCATTTCTTACACTGTCATATCCTTTACACCCTGTT
921774 CTGTGCCGTCCATTTCTTACACTGTCATATCCTTTACACCCTGTT
1 CTGTGCCGTCCATTTCTTACACTGTCATATCCTTTACACCCTGTT
* *
921819 CTGTCCCGTCCATCTCTT
1 CTGTGCCGTCCATTTCTT
921837 TTACTGTCCT
Statistics
Matches: 146, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 146 1.00
ACGTcount: A:0.14, C:0.36, G:0.10, T:0.39
Consensus pattern (45 bp):
CTGTGCCGTCCATTTCTTACACTGTCATATCCTTTACACCCTGTT
Found at i:929017 original size:45 final size:45
Alignment explanation
Indices: 928953--931046 Score: 1989
Period size: 45 Copynumber: 46.6 Consensus size: 45
928943 AAAAAAGTTG
* *
928953 TAGATTATAACGTGTACCAGTGCCTTACTAACCGTATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* **
928998 TAGATCATAACGTGTACCAGTGCCGTACTAACCATATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* *
929043 TAGATTATAACGTGTACCAGTGCCTTACTAACCGTATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* **
929088 TAGATCATAACGTGTACCAGTGCCGTACTAACCATATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* **
929133 TAGATTATAACGTGTACCAGTGCCTTACTAACCATATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * *
929178 TAGATTATAACGTGTACCAGTGCCTTACTAACCGTATTGCCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * * * * *
929223 TAGATTATGACGTGTACCAATGCTGTATTAACCGCATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * * **
929268 TAGATTGTAACGTGTACAAGTGCCGTACTAACCGTATTGTCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * *
929313 TAGATTATAACGTGTACCAATGCTGTACTAACCGTATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* ** * * *
929358 TAGATTATAACGTGTATCAGAACCGTAC-AAATCGTATCACCATAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACT-GTATTACCGTAA
* * ***
929403 TTGATTATAACGTGTACTAGTGCCGTACTAACTGTAATT-TTATAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGT-ATTACCGTAA
* * * ***
929448 TAGATTATAACGTGCACTAGTGCTGTACTAACTGTAATT-TTATAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGT-ATTACCGTAA
* * ***
929493 TAGATTATAACGTGTACTAGTGCCGTACTAAATGTAATT-TTATAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGT-ATTACCGTAA
* * * * * *
929538 TAGAATATAACGTCTACCAATGCCGTACTAACTGAATCACTGTTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCG-TAA
* * * * * *
929584 -AGATTATAATGTGAACCAGTTCTGTACTAAGTGTATTATCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * **
929628 TGGATTATAAAGTGTACCAGAACCGTACTAACTGTATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * *
929673 TAGATCATAACGTGTACCAGTGCC-TACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
** * * * *
929717 TAGATTATAACGTGTACCAGAACTGTACTAGCTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
** * * * *
929762 TAGATTATAACGTGTACCAGAACTGTACTAGCTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* ** * * *
929807 TAGATTATAAAGTGTACCAGAACCGTACTAACTGAATCAACGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * ** * * *
929852 TAGATAATAACGTTTACCAGAACCATACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * ** * * *
929897 TTGATTATAACGTTTACCAGAACCATACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * ** * * *
929942 TAGATTATTACGTTTACCAGAACCATACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* *
929987 TAGATTATAACGTGTACCAGTGTCGTACTAACCGTATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* **
930032 TAGATCATAACGTGTACCAGTGCCGTACTAACCATATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * *
930077 TAGATTATAACGTGTACCAGTGCCTTACTAACCGTATTGCCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * * * *
930122 TAGATTATGACGTGTACCAATGCTGTACTAACCGCATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * * **
930167 TAGATTGTAACGTGTACAAGTGCCGTACTAACCGTATTGTCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * *
930212 TAGATTATAACGTGTACCAATGCTGTACTAACCGTATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* ** * *
930257 TAGATTATAACGTGTATCAGAACCGTAC-AAATCGTATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACT-GTATTACCGTAA
* * * ***
930302 TTGATTATAACGTGTACTAGTGCCGTACCAACTGTAATT-TTATAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGT-ATTACCGTAA
* * * ***
930347 TAGATTATAACGTGCACTAGTGCTGTACTAACTGTAATT-TTATAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGT-ATTACCGTAA
* * ***
930392 TAGATTATAACGTGTACTAGTGCCGTACTAAATGTAATT-TTATAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGT-ATTACCGTAA
* * * * *
930437 TAGATTATAACGTCTACCAATGCCGTACTAACTGAATCACTGTTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCG-TAA
* * * * * *
930483 -AGATTATAATGTGAACCAGTTCTGTACTAAGTGTATTATCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * **
930527 TGGATTATAAAGTGTACCAGAACCGTACTAACTGTATTACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * *
930572 TAGATCATAACGTGTACCAGTGCC-TACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
** * * * *
930616 TAGATTATAACGTGTACCAGAACTGTACTAGCTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
** * * * *
930661 TAGATTATAACGTGTACCAGAACTGTACTAGCTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* ** * * *
930706 TAGATTATAAAGTGTACCAGAACCGTACTAACTGAATCAACGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * ** * * *
930751 TAGATAATAACGTTTACCAGAACCATACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* ** * * *
930796 TAGATTATAACGTTTACCAGAACCATACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* ** * * *
930841 TAGATTATAACGTTTACCAGAACCATACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
** ** * * *
930886 TAGATTCGAACGTGTACCAGAACCATACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * *
930931 TAGATTATAACGTGTACTAGTGCCGTACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
** * *
930976 TAGATTATAACGTGTACCAGAACCGTACTAACTGAATCACCGTAA
1 TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
* * *
931021 TAGATTCTAACGTGTACTATTGCCGT
1 TAGATTATAACGTGTACCAGTGCCGT
931047 TATATCGTAA
Statistics
Matches: 1795, Mismatches: 240, Indels: 28
0.87 0.12 0.01
Matches are distributed among these distances:
44 90 0.05
45 1689 0.94
46 16 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (45 bp):
TAGATTATAACGTGTACCAGTGCCGTACTAACTGTATTACCGTAA
Found at i:931095 original size:36 final size:36
Alignment explanation
Indices: 931014--931100 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
931004 TAACTGAATC
* *
931014 ACCGTAATAGATTCTAACGTGTACTATTGCCGTTAT
1 ACCGTAATAGATTATAACGTGTACTATTGCCCTTAT
* *
931050 ATCGTAATAGATTATAACGTGTACT-TGTGCCCTTTT
1 ACCGTAATAGATTATAACGTGTACTAT-TGCCCTTAT
*
931086 ACCGAAATAGATTAT
1 ACCGTAATAGATTAT
931101 GATGTTTACC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
35 1 0.02
36 43 0.98
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (36 bp):
ACCGTAATAGATTATAACGTGTACTATTGCCCTTAT
Found at i:931402 original size:40 final size:40
Alignment explanation
Indices: 931358--931579 Score: 381
Period size: 40 Copynumber: 5.5 Consensus size: 40
931348 ACTAACCCTG
931358 CTACCGTAATAGATTATTACGTGTACCATCCAGTACCATC
1 CTACCGTAATAGATTATTACGTGTACCATCCAGTACCATC
* *
931398 CTACCGTAATAGATTATTACGTGTTCCATCTAGTACCATC
1 CTACCGTAATAGATTATTACGTGTACCATCCAGTACCATC
931438 CTACCGTAATAGATTATTACGTGTACCATCCAGTACCATC
1 CTACCGTAATAGATTATTACGTGTACCATCCAGTACCATC
* *
931478 CTACCGTAATAGATTATTACGTGTACCATCTAGTACTATC
1 CTACCGTAATAGATTATTACGTGTACCATCCAGTACCATC
*
931518 CTATCGTAATAGATTATTACGTGTACCATCCAGTACCATC
1 CTACCGTAATAGATTATTACGTGTACCATCCAGTACCATC
* *
931558 CTACCGTAATATATTATAACGT
1 CTACCGTAATAGATTATTACGT
931580 ATGCCGTATA
Statistics
Matches: 170, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 170 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (40 bp):
CTACCGTAATAGATTATTACGTGTACCATCCAGTACCATC
Found at i:940919 original size:56 final size:56
Alignment explanation
Indices: 940832--940940 Score: 175
Period size: 56 Copynumber: 1.9 Consensus size: 56
940822 ATCACAGTTG
*
940832 ATTGATATAATCTTAGACTAATTGACTGTTATATCATACTCTGTGGTAAGTCCCCCC
1 ATTGATATAATCTTAGACTAATTGACTGTTATATCATACTCTGTGCT-AGTCCCCCC
* *
940889 ATTGATATAGT-TTGGACTAATTGACTGTTATATCATACTCTGTGCTAGTCCC
1 ATTGATATAATCTTAGACTAATTGACTGTTATATCATACTCTGTGCTAGTCCC
940941 TCTATCAACT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
55 6 0.12
56 33 0.67
57 10 0.20
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (56 bp):
ATTGATATAATCTTAGACTAATTGACTGTTATATCATACTCTGTGCTAGTCCCCCC
Found at i:959944 original size:31 final size:31
Alignment explanation
Indices: 959909--960091 Score: 106
Period size: 31 Copynumber: 6.0 Consensus size: 31
959899 TTTCAGTTAT
* * *
959909 AACTACACTTTAGAGGTGAGATTTTCACTAC
1 AACTAAACTTGAGAGGTGAGATTTTCACTAA
* *
959940 AACTAAAGTTGAGAGGTGAG--TTCCACTAA
1 AACTAAACTTGAGAGGTGAGATTTTCACTAA
* * *
959969 AACTAAAGTTGAGAGGTGAGATTATCACCATA
1 AACTAAACTTGAGAGGTGAGATTTTCACTA-A
* ** * * *
960001 ATCT-AACTCAAGAGGTGAGATTATAACTATT
1 AACTAAACTTGAGAGGTGAGATTTTCACTA-A
* ** *
960032 ACCT-TCCTTGAGAGGTGAGATTATCACTATA
1 AACTAAACTTGAGAGGTGAGATTTTCACTA-A
** * *
960063 GCCT-TACTTGAGAGGTGAGATTATCACTA
1 AACTAAACTTGAGAGGTGAGATTTTCACTA
960092 TAGCATTGAG
Statistics
Matches: 125, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
29 27 0.22
31 94 0.75
32 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (31 bp):
AACTAAACTTGAGAGGTGAGATTTTCACTAA
Found at i:959975 original size:29 final size:30
Alignment explanation
Indices: 959920--959991 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
959910 ACTACACTTT
* *
959920 AGAGGTGAGATTTTCACTACAACTAAAGTTG
1 AGAGGTGAGA-TTCCACTAAAACTAAAGTTG
959951 AGAGGTGAG-TTCCACTAAAACTAAAGTTG
1 AGAGGTGAGATTCCACTAAAACTAAAGTTG
959980 AGAGGTGAGATT
1 AGAGGTGAGATT
959992 ATCACCATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 27 0.71
30 2 0.05
31 9 0.24
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.26
Consensus pattern (30 bp):
AGAGGTGAGATTCCACTAAAACTAAAGTTG
Found at i:960092 original size:31 final size:31
Alignment explanation
Indices: 959977--960095 Score: 150
Period size: 31 Copynumber: 3.8 Consensus size: 31
959967 AAAACTAAAG
* ** *
959977 TTGAGAGGTGAGATTATCACCATAATCTAAC
1 TTGAGAGGTGAGATTATCACTATAGCCTTAC
** * *
960008 TCAAGAGGTGAGATTATAACTATTA-CCTTCC
1 TTGAGAGGTGAGATTATCACTA-TAGCCTTAC
960039 TTGAGAGGTGAGATTATCACTATAGCCTTAC
1 TTGAGAGGTGAGATTATCACTATAGCCTTAC
960070 TTGAGAGGTGAGATTATCACTATAGC
1 TTGAGAGGTGAGATTATCACTATAGC
960096 ATTGAGTTGC
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
30 2 0.03
31 71 0.95
32 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (31 bp):
TTGAGAGGTGAGATTATCACTATAGCCTTAC
Found at i:960264 original size:39 final size:39
Alignment explanation
Indices: 960209--960734 Score: 626
Period size: 39 Copynumber: 13.2 Consensus size: 39
960199 AATCCCTTTA
* *
960209 CCTGTGAAGCTT-TATAGCCTTA-TTAGAGTGACTAGCTGT
1 CCTGTGAA-CTTCTATAGCCTTACTT-GAGTGGCTAGCTGC
* * *
960248 CCTGTGAACTTCTATAGCCTTAAGTGGCTAGCTCCCCCGCTAGCTGC
1 CCTGTGAACTTCTATAGCCTT-ACTTG--AG-T----GGCTAGCTGC
*
960295 CTTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
1 CCTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
* * *
960334 CCTGTGAAGTTTTAAAGCCTTACTTGAGTGGCTAGCTGC
1 CCTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
*
960373 CCTGTGAACTTCTAAAGCCTTACTTGAGTGGCTAGCTGC
1 CCTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
* *
960412 CCTGTGAACTTCTATAGTCTTACTTGAGTGCCTAGCTGC
1 CCTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
*
960451 CCTGTGAACTTCTGTAGCCTTACTTGAGTGGCTAGCTGC
1 CCTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
*
960490 CCTGTGAACTTCTATAGCCTTAATTGAGTGGCTAGCTGC
1 CCTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
* * * *
960529 CCTGTGAAGTTTTAAAGCCTTAATTGAGTGGCTAGCTGC
1 CCTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
* *
960568 CCTGTGAAGTTTTATAGCCTTACTTGAGTGGCTAGCTGC
1 CCTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
* *
960607 CCTGTGAAGTTTTATAGCCTTACTTGAGTGGCTAGCTGC
1 CCTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
* * * *
960646 CCTGTGAAGTTTTAT-TCACTTACTTTAGTGGCTAGCTGC
1 CCTGTGAACTTCTATAGC-CTTACTTGAGTGGCTAGCTGC
* * * * *
960685 CTAGCTGTGAAGTTTTATTGACTTACTTGAGTGGCTAGCTGT
1 C---CTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
960727 CCTGTGAA
1 CCTGTGAA
960735 GCAGTAGAAA
Statistics
Matches: 439, Mismatches: 33, Indels: 30
0.87 0.07 0.06
Matches are distributed among these distances:
38 4 0.01
39 362 0.82
40 2 0.00
41 1 0.00
42 36 0.08
43 2 0.00
44 2 0.00
46 3 0.01
47 27 0.06
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (39 bp):
CCTGTGAACTTCTATAGCCTTACTTGAGTGGCTAGCTGC
Found at i:964671 original size:17 final size:17
Alignment explanation
Indices: 964637--964845 Score: 267
Period size: 17 Copynumber: 12.7 Consensus size: 17
964627 TTCTGTCCTT
*
964637 TCCATTCTC-CTATCTC
1 TCCATTCTCTCTTTCTC
964653 TCCATTCTCTCTTTCTC
1 TCCATTCTCTCTTTCTC
*
964670 TCCATTCTCTCTTTCTT
1 TCCATTCTCTCTTTCTC
*
964687 TACCATTC-C-CTTTCTT
1 T-CCATTCTCTCTTTCTC
*
964703 TACCATTCCCTCTTTCTC
1 T-CCATTCTCTCTTTCTC
964721 TCCA-T-TCTCTTTCTC
1 TCCATTCTCTCTTTCTC
964736 TCCATT-TCCTCTTTCTC
1 TCCATTCT-CTCTTTCTC
*
964753 TCCATTCCCTCTTTCTC
1 TCCATTCTCTCTTTCTC
964770 TCCATTCTCTCTTTCTC
1 TCCATTCTCTCTTTCTC
*
964787 TCCATTCCCTCTTTCTC
1 TCCATTCTCTCTTTCTC
964804 TCCA-T-TCTC--TCTC
1 TCCATTCTCTCTTTCTC
964817 TCCATTCTCTCTTTCTC
1 TCCATTCTCTCTTTCTC
964834 TCCATTCTCTCT
1 TCCATTCTCTCT
964846 GTTTCTATGT
Statistics
Matches: 174, Mismatches: 8, Indels: 21
0.86 0.04 0.10
Matches are distributed among these distances:
13 8 0.05
14 1 0.01
15 20 0.11
16 28 0.16
17 104 0.60
18 13 0.07
ACGTcount: A:0.08, C:0.42, G:0.00, T:0.50
Consensus pattern (17 bp):
TCCATTCTCTCTTTCTC
Found at i:964851 original size:83 final size:83
Alignment explanation
Indices: 964637--964851 Score: 298
Period size: 83 Copynumber: 2.6 Consensus size: 83
964627 TTCTGTCCTT
*
964637 TCCATTCTCCTATCTCTCCATTCTCTCTTTCTCTCCATTCTCTC-TTTCTTTACCATTCCCTTTC
1 TCCATTCT-CT-TCTCTCCATTCTCTCTTTCTCTCCATTCTCTCTTTTCTCTACCATTCCCTTTC
*
964701 TTTACCATTCCCTCTTTCTC
64 TCTACCATTCCCTCTTTCTC
*
964721 TCCATTCTCTTTCTCTCCATT-TCCTCTTTCTCTCCATTCCCTC-TTTCTCT-CCATTCTCTCTT
1 TCCATTCTC-TTCTCTCCATTCT-CTCTTTCTCTCCATTCTCTCTTTTCTCTACCATTC-C-CTT
964783 TCTCT-CCATTCCCTCTTTCTC
62 TCTCTACCATTCCCTCTTTCTC
964804 TCCATTCTC-TCTCTCCATTCTCTCTTTCTCTCCATTCTCTCTGTTTCT
1 TCCATTCTCTTCTCTCCATTCTCTCTTTCTCTCCATTCTCTCT-TTTCT
964852 ATGTCTGCCC
Statistics
Matches: 120, Mismatches: 4, Indels: 15
0.86 0.03 0.11
Matches are distributed among these distances:
81 29 0.24
82 8 0.07
83 67 0.56
84 16 0.13
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.51
Consensus pattern (83 bp):
TCCATTCTCTTCTCTCCATTCTCTCTTTCTCTCCATTCTCTCTTTTCTCTACCATTCCCTTTCTC
TACCATTCCCTCTTTCTC
Found at i:967066 original size:24 final size:24
Alignment explanation
Indices: 967046--967133 Score: 158
Period size: 24 Copynumber: 3.7 Consensus size: 24
967036 TCATACAACA
967046 CATTAGCTTACCTGTTCTACAATT
1 CATTAGCTTACCTGTTCTACAATT
*
967070 CATTAGCTTACCTGTTTTACAATT
1 CATTAGCTTACCTGTTCTACAATT
*
967094 CATTAGCTTACCTGTTTTACAATT
1 CATTAGCTTACCTGTTCTACAATT
967118 CATTAGCTTACCTGTT
1 CATTAGCTTACCTGTT
967134 GTACTGCATG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (24 bp):
CATTAGCTTACCTGTTCTACAATT
Found at i:972994 original size:5 final size:5
Alignment explanation
Indices: 972984--973027 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
972974 ATCTCTTCAT
* *
972984 AATTC AATTC AATTC AATTC AATTC AATTC AATTG AATTG AATT
1 AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATT
973028 TCTTTATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (5 bp):
AATTC
Found at i:973104 original size:18 final size:18
Alignment explanation
Indices: 973077--973117 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
973067 AAGACTGTTG
* *
973077 ACATACAACATCCAATGA
1 ACATAAAACATCCAATAA
*
973095 ACATAAAACATTCAATAA
1 ACATAAAACATCCAATAA
973113 ACATA
1 ACATA
973118 TACAAGAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.22, G:0.02, T:0.20
Consensus pattern (18 bp):
ACATAAAACATCCAATAA
Found at i:976923 original size:2 final size:2
Alignment explanation
Indices: 976916--976965 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
976906 ACCACTGAAA
976916 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
976958 TC TC TC TC
1 TC TC TC TC
976966 GAGATCGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:979665 original size:2 final size:2
Alignment explanation
Indices: 979658--979696 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
979648 GTGATTGTTT
*
979658 TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
979697 TAAAAAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:979992 original size:86 final size:86
Alignment explanation
Indices: 979847--980017 Score: 297
Period size: 86 Copynumber: 2.0 Consensus size: 86
979837 TGTCCATCTC
* *
979847 TGACACTATTTTAACAAGGTGCCTGTACTTACAGGGTCTTGTACTACTGCCACAGGGGGTACAGG
1 TGACACTATTTTAACAAGGCGCCTGTACTTACAGGGTCCTGTACTACTGCCACAGGGGGTACAGG
979912 TTTATCCTCCTGTGTTTCTTT
66 TTTATCCTCCTGTGTTTCTTT
* * *
979933 TGACACTATTTTAACTAGGCGCCTGTACTTACAGGGTCCTGTACTACTGCCCCGGGGGGTACAGG
1 TGACACTATTTTAACAAGGCGCCTGTACTTACAGGGTCCTGTACTACTGCCACAGGGGGTACAGG
979998 TTTATCCTCCTGTGTTTCTT
66 TTTATCCTCCTGTGTTTCTT
980018 GTGTCGAACT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (86 bp):
TGACACTATTTTAACAAGGCGCCTGTACTTACAGGGTCCTGTACTACTGCCACAGGGGGTACAGG
TTTATCCTCCTGTGTTTCTTT
Found at i:980295 original size:29 final size:29
Alignment explanation
Indices: 980260--980318 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
980250 CTCACTGAAC
980260 ATCATTAATTATCCTACAGGTTAATATCA
1 ATCATTAATTATCCTACAGGTTAATATCA
*
980289 ATCATTAATTATCCTACCGGTTAATATCA
1 ATCATTAATTATCCTACAGGTTAATATCA
980318 A
1 A
980319 CCATAATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (29 bp):
ATCATTAATTATCCTACAGGTTAATATCA
Found at i:983567 original size:52 final size:52
Alignment explanation
Indices: 983492--983687 Score: 302
Period size: 52 Copynumber: 3.8 Consensus size: 52
983482 TAAGGAGAGT
* *
983492 TCAAAGGGAGGACACAGTTAATATCATACCTCTGTCTTTTAGCTCCCTGTTA
1 TCAAAGGGAGAACACAGTAAATATCATACCTCTGTCTTTTAGCTCCCTGTTA
* * * *
983544 TCAAAGGGAGAACACTGTAAATATTATACCCCTGCCTTTTAGCTCCCTGTTA
1 TCAAAGGGAGAACACAGTAAATATCATACCTCTGTCTTTTAGCTCCCTGTTA
* * *
983596 TCAAAGGGAGGACACTGTTAATATCATACCTCTGTCTTTTAGCTCCCTGTTA
1 TCAAAGGGAGAACACAGTAAATATCATACCTCTGTCTTTTAGCTCCCTGTTA
*
983648 TCAAAGGGAGAACACAGTAAATATTATACCTCTGTCTTTT
1 TCAAAGGGAGAACACAGTAAATATCATACCTCTGTCTTTT
983688 GATGTAATGT
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 129 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (52 bp):
TCAAAGGGAGAACACAGTAAATATCATACCTCTGTCTTTTAGCTCCCTGTTA
Found at i:983672 original size:104 final size:104
Alignment explanation
Indices: 983492--983687 Score: 356
Period size: 104 Copynumber: 1.9 Consensus size: 104
983482 TAAGGAGAGT
983492 TCAAAGGGAGGACACAGTTAATATCATACCTCTGTCTTTTAGCTCCCTGTTATCAAAGGGAGAAC
1 TCAAAGGGAGGACACAGTTAATATCATACCTCTGTCTTTTAGCTCCCTGTTATCAAAGGGAGAAC
*
983557 ACTGTAAATATTATACCCCTGCCTTTTAGCTCCCTGTTA
66 ACAGTAAATATTATACCCCTGCCTTTTAGCTCCCTGTTA
*
983596 TCAAAGGGAGGACACTGTTAATATCATACCTCTGTCTTTTAGCTCCCTGTTATCAAAGGGAGAAC
1 TCAAAGGGAGGACACAGTTAATATCATACCTCTGTCTTTTAGCTCCCTGTTATCAAAGGGAGAAC
* *
983661 ACAGTAAATATTATACCTCTGTCTTTT
66 ACAGTAAATATTATACCCCTGCCTTTT
983688 GATGTAATGT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 88 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (104 bp):
TCAAAGGGAGGACACAGTTAATATCATACCTCTGTCTTTTAGCTCCCTGTTATCAAAGGGAGAAC
ACAGTAAATATTATACCCCTGCCTTTTAGCTCCCTGTTA
Found at i:984111 original size:51 final size:49
Alignment explanation
Indices: 983959--984287 Score: 493
Period size: 51 Copynumber: 6.7 Consensus size: 49
983949 TTAAATAGAC
* * * * *
983959 ACCTTTCAGGGAGATTACCGAGTACACTTCC-TCTTTCAGCTAATATGT
1 ACCTTACAGAGAGATTACTGAGTACACTTCCTTCTTCCAGCTAACATGT
* *
984007 ACCTTTCAGGGAGATTACTGAGTACACTTCC-TCTTCCAGCTAACATGT
1 ACCTTACAGAGAGATTACTGAGTACACTTCCTTCTTCCAGCTAACATGT
*
984055 ACCTTACAGAGAGATTACTGAGTACACTTCCTGATCTTCCAGCTATCATGT
1 ACCTTACAGAGAGATTACTGAGTACACTTCCT--TCTTCCAGCTAACATGT
984106 ACCTTACAGAGAGATTACTGAGTACACTTCCTGATCTTCCAGCTAACATGT
1 ACCTTACAGAGAGATTACTGAGTACACTTCCT--TCTTCCAGCTAACATGT
* *
984157 ACCTTACAGAGAGATTACTGAGTACACTTCCTGATCTTTCAGCTAACATAT
1 ACCTTACAGAGAGATTACTGAGTACACTTCCT--TCTTCCAGCTAACATGT
984208 ACCTTACAGAGAGATTACTGAGTACACTTCC-TCTTCCAGCTAACATGT
1 ACCTTACAGAGAGATTACTGAGTACACTTCCTTCTTCCAGCTAACATGT
984256 ACCTTACAGAGAGATTACTGAGTACACTTCCT
1 ACCTTACAGAGAGATTACTGAGTACACTTCCT
984288 CNNNNNNNNN
Statistics
Matches: 266, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
48 120 0.45
51 146 0.55
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (49 bp):
ACCTTACAGAGAGATTACTGAGTACACTTCCTTCTTCCAGCTAACATGT
Found at i:986385 original size:52 final size:53
Alignment explanation
Indices: 986243--986457 Score: 215
Period size: 52 Copynumber: 4.1 Consensus size: 53
986233 GTAGGCAAGA
* * * * * *
986243 TACTCAACTGTTAAATATGAAACATGTTACTTACCAAAAGCTAA-TGTTAGGTTAC
1 TACTCCACTGTTAAATATAAAACATGTTTCTTAACAAAAGCTAACAGGTAGG---C
* * * *
986298 GTACTTCACTGTTAAATATAAAACATGTTACTTAACAAAAGCTAACA-TTGGGC
1 -TACTCCACTGTTAAATATAAAACATGTTTCTTAACAAAAGCTAACAGGTAGGC
*
986351 TA-TGCCACTGTTAAATATAAAACATGTTTTTTAACAAAAGCTAA-AGGTAGGC
1 TACT-CCACTGTTAAATATAAAACATGTTTCTTAACAAAAGCTAACAGGTAGGC
* * * *
986403 TACTCCACTGTCAAATATAAAACATGTTTCTTCACAAAAGTTAAC-GCTAGGC
1 TACTCCACTGTTAAATATAAAACATGTTTCTTAACAAAAGCTAACAGGTAGGC
986455 TAC
1 TAC
986458 GTCTCTACTC
Statistics
Matches: 138, Mismatches: 16, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
51 2 0.01
52 90 0.65
53 2 0.01
56 44 0.32
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.31
Consensus pattern (53 bp):
TACTCCACTGTTAAATATAAAACATGTTTCTTAACAAAAGCTAACAGGTAGGC
Found at i:986456 original size:104 final size:106
Alignment explanation
Indices: 986249--986456 Score: 258
Period size: 104 Copynumber: 2.0 Consensus size: 106
986239 AAGATACTCA
* * * * * *
986249 ACTGTTAAATATGAAACATGTTACTTACCAAAAGCTAATGTTAGGTTACGTACTTCACTGTTAAA
1 ACTGTTAAATATAAAACATGTTACTTAACAAAAGCTAAAGGTAGG-T-CGTACTCCACTGTCAAA
* *
986314 TATAAAACATGTTACTTAACAAAAGCTAACATTGGGCTATGCC
64 TATAAAACATGTTACTTAACAAAAGCTAACACTAGGCTATGCC
**
986357 ACTGTTAAATATAAAACATGTTTTTTAACAAAAGCTAAAGGTAGG-C-TACTCCACTGTCAAATA
1 ACTGTTAAATATAAAACATGTTACTTAACAAAAGCTAAAGGTAGGTCGTACTCCACTGTCAAATA
* * * *
986420 TAAAACATGTTTCTTCACAAAAGTTAACGCTAGGCTA
66 TAAAACATGTTACTTAACAAAAGCTAACACTAGGCTA
986457 CGTCTCTACT
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
104 46 0.53
105 1 0.01
108 39 0.45
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (106 bp):
ACTGTTAAATATAAAACATGTTACTTAACAAAAGCTAAAGGTAGGTCGTACTCCACTGTCAAATA
TAAAACATGTTACTTAACAAAAGCTAACACTAGGCTATGCC
Found at i:987934 original size:2 final size:2
Alignment explanation
Indices: 987929--987977 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
987919 ATTAAGGGGG
987929 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
987971 GA GA GA G
1 GA GA GA G
987978 GGGAGGGTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:989432 original size:22 final size:22
Alignment explanation
Indices: 989394--989678 Score: 403
Period size: 22 Copynumber: 13.0 Consensus size: 22
989384 CAAGCAAAAC
*
989394 GGATAGTGTAATCATACAGAAA
1 GGATAGTGTAATTATACAGAAA
* *
989416 GGACAGTGTACTTATACAGAAA
1 GGATAGTGTAATTATACAGAAA
** * *
989438 CTATAG-GTTATTAAACAGAAA
1 GGATAGTGTAATTATACAGAAA
**
989459 GGATAGTGTTGTTATACAGAAA
1 GGATAGTGTAATTATACAGAAA
989481 GGATAGTGTAATTATACAGAAA
1 GGATAGTGTAATTATACAGAAA
989503 GGATAGTGTAATTATACAGAAA
1 GGATAGTGTAATTATACAGAAA
989525 GGATAGTGTAATTATACAGAAA
1 GGATAGTGTAATTATACAGAAA
989547 GGATAGTGTAATTATACAGAAA
1 GGATAGTGTAATTATACAGAAA
** *
989569 CTATAGTGTTATTATACAGAAA
1 GGATAGTGTAATTATACAGAAA
989591 GGATAGTG-ATATTATACAGAAA
1 GGATAGTGTA-ATTATACAGAAA
* *
989613 GGACAGTGTGATTATACAGAAA
1 GGATAGTGTAATTATACAGAAA
**
989635 GGATAGTGTAATTATTTAGAAA
1 GGATAGTGTAATTATACAGAAA
989657 GGATAGTGTAATTATACAGAAA
1 GGATAGTGTAATTATACAGAAA
989679 TACAGAAGGA
Statistics
Matches: 231, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
21 16 0.07
22 215 0.93
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (22 bp):
GGATAGTGTAATTATACAGAAA
Found at i:990564 original size:34 final size:34
Alignment explanation
Indices: 990521--990661 Score: 264
Period size: 34 Copynumber: 4.1 Consensus size: 34
990511 TCACAGGTAG
990521 CTTTCATCTTGTGGGGGTTATACTTAGTATCGCC
1 CTTTCATCTTGTGGGGGTTATACTTAGTATCGCC
*
990555 CTTTCATCTTGGGGGGGTTATACTTAGTATCGCC
1 CTTTCATCTTGTGGGGGTTATACTTAGTATCGCC
990589 CTTTCATCTTGTGGGGGTTATACTTAGTATCGCC
1 CTTTCATCTTGTGGGGGTTATACTTAGTATCGCC
*
990623 CTTTCATCTTGTGGGGGTTATACTTAGTATCGTC
1 CTTTCATCTTGTGGGGGTTATACTTAGTATCGCC
990657 CTTTC
1 CTTTC
990662 TTAAAGTTTC
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 104 1.00
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.42
Consensus pattern (34 bp):
CTTTCATCTTGTGGGGGTTATACTTAGTATCGCC
Found at i:991330 original size:10 final size:10
Alignment explanation
Indices: 991315--991373 Score: 109
Period size: 10 Copynumber: 5.8 Consensus size: 10
991305 CACGTCTTTT
991315 AACCCCAAGG
1 AACCCCAAGG
991325 AACCCCAAGG
1 AACCCCAAGG
991335 AACCCCAAGG
1 AACCCCAAGG
991345 AAACCCCAAGG
1 -AACCCCAAGG
991356 AACCCCAAGG
1 AACCCCAAGG
991366 AACCCCAA
1 AACCCCAA
991374 TGACAGAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
10 38 0.79
11 10 0.21
ACGTcount: A:0.42, C:0.41, G:0.17, T:0.00
Consensus pattern (10 bp):
AACCCCAAGG
Found at i:991351 original size:21 final size:20
Alignment explanation
Indices: 991315--991373 Score: 109
Period size: 21 Copynumber: 2.9 Consensus size: 20
991305 CACGTCTTTT
991315 AACCCCAAGGAACCCCAAGG
1 AACCCCAAGGAACCCCAAGG
991335 AACCCCAAGGAAACCCCAAGG
1 AACCCCAAGG-AACCCCAAGG
991356 AACCCCAAGGAACCCCAA
1 AACCCCAAGGAACCCCAA
991374 TGACAGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 18 0.47
21 20 0.53
ACGTcount: A:0.42, C:0.41, G:0.17, T:0.00
Consensus pattern (20 bp):
AACCCCAAGGAACCCCAAGG
Found at i:991353 original size:31 final size:31
Alignment explanation
Indices: 991315--991373 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
991305 CACGTCTTTT
991315 AACCCCAAGGAACCCCAAGGAACCCCAAGGA
1 AACCCCAAGGAACCCCAAGGAACCCCAAGGA
991346 AACCCCAAGGAACCCCAAGGAACCCCAA
1 AACCCCAAGGAACCCCAAGGAACCCCAA
991374 TGACAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.41, G:0.17, T:0.00
Consensus pattern (31 bp):
AACCCCAAGGAACCCCAAGGAACCCCAAGGA
Found at i:991974 original size:173 final size:173
Alignment explanation
Indices: 991547--992220 Score: 1024
Period size: 173 Copynumber: 3.9 Consensus size: 173
991537 GATACCCTAA
* * * * *
991547 TAATACAAATTTTAAACTCTTGGTACCCCTGGGGACTCACTGGTATTCCAGACACACCTCTAAGA
1 TAATACAAATTTAAAACTCTTGATAACCCTGGGGACTCATTGGTATTCCAGATACACCTCTAAGA
* *
991612 A-CCACAGGGAACCCCAGGGATATCCCAAGGAACTCGAAGAATATCCTAATAATACAGAATCATA
66 ATCC-CAGGGAACCCCAGGGATATCCCAAGGAACTCCAAGAATACCCTAATAATACAGAATCATA
991676 ACTCTTGATACTCCATAGAACCCCAAGGATACCC---TA-A-TG
130 ACTCTTGATACTCCATAGAACCCCAAGGATACCCTAATACATTG
* * *
991715 --ATACAAATTTAAAACTCTT-ATTAACACTGAGGACTCATTGGTATTCCAGATACACCTCTAGG
1 TAATACAAATTTAAAACTCTTGA-TAACCCTGGGGACTCATTGGTATTCCAGATACACCTCTAAG
* * *
991777 AATCCCAGGGAACCCCATGGATATCCCAAGGAACTCCAAAAATACCCTTATAATACAGAATCATA
65 AATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAAGAATACCCTAATAATACAGAATCATA
*
991842 ACTCTTAATACTCCATAGAACCCCAAGGATACCCTAATACATTG
130 ACTCTTGATACTCCATAGAACCCCAAGGATACCCTAATACATTG
*
991886 TAATACAAATGTAAAACTCTTGATAACCCTGGGGACTCATTGGTATTCCAGATACACCTCTAAGA
1 TAATACAAATTTAAAACTCTTGATAACCCTGGGGACTCATTGGTATTCCAGATACACCTCTAAGA
*
991951 ATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAAGAATACCCTAATAATACAGAATTATAA
66 ATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAAGAATACCCTAATAATACAGAATCATAA
* * *
992016 ATCTTGATACTCCATAGAACCCCAAGGATACCGTAATACGTTG
131 CTCTTGATACTCCATAGAACCCCAAGGATACCCTAATACATTG
*
992059 TAATACAAATTTAAAACTCTTGATAACCCTGGGGACTCATTGGTATTCCAGATACACCTGTAAGA
1 TAATACAAATTTAAAACTCTTGATAACCCTGGGGACTCATTGGTATTCCAGATACACCTCTAAGA
* * * * *
992124 ATCCCAGGGAACCCCAGGGATATCCCAAAGAACTCCAAGAATACCCTAAAAATACAGATTCGTTA
66 ATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAAGAATACCCTAATAATACAGAATCATAA
* *
992189 CTCTTGATACACCACAGAACCCCAAGGATACC
131 CTCTTGATACTCCATAGAACCCCAAGGATACC
992221 TCAAGGAACT
Statistics
Matches: 459, Mismatches: 37, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
166 143 0.31
167 2 0.00
169 2 0.00
170 1 0.00
171 2 0.00
173 308 0.67
174 1 0.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (173 bp):
TAATACAAATTTAAAACTCTTGATAACCCTGGGGACTCATTGGTATTCCAGATACACCTCTAAGA
ATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAAGAATACCCTAATAATACAGAATCATAA
CTCTTGATACTCCATAGAACCCCAAGGATACCCTAATACATTG
Found at i:996667 original size:21 final size:20
Alignment explanation
Indices: 996618--996676 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
996608 ATTTCTATTA
996618 TTGGGGT-TACTTGGGGTTC
1 TTGGGGTATACTTGGGGTTC
*
996637 TAAT-GAGTATACTTGGGGTTCC
1 T--TGGGGTATACTTGGGGTT-C
*
996659 TTGGGGTATCCTTGGGGT
1 TTGGGGTATACTTGGGGT
996677 ACTACGAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 25 0.78
22 2 0.06
ACGTcount: A:0.12, C:0.12, G:0.37, T:0.39
Consensus pattern (20 bp):
TTGGGGTATACTTGGGGTTC
Found at i:996672 original size:11 final size:11
Alignment explanation
Indices: 996643--996677 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
996633 GTTCTAATGA
*
996643 GTATACTTGGG
1 GTATCCTTGGG
996654 GT-TCCTTGGG
1 GTATCCTTGGG
996664 GTATCCTTGGG
1 GTATCCTTGGG
996675 GTA
1 GTA
996678 CTACGAGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.11, C:0.14, G:0.37, T:0.37
Consensus pattern (11 bp):
GTATCCTTGGG
Found at i:996910 original size:195 final size:196
Alignment explanation
Indices: 996577--996953 Score: 515
Period size: 195 Copynumber: 1.9 Consensus size: 196
996567 ATAGGGGTAT
* * * * * *
996577 AATGAGACTCCTGGGGTATCACTAGTTACTAATTTCTATTATTGGGGTTACTTGGGGTTCTAATG
1 AATGAGACCCCTGGGGTATCACTAGTTAATAACTTCTATCATTGGGGTTACATGGGGTTCTAACG
* * * * *
996642 AGTATACTTGGGGTTCCTTGGGGTATCCTTGGGGTACTACGAGGTGACCCTTGGATTCAAATGAG
66 AGTATACTTGGGGTTCCTTGGGGTACCCTTGGGGTACTAAGAGGTGACCCTTGAAGTCAAATAAG
996707 ACCCCTTGGGTA-TAAATAGTTATTAATTTCTATCACTGGGGTACCTTGGGGTGAGCCTTTGATT
131 ACCCCTTGGGTATTAAA-AGTTATTAATTTCTATCACTGGGGTACCTTGGGGTGAGCCTTTGATT
996771 CG
195 CG
* * * *
996773 AATGAGACCCCTGGGGTATCACTGGTTAATAACTT-TATCATTTGGGTTCCATGGGGTTCTTACG
1 AATGAGACCCCTGGGGTATCACTAGTTAATAACTTCTATCATTGGGGTTACATGGGGTTCTAACG
* * * *
996837 GGTTTCCTTGGGGTTCCTTGGGGTACCCTTGGGGTACTAAGAGGTGACCCTTGAAGTCCAATAAG
66 AGTATACTTGGGGTTCCTTGGGGTACCCTTGGGGTACTAAGAGGTGACCCTTGAAGTCAAATAAG
* * * * *
996902 ACCCCTTGGGTATTAAAATTTATTAATTTTTGTCATTGGGGTTCCTTGGGGT
131 ACCCCTTGGGTATTAAAAGTTATTAATTTCTATCACTGGGGTACCTTGGGGT
996954 ATCCTTGAGG
Statistics
Matches: 156, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
195 121 0.78
196 35 0.22
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (196 bp):
AATGAGACCCCTGGGGTATCACTAGTTAATAACTTCTATCATTGGGGTTACATGGGGTTCTAACG
AGTATACTTGGGGTTCCTTGGGGTACCCTTGGGGTACTAAGAGGTGACCCTTGAAGTCAAATAAG
ACCCCTTGGGTATTAAAAGTTATTAATTTCTATCACTGGGGTACCTTGGGGTGAGCCTTTGATTC
G
Found at i:996952 original size:10 final size:10
Alignment explanation
Indices: 996937--997006 Score: 113
Period size: 10 Copynumber: 6.8 Consensus size: 10
996927 ATTTTTGTCA
996937 TTGGGGTTCC
1 TTGGGGTTCC
996947 TTGGGGTATCC
1 TTGGGGT-TCC
*
996958 TTGAGGTTCC
1 TTGGGGTTCC
996968 TTGGGGTTTCC
1 TTGGGG-TTCC
996979 TTGGGGTTCC
1 TTGGGGTTCC
996989 TTGGGGTTCC
1 TTGGGGTTCC
996999 TTGGGGTT
1 TTGGGGTT
997007 AAAAGACGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
10 37 0.66
11 19 0.34
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (10 bp):
TTGGGGTTCC
Found at i:996967 original size:21 final size:20
Alignment explanation
Indices: 996937--997006 Score: 113
Period size: 21 Copynumber: 3.4 Consensus size: 20
996927 ATTTTTGTCA
996937 TTGGGGTTCCTTGGGGTATCC
1 TTGGGGTTCCTTGGGGT-TCC
*
996958 TTGAGGTTCCTTGGGGTTTCC
1 TTGGGGTTCCTTGGGG-TTCC
996979 TTGGGGTTCCTTGGGGTTCC
1 TTGGGGTTCCTTGGGGTTCC
996999 TTGGGGTT
1 TTGGGGTT
997007 AAAAGACGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 12 0.26
21 33 0.72
22 1 0.02
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (20 bp):
TTGGGGTTCCTTGGGGTTCC
Found at i:996975 original size:31 final size:30
Alignment explanation
Indices: 996937--997006 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 30
996927 ATTTTTGTCA
996937 TTGGGGTTCCTTGGGGTATCCTTGAGGTTCC
1 TTGGGGTTCCTTGGGGT-TCCTTGAGGTTCC
*
996968 TTGGGGTTTCCTTGGGGTTCCTTGGGGTTCC
1 TTGGGG-TTCCTTGGGGTTCCTTGAGGTTCC
996999 TTGGGGTT
1 TTGGGGTT
997007 AAAAGACGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 2 0.05
31 24 0.65
32 11 0.30
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (30 bp):
TTGGGGTTCCTTGGGGTTCCTTGAGGTTCC
Found at i:998596 original size:1 final size:1
Alignment explanation
Indices: 998585--998618 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
998575 GTTCTTGTAA
*
998585 CCCCCCTCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
998619 ACAACCTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:1000874 original size:2 final size:2
Alignment explanation
Indices: 1000867--1000920 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
1000857 CCACGAAATA
* *
1000867 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CC
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1000909 CT CT CT CT CT CT
1 CT CT CT CT CT CT
1000921 TTTAGTAGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:1006436 original size:63 final size:63
Alignment explanation
Indices: 1006333--1006454 Score: 192
Period size: 63 Copynumber: 1.9 Consensus size: 63
1006323 GAACTTATTC
* * *
1006333 AACACCAGACAATAACATTTATATATTAAAAAACTCCCAGACAATAACATCTATATATATAAA
1 AACACCAGACAATAACATCTATATATAAAAAAACTACCAGACAATAACATCTATATATATAAA
*
1006396 AACACCAGACAATAACATCTATATATAAAAAAAAC-ACCAGACAATAACATTTATATATA
1 AACACCAGACAATAACATCTATATAT-AAAAAAACTACCAGACAATAACATCTATATATA
1006455 ACATCTATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 47 0.87
64 7 0.13
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (63 bp):
AACACCAGACAATAACATCTATATATAAAAAAACTACCAGACAATAACATCTATATATATAAA
Found at i:1006454 original size:32 final size:31
Alignment explanation
Indices: 1006333--1006455 Score: 183
Period size: 32 Copynumber: 3.9 Consensus size: 31
1006323 GAACTTATTC
* *
1006333 AACACCAGACAATAACATTTATATATTAAAA
1 AACACCAGACAATAACATCTATATATAAAAA
* *
1006364 AACTCCCAGACAATAACATCTATATATATAAA
1 AAC-ACCAGACAATAACATCTATATATAAAAA
1006396 AACACCAGACAATAACATCTATATATAAAAAA
1 AACACCAGACAATAACATCTATATAT-AAAAA
*
1006428 AACACCAGACAATAACATTTATATATAA
1 AACACCAGACAATAACATCTATATATAA
1006456 CATCTATATA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
31 27 0.33
32 56 0.67
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (31 bp):
AACACCAGACAATAACATCTATATATAAAAA
Found at i:1008150 original size:19 final size:19
Alignment explanation
Indices: 1008126--1008293 Score: 320
Period size: 19 Copynumber: 8.9 Consensus size: 19
1008116 GGTAGCACAT
1008126 CAATGAGATTAGTTGTACA
1 CAATGAGATTAGTTGTACA
1008145 CAATGAGATTAGTTGTACA
1 CAATGAGATTAGTTGTACA
1008164 CAATGAGATTAGTTGTACA
1 CAATGAGATTAGTTGTACA
1008183 CAATGAGATTAGTTGTACA
1 CAATGAGATTAGTTGTACA
1008202 CAATGAGATTAGTTGTACA
1 CAATGAGATTAGTTGTACA
1008221 CAATGAGATTAGTTGTACA
1 CAATGAGATTAGTTGTACA
*
1008240 CAATGAGATTAGTTGTA-T
1 CAATGAGATTAGTTGTACA
1008258 CAATGAGATTAGTTGTACA
1 CAATGAGATTAGTTGTACA
1008277 CAATGAGATTAGTTGTA
1 CAATGAGATTAGTTGTA
1008294 TCAAAGGGCT
Statistics
Matches: 146, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
18 17 0.12
19 129 0.88
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (19 bp):
CAATGAGATTAGTTGTACA
Found at i:1009397 original size:14 final size:14
Alignment explanation
Indices: 1009378--1009812 Score: 519
Period size: 14 Copynumber: 31.1 Consensus size: 14
1009368 CATTGCGAAT
1009378 TCTGCGAGGTAAGG
1 TCTGCGAGGTAAGG
1009392 TCTGCGAGGTAAGG
1 TCTGCGAGGTAAGG
* ** *
1009406 ACTGTAAGGTAACG
1 TCTGCGAGGTAAGG
*
1009420 TCTGCGGGGTAAGG
1 TCTGCGAGGTAAGG
*
1009434 TCTGTGAGGTAAGG
1 TCTGCGAGGTAAGG
* *
1009448 TCTGTGAGGTAATG
1 TCTGCGAGGTAAGG
1009462 TCTGCGAGGTAAGG
1 TCTGCGAGGTAAGG
* * *
1009476 ACTGTGAGGTAATG
1 TCTGCGAGGTAAGG
*
1009490 TCTGCGGGGTAAGG
1 TCTGCGAGGTAAGG
*
1009504 TCTGTGAGGTAAGG
1 TCTGCGAGGTAAGG
* *
1009518 TCTGTGAGGTAATG
1 TCTGCGAGGTAAGG
1009532 TCTGCGAGGTAAGG
1 TCTGCGAGGTAAGG
*
1009546 GCTGCGAGGTAAGG
1 TCTGCGAGGTAAGG
* *
1009560 TCTGTGAGGTAATG
1 TCTGCGAGGTAAGG
*
1009574 TCTGCGAGGTAATG
1 TCTGCGAGGTAAGG
1009588 TCTGCGAGGTAAGG
1 TCTGCGAGGTAAGG
*
1009602 TCTGCGAGGTAATG
1 TCTGCGAGGTAAGG
*
1009616 TCTGCGAGGTAAAG
1 TCTGCGAGGTAAGG
*
1009630 TCTGCGAGGTCAGG
1 TCTGCGAGGTAAGG
* *
1009644 TCTGTGAGGTAATG
1 TCTGCGAGGTAAGG
1009658 TCTGCGAGGTAAGG
1 TCTGCGAGGTAAGG
* *
1009672 ACTGCGAGGTAAAG
1 TCTGCGAGGTAAGG
1009686 TCTGCGAGGTAAGG
1 TCTGCGAGGTAAGG
* *
1009700 ACTGCGAGGTCAGG
1 TCTGCGAGGTAAGG
* *
1009714 ACTGCGAGGTCAGG
1 TCTGCGAGGTAAGG
* *
1009728 TCTGTGAGGTCAGG
1 TCTGCGAGGTAAGG
* *
1009742 TCTGTGAGGTCAGG
1 TCTGCGAGGTAAGG
* *
1009756 TCTGTGAGGTAATG
1 TCTGCGAGGTAAGG
*
1009770 TCTGCGAGGTCAGG
1 TCTGCGAGGTAAGG
*
1009784 TCTGCGAGGTCAGG
1 TCTGCGAGGTAAGG
*
1009798 TCTGTGAGGTAAGG
1 TCTGCGAGGTAAGG
1009812 T
1 T
1009813 TTTAGGAGCA
Statistics
Matches: 365, Mismatches: 56, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 365 1.00
ACGTcount: A:0.21, C:0.13, G:0.41, T:0.25
Consensus pattern (14 bp):
TCTGCGAGGTAAGG
Found at i:1010866 original size:40 final size:40
Alignment explanation
Indices: 1010808--1010889 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
1010798 AATAAAAAGC
1010808 TAGTCGATCATCAATAAACATTAGTCCCCATAGTGAGGCA
1 TAGTCGATCATCAATAAACATTAGTCCCCATAGTGAGGCA
*
1010848 TAGTCGATCATCAGTAAACATTAGTCCCCATAGTGAGGCA
1 TAGTCGATCATCAATAAACATTAGTCCCCATAGTGAGGCA
1010888 TA
1 TA
1010890 ACGATGAATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (40 bp):
TAGTCGATCATCAATAAACATTAGTCCCCATAGTGAGGCA
Found at i:1011005 original size:34 final size:34
Alignment explanation
Indices: 1010962--1011066 Score: 192
Period size: 34 Copynumber: 3.1 Consensus size: 34
1010952 GAATTATCCC
*
1010962 ACTGGTCCCAGCGGACCAACAACATTCTAGTATG
1 ACTGGTCCCAGCGGACCAACAACATTCTAGTAGG
*
1010996 ACTGGTCCCAGCGGACCAACAACATTTTAGTAGG
1 ACTGGTCCCAGCGGACCAACAACATTCTAGTAGG
1011030 ACTGGTCCCAGCGGACCAACAACATTCTAGTAGG
1 ACTGGTCCCAGCGGACCAACAACATTCTAGTAGG
1011064 ACT
1 ACT
1011067 TTTGTTGTAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.20
Consensus pattern (34 bp):
ACTGGTCCCAGCGGACCAACAACATTCTAGTAGG
Found at i:1011198 original size:30 final size:29
Alignment explanation
Indices: 1011164--1011221 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
1011154 TGAATATACT
* * *
1011164 TGTCTGTAATATACCTGTTTGTTCTGTAAC
1 TGTCTGTAATAAACATGTCTG-TCTGTAAC
1011194 TGTCTGTAATAAACATGTCTGTCTGTAA
1 TGTCTGTAATAAACATGTCTGTCTGTAA
1011222 TTATACCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (29 bp):
TGTCTGTAATAAACATGTCTGTCTGTAAC
Found at i:1011277 original size:20 final size:20
Alignment explanation
Indices: 1011252--1011295 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1011242 TGTATCTATT
1011252 TGTAACTGTACCA-TTTTGTC
1 TGTAACTGTACCAGTTTT-TC
1011272 TGTAACTGTACCAGTTTTTC
1 TGTAACTGTACCAGTTTTTC
1011292 TGTA
1 TGTA
1011296 TTTGCACCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTAACTGTACCAGTTTTTC
Found at i:1012843 original size:2 final size:2
Alignment explanation
Indices: 1012838--1012898 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1012828 AAAAAAAAAA
1012838 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1012880 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
1012899 ATACATGTAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1023598 original size:16 final size:16
Alignment explanation
Indices: 1023579--1023613 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1023569 TATATCAATT
1023579 TATAAGTAAATAAAAA
1 TATAAGTAAATAAAAA
*
1023595 TATAAGTAAATAAATA
1 TATAAGTAAATAAAAA
1023611 TAT
1 TAT
1023614 GGGGTTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
TATAAGTAAATAAAAA
Found at i:1024952 original size:25 final size:25
Alignment explanation
Indices: 1024924--1024997 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
1024914 CGACAGCGTC
1024924 ATCGATTGACATCACAATGGTAAAT
1 ATCGATTGACATCACAATGGTAAAT
* *
1024949 ATCGA-T--CA--ATAAT-G--ATT
1 ATCGATTGACATCACAATGGTAAAT
1024966 CATCGATTGACATCACAATGGTAAAT
1 -ATCGATTGACATCACAATGGTAAAT
1024992 ATCGAT
1 ATCGAT
1024998 CAATATTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
17 2 0.06
18 5 0.14
19 2 0.06
20 4 0.11
21 2 0.06
22 2 0.06
23 4 0.11
24 2 0.06
25 11 0.31
26 2 0.06
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (25 bp):
ATCGATTGACATCACAATGGTAAAT
Found at i:1024970 original size:43 final size:43
Alignment explanation
Indices: 1024922--1025181 Score: 450
Period size: 43 Copynumber: 6.1 Consensus size: 43
1024912 GTCGACAGCG
*
1024922 TCATCGATTGACATCACAATGGTAAATATCGATCAATAATGAT
1 TCATCGATTGACATCACAATGGTAAATATCGATCAATATTGAT
1024965 TCATCGATTGACATCACAATGGTAAATATCGATCAATATTGAT
1 TCATCGATTGACATCACAATGGTAAATATCGATCAATATTGAT
* * *
1025008 TCATCGATTGACATCAAAATGGTAAATACCGATCAATATTCAT
1 TCATCGATTGACATCACAATGGTAAATATCGATCAATATTGAT
1025051 TCATCGATTGAC-TCACAATGGTAAATATCGATCAATATTGAT
1 TCATCGATTGACATCACAATGGTAAATATCGATCAATATTGAT
*
1025093 TCATCTATTGACATCACAATGGTAAATATCGATCAATATTGAT
1 TCATCGATTGACATCACAATGGTAAATATCGATCAATATTGAT
* *
1025136 TCATCGATTGACATCAAAATGGTAGATATCGATCAATATTGAT
1 TCATCGATTGACATCACAATGGTAAATATCGATCAATATTGAT
1025179 TCA
1 TCA
1025182 ACTGTCCCAT
Statistics
Matches: 205, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
42 38 0.19
43 167 0.81
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (43 bp):
TCATCGATTGACATCACAATGGTAAATATCGATCAATATTGAT
Found at i:1025169 original size:128 final size:129
Alignment explanation
Indices: 1024922--1025181 Score: 468
Period size: 128 Copynumber: 2.0 Consensus size: 129
1024912 GTCGACAGCG
1024922 TCATCGATTGACATCACAATGGTAAATATCGATCAATAATGATTCATCGATTGACATCACAATGG
1 TCATCGATTGACATCACAATGGTAAATATCGATCAATAATGATTCATCGATTGACATCACAATGG
1024987 TAAATATCGATCAATATTGATTCATCGATTGACATCAAAATGGTAAATACCGATCAATATTCAT
66 TAAATATCGATCAATATTGATTCATCGATTGACATCAAAATGGTAAATACCGATCAATATTCAT
* *
1025051 TCATCGATTGAC-TCACAATGGTAAATATCGATCAATATTGATTCATCTATTGACATCACAATGG
1 TCATCGATTGACATCACAATGGTAAATATCGATCAATAATGATTCATCGATTGACATCACAATGG
* * *
1025115 TAAATATCGATCAATATTGATTCATCGATTGACATCAAAATGGTAGATATCGATCAATATTGAT
66 TAAATATCGATCAATATTGATTCATCGATTGACATCAAAATGGTAAATACCGATCAATATTCAT
1025179 TCA
1 TCA
1025182 ACTGTCCCAT
Statistics
Matches: 126, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
128 114 0.90
129 12 0.10
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (129 bp):
TCATCGATTGACATCACAATGGTAAATATCGATCAATAATGATTCATCGATTGACATCACAATGG
TAAATATCGATCAATATTGATTCATCGATTGACATCAAAATGGTAAATACCGATCAATATTCAT
Found at i:1028745 original size:228 final size:227
Alignment explanation
Indices: 1028313--1028722 Score: 784
Period size: 228 Copynumber: 1.8 Consensus size: 227
1028303 ACAACTACAC
1028313 GAAGTCCAACCTCTTGAAAAAATGGTTCCAATTTTTATCATCATTTTTTAACCTAATTTACATAA
1 GAAGTCCAACCTCTTGAAAAAATGGTTCCAATTTTTATCATCATTTTTTAACCTAATTTACATAA
1028378 TATGATGCATGTTTTGTCGTTTGGTTAACGAGGTCAAAACTGCATGTAAGGTGAGCAAACGATAG
66 TATGATGCATGTTTTGTCGTTTGGTTAACGAGGTCAAAACTGCATGTAAGGTGAGCAAACGATAG
** *
1028443 ATTCGTTTTAAAATTGAATATCAAATCCGTAGTAAAATGATATAAATGATATATTATATTATACC
131 ATTCGTTTTAAAATTGAATATCAAATCCGTAGTAAAATGATATAAATGATATATTATACGACACC
1028508 TCTTATACATTGGCGTCGGAAACTTGGGGGGG
196 TCTTATACATTGGCGTCGGAAACTTGGGGGGG
1028540 NGAAGTCCAACCTCTTGAAAAAATGGTTCCAATTTTTATCATCATTTTTTAACCTAATTTACATA
1 -GAAGTCCAACCTCTTGAAAAAATGGTTCCAATTTTTATCATCATTTTTTAACCTAATTTACATA
1028605 ATATGATGCATGTTTTGTCGTTTGGTTAACGAGGTCAAAACTGCATGTAAGGTGAGCAAACGATA
65 ATATGATGCATGTTTTGTCGTTTGGTTAACGAGGTCAAAACTGCATGTAAGGTGAGCAAACGATA
1028670 GATTCGTTTTAAAATTGAATATCAAATCCGTAGTAAAATGATATAAATGATAT
130 GATTCGTTTTAAAATTGAATATCAAATCCGTAGTAAAATGATATAAATGATAT
1028723 NTTCCAACGC
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
228 182 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (227 bp):
GAAGTCCAACCTCTTGAAAAAATGGTTCCAATTTTTATCATCATTTTTTAACCTAATTTACATAA
TATGATGCATGTTTTGTCGTTTGGTTAACGAGGTCAAAACTGCATGTAAGGTGAGCAAACGATAG
ATTCGTTTTAAAATTGAATATCAAATCCGTAGTAAAATGATATAAATGATATATTATACGACACC
TCTTATACATTGGCGTCGGAAACTTGGGGGGG
Found at i:1029472 original size:102 final size:102
Alignment explanation
Indices: 1029296--1029550 Score: 476
Period size: 102 Copynumber: 2.5 Consensus size: 102
1029286 TTTGTTTAAC
1029296 TAATTAATAAATTGATTATGAAAAGTTAGTAAAATTCACTAAATTACTGTTAAAGGGACGATTTG
1 TAATTAATAAATTGATTATGAAAAGTTAGTAAAATTCACTAAATTACTGTTAAAGGGACGATTTG
1029361 AGATCAAAAATTTAATTTTTATTTTCCTTATTTTAGT
66 AGATCAAAAATTTAATTTTTATTTTCCTTATTTTAGT
1029398 TAATTAATAAATTGATTATGAAAAGTTAGTAAAATTCACTAAATTACTGTTAAAGGGACGATTTG
1 TAATTAATAAATTGATTATGAAAAGTTAGTAAAATTCACTAAATTACTGTTAAAGGGACGATTTG
1029463 AGATCAAAAATTTAATTTTTATTTTCCTTATTTTAGT
66 AGATCAAAAATTTAATTTTTATTTTCCTTATTTTAGT
* *
1029500 TAATTAATAAATTGGTTATGAAAAGTAACG-AAAATTCACTAAATTACTGTT
1 TAATTAATAAATTGATTATGAAAAGTTA-GTAAAATTCACTAAATTACTGTT
1029551 GATGTACATA
Statistics
Matches: 150, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
102 149 0.99
103 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (102 bp):
TAATTAATAAATTGATTATGAAAAGTTAGTAAAATTCACTAAATTACTGTTAAAGGGACGATTTG
AGATCAAAAATTTAATTTTTATTTTCCTTATTTTAGT
Found at i:1030042 original size:21 final size:20
Alignment explanation
Indices: 1030016--1030063 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
1030006 ACGTAGAAGA
*
1030016 GTCAGATCAAAATATTTATTT
1 GTCAGA-CAAAATATGTATTT
*
1030037 GTCAGACGAAATATGTATTT
1 GTCAGACAAAATATGTATTT
1030057 GTTCAGA
1 G-TCAGA
1030064 AATATTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (20 bp):
GTCAGACAAAATATGTATTT
Found at i:1030050 original size:20 final size:21
Alignment explanation
Indices: 1030025--1030063 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1030015 AGTCAGATCA
*
1030025 AAATATTTATTTG-TCAGACG
1 AAATATGTATTTGTTCAGACG
1030045 AAATATGTATTTGTTCAGA
1 AAATATGTATTTGTTCAGA
1030064 AATATTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (21 bp):
AAATATGTATTTGTTCAGACG
Found at i:1033109 original size:85 final size:85
Alignment explanation
Indices: 1032979--1033184 Score: 261
Period size: 85 Copynumber: 2.4 Consensus size: 85
1032969 AAAAGAGACT
* * *
1032979 ATTGAAGCTAAATGGAAAGCAATCTTATACTAATACTAATCTTAACGCAAACCAATCTTAAACTA
1 ATTGAAGCTAAATGCAAAGAAATCTTAAACTAATACTAATCTTAACGCAAACCAATCTTAAACTA
*
1033044 ATGCTTATTCTAACTCAAGA
66 ATGCTTATTCTAACTCAAAA
* * * *
1033064 ATTGTAGCTAAATGCAAA-AAATTCTTAAACTAATTCTTATTTTAACGCAAACCAATCTTAAACT
1 ATTGAAGCTAAATGCAAAGAAA-TCTTAAACTAATACTAATCTTAACGCAAACCAATCTTAAACT
*
1033128 AATGCTTATTTTAACTCAAAA
65 AATGCTTATTCTAACTCAAAA
* ** * * *
1033149 ATTAAAGCTAAATAAAAACAAATATTATACTAATAC
1 ATTGAAGCTAAATGCAAAGAAATCTTAAACTAATAC
1033185 CAATTTTTAA
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
84 2 0.02
85 98 0.95
86 3 0.03
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.32
Consensus pattern (85 bp):
ATTGAAGCTAAATGCAAAGAAATCTTAAACTAATACTAATCTTAACGCAAACCAATCTTAAACTA
ATGCTTATTCTAACTCAAAA
Found at i:1033114 original size:33 final size:32
Alignment explanation
Indices: 1033077--1033149 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
1033067 GTAGCTAAAT
*
1033077 GCAAAAAATTCTTAAACTAATTCTTATTTTAAC
1 GCAAAAAA-TCTTAAACTAATGCTTATTTTAAC
*
1033110 GCAAACCAATCTTAAACTAATGCTTATTTTAAC
1 GCAAA-AAATCTTAAACTAATGCTTATTTTAAC
*
1033143 TCAAAAA
1 GCAAAAA
1033150 TTAAAGCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 1 0.03
33 32 0.91
34 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (32 bp):
GCAAAAAATCTTAAACTAATGCTTATTTTAAC
Found at i:1033281 original size:54 final size:53
Alignment explanation
Indices: 1033191--1033301 Score: 150
Period size: 54 Copynumber: 2.1 Consensus size: 53
1033181 ATACCAATTT
* ** * ** *
1033191 TTAAACTAATGCTTATTTAACTCAAGAATTGTAGCTAACTGGGAAATAAAATC
1 TTAAACTAATACTTATTTAACTCAAGAATTAAAGCTAAATGAAAAAAAAAATC
1033244 TTAAACTAATACTTATTTTAACTCAAGAATTAAAGCTAAATGAAAAAAAAAATC
1 TTAAACTAATACTTA-TTTAACTCAAGAATTAAAGCTAAATGAAAAAAAAAATC
1033298 TTAA
1 TTAA
1033302 TTTTAACGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 14 0.28
54 36 0.72
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.32
Consensus pattern (53 bp):
TTAAACTAATACTTATTTAACTCAAGAATTAAAGCTAAATGAAAAAAAAAATC
Found at i:1033452 original size:84 final size:79
Alignment explanation
Indices: 1033240--1033505 Score: 317
Period size: 84 Copynumber: 3.3 Consensus size: 79
1033230 TGGGAAATAA
* * ** *
1033240 AATCTTAAACTAATACTTATTTTAACTCAAGAATTAAAGCTAAATGAAAAAAAAA-AT-CT--TA
1 AATCTTACACTAATGC-TATTTTAACTCAAGAATTGTAGCTAAATGAAAAAAAAATATAATACTA
1033301 ATTTTAACGCAAACC
65 ATTTTAACGCAAACC
* *
1033316 AATCTTACACTAATGCGTATTTTAGCTCAAGAATTGTAGCTAAATGGAAAAAAATGTTATAGTAA
1 AATCTTACACTAATGC-TATTTTAACTCAAGAATTGTAGCTAAAT-GAAAAAAA---AATA-TAA
*
1033381 TACTTATTTTAACG-AAACC
60 TACTAATTTTAACGCAAACC
* *
1033400 AATCTTATACTAATGCTAATTTTAACTCAAGAATTGTAGCTAAATGAAAAAAAAATATTATACTA
1 AATCTTACACTAATGCT-ATTTTAACTCAAGAATTGTAGCTAAATGAAAAAAAAATATAATACTA
1033465 ATTTTAACGCAAACC
65 ATTTTAACGCAAACC
*
1033480 AATCTTACACTAAGGCTTATTTTAAC
1 AATCTTACACTAATGC-TATTTTAAC
1033506 GCAGACCACT
Statistics
Matches: 162, Mismatches: 16, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
76 39 0.24
77 8 0.05
79 15 0.09
80 31 0.19
81 2 0.01
82 1 0.01
83 10 0.06
84 46 0.28
85 10 0.06
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (79 bp):
AATCTTACACTAATGCTATTTTAACTCAAGAATTGTAGCTAAATGAAAAAAAAATATAATACTAA
TTTTAACGCAAACC
Found at i:1041523 original size:3 final size:3
Alignment explanation
Indices: 1041515--1041854 Score: 232
Period size: 3 Copynumber: 113.3 Consensus size: 3
1041505 GTCGACGGCG
* * * *
1041515 CTC CTC CTC CTC TTC CTC CTC CTC TTC CTC CTC CTC CCC CAC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * * *
1041563 GAT- GTC CCC CTC TTC CTC CAC CAC CAC CAC CTC CTC CTC CTC CTC
1 -CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* ** * * * * * * *
1041608 CTC CTC TTC CAA CAC CTC CTC CTC TTC CTC CTC CAC CGC CAC CAC CAC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * *
1041656 CTC CTC TTC CTC CTC CTC CTC CAC CAC CTC CTC CTC TTC CTC CTC CAC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * * *
1041704 CGC CAC CTC CTC CTC TTC CTC CTC CAC CGC CAC CTC CTC CTC TTC CTA
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * *
1041752 CTC CTC CAC CAC CTC CTC CTC TTC CTC CTC CAC CAC CAC CTC CTC TTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * *
1041800 CTA CTC CTC CTC CAC CTC CTC CTC TTC CTC CAC CAC CTC CTC TTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1041848 CTC CTC C
1 CTC CTC C
1041855 ACCAAGATCG
Statistics
Matches: 269, Mismatches: 66, Indels: 4
0.79 0.19 0.01
Matches are distributed among these distances:
2 1 0.00
3 267 0.99
4 1 0.00
ACGTcount: A:0.09, C:0.62, G:0.01, T:0.28
Consensus pattern (3 bp):
CTC
Found at i:1041551 original size:30 final size:30
Alignment explanation
Indices: 1041515--1041853 Score: 264
Period size: 30 Copynumber: 11.8 Consensus size: 30
1041505 GTCGACGGCG
* **
1041515 CTCCTCCTCCTCTTCCTCCTCCTCTTCCTC
1 CTCCTCCTCCACCACCTCCTCCTCTTCCTC
* * * * * *
1041545 CTCCTCCCCCACCTCCTCGATGTCCCCCTCTTC
1 CTCCTCCTCCACCACCTC---CTCCTCTTCCTC
* * *
1041578 CTCCACCACCACCACCTCCTCCTCCTCCTC
1 CTCCTCCTCCACCACCTCCTCCTCTTCCTC
* *
1041608 CTCCTCTTCCAACACCTCCTCCTCTTCCTC
1 CTCCTCCTCCACCACCTCCTCCTCTTCCTC
* * *
1041638 CTCCACCGCCACCACCACCTCCTCTTCCTC
1 CTCCTCCTCCACCACCTCCTCCTCTTCCTC
1041668 CTCCTCCTCCACCACCTCCTCCTC-T--TC
1 CTCCTCCTCCACCACCTCCTCCTCTTCCTC
* *
1041695 CTCCTCCACCGCCACCTCCTCCTC-T--TC
1 CTCCTCCTCCACCACCTCCTCCTCTTCCTC
* *
1041722 CTCCTCCACCGCCACCTCCTCCTC-T--TC
1 CTCCTCCTCCACCACCTCCTCCTCTTCCTC
*
1041749 CTACTCCTCCACCACCTCCT-C-C-T-CT-
1 CTCCTCCTCCACCACCTCCTCCTCTTCCTC
* *
1041774 -TCCTCCTCCACCACCACCTCCTCTTCCTA
1 CTCCTCCTCCACCACCTCCTCCTCTTCCTC
1041803 CTCCTCCT---CCACCTCCTCCTCTTCCTC
1 CTCCTCCTCCACCACCTCCTCCTCTTCCTC
* * * **
1041830 CACCACCTCCTCTTCCTCCTCCTC
1 CTCCTCCTCCACCACCTCCTCCTC
1041854 CACCAAGATC
Statistics
Matches: 257, Mismatches: 39, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
24 17 0.07
25 3 0.01
26 3 0.01
27 95 0.37
28 2 0.01
29 1 0.00
30 113 0.44
33 23 0.09
ACGTcount: A:0.09, C:0.62, G:0.01, T:0.28
Consensus pattern (30 bp):
CTCCTCCTCCACCACCTCCTCCTCTTCCTC
Found at i:1041559 original size:27 final size:27
Alignment explanation
Indices: 1041515--1041830 Score: 269
Period size: 27 Copynumber: 11.1 Consensus size: 27
1041505 GTCGACGGCG
* **
1041515 CTCCTCCTCCTCTTCCTCCTCCTCTTC
1 CTCCTCCTCCACCACCTCCTCCTCTTC
* * *
1041542 CTCCTCCTCCCCCACCTCCTCGATGTCCCCCTC
1 CTCCTCCTCCACCACCT-C-C----TCCTCTTC
* *
1041575 TTCCTCCACCACCACCACCTCCTCCTCCTCCTC
1 CTCCTCCTCCACCA---CCTCCTCCT-CT--TC
* *
1041608 CTCCTCTTCCAACACCTCCTCCTCTTC
1 CTCCTCCTCCACCACCTCCTCCTCTTC
* *
1041635 CTCCTCCACCGCCACCACCACCTCCTCTTCCTC
1 CTCCT---CCTCCACCACCTCCTCCTC-T--TC
1041668 CTCCTCCTCCACCACCTCCTCCTCTTC
1 CTCCTCCTCCACCACCTCCTCCTCTTC
* *
1041695 CTCCTCCACCGCCACCTCCTCCTCTTC
1 CTCCTCCTCCACCACCTCCTCCTCTTC
* *
1041722 CTCCTCCACCGCCACCTCCTCCTCTTC
1 CTCCTCCTCCACCACCTCCTCCTCTTC
*
1041749 CTACTCCTCCACCACCTCCTCCTC-T-
1 CTCCTCCTCCACCACCTCCTCCTCTTC
*
1041774 -TCCTCCTCCACCACCACCTCCTCTTC
1 CTCCTCCTCCACCACCTCCTCCTCTTC
* *
1041800 CTACTCCTCCTCCACCTCCTCCTCTTC
1 CTCCTCCTCCACCACCTCCTCCTCTTC
1041827 CTCC
1 CTCC
1041831 ACCACCTCCT
Statistics
Matches: 237, Mismatches: 31, Indels: 42
0.76 0.10 0.14
Matches are distributed among these distances:
24 21 0.09
25 1 0.00
26 1 0.00
27 122 0.51
28 1 0.00
29 4 0.02
30 44 0.19
31 2 0.01
33 36 0.15
34 1 0.00
35 1 0.00
36 3 0.01
ACGTcount: A:0.09, C:0.62, G:0.02, T:0.28
Consensus pattern (27 bp):
CTCCTCCTCCACCACCTCCTCCTCTTC
Found at i:1041838 original size:27 final size:27
Alignment explanation
Indices: 1041571--1041850 Score: 287
Period size: 27 Copynumber: 10.1 Consensus size: 27
1041561 TCGATGTCCC
* *
1041571 CCTCTTCCTCCACCACCACCACCTCCT
1 CCTCTTCCTCCTCCACCTCCACCTCCT
* * *
1041598 CCTCCTCCTCCTCCTCTTCCAACACCTCCT
1 CCTCTTCCTCCTCCACCT-C--CACCTCCT
* *
1041628 CCTCTTCCTCCTCCACCGCCACCACCACCT
1 CCTCTTCCTCCTCCA---CCTCCACCTCCT
*
1041658 CCTCTTCCTCCTCCTCCTCCACCACCTCCT
1 CCTCTTCCTCCTCCACCT---CCACCTCCT
*
1041688 CCTCTTCCTCCTCCACCGCCACCTCCT
1 CCTCTTCCTCCTCCACCTCCACCTCCT
*
1041715 CCTCTTCCTCCTCCACCGCCACCTCCT
1 CCTCTTCCTCCTCCACCTCCACCTCCT
* * *
1041742 CCTCTTCCTACTCCTCCACCACCTCCT
1 CCTCTTCCTCCTCCACCTCCACCTCCT
*
1041769 CCTCTTCCTCCTCCA---CCACCACCT
1 CCTCTTCCTCCTCCACCTCCACCTCCT
* *
1041793 CCTCTTCCTACTCCTCCTCCACCTCCT
1 CCTCTTCCTCCTCCACCTCCACCTCCT
* * *
1041820 CCTCTTCCTCCACCACCTCCTCTTCCT
1 CCTCTTCCTCCTCCACCTCCACCTCCT
1041847 CCTC
1 CCTC
1041851 CTCCACCAAG
Statistics
Matches: 212, Mismatches: 29, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
24 21 0.10
27 122 0.58
28 1 0.00
30 66 0.31
32 1 0.00
33 1 0.00
ACGTcount: A:0.10, C:0.62, G:0.01, T:0.28
Consensus pattern (27 bp):
CCTCTTCCTCCTCCACCTCCACCTCCT
Found at i:1041954 original size:4 final size:4
Alignment explanation
Indices: 1041945--1042058 Score: 205
Period size: 4 Copynumber: 29.0 Consensus size: 4
1041935 TGATGTTGTG
1041945 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
*
1041993 AGAC AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1042041 AGAT AGAT --AT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT
1042059 GACAAAAAAG
Statistics
Matches: 106, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
4 104 0.98
ACGTcount: A:0.50, C:0.01, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:1043604 original size:1 final size:1
Alignment explanation
Indices: 1043598--1043627 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1043588 TATATATATA
1043598 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1043628 ACATCTACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1043775 original size:15 final size:16
Alignment explanation
Indices: 1043750--1043783 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1043740 GTCGAAACCT
1043750 ACAGCGACTGAAACTG
1 ACAGCGACTGAAACTG
*
1043766 ACAG-GACTGAAATTG
1 ACAGCGACTGAAACTG
1043781 ACA
1 ACA
1043784 CGCCCTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.15
Consensus pattern (16 bp):
ACAGCGACTGAAACTG
Found at i:1045170 original size:41 final size:39
Alignment explanation
Indices: 1045124--1045264 Score: 115
Period size: 41 Copynumber: 3.5 Consensus size: 39
1045114 TAATTTAAAT
*
1045124 ATACAATGCAAATAGAAAGTTTTTGAATACAATTGAAAAA
1 ATACAATGCAAATAGAAA-TTTTTGAATACAAATGAAAAA
* * * * *
1045164 GATACAATGCAAATGGAAAATCATAT-AATTCAAATGAAAATT
1 -ATACAATGCAAATAG-AAAT-TTTTGAATACAAATGAAAA-A
* *
1045206 ATACAATGCAAATGAGAAA-TTTAGAATACAAATGAAATTA
1 ATACAATGCAAAT-AGAAATTTTTGAATACAAATGAAA-AA
*
1045246 ATAACAATGCAAATGGAAA
1 AT-ACAATGCAAATAGAAA
1045265 ATCATATAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
39 1 0.01
40 18 0.23
41 54 0.68
42 6 0.08
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.25
Consensus pattern (39 bp):
ATACAATGCAAATAGAAATTTTTGAATACAAATGAAAAA
Found at i:1045202 original size:20 final size:20
Alignment explanation
Indices: 1045165--1045270 Score: 97
Period size: 20 Copynumber: 5.2 Consensus size: 20
1045155 ATTGAAAAAG
1045165 ATACAATGCAAATGGAAAATC
1 ATACAATGCAAAT-GAAAATC
* * *
1045186 ATATAATTCAAATGAAAATT
1 ATACAATGCAAATGAAAATC
1045206 ATACAATGCAAATGAGAAAT-
1 ATACAATGCAAATGA-AAATC
* * * * *
1045226 TTAGAATACAAATGAAATTA
1 ATACAATGCAAATGAAAATC
1045246 ATAACAATGCAAATGGAAAATC
1 AT-ACAATGCAAAT-GAAAATC
1045268 ATA
1 ATA
1045271 TAAATCAAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.04
20 32 0.48
21 25 0.37
22 7 0.10
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (20 bp):
ATACAATGCAAATGAAAATC
Found at i:1045253 original size:82 final size:81
Alignment explanation
Indices: 1045123--1045279 Score: 228
Period size: 82 Copynumber: 1.9 Consensus size: 81
1045113 TTAATTTAAA
* *
1045123 TATACAATGCAAATAGAAAGTTTTTGAATACAATTGAAAAAGATACAATGCAAATGGAAAATCAT
1 TATACAATGCAAATAGAAAG-TTTAGAATACAAATGAAAAAGATACAATGCAAATGGAAAATCAT
*
1045188 ATAATTCAAATGAAAAT
65 ATAAATCAAATGAAAAT
*
1045205 TATACAATGCAAATGAGAAA-TTTAGAATACAAATGAAATTA-ATAACAATGCAAATGGAAAATC
1 TATACAATGCAAAT-AGAAAGTTTAGAATACAAATGAAA-AAGAT-ACAATGCAAATGGAAAATC
1045268 ATATAAATCAAA
63 ATATAAATCAAA
1045280 ATAATTAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
81 18 0.26
82 45 0.66
83 5 0.07
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.25
Consensus pattern (81 bp):
TATACAATGCAAATAGAAAGTTTAGAATACAAATGAAAAAGATACAATGCAAATGGAAAATCATA
TAAATCAAATGAAAAT
Found at i:1045286 original size:41 final size:40
Alignment explanation
Indices: 1045165--1045287 Score: 114
Period size: 41 Copynumber: 3.0 Consensus size: 40
1045155 ATTGAAAAAG
* *
1045165 ATACAATGCAAATGGAAAATCATATAATTCAAATGAAAATT-
1 ATACAATGCAAATGGAAAATCATATAAATCAAA--ATAATTA
1045206 ATACAATGCAAAT-GAGAAAT--T-TAGAAT-ACAAATGAAATTA
1 ATACAATGCAAATGGA-AAATCATATA-AATCA-AAAT--AATTA
1045246 ATAACAATGCAAATGGAAAATCATATAAATCAAAATAATTA
1 AT-ACAATGCAAATGGAAAATCATATAAATCAAAATAATTA
1045287 A
1 A
1045288 AAATGAAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 24
0.72 0.02 0.26
Matches are distributed among these distances:
37 1 0.01
38 3 0.04
39 9 0.13
40 4 0.06
41 38 0.56
42 2 0.03
43 8 0.12
44 3 0.04
ACGTcount: A:0.56, C:0.09, G:0.10, T:0.25
Consensus pattern (40 bp):
ATACAATGCAAATGGAAAATCATATAAATCAAAATAATTA
Found at i:1045337 original size:21 final size:20
Alignment explanation
Indices: 1045288--1045340 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
1045278 AAATAATTAA
*
1045288 AAATGAAAATTATAGATCAC
1 AAATGAAAATTATAAATCAC
1045308 AAATAGAAAATTAATGAAAT-AC
1 AAAT-GAAAATT-AT-AAATCAC
1045330 AAATGAAAATT
1 AAATGAAAATT
1045341 TACACAATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.14
21 14 0.48
22 8 0.28
23 3 0.10
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.25
Consensus pattern (20 bp):
AAATGAAAATTATAAATCAC
Found at i:1047669 original size:2 final size:2
Alignment explanation
Indices: 1047662--1047690 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1047652 GCGCTTGTTA
1047662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1047691 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1048354 original size:17 final size:17
Alignment explanation
Indices: 1048332--1048374 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1048322 TGTATTCTTA
1048332 TAATCGATACACTGTCG
1 TAATCGATACACTGTCG
1048349 TAATCGATACACTGTCG
1 TAATCGATACACTGTCG
*
1048366 TAATTGATA
1 TAATCGATA
1048375 GATTTACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (17 bp):
TAATCGATACACTGTCG
Found at i:1048622 original size:36 final size:37
Alignment explanation
Indices: 1048572--1048650 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 37
1048562 ACTCATACCT
* *
1048572 CAATGTTATACAAT-ATTAACCTTCTCATGCCT-CATA
1 CAATATTATACAATAATTAACATTCTCATGCCTCCA-A
1048608 CAATATTATACAATACATTAACATTCTCATGCCTCCAA
1 CAATATTATACAATA-ATTAACATTCTCATGCCTCCAA
1048646 CAATA
1 CAATA
1048651 CGATACAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 13 0.34
38 23 0.61
39 2 0.05
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (37 bp):
CAATATTATACAATAATTAACATTCTCATGCCTCCAA
Found at i:1048657 original size:38 final size:38
Alignment explanation
Indices: 1048586--1048667 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
1048576 GTTATACAAT
* **
1048586 ATTAACCTTCTCATGCCTCATACAATATTATACAATAC
1 ATTAACATTCTCATGCCTCATACAATACGATACAATAC
*
1048624 ATTAACATTCTCATGCCTCCA-ACAATACGATACAGTAC
1 ATTAACATTCTCATGCCT-CATACAATACGATACAATAC
*
1048662 AATAAC
1 ATTAAC
1048668 GTCAATATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 36 0.95
39 2 0.05
ACGTcount: A:0.39, C:0.27, G:0.05, T:0.29
Consensus pattern (38 bp):
ATTAACATTCTCATGCCTCATACAATACGATACAATAC
Found at i:1048942 original size:12 final size:15
Alignment explanation
Indices: 1048875--1048945 Score: 117
Period size: 15 Copynumber: 4.7 Consensus size: 15
1048865 GATCTTCATA
1048875 ATAGAGTAGTATATT
1 ATAGAGTAGTATATT
1048890 ATAGAGTTA-TATATT
1 ATAGAG-TAGTATATT
1048905 ATAGAGTAGTATATT
1 ATAGAGTAGTATATT
1048920 ATAGAGTAGTATATT
1 ATAGAGTAGTATATT
*
1048935 AAAGAGTAGTA
1 ATAGAGTAGTA
1048946 AAGTTTGTGG
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
14 2 0.04
15 49 0.92
16 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (15 bp):
ATAGAGTAGTATATT
Found at i:1051653 original size:14 final size:15
Alignment explanation
Indices: 1051626--1051654 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1051616 CTAAACAATC
1051626 AAGTAAAAATCATTA
1 AAGTAAAAATCATTA
1051641 AAGTAAAAA-CATTA
1 AAGTAAAAATCATTA
1051655 CCAAGATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (15 bp):
AAGTAAAAATCATTA
Found at i:1051972 original size:54 final size:54
Alignment explanation
Indices: 1051855--1052291 Score: 704
Period size: 54 Copynumber: 8.1 Consensus size: 54
1051845 AATTATTGTA
* *
1051855 GTACTCCTCAGTTTGTTATAACGAGTCAATGTATA-TCCTCAGTCCAAGACTGT
1 GTACTCCTCAGTGTCTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
*
1051908 GTACTCCTCAGTGTATTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
1 GTACTCCTCAGTGTCTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
* *
1051962 GTACTCCTCAGTGTCTTATAACGAGTCAATGTGTATTCCTCAGTCCAAGACTGC
1 GTACTCCTCAGTGTCTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
*
1052016 GTACTCCTCAGTGTGTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
1 GTACTCCTCAGTGTCTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
1052070 GTACTCCTCA-TCGTCTTATAACGAGTCAATGTATA-TCCTCAGTCCAAGACTGT
1 GTACTCCTCAGT-GTCTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
1052123 GTACTCCTCAGTGTCTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
1 GTACTCCTCAGTGTCTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
*
1052177 GTACTCCTCA-TCGTCTTATAACGAGTCAATGTATATTCCTTATGCAGTCTAAGACTGT
1 GTACTCCTCAGT-GTCTTATAACGAGTCAATGTATATTCC---T-CAGTCCAAGACTGT
* *
1052235 GTACTCCTCAGTTTGTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACT-T
1 GTACTCCTCAGTGTCTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
1052288 GTAC
1 GTAC
1052292 GTGTATACGT
Statistics
Matches: 361, Mismatches: 13, Indels: 20
0.92 0.03 0.05
Matches are distributed among these distances:
53 91 0.25
54 219 0.61
55 1 0.00
57 1 0.00
58 48 0.13
59 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (54 bp):
GTACTCCTCAGTGTCTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGT
Found at i:1052120 original size:161 final size:162
Alignment explanation
Indices: 1051855--1052291 Score: 713
Period size: 161 Copynumber: 2.7 Consensus size: 162
1051845 AATTATTGTA
*
1051855 GTACTCCTCAGTTTGTTATAACGAGTCAATGTATA-TCCTCAGTCCAAGACTGTGTACTCCTCAG
1 GTACTCCTCAGTGTGTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGTGTACTCCTCAG
1051919 TGTATTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGTGTACTCCTCAGTGTCTTATAAC
66 TGTATTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGTGTACTCCTCAGTGTCTTATAAC
*
1051984 GAGTCAATGTGTATTCCTCAGTCCAAGACTGC
131 GAGTCAATGTATATTCCTCAGTCCAAGACTGC
1052016 GTACTCCTCAGTGTGTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGTGTACTCCTCA-
1 GTACTCCTCAGTGTGTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGTGTACTCCTCAG
*
1052080 TCGTCTTATAACGAGTCAATGTATA-TCCTCAGTCCAAGACTGTGTACTCCTCAGTGTCTTATAA
66 T-GTATTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGTGTACTCCTCAGTGTCTTATAA
*
1052144 CGAGTCAATGTATATTCCTCAGTCCAAGACTGT
130 CGAGTCAATGTATATTCCTCAGTCCAAGACTGC
* *
1052177 GTACTCCTCA-TCGTCTTATAACGAGTCAATGTATATTCCTTATGCAGTCTAAGACTGTGTACTC
1 GTACTCCTCAGT-GTGTTATAACGAGTCAATGTATATTCC---T-CAGTCCAAGACTGTGTACTC
* *
1052241 CTCAGTTTGTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACT-TGTAC
61 CTCAGTGTATTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGTGTAC
1052292 GTGTATACGT
Statistics
Matches: 259, Mismatches: 8, Indels: 14
0.92 0.03 0.05
Matches are distributed among these distances:
160 1 0.00
161 141 0.54
162 50 0.19
164 1 0.00
165 49 0.19
166 17 0.07
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (162 bp):
GTACTCCTCAGTGTGTTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGTGTACTCCTCAG
TGTATTATAACGAGTCAATGTATATTCCTCAGTCCAAGACTGTGTACTCCTCAGTGTCTTATAAC
GAGTCAATGTATATTCCTCAGTCCAAGACTGC
Found at i:1058374 original size:2 final size:2
Alignment explanation
Indices: 1058369--1058400 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1058359 TTCTAAATAA
1058369 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1058401 ATATTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1059947 original size:21 final size:21
Alignment explanation
Indices: 1059918--1060134 Score: 194
Period size: 21 Copynumber: 10.6 Consensus size: 21
1059908 TGGATATGGA
*
1059918 GGATATGGCGGGATTGGAGGT
1 GGATATGGCGGCATTGGAGGT
*
1059939 GGCTATGGCGGCATTGGAGGT
1 GGATATGGCGGCATTGGAGGT
*
1059960 GGCTATGGCGGCATTGGAGGT
1 GGATATGGCGGCATTGGAGGT
*
1059981 GGATATGGCGGGATTGGAGGT
1 GGATATGGCGGCATTGGAGGT
* * * *
1060002 GGATACGGTGGAATCGGAGGT
1 GGATATGGCGGCATTGGAGGT
*
1060023 GGATATGGTGGC-TT--AGGT
1 GGATATGGCGGCATTGGAGGT
* * * *
1060041 GGATATGGTGGAATCGGGGGT
1 GGATATGGCGGCATTGGAGGT
* * * *
1060062 GGTTATGGTGGAATCGGAGGT
1 GGATATGGCGGCATTGGAGGT
1060083 GGATATGGCGGC-TT-G-GGT
1 GGATATGGCGGCATTGGAGGT
* * * *
1060101 GGATATGGTGGAATCGGGGGT
1 GGATATGGCGGCATTGGAGGT
*
1060122 GGATATGGTGGCA
1 GGATATGGCGGCA
1060135 AAATGAATTA
Statistics
Matches: 166, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
18 28 0.17
19 3 0.02
20 3 0.02
21 132 0.80
ACGTcount: A:0.18, C:0.08, G:0.49, T:0.25
Consensus pattern (21 bp):
GGATATGGCGGCATTGGAGGT
Found at i:1059978 original size:60 final size:60
Alignment explanation
Indices: 1059915--1060132 Score: 229
Period size: 60 Copynumber: 3.6 Consensus size: 60
1059905 TGGTGGATAT
* * * * *
1059915 GGAGGATATGGCGGGATTGGAGGTGGCTATGGCGGCATTGGAGGTGGCTATGGCGGCATTGGA
1 GGAGGATATGGCGGGATTGGAGGTGGATATGGTGGAATCGGAGGTGGATATGGCGGC-TT--A
* * *
1059978 GGTGGATATGGCGGGATTGGAGGTGGATACGGTGGAATCGGAGGTGGATATGGTGGCTTA
1 GGAGGATATGGCGGGATTGGAGGTGGATATGGTGGAATCGGAGGTGGATATGGCGGCTTA
* * * * * * *
1060038 GGTGGATATGGTGGAATCGGGGGTGGTTATGGTGGAATCGGAGGTGGATATGGCGGCTTG
1 GGAGGATATGGCGGGATTGGAGGTGGATATGGTGGAATCGGAGGTGGATATGGCGGCTTA
* * * * *
1060098 GGTGGATATGGTGGAATCGGGGGTGGATATGGTGG
1 GGAGGATATGGCGGGATTGGAGGTGGATATGGTGG
1060133 CAAAATGAAT
Statistics
Matches: 138, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
60 87 0.63
62 2 0.01
63 49 0.36
ACGTcount: A:0.18, C:0.07, G:0.50, T:0.25
Consensus pattern (60 bp):
GGAGGATATGGCGGGATTGGAGGTGGATATGGTGGAATCGGAGGTGGATATGGCGGCTTA
Found at i:1061611 original size:2 final size:2
Alignment explanation
Indices: 1061604--1061635 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1061594 ATGTCATGGC
1061604 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1061636 GTGTCAGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1062796 original size:4 final size:4
Alignment explanation
Indices: 1062787--1062821 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1062777 AAAGTTTATG
*
1062787 GACA GACA GACA GACA GGCA GACA GAC- GACA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA
1062822 AAATGTGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.46, C:0.26, G:0.29, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:1069909 original size:34 final size:34
Alignment explanation
Indices: 1069866--1070299 Score: 696
Period size: 34 Copynumber: 12.8 Consensus size: 34
1069856 CTTGTTTAAG
1069866 TCTTATGATATAGAGGATACCCATGTTGATCTAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
1069900 TCTTATGATATAGAGGATACGTACCCATGTTGATCTAT
1 TCTTATGATATAGAGG--A--TACCCATGTTGATCTAT
*
1069938 TCTTATGATATAGAGGATACCCATGTTGATTTAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
*
1069972 TCTTATGATATAG-GTATACCCATGTTGATCTAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
*
1070005 TCTTATGATATAGAGGATACCCATGTTGATTTAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
*
1070039 TCTTATGATATAG-GTATACCCATGTTGATCTAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
*
1070072 TCTTATGATATAGAGGATACCCATGTTGATTTAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
*
1070106 TCTTATGATATAG-GTATACCCATGTTGATCTAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
1070139 TCTTATGATATAGAGGATACCCATGTTGATCTAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
*
1070173 TCTTATGATATAG-GTATACCCATGTTGATCTAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
*
1070206 TCTTATGACATAGAGGATACCCATGTTGATCTAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
* * *
1070240 TTTTATGATATATAGGATACCCATGTTGATATAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTAT
*
1070274 TCTTATGACATAGAGGATACCCATGT
1 TCTTATGATATAGAGGATACCCATGT
1070300 CAACTTGATC
Statistics
Matches: 370, Mismatches: 22, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
33 124 0.34
34 211 0.57
36 2 0.01
38 33 0.09
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (34 bp):
TCTTATGATATAGAGGATACCCATGTTGATCTAT
Found at i:1070029 original size:67 final size:67
Alignment explanation
Indices: 1069866--1070299 Score: 735
Period size: 67 Copynumber: 6.4 Consensus size: 67
1069856 CTTGTTTAAG
1069866 TCTTATGATATAGAGGATACCCATGTTGATCTATTCTTATGATATAGAGGATACGTACCCATGTT
1 TCTTATGATATAGAGGATACCCATGTTGATCTATTCTTATGATAT--AGG-TA--TACCCATGTT
1069931 GATCTAT
61 GATCTAT
*
1069938 TCTTATGATATAGAGGATACCCATGTTGATTTATTCTTATGATATAGGTATACCCATGTTGATCT
1 TCTTATGATATAGAGGATACCCATGTTGATCTATTCTTATGATATAGGTATACCCATGTTGATCT
1070003 AT
66 AT
*
1070005 TCTTATGATATAGAGGATACCCATGTTGATTTATTCTTATGATATAGGTATACCCATGTTGATCT
1 TCTTATGATATAGAGGATACCCATGTTGATCTATTCTTATGATATAGGTATACCCATGTTGATCT
1070070 AT
66 AT
*
1070072 TCTTATGATATAGAGGATACCCATGTTGATTTATTCTTATGATATAGGTATACCCATGTTGATCT
1 TCTTATGATATAGAGGATACCCATGTTGATCTATTCTTATGATATAGGTATACCCATGTTGATCT
1070137 AT
66 AT
1070139 TCTTATGATATAGAGGATACCCATGTTGATCTATTCTTATGATATAGGTATACCCATGTTGATCT
1 TCTTATGATATAGAGGATACCCATGTTGATCTATTCTTATGATATAGGTATACCCATGTTGATCT
1070204 AT
66 AT
* *
1070206 TCTTATGACATAGAGGATACCCATGTTGATCTATTTTTATGATATATAGG-ATACCCATGTTGAT
1 TCTTATGATATAGAGGATACCCATGTTGATCTATTCTTATG--ATATAGGTATACCCATGTTGAT
*
1070270 ATAT
64 CTAT
*
1070274 TCTTATGACATAGAGGATACCCATGT
1 TCTTATGATATAGAGGATACCCATGT
1070300 CAACTTGATC
Statistics
Matches: 355, Mismatches: 5, Indels: 8
0.96 0.01 0.02
Matches are distributed among these distances:
67 256 0.72
68 43 0.12
69 9 0.03
70 3 0.01
72 44 0.12
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (67 bp):
TCTTATGATATAGAGGATACCCATGTTGATCTATTCTTATGATATAGGTATACCCATGTTGATCT
AT
Found at i:1070588 original size:17 final size:16
Alignment explanation
Indices: 1070568--1070606 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1070558 AAAAAAAAGG
*
1070568 AAACATCAATAAAATAC
1 AAACATCAACAAAA-AC
*
1070585 AAACAACAACAAAAAC
1 AAACATCAACAAAAAC
1070601 AAACAT
1 AAACAT
1070607 GAAAATTCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.69, C:0.21, G:0.00, T:0.10
Consensus pattern (16 bp):
AAACATCAACAAAAAC
Found at i:1074619 original size:4 final size:4
Alignment explanation
Indices: 1074588--1074642 Score: 67
Period size: 4 Copynumber: 14.0 Consensus size: 4
1074578 TTTTACGAAT
* * **
1074588 TAAA -AAA TACA TAAA TAGA TCGA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1074635 TAAA TAAA
1 TAAA TAAA
1074643 GTTTCTCTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 3 0.07
4 41 0.93
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:1075002 original size:2 final size:2
Alignment explanation
Indices: 1074995--1075057 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1074985 AATCAGTTTG
1074995 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1075037 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
1075058 GTCGGACCGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1076634 original size:15 final size:15
Alignment explanation
Indices: 1076616--1076669 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1076606 CTTACGGGTA
1076616 ACAAATTTACAGATC
1 ACAAATTTACAGATC
** *
1076631 ACAAACGTACACATC
1 ACAAATTTACAGATC
*
1076646 AC-AATCTTATAGATC
1 ACAAAT-TTACAGATC
1076661 ACAAATTTA
1 ACAAATTTA
1076670 ACTTATAGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 2 0.07
15 25 0.83
16 3 0.10
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (15 bp):
ACAAATTTACAGATC
Found at i:1076690 original size:20 final size:20
Alignment explanation
Indices: 1076651--1076690 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1076641 ACATCACAAT
*
1076651 CTTATAGATCACAAATTTAA
1 CTTATAGATCACAAACTTAA
*
1076671 CTTATAGATCACGAACTTAA
1 CTTATAGATCACAAACTTAA
1076691 AGATCACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (20 bp):
CTTATAGATCACAAACTTAA
Found at i:1079380 original size:33 final size:33
Alignment explanation
Indices: 1079340--1079402 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
1079330 ACAGAACCAG
*
1079340 AGACAGGATTATCTTAAGGTAAGAAACAGATAT
1 AGACAGGATTATCTCAAGGTAAGAAACAGATAT
1079373 AGACAGGATTATCTCAAGGTAAGAAACAGA
1 AGACAGGATTATCTCAAGGTAAGAAACAGA
1079403 ATTATCTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21
Consensus pattern (33 bp):
AGACAGGATTATCTCAAGGTAAGAAACAGATAT
Found at i:1079406 original size:23 final size:23
Alignment explanation
Indices: 1079375--1079443 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1079365 ACAGATATAG
*
1079375 ACAGGATTATCTCAAGGTAAGAA
1 ACAGAATTATCTCAAGGTAAGAA
*
1079398 ACAGAATTATCTCAAGGTATGAA
1 ACAGAATTATCTCAAGGTAAGAA
* * *
1079421 ACAGACTTATCTGAACGTAAGAA
1 ACAGAATTATCTCAAGGTAAGAA
1079444 CCACACAAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.23
Consensus pattern (23 bp):
ACAGAATTATCTCAAGGTAAGAA
Done.