Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1154
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: 1159333
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.30
Warning! 97731 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:527578 original size:83 final size:84
Alignment explanation
Indices: 527439--527602 Score: 276
Period size: 83 Copynumber: 2.0 Consensus size: 84
527429 TAATGCTCTA
*
527439 CTAATAGTTTAAAGAAATAACTCAAACAGGGTAGCAAATGATATTGAATTAG-TTTTTTTTACAA
1 CTAATAGTTTAAAGAAATAACTCAAACAGGGTAGCAAATGATATTCAATTAGTTTTTTTTTACAA
527503 TTATTAATTTAATTTTATT
66 TTATTAATTTAATTTTATT
* *
527522 CTAATAGTTTAAAGAAATAACTCAAACAGGGTAGCAAATGATATTCAGTTAGTTTTTTTTTTCCA
1 CTAATAGTTTAAAGAAATAACTCAAACAGGGTAGCAAATGATATTCAATTAG-TTTTTTTTTACA
*
527587 ATTTTTAATTTAATTT
65 ATTATTAATTTAATTT
527603 AATTAGGGTA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
83 50 0.67
85 25 0.33
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (84 bp):
CTAATAGTTTAAAGAAATAACTCAAACAGGGTAGCAAATGATATTCAATTAGTTTTTTTTTACAA
TTATTAATTTAATTTTATT
Found at i:531259 original size:4 final size:4
Alignment explanation
Indices: 531250--531293 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
531240 ACTTTCAAGT
531250 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
531294 TATATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:531298 original size:2 final size:2
Alignment explanation
Indices: 531291--531322 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
531281 AGATAGATAG
531291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
531323 NNNNNNNNNN
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:534475 original size:2 final size:2
Alignment explanation
Indices: 534470--534513 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
534460 NNNNNNTACC
534470 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
534512 TA
1 TA
534514 AGCTAAACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:549268 original size:21 final size:21
Alignment explanation
Indices: 549205--549270 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
549195 GGCAAGCCAG
549205 TTATTTATGTCACAT-T-CAAC
1 TTATTTATGTCA-ATATGCAAC
* ** * **
549225 TTAGTTATGTTGACATGTTAC
1 TTATTTATGTCAATATGCAAC
549246 TTATTTATGTCAATATGCAAC
1 TTATTTATGTCAATATGCAAC
549267 TTAT
1 TTAT
549271 GTTGGCATGC
Statistics
Matches: 32, Mismatches: 12, Indels: 3
0.68 0.26 0.06
Matches are distributed among these distances:
19 1 0.03
20 10 0.31
21 21 0.66
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.47
Consensus pattern (21 bp):
TTATTTATGTCAATATGCAAC
Found at i:549334 original size:21 final size:21
Alignment explanation
Indices: 549283--549335 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
549273 TGGCATGCAT
**
549283 CTTATTTATGTTGACATGCAA
1 CTTATTTATGTTGACATAAAA
* *
549304 CATGA-ATATGTTGACATAAAA
1 C-TTATTTATGTTGACATAAAA
549325 CTTATTTATGT
1 CTTATTTATGT
549336 CAACATACGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (21 bp):
CTTATTTATGTTGACATAAAA
Found at i:549341 original size:21 final size:21
Alignment explanation
Indices: 549317--549356 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
549307 GAATATGTTG
*
549317 ACATAAAACTTATTTATGTCA
1 ACATAAAACTTAATTATGTCA
**
549338 ACATACGACTTAATTATGT
1 ACATAAAACTTAATTATGT
549357 TTAAATACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (21 bp):
ACATAAAACTTAATTATGTCA
Found at i:573711 original size:30 final size:30
Alignment explanation
Indices: 573686--574143 Score: 684
Period size: 30 Copynumber: 15.3 Consensus size: 30
573676 CAGCCCAAAA
* *
573686 ATCCAAAACAAGAAACTGAAAAGCCCAGAG
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
*
573716 ATCCAATACAAGAAACTGAAAAGCCCAGAG
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
* *
573746 ATCCAATACAAGAAACTGAAAAGCCCAGAA
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
*
573776 ATCCAATACAAGAAACTGAAAAGCCCAGAG
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
*
573806 ATCCGATACAGGAAACTGAAAAGCCCAGAG
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
* * *
573836 ATCCAATACAAGAAACTGAAGAGCCCAGAA
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
*
573866 ATCCAATACAGAAAACTGAAAAGCCCAGAG
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
* * * *
573896 ATCCAGTAAAGGAAACTGAAAAGTCCAGAA
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
573926 ATCCAATACAGGAAACTGAAAAGCCCAGAG
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
* *
573956 ATCCAATACAAGAAACTGAAAAGCCCAGAA
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
*
573986 ATTCAATACAGGAAACTGAAAAGCCCAGAG
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
* * * *
574016 ATCCAGTA-ATGGAAACTAAAAAGTCCAGAA
1 ATCCAATACA-GGAAACTGAAAAGCCCAGAG
574046 ATCCAATACAGGAAACTGAAAAGCCCAGAG
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
574076 ATCCAATACAGGAAACTGAAAAGCCCAGAG
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
* *
574106 ATCCAATACAGGAAACTGAAAAGTCCAGAA
1 ATCCAATACAGGAAACTGAAAAGCCCAGAG
574136 ATCCAATA
1 ATCCAATA
574144 AAGAAGCAGC
Statistics
Matches: 388, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
29 1 0.00
30 386 0.99
31 1 0.00
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.11
Consensus pattern (30 bp):
ATCCAATACAGGAAACTGAAAAGCCCAGAG
Found at i:575880 original size:2 final size:2
Alignment explanation
Indices: 575873--575911 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
575863 AACAGAGAAA
* *
575873 CT CT CT CT CT CC CT CT CT CT CT CT CT CT TT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
575912 GTGAATTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:576138 original size:43 final size:45
Alignment explanation
Indices: 576077--576289 Score: 169
Period size: 47 Copynumber: 4.8 Consensus size: 45
576067 TTTGAGGTAT
* *
576077 TTTCTGATATCAGAAAATGA-T-TTTTTGATATCAAGATTTCTAA
1 TTTCTGATATCAGAAAATGATTATTTTTGATATCAAGAATTCGAA
*
576120 TTTCTGATATCAGAAAATGATTTAATTTTTGATATCAAGAATTCGGA
1 TTTCTGATATCAGAAAATGA-TT-ATTTTTGATATCAAGAATTCGAA
* * * * *
576167 -TTCTTGATATCAGAAAATACGATCCATTTTTCTTATATCAAAAAATCGAT
1 TTTC-TGATATCAGAAAAT--GAT-TA-TTTT-TGATATCAAGAATTCGAA
* *
576217 TTTGTGATATC--AAAAT-ATCA-TTTTGATATC-AGAAATTCG-A
1 TTTCTGATATCAGAAAATGATTATTTTTGATATCAAG-AATTCGAA
*
576257 TTTTTGATATCAGAAAATGA-T-TTTTTGATATCA
1 TTTCTGATATCAGAAAATGATTATTTTTGATATCA
576290 GAAATTCAAA
Statistics
Matches: 137, Mismatches: 16, Indels: 34
0.73 0.09 0.18
Matches are distributed among these distances:
40 11 0.08
41 11 0.08
42 18 0.13
43 21 0.15
44 2 0.01
45 3 0.02
46 3 0.02
47 33 0.24
48 7 0.05
49 6 0.04
50 20 0.15
51 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (45 bp):
TTTCTGATATCAGAAAATGATTATTTTTGATATCAAGAATTCGAA
Found at i:576239 original size:21 final size:22
Alignment explanation
Indices: 576075--576343 Score: 125
Period size: 22 Copynumber: 11.8 Consensus size: 22
576065 TTTTTGAGGT
576075 ATTTTCTGATATCAGAAA-AT-G
1 ATTTT-TGATATCAGAAATATCG
* * *
576096 ATTTTTTGATATCA-AGATTTCTA
1 A-TTTTTGATATCAGAAATATC-G
* **
576119 ATTTCTGATATCAGAAAATGATTTA
1 ATTTTTGATATCAG-AAAT-A-TCG
576144 ATTTTTGATATCA-AGAAT-TCGG
1 ATTTTTGATATCAGA-AATATC-G
* *
576166 ATTCTTGATATCAGAAAATACGATCC
1 ATTTTTGATATCAG-AAAT---ATCG
* *
576192 ATTTTTCTTATATCA-AAAAATCG
1 A-TTTT-TGATATCAGAAATATCG
576215 ATTTTGTGATATCA-AAATATC-
1 ATTTT-TGATATCAGAAATATCG
576236 A-TTTTGATATCAGAAAT-TCG
1 ATTTTTGATATCAGAAATATCG
576256 ATTTTTGATATCAGAAA-AT-G
1 ATTTTTGATATCAGAAATATCG
*
576276 ATTTTTTGATATCAGAAATTCAAACTG
1 A-TTTTTGATATCAGAAA-T--ATC-G
*
576303 ATTTTTTGATATCAAGAATTAT--
1 A-TTTTTGATATC-AGAAATATCG
576325 ATTTTTTGATATCAGAAAT
1 A-TTTTTGATATCAGAAAT
576344 TCAAATAAAA
Statistics
Matches: 195, Mismatches: 23, Indels: 60
0.70 0.08 0.22
Matches are distributed among these distances:
19 10 0.05
20 12 0.06
21 49 0.25
22 57 0.29
23 9 0.05
24 7 0.04
25 15 0.08
26 5 0.03
27 20 0.10
28 11 0.06
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (22 bp):
ATTTTTGATATCAGAAATATCG
Found at i:576259 original size:20 final size:21
Alignment explanation
Indices: 576201--576345 Score: 111
Period size: 21 Copynumber: 6.6 Consensus size: 21
576191 CATTTTTCTT
* *
576201 ATATCAAAAAATCGATTTTGTG
1 ATATCAGAAATTCGATTTT-TG
576223 ATATCA-AAATATC-A-TTTTG
1 ATATCAGAAAT-TCGATTTTTG
576242 ATATCAGAAATTCGATTTTTG
1 ATATCAGAAATTCGATTTTTG
*
576263 ATATCAGAAAAT-GATTTTTTG
1 ATATCAGAAATTCGA-TTTTTG
576284 ATATCAGAAATTCAAACTGATTTTTTG
1 ATATCAGAAATT----C-GA-TTTTTG
**
576311 ATATCA-AGAATTATATTTTTTG
1 ATATCAGA-AATTCGA-TTTTTG
576333 ATATCAGAAATTC
1 ATATCAGAAATTC
576346 AAATAAAATG
Statistics
Matches: 104, Mismatches: 6, Indels: 26
0.76 0.04 0.19
Matches are distributed among these distances:
19 10 0.10
20 10 0.10
21 37 0.36
22 26 0.25
23 1 0.01
26 1 0.01
27 19 0.18
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (21 bp):
ATATCAGAAATTCGATTTTTG
Found at i:576283 original size:42 final size:41
Alignment explanation
Indices: 576201--576345 Score: 141
Period size: 49 Copynumber: 3.3 Consensus size: 41
576191 CATTTTTCTT
* * *
576201 ATATCAAAAAATCGATTTTGTGATATC--AAAATATCATTTTG
1 ATATCAGAAATTCGATTTT-TGATATCAGAAAATAT-TTTTTG
576242 ATATCAGAAATTCGATTTTTGATATCAGAAAATGATTTTTTG
1 ATATCAGAAATTCGATTTTTGATATCAGAAAAT-ATTTTTTG
*
576284 ATATCAGAAATTCAAACTGATTTTTTGATATCAAGAATTATATTTTTTG
1 ATATCAGAAATT----C-GA-TTTTTGATATC-AGAA-AATATTTTTTG
576333 ATATCAGAAATTC
1 ATATCAGAAATTC
576346 AAATAAAATG
Statistics
Matches: 89, Mismatches: 4, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
40 7 0.08
41 17 0.19
42 22 0.25
43 2 0.02
45 1 0.01
46 1 0.01
47 2 0.02
48 11 0.12
49 24 0.27
50 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (41 bp):
ATATCAGAAATTCGATTTTTGATATCAGAAAATATTTTTTG
Found at i:576312 original size:27 final size:26
Alignment explanation
Indices: 576271--576349 Score: 105
Period size: 27 Copynumber: 3.2 Consensus size: 26
576261 TGATATCAGA
576271 AAATGATTTTTTGATATCAGAAATTC
1 AAATGATTTTTTGATATCAGAAATTC
576297 AAACTGATTTTTTGATATCA-AGAATT-
1 AAA-TGATTTTTTGATATCAGA-AATTC
576323 --AT-ATTTTTTGATATCAGAAATTC
1 AAATGATTTTTTGATATCAGAAATTC
576346 AAAT
1 AAAT
576350 AAAATGGCGA
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
22 18 0.38
23 2 0.04
24 1 0.02
25 2 0.04
26 4 0.09
27 20 0.43
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (26 bp):
AAATGATTTTTTGATATCAGAAATTC
Found at i:577052 original size:22 final size:22
Alignment explanation
Indices: 577024--577153 Score: 129
Period size: 22 Copynumber: 5.7 Consensus size: 22
577014 TGTAGGTCTT
577024 ATTTTCTGATATCAAAAAATCG
1 ATTTTCTGATATCAAAAAATCG
*
577046 ATTTTCTGATATCAGAAAATACAAATG
1 ATTTTCTGATATCAAAAAAT-C----G
* *
577073 ATTTTTTGATATGAAAAAAT-G
1 ATTTTCTGATATCAAAAAATCG
* *
577094 ATTTTTCTGATATCAAGAATTCG
1 A-TTTTCTGATATCAAAAAATCG
*
577117 ATTTTTTTGATATCAAAAAAT-G
1 A-TTTTCTGATATCAAAAAATCG
577139 ATTTTCTGATATCAA
1 ATTTTCTGATATCAA
577154 GAATTCAAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
21 15 0.17
22 36 0.40
23 20 0.22
27 18 0.20
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (22 bp):
ATTTTCTGATATCAAAAAATCG
Found at i:577091 original size:27 final size:28
Alignment explanation
Indices: 577040--577092 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
577030 TGATATCAAA
*
577040 AAATCGATTTTCTGATATCAGAAAATAC
1 AAATCGATTTTCTGATATCAAAAAATAC
* *
577068 AAAT-GATTTTTTGATATGAAAAAAT
1 AAATCGATTTTCTGATATCAAAAAAT
577093 GATTTTTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (28 bp):
AAATCGATTTTCTGATATCAAAAAATAC
Found at i:577135 original size:44 final size:46
Alignment explanation
Indices: 577023--577162 Score: 185
Period size: 49 Copynumber: 3.0 Consensus size: 46
577013 ATGTAGGTCT
* * *
577023 TATTTTCTGATATCAAAAAATCGATTTTCTGATATCAGAAAATACAAA
1 TATTTTTTGATATCAAAAAAT-GATTTTCTGATATCA-AGAATTCAAA
* *
577071 TGATTTTTTGATATGAAAAAATGATTTTTCTGATATCAAGAATTC-GA
1 T-ATTTTTTGATATCAAAAAATGA-TTTTCTGATATCAAGAATTCAAA
577118 T-TTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCAAA
1 TATTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCAAA
577163 AAAATAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
44 20 0.24
45 21 0.26
47 2 0.02
48 8 0.10
49 31 0.38
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (46 bp):
TATTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCAAA
Found at i:577293 original size:22 final size:21
Alignment explanation
Indices: 577257--577325 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
577247 GAATTTGTGG
577257 TATCAAAAAATGATTTTCTGA
1 TATCAAAAAATGATTTTCTGA
* *
577278 TATCACAAAATAGATTTTTTGA
1 TATCAAAAAAT-GATTTTCTGA
* * *
577300 TATC-AATAATTATTTTATGA
1 TATCAAAAAATGATTTTCTGA
577320 TATCAA
1 TATCAA
577326 TAATTCGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 12 0.30
21 15 0.38
22 13 0.32
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (21 bp):
TATCAAAAAATGATTTTCTGA
Found at i:577320 original size:20 final size:20
Alignment explanation
Indices: 577291--577330 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
577281 CACAAAATAG
*
577291 ATTTTTTGATATCAATAATT
1 ATTTTATGATATCAATAATT
577311 ATTTTATGATATCAATAATT
1 ATTTTATGATATCAATAATT
577331 CGAATTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
ATTTTATGATATCAATAATT
Found at i:577342 original size:42 final size:40
Alignment explanation
Indices: 577226--577368 Score: 124
Period size: 42 Copynumber: 3.4 Consensus size: 40
577216 GAAATTCATC
* * *
577226 ATTTTTTGATATCAAGAATTCGAATTTGTGGTATCAAAAAATG
1 ATTTTTTGATATCAA-AATTCGAATTT-TGATATC-AATAATT
* * * *
577269 ATTTTCTGATATCACAAAATAGATTTTTTGATATCAATAATT
1 ATTTTTTGATATCA-AAATTCGA-ATTTTGATATCAATAATT
* *
577311 ATTTTATGATATCAATAATTCGAATTATTGATATCAGATATTT
1 ATTTTTTGATATCAA-AATTCGAATT-TTGATATCA-ATAATT
577354 ATTTTTTTGATATCA
1 A-TTTTTTGATATCA
577369 GAAAATACCT
Statistics
Matches: 81, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
41 3 0.04
42 32 0.40
43 30 0.37
44 16 0.20
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.45
Consensus pattern (40 bp):
ATTTTTTGATATCAAAATTCGAATTTTGATATCAATAATT
Found at i:577345 original size:22 final size:19
Alignment explanation
Indices: 577296--577356 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 19
577286 AATAGATTTT
*
577296 TTGATATCAATAATTATTT
1 TTGATATCAATAATTATTA
577315 TATGATATCAATAATTCGAATTA
1 T-TGATATCAATAATT---ATTA
*
577338 TTGATATCAGATATTTATT
1 TTGATATCA-ATAATTATT
577357 TTTTTGATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 1 0.03
20 17 0.49
22 8 0.23
23 9 0.26
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48
Consensus pattern (19 bp):
TTGATATCAATAATTATTA
Found at i:577370 original size:22 final size:20
Alignment explanation
Indices: 577291--577368 Score: 75
Period size: 22 Copynumber: 3.7 Consensus size: 20
577281 CACAAAATAG
*
577291 ATTTTTTGATATCAATAATT
1 ATTTTTTGATATCAATATTT
* *
577311 ATTTTATGATATCAATAATTCG
1 ATTTTTTGATATCAAT-ATT-T
* *
577333 AATTATTGATATCAGATATTT
1 ATTTTTTGATATCA-ATATTT
577354 ATTTTTTTGATATCA
1 A-TTTTTTGATATCA
577369 GAAAATACCT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 15 0.33
21 3 0.07
22 25 0.56
23 2 0.04
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTTTTTGATATCAATATTT
Found at i:577933 original size:21 final size:21
Alignment explanation
Indices: 577909--577977 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
577899 AAATTACAGT
* *
577909 ATATAATTATGTTAGC-ACTGC
1 ATATAATGATGTTA-CAAATGC
577930 ATATAATGATGTTACAAATGC
1 ATATAATGATGTTACAAATGC
* * * *
577951 ATATAATGTTATTACTATTGC
1 ATATAATGATGTTACAAATGC
577972 ATATAA
1 ATATAA
577978 AAGATATACC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 1 0.02
21 40 0.98
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
ATATAATGATGTTACAAATGC
Found at i:578775 original size:19 final size:19
Alignment explanation
Indices: 578751--578789 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
578741 TTCAAAGGGC
*
578751 ACCTGCACCAAAAACTTTA
1 ACCTGCACCAAAAACCTTA
* *
578770 ACCTGCTCTAAAAACCTTA
1 ACCTGCACCAAAAACCTTA
578789 A
1 A
578790 TCTCCTCCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.31, G:0.05, T:0.23
Consensus pattern (19 bp):
ACCTGCACCAAAAACCTTA
Found at i:579245 original size:18 final size:20
Alignment explanation
Indices: 579222--579262 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
579212 TTGAGTTTTT
579222 TCAAAT-TT-GAGAAAAAAC
1 TCAAATATTGGAGAAAAAAC
579240 TCAAATATTGGAGAAAAAAC
1 TCAAATATTGGAGAAAAAAC
579260 TCA
1 TCA
579263 GACTTTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
19 2 0.10
20 13 0.62
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (20 bp):
TCAAATATTGGAGAAAAAAC
Found at i:583268 original size:16 final size:16
Alignment explanation
Indices: 583245--583294 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
583235 GCCCGAGTTT
583245 CAGGAGAAAACGTACC
1 CAGGAGAAAACGTACC
*
583261 CGGGAGAAAACGTACC
1 CAGGAGAAAACGTACC
*
583277 CAGGAGAAAACATACC
1 CAGGAGAAAACGTACC
583293 CA
1 CA
583295 ATCTTTACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.44, C:0.26, G:0.24, T:0.06
Consensus pattern (16 bp):
CAGGAGAAAACGTACC
Found at i:587470 original size:47 final size:47
Alignment explanation
Indices: 587416--587580 Score: 224
Period size: 47 Copynumber: 3.5 Consensus size: 47
587406 CCTTACAACA
* *
587416 AACTACAGGTAAGTACCCTTCATTCCAAAGACAGTGTAACATTGACC
1 AACTACAGGTAAGTACCGTTCATTCCAAAGACAGTGTAACATTAACC
* *
587463 AACTACAGGTAAGTACCGTTCATTCCAATGACAGTGTACCATTAACC
1 AACTACAGGTAAGTACCGTTCATTCCAAAGACAGTGTAACATTAACC
* * ** *
587510 ACCTACAGGTAAGTACTGTTCATTCCATGGACAGTGT-ACTGTTAACC
1 AACTACAGGTAAGTACCGTTCATTCCAAAGACAGTGTAAC-ATTAACC
*
587557 AACTACAGGTAAGTACCGATCATT
1 AACTACAGGTAAGTACCGTTCATT
587581 TGATGGTCAT
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 1 0.01
47 103 0.99
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (47 bp):
AACTACAGGTAAGTACCGTTCATTCCAAAGACAGTGTAACATTAACC
Found at i:587600 original size:47 final size:47
Alignment explanation
Indices: 587416--587651 Score: 192
Period size: 47 Copynumber: 5.0 Consensus size: 47
587406 CCTTACAACA
** ** * * *
587416 AACTACAGGTAAGTACCCTTCATTCCAAAGACAGTGTAAC-ATTGACC
1 AACTACAGGTAAGTACCGATCATTCCATGGACAGTCT-ACTGTTAACC
* * **
587463 AACTACAGGTAAGTACCGTTCATTCCAAT-GACAGTGTACCATTAACC
1 AACTACAGGTAAGTACCGATCATTCC-ATGGACAGTCTACTGTTAACC
* * * *
587510 ACCTACAGGTAAGTACTGTTCATTCCATGGACAGTGTACTGTTAACC
1 AACTACAGGTAAGTACCGATCATTCCATGGACAGTCTACTGTTAACC
** * *
587557 AACTACAGGTAAGTACCGATCATTTGATGGTCA-TACTATTGTTAACC
1 AACTACAGGTAAGTACCGATCATTCCATGGACAGT-CTACTGTTAACC
* ** * *
587604 AACTACAGGTAAGTAAC-ATTCATTCCACAGTCAGTGTACTGTTAACC
1 AACTACAGGTAAGTACCGA-TCATTCCATGGACAGTCTACTGTTAACC
587651 A
1 A
587652 CTTTTATTGT
Statistics
Matches: 161, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
46 6 0.04
47 153 0.95
48 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (47 bp):
AACTACAGGTAAGTACCGATCATTCCATGGACAGTCTACTGTTAACC
Found at i:590078 original size:53 final size:51
Alignment explanation
Indices: 589952--590381 Score: 169
Period size: 51 Copynumber: 8.5 Consensus size: 51
589942 TTAACAGTAT
* *
589952 AGTCTGGCTACCTGATGCA--TGTTAACTT-T-TTATCTATTTTTACAGTTAG
1 AGTCTGGCTACCTGATGCATGTGTTAA-TTGTCTGA-CTATTATTACAGTTAG
* * *
590001 AGTCCT-GCCACCTGAAGTATGTGTTAATTGTCTGACTATTATTACAGGTATAG
1 AGT-CTGGCTACCTGATGCATGTGTTAATTGTCTGACTATTATTACA-GT-TAG
* * * * *
590054 CGTCTGGCTACCTGATGCATGTGTTAA-TGTCAGACTTTTGTTAGAG-T-G
1 AGTCTGGCTACCTGATGCATGTGTTAATTGTCTGACTATTATTACAGTTAG
* ** *** * *
590102 A--CTGGTTACCTCCTGCACACAG-TAACTT-TCTGGCTATTGTTACAGTTAG
1 AGTCTGGCTACCTGATGCA-TGTGTTAA-TTGTCTGACTATTATTACAGTTAG
* * * * * * * * * * *
590151 AATCTGGCTACATGAAGCATTTGTTGACTGTGTGTCCATTTTTATAGTTAG
1 AGTCTGGCTACCTGATGCATGTGTTAATTGTCTGACTATTATTACAGTTAG
* * * *
590202 ATTCTGGCTACCTG-T--ATGGTGTTAA-TGTCAGACTTTTGTTACAGTTAG
1 AGTCTGGCTACCTGATGCAT-GTGTTAATTGTCTGACTATTATTACAGTTAG
* * * * * * * *
590250 AGTCTGGCTACTTGAAGCATGTGTTAACTGCCTGGCTATTGTTTCAGTGAG
1 AGTCTGGCTACCTGATGCATGTGTTAATTGTCTGACTATTATTACAGTTAG
* * * *
590301 AGTCTGGTTACTTGAAGCATTTAATTTGTTAACTT-TCT-ATCTAATT-TTACAGTTAG
1 AGTCTGGCTACCTGATGC-----ATGTGTTAA-TTGTCTGA-CT-ATTATTACAGTTAG
*
590357 AGTCTGGCTACCTGAAGCATGTGTT
1 AGTCTGGCTACCTGATGCATGTGTT
590382 TTCAGTATTT
Statistics
Matches: 281, Mismatches: 70, Indels: 58
0.69 0.17 0.14
Matches are distributed among these distances:
46 16 0.06
47 14 0.05
48 33 0.12
49 21 0.07
50 13 0.05
51 101 0.36
52 20 0.07
53 23 0.08
56 36 0.13
57 4 0.01
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (51 bp):
AGTCTGGCTACCTGATGCATGTGTTAATTGTCTGACTATTATTACAGTTAG
Found at i:591049 original size:8 final size:8
Alignment explanation
Indices: 591036--591094 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
591026 GGAATCACCT
591036 TGTCCGTC
1 TGTCCGTC
591044 TGTCCGTC
1 TGTCCGTC
591052 TGTCCGTC
1 TGTCCGTC
* *
591060 CGTCTGTC
1 TGTCCGTC
* *
591068 CGTCAGTC
1 TGTCCGTC
591076 TGTCCGTC
1 TGTCCGTC
* *
591084 CGTCTGTC
1 TGTCCGTC
591092 TGT
1 TGT
591095 GCAATCGTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.02, C:0.36, G:0.25, T:0.37
Consensus pattern (8 bp):
TGTCCGTC
Found at i:591062 original size:12 final size:12
Alignment explanation
Indices: 591045--591091 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
591035 TTGTCCGTCT
591045 GTCCGTCTGTCC
1 GTCCGTCTGTCC
591057 GTCCGTCTGTCC
1 GTCCGTCTGTCC
*
591069 GTCAGTCTGTCC
1 GTCCGTCTGTCC
591081 GTCCGTCTGTC
1 GTCCGTCTGTC
591092 TGTGCAATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.02, C:0.38, G:0.26, T:0.34
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:591094 original size:4 final size:4
Alignment explanation
Indices: 591037--591087 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
591027 GAATCACCTT
* * * * *
591037 GTCC GTCT GTCC GTCT GTCC GTCC GTCT GTCC GTCA GTCT GTCC GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
591085 GTC
1 GTC
591088 TGTCTGTGCA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.02, C:0.39, G:0.25, T:0.33
Consensus pattern (4 bp):
GTCC
Found at i:591902 original size:146 final size:146
Alignment explanation
Indices: 591099--591900 Score: 1149
Period size: 146 Copynumber: 5.5 Consensus size: 146
591089 GTCTGTGCAA
591099 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
591164 TTATGACCTAAGGGTGTGTC-TGACCTTGACCCAAGGTCATTCGGGCAATGTCAAGGTAACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
*
591228 AGAAATAA-TACAAAAT
131 AGAAA-AAGTGCAAAAT
* *
591244 TCGTGTCCGGTCCATATCTTTCTTATTGAGAAACATTGGAAGTTCTTAATTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * *
591309 TTATGACCTAAGGGTGTGTAATGACCTTGACCCAAGGTTATTCGGGCAAGGTCAAGGTCACTGGT
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
* *
591374 AGAAAAAATACAAAAAT
131 AGAAAAAGTGC-AAAAT
* * * *
591391 TCTTGTCCGGTCCACATCTTTCGTATGGAGAAACATTGGAAATTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
591456 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
591521 AGAAAAAAG-GCAAAAGT
131 AG-AAAAAGTGCAAAA-T
*
591538 T-GTGTCCGGCCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTTA-TTCACACAAAGATTG
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTC-TTACTTCACACAAAGATTG
* * * **
591601 CTTATGACTTAATGGTGTGTCATGACCTTGATCCAAGGTCATTCGGGCAAGGTCAAGGTCGTTGG
65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGG
591666 --GAAAATAGTGCAAAAT
130 CAGAAAA-AGTGCAAAAT
* * * * *
591682 TCGTGTCCGGT-CATTATCTTACTTATGGAGAAGCATT-GAATGTTCTAACTTAACACAAATATT
1 TCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT
* * * *
591745 GCTTAGGACCAAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTTAAGGTCACTG
64 GCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTG
591810 GCAGAAAAAGTGCAAAAT
129 GCAGAAAAAGTGCAAAAT
* * *
591828 TCGTGTCTGGT-CATTATCTTTCTTATGGAGAAGCATT-GAATGTTCTTACTTCACACAAATATT
1 TCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT
591891 GCTTATGACC
64 GCTTATGACC
591901 AACAGTTTTA
Statistics
Matches: 595, Mismatches: 48, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
143 4 0.01
144 12 0.02
145 192 0.32
146 243 0.41
147 139 0.23
148 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (146 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
AGAAAAAGTGCAAAAT
Found at i:594174 original size:15 final size:15
Alignment explanation
Indices: 594132--594174 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
594122 CTTTGCACAG
594132 TATTTTTTATTCTATTT
1 TATTTTTT-TT-TATTT
* *
594149 TAATTTATTTTATTT
1 TATTTTTTTTTATTT
594164 TATTTTTTTTT
1 TATTTTTTTTT
594175 TTAGAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 2 0.09
17 6 0.27
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TATTTTTTTTTATTT
Found at i:594176 original size:5 final size:5
Alignment explanation
Indices: 594136--594173 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
594126 GCACAGTATT
* *
594136 TTTTA TTCTA TTTTA ATTTA TTTTA TTTTA TTTT- TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
594174 TTTAGAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:597042 original size:13 final size:13
Alignment explanation
Indices: 597024--597085 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 13
597014 TAGATTGTAC
597024 TGTGTAAATGAAA
1 TGTGTAAATGAAA
*
597037 TGTGTAAATGTAA
1 TGTGTAAATGAAA
*
597050 TGTGTAAGTGTAAA
1 TGTGTAAATG-AAA
597064 --TGTAAAT-ATAA
1 TGTGTAAATGA-AA
597075 TGTGTAAATGA
1 TGTGTAAATGA
597086 CTCTGTGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 1 0.03
11 2 0.05
12 6 0.15
13 28 0.70
14 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (13 bp):
TGTGTAAATGAAA
Found at i:597079 original size:19 final size:19
Alignment explanation
Indices: 597026--597084 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
597016 GATTGTACTG
597026 TGTAAATGA-AATGTGTAAA
1 TGTAAAT-ATAATGTGTAAA
* *
597045 TGTAATGTGTAA-GTGTAAA
1 TGTAA-ATATAATGTGTAAA
597064 TGTAAATATAATGTGTAAA
1 TGTAAATATAATGTGTAAA
597083 TG
1 TG
597085 ACTCTGTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.12
19 26 0.79
20 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (19 bp):
TGTAAATATAATGTGTAAA
Found at i:598821 original size:4 final size:4
Alignment explanation
Indices: 598806--598843 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
598796 ATCACCCGTT
* *
598806 GTCC GT-C GTCC GTCC GTCC GTCT GTCT GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
598844 TGTAAACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.42, G:0.26, T:0.32
Consensus pattern (4 bp):
GTCC
Found at i:598838 original size:16 final size:16
Alignment explanation
Indices: 598806--598846 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
598796 ATCACCCGTT
598806 GTCCGTC-GTCCGTCC
1 GTCCGTCTGTCCGTCC
*
598821 GTCCGTCTGTCTGTCC
1 GTCCGTCTGTCCGTCC
598837 GTCCGTCTGT
1 GTCCGTCTGT
598847 AAACTTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.00, C:0.39, G:0.27, T:0.34
Consensus pattern (16 bp):
GTCCGTCTGTCCGTCC
Found at i:599622 original size:333 final size:331
Alignment explanation
Indices: 599013--600183 Score: 1888
Period size: 333 Copynumber: 3.6 Consensus size: 331
599003 GGTGCATGTC
599013 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTTA
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTTA
599078 ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
66 ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
599143 GTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTTAAAAATCTTCTTCTCAAGAACCACTG
131 GTTCAAAGTTTAACATAGAAATACATAGGAAAATG-TTTAAAAATCTTCTTCTCAAGAACCACTG
* * * *
599208 CACCAGAAATGCCAATATTTACACAAAAACTTGTATATATAGTGAAGATTCTAAATTGTAAAAAT
195 CACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAAAT
*** *
599273 CGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTTCAAAGTTTAACATGGAACTACATATG
260 CGTGACCCTCGGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATATG
599338 GAAAATG
325 GAAAATG
*
599345 TTTAAAAAATCTTCTTCTCAAGAACTACTGCACCAGAAATGCCAATATTTACACAAAAGCTTG-T
1 TTT-AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTT
*
599409 ATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCG
65 A-ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCG
*
599474 GGGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAAAATCTTCTTCTCAAGAACTAC
129 GGGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTT-AAAAATCTTCTTCTCAAGAACCAC
599539 TGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAA
193 TGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAA
*
599604 ATCGTGACCCTCGGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAAATACATA
258 ATCGTGACCCTCGGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATA
599669 -GGAAAATG
323 TGGAAAATG
*
599677 TTTAAAAATCTTCTTCTCAAGAACCACTGCATCAGAAATGCCAATATTTACACAAAAGCTTGTTA
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTTA
599742 ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
66 ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
599807 GTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAAATCTTCTTCTCAAGAACCACTGC
131 GTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAAATCTTCTTCTCAAGAACCACTGC
*
599872 ATCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAAATC
196 ACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAAATC
* *
599937 GTGACCCTCAGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATATGA
261 GTGACCCTCGGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATATGG
600002 AAAATG
326 AAAATG
* * * ** *
600008 TTTAAAAATTTTCTTCTCAAGAACCACTTCACCAAAAATGCCAATACATACACAAAAGGTTG-TA
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTTA
* * * * * **
600072 TATATAGTGAAG-------ATTGTAAAAATCGTGACCCCCGAACAAAAAGTGGGGCCCCAGTAGG
66 -ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
* * * *
600130 GGTTTAGATTTTAACAT----AT--ATAGGAAAATGTTTTAAAATCTTCTTCTCAAGAAC
130 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAAATCTTCTTCTCAAGAAC
600184 TATAGTGCAA
Statistics
Matches: 795, Mismatches: 38, Indels: 26
0.93 0.04 0.03
Matches are distributed among these distances:
318 34 0.04
320 2 0.00
324 54 0.07
330 152 0.19
331 231 0.29
332 21 0.03
333 301 0.38
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (331 bp):
TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTTA
ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
GTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAAATCTTCTTCTCAAGAACCACTGC
ACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAAATC
GTGACCCTCGGACCAAAACTACAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATATGG
AAAATG
Found at i:599776 original size:165 final size:165
Alignment explanation
Indices: 599013--600183 Score: 1814
Period size: 166 Copynumber: 7.1 Consensus size: 165
599003 GGTGCATGTC
599013 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGT-T
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
*
599077 AACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
66 -ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
599142 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG
130 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG
*
599178 TTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAACTTGTA
1 -TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA
599243 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
65 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
* *
599308 GGTTCAAAGTTTAACATGGAACTACATATGGAAAATG
130 GGTTCAAAGTTTAACATAGAAATACATA-GGAAAATG
*
599345 TTTAAAAAATCTTCTTCTCAAGAACTACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA
1 TTT-AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA
599410 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
65 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
599475 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG
130 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG
*
599511 TTTAAAAAATCTTCTTCTCAAGAACTACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA
1 TTT-AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA
* * * ***
599576 TGTATAATGAAGATTCTAAATTGTAGAAATCGTGACCCTCGGACCAAAACTACAGCCCCAGGCGG
65 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
599641 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG
130 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG
*
599677 TTTAAAAATCTTCTTCTCAAGAACCACTGCATCAGAAATGCCAATATTTACACAAAAGCTTGT-T
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
*
599741 AACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
66 -ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
599806 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG
130 GGTTCAAAGTTTAACATAGAAATACATAGGAAAATG
*
599842 TTTAAAAATCTTCTTCTCAAGAACCACTGCATCAGAAATGCCAATATTTACACAAAAGCTTGTAT
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
* * * * ***
599907 GTATAATGAAGATTCTAAATTGTAGAAATCGTGACCCTCAGACCAAAACTACAGCCCCAGGCGGG
66 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
* *
599972 GTTCAAAGTTTAACATAGAACTACATATGAAAAATG
131 GTTCAAAGTTTAACATAGAAATACATA-GGAAAATG
* * * ** *
600008 TTTAAAAATTTTCTTCTCAAGAACCACTTCACCAAAAATGCCAATACATACACAAAAGGTTGTAT
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
* * * * **
600073 ATATAGTGAAG-------ATTGTAAAAATCGTGACCCCCGAACAAAAAGTGGGGCCCCAGTAGGG
66 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
* * *
600131 GTTTAGATTTTAACAT----AT--ATAGGAAAATG
131 GTTCAAAGTTTAACATAGAAATACATAGGAAAATG
*
600160 TTTTAAAATCTTCTTCTCAAGAAC
1 TTTAAAAATCTTCTTCTCAAGAAC
600184 TATAGTGCAA
Statistics
Matches: 939, Mismatches: 60, Indels: 26
0.92 0.06 0.03
Matches are distributed among these distances:
152 29 0.03
153 3 0.00
155 1 0.00
159 49 0.05
164 1 0.00
165 297 0.32
166 400 0.43
167 159 0.17
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (165 bp):
TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
GTTCAAAGTTTAACATAGAAATACATAGGAAAATG
Found at i:607358 original size:4 final size:4
Alignment explanation
Indices: 607351--607392 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
607341 AGAGAGAGAG
*
607351 AGAC AGAC AGAC AGAC AG-- AGAC AGAC GGAC AGAC AGAC AGAC
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
607393 TGACTGACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
4 32 0.94
ACGTcount: A:0.48, C:0.24, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:607372 original size:18 final size:18
Alignment explanation
Indices: 607349--607387 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
607339 CTAGAGAGAG
607349 AGAGACAGACAGACAGAC
1 AGAGACAGACAGACAGAC
*
607367 AGAGACAGACGGACAGAC
1 AGAGACAGACAGACAGAC
607385 AGA
1 AGA
607388 CAGACTGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.31, T:0.00
Consensus pattern (18 bp):
AGAGACAGACAGACAGAC
Found at i:607376 original size:22 final size:22
Alignment explanation
Indices: 607345--607391 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
607335 TAGTCTAGAG
*
607345 AGAGAGAGACAGACAGACAGAC
1 AGAGACAGACAGACAGACAGAC
*
607367 AGAGACAGACGGACAGACAGAC
1 AGAGACAGACAGACAGACAGAC
607389 AGA
1 AGA
607392 CTGACTGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.19, G:0.32, T:0.00
Consensus pattern (22 bp):
AGAGACAGACAGACAGACAGAC
Found at i:625293 original size:8 final size:8
Alignment explanation
Indices: 625272--625329 Score: 82
Period size: 8 Copynumber: 7.4 Consensus size: 8
625262 GATCACATTT
625272 TGTCCGTC
1 TGTCCGTC
625280 -GTCCGTC
1 TGTCCGTC
625287 TGTCCGTC
1 TGTCCGTC
*
625295 CGTCCGTC
1 TGTCCGTC
*
625303 TGTCTGTC
1 TGTCCGTC
*
625311 TGTCTGTC
1 TGTCCGTC
625319 TGTCCGTC
1 TGTCCGTC
625327 TGT
1 TGT
625330 AAACTTTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
7 7 0.16
8 38 0.84
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40
Consensus pattern (8 bp):
TGTCCGTC
Found at i:625296 original size:12 final size:12
Alignment explanation
Indices: 625273--625329 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
625263 ATCACATTTT
625273 GTCCGTC-GTCC
1 GTCCGTCTGTCC
* *
625284 GTCTGTCCGTCC
1 GTCCGTCTGTCC
*
625296 GTCCGTCTGTCT
1 GTCCGTCTGTCC
* *
625308 GTCTGTCTGTCT
1 GTCCGTCTGTCC
625320 GTCCGTCTGT
1 GTCCGTCTGT
625330 AAACTTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
11 6 0.15
12 33 0.85
ACGTcount: A:0.00, C:0.35, G:0.26, T:0.39
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:634047 original size:41 final size:41
Alignment explanation
Indices: 633976--634343 Score: 529
Period size: 41 Copynumber: 9.0 Consensus size: 41
633966 TACACCAAAG
* * ** * * *
633976 TCATATCCACTGGTTACACCGCGCTGTGTACCAGTACTTGC
1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC
* *
634017 TCATTTCCACTAGCTACACCATGCTATGTACCAGCACTTAC
1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC
*
634058 TCATATCCACTGGCTACACCATGCTATGTACCAGGACTTAC
1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC
* *
634099 TCATATCCACTGGCTACACCATGCTATGTACCAGAACTTAC
1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC
* * * *
634140 TCAATTCCACTGGCTACACCATGCTATATGCCAGGACTTGC
1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC
* *
634181 TCATTTCAACTGGCTACACCATGCTATGTACCAGGACTTGC
1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC
*
634222 TCATTTCAACTGGCTACACCATGCTATGTACCAGGACTTAC
1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC
** *
634263 TCAACTCCACTGGCTACACCATGCTATGTACCAGGACTTGC
1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC
*
634304 TCATTTCAACTGGCTACACCATGCTATGTACCAGGACTTA
1 TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTA
634344 ACTCCAAAAA
Statistics
Matches: 296, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 296 1.00
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (41 bp):
TCATTTCCACTGGCTACACCATGCTATGTACCAGGACTTAC
Found at i:636162 original size:19 final size:19
Alignment explanation
Indices: 636115--636168 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
636105 AGACCACTCT
636115 CCCAAATGGGATATAATAG
1 CCCAAATGGGATATAATAG
***
636134 CCCGTTTGGGATATAATAG
1 CCCAAATGGGATATAATAG
636153 CCCAAATGGGATATAA
1 CCCAAATGGGATATAA
636169 ATTTTAAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (19 bp):
CCCAAATGGGATATAATAG
Found at i:645872 original size:167 final size:167
Alignment explanation
Indices: 645596--645931 Score: 672
Period size: 167 Copynumber: 2.0 Consensus size: 167
645586 TATCATTGGC
645596 ATGATATGTACACAAAAGTAATGTAATTAGAACCATTTTAACTATAGCTTGGACTTTGGGTAGTT
1 ATGATATGTACACAAAAGTAATGTAATTAGAACCATTTTAACTATAGCTTGGACTTTGGGTAGTT
645661 GTGTCAAACAGCAATGTGACGTAGGCCTGTCTATTTCATTGCTGGCCACTCAGCCAAGGCTCTGT
66 GTGTCAAACAGCAATGTGACGTAGGCCTGTCTATTTCATTGCTGGCCACTCAGCCAAGGCTCTGT
645726 GACATTAACAAGATGTGTCTGGCTTTTGAGCTAAGAT
131 GACATTAACAAGATGTGTCTGGCTTTTGAGCTAAGAT
645763 ATGATATGTACACAAAAGTAATGTAATTAGAACCATTTTAACTATAGCTTGGACTTTGGGTAGTT
1 ATGATATGTACACAAAAGTAATGTAATTAGAACCATTTTAACTATAGCTTGGACTTTGGGTAGTT
645828 GTGTCAAACAGCAATGTGACGTAGGCCTGTCTATTTCATTGCTGGCCACTCAGCCAAGGCTCTGT
66 GTGTCAAACAGCAATGTGACGTAGGCCTGTCTATTTCATTGCTGGCCACTCAGCCAAGGCTCTGT
645893 GACATTAACAAGATGTGTCTGGCTTTTGAGCTAAGAT
131 GACATTAACAAGATGTGTCTGGCTTTTGAGCTAAGAT
645930 AT
1 AT
645932 TTGAGGCAAT
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 169 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (167 bp):
ATGATATGTACACAAAAGTAATGTAATTAGAACCATTTTAACTATAGCTTGGACTTTGGGTAGTT
GTGTCAAACAGCAATGTGACGTAGGCCTGTCTATTTCATTGCTGGCCACTCAGCCAAGGCTCTGT
GACATTAACAAGATGTGTCTGGCTTTTGAGCTAAGAT
Found at i:651614 original size:165 final size:166
Alignment explanation
Indices: 651342--651968 Score: 852
Period size: 166 Copynumber: 3.8 Consensus size: 166
651332 GTGAATATGC
* * * * *
651342 AAAATAAGCAAAGTCGA-CATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCAC
1 AAAATAAACAAAGTC-ATCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCAC
* * * * *
651406 AATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG
65 CATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
**
651471 AAATCTGAGAGGAAAATTTGTTTGAAAATTTTGGCT-
130 AAATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCTA
* **
651507 AAAATAAACAAAGT-ACTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATAAATATCAC
1 AAAATAAACAAAGTCA-TCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCAC
* * * *
651571 GATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAAAAGCTGCTGAG
65 CATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
*
651636 AAATCTTTGA-CATAAATTTGTTTGAAAATTTTGGCTA
130 AAATCTTTGAGGA-AAATTTGTTTGAAAATTTTGGCTA
* * * * *
651673 AAAAAAAACAAAGTCATTATTTCACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACC
1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACC
* *
651738 ATATGGCATGCC-TATACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
66 ATATGGCATGCCTTA-ACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
*
651802 AAATCTTTGACGG-AAATTTGTTTGAAAATTTTTGCTA
130 AAATCTTTGA-GGAAAATTTGTTTGAAAATTTTGGCTA
* * * *
651839 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGGCGTCCGATTGGTACAAAAATATATCCCACC
1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACC
* * *
651904 ATATGGCATACCTTAACAAACACCGTGTTAAAATTTCAAGCATCTGCGACAAATAGTTGCTGAGA
66 ATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
651969 TAAATGCGAC
Statistics
Matches: 407, Mismatches: 46, Indels: 17
0.87 0.10 0.04
Matches are distributed among these distances:
163 1 0.00
164 1 0.00
165 144 0.35
166 258 0.63
167 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (166 bp):
AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACC
ATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
AATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCTA
Found at i:652012 original size:12 final size:12
Alignment explanation
Indices: 651995--652030 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
651985 TTTTGTTACG
651995 GACGGACAGACA
1 GACGGACAGACA
*
652007 GACGGACTGACA
1 GACGGACAGACA
*
652019 GACAGACAGACA
1 GACGGACAGACA
652031 CACAAGGGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.25, G:0.31, T:0.03
Consensus pattern (12 bp):
GACGGACAGACA
Found at i:652013 original size:16 final size:16
Alignment explanation
Indices: 651992--652025 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
651982 AATTTTTGTT
651992 ACGGACGGACAGACAG
1 ACGGACGGACAGACAG
*
652008 ACGGACTGACAGACAG
1 ACGGACGGACAGACAG
652024 AC
1 AC
652026 AGACACACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.26, G:0.32, T:0.03
Consensus pattern (16 bp):
ACGGACGGACAGACAG
Found at i:657814 original size:160 final size:158
Alignment explanation
Indices: 657504--657989 Score: 589
Period size: 160 Copynumber: 3.0 Consensus size: 158
657494 AATGAATGTG
** * * *
657504 AACTGCAAATATTTGGAACTTTTCTATGTCCAAGAGCCATAACTCTGTCGAAAATTGCTCTATCA
1 AACTGCAAATAACTGGAATTTTTCTACGTCCAAGAGCCATAACTCTGTCGAAAATTGCTCGAT-A
* * * * *
657569 TACCCAAAATCAAACCTGAGCTAGATATTATCATGATAAACCTGTATACAAAATTTCTTATCAGT
65 TACCCAATATC-AACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCTT-TCAAT
* *
657634 ATGTGCACCCTCTG-AAAGAAAATGAGCGGA
128 ATGTTCATCCTCTGCAAAGAAAATGAGCGGA
* * * *
657664 AACTGCAAATAACTGGAATTTTTCTACGTCTAAGAGCCATAACTCTG-CTGAAAATTACTCGCTG
1 AACTGCAAATAACTGGAATTTTTCTACGTCCAAGAGCCATAACTCTGTC-GAAAATTGCTCGATA
* * *
657728 TACCCAATATCATACTTGACCTAGATGTAATCATGATAAACATGTATACCAAATTTCGTTTCAAT
65 TACCCAATATCA-ACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTC-TTTCAAT
657793 ATGTTCATCCTCTGCAAAGAAAATGAGCGGA
128 ATGTTCATCCTCTGCAAAGAAAATGAGCGGA
* * * * * * * *
657824 AACTGCAAATAACTGAAATTTTTCAACGTCCAAGGGCTATCACTCTGTCGAAAACTGCTTGATCT
1 AACTGCAAATAACTGGAATTTTTCTACGTCCAAGAGCCATAACTCTGTCGAAAATTGCTCGATAT
* *
657889 ACCCAATATTGAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATGTCATTTTCAAT
66 ACCCAATA-TCAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTC--TTTCAAT
* **
657954 ATGTTCATCCTCTGCGAAGAAAATGAAAGGA
128 ATGTTCATCCTCTGCAAAGAAAATGAGCGGA
657985 AACTG
1 AACTG
657990 TAGATGGACC
Statistics
Matches: 280, Mismatches: 39, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
158 1 0.00
159 65 0.23
160 171 0.61
161 43 0.15
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (158 bp):
AACTGCAAATAACTGGAATTTTTCTACGTCCAAGAGCCATAACTCTGTCGAAAATTGCTCGATAT
ACCCAATATCAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCTTTCAATATG
TTCATCCTCTGCAAAGAAAATGAGCGGA
Found at i:659857 original size:13 final size:13
Alignment explanation
Indices: 659839--659880 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
659829 AAAGCATTGT
659839 AAATATTTGTTGA
1 AAATATTTGTTGA
659852 AAATATTTG-T--
1 AAATATTTGTTGA
659862 AAATATTTGTTGA
1 AAATATTTGTTGA
659875 AAATAT
1 AAATAT
659881 GTAAATATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.35
11 1 0.04
12 1 0.04
13 15 0.58
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (13 bp):
AAATATTTGTTGA
Found at i:659861 original size:23 final size:22
Alignment explanation
Indices: 659834--659888 Score: 94
Period size: 23 Copynumber: 2.5 Consensus size: 22
659824 GTTTTAAAGC
659834 ATTGTAAATATTTGTTGAAAAT
1 ATTGTAAATATTTGTTGAAAAT
659856 ATTTGTAAATATTTGTTGAAAAT
1 A-TTGTAAATATTTGTTGAAAAT
659879 A-TGTAAATAT
1 ATTGTAAATAT
659889 ACTTCCAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.28
22 1 0.03
23 22 0.69
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (22 bp):
ATTGTAAATATTTGTTGAAAAT
Found at i:666015 original size:45 final size:45
Alignment explanation
Indices: 665949--666034 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
665939 GGAGGGTAAC
*
665949 AGTTGAAATTGACACCCCGAGAAAACCACTGTCAACTGACGTGAA
1 AGTTGAAATTGACACCCCGAGAAAACCACTGTCAACCGACGTGAA
* *
665994 AGTTGAAATTGACACCTCGAGAAAACCATTGTCAACCGACG
1 AGTTGAAATTGACACCCCGAGAAAACCACTGTCAACCGACG
666035 CGAAGTGGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (45 bp):
AGTTGAAATTGACACCCCGAGAAAACCACTGTCAACCGACGTGAA
Found at i:667109 original size:44 final size:44
Alignment explanation
Indices: 667011--668010 Score: 1334
Period size: 44 Copynumber: 23.3 Consensus size: 44
667001 AACAATAATT
*
667011 CACTGACAAAGCTGTGTACTTTACTTTACTGACACACAGACTCACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACA
667057 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
* ** *
667101 CACAGACAATTCTGTGTACTTTACTTTACTGACACACAGACTAACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACA
* * *
667147 CACTAACAAAGCTGGGTAGTTTACTTTACTGACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
667191 CACTGACAAAGCTGTGTACTTTACTTTACTGACACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACA
* * **
667237 CACTGACAAAGCTATGTACTTTACTTTATTGACATACAGACAAACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGAC--ACAGACTTACA
* * *
667283 CACTGACAAAGCTGTATACTTTACTTTACTAACACACAGACTAACA
1 CACTGACAAAGCTGTGTACTTTACTTTACT--GACACAGACTTACA
* * * *
667329 CACTGAGAAAGCTGTGTACTTCACTTTACTGACACACAGTCTAACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACA
* *
667375 CAATGACAAAGCTGTGTACTTTACTTCACTGACACAGACTT--A
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
* *
667417 TACTGACAAAGCTGTGTACTTTACTTCACTGACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
* *
667461 CACTGACAAAGCTGTGTACTTTACTTCACTGACACAGACTAACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
*
667505 CACTGACAAAGCTGTGTACTTTAC-TAAC--ACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
* * *
667546 CACTGACAAAGTTTTGTACTTTACTTCACTGACACAGACTT--A
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
667588 CACTGACAAAGCTGTG-----TACTTTACTG--ACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
667625 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
667669 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
667713 CACTGACAAAGCTGTG-----TACTTTACTGACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
* * *
667752 CACTGACAAAGCTGTGTACTTTAC-TGAC--ACACATACTAACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
*
667793 CACTGACAAAACTGTGTACTTTACTTTACTGACACAGACTT---
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
667834 -ACTGACAAAGCTGTG-----TACTTTACTGACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
667872 CACTGACAAAGCTGTG-----TACTTTACTGACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
667911 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
*
667955 CACTGACAAAGCTGTGTACTTCACTTTACTGACACAGACTTACA
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
667999 CACTGACAAAGC
1 CACTGACAAAGC
668011 GTAATGTGTA
Statistics
Matches: 857, Mismatches: 56, Indels: 84
0.86 0.06 0.08
Matches are distributed among these distances:
35 28 0.03
37 26 0.03
39 93 0.11
40 14 0.02
41 68 0.08
42 71 0.08
43 6 0.01
44 327 0.38
46 222 0.26
48 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (44 bp):
CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACA
Found at i:667122 original size:90 final size:88
Alignment explanation
Indices: 667011--668010 Score: 1334
Period size: 90 Copynumber: 11.6 Consensus size: 88
667001 AACAATAATT
*
667011 CACTGACAAAGCTGTGTACTTTACTTTACTGACACACAGACTCACACACTGACAAAGCTGTGTAC
1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACACACTGACAAAGCTGTGTAC
667076 TTTACTTTACTGACACAGACTTACA
64 TTTACTTTACTGACACAGACTTACA
* ** * * * *
667101 CACAGACAATTCTGTGTACTTTACTTTACTGACACACAGACTAACACACTAACAAAGCTGGGTAG
1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACACACTGACAAAGCTGTGTAC
667166 TTTACTTTACTGACACAGACTTACA
64 TTTACTTTACTGACACAGACTTACA
*
667191 CACTGACAAAGCTGTGTACTTTACTTTACTGACACACAGACTTACACACTGACAAAGCTATGTAC
1 CACTGACAAAGCTGTGTACTTTACTTTACTG--ACACAGACTTACACACTGACAAAGCTGTGTAC
* **
667256 TTTACTTTATTGACATACAGACAAACA
64 TTTACTTTACTGAC--ACAGACTTACA
* * * *
667283 CACTGACAAAGCTGTATACTTTACTTTACTAACACACAGACTAACACACTGAGAAAGCTGTGTAC
1 CACTGACAAAGCTGTGTACTTTACTTTACT--GACACAGACTTACACACTGACAAAGCTGTGTAC
* * *
667348 TTCACTTTACTGACACACAGTCTAACA
64 TTTACTTTACTG--ACACAGACTTACA
* * *
667375 CAATGACAAAGCTGTGTACTTTACTTCACTGACACAGACTT--ATACTGACAAAGCTGTGTACTT
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
*
667438 TACTTCACTGACACAGACTTACA
66 TACTTTACTGACACAGACTTACA
* *
667461 CACTGACAAAGCTGTGTACTTTACTTCACTGACACAGACTAACACACTGACAAAGCTGTGTACTT
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
*
667526 TAC-TAAC--ACACAGACTTACA
66 TACTTTACTGACACAGACTTACA
* * *
667546 CACTGACAAAGTTTTGTACTTTACTTCACTGACACAGACTT--ACACTGACAAAGCTGTG-----
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
667604 TACTTTACTG--ACAGACTTACA
66 TACTTTACTGACACAGACTTACA
667625 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
667690 TACTTTACTGACACAGACTTACA
66 TACTTTACTGACACAGACTTACA
667713 CACTGACAAAGCTGTG-----TACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
* * *
667773 TAC-TGAC--ACACATACTAACA
66 TACTTTACTGACACAGACTTACA
*
667793 CACTGACAAAACTGTGTACTTTACTTTACTGACACAGACTT----ACTGACAAAGCTGTG-----
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
667849 TACTTTACTGACACAGACTTACA
66 TACTTTACTGACACAGACTTACA
667872 CACTGACAAAGCTGTG-----TACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
667932 TACTTTACTGACACAGACTTACA
66 TACTTTACTGACACAGACTTACA
*
667955 CACTGACAAAGCTGTGTACTTCACTTTACTGACACAGACTTACACACTGACAAAGC
1 CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGC
668011 GTAATGTGTA
Statistics
Matches: 810, Mismatches: 58, Indels: 86
0.85 0.06 0.09
Matches are distributed among these distances:
74 20 0.02
76 3 0.00
77 3 0.00
78 18 0.02
79 78 0.10
80 26 0.03
81 32 0.04
82 3 0.00
83 103 0.13
85 71 0.09
86 60 0.07
87 3 0.00
88 113 0.14
90 162 0.20
92 113 0.14
94 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (88 bp):
CACTGACAAAGCTGTGTACTTTACTTTACTGACACAGACTTACACACTGACAAAGCTGTGTACTT
TACTTTACTGACACAGACTTACA
Found at i:667449 original size:26 final size:26
Alignment explanation
Indices: 667418--667494 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 26
667408 ACAGACTTAT
667418 ACTGACAAAGCTGTGTACTTTACTTC
1 ACTGACAAAGCTGTGTACTTTACTTC
* *
667444 ACTGAC--A-C--AG-AC-TTAC-AC
1 ACTGACAAAGCTGTGTACTTTACTTC
667462 ACTGACAAAGCTGTGTACTTTACTTC
1 ACTGACAAAGCTGTGTACTTTACTTC
667488 ACTGACA
1 ACTGACA
667495 CAGACTAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
18 7 0.18
19 4 0.10
20 3 0.08
21 2 0.05
23 2 0.05
24 3 0.08
25 4 0.10
26 14 0.36
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (26 bp):
ACTGACAAAGCTGTGTACTTTACTTC
Found at i:667613 original size:21 final size:21
Alignment explanation
Indices: 667589--667649 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
667579 ACAGACTTAC
667589 ACTGACAAAGCTGTGTACTTT
1 ACTGACAAAGCTGTGTACTTT
* **
667610 ACTGACAGA-C--T-TAC-AC
1 ACTGACAAAGCTGTGTACTTT
667626 ACTGACAAAGCTGTGTACTTT
1 ACTGACAAAGCTGTGTACTTT
667647 ACT
1 ACT
667650 TTACTGACAC
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
16 8 0.28
17 4 0.14
18 1 0.03
19 1 0.03
20 4 0.14
21 11 0.38
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (21 bp):
ACTGACAAAGCTGTGTACTTT
Found at i:667655 original size:26 final size:26
Alignment explanation
Indices: 667626--667702 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
667616 AGACTTACAC
667626 ACTGACAAAGCTGTGTACTTTACTTT
1 ACTGACAAAGCTGTGTACTTTACTTT
*
667652 ACTGACACAGAC--T-TAC---AC---
1 ACTGACAAAG-CTGTGTACTTTACTTT
667670 ACTGACAAAGCTGTGTACTTTACTTT
1 ACTGACAAAGCTGTGTACTTTACTTT
667696 ACTGACA
1 ACTGACA
667703 CAGACTTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 20
0.64 0.03 0.33
Matches are distributed among these distances:
17 1 0.03
18 9 0.23
19 1 0.03
20 3 0.08
21 2 0.05
23 2 0.05
24 3 0.08
25 1 0.03
26 16 0.41
27 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (26 bp):
ACTGACAAAGCTGTGTACTTTACTTT
Found at i:667719 original size:18 final size:18
Alignment explanation
Indices: 667696--667759 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
667686 ACTTTACTTT
667696 ACTGACACAGACTTACAC
1 ACTGACACAGACTTACAC
* **
667714 ACTGACAAAG-CTGTGTACTTT
1 ACTGACACAGAC--T-TAC-AC
667735 ACTGACACAGACTTACAC
1 ACTGACACAGACTTACAC
667753 ACTGACA
1 ACTGACA
667760 AAGCTGTGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
17 1 0.03
18 16 0.46
19 4 0.11
20 4 0.11
21 9 0.26
22 1 0.03
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (18 bp):
ACTGACACAGACTTACAC
Found at i:667740 original size:21 final size:21
Alignment explanation
Indices: 667714--667780 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
667704 AGACTTACAC
667714 ACTGACAAAGCTGTGTACTTT
1 ACTGACAAAGCTGTGTACTTT
* **
667735 ACTGACACAGAC--T-TAC-AC
1 ACTGACAAAG-CTGTGTACTTT
667753 ACTGACAAAGCTGTGTACTTT
1 ACTGACAAAGCTGTGTACTTT
667774 ACTGACA
1 ACTGACA
667781 CACATACTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
17 1 0.03
18 9 0.26
19 4 0.11
20 4 0.11
21 16 0.46
22 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (21 bp):
ACTGACAAAGCTGTGTACTTT
Found at i:667856 original size:21 final size:21
Alignment explanation
Indices: 667832--667935 Score: 80
Period size: 21 Copynumber: 5.2 Consensus size: 21
667822 TGACACAGAC
667832 TTACTGACAAAGCTGTGTACT
1 TTACTGACAAAGCTGTGTACT
*
667853 TTACTGACACAGAC--T-TAC-
1 TTACTGACAAAG-CTGTGTACT
**
667871 ACACTGACAAAGCTGTGTACT
1 TTACTGACAAAGCTGTGTACT
*
667892 TTACTGACACAGAC--T-TAC-
1 TTACTGACAAAG-CTGTGTACT
**
667910 ACACTGACAAAGCTGTGTACT
1 TTACTGACAAAGCTGTGTACT
667931 TTACT
1 TTACT
667936 TTACTGACAC
Statistics
Matches: 61, Mismatches: 12, Indels: 20
0.66 0.13 0.22
Matches are distributed among these distances:
17 2 0.03
18 18 0.30
19 8 0.13
20 8 0.13
21 23 0.38
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (21 bp):
TTACTGACAAAGCTGTGTACT
Found at i:667878 original size:18 final size:18
Alignment explanation
Indices: 667855--667918 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
667845 TGTGTACTTT
667855 ACTGACACAGACTTACAC
1 ACTGACACAGACTTACAC
* **
667873 ACTGACAAAG-CTGTGTACTTT
1 ACTGACACAGAC--T-TAC-AC
667894 ACTGACACAGACTTACAC
1 ACTGACACAGACTTACAC
667912 ACTGACA
1 ACTGACA
667919 AAGCTGTGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
17 1 0.03
18 16 0.46
19 4 0.11
20 4 0.11
21 9 0.26
22 1 0.03
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (18 bp):
ACTGACACAGACTTACAC
Found at i:668935 original size:128 final size:128
Alignment explanation
Indices: 668775--669009 Score: 409
Period size: 128 Copynumber: 1.8 Consensus size: 128
668765 CTATATGATT
668775 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAAT-A
1 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAA
668839 CTAAAACACTATAAGTATACATGTTTAATAGATACAAATTATATGTTACATTTATCATATAAAC
66 CTAAAACACTA-AAGTATACATGTTTAATAGATACAAATTATATGTTACATTTATCATATAAAC
* * * * *
668903 AGTAAATAGCAAAAAGACTTTCCTATTCTATAAATGACTTTCATGTATTTGACTTTATTCAATAA
1 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAA
668968 CTAAAACACTAAAGTATACATGTTTAATAGATACAAATTATA
66 CTAAAACACTAAAGTATACATGTTTAATAGATACAAATTATA
669010 CATCCTATTA
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
128 89 0.88
129 12 0.12
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (128 bp):
AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAA
CTAAAACACTAAAGTATACATGTTTAATAGATACAAATTATATGTTACATTTATCATATAAAC
Found at i:669026 original size:128 final size:128
Alignment explanation
Indices: 668775--669043 Score: 398
Period size: 128 Copynumber: 2.1 Consensus size: 128
668765 CTATATGATT
668775 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAC
1 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAC
** * *
668840 TAAAACACTATAAGTATACATGTTTAATAGATACAAATTATATGTTACATTTATCATATAAAC
66 TAAAACACTATAAGTATACATGTTTAATAGATACAAATTATATCATACATTAACCATATAAAC
* * * * *
668903 AGTAAATAGCAAAAAGACTTTCCTATTCTATAAATGACTTTCATGTATTTGACTTTATTCAATAA
1 AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAAT-A
*
668968 CTAAAACACTA-AAGTATACATGTTTAATAGATACAAATTATA-CATCCTATTAACCATATAAAC
65 CTAAAACACTATAAGTATACATGTTTAATAGATACAAATTATATCATAC-ATTAACCATATAAAC
* *
669031 AGTTAATGGCAAA
1 AGTAAATAGCAAA
669044 CATCTTTTCT
Statistics
Matches: 127, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
127 2 0.02
128 113 0.89
129 12 0.09
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.34
Consensus pattern (128 bp):
AGTAAATAGCAAAAAAACTTTCCTATTCTATAAATGACTTTCATATATTCGACTTCAATCAATAC
TAAAACACTATAAGTATACATGTTTAATAGATACAAATTATATCATACATTAACCATATAAAC
Found at i:670171 original size:180 final size:180
Alignment explanation
Indices: 669869--670303 Score: 845
Period size: 180 Copynumber: 2.4 Consensus size: 180
669859 ACCCTACATG
669869 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTC-ATAAATTATC
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTA-TTTTTTCGATAAATTATC
669933 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
65 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
669998 CTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
130 CTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
*
670049 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
670114 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
670179 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
670229 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
670294 GAAATCAAAA
66 GAAATCAAAA
670304 NNNNNNNNNN
Statistics
Matches: 252, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
179 7 0.03
180 245 0.97
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (180 bp):
TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
Found at i:673379 original size:41 final size:41
Alignment explanation
Indices: 673334--673415 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
673324 CCCCCTTCTT
*
673334 TTGAAACATCTGTGAAA-AAAATGAATGGAAACTGCAAATAA
1 TTGAAACATCTG-CAAAGAAAATGAATGGAAACTGCAAATAA
673375 TTGAAACATCTGCAAAGAAAATGAATGGAAACTGCAAATAA
1 TTGAAACATCTGCAAAGAAAATGAATGGAAACTGCAAATAA
673416 CTGGAATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 3 0.08
41 36 0.92
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (41 bp):
TTGAAACATCTGCAAAGAAAATGAATGGAAACTGCAAATAA
Found at i:673737 original size:161 final size:158
Alignment explanation
Indices: 673383--673891 Score: 574
Period size: 161 Copynumber: 3.2 Consensus size: 158
673373 AATTGAAACA
* * **
673383 TCTGCAAAGAAAATGAATGGAAACTGCAAATAACTGGAATTTTTCTA-AGTCCAAGGGACATAAC
1 TCTGCGAAGAAAATGAACGGAAACTGCAAATAA-TTAAATTTTTCTACA-TCCAAGGG-CATAAC
* * * * * * *
673447 TCTGTATTAATTTTGCTTGTTCAAACTCAATATAAAACTTGACCTAGATGTTATCATGATAAACC
63 TCTGTA-TAA-ATTGCTCGATCGAACCCAATATAGAACTTGACCTAGATATTATCATGATAAACC
* *
673512 TGTATACCAAATTTCATTTCAATATCTTCATCC
126 TGAATACCAAATTTCATTTCAATATGTTCATCC
* * * **
673545 TCTGCAAAGAAAATGAATGGAAACGGCAAATAATTCAAATTTTTCTACATCCAATGGGCATTGCT
1 TCTGCGAAGAAAATGAACGGAAACTGCAAATAATT-AAATTTTTCTACATCCAA-GGGCATAACT
* * * *
673610 CTGTATAAACTTGCTCGATCGAACCCAATATGGAACTTAACCTAGATATTATCATGATTAACATG
64 CTGTATAAA-TTGCTCGATCGAACCCAATATAGAACTTGACCTAGATATTATCATGATAAACCTG
* * *
673675 CATTCCAAAGTTC-TATTCAATATGTTCATCC
128 AATACCAAATTTCAT-TTCAATATGTTCATCC
* * * * * *
673706 TCTGTGAAGAAAATGAGCAGAAACTGCAAATAATTAGAATTTTTCTGCGTCCAAGAGGCATACCT
1 TCTGCGAAGAAAATGAACGGAAACTGCAAATAATTA-AATTTTTCTACATCCAAG-GGCATAACT
** * *
673771 CTGTCGAAATTGCTCAATCGAACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTGA
64 CTGTATAAATTGCTCGATCGAACCCAATATAGAACTTGACCTAGATATTATCATGATAAACCTGA
673836 ATACCAAATTTCATTTCAATATGTTCA-CC
129 ATACCAAATTTCATTTCAATATGTTCATCC
673865 TTCTGCGAAGAAAATGAACGGAAACTG
1 -TCTGCGAAGAAAATGAACGGAAACTG
673892 TTGGTGGACT
Statistics
Matches: 295, Mismatches: 43, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
159 2 0.01
160 99 0.34
161 133 0.45
162 57 0.19
163 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (158 bp):
TCTGCGAAGAAAATGAACGGAAACTGCAAATAATTAAATTTTTCTACATCCAAGGGCATAACTCT
GTATAAATTGCTCGATCGAACCCAATATAGAACTTGACCTAGATATTATCATGATAAACCTGAAT
ACCAAATTTCATTTCAATATGTTCATCC
Found at i:682051 original size:2 final size:2
Alignment explanation
Indices: 682044--682089 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
682034 TATGAGATAC
682044 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
682086 AG AG
1 AG AG
682090 TTTTAAATTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:685451 original size:1 final size:1
Alignment explanation
Indices: 685409--685442 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
685399 TACTTCTTTC
685409 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
685443 AGAATTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:685868 original size:2 final size:2
Alignment explanation
Indices: 685861--685885 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
685851 TTTTGATAAG
685861 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 A
685886 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:697604 original size:2 final size:2
Alignment explanation
Indices: 697597--697668 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
697587 TGACATTATA
697597 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
697639 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
697669 GNNNNNNNNN
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:701577 original size:1 final size:1
Alignment explanation
Indices: 701573--701616 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
701563 NNNGGGGGGG
701573 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
701617 ACAAAAAACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:705749 original size:10 final size:10
Alignment explanation
Indices: 705734--705768 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
705724 CTAAGAAAAG
705734 TTTTTTATAT
1 TTTTTTATAT
705744 TTTTTTATAT
1 TTTTTTATAT
*
705754 ATTTTATATAT
1 -TTTTTTATAT
705765 TTTT
1 TTTT
705769 GTTACCATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:711287 original size:4 final size:4
Alignment explanation
Indices: 711278--711306 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
711268 CTTTGTGCCC
711278 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
711307 GTGAGACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:720357 original size:53 final size:54
Alignment explanation
Indices: 720276--720389 Score: 185
Period size: 53 Copynumber: 2.1 Consensus size: 54
720266 CTTAATTATT
*
720276 TATATTAATCAAATAAGAAAGTGCTATCTAATCGAAG-TATATGTATTTTGATAG
1 TATA-TAATCAAATAAGAAAGTGCTATCTAATCAAAGATATATGTATTTTGATAG
*
720330 TATATAATCAAATGAGAAAGTGCTATCTAATCAAAGTATATATGTATTTTGATAG
1 TATATAATCAAATAAGAAAGTGCTATCTAATCAAAG-ATATATGTATTTTGATAG
720385 TATAT
1 TATAT
720390 CTATGAAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
53 30 0.54
54 4 0.07
55 22 0.39
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (54 bp):
TATATAATCAAATAAGAAAGTGCTATCTAATCAAAGATATATGTATTTTGATAG
Found at i:722341 original size:22 final size:22
Alignment explanation
Indices: 722315--722362 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
722305 AAATATCACA
722315 AACATATTGACACATGTAATAC
1 AACATATTGACACATGTAATAC
722337 AACATATTGACACATGTAATAC
1 AACATATTGACACATGTAATAC
722359 AACA
1 AACA
722363 ATGTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (22 bp):
AACATATTGACACATGTAATAC
Found at i:726647 original size:22 final size:22
Alignment explanation
Indices: 726619--726681 Score: 126
Period size: 22 Copynumber: 2.9 Consensus size: 22
726609 TCTGGCTGGG
726619 TTACCTGATGTCATTAATGTCA
1 TTACCTGATGTCATTAATGTCA
726641 TTACCTGATGTCATTAATGTCA
1 TTACCTGATGTCATTAATGTCA
726663 TTACCTGATGTCATTAATG
1 TTACCTGATGTCATTAATG
726682 GCCCCCGATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (22 bp):
TTACCTGATGTCATTAATGTCA
Found at i:726653 original size:13 final size:13
Alignment explanation
Indices: 726619--726678 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 13
726609 TCTGGCTGGG
726619 TTACCTGATGTCA
1 TTACCTGATGTCA
726632 TTA----ATGTCA
1 TTACCTGATGTCA
726641 TTACCTGATGTCA
1 TTACCTGATGTCA
726654 TTA----ATGTCA
1 TTACCTGATGTCA
726663 TTACCTGATGTCA
1 TTACCTGATGTCA
726676 TTA
1 TTA
726679 ATGGCCCCCG
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
9 18 0.46
13 21 0.54
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (13 bp):
TTACCTGATGTCA
Found at i:726867 original size:21 final size:21
Alignment explanation
Indices: 726841--727021 Score: 118
Period size: 21 Copynumber: 8.6 Consensus size: 21
726831 CAATGACTAT
*
726841 AAAGGTCAAATCATAGCATCA
1 AAAGGTCATATCATAGCATCA
* *
726862 AAAGGTGATATCTTAGCATCA
1 AAAGGTCATATCATAGCATCA
* *
726883 AAAGGTGATATCTTAGCATCA
1 AAAGGTCATATCATAGCATCA
* *
726904 AAGGGTCACATCATAGCA-CTA
1 AAAGGTCATATCATAGCATC-A
** * *
726925 AAAGGTCGCATCAAAGCATTTA
1 AAAGGTCATATCATAGCA-TCA
**
726947 AAA-AACATGAT-ATAGCATCA
1 AAAGGTCAT-ATCATAGCATCA
* * **
726967 AAAGGTCACATCAAATTATCA
1 AAAGGTCATATCATAGCATCA
*
726988 AAATGTCATATCATA-CTATCA
1 AAAGGTCATATCATAGC-ATCA
* *
727009 AAAGATCACATCA
1 AAAGGTCATATCA
727022 AAAGACATAT
Statistics
Matches: 123, Mismatches: 30, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
20 8 0.07
21 109 0.89
22 6 0.05
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (21 bp):
AAAGGTCATATCATAGCATCA
Found at i:727111 original size:20 final size:21
Alignment explanation
Indices: 727058--727129 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
727048 ATCAAATCAC
*
727058 CAAAAGGACATATCTTAGCAT
1 CAAAAGGTCATATCTTAGCAT
727079 CAAAAGGTCATATCTTAGCAT
1 CAAAAGGTCATATCTTAGCAT
* * *
727100 CAAAA-TTCATATCATAACAT
1 CAAAAGGTCATATCTTAGCAT
*
727120 CTAAAGGTCA
1 CAAAAGGTCA
727130 ATCATATCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (21 bp):
CAAAAGGTCATATCTTAGCAT
Found at i:727152 original size:16 final size:16
Alignment explanation
Indices: 727131--727161 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
727121 TAAAGGTCAA
727131 TCATATCATCAGTTCG
1 TCATATCATCAGTTCG
*
727147 TCATATCGTCAGTTC
1 TCATATCATCAGTTC
727162 AAATTATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39
Consensus pattern (16 bp):
TCATATCATCAGTTCG
Found at i:735174 original size:2 final size:2
Alignment explanation
Indices: 735167--735214 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
735157 TCTTCATAAC
735167 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
735209 AG AG AG
1 AG AG AG
735215 CTACCCACCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:739564 original size:16 final size:16
Alignment explanation
Indices: 739543--739573 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
739533 TAAATTTATT
*
739543 GTCTAAATGGAAAAAA
1 GTCTAAATAGAAAAAA
739559 GTCTAAATAGAAAAA
1 GTCTAAATAGAAAAA
739574 TATTTGTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (16 bp):
GTCTAAATAGAAAAAA
Found at i:746581 original size:4 final size:4
Alignment explanation
Indices: 746566--746623 Score: 73
Period size: 4 Copynumber: 14.8 Consensus size: 4
746556 ATCACTTTTT
* * *
746566 GTCC GT-C GTCC GTCC GTCC GTCC GTCT GTCC GTCC GTCT GTCC GTCT
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
*
746613 GTCT GTCC GTC
1 GTCC GTCC GTC
746624 TGTAAACTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 3 0.06
4 44 0.94
ACGTcount: A:0.00, C:0.41, G:0.26, T:0.33
Consensus pattern (4 bp):
GTCC
Found at i:746626 original size:12 final size:12
Alignment explanation
Indices: 746572--746623 Score: 86
Period size: 12 Copynumber: 4.3 Consensus size: 12
746562 TTTTGTCCGT
*
746572 CGTCCGTCCGTC
1 CGTCCGTCTGTC
746584 CGTCCGTCTGTC
1 CGTCCGTCTGTC
746596 CGTCCGTCTGTC
1 CGTCCGTCTGTC
*
746608 CGTCTGTCTGTC
1 CGTCCGTCTGTC
746620 CGTC
1 CGTC
746624 TGTAAACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.00, C:0.42, G:0.25, T:0.33
Consensus pattern (12 bp):
CGTCCGTCTGTC
Found at i:751028 original size:31 final size:31
Alignment explanation
Indices: 750993--751086 Score: 88
Period size: 31 Copynumber: 3.2 Consensus size: 31
750983 CAGCCCTAGT
* *
750993 GAACACAGCCAGGGATAGTCCATCCCTCATA
1 GAACACATCCAGGGATAGTCCATCCATCATA
* *
751024 GAACACATCC----ATAGTCTATCCTTCATA
1 GAACACATCCAGGGATAGTCCATCCATCATA
* * *
751051 TAACAAATTCAGGGATAGTCCATCCATCATA
1 GAACACATCCAGGGATAGTCCATCCATCATA
*
751082 AAACA
1 GAACA
751087 TGTCTAGGGA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
27 22 0.44
31 28 0.56
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22
Consensus pattern (31 bp):
GAACACATCCAGGGATAGTCCATCCATCATA
Found at i:753686 original size:25 final size:25
Alignment explanation
Indices: 753652--753706 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
753642 GAAATGCAAA
753652 AACAATTAAAATATGATTTCCCAAT
1 AACAATTAAAATATGATTTCCCAAT
*
753677 AACAATTAAAATATTATTTCCCAAT
1 AACAATTAAAATATGATTTCCCAAT
753702 AACAA
1 AACAA
753707 AAACTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (25 bp):
AACAATTAAAATATGATTTCCCAAT
Found at i:756357 original size:13 final size:13
Alignment explanation
Indices: 756339--756365 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
756329 GTAAAATGTC
756339 AATAATTGTTTGT
1 AATAATTGTTTGT
756352 AATAATTGTTTGT
1 AATAATTGTTTGT
756365 A
1 A
756366 CTTAAGCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (13 bp):
AATAATTGTTTGT
Found at i:763385 original size:17 final size:17
Alignment explanation
Indices: 763363--763477 Score: 126
Period size: 22 Copynumber: 6.3 Consensus size: 17
763353 ACAGCACTAT
763363 GCCACTGTAACACTACA
1 GCCACTGTAACACTACA
763380 GCCACTGTAACACTACA
1 GCCACTGTAACACTACA
763397 GCCACTGTAACGTAACACTACA
1 GCCAC--T---GTAACACTACA
763419 GCCACTGTAACGTAACACTACA
1 GCCAC--T---GTAACACTACA
763441 GCCACTGTAACACTA-A
1 GCCACTGTAACACTACA
763457 GCCACTGTAACACTA-A
1 GCCACTGTAACACTACA
763473 GCCAC
1 GCCAC
763478 CTGATGCTCA
Statistics
Matches: 93, Mismatches: 0, Indels: 11
0.89 0.00 0.11
Matches are distributed among these distances:
16 22 0.24
17 31 0.33
19 1 0.01
20 1 0.01
22 38 0.41
ACGTcount: A:0.36, C:0.34, G:0.13, T:0.17
Consensus pattern (17 bp):
GCCACTGTAACACTACA
Found at i:763411 original size:22 final size:22
Alignment explanation
Indices: 763386--763451 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
763376 TACAGCCACT
763386 GTAACACTACAGCCACTGTAAC
1 GTAACACTACAGCCACTGTAAC
763408 GTAACACTACAGCCACTGTAAC
1 GTAACACTACAGCCACTGTAAC
763430 GTAACACTACAGCCACTGTAAC
1 GTAACACTACAGCCACTGTAAC
763452 ACTAAGCCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.36, C:0.32, G:0.14, T:0.18
Consensus pattern (22 bp):
GTAACACTACAGCCACTGTAAC
Found at i:763412 original size:39 final size:40
Alignment explanation
Indices: 763366--763477 Score: 135
Period size: 39 Copynumber: 2.9 Consensus size: 40
763356 GCACTATGCC
* *
763366 ACTGTAACACTACAGCCACTGTAACACTACAGCCACTGTA
1 ACTGTAACACTACAGCCACTGTAACACTACAGCCACAGCA
* * *
763406 AC-GTAACACTACAGCCACTGTAAC-GTAACA-CTACAGCC
1 ACTGTAACACTACAGCCACTGTAACACT-ACAGCCACAGCA
763444 ACTGTAACACTA-AGCCACTGTAACACTA-AGCCAC
1 ACTGTAACACTACAGCCACTGTAACACTACAGCCAC
763478 CTGATGCTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
37 1 0.02
38 23 0.38
39 35 0.57
40 2 0.03
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.18
Consensus pattern (40 bp):
ACTGTAACACTACAGCCACTGTAACACTACAGCCACAGCA
Found at i:768814 original size:15 final size:15
Alignment explanation
Indices: 768790--768819 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
768780 TCAAAGTTTG
768790 CAATAATTTTGTTGT
1 CAATAATTTTGTTGT
*
768805 CAATATTTTTGTTGT
1 CAATAATTTTGTTGT
768820 TGTAAACCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (15 bp):
CAATAATTTTGTTGT
Found at i:774824 original size:15 final size:16
Alignment explanation
Indices: 774795--774824 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
774785 CAACCAAAAA
774795 AACCAAAAGGTGTACC
1 AACCAAAAGGTGTACC
774811 AACCAAAA-GTGTAC
1 AACCAAAAGGTGTAC
774825 AAAAAACCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (16 bp):
AACCAAAAGGTGTACC
Found at i:777666 original size:2 final size:2
Alignment explanation
Indices: 777659--777707 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
777649 AAAATACAGA
777659 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
777701 AG AG AG A
1 AG AG AG A
777708 TATGACTGTG
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:791262 original size:17 final size:18
Alignment explanation
Indices: 791240--791274 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
791230 GCTACAACAT
791240 TTTAAAAA-TTTGAATAA
1 TTTAAAAATTTTGAATAA
791257 TTTAAAAATTTTGAATAA
1 TTTAAAAATTTTGAATAA
791275 ACTGATATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTAAAAATTTTGAATAA
Found at i:800972 original size:2 final size:2
Alignment explanation
Indices: 800965--800994 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
800955 TCTCAATTTT
800965 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
800995 TTTAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:803147 original size:3 final size:3
Alignment explanation
Indices: 803141--803191 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
803131 AAATTTAAAT
803141 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
803189 GAA
1 GAA
803192 ATTTATACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:803769 original size:2 final size:2
Alignment explanation
Indices: 803762--803821 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
803752 GTTATTGCAA
803762 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
803803 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
803822 GAGAATTATT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:806969 original size:7 final size:7
Alignment explanation
Indices: 806938--806969 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
806928 CCCCCCCCCC
806938 AAAAA-A
1 AAAAACA
806944 AAAAA-A
1 AAAAACA
806950 AAAAACA
1 AAAAACA
806957 AAAAACA
1 AAAAACA
806964 AAAAAC
1 AAAAAC
806970 CAGACAAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 11 0.44
7 14 0.56
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:817020 original size:2 final size:2
Alignment explanation
Indices: 817013--817065 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
817003 CAAATCTCAC
817013 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
817055 GA GA GA GA GA G
1 GA GA GA GA GA G
817066 GGGTTTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:817482 original size:18 final size:18
Alignment explanation
Indices: 817459--817493 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
817449 TCTAACAAGA
817459 GCTGCTGATTATATAATC
1 GCTGCTGATTATATAATC
817477 GCTGCTGATTATATAAT
1 GCTGCTGATTATATAAT
817494 TTAGATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (18 bp):
GCTGCTGATTATATAATC
Found at i:826506 original size:2 final size:2
Alignment explanation
Indices: 826499--826532 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
826489 ATTTAATGTA
826499 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
826533 AGAGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:826537 original size:2 final size:2
Alignment explanation
Indices: 826532--826588 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
826522 GTGTGTGTGT
826532 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
826574 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
826589 GTGTACACAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:828187 original size:22 final size:22
Alignment explanation
Indices: 828132--828187 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
828122 AAAACATGAA
828132 ATAAATTAAACT-GAAATATATT
1 ATAAATTAAA-TGGAAATATATT
* **
828154 ATAAGTGGAATGGATAATA-ATT
1 ATAAATTAAATGGA-AATATATT
828176 ATAAATTAAATG
1 ATAAATTAAATG
828188 TGATTGAAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
21 1 0.04
22 21 0.81
23 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (22 bp):
ATAAATTAAATGGAAATATATT
Found at i:828254 original size:2 final size:2
Alignment explanation
Indices: 828247--828273 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
828237 GCAATACGCC
828247 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
828274 TCTTTACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:835418 original size:151 final size:153
Alignment explanation
Indices: 835174--835475 Score: 454
Period size: 151 Copynumber: 2.0 Consensus size: 153
835164 ACCTTATTGT
* * *
835174 AAACTATTTTGAATTTTTTTTTATATACACATGTATGACATTTTATTTGCATGTGAAAAAGTATA
1 AAACTATTTTGAATTTTTATTTAAATACACATGTATGACATTTTATTTGCATGTGAAAAAGTACA
*
835239 TCAATTATTGTAAAGGGAGAGGGCTACATAAGTTTTA-GAA-CT-TGTGCCCAATCGCATCGTAA
66 TCAATTATTGTAAAGGGAGAGGGCTACATAAG-TTTAGGAACCTGTGTGCCCAATCCCATCGTAA
835301 -TATATTAAAATAAAATAAGATAA
130 TTATATTAAAATAAAATAAGATAA
835324 AAAC-ATTTTGAATCTTTATATTTAAATACACATGTATGACATTTTATTTGCATGTGAAAAATGT
1 AAACTATTTTGAAT-TTT-TATTTAAATACACATGTATGACATTTTATTTGCATGTGAAAAA-GT
* *
835388 ACATCAATTATTGTAAAGGGAG-GGGTTACATAAGTTTAGGAACCTGTGTGCCCAATCCCATTGT
63 ACATCAATTATTGTAAAGGGAGAGGGCTACATAAGTTTAGGAACCTGTGTGCCCAATCCCATCGT
* *
835452 AATTGTATTACAATAAAATAAGAT
128 AATTATATTAAAATAAAATAAGAT
835476 CAAACCAAAC
Statistics
Matches: 137, Mismatches: 8, Indels: 10
0.88 0.05 0.06
Matches are distributed among these distances:
149 9 0.07
150 11 0.08
151 55 0.40
152 25 0.18
153 18 0.13
154 19 0.14
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (153 bp):
AAACTATTTTGAATTTTTATTTAAATACACATGTATGACATTTTATTTGCATGTGAAAAAGTACA
TCAATTATTGTAAAGGGAGAGGGCTACATAAGTTTAGGAACCTGTGTGCCCAATCCCATCGTAAT
TATATTAAAATAAAATAAGATAA
Found at i:837896 original size:2 final size:2
Alignment explanation
Indices: 837889--837938 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
837879 CACCTGCATA
837889 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
837931 TC TC TC TC
1 TC TC TC TC
837939 AAAATCAGCT
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:838094 original size:18 final size:19
Alignment explanation
Indices: 838071--838112 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
838061 TTGTGAAATG
* *
838071 AAAAACCCAATAAAA-AAA
1 AAAAACCAAAAAAAACAAA
838089 AAAAA-CAAAAAAAACAAA
1 AAAAACCAAAAAAAACAAA
838107 AAAAAC
1 AAAAAC
838113 AACAACAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.02
Consensus pattern (19 bp):
AAAAACCAAAAAAAACAAA
Found at i:838100 original size:9 final size:9
Alignment explanation
Indices: 838082--838114 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
838072 AAAACCCAAT
838082 AAAA-AAAA
1 AAAACAAAA
838090 AAAACAAAA
1 AAAACAAAA
838099 AAAACAAAA
1 AAAACAAAA
838108 AAAACAA
1 AAAACAA
838115 CAACAACGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 20 0.83
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAACAAAA
Found at i:848078 original size:2 final size:2
Alignment explanation
Indices: 848071--848097 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
848061 CACCTTACAT
848071 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
848098 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:848124 original size:2 final size:2
Alignment explanation
Indices: 848119--848150 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
848109 NNNNNNNNNN
848119 TA TA 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 TA TA
848151 AGACAGGGCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:850983 original size:2 final size:2
Alignment explanation
Indices: 850976--851034 Score: 75
Period size: 2 Copynumber: 29.5 Consensus size: 2
850966 AAGATAATTG
* * *
850976 CT CT CT CT CT CT CT CT CT CT CAT -T CT CT CT CT CA CA CA CT CT
1 CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT CT CT
851018 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
851035 CGTCTGAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 1 0.02
2 51 0.96
3 1 0.02
ACGTcount: A:0.07, C:0.49, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:851217 original size:5 final size:5
Alignment explanation
Indices: 851207--851307 Score: 118
Period size: 5 Copynumber: 20.4 Consensus size: 5
851197 GTATAAATTC
* * *
851207 CGTTT CGTTT CGTTT CGATT --TTT GGTTT CGTTT CGTTT TGTTT CGTTT
1 CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT
* *
851255 CGTTT CGATT GGTTT CGTTT CGTTT CG-TT CGATTT CGTTT CGATTT CGTTT
1 CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CG-TTT CGTTT CG-TTT CGTTT
851306 CG
1 CG
851308 CACTTTACAG
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
3 2 0.02
4 4 0.05
5 67 0.82
6 9 0.11
ACGTcount: A:0.04, C:0.17, G:0.22, T:0.57
Consensus pattern (5 bp):
CGTTT
Found at i:853940 original size:2 final size:2
Alignment explanation
Indices: 853933--853959 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
853923 AATTAGGCCA
853933 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
853960 TAAGATGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:862776 original size:15 final size:14
Alignment explanation
Indices: 862744--862788 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
862734 GTGGTACTTT
* *
862744 TTTGTTTTTGTTTG
1 TTTGTTTTTTTTTA
862758 TTTGGTTTTTTTTTA
1 TTT-GTTTTTTTTTA
862773 TTTGTTTCTTTTTTA
1 TTTGTTT-TTTTTTA
862788 T
1 T
862789 ATTCTCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.04, C:0.02, G:0.13, T:0.80
Consensus pattern (14 bp):
TTTGTTTTTTTTTA
Found at i:862785 original size:19 final size:19
Alignment explanation
Indices: 862742--862786 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
862732 AAGTGGTACT
* *
862742 TTTTTGTTTTTGTTTGTTTG
1 TTTTT-TTTTTATTTGTTTC
*
862762 GTTTTTTTTTATTTGTTTC
1 TTTTTTTTTTATTTGTTTC
862781 TTTTTT
1 TTTTTT
862787 ATATTCTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTTATTTGTTTC
Found at i:867394 original size:106 final size:106
Alignment explanation
Indices: 867226--867424 Score: 380
Period size: 106 Copynumber: 1.9 Consensus size: 106
867216 TTCTTTATAT
*
867226 GCGTTAATGGAAACGTAGATCAGCAAGGGGTTCTTTGTCGTGCAAGCACCCACTTAATAGATTGT
1 GCGTTAATGGAAACGTAGATCAGCAAGGGGTTCTTTGTCATGCAAGCACCCACTTAATAGATTGT
867291 TACACGGATCTAAAACGATGACAAATATTTTTTCCGTTATG
66 TACACGGATCTAAAACGATGACAAATATTTTTTCCGTTATG
*
867332 GCGTTAATGGAAACGTAGATCAGCAAGGGGTTCTTTGTCATGCAAGCACCTACTTAATAGATTGT
1 GCGTTAATGGAAACGTAGATCAGCAAGGGGTTCTTTGTCATGCAAGCACCCACTTAATAGATTGT
867397 TACACGGATCTAAAACGATGACAAATAT
66 TACACGGATCTAAAACGATGACAAATAT
867425 CGAAAAGGCA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 91 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (106 bp):
GCGTTAATGGAAACGTAGATCAGCAAGGGGTTCTTTGTCATGCAAGCACCCACTTAATAGATTGT
TACACGGATCTAAAACGATGACAAATATTTTTTCCGTTATG
Done.