Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1009
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: 1861391
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 223269 characters in sequence are not A, C, G, or T
File 6 of 5
Found at i:1522799 original size:21 final size:21
Alignment explanation
Indices: 1522773--1522814 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1522763 ATAATTTGAA
*
1522773 AGCATT-AGCACAACAATAATG
1 AGCATTCAGAACAACAA-AATG
1522794 AGCATTCAGAACAACAAAATG
1 AGCATTCAGAACAACAAAATG
1522815 GTAAATACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (21 bp):
AGCATTCAGAACAACAAAATG
Found at i:1524370 original size:2 final size:2
Alignment explanation
Indices: 1524365--1524423 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1524355 TGTTAAAAAT
1524365 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
1524407 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
1524424 TGTGAGTAGC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1527235 original size:15 final size:15
Alignment explanation
Indices: 1527215--1527249 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1527205 ATGACTTGCA
1527215 TTATATTTT-TGATTT
1 TTATATTTTAT-ATTT
1527230 TTATATTTTATATTT
1 TTATATTTTATATTT
1527245 TTATA
1 TTATA
1527250 AACTGAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTATATTTTATATTT
Found at i:1531347 original size:13 final size:13
Alignment explanation
Indices: 1531329--1531358 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1531319 CACAACAAGA
1531329 TTCATATGGGATT
1 TTCATATGGGATT
*
1531342 TTCATATGGGGTT
1 TTCATATGGGATT
1531355 TTCA
1 TTCA
1531359 CGAAATTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.10, G:0.23, T:0.47
Consensus pattern (13 bp):
TTCATATGGGATT
Found at i:1534532 original size:2 final size:2
Alignment explanation
Indices: 1534525--1534573 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1534515 TATTTAAATA
1534525 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
1534567 TC TC TC T
1 TC TC TC T
1534574 GTTAATCATC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1538606 original size:56 final size:54
Alignment explanation
Indices: 1538540--1538662 Score: 138
Period size: 55 Copynumber: 2.2 Consensus size: 54
1538530 TATAAAGTGG
* *
1538540 ATGAAAAAATATCAAAGAGACCATTAAAATGTAAAATGAAGTGCTACTTATCATTT
1 ATGAATAAATATCAAA-AGA-CATGAAAATGTAAAATGAAGTGCTACTTATCATTT
*** * * *
1538596 ATGAATAAATATTTTTAAGATATGCAAATGTAAAATTAAGTGCTACTTATCATTT
1 ATGAATAAATA-TCAAAAGACATGAAAATGTAAAATGAAGTGCTACTTATCATTT
*
1538651 GTGAATAAATAT
1 ATGAATAAATAT
1538663 TGTAGTTGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
54 1 0.02
55 41 0.72
56 13 0.23
57 2 0.04
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (54 bp):
ATGAATAAATATCAAAAGACATGAAAATGTAAAATGAAGTGCTACTTATCATTT
Found at i:1540223 original size:2 final size:2
Alignment explanation
Indices: 1540216--1540255 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1540206 AATTTTTCAC
* *
1540216 CT CT CT CT CT CT CT CT CT CT CT CT TT TT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1540256 TTCAAATTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
CT
Found at i:1549656 original size:2 final size:2
Alignment explanation
Indices: 1549651--1549692 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1549641 TATATATATA
1549651 TG TG TG TG 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 TG TG TG TG
1549693 ACAAGACATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1553158 original size:21 final size:21
Alignment explanation
Indices: 1553133--1553266 Score: 171
Period size: 21 Copynumber: 6.4 Consensus size: 21
1553123 ATATGCCACC
1553133 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
**
1553154 ACTTGTCAGATCTTTATGTCG
1 ACTTGTCAGATAATTATGTCG
1553175 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
*
1553196 ACTTGTCAGAT-CTTGATGTCG
1 ACTTGTCAGATAATT-ATGTCG
* *
1553217 ACTTGTCAGATAATCATGTTG
1 ACTTGTCAGATAATTATGTCG
* ** *
1553238 ACTTGTCAGTTCTTTAAGTCG
1 ACTTGTCAGATAATTATGTCG
1553259 ACTTGTCA
1 ACTTGTCA
1553267 CTTATTCACG
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
20 2 0.02
21 94 0.97
22 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCG
Found at i:1553192 original size:42 final size:42
Alignment explanation
Indices: 1553133--1553266 Score: 223
Period size: 42 Copynumber: 3.2 Consensus size: 42
1553123 ATATGCCACC
1553133 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTTATGTCG
1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTTATGTCG
*
1553175 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTTATGTCG
* * * *
1553217 ACTTGTCAGATAATCATGTTGACTTGTCAGTTCTTTAAGTCG
1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTTATGTCG
1553259 ACTTGTCA
1 ACTTGTCA
1553267 CTTATTCACG
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 86 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (42 bp):
ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTTATGTCG
Found at i:1553367 original size:21 final size:21
Alignment explanation
Indices: 1553343--1553502 Score: 182
Period size: 21 Copynumber: 7.7 Consensus size: 21
1553333 AATAATATTT
**
1553343 TCTGACAAGTCGACATAAGGA
1 TCTGACAAGTCGACATAATTA
*
1553364 TCTGACAAGTTGACATAATCATA
1 TCTGACAAGTCGACATAAT--TA
*
1553387 TTTG--AAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
* *
1553406 TTTGACAAGGCGACATAATTA
1 TCTGACAAGTCGACATAATTA
1553427 TCTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
* * *
1553448 TTTGACAAGACGACATAA-CA
1 TCTGACAAGTCGACATAATTA
* *
1553468 TCTGACAAGTCAACATCATTA
1 TCTGACAAGTCGACATAATTA
1553489 TCTGACAAGTCGAC
1 TCTGACAAGTCGAC
1553503 TTATAATATG
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 6 0.05
20 15 0.13
21 92 0.79
23 4 0.03
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (21 bp):
TCTGACAAGTCGACATAATTA
Found at i:1553734 original size:21 final size:21
Alignment explanation
Indices: 1553709--1553789 Score: 99
Period size: 21 Copynumber: 3.9 Consensus size: 21
1553699 ATAGTTATTT
* *
1553709 TCTGACATGTCAACATAAAGA
1 TCTGACAAGTCAACATAAACA
** *
1553730 TCTGACAAGTTGACATAAATA
1 TCTGACAAGTCAACATAAACA
*
1553751 TCTGACAAGTCAACATAATCA
1 TCTGACAAGTCAACATAAACA
*
1553772 TCTGACAAGTCGACATAA
1 TCTGACAAGTCAACATAA
1553790 TTTTCTGACA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.25
Consensus pattern (21 bp):
TCTGACAAGTCAACATAAACA
Found at i:1553768 original size:42 final size:42
Alignment explanation
Indices: 1553709--1553802 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
1553699 ATAGTTATTT
* * *
1553709 TCTGACATGTCAACATAAAGATCTGACAAGTTGACATAAATA
1 TCTGACAAGTCAACATAAACATCTGACAAGTCGACATAAATA
* * *
1553751 TCTGACAAGTCAACATAATCATCTGACAAGTCGACATAATTT
1 TCTGACAAGTCAACATAAACATCTGACAAGTCGACATAAATA
1553793 TCTGACAAGT
1 TCTGACAAGT
1553803 GGTGGCAGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (42 bp):
TCTGACAAGTCAACATAAACATCTGACAAGTCGACATAAATA
Found at i:1553790 original size:21 final size:20
Alignment explanation
Indices: 1553709--1553802 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 20
1553699 ATAGTTATTT
* *
1553709 TCTGACATGTCAACATAAAGA
1 TCTGACAAGTCAACAT-AATA
**
1553730 TCTGACAAGTTGACATAAATA
1 TCTGACAAGTCAACAT-AATA
1553751 TCTGACAAGTCAACATAATCA
1 TCTGACAAGTCAACATAAT-A
* *
1553772 TCTGACAAGTCGACATAATTT
1 TCTGACAAGTCAACATAA-TA
1553793 TCTGACAAGT
1 TCTGACAAGT
1553803 GGTGGCAGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (20 bp):
TCTGACAAGTCAACATAATA
Found at i:1560316 original size:18 final size:18
Alignment explanation
Indices: 1560289--1560323 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1560279 GAGGACGGAC
*
1560289 AGTGATAAAAGTAATAAA
1 AGTGACAAAAGTAATAAA
1560307 AGTGACAAAAGTAATAA
1 AGTGACAAAAGTAATAA
1560324 TTCCTTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (18 bp):
AGTGACAAAAGTAATAAA
Found at i:1575918 original size:2 final size:2
Alignment explanation
Indices: 1575911--1575959 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1575901 CCTCGTTTTA
1575911 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
1575953 AG AG AG A
1 AG AG AG A
1575960 ATTATTTATT
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:1589139 original size:2 final size:2
Alignment explanation
Indices: 1589132--1589162 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1589122 CCTGTCTGAN
1589132 TC TC 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 TC TC T
1589163 AACCTAGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1596027 original size:18 final size:17
Alignment explanation
Indices: 1596000--1596036 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1595990 CCCATGTCCC
1596000 CAAACACTGTACATATA
1 CAAACACTGTACATATA
*
1596017 CAAACCACTGTATATATA
1 CAAA-CACTGTACATATA
1596035 CA
1 CA
1596037 TGTGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (17 bp):
CAAACACTGTACATATA
Found at i:1596295 original size:2 final size:2
Alignment explanation
Indices: 1596288--1596321 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1596278 GACGAATGAT
1596288 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
1596322 CCGTATAGAA
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1609762 original size:22 final size:23
Alignment explanation
Indices: 1609733--1609999 Score: 154
Period size: 22 Copynumber: 11.8 Consensus size: 23
1609723 NNNNNNNNAA
1609733 TTTCTGATATCAGAAAATATAAT
1 TTTCTGATATCAGAAAATATAAT
* *
1609756 TCT-TGATATCAAAAAATCAGTTTCAA-
1 TTTCTGATATCAGAAAAT-A---T-AAT
*
1609782 TTTCTGATATCA-AAAA-ATCAT
1 TTTCTGATATCAGAAAATATAAT
* **
1609803 TTTCTGATATCAAAAAATCGAA-
1 TTTCTGATATCAGAAAATATAAT
1609825 TTTCTGATATCAGAAAATGAT--T
1 TTTCTGATATCAGAAAAT-ATAAT
**
1609847 TTT-TGATATCAGAAAAT-CGAT
1 TTTCTGATATCAGAAAATATAAT
* *
1609868 TTTTTGATATCAGAAAATGGATCGTAT
1 TTTCTGATATCAGAAAAT--AT--AAT
*
1609895 TTTCTGATATCA-AGAAT-TCGAA-
1 TTTCTGATATCAGAAAATAT--AAT
*
1609917 TTTCTGATATCA-AAAA-ATCAT
1 TTTCTGATATCAGAAAATATAAT
* **
1609938 TTTCTGATATCAGAAATTCGAAT
1 TTTCTGATATCAGAAAATATAAT
* *
1609961 TCT-TGATATCA-AAAA-ATCAT
1 TTTCTGATATCAGAAAATATAAT
1609981 TTTCTGATATCAGAAAATA
1 TTTCTGATATCAGAAAATA
1610000 CCTCAAAAAT
Statistics
Matches: 190, Mismatches: 28, Indels: 52
0.70 0.10 0.19
Matches are distributed among these distances:
20 6 0.03
21 54 0.28
22 82 0.43
23 13 0.07
24 1 0.01
26 11 0.06
27 23 0.12
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (23 bp):
TTTCTGATATCAGAAAATATAAT
Found at i:1609832 original size:43 final size:43
Alignment explanation
Indices: 1609731--1609998 Score: 279
Period size: 43 Copynumber: 6.0 Consensus size: 43
1609721 NNNNNNNNNN
* *
1609731 AATTTCTGATATCAGAAAAT-ATAATTCTTGATATCAAAAAATCAG
1 AATTTCTGATATCAAAAAATCAT-TTTC-TGATATCAAAAAATC-G
1609776 TTTCAATTTCTGATATCAAAAAATCATTTTCTGATATCAAAAAATCG
1 ----AATTTCTGATATCAAAAAATCATTTTCTGATATCAAAAAATCG
* * * *
1609823 AATTTCTGATATCAGAAAATGATTTTTTGATATCAGAAAATCG
1 AATTTCTGATATCAAAAAATCATTTTCTGATATCAAAAAATCG
* * * *
1609866 ATTTTTTGATATCAGAAAATGGATCGTATTTTCTGATATCAAGAATTCG
1 AATTTCTGATATCA-AAAA---ATC--ATTTTCTGATATCAAAAAATCG
* *
1609915 AATTTCTGATATCAAAAAATCATTTTCTGATATCAGAAATTCG
1 AATTTCTGATATCAAAAAATCATTTTCTGATATCAAAAAATCG
*
1609958 AA-TTCTTGATATCAAAAAATCATTTTCTGATATCAGAAAAT
1 AATTTC-TGATATCAAAAAATCATTTTCTGATATCAAAAAAT
1609999 ACCTCAAAAA
Statistics
Matches: 192, Mismatches: 19, Indels: 22
0.82 0.08 0.09
Matches are distributed among these distances:
42 3 0.02
43 107 0.56
44 3 0.02
45 3 0.02
47 3 0.02
48 19 0.10
49 52 0.27
50 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (43 bp):
AATTTCTGATATCAAAAAATCATTTTCTGATATCAAAAAATCG
Found at i:1609897 original size:92 final size:85
Alignment explanation
Indices: 1609731--1609998 Score: 302
Period size: 92 Copynumber: 3.0 Consensus size: 85
1609721 NNNNNNNNNN
* * *
1609731 AATTTCTGATATCAGAAAATATAATTCTTGATATCAAAAAATCAGTTTCAATTTCTGATATCAAA
1 AATTTCTGATATCAGAAAATAT--TTTTTGATATCAGAAAATC-GATT---TTT-TGATATCAAA
1609796 AAATCATTTTCTGATATCAAAAAATCG
59 AAATCATTTTCTGATATCAAAAAATCG
1609823 AATTTCTGATATCAGAAAATGATTTTTTGATATCAGAAAATCGATTTTTTGATATCAGAAAATGG
1 AATTTCTGATATCAGAAAAT-ATTTTTTGATATCAGAAAATCGATTTTTTGATATCA-AAAA---
* *
1609888 ATCGTATTTTCTGATATCAAGAATTCG
61 ATC--ATTTTCTGATATCAAAAAATCG
* * * * *
1609915 AATTTCTGATATCAAAAAATCATTTTCTGATATCAGAAATTCGAATTCTTGATATCAAAAAATCA
1 AATTTCTGATATCAGAAAAT-ATTTTTTGATATCAGAAAATCGATTTTTTGATATCAAAAAATCA
*
1609980 TTTTCTGATATCAGAAAAT
65 TTTTCTGATATCAAAAAAT
1609999 ACCTCAAAAA
Statistics
Matches: 155, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
86 25 0.16
87 7 0.05
88 3 0.02
90 6 0.04
91 21 0.14
92 91 0.59
93 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (85 bp):
AATTTCTGATATCAGAAAATATTTTTTGATATCAGAAAATCGATTTTTTGATATCAAAAAATCAT
TTTCTGATATCAAAAAATCG
Found at i:1613888 original size:63 final size:63
Alignment explanation
Indices: 1613683--1613897 Score: 198
Period size: 63 Copynumber: 3.4 Consensus size: 63
1613673 CTTCTGGTGC
* ** * * * * * *
1613683 TGCAGTTATTTCAGGTGATTTTTCTTGGCTTGGTGTAGTTAGCTCAGAAGATTCTTCCAGAGC
1 TGCAGTTATTTTAGACGATTTTTCTTGGCTTGATGTAGTTAACTTAGAGGATTCTTCCAGTGA
* * * * * * *
1613746 TGCAATTTTTTTGGACGATTTTTCCTGGCTTGATATAGTT-ACTTCAGAGGATTCTTCCATTGT
1 TGCAGTTATTTTAGACGATTTTTCTTGGCTTGATGTAGTTAACTT-AGAGGATTCTTCCAGTGA
** * * *
1613809 TATAGTTATTTCAGACGATTTTTCTTGGTTTGATGTAGTTAAATTAGAGGATTCTTCCAGTGA
1 TGCAGTTATTTTAGACGATTTTTCTTGGCTTGATGTAGTTAACTTAGAGGATTCTTCCAGTGA
** *
1613872 TGCAGTCGTTTTAGACGATTCTTCTT
1 TGCAGTTATTTTAGACGATTTTTCTT
1613898 CATCTAATGA
Statistics
Matches: 117, Mismatches: 33, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
62 2 0.02
63 112 0.96
64 3 0.03
ACGTcount: A:0.20, C:0.14, G:0.21, T:0.44
Consensus pattern (63 bp):
TGCAGTTATTTTAGACGATTTTTCTTGGCTTGATGTAGTTAACTTAGAGGATTCTTCCAGTGA
Found at i:1614275 original size:15 final size:15
Alignment explanation
Indices: 1614255--1614288 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1614245 TCTGTTATAA
1614255 CTGTTTCAGATGAAT
1 CTGTTTCAGATGAAT
1614270 CTGTTTCAGATGAAT
1 CTGTTTCAGATGAAT
1614285 CTGT
1 CTGT
1614289 GAAAGCTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.41
Consensus pattern (15 bp):
CTGTTTCAGATGAAT
Found at i:1616934 original size:2 final size:2
Alignment explanation
Indices: 1616929--1616974 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1616919 GAAAGGTGTG
1616929 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1616971 CT CT
1 CT CT
1616975 ATTTATACGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1621732 original size:9 final size:9
Alignment explanation
Indices: 1621718--1621794 Score: 100
Period size: 9 Copynumber: 8.2 Consensus size: 9
1621708 CATGTACTTA
1621718 TTGTTCTTC
1 TTGTTCTTC
1621727 TTGTTCTTC
1 TTGTTCTTC
*
1621736 TTCTTCTTGTTC
1 TTGTTC---TTC
1621748 TTGTTCTTC
1 TTGTTCTTC
1621757 TTGTTCTTC
1 TTGTTCTTC
1621766 TTGTTCTTC
1 TTGTTCTTC
*
1621775 TTCTTCTTC
1 TTGTTCTTC
*
1621784 TTCTTCTTC
1 TTGTTCTTC
1621793 TT
1 TT
1621795 TTCAAAGAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
9 54 0.87
12 8 0.13
ACGTcount: A:0.00, C:0.25, G:0.08, T:0.68
Consensus pattern (9 bp):
TTGTTCTTC
Found at i:1621739 original size:6 final size:6
Alignment explanation
Indices: 1621721--1621794 Score: 103
Period size: 6 Copynumber: 12.3 Consensus size: 6
1621711 GTACTTATTG
* * * * *
1621721 TTCTTC TTGTTC TTCTTC TTCTTG TTCTTG TTCTTC TTGTTC TTCTTG
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
1621769 TTCTTC TTCTTC TTCTTC TTCTTC TT
1 TTCTTC TTCTTC TTCTTC TTCTTC TT
1621795 TTCAAAGAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.68
Consensus pattern (6 bp):
TTCTTC
Found at i:1621741 original size:15 final size:15
Alignment explanation
Indices: 1621721--1621794 Score: 112
Period size: 15 Copynumber: 4.9 Consensus size: 15
1621711 GTACTTATTG
1621721 TTCTTCTTGTTCTTC
1 TTCTTCTTGTTCTTC
*
1621736 TTCTTCTTGTTCTTG
1 TTCTTCTTGTTCTTC
1621751 TTCTTCTTGTTCTTC
1 TTCTTCTTGTTCTTC
* *
1621766 TTGTTCTTCTTCTTC
1 TTCTTCTTGTTCTTC
*
1621781 TTCTTCTTCTTCTT
1 TTCTTCTTGTTCTT
1621795 TTCAAAGAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 54 1.00
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.68
Consensus pattern (15 bp):
TTCTTCTTGTTCTTC
Found at i:1627890 original size:20 final size:20
Alignment explanation
Indices: 1627865--1627921 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1627855 TTTTAAATTA
1627865 TATATAATTTATAATTATAT
1 TATATAATTTATAATTATAT
**
1627885 TATAT-ATGAATAAATTATAT
1 TATATAATTTAT-AATTATAT
1627905 TATCATAATTTTATAAT
1 TAT-ATAA-TTTATAAT
1627922 ACATGTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 4 0.14
20 16 0.55
21 2 0.07
22 4 0.14
23 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TATATAATTTATAATTATAT
Found at i:1628841 original size:12 final size:12
Alignment explanation
Indices: 1628818--1628847 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1628808 ATCACATTTT
1628818 GTCTGT-CGTCC
1 GTCTGTCCGTCC
1628829 GTCTGTCCGTCC
1 GTCTGTCCGTCC
1628841 GTCTGTC
1 GTCTGTC
1628848 TGTCTGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.00, C:0.37, G:0.27, T:0.37
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:1633352 original size:2 final size:2
Alignment explanation
Indices: 1633345--1633389 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1633335 NNNNNNNNNN
1633345 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
1633387 TC T
1 TC T
1633390 TTTACAAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1638446 original size:169 final size:169
Alignment explanation
Indices: 1638060--1638557 Score: 741
Period size: 169 Copynumber: 2.9 Consensus size: 169
1638050 AGAACCATTA
* * *
1638060 AGCCAGGAAAGCTGAAACTTTTGTGGAAGCATCTTCAGGTAGTGTAGATTCAAAATTGTGAAAAT
1 AGCCAGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
* * *
1638125 CATGACTTCTAGGGGTAGGGTGGGGCCACAAT--GGGGGGGGGGTCAAAGTTTAACATAGGAATA
66 CATGACTTCTGGGGGTAGGGTGGGACCACAATGGGGGGGGGGGGTCAAAGTTTAACATTGGAATA
* * *
1638188 TATAGAGTAAATCTCTATAAATCTTCTTTACAAAAACTAATC
131 TATTGAGTAAATCT-TAAAAAT-TT-TCTACAAAAACTAATC
* *
1638230 AGCCAGGAAAGCTTAAACTTATGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAGTTGTGAAAAT
1 AGCCAGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
* * *
1638295 CATGACTTCTGGGGGAAGGATGGGACCACAATGGGGGGAGGGGGGTCAAAATTTAACATTGGAAT
66 CATGACTTCTGGGGGTAGGGTGGGACCACAATGGGGGG-GGGGGGTCAAAGTTTAACATTGGAAT
**
1638360 ATATTGAGTAAATCTTAAAAATTTTCT-CAGTAACTAATC
130 ATATTGAGTAAATCTTAAAAATTTTCTACAAAAACTAATC
* *
1638399 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTAAAAAT
1 AGCCAGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
1638464 CATGACTTCTGGGGGTAGGGTGGGACCACAATTGGGGGGGGGGGGTGTCAAAGTTTAACATTGGA
66 CATGACTTCTGGGGGTAGGGTGGGACCACAA-T-GGGGGGGGGGG-GTCAAAGTTTAACATTGGA
*
1638529 ATATATTGAGTAAATCTTAAAAATCTTCT
128 ATATATTGAGTAAATCTTAAAAATTTTCT
1638558 TCTCTTTATG
Statistics
Matches: 298, Mismatches: 24, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
169 100 0.34
170 96 0.32
171 54 0.18
172 10 0.03
173 38 0.13
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (169 bp):
AGCCAGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
CATGACTTCTGGGGGTAGGGTGGGACCACAATGGGGGGGGGGGGTCAAAGTTTAACATTGGAATA
TATTGAGTAAATCTTAAAAATTTTCTACAAAAACTAATC
Found at i:1639381 original size:172 final size:170
Alignment explanation
Indices: 1638836--1639513 Score: 895
Period size: 168 Copynumber: 4.0 Consensus size: 170
1638826 AGAACCATTA
* * * *
1638836 AGCCAGGAAAGCTGATACTTGTTTGGAAGCATCTTCAGGTAGTGTAGATTCAAAATTGTGAAAAT
1 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
* * * *
1638901 CATGA--CTTTGGGGGTAGGGTGGGGCCACAATGGGGGGGGGGGTCGCAGTTTAACATAGGAATA
66 CATGACCCCTT-GGCGTAGGGT-GGGCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATA
* * * *
1638964 TATAGAGTAAATCTTTATAAATCTTCTTTACAAAAACTAATC
129 TATTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATC
* * *
1639006 GGCCAGGAAAGCTTAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAAT
1 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
* * * *
1639071 CATGACCCCCTTGGCGTAGGGTTGTCCACAAT---GGGGGGGATCCAAGTTTTACATAGGAATAT
66 CATGA-CCCCTTGGCGTAGGGTGGGCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATAT
* *
1639133 ATAT-AGTAAATCTTTAAAAAAACTTCTTTTCAGAAACAAATC
130 AT-TGAGTAAATCTTT-AAAAATCTTCTTTTCAGAAACTAATC
* *
1639175 AGCCAGGAAAGCTTAAACTTGTGTGGAAGCATCCTCAGG-AGTGTAGATTTAAAGTTGTGAAAAT
1 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
* * *
1639239 CATGACCCCCTTGGCGTAGAGCT-GTCCACAACTGGGGGAGGGGGATCGAAGTTTTACATAGGAA
66 CATGA-CCCCTTGGCGTAG-GGTGGGCCACAA-TGGGGG-GGGGGATCGAAGTTTAACATAGGAA
1639303 TATATTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATC
127 TATATTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATC
1639347 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
1 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
** * * * * * *
1639412 CATGACTTCTGGGGGTAGGGTGGGGCCACAATGGGGGGGGGGGTCAAAATTTAACATTGGAATAT
66 CATGACCCCTTGGCGTAGGGT-GGGCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATAT
*
1639477 ATTGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
130 ATTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACT
1639514 CGGCTTTAGG
Statistics
Matches: 453, Mismatches: 40, Indels: 29
0.87 0.08 0.06
Matches are distributed among these distances:
168 91 0.20
169 62 0.14
170 63 0.14
171 69 0.15
172 89 0.20
173 79 0.17
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (170 bp):
AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
CATGACCCCTTGGCGTAGGGTGGGCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATATA
TTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATC
Found at i:1639513 original size:171 final size:171
Alignment explanation
Indices: 1638796--1639513 Score: 886
Period size: 172 Copynumber: 4.2 Consensus size: 171
1638786 ATGAAAATTT
* * * *
1638796 TTGAG-AAAT-TTTCAAAAATCTTCCTTCTCA-AGAACCATTAAGCCAGGAAAGCTGATACTTGT
1 TTGAGTAAATCTTT-AAAAATCTT-CTTCTCAGA-AACTAATCAGCCAGGAAAGCTGAAACTTGT
* * * ** *
1638858 TTGGAAGCATCTTCAGGTAGTGTAGATTCAAAATTGTGAAAATCATGA--CTTTGGGGGTAGGGT
63 GTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCTGGGCGTAGGGT
* *
1638921 GGGGCCACAATGGGGGGGGGGGTCGCAGTTTAACATAGGAATATA
128 -GGGCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATATA
* * * * *
1638966 TAGAGTAAATCTTTATAAATCTTCTT-TACAAAAACTAATCGGCCAGGAAAGCTTAAACTTGTGT
1 TTGAGTAAATCTTTAAAAATCTTCTTCT-CAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGT
* * *
1639030 GGAAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAATCATGACCCCCTTGGCGTAGGGTTG
65 GGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCTGGGCGTAGGGTGG
* * *
1639095 TCCACAAT---GGGGGGGATCCAAGTTTTACATAGGAATATA
130 GCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATATA
* * * *
1639134 TAT-AGTAAATCTTTAAAAAAACTTCTTTTCAGAAACAAATCAGCCAGGAAAGCTTAAACTTGTG
1 T-TGAGTAAATCTTT-AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG
* * *
1639198 TGGAAGCATCCTCAGG-AGTGTAGATTTAAAGTTGTGAAAATCATGACCCCCTTGGCGTAGAGCT
64 TGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCTGGGCGTAG-GGT
* *
1639262 -GTCCACAACTGGGGGAGGGGGATCGAAGTTTTACATAGGAATATA
128 GGGCCACAA-TGGGGG-GGGGGATCGAAGTTTAACATAGGAATATA
*
1639307 TTGAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTG
1 TTGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTG
** *
1639372 GAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGA-CTTCTGGGGGTAGGGTGGG
66 GAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCTGGGCGTAGGGT-GG
* * * *
1639436 GCCACAATGGGGGGGGGGGTCAAAATTTAACATTGGAATATA
130 GCCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATATA
1639478 TTGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
1 TTGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
1639514 CGGCTTTAGG
Statistics
Matches: 483, Mismatches: 46, Indels: 37
0.85 0.08 0.07
Matches are distributed among these distances:
168 91 0.19
169 62 0.13
170 78 0.16
171 82 0.17
172 94 0.19
173 76 0.16
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (171 bp):
TTGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTG
GAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCTGGGCGTAGGGTGGG
CCACAATGGGGGGGGGGATCGAAGTTTAACATAGGAATATA
Found at i:1643462 original size:30 final size:30
Alignment explanation
Indices: 1643426--1643488 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
1643416 GGTTCCGACG
1643426 CCTATGAGCTATTCACTGCGTATGAATTTA
1 CCTATGAGCTATTCACTGCGTATGAATTTA
1643456 CCTATGAGCTATTCACTGCGTATGAATTTA
1 CCTATGAGCTATTCACTGCGTATGAATTTA
1643486 CCT
1 CCT
1643489 GTAATTTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (30 bp):
CCTATGAGCTATTCACTGCGTATGAATTTA
Found at i:1647037 original size:27 final size:27
Alignment explanation
Indices: 1646984--1647040 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1646974 GATCTTTAAC
**
1646984 TGCAGCCCTTCTAAATAGAGTTGTGCA
1 TGCAGCCCTTCTAAATAGAGTCCTGCA
1647011 TGCAGCCCTTCTAAAT-GAAGTCCTGCA
1 TGCAGCCCTTCTAAATAG-AGTCCTGCA
1647038 TGC
1 TGC
1647041 CTATAAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (27 bp):
TGCAGCCCTTCTAAATAGAGTCCTGCA
Found at i:1648310 original size:16 final size:16
Alignment explanation
Indices: 1648289--1648333 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1648279 CATACGGTAT
1648289 CAGGAGAAAACGTACC
1 CAGGAGAAAACGTACC
1648305 CAGGAGAAAACGTACC
1 CAGGAGAAAACGTACC
*
1648321 CAAGAGAAAACGT
1 CAGGAGAAAACGT
1648334 TCCTAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.47, C:0.22, G:0.24, T:0.07
Consensus pattern (16 bp):
CAGGAGAAAACGTACC
Found at i:1649457 original size:16 final size:16
Alignment explanation
Indices: 1649439--1649502 Score: 101
Period size: 16 Copynumber: 4.0 Consensus size: 16
1649429 CCCTAGAAAT
*
1649439 TGGGTACGTTTTCTCT
1 TGGGTACGTTTTCTCC
1649455 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
1649471 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
* *
1649487 TAGGTATGTTTTCTCC
1 TGGGTACGTTTTCTCC
1649503 AGCATTCTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.22, G:0.23, T:0.47
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:1651033 original size:2 final size:2
Alignment explanation
Indices: 1651026--1651051 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1651016 TTGTATACAT
1651026 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
1651052 ATGAGAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1661202 original size:24 final size:24
Alignment explanation
Indices: 1661175--1661247 Score: 146
Period size: 24 Copynumber: 3.0 Consensus size: 24
1661165 GCGGTCGTTG
1661175 TACATGTATATGGATCAATTGTTA
1 TACATGTATATGGATCAATTGTTA
1661199 TACATGTATATGGATCAATTGTTA
1 TACATGTATATGGATCAATTGTTA
1661223 TACATGTATATGGATCAATTGTTA
1 TACATGTATATGGATCAATTGTTA
1661247 T
1 T
1661248 GTTAAGAATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.42
Consensus pattern (24 bp):
TACATGTATATGGATCAATTGTTA
Found at i:1666901 original size:27 final size:27
Alignment explanation
Indices: 1666878--1667305 Score: 608
Period size: 27 Copynumber: 15.9 Consensus size: 27
1666868 TACTGTAATT
*
1666878 TAACGATACTATATGGTATATGTACTG
1 TAACGATACTATATGGTACATGTACTG
* *
1666905 TAATGATACTATATGGTGCATGTACTG
1 TAACGATACTATATGGTACATGTACTG
* * * *
1666932 TTATGATACTATATGGTAGAGGTACTG
1 TAACGATACTATATGGTACATGTACTG
*
1666959 TAACAATACTATATGGTACATGTACTG
1 TAACGATACTATATGGTACATGTACTG
* * *
1666986 TAACAAGACTATATGGTTCATGTACTG
1 TAACGATACTATATGGTACATGTACTG
1667013 TAACGATACTATATGGTACATGTACTG
1 TAACGATACTATATGGTACATGTACTG
1667040 TAACGATACTATATGGTACATGTACTG
1 TAACGATACTATATGGTACATGTACTG
*
1667067 TAACGGTACTATATGGTACATGTACT-
1 TAACGATACTATATGGTACATGTACTG
* **
1667093 CAAGCGATTTTATATGGTACATGTACTG
1 TAA-CGATACTATATGGTACATGTACTG
1667121 TAACGATACTATATGGTACATGTACTG
1 TAACGATACTATATGGTACATGTACTG
*
1667148 TAACGATACTATATTGTACATGTACTG
1 TAACGATACTATATGGTACATGTACTG
* *
1667175 TAATGTTACTATATGGTACATGTACTG
1 TAACGATACTATATGGTACATGTACTG
* *
1667202 TAACAATACTCTATGGTACATGTACTG
1 TAACGATACTATATGGTACATGTACTG
* *
1667229 TAAGGATAGTA-ATTGGTACATGTACTG
1 TAACGATACTATA-TGGTACATGTACTG
*
1667256 TAACAATACTATATGGTACATGTACTG
1 TAACGATACTATATGGTACATGTACTG
*
1667283 TAACGATATTATATGGTACATGT
1 TAACGATACTATATGGTACATGT
1667306 NCTCGAAAAC
Statistics
Matches: 355, Mismatches: 42, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
26 3 0.01
27 349 0.98
28 3 0.01
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (27 bp):
TAACGATACTATATGGTACATGTACTG
Found at i:1667496 original size:27 final size:27
Alignment explanation
Indices: 1667408--1667487 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
1667398 TATTTATATA
*
1667408 ATGGTGCATGTACTGTAACGATACTAT
1 ATGGTACATGTACTGTAACGATACTAT
*
1667435 ATGGTATATGTACTGTAACGATACTAT
1 ATGGTACATGTACTGTAACGATACTAT
*
1667462 ATGGTACATGTACTGTAATGATACTA
1 ATGGTACATGTACTGTAACGATACTA
1667488 AACTTTACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (27 bp):
ATGGTACATGTACTGTAACGATACTAT
Found at i:1667552 original size:20 final size:20
Alignment explanation
Indices: 1667523--1667613 Score: 128
Period size: 20 Copynumber: 4.5 Consensus size: 20
1667513 TTCACTATGT
* *
1667523 AAGTTCTGTAAGGATACTAC
1 AAGTACTGTAACGATACTAC
*
1667543 AAGTATTGTAACGATACTAC
1 AAGTACTGTAACGATACTAC
*
1667563 AAGTATTGTAACGATACTAC
1 AAGTACTGTAACGATACTAC
*
1667583 AAGTACTGTAACGATATTAC
1 AAGTACTGTAACGATACTAC
*
1667603 ATGTACTGTAA
1 AAGTACTGTAA
1667614 AGACCCTAGG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (20 bp):
AAGTACTGTAACGATACTAC
Found at i:1674902 original size:16 final size:18
Alignment explanation
Indices: 1674881--1674918 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1674871 TCAATGCGTT
1674881 ACATAG-TAC-TAGTGTA
1 ACATAGATACATAGTGTA
1674897 ACATAGTATACATAGTGTA
1 ACATAG-ATACATAGTGTA
1674916 ACA
1 ACA
1674919 CTAAATCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (18 bp):
ACATAGATACATAGTGTA
Found at i:1676372 original size:23 final size:23
Alignment explanation
Indices: 1676342--1676391 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1676332 ATATCGAAAC
1676342 CAGGGCGTGGTCGCTGTATATAT
1 CAGGGCGTGGTCGCTGTATATAT
1676365 CAGGGCGTGGTCGCTGTATATAT
1 CAGGGCGTGGTCGCTGTATATAT
1676388 CAGG
1 CAGG
1676392 ATTCCGGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.28
Consensus pattern (23 bp):
CAGGGCGTGGTCGCTGTATATAT
Found at i:1679225 original size:10 final size:11
Alignment explanation
Indices: 1679194--1679224 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1679184 CCCCCCCCAA
1679194 AAAAAAAAAAC
1 AAAAAAAAAAC
1679205 AAAAAAAAAAC
1 AAAAAAAAAAC
1679216 AAAAAAAAA
1 AAAAAAAAA
1679225 CCCCCAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:1679445 original size:30 final size:30
Alignment explanation
Indices: 1679411--1679531 Score: 206
Period size: 30 Copynumber: 4.0 Consensus size: 30
1679401 TTTTCTCGAC
* * *
1679411 TTGACGAAAAAGGCCGAGCAATGTTTCGAT
1 TTGACGGAAAAGGCCGAGCGATGTTCCGAT
1679441 TTGACGGAAAAGGCCGAGCGATGTTCCGAT
1 TTGACGGAAAAGGCCGAGCGATGTTCCGAT
1679471 TTGACGGAAAAGGCCGAGCGATGTTCCGAT
1 TTGACGGAAAAGGCCGAGCGATGTTCCGAT
*
1679501 TTTACGGAAAAGGCCGAGCGATGTTCCGAT
1 TTGACGGAAAAGGCCGAGCGATGTTCCGAT
1679531 T
1 T
1679532 AATAATACTC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (30 bp):
TTGACGGAAAAGGCCGAGCGATGTTCCGAT
Found at i:1687687 original size:2 final size:2
Alignment explanation
Indices: 1687680--1687723 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1687670 TTGTTTAATA
1687680 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1687722 CT
1 CT
1687724 GTTATATACA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1688057 original size:17 final size:17
Alignment explanation
Indices: 1688037--1688071 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1688027 CCCAAAAAAT
1688037 ACAAAAGAAA-AAAACAA
1 ACAAAA-AAACAAAACAA
1688054 ACAAAAAAACAAAACAA
1 ACAAAAAAACAAAACAA
1688071 A
1 A
1688072 ATTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (17 bp):
ACAAAAAAACAAAACAA
Found at i:1688059 original size:12 final size:13
Alignment explanation
Indices: 1688029--1688072 Score: 63
Period size: 12 Copynumber: 3.4 Consensus size: 13
1688019 CCCCCGCCCC
1688029 CAAAAAATACAAAA
1 CAAAAAA-ACAAAA
*
1688043 GAAAAAAAC-AAA
1 CAAAAAAACAAAA
1688055 CAAAAAAACAAAA
1 CAAAAAAACAAAA
1688068 CAAAA
1 CAAAA
1688073 TTTAAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 11 0.41
13 10 0.37
14 6 0.22
ACGTcount: A:0.82, C:0.14, G:0.02, T:0.02
Consensus pattern (13 bp):
CAAAAAAACAAAA
Found at i:1690194 original size:2 final size:2
Alignment explanation
Indices: 1690187--1690254 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
1690177 AATCTAGCAT
1690187 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
* *
1690229 TC TC TC TC CC TC TC TC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1690255 CATTTATCTC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1692923 original size:200 final size:200
Alignment explanation
Indices: 1692580--1692980 Score: 802
Period size: 200 Copynumber: 2.0 Consensus size: 200
1692570 CGGAGGGGTC
1692580 ATTTTGGTCAGCTCCTGCAACAGCAGATTCTGTGAATGTGGTGAGTCGTTAGGAGATGAATAAGT
1 ATTTTGGTCAGCTCCTGCAACAGCAGATTCTGTGAATGTGGTGAGTCGTTAGGAGATGAATAAGT
1692645 CCGCTGCCAGCCTTGTGCTCCAGAATTCCGTGGTCAATACTTGTAGCTGGTTTCACCAGTGGAAA
66 CCGCTGCCAGCCTTGTGCTCCAGAATTCCGTGGTCAATACTTGTAGCTGGTTTCACCAGTGGAAA
1692710 TTAAGCAATTATATTACTGGAATTGTCTTGACTTGCAGGTCAGTTTTCCAATCAATTGATTTGAA
131 TTAAGCAATTATATTACTGGAATTGTCTTGACTTGCAGGTCAGTTTTCCAATCAATTGATTTGAA
1692775 GCTAA
196 GCTAA
1692780 ATTTTGGTCAGCTCCTGCAACAGCAGATTCTGTGAATGTGGTGAGTCGTTAGGAGATGAATAAGT
1 ATTTTGGTCAGCTCCTGCAACAGCAGATTCTGTGAATGTGGTGAGTCGTTAGGAGATGAATAAGT
1692845 CCGCTGCCAGCCTTGTGCTCCAGAATTCCGTGGTCAATACTTGTAGCTGGTTTCACCAGTGGAAA
66 CCGCTGCCAGCCTTGTGCTCCAGAATTCCGTGGTCAATACTTGTAGCTGGTTTCACCAGTGGAAA
1692910 TTAAGCAATTATATTACTGGAATTGTCTTGACTTGCAGGTCAGTTTTCCAATCAATTGATTTGAA
131 TTAAGCAATTATATTACTGGAATTGTCTTGACTTGCAGGTCAGTTTTCCAATCAATTGATTTGAA
1692975 GCTAA
196 GCTAA
1692980 A
1 A
1692981 GATAAGGACT
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 201 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (200 bp):
ATTTTGGTCAGCTCCTGCAACAGCAGATTCTGTGAATGTGGTGAGTCGTTAGGAGATGAATAAGT
CCGCTGCCAGCCTTGTGCTCCAGAATTCCGTGGTCAATACTTGTAGCTGGTTTCACCAGTGGAAA
TTAAGCAATTATATTACTGGAATTGTCTTGACTTGCAGGTCAGTTTTCCAATCAATTGATTTGAA
GCTAA
Found at i:1720573 original size:21 final size:21
Alignment explanation
Indices: 1720549--1720888 Score: 366
Period size: 21 Copynumber: 16.2 Consensus size: 21
1720539 ATTGAATCCG
1720549 AAGATTAAAGTTGGAAATTCC
1 AAGATTAAAGTTGGAAATTCC
1720570 AAGATTAAAGTTGGAAATTCC
1 AAGATTAAAGTTGGAAATTCC
** *
1720591 AACTTTAAAGTTGGAAAAAT-C
1 AAGATTAAAGTTGG-AAATTCC
** *
1720612 AACTTTAAAGTTGGAAAAAT-C
1 AAGATTAAAGTTGG-AAATTCC
**
1720633 AACTTTAAAGTTGGAAATTCC
1 AAGATTAAAGTTGGAAATTCC
1720654 AAGATTAAAGTTGGAAATTCC
1 AAGATTAAAGTTGGAAATTCC
*
1720675 AAGATTAAAGTTGGAATTTCC
1 AAGATTAAAGTTGGAAATTCC
** *
1720696 AACTTTAAAGTTGGAAAAAT-C
1 AAGATTAAAGTTGG-AAATTCC
** *
1720717 AACTTTAAAATTGGAAATTCC
1 AAGATTAAAGTTGGAAATTCC
** *
1720738 AACTTTAAAGTTTGAAATTCC
1 AAGATTAAAGTTGGAAATTCC
1720759 AAGATTAAAGTTGGAAATTCC
1 AAGATTAAAGTTGGAAATTCC
*
1720780 AAGATTAAAGTTGGAATTTCC
1 AAGATTAAAGTTGGAAATTCC
*
1720801 AACG-TTAAAGTTGGAAAAAT-C
1 AA-GATTAAAGTTGG-AAATTCC
** *
1720822 AACTTTAAAGTTTGAAATTCC
1 AAGATTAAAGTTGGAAATTCC
1720843 AAGATTAAAGTTGGAAATTCC
1 AAGATTAAAGTTGGAAATTCC
** *
1720864 AACTTTAAAGTTCGAAATTCC
1 AAGATTAAAGTTGGAAATTCC
1720885 AAGA
1 AAGA
1720889 AAAAAAAAAT
Statistics
Matches: 279, Mismatches: 32, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.04
21 256 0.92
22 11 0.04
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31
Consensus pattern (21 bp):
AAGATTAAAGTTGGAAATTCC
Found at i:1720731 original size:105 final size:105
Alignment explanation
Indices: 1720549--1720888 Score: 565
Period size: 105 Copynumber: 3.2 Consensus size: 105
1720539 ATTGAATCCG
*
1720549 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAAAATCAA
1 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTTAAAGTTGGAAAAATCAA
*
1720614 CTTTAAAGTTGGAAAAAT-CAACTTTAAAGTTGGAAATTCC
66 CTTTAAAGTTGG-AAATTCCAACTTTAAAGTTGGAAATTCC
1720654 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTTAAAGTTGGAAAAATCAA
1 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTTAAAGTTGGAAAAATCAA
* *
1720719 CTTTAAAATTGGAAATTCCAACTTTAAAGTTTGAAATTCC
66 CTTTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCC
*
1720759 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACGTTAAAGTTGGAAAAATCAA
1 AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTTAAAGTTGGAAAAATCAA
* **
1720824 CTTTAAAGTTTGAAATTCCAAGATTAAAGTTGGAAATTCC
66 CTTTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCC
** *
1720864 AACTTTAAAGTTCGAAATTCCAAGA
1 AAGATTAAAGTTGGAAATTCCAAGA
1720889 AAAAAAAAAT
Statistics
Matches: 221, Mismatches: 13, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
104 4 0.02
105 217 0.98
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31
Consensus pattern (105 bp):
AAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTTAAAGTTGGAAAAATCAA
CTTTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCC
Found at i:1720886 original size:84 final size:84
Alignment explanation
Indices: 1720553--1720880 Score: 446
Period size: 84 Copynumber: 3.9 Consensus size: 84
1720543 AATCCGAAGA
** ** *
1720553 TTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAAAAT-CAACTT
1 TTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCCAAGATTAAAGTTGG-AAATTCCAACTT
1720617 TAAAGTTGGAAAAATCAACT
65 TAAAGTTGGAAAAATCAACT
** *
1720637 TTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAAGATTAAAGTTGGAATTTCCAACTTT
1 TTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTTT
1720702 AAAGTTGGAAAAATCAACT
66 AAAGTTGGAAAAATCAACT
* * **
1720721 TTAAAATTGGAAATTCCAACTTTAAAGTTTGAAATTCCAAGATTAAAGTTGGAAATTCCAAGATT
1 TTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTTT
** *
1720786 AAAGTTGG-AATTTCCAACG
66 AAAGTTGGAAAAAT-CAACT
* *
1720805 TTAAAGTTGGAAAAAT-CAACTTTAAAGTTTGAAATTCCAAGATTAAAGTTGGAAATTCCAACTT
1 TTAAAGTTGG-AAATTCCAACTTTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTT
*
1720869 TAAAGTTCGAAA
65 TAAAGTTGGAAA
1720881 TTCCAAGAAA
Statistics
Matches: 221, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
83 6 0.03
84 209 0.95
85 6 0.03
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (84 bp):
TTAAAGTTGGAAATTCCAACTTTAAAGTTGGAAATTCCAAGATTAAAGTTGGAAATTCCAACTTT
AAAGTTGGAAAAATCAACT
Found at i:1729039 original size:145 final size:145
Alignment explanation
Indices: 1728765--1729060 Score: 436
Period size: 145 Copynumber: 2.0 Consensus size: 145
1728755 ACATGACACA
1728765 GACA-GAATTTAGCATTTTTGAAACAATGACCTTGAACTTCCTCAATTGACCTTGGGTCAAGGTC
1 GACACGAATTTAGCATTTTTGAAACAATGACCTTGAACTTCCTCAATTGACCTTGGGTCAAGGTC
* * * *
1728829 ATGACATACCCTTTGGTTATAAGCAATATTTGTGTGAAGTAAGAACATTCAATGCTTCTCAATAA
66 AAGACACACCCTTAGGTTATAAGCAATATTTGTGTGAAGTAAGAACATTCAATGCTTATCAATAA
1728894 GAAAGATATGGACCG
131 GAAAGATATGGACCG
* * *
1728909 GACACGAATTTAGCATTTTTGAAACAATGACCTTGACCTTGCC-CGATTGACCTTGGGTCATGGT
1 GACACGAATTTAGCATTTTTGAAACAATGACCTTGAACTT-CCTCAATTGACCTTGGGTCAAGGT
* * * * *
1728973 CAAGACACACCCTTAGGTTATAAGCAATCTTTGTGTGAAGTAAGAA-TTTCCCATGTTTATCCAT
65 CAAGACACACCCTTAGGTTATAAGCAATATTTGTGTGAAGTAAGAACATT-CAATGCTTATCAAT
*
1729037 AAGAAAGATATGGACTG
129 AAGAAAGATATGGACCG
1729054 GACACGA
1 GACACGA
1729061 TTGCACAGAC
Statistics
Matches: 136, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
144 6 0.04
145 128 0.94
146 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (145 bp):
GACACGAATTTAGCATTTTTGAAACAATGACCTTGAACTTCCTCAATTGACCTTGGGTCAAGGTC
AAGACACACCCTTAGGTTATAAGCAATATTTGTGTGAAGTAAGAACATTCAATGCTTATCAATAA
GAAAGATATGGACCG
Found at i:1745966 original size:1 final size:1
Alignment explanation
Indices: 1745960--1745998 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
1745950 TCTCTCCTCA
1745960 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1745999 TTTCTTCAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1761039 original size:2 final size:2
Alignment explanation
Indices: 1761032--1761088 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1761022 ATCCTGTCAT
1761032 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
1761074 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
1761089 GTTTTAAAAA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1764075 original size:199 final size:199
Alignment explanation
Indices: 1763735--1764137 Score: 806
Period size: 199 Copynumber: 2.0 Consensus size: 199
1763725 CATGAATATC
1763735 ATTTTATTTAAAATAAAAACATCTTGAATATTCATAACATGTACTTCATGCAAAAAATATAAATA
1 ATTTTATTTAAAATAAAAACATCTTGAATATTCATAACATGTACTTCATGCAAAAAATATAAATA
1763800 ACATTTAAAAATCATATGAAATCTGAACAACATATTTTAATTAAATTACATTTCACATTACAAAA
66 ACATTTAAAAATCATATGAAATCTGAACAACATATTTTAATTAAATTACATTTCACATTACAAAA
1763865 ATAAACTCGTAATTATACATGTCCAATGTTCAAAGTTCAATGATTGTACTGTAAAATAAATATTC
131 ATAAACTCGTAATTATACATGTCCAATGTTCAAAGTTCAATGATTGTACTGTAAAATAAATATTC
1763930 ATGT
196 ATGT
1763934 ATTTTATTTAAAATAAAAACATCTTGAATATTCATAACATGTACTTCATGCAAAAAATATAAATA
1 ATTTTATTTAAAATAAAAACATCTTGAATATTCATAACATGTACTTCATGCAAAAAATATAAATA
1763999 ACATTTAAAAATCATATGAAATCTGAACAACATATTTTAATTAAATTACATTTCACATTACAAAA
66 ACATTTAAAAATCATATGAAATCTGAACAACATATTTTAATTAAATTACATTTCACATTACAAAA
1764064 ATAAACTCGTAATTATACATGTCCAATGTTCAAAGTTCAATGATTGTACTGTAAAATAAATATTC
131 ATAAACTCGTAATTATACATGTCCAATGTTCAAAGTTCAATGATTGTACTGTAAAATAAATATTC
1764129 ATGT
196 ATGT
1764133 ATTTT
1 ATTTT
1764138 TGAACAGTAT
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 204 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (199 bp):
ATTTTATTTAAAATAAAAACATCTTGAATATTCATAACATGTACTTCATGCAAAAAATATAAATA
ACATTTAAAAATCATATGAAATCTGAACAACATATTTTAATTAAATTACATTTCACATTACAAAA
ATAAACTCGTAATTATACATGTCCAATGTTCAAAGTTCAATGATTGTACTGTAAAATAAATATTC
ATGT
Found at i:1774904 original size:4 final size:4
Alignment explanation
Indices: 1774895--1775026 Score: 264
Period size: 4 Copynumber: 33.0 Consensus size: 4
1774885 NNNNNNNNNN
1774895 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1774943 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1774991 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1775027 GTTTCTGAAA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 128 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:1783275 original size:22 final size:22
Alignment explanation
Indices: 1783222--1783275 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1783212 AAACGGTGAG
*
1783222 TGAACCCAAAGTAAACCCGGAG
1 TGAACCCAAAGTAAACCCGGAC
*
1783244 TGGACCCAAAGTAAACACC-GAC
1 TGAACCCAAAGTAAAC-CCGGAC
*
1783266 TGAACACAAA
1 TGAACCCAAA
1783276 TTTTCAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
TGAACCCAAAGTAAACCCGGAC
Found at i:1794827 original size:12 final size:12
Alignment explanation
Indices: 1794810--1794835 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1794800 TTTATATTGC
1794810 GTTTATCAGGTT
1 GTTTATCAGGTT
1794822 GTTTATCAGGTT
1 GTTTATCAGGTT
1794834 GT
1 GT
1794836 CAGAACTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.27, T:0.50
Consensus pattern (12 bp):
GTTTATCAGGTT
Found at i:1804793 original size:17 final size:18
Alignment explanation
Indices: 1804763--1804803 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1804753 CATTTAAATA
*
1804763 GAAAATAACATTTTGCAT
1 GAAAATAACATTTTACAT
1804781 -AAAATAA-ATTTTTACAT
1 GAAAATAACA-TTTTACAT
1804798 GAAAAT
1 GAAAAT
1804804 TGCACTGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (18 bp):
GAAAATAACATTTTACAT
Found at i:1814121 original size:2 final size:2
Alignment explanation
Indices: 1814114--1814147 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1814104 TCTATTTTGC
1814114 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1814148 GTGGCACATT
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1825948 original size:11 final size:11
Alignment explanation
Indices: 1825932--1825971 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1825922 TAAGCAAGTC
1825932 CTTAAAGGTGG
1 CTTAAAGGTGG
*
1825943 CTTAAAGGTGA
1 CTTAAAGGTGG
*
1825954 CTTAAAGG-AG
1 CTTAAAGGTGG
1825964 CTTAAAGG
1 CTTAAAGG
1825972 CTATACAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:1826090 original size:10 final size:11
Alignment explanation
Indices: 1826042--1826091 Score: 84
Period size: 11 Copynumber: 4.6 Consensus size: 11
1826032 GTCCAAACTT
1826042 CTTTAAGCCAC
1 CTTTAAGCCAC
1826053 CTTTAAGCCAC
1 CTTTAAGCCAC
1826064 CTTTAAGCCAC
1 CTTTAAGCCAC
*
1826075 CTTTAAG-CAT
1 CTTTAAGCCAC
1826085 CTTTAAG
1 CTTTAAG
1826092 TGGCATTTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1826141 original size:22 final size:22
Alignment explanation
Indices: 1826084--1826144 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
1826074 CCTTTAAGCA
* *
1826084 TCTTTAAGTGGCATTTACGCTC
1 TCTTTAAGTGGCCTTTACACTC
* *
1826106 TCTTTACACT-GCCTTTACACTG
1 TCTTTA-AGTGGCCTTTACACTC
1826128 TCTTTAAGTGGCCTTTA
1 TCTTTAAGTGGCCTTTA
1826145 AGTCAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43
Consensus pattern (22 bp):
TCTTTAAGTGGCCTTTACACTC
Found at i:1826478 original size:2 final size:2
Alignment explanation
Indices: 1826473--1826516 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1826463 GTGAAAAAAA
1826473 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
1826515 TC
1 TC
1826517 AGTTCATCCG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1826928 original size:112 final size:112
Alignment explanation
Indices: 1826731--1826953 Score: 428
Period size: 112 Copynumber: 2.0 Consensus size: 112
1826721 AGTTTTGTTC
*
1826731 GTTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
*
1826796 GAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCAT
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
1826843 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1826908 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
1826954 CGTCAGGGTT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (112 bp):
GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
Found at i:1827978 original size:11 final size:11
Alignment explanation
Indices: 1827964--1828017 Score: 99
Period size: 11 Copynumber: 4.9 Consensus size: 11
1827954 TTTTTTTTAA
1827964 TGGCTTAAAGG
1 TGGCTTAAAGG
1827975 TGGCTTAAAGG
1 TGGCTTAAAGG
*
1827986 TAGCTTAAAGG
1 TGGCTTAAAGG
1827997 TGGCTTAAAGG
1 TGGCTTAAAGG
1828008 TGGCTTAAAG
1 TGGCTTAAAG
1828018 AAGTTTGGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.30, C:0.09, G:0.33, T:0.28
Consensus pattern (11 bp):
TGGCTTAAAGG
Found at i:1828196 original size:11 final size:11
Alignment explanation
Indices: 1828180--1828218 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1828170 TAAAGATCGT
1828180 CTTTAAGCTAC
1 CTTTAAGCTAC
*
1828191 CTTTAAAC-AC
1 CTTTAAGCTAC
*
1828201 CTTTAAGCTAT
1 CTTTAAGCTAC
1828212 CTTTAAG
1 CTTTAAG
1828219 GAGGACTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:1853277 original size:2 final size:2
Alignment explanation
Indices: 1853270--1853294 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1853260 NNNNNNNNNN
1853270 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 T
1853295 CTTAGCCATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1854772 original size:12 final size:12
Alignment explanation
Indices: 1854755--1854780 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1854745 AGCAATTTCA
1854755 AACAGACTTTTT
1 AACAGACTTTTT
1854767 AACAGACTTTTT
1 AACAGACTTTTT
1854779 AA
1 AA
1854781 TATTATACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (12 bp):
AACAGACTTTTT
Done.