Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 9 of 17
Found at i:1247784 original size:25 final size:25
Alignment explanation
Indices: 1247754--1247805 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1247744 CGATACTACT
*
1247754 TCTATGCTACTTACTATTAAAAGAA
1 TCTATGCTACTAACTATTAAAAGAA
*
1247779 TCTATGCTACTAACTATTAGAAGAA
1 TCTATGCTACTAACTATTAAAAGAA
1247804 TC
1 TC
1247806 GCATCGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (25 bp):
TCTATGCTACTAACTATTAAAAGAA
Found at i:1250088 original size:27 final size:27
Alignment explanation
Indices: 1250050--1250103 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1250040 GAACATGTAT
*
1250050 GCACTAAGTTATAATAAGATGACTGAC
1 GCACCAAGTTATAATAAGATGACTGAC
*
1250077 GCACCAAGTTATGATAAGATGACTGAC
1 GCACCAAGTTATAATAAGATGACTGAC
1250104 CAAAGGGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (27 bp):
GCACCAAGTTATAATAAGATGACTGAC
Found at i:1251785 original size:16 final size:16
Alignment explanation
Indices: 1251752--1251808 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
1251742 AGGTATTTTG
1251752 AAAAATA-AAATA-TT
1 AAAAATATAAATATTT
*
1251766 AAAAATATATATATTT
1 AAAAATATAAATATTT
1251782 -AAAATAATAAATATTT
1 AAAAAT-ATAAATATTT
1251798 AAAAATATAAA
1 AAAAATATAAA
1251809 AATAATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
14 7 0.19
15 9 0.24
16 16 0.43
17 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATATAAATATTT
Found at i:1253109 original size:72 final size:72
Alignment explanation
Indices: 1252990--1253166 Score: 282
Period size: 72 Copynumber: 2.5 Consensus size: 72
1252980 CGATAATTCA
* * *
1252990 AGATAATTTGCACGATAAATACAATCAACAACTATTTTTGCATATTTAAAACTACTATCAACAAA
1 AGATAATTTACACGATAAATACAATCAACAACTATTTCTGCACATTTAAAACTACTATCAACAAA
1253055 TAATCTG
66 TAATCTG
* * *
1253062 AGATAATCTACACGATAAATACAATCAACAACTATTTCTGTACATTTAAAACTACTATCAACAAT
1 AGATAATTTACACGATAAATACAATCAACAACTATTTCTGCACATTTAAAACTACTATCAACAAA
1253127 TAATCTG
66 TAATCTG
* *
1253134 AAATAATTTACACGATAACTACAATCAACAACT
1 AGATAATTTACACGATAAATACAATCAACAACT
1253167 TTGTGTGCCA
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 96 1.00
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (72 bp):
AGATAATTTACACGATAAATACAATCAACAACTATTTCTGCACATTTAAAACTACTATCAACAAA
TAATCTG
Found at i:1253477 original size:26 final size:27
Alignment explanation
Indices: 1253426--1253484 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
1253416 TTGGGTCATG
*
1253426 GTAGGATATGATGAGTATGGAGGTTGA
1 GTAGGATATGACGAGTATGGAGGTTGA
* *
1253453 GTAGGATATGGCG-GTATGGATGTTGA
1 GTAGGATATGACGAGTATGGAGGTTGA
1253479 GTAGGA
1 GTAGGA
1253485 AAATATGCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.27, C:0.02, G:0.42, T:0.29
Consensus pattern (27 bp):
GTAGGATATGACGAGTATGGAGGTTGA
Found at i:1257449 original size:79 final size:79
Alignment explanation
Indices: 1257319--1257467 Score: 217
Period size: 79 Copynumber: 1.9 Consensus size: 79
1257309 ATGATTATGA
* ***
1257319 AAAATCGGTGTTCTGGAAATAAAATCAGGGTTGGAGTATCCCCTTGGAAATAACAAGGTTCGAGT
1 AAAATCGGTGTTCTGAAAATAAAATCAGGGTTGGAGTATCCCCTAAAAAATAACAAGGTTCGAGT
1257384 ATCCCTAATTATAG
66 ATCCCTAATTATAG
* * ** *
1257398 AAAATTGGTGTTTTGAAAATAAAATCAGGGTTGGAGTATCCCCTAAAAAATAACGGGGTTTGAGT
1 AAAATCGGTGTTCTGAAAATAAAATCAGGGTTGGAGTATCCCCTAAAAAATAACAAGGTTCGAGT
1257463 ATCCC
66 ATCCC
1257468 CGCGAAAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (79 bp):
AAAATCGGTGTTCTGAAAATAAAATCAGGGTTGGAGTATCCCCTAAAAAATAACAAGGTTCGAGT
ATCCCTAATTATAG
Found at i:1257462 original size:28 final size:28
Alignment explanation
Indices: 1257425--1257498 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
1257415 AATAAAATCA
*
1257425 GGGTTGGAGTATCCCCTAAAAAATAACG
1 GGGTTTGAGTATCCCCTAAAAAATAACG
***
1257453 GGGTTTGAGTATCCCCGCGAAAATAACG
1 GGGTTTGAGTATCCCCTAAAAAATAACG
1257481 GGG-TTGAAGTATCCCCTA
1 GGGTTTG-AGTATCCCCTA
1257499 TTGTGAGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 3 0.08
28 36 0.92
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (28 bp):
GGGTTTGAGTATCCCCTAAAAAATAACG
Found at i:1257534 original size:79 final size:80
Alignment explanation
Indices: 1257451--1257654 Score: 322
Period size: 79 Copynumber: 2.6 Consensus size: 80
1257441 TAAAAAATAA
* *
1257451 CGGGGTTTGAGTATCCCCGCGAAAATAACGGGGTTGAAGTATCCCCT-ATTGTGAGAAATCAATA
1 CGGGGTTTGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCTGATTGTGAGAAATCAATA
*
1257515 TTTTAGAAATAAAAT
66 TTTTAGAAATAAAAC
*
1257530 CGGGGTTTGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT-CGCTGATTGTGAGAAATCAATA
1 CGGGGTTTGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCTGATTGTGAGAAATCAATA
* *
1257594 TTTTAGGAATAAAGC
66 TTTTAGAAATAAAAC
* *
1257609 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCC
1 CGGGGTTTGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
1257655 GATGATTAAC
Statistics
Matches: 114, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
78 3 0.03
79 109 0.96
80 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (80 bp):
CGGGGTTTGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCTGATTGTGAGAAATCAATA
TTTTAGAAATAAAAC
Found at i:1257672 original size:27 final size:28
Alignment explanation
Indices: 1257609--1257684 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
1257599 GGAATAAAGC
***
1257609 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1257637 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1257664 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1257685 TATGAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1257713 original size:186 final size:186
Alignment explanation
Indices: 1257292--1257733 Score: 444
Period size: 186 Copynumber: 2.4 Consensus size: 186
1257282 GGAGATGACG
* * * * * *
1257292 ACGGGGCTGGAGTA-CCCATGATTATGAAAAATCGGTGTTCTGGAAATAAAATCAGGGTTGGAGT
1 ACGGGGTTGGAGTATCCC-CGATTATGAAAAATCGGTGTTTTTGAAATAAAATCGGGGTTAGAGT
* * *** *
1257356 ATCCCCTTGGAAATAACAAGGTTCGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAA
65 ATCCCCTCGAAAATAACAAGGTTCGAGTATCCCTAATTATAGAAAATCAATATTTTGAAAATAAA
* *
1257421 ATCAGGGTTGGAGTATCCCCTAAAAAATAACGGGGTTTGAGTATCCCCGCGAAAATA
130 ACCAGGGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGCGAAAATA
* * * * ** * * *
1257478 ACGGGGTTGAAGTATCCCCTATTGTGAGAAATCAATATTTTAGAAATAAAATCGGGGTTTGAGTA
1 ACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTTGAAATAAAATCGGGGTTAGAGTA
** * * * * *
1257543 TCCCCTCGAAAATAACGGGGTTGGAGTATCGCTGATTGT-GAGAAATCAATATTTT-AGGAATAA
66 TCCCCTCGAAAATAACAAGGTTCGAGTATCCCTAATTATAGA-AAATCAATATTTTGA-AAATAA
* * *** * *
1257606 AGCCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTAT-CCC-CGATGATTA
129 AACCAGGGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGCGA-AAATA
* **
1257663 ACGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGAAAATAAAATCGAAGTTAGAGT
1 ACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTTG-AAATAAAATCGGGGTTAGAGT
1257728 ATCCCC
65 ATCCCC
1257734 GATTATAGAA
Statistics
Matches: 204, Mismatches: 47, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
184 3 0.01
185 43 0.21
186 155 0.76
187 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (186 bp):
ACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTTGAAATAAAATCGGGGTTAGAGTA
TCCCCTCGAAAATAACAAGGTTCGAGTATCCCTAATTATAGAAAATCAATATTTTGAAAATAAAA
CCAGGGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGCGAAAATA
Found at i:1257855 original size:102 final size:103
Alignment explanation
Indices: 1257664--1257901 Score: 329
Period size: 102 Copynumber: 2.3 Consensus size: 103
1257654 CGATGATTAA
**
1257664 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGAAAATAAAATCGAAGTTAGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTCAAAAATAAAATCGAAGTTAGAGTA
* *
1257729 TCCCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAAC
66 TCCCCAATTATAGAAAATTAGTGTTTTAG-AAATAAAAC
* * *
1257767 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTG-TTTCAAAAATAAAATCGGAGTTAGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTCAAAAATAAAATCGAAGTTAGAGTA
* * *
1257831 TCCCCAATTGTGGAAAATTAGTGTTTTAGGAATAAAAC
66 TCCCCAATTATAGAAAATTAGTGTTTTAGAAATAAAAC
**
1257869 CGGGGTTAAAGTA-CCCACGATTATGAAAAATTG
1 CGGGGTTGGAGTATCCC-CGATTATGAAAAATTG
1257902 AGAAACTTAA
Statistics
Matches: 119, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
101 3 0.03
102 81 0.68
103 35 0.29
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (103 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTCAAAAATAAAATCGAAGTTAGAGTA
TCCCCAATTATAGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:1257899 original size:51 final size:52
Alignment explanation
Indices: 1257664--1257901 Score: 270
Period size: 51 Copynumber: 4.6 Consensus size: 52
1257654 CGATGATTAA
* * *
1257664 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGAAAATAAAAT
1 CGGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAAATAAAAC
**
1257716 CGAAGTTAGAGTATCCCCGATTAT-AGAAAATTGGTGTTTT-GAAAATAAAAC
1 CGGGGTTAGAGTATCCCCGATTATGA-AAAATTGGTGTTTTAGAAAATAAAAC
* * * * *
1257767 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTCA-AAAATAAAAT
1 CGGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAAATAAAAC
* * * * * *
1257818 CGGAGTTAGAGTATCCCCAATTGTGGAAAATTAGTGTTTTAG-GAATAAAAC
1 CGGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAAATAAAAC
*
1257869 CGGGGTTAAAGTA-CCCACGATTATGAAAAATTG
1 CGGGGTTAGAGTATCCC-CGATTATGAAAAATTG
1257902 AGAAACTTAA
Statistics
Matches: 157, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
50 3 0.02
51 119 0.76
52 35 0.22
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (52 bp):
CGGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAAATAAAAC
Found at i:1259346 original size:21 final size:19
Alignment explanation
Indices: 1259297--1259348 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1259287 AGCGATACAT
*
1259297 TGTATCGATACATTACTTA
1 TGTATCGATACATTACTAA
*
1259316 TGTGTCGATACATTTACTGAA
1 TGTATCGATACA-TTACT-AA
*
1259337 TTTATCGATACA
1 TGTATCGATACA
1259349 AATTATTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.41
20 5 0.19
21 11 0.41
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATTACTAA
Found at i:1263459 original size:35 final size:34
Alignment explanation
Indices: 1263405--1263523 Score: 166
Period size: 34 Copynumber: 3.5 Consensus size: 34
1263395 TCTTTGTTTA
* **
1263405 ATGTGTTAGGTAAATATATTAGGTGTGTTAGGTG
1 ATGTGTTAGGTGAGCATATTAGGTGTGTTAGGTG
* * *
1263439 GTTTGTTATGTGAAGCATATTAGGTGTGTTAGGTG
1 ATGTGTTAGGTG-AGCATATTAGGTGTGTTAGGTG
*
1263474 ATGTGTTAGGTGAGCATATTAGGTGTGTTAGGTA
1 ATGTGTTAGGTGAGCATATTAGGTGTGTTAGGTG
1263508 ATGTGTTAGGTGAGCA
1 ATGTGTTAGGTGAGCA
1263524 AGATATTTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
34 45 0.61
35 29 0.39
ACGTcount: A:0.24, C:0.03, G:0.34, T:0.39
Consensus pattern (34 bp):
ATGTGTTAGGTGAGCATATTAGGTGTGTTAGGTG
Found at i:1263480 original size:12 final size:12
Alignment explanation
Indices: 1263463--1263520 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
1263453 GCATATTAGG
1263463 TGTGTTAGGTGA
1 TGTGTTAGGTGA
1263475 TGTGTTAGGTGA
1 TGTGTTAGGTGA
*
1263487 -GCATATTA-G-G-
1 TG--TGTTAGGTGA
*
1263497 TGTGTTAGGTAA
1 TGTGTTAGGTGA
1263509 TGTGTTAGGTGA
1 TGTGTTAGGTGA
1263521 GCAAGATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
9 4 0.11
10 1 0.03
11 3 0.08
12 24 0.67
13 4 0.11
ACGTcount: A:0.21, C:0.02, G:0.38, T:0.40
Consensus pattern (12 bp):
TGTGTTAGGTGA
Found at i:1267525 original size:13 final size:13
Alignment explanation
Indices: 1267507--1267532 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1267497 CAATTTTTTG
1267507 TGTATCGATACAT
1 TGTATCGATACAT
1267520 TGTATCGATACAT
1 TGTATCGATACAT
1267533 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1267547 original size:32 final size:33
Alignment explanation
Indices: 1267487--1267550 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1267477 TACAAGCCAA
** *
1267487 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1267520 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1267551 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1268270 original size:21 final size:21
Alignment explanation
Indices: 1268229--1268272 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1268219 CTCCCCTTTA
* *
1268229 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1268250 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1268271 TC
1 TC
1268273 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1269620 original size:21 final size:20
Alignment explanation
Indices: 1269591--1269633 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1269581 GGCTAGTGTG
* *
1269591 GGGACTGCCCGGTTATGACCT
1 GGGACTG-CCGGTCACGACCT
*
1269612 GGGAGTGCCGGTCACGACCT
1 GGGACTGCCGGTCACGACCT
1269632 GG
1 GG
1269634 TGATGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.14, C:0.28, G:0.40, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCACGACCT
Found at i:1272198 original size:15 final size:15
Alignment explanation
Indices: 1272178--1272208 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1272168 ATTTCGTTTG
*
1272178 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1272193 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1272208 G
1 G
1272209 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1274040 original size:21 final size:21
Alignment explanation
Indices: 1274011--1274055 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1274001 AAGTTTTCAT
*
1274011 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1274031 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1274053 TTT
1 TTT
1274056 CATCTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1276288 original size:13 final size:13
Alignment explanation
Indices: 1276270--1276295 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1276260 CAATTTTTTG
1276270 TGTATCGATACAT
1 TGTATCGATACAT
1276283 TGTATCGATACAT
1 TGTATCGATACAT
1276296 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1276310 original size:32 final size:33
Alignment explanation
Indices: 1276250--1276313 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1276240 TACAAGCCAA
** *
1276250 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1276283 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1276314 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1277542 original size:79 final size:79
Alignment explanation
Indices: 1277439--1277645 Score: 247
Period size: 79 Copynumber: 2.6 Consensus size: 79
1277429 GAGATAATAA
* * * *
1277439 CGGGGTTGGAGTATTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGTA-TCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
1277503 A-TTTAAAAAAAAAAT
64 ATTTTAAAAAAAAAAC
* *
1277518 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
*** * *
1277583 TTTGGGAATAAAGC
66 TTTAAAAAAAAAAC
* * *
1277597 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1277646 GAAATAACGA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
78 7 0.06
79 102 0.94
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTTAAAAAAAAAAC
Found at i:1277637 original size:28 final size:28
Alignment explanation
Indices: 1277597--1277668 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1277587 GGAATAAAGC
** *
1277597 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1277625 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1277653 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1277669 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1280076 original size:20 final size:20
Alignment explanation
Indices: 1280051--1280170 Score: 73
Period size: 20 Copynumber: 5.8 Consensus size: 20
1280041 AAAATGCCTG
1280051 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGTAA
1280071 AATGTATCGATACATATGGGTAA
1 AATGTATCGATACAT-T--GTAA
* ** * *
1280094 AAT-T-TCCAAATGTATCGATAC
1 AATGTAT-C-GATACATTG-TAA
** *
1280115 AATGTATCGATACACAGAAA
1 AATGTATCGATACATTGTAA
** *
1280135 AATGTATCGATACACAGAAA
1 AATGTATCGATACATTGTAA
1280155 AATGTATCGATACATT
1 AATGTATCGATACATT
1280171 TCCTTGGCAG
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
20 51 0.65
21 11 0.14
22 4 0.05
23 12 0.15
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACATTGTAA
Found at i:1280120 original size:13 final size:13
Alignment explanation
Indices: 1280102--1280128 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1280092 AAAATTTCCA
1280102 AATGTATCGATAC
1 AATGTATCGATAC
1280115 AATGTATCGATAC
1 AATGTATCGATAC
1280128 A
1 A
1280129 CAGAAAAATG
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1280212 original size:19 final size:18
Alignment explanation
Indices: 1280188--1280255 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1280178 CAGTAGCTAA
1280188 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1280207 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1280222 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1280239 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1280256 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1280228 original size:13 final size:13
Alignment explanation
Indices: 1280210--1280234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1280200 ACAATACTTA
1280210 TGTATCGATACAT
1 TGTATCGATACAT
1280223 TGTATCGATACA
1 TGTATCGATACA
1280235 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1280232 original size:32 final size:32
Alignment explanation
Indices: 1280191--1280253 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1280181 TAGCTAATTA
*
1280191 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1280223 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1280254 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1282287 original size:12 final size:12
Alignment explanation
Indices: 1282270--1282294 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1282260 AAACATATTA
1282270 GGTGTGTTAGGT
1 GGTGTGTTAGGT
1282282 GGTGTGTTAGGT
1 GGTGTGTTAGGT
1282294 G
1 G
1282295 AAGCATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.52, T:0.40
Consensus pattern (12 bp):
GGTGTGTTAGGT
Found at i:1282287 original size:34 final size:34
Alignment explanation
Indices: 1282250--1282367 Score: 173
Period size: 34 Copynumber: 3.4 Consensus size: 34
1282240 CTTTGTTAAG
* *
1282250 TGTGTTAGGTAAACATATTAGGTGTGTTAGGTGG
1 TGTGTTAGGTAAGCATATTAGGTGTGTTAGGTGA
1282284 TGTGTTAGGTGAAGCATATTAGGTGTGTTAGGTGA
1 TGTGTTAGGT-AAGCATATTAGGTGTGTTAGGTGA
* * * *
1282319 TGTGTCAGGTGAGTATATTAGGTGTGTTAGGTAA
1 TGTGTTAGGTAAGCATATTAGGTGTGTTAGGTGA
1282353 TGTGTTAGGTAAGCA
1 TGTGTTAGGTAAGCA
1282368 AGATATTTTA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 43 0.58
35 31 0.42
ACGTcount: A:0.24, C:0.03, G:0.36, T:0.37
Consensus pattern (34 bp):
TGTGTTAGGTAAGCATATTAGGTGTGTTAGGTGA
Found at i:1283291 original size:15 final size:15
Alignment explanation
Indices: 1283273--1283313 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1283263 TGATCCTATC
*
1283273 CATCCACCACCCTTG
1 CATCCACCACCCGTG
*
1283288 CATCCACAACCCGTG
1 CATCCACCACCCGTG
1283303 CATCCACCACC
1 CATCCACCACC
1283314 TGTTTACCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.24, C:0.54, G:0.07, T:0.15
Consensus pattern (15 bp):
CATCCACCACCCGTG
Found at i:1283449 original size:27 final size:27
Alignment explanation
Indices: 1283413--1283472 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
1283403 CTCCATATTT
*
1283413 TCCTACTCAACCTCTATACCCGTCATA
1 TCCTACTCAACCTCTATACCCATCATA
*
1283440 TCCTACTCAACCTTTATACCCATCATA
1 TCCTACTCAACCTCTATACCCATCATA
1283467 TCCTAC
1 TCCTAC
1283473 CACGACCCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.27, C:0.40, G:0.02, T:0.32
Consensus pattern (27 bp):
TCCTACTCAACCTCTATACCCATCATA
Found at i:1283850 original size:72 final size:72
Alignment explanation
Indices: 1283730--1283912 Score: 233
Period size: 72 Copynumber: 2.6 Consensus size: 72
1283720 TGGCACACAA
* * *
1283730 AGTTGTTGATTGTAGTTATCGTGCATATTATCTCAGATTAGTTATTGATAGTAGTTTTAAATATG
1 AGTTGTTGATTGTATTTATCGTGCAGATTATCTTAGATTAGTTATTGATAGTAGTTTTAAATATG
*
1283795 CAGAAAT
66 CAAAAAT
* * * * *
1283802 AGTTGTTGATTCTATTTATCGTGCAGATTATCTTGGATTAGTTGTTGATTGTATTTTTAAATATG
1 AGTTGTTGATTGTATTTATCGTGCAGATTATCTTAGATTAGTTATTGATAGTAGTTTTAAATATG
1283867 CAAAAAT
66 CAAAAAT
* * * * *
1283874 AGTTATTAATTGTATTTAGCGT-AAGATTATCTTAAATTA
1 AGTTGTTGATTGTATTTATCGTGCAGATTATCTTAGATTA
1283913 TCGTTTCATC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
71 14 0.15
72 81 0.85
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (72 bp):
AGTTGTTGATTGTATTTATCGTGCAGATTATCTTAGATTAGTTATTGATAGTAGTTTTAAATATG
CAAAAAT
Found at i:1286716 original size:26 final size:26
Alignment explanation
Indices: 1286687--1286767 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
1286677 AAATGCAACC
1286687 ATTTGTATTTGTCAAATATGGTGG-TT
1 ATTTGT-TTTGTCAAATATGGTGGCTT
* * * *
1286713 ATTTTTGTTTGTAAAAAATAGTGGCTT
1 ATTTGT-TTTGTCAAATATGGTGGCTT
* *
1286740 A-TTG-TTTGTCAAATTTGGTGGCTA
1 ATTTGTTTTGTCAAATATGGTGGCTT
1286764 ATTT
1 ATTT
1286768 TTATTAGAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
24 16 0.38
25 2 0.05
26 21 0.50
27 3 0.07
ACGTcount: A:0.25, C:0.05, G:0.21, T:0.49
Consensus pattern (26 bp):
ATTTGTTTTGTCAAATATGGTGGCTT
Found at i:1291246 original size:26 final size:24
Alignment explanation
Indices: 1291217--1291282 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
1291207 ACCATTTGTA
*
1291217 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAATATGGTGG--ATTGTTG
* * * *
1291243 TTTGTAAAAAATAGTGGCTTGTTG
1 TTTGTCAAATATGGTGGATTGTTG
*
1291267 TTTGTCAAATTTGGTG
1 TTTGTCAAATATGGTG
1291283 ACTAATTTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 17 0.55
26 14 0.45
ACGTcount: A:0.23, C:0.05, G:0.24, T:0.48
Consensus pattern (24 bp):
TTTGTCAAATATGGTGGATTGTTG
Found at i:1293133 original size:35 final size:38
Alignment explanation
Indices: 1293064--1293134 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 38
1293054 ATATTAAAAA
*
1293064 TTATAATATTAAATTAAATAAATATTTTTATTAATTAT
1 TTATAATATTAAATTAAATAAATATTTTAATTAATTAT
* *
1293102 TTATAATATTTAA-T-ATTAAA-ATTTTAATTAATT
1 TTATAATATTAAATTAAATAAATATTTTAATTAATT
1293135 TGAAGTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 12 0.40
36 5 0.17
37 1 0.03
38 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (38 bp):
TTATAATATTAAATTAAATAAATATTTTAATTAATTAT
Found at i:1300448 original size:13 final size:13
Alignment explanation
Indices: 1300432--1300462 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1300422 TTATAATTAT
1300432 TAATTTTTTAAAA
1 TAATTTTTTAAAA
1300445 TAA-TTTTTAAAA
1 TAATTTTTTAAAA
1300457 TAATTT
1 TAATTT
1300463 ATGATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTTTTTAAAA
Found at i:1300928 original size:16 final size:16
Alignment explanation
Indices: 1300909--1300946 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1300899 AAAATAAATA
1300909 TAAAAATATAATTTTT
1 TAAAAATATAATTTTT
*
1300925 TAAATATATAATTTTT
1 TAAAAATATAATTTTT
1300941 TAAAAA
1 TAAAAA
1300947 ATTAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAAATATAATTTTT
Found at i:1301504 original size:32 final size:29
Alignment explanation
Indices: 1301433--1301513 Score: 81
Period size: 32 Copynumber: 2.7 Consensus size: 29
1301423 ATTAGTATTA
* *
1301433 ATTTTAAATTTAATGAATTAGATATAATT
1 ATTTTAAATTTAATGAATTAAATAAAATT
* *
1301462 ATTTAAAAATTTGATGAATATTAAATAAAATT
1 ATTT-TAAATTTAATG-A-ATTAAATAAAATT
*
1301494 ATTTGTAAATTTAATAAATT
1 ATTT-TAAATTTAATGAATT
1301514 TGATAGTCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
29 4 0.10
30 12 0.29
31 2 0.05
32 23 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (29 bp):
ATTTTAAATTTAATGAATTAAATAAAATT
Found at i:1305245 original size:20 final size:20
Alignment explanation
Indices: 1305220--1305294 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1305210 TGACCCAAAG
*
1305220 GTATCGATACATTCTTTAAT
1 GTATCGATACATTCTTCAAT
* *
1305240 GTATCGATACATGT-ATGAAT
1 GTATCGATACAT-TCTTCAAT
*
1305260 GTATCGATACATTCGTCAAT
1 GTATCGATACATTCTTCAAT
*
1305280 ATATCGATACATTCT
1 GTATCGATACATTCT
1305295 GTCATTTTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
GTATCGATACATTCTTCAAT
Found at i:1305307 original size:91 final size:91
Alignment explanation
Indices: 1305132--1305342 Score: 295
Period size: 91 Copynumber: 2.4 Consensus size: 91
1305122 TTATCCAGAT
* * * *
1305132 GTATTGATACA-TCTTT--TGTATCGATACATGTATGAATATATTGATATATTCTTCAATATATC
1 GTATCGATACATTCTTTAATGTATCGATACATGTATGAATATATCGATACATTCGTCAATATATC
*
1305194 GATACATTTTGTCTTTTGACCCAAAG
66 GATACATTCTGTCTTTTGACCCAAAG
*
1305220 GTATCGATACATTCTTTAATGTATCGATACATGTATGAATGTATCGATACATTCGTCAATATATC
1 GTATCGATACATTCTTTAATGTATCGATACATGTATGAATATATCGATACATTCGTCAATATATC
*
1305285 GATACATTCTGTCATTTT-ACCCAAAT
66 GATACATTCTGTC-TTTTGACCCAAAG
* * *
1305311 TTATCGATACATTATTCAATGTATCGATACAT
1 GTATCGATACATTCTTTAATGTATCGATACAT
1305343 CTAATTAAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
88 10 0.09
89 5 0.05
91 90 0.83
92 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (91 bp):
GTATCGATACATTCTTTAATGTATCGATACATGTATGAATATATCGATACATTCGTCAATATATC
GATACATTCTGTCTTTTGACCCAAAG
Found at i:1313269 original size:28 final size:28
Alignment explanation
Indices: 1313233--1313726 Score: 562
Period size: 28 Copynumber: 17.5 Consensus size: 28
1313223 TATCGACTTG
1313233 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1313261 TGTGGGCTTTTAAAGGGTATGCCACTGACT
1 TGTGGGCTTTGAAAGGG--TGCCACTGACT
*
1313291 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1313319 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1313347 TATAGGCTTTGAAAAGGTACCAC-GAACT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * *
1313375 TGTGGGCTTTGGAGGGGTATGCCACGGACT
1 TGTGGGCTTTGAAAGGG--TGCCACTGACT
*
1313405 TATGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1313433 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1313461 TGTGGGCTTTTAAAAGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1313489 TATGGGCTTTGCAAA-GGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1313517 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** **
1313545 CGTGGTTTTTTG-AAGAAATGCCACTGACT
1 TGTGG-GCTTTGAAAG-GGTGCCACTGACT
* *
1313574 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1313602 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** *
1313630 TGCGAGCTTTGAAAGAATGCCACTGACC
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * *
1313658 TGTAAGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1313686 TGTGGGCTTTGAAAGGATACCACTGACC
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1313714 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
1313727 GAGATGAACG
Statistics
Matches: 400, Mismatches: 55, Indels: 22
0.84 0.12 0.05
Matches are distributed among these distances:
27 4 0.01
28 321 0.80
29 25 0.06
30 49 0.12
31 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:1314985 original size:4 final size:4
Alignment explanation
Indices: 1314976--1315031 Score: 73
Period size: 4 Copynumber: 14.8 Consensus size: 4
1314966 AGACCCCTTT
* *
1314976 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG -TT- TTTG TTTC TTTA
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG
1315022 TTT- TTTG TTT
1 TTTG TTTG TTT
1315032 TTCTATTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 7 0.15
4 40 0.85
ACGTcount: A:0.02, C:0.02, G:0.18, T:0.79
Consensus pattern (4 bp):
TTTG
Found at i:1315058 original size:18 final size:17
Alignment explanation
Indices: 1314974--1315071 Score: 65
Period size: 18 Copynumber: 5.4 Consensus size: 17
1314964 CTAGACCCCT
*
1314974 TTTTTGTTTGTTTGTTTG
1 TTTTTGTTT-TTTTTTTG
*
1314992 --TTTGTTTGTTTGTTTG
1 TTTTTGTTT-TTTTTTTG
1315008 TTTTTGTTTCTTTATTTTTTG
1 TTTTTG--T-TTT-TTTTTTG
* *
1315029 TTTTTCTATTTTTTTATG
1 TTTTTGT-TTTTTTTTTG
*
1315047 TTTTTGTTTTTTTCTTTT
1 TTTTTGTTTTTTT-TTTG
1315065 TTTTTGT
1 TTTTTGT
1315072 ACGAAGGACG
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
16 16 0.24
17 6 0.09
18 25 0.38
19 4 0.06
20 2 0.03
21 13 0.20
ACGTcount: A:0.03, C:0.03, G:0.13, T:0.81
Consensus pattern (17 bp):
TTTTTGTTTTTTTTTTG
Found at i:1315059 original size:8 final size:8
Alignment explanation
Indices: 1314973--1315067 Score: 75
Period size: 8 Copynumber: 11.8 Consensus size: 8
1314963 TCTAGACCCC
1314973 TTTTTTGT
1 TTTTTTGT
*
1314981 TTGTTTGT
1 TTTTTTGT
*
1314989 TTGTTTGT
1 TTTTTTGT
*
1314997 TTGTTTGTT
1 TTTTTTG-T
1315006 TGTTTTTGT
1 T-TTTTTGT
* *
1315015 TTCTTT-A
1 TTTTTTGT
1315022 TTTTTTGT
1 TTTTTTGT
* *
1315030 TTTTCTAT
1 TTTTTTGT
*
1315038 TTTTTTAT
1 TTTTTTGT
*
1315046 GTTTTTGT
1 TTTTTTGT
*
1315054 TTTTTTCT
1 TTTTTTGT
1315062 TTTTTT
1 TTTTTT
1315068 TTGTACGAAG
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
7 5 0.07
8 57 0.80
9 4 0.06
10 5 0.07
ACGTcount: A:0.03, C:0.03, G:0.13, T:0.81
Consensus pattern (8 bp):
TTTTTTGT
Found at i:1327326 original size:10 final size:10
Alignment explanation
Indices: 1327304--1327333 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
1327294 GAAGTTTTTA
1327304 TGAAAAATGTT
1 TGAAAAAT-TT
1327315 TGAAAAATTT
1 TGAAAAATTT
1327325 TGAAAAATT
1 TGAAAAATT
1327334 ATCTAGTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (10 bp):
TGAAAAATTT
Found at i:1329031 original size:20 final size:20
Alignment explanation
Indices: 1329002--1329039 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1328992 GTAAAAAGAC
*
1329002 AGAATGTATCGATACATTGA
1 AGAATATATCGATACATTGA
1329022 AGAATATATCGATACATT
1 AGAATATATCGATACATT
1329040 TAGGTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATATATCGATACATTGA
Found at i:1339767 original size:1 final size:1
Alignment explanation
Indices: 1339761--1339818 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
1339751 CCTTCGTACC
* ** * * * *
1339761 AAAAAAAAGAAAAAAACCAAGAAAAAAAACAAAAAACAAAAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1339819 CAAACAAGAA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:1339787 original size:20 final size:17
Alignment explanation
Indices: 1339760--1339811 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 17
1339750 TCCTTCGTAC
*
1339760 CAAAAAAAAGAAAAAAAC
1 CAAAAAAAA-AAAAAAAA
1339778 CAAGAAAAAAAACAAAAAA
1 CAA-AAAAAAAA-AAAAAA
1339797 CAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
1339812 GAAAAAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 4 0.13
18 13 0.42
19 14 0.45
ACGTcount: A:0.87, C:0.10, G:0.04, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAAAAAAAAA
Found at i:1339801 original size:12 final size:11
Alignment explanation
Indices: 1339761--1339825 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
1339751 CCTTCGTACC
*
1339761 AAAAAAA-AGA
1 AAAAAAACAAA
*
1339771 AAAAAACCAAGA
1 AAAAAAACAA-A
1339783 AAAAAAACAAA
1 AAAAAAACAAA
1339794 AAACAAAA-AAA
1 AAA-AAAACAAA
*
1339805 AAAAAAAGAAA
1 AAAAAAACAAA
*
1339816 AAACAAACAA
1 AAAAAAACAA
1339826 GAAAGGTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
10 10 0.22
11 22 0.48
12 14 0.30
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:1339801 original size:15 final size:14
Alignment explanation
Indices: 1339763--1339822 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
1339753 TTCGTACCAA
1339763 AAAAAAGAAAAAAAC
1 AAAAAA-AAAAAAAC
* *
1339778 -CAAGAAAAAAAAC
1 AAAAAAAAAAAAAC
1339791 AAAAAACAAAAAAA-
1 AAAAAA-AAAAAAAC
1339805 AAAAAAAGAAAAAAC
1 AAAAAAA-AAAAAAC
1339820 AAA
1 AAA
1339823 CAAGAAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 9 0.24
14 18 0.49
15 10 0.27
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:1339819 original size:22 final size:22
Alignment explanation
Indices: 1339761--1339822 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
1339751 CCTTCGTACC
** *
1339761 AAAAAAAAGAAAAAA-ACCAAG
1 AAAAAAAAGAAAAAACAAAAAA
*
1339782 AAAAAAAACAAAAAACAAAAAA
1 AAAAAAAAGAAAAAACAAAAAA
1339804 AAAAAAAAGAAAAAACAAA
1 AAAAAAAAGAAAAAACAAA
1339823 CAAGAAAGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGAAAAAACAAAAAA
Found at i:1339827 original size:14 final size:13
Alignment explanation
Indices: 1339791--1339829 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
1339781 GAAAAAAAAC
1339791 AAAAAACAA-AAA
1 AAAAAACAAGAAA
*
1339803 AAAAAAAAAGAAA
1 AAAAAACAAGAAA
1339816 AAACAAACAAGAAA
1 AAA-AAACAAGAAA
1339830 GGTGTTCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 8 0.35
13 6 0.26
14 9 0.39
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (13 bp):
AAAAAACAAGAAA
Found at i:1341102 original size:28 final size:28
Alignment explanation
Indices: 1341068--1342032 Score: 865
Period size: 28 Copynumber: 34.6 Consensus size: 28
1341058 CGTTCATCTC
*
1341068 TTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1341096 TTCAAAGCCCATAAGTCAGTGGCA-CCTTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC--T
* *
1341125 TTCAAAGCCCACAAGTCAGTAGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1341153 TT------CC-TAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
1341174 TTTATAGCCCACAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
1341202 TTCATAGCCCACAAGTCAGTGG-AACCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
1341230 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
1341258 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1341286 TTCAAAGCTCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1341314 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1341342 TTCATAGCCCACAAGTCAGTAGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
1341370 TTCATAA-CCTACAAGTCAGTGGCA-CATT
1 TTCA-AAGCCCACAAGTCAGTGGCATC-CT
*
1341398 TTCAAAGCCCACAAGTCAGTGGCATTCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1341426 TTCAAAGTCCACAAGTTAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* **
1341455 TTCAAAGCCTACAAGTCAGTGATATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1341483 TTCAAAGCGCACAAGTTAGTGGCA-CTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
**
1341510 TGTCAAAGCCCACAAGTCAGTGGCATATT
1 T-TCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
1341539 TTCAAAGCGCACAAGTTAATGACATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1341567 TTCAAAGCCCACAAGTTAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* * *
1341595 TTCATAGCCTATAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
1341623 TTCATAGCCCATAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* * * *
1341651 TTCATAGCCTATAAGTCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
1341680 TTCAAAGCCCACAAGTCAATGGCA-CTTT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* * *
1341708 TTCATAGCCCATAAGTCATTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
1341736 TTCATAGCCCACAAGTCAGTGGCA-CATT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* *
1341764 TTCAAAGCCCACGAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1341792 TTCAAAGCCCACAAGTCAGTGACA--CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1341818 TCTCAGAA-CCTACAAGTTAGTGGCA-CCTT
1 T-TCA-AAGCCCACAAGTCAGTGGCATCC-T
* * *
1341847 TTCATAGCCCAGAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1341875 TTCAAAACCCATAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1341902 CTTCAAGGCCCATAAGAT-AGTGGCATCCT
1 -TTCAAAGCCCACAAG-TCAGTGGCATCCT
* *
1341931 TCCAAAGCCCACGAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1341958 CTTCAAAGCCCACAAGTCAGAGGCAT-AT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1341986 TCTCAGAA-CCCACAAGTTAGTGGCATTCT
1 T-TCA-AAGCCCACAAGTCAGTGGCATCCT
*
1342015 TTTAAAGGCCACACAAGT
1 TTCAAA-GCC-CACAAGT
1342033 TGGTGGCAAC
Statistics
Matches: 793, Mismatches: 100, Indels: 86
0.81 0.10 0.09
Matches are distributed among these distances:
20 1 0.00
21 14 0.02
22 2 0.00
26 3 0.00
27 39 0.05
28 636 0.80
29 90 0.11
30 8 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1347036 original size:29 final size:29
Alignment explanation
Indices: 1347002--1347072 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1346992 TTGATTTGAG
** * *
1347002 TATTAATTTGTATCAATTATATTAGTTTA
1 TATTAATTCATATCAATTATATCACTTTA
**
1347031 TATTAATTCATATTGATTATATCACTTTA
1 TATTAATTCATATCAATTATATCACTTTA
*
1347060 TATTAATTGATAT
1 TATTAATTCATAT
1347073 AAAATTTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (29 bp):
TATTAATTCATATCAATTATATCACTTTA
Found at i:1347038 original size:19 final size:20
Alignment explanation
Indices: 1347002--1347072 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 20
1346992 TTGATTTGAG
*
1347002 TATTAATTTGTATCAATT-A
1 TATTAATTTATATCAATTCA
* *
1347021 TATTAGTTTATATTAATTCA
1 TATTAATTTATATCAATTCA
* * *
1347041 TATTGA-TTATATCACTTTA
1 TATTAATTTATATCAATTCA
*
1347060 TATTAATTGATAT
1 TATTAATTTATAT
1347073 AAAATTTTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (20 bp):
TATTAATTTATATCAATTCA
Found at i:1349036 original size:21 final size:21
Alignment explanation
Indices: 1349010--1349066 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1349000 ACATGTTGCA
1349010 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1349031 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1349052 ATGTATCGATACATG
1 ATGTATCGATACATG
1349067 TTATTGGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1349121 original size:19 final size:19
Alignment explanation
Indices: 1349097--1349161 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
1349087 TAGCCAAACT
1349097 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
1349116 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
1349129 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
1349150 TGTATCGATACA
1 TGTATCGATACA
1349162 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:1349133 original size:13 final size:13
Alignment explanation
Indices: 1349115--1349140 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1349105 TACACAAAAT
1349115 ATGTATCGATACA
1 ATGTATCGATACA
1349128 ATGTATCGATACA
1 ATGTATCGATACA
1349141 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1349138 original size:32 final size:33
Alignment explanation
Indices: 1349097--1349161 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
1349087 TAGCCAAACT
1349097 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
1349129 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
1349162 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:1351745 original size:13 final size:13
Alignment explanation
Indices: 1351727--1351751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1351717 TATAAAGTGT
1351727 TGTATCGATACAA
1 TGTATCGATACAA
1351740 TGTATCGATACA
1 TGTATCGATACA
1351752 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1351749 original size:33 final size:33
Alignment explanation
Indices: 1351707--1351773 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1351697 TTCAACGATT
*
1351707 TGTATCGATATATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1351740 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1351773 T
1 T
1351774 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1351811 original size:13 final size:13
Alignment explanation
Indices: 1351793--1351817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1351783 TGCCAAAAAA
1351793 TGTATCGATACAT
1 TGTATCGATACAT
1351806 TGTATCGATACA
1 TGTATCGATACA
1351818 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1356757 original size:15 final size:15
Alignment explanation
Indices: 1356737--1356767 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1356727 TAAAAATGTC
*
1356737 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1356752 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1356767 C
1 C
1356768 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1358867 original size:13 final size:13
Alignment explanation
Indices: 1358849--1358886 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1358839 CATTTTTCTT
1358849 TGTATCGATACAA
1 TGTATCGATACAA
*
1358862 TGTATCGATACAC
1 TGTATCGATACAA
1358875 TGTATCGATACA
1 TGTATCGATACA
1358887 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1359041 original size:20 final size:20
Alignment explanation
Indices: 1358998--1359043 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1358988 AAATCTTTTG
1358998 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1359019 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1359039 CAAAA
1 CAAAA
1359044 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1361375 original size:21 final size:21
Alignment explanation
Indices: 1361349--1361405 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1361339 ACATGTTGCA
1361349 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1361370 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1361391 ATGTATCGATACATG
1 ATGTATCGATACATG
1361406 TCATTGGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1361477 original size:32 final size:33
Alignment explanation
Indices: 1361436--1361500 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
1361426 TAGCCAAACT
*
1361436 TGTATCG-ATACACAAAATATGTATCGATACAA
1 TGTATCGAATACAAAAAATATGTATCGATACAA
1361468 TGTATCGATATACAAAAAATATGTATCGATACA
1 TGTATCGA-ATACAAAAAATATGTATCGATACA
1361501 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 7 0.23
34 23 0.77
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (33 bp):
TGTATCGAATACAAAAAATATGTATCGATACAA
Found at i:1365478 original size:49 final size:49
Alignment explanation
Indices: 1365406--1365505 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
1365396 TTATCCTTTA
1365406 TGAAAAAAATCTTTTGAATAGAGAGTTAGATTTTGAAGAAAAACGAGAT
1 TGAAAAAAATCTTTTGAATAGAGAGTTAGATTTTGAAGAAAAACGAGAT
*
1365455 TGAAAAAAATCTTTTGAATAGAGAGTTAGATTTTGAAGAAAACCGAGAT
1 TGAAAAAAATCTTTTGAATAGAGAGTTAGATTTTGAAGAAAAACGAGAT
1365504 TG
1 TG
1365506 GAGTATCCCC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (49 bp):
TGAAAAAAATCTTTTGAATAGAGAGTTAGATTTTGAAGAAAAACGAGAT
Found at i:1367347 original size:13 final size:13
Alignment explanation
Indices: 1367329--1367353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1367319 ATTTTGCTAA
1367329 GTATCGATACATT
1 GTATCGATACATT
1367342 GTATCGATACAT
1 GTATCGATACAT
1367354 AGCATTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1367428 original size:22 final size:22
Alignment explanation
Indices: 1367401--1367474 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
1367391 TCACTATTCA
*
1367401 CACTGTTTATGTATCGATACAT
1 CACTGTTCATGTATCGATACAT
* * *
1367423 CACTGTTCA--TCTCTATTCAT
1 CACTGTTCATGTATCGATACAT
1367443 CACTGTTCATGTATCGATACAT
1 CACTGTTCATGTATCGATACAT
1367465 CACTGTTCAT
1 CACTGTTCAT
1367475 CACTGTACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 17 0.40
22 26 0.60
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (22 bp):
CACTGTTCATGTATCGATACAT
Found at i:1367451 original size:10 final size:10
Alignment explanation
Indices: 1367381--1367480 Score: 53
Period size: 10 Copynumber: 9.7 Consensus size: 10
1367371 AATCTTATTT
1367381 TCACTGTTCA
1 TCACTGTTCA
*
1367391 TCACTATTCA
1 TCACTGTTCA
*
1367401 -CACTGTTTA
1 TCACTGTTCA
* *
1367410 TGTA-TCGATACA
1 T-CACT-G-TTCA
1367422 TCACTGTTCA
1 TCACTGTTCA
* *
1367432 TCTCTATTCA
1 TCACTGTTCA
1367442 TCACTGTTCA
1 TCACTGTTCA
* *
1367452 TGTA-TCGATACA
1 T-CACT-G-TTCA
1367464 TCACTGTTCA
1 TCACTGTTCA
1367474 TCACTGT
1 TCACTGT
1367481 ACATTGAGCC
Statistics
Matches: 65, Mismatches: 16, Indels: 18
0.66 0.16 0.18
Matches are distributed among these distances:
9 7 0.11
10 41 0.63
11 8 0.12
12 9 0.14
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:1367460 original size:42 final size:41
Alignment explanation
Indices: 1367381--1367478 Score: 169
Period size: 42 Copynumber: 2.4 Consensus size: 41
1367371 AATCTTATTT
*
1367381 TCACTGTTCATCACTATTCACACTGTTTATGTATCGATACA
1 TCACTGTTCATCACTATTCACACTGTTCATGTATCGATACA
*
1367422 TCACTGTTCATCTCTATTCATCACTGTTCATGTATCGATACA
1 TCACTGTTCATCACTATTCA-CACTGTTCATGTATCGATACA
1367464 TCACTGTTCATCACT
1 TCACTGTTCATCACT
1367479 GTACATTGAG
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 19 0.36
42 34 0.64
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (41 bp):
TCACTGTTCATCACTATTCACACTGTTCATGTATCGATACA
Found at i:1367549 original size:22 final size:22
Alignment explanation
Indices: 1367521--1367563 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1367511 ATTCATCACA
1367521 GTATCGATACATCACTGTTCAT
1 GTATCGATACATCACTGTTCAT
1367543 GTATCGATACATCACTGTTCA
1 GTATCGATACATCACTGTTCA
1367564 CACTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (22 bp):
GTATCGATACATCACTGTTCAT
Found at i:1368062 original size:34 final size:35
Alignment explanation
Indices: 1367999--1368065 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
1367989 CTAAGTGATT
1367999 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
*
1368035 GAGAGGTTTTTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1368066 TGTTGTAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
36 9 0.31
37 12 0.41
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1372948 original size:13 final size:13
Alignment explanation
Indices: 1372930--1372954 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1372920 ATTTTGCTAA
1372930 GTATCGATACATT
1 GTATCGATACATT
1372943 GTATCGATACAT
1 GTATCGATACAT
1372955 AGCATTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1373030 original size:22 final size:22
Alignment explanation
Indices: 1373003--1373076 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
1372993 AACTATTCAC
*
1373003 CACTGTTTATGTATCGATACAT
1 CACTGTTCATGTATCGATACAT
* * *
1373025 CACTGTTCA--TCTCTATTCAT
1 CACTGTTCATGTATCGATACAT
1373045 CACTGTTCATGTATCGATACAT
1 CACTGTTCATGTATCGATACAT
1373067 CACTGTTCAT
1 CACTGTTCAT
1373077 CACTGTACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 17 0.40
22 26 0.60
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (22 bp):
CACTGTTCATGTATCGATACAT
Found at i:1373041 original size:42 final size:42
Alignment explanation
Indices: 1372982--1373080 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
1372972 AATCTTATTT
* *
1372982 TCACTGTTCATAACTATTCACCACTGTTTATGTATCGATACA
1 TCACTGTTCATCACTATTCACCACTGTTCATGTATCGATACA
* *
1373024 TCACTGTTCATCTCTATTCATCACTGTTCATGTATCGATACA
1 TCACTGTTCATCACTATTCACCACTGTTCATGTATCGATACA
1373066 TCACTGTTCATCACT
1 TCACTGTTCATCACT
1373081 GTACATTGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.25, C:0.26, G:0.09, T:0.39
Consensus pattern (42 bp):
TCACTGTTCATCACTATTCACCACTGTTCATGTATCGATACA
Found at i:1373053 original size:10 final size:10
Alignment explanation
Indices: 1373022--1373082 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
1373012 TGTATCGATA
1373022 CATCACTGTT
1 CATCACTGTT
* *
1373032 CATCTCTATT
1 CATCACTGTT
1373042 CATCACTGTT
1 CATCACTGTT
* *
1373052 CATGTA-TCGATA
1 CAT-CACT-G-TT
1373064 CATCACTGTT
1 CATCACTGTT
1373074 CATCACTGT
1 CATCACTGT
1373083 ACATTGAGCC
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
10 30 0.77
11 4 0.10
12 5 0.13
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.39
Consensus pattern (10 bp):
CATCACTGTT
Found at i:1373158 original size:22 final size:22
Alignment explanation
Indices: 1373133--1373175 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1373123 ATTCATCACA
*
1373133 GTATCGATACATCATTGTTCAT
1 GTATCGATACATCACTGTTCAT
1373155 GTATCGATACATCACTGTTCA
1 GTATCGATACATCACTGTTCA
1373176 CACTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (22 bp):
GTATCGATACATCACTGTTCAT
Found at i:1373674 original size:34 final size:35
Alignment explanation
Indices: 1373611--1373677 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
1373601 CTAAGTGATT
1373611 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
*
1373647 GAGAGGTTTTTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1373678 TGTTATAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
36 9 0.31
37 12 0.41
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1376182 original size:16 final size:16
Alignment explanation
Indices: 1376163--1376204 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 16
1376153 AGGAATTAAT
1376163 TTTTGAAAAAAAATTG
1 TTTTGAAAAAAAATTG
1376179 TTTTGAGAAAAAAAATTG
1 TTTT--GAAAAAAAATTG
1376197 TTTTGAAA
1 TTTTGAAA
1376205 GGAAGTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
18 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (16 bp):
TTTTGAAAAAAAATTG
Found at i:1378518 original size:17 final size:19
Alignment explanation
Indices: 1378486--1378525 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1378476 TAAATATTCA
1378486 CTTTTGTCTCTTTA-TTTT
1 CTTTTGTCTCTTTATTTTT
*
1378504 CTTTTTTCT-TTTATTTTT
1 CTTTTGTCTCTTTATTTTT
1378522 CTTT
1 CTTT
1378526 CTCTCATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.78
Consensus pattern (19 bp):
CTTTTGTCTCTTTATTTTT
Found at i:1378617 original size:305 final size:310
Alignment explanation
Indices: 1378169--1378787 Score: 1052
Period size: 305 Copynumber: 2.0 Consensus size: 310
1378159 TAATCCAAGC
*
1378169 AAATATTCACTTTTCTCTCTTTATTTTCATTTTTCTTTTATTTTTCTTTCTCTCATTTCCTTTCT
1 AAATATTCACTTTTCTCTCTTTATTTTCATTTTTCTTTTATTTTTCTTTCTCTCATTTCCTTTAT
* *
1378234 TTTCATTTCATTTTCTTTTCCTTCTTTGTTGAGAGAGAAAAAAATTAAAGAGAGGGGCCTTTTAA
66 TTTCATTTCAATTTCTTTTCCTTCTTTGTTGAGAGAGAAAAAAATTAAAGAGAAGGGCCTTTTAA
1378299 TCATGAATTCCGAAATTCATTTAAGAAGGGAAAATGACCCTTGTTTCTATC-TTTTTTTTTT-CA
131 TCATGAATTCCGAAATTCATTTAAGAAGGGAAAATGACCCTTGTTTC-ATCTTTTTTTTTTTGCA
*
1378362 TGCACAAAATGGTCCCTTTTTATCCTAACTCTCTCCATTCGTTAATTTCC-TTTAATTTAGGACC
195 TGCAAAAAATGGTCCCTTTTTATCCTAACTCTCTCCATTCGTTAATTTCCTTTTAATTTAGGACC
1378426 AACGAAGCCTTTGATTGGCTACTCTGTGTACTTATCCCCCAACAAAAAATT
260 AACGAAGCCTTTGATTGGCTACTCTGTGTACTTATCCCCCAACAAAAAATT
* *
1378477 AAATATTCACTTTTGTCTCTTTATTTTCTTTTTTCTTTTATTTTTCTTTCTCTCATTTCCTTTAT
1 AAATATTCACTTTTCTCTCTTTATTTTCATTTTTCTTTTATTTTTCTTTCTCTCATTTCCTTTAT
*
1378542 TTTCA-TT-AATTT-TTTTCCTTCTTTGTTGAGAGAGAAAAAAATTAAAGAGAAGGGCCTTTTGA
66 TTTCATTTCAATTTCTTTTCCTTCTTTGTTGAGAGAGAAAAAAATTAAAGAGAAGGGCCTTTTAA
1378604 TCATGAATTCCGAAATTCATTTAAGAAGGGAAAATGACCCTTGTTTCATCTTTTTTTTTTTTTTT
131 TCATGAATTCCGAAATTCATTTAAGAAGGGAAAATGACCCTTGTTTCATC-------TTTTTTTT
*
1378669 TTTGCATGCAAAAAATGGTCCCTTTTTATCCTAGCTCTCTCCATTCGTTAATTTCCTTTTAATTT
189 TTTGCATGCAAAAAATGGTCCCTTTTTATCCTAACTCTCTCCATTCGTTAATTTCCTTTTAATTT
1378734 AGGACCAACGAAGCCTTTGATTGGCTACTCTGTGTACTTATCCCCCAACAAAAA
254 AGGACCAACGAAGCCTTTGATTGGCTACTCTGTGTACTTATCCCCCAACAAAAA
1378788 TAAAAATGCC
Statistics
Matches: 293, Mismatches: 8, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
304 3 0.01
305 95 0.32
306 4 0.01
307 2 0.01
308 67 0.23
312 10 0.03
313 50 0.17
314 62 0.21
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (310 bp):
AAATATTCACTTTTCTCTCTTTATTTTCATTTTTCTTTTATTTTTCTTTCTCTCATTTCCTTTAT
TTTCATTTCAATTTCTTTTCCTTCTTTGTTGAGAGAGAAAAAAATTAAAGAGAAGGGCCTTTTAA
TCATGAATTCCGAAATTCATTTAAGAAGGGAAAATGACCCTTGTTTCATCTTTTTTTTTTTGCAT
GCAAAAAATGGTCCCTTTTTATCCTAACTCTCTCCATTCGTTAATTTCCTTTTAATTTAGGACCA
ACGAAGCCTTTGATTGGCTACTCTGTGTACTTATCCCCCAACAAAAAATT
Found at i:1380570 original size:14 final size:14
Alignment explanation
Indices: 1380551--1380577 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1380541 TTCTTTTATT
1380551 TTTTCATAATAAAA
1 TTTTCATAATAAAA
1380565 TTTTCATAATAAA
1 TTTTCATAATAAA
1380578 TGAAAAGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTTCATAATAAAA
Found at i:1381926 original size:15 final size:16
Alignment explanation
Indices: 1381896--1381927 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1381886 CAAAACGTGA
1381896 ACATTGTGATTTAAGG
1 ACATTGTGATTTAAGG
1381912 ACATTGTGA-TTAAGG
1 ACATTGTGATTTAAGG
1381927 A
1 A
1381928 GCAACTTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
ACATTGTGATTTAAGG
Found at i:1389026 original size:17 final size:16
Alignment explanation
Indices: 1388985--1389026 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1388975 TGGCAAAAAG
*
1388985 ATTGACTTTTTTAATA
1 ATTGACTTTTTTAACA
*
1389001 ATTGA-TTTTATTTACA
1 ATTGACTTTT-TTAACA
1389017 ATTGACTTTT
1 ATTGACTTTT
1389027 GACTTATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (16 bp):
ATTGACTTTTTTAACA
Found at i:1389533 original size:27 final size:27
Alignment explanation
Indices: 1389489--1389548 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1389479 AGAATGTAAT
*
1389489 AACTCCGTGGCACATTTTTAAGTCCAC
1 AACTCCGTGACACATTTTTAAGTCCAC
* * *
1389516 AACTCTGTGACACCTTTTTAAGTTCAC
1 AACTCCGTGACACATTTTTAAGTCCAC
1389543 AACTCC
1 AACTCC
1389549 ATGGCATCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.32
Consensus pattern (27 bp):
AACTCCGTGACACATTTTTAAGTCCAC
Found at i:1389659 original size:27 final size:27
Alignment explanation
Indices: 1389622--1389692 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
1389612 TCTTTTTCTT
1389622 TTTTAAGTCCACAACTCCATGGCACCC
1 TTTTAAGTCCACAACTCCATGGCACCC
* *
1389649 TTTTAAGTCCACAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCATGGCACCC
** *
1389676 TTCAAAGTCCACGACTC
1 TTTTAAGTCCACAACTC
1389693 AGTGGCATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.25, C:0.35, G:0.13, T:0.27
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCATGGCACCC
Found at i:1389697 original size:27 final size:27
Alignment explanation
Indices: 1389626--1389706 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
1389616 TTTCTTTTTT
* **
1389626 AAGTCCACAACTCCA-TGGCACCCTTTT
1 AAGTCCACAACT-CAGTGGCATCCTTCA
*
1389653 AAGTCCACAACTCCGTGGCATCCTTCA
1 AAGTCCACAACTCAGTGGCATCCTTCA
*
1389680 AAGTCCACGACTCAGTGGCATCTCTTC
1 AAGTCCACAACTCAGTGGCATC-CTTC
1389707 TCCATGTCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.02
27 41 0.89
28 4 0.09
ACGTcount: A:0.25, C:0.36, G:0.15, T:0.25
Consensus pattern (27 bp):
AAGTCCACAACTCAGTGGCATCCTTCA
Found at i:1389716 original size:118 final size:117
Alignment explanation
Indices: 1389503--1389797 Score: 369
Period size: 118 Copynumber: 2.5 Consensus size: 117
1389493 CCGTGGCACA
* * * * *
1389503 TTTTTAAGTCCACAACTCTGTGACACCTTTTTAAGTTCACAACTCCATGGCATCCTTTAAAGTCC
1 TTTTTAAGTCCACAACTCTATGGCACCTTTTTAAGTCCACAACTCCGTGGCATCCTTCAAAGTCC
* * *
1389568 ATGACTCAATGGCATTTCTTCTCCAAGTCCACGACTTAGTGGCATCTTTTTCT
66 ACGACTCAATGGCATCTCTTCTCCAAGTCCACGACTTAGTGGCATCCTTTT-T
* *
1389621 TTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTCAAAGTCC
1 TTTTTAAGTCCACAACTCTATGGCACCTTTTTAAGTCCACAACTCCGTGGCATCCTTCAAAGTCC
* * *
1389686 ACGACTCAGTGGCATCTCTTCTCCATGTCCACGACTTAGTGGTATCCTTTTT
66 ACGACTCAATGGCATCTCTTCTCCAAGTCCACGACTTAGTGGCATCCTTTTT
** ** *
1389738 TTTCCAAGTCCATGACT-TAGTGGCATCTTTTCTCTAAGTCCACAACTCCGTGGCA-CCTTC
1 TTTTTAAGTCCACAACTCTA-TGGCA-CCTTT-T-TAAGTCCACAACTCCGTGGCATCCTTC
1389798 TTCTTTTAAG
Statistics
Matches: 153, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
116 1 0.01
117 19 0.12
118 106 0.69
119 6 0.04
120 21 0.14
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.34
Consensus pattern (117 bp):
TTTTTAAGTCCACAACTCTATGGCACCTTTTTAAGTCCACAACTCCGTGGCATCCTTCAAAGTCC
ACGACTCAATGGCATCTCTTCTCCAAGTCCACGACTTAGTGGCATCCTTTTT
Found at i:1389718 original size:30 final size:31
Alignment explanation
Indices: 1389562--1389801 Score: 135
Period size: 30 Copynumber: 7.9 Consensus size: 31
1389552 GCATCCTTTA
* *
1389562 AAGTCCATGACTCAATGGCAT-TTCTTCTCC
1 AAGTCCACGACTCAGTGGCATCTTCTTCTCC
* * **
1389592 AAGTCCACGACTTAGTGGCATCTTTTTCTTTTTT
1 AAGTCCACGACTCAGTGGCATC---TTCTTCTCC
* * *
1389626 AAGTCCACAACTCCA-TGGCA-C-CCTT-T-T
1 AAGTCCACGACT-CAGTGGCATCTTCTTCTCC
* * *
1389653 AAGTCCACAACTCCGTGGCATC--C-T-TCA
1 AAGTCCACGACTCAGTGGCATCTTCTTCTCC
1389680 AAGTCCACGACTCAGTGGCATC-TCTTCTCC
1 AAGTCCACGACTCAGTGGCATCTTCTTCTCC
* * * * *
1389710 ATGTCCACGACTTAGTGGTATCCTTTTTTTTCC
1 AAGTCCACGACTCAGTGGCAT-C-TTCTTCTCC
* * *
1389743 AAGTCCATGACTTAGTGGCATCTT-TTCTCT
1 AAGTCCACGACTCAGTGGCATCTTCTTCTCC
* * *
1389773 AAGTCCACAACTCCGTGGCACCTTCTTCT
1 AAGTCCACGACTCAGTGGCATCTTCTTCT
1389802 TTTAAGTCCA
Statistics
Matches: 166, Mismatches: 29, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
26 3 0.02
27 39 0.23
28 3 0.02
29 4 0.02
30 61 0.37
31 7 0.04
32 1 0.01
33 25 0.15
34 22 0.13
35 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (31 bp):
AAGTCCACGACTCAGTGGCATCTTCTTCTCC
Found at i:1389755 original size:33 final size:32
Alignment explanation
Indices: 1389680--1389768 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 32
1389670 GCATCCTTCA
* * *
1389680 AAGTCCACGACTCAGTGGCATC--TCTTCTCC
1 AAGTCCACGACTTAGTGGCATCTTTTTTTTCC
* *
1389710 ATGTCCACGACTTAGTGGTATCCTTTTTTTTCC
1 AAGTCCACGACTTAGTGGCAT-CTTTTTTTTCC
*
1389743 AAGTCCATGACTTAGTGGCATCTTTT
1 AAGTCCACGACTTAGTGGCATCTTTT
1389769 CTCTAAGTCC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 18 0.38
31 1 0.02
32 5 0.10
33 24 0.50
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (32 bp):
AAGTCCACGACTTAGTGGCATCTTTTTTTTCC
Found at i:1389809 original size:32 final size:32
Alignment explanation
Indices: 1389772--1390073 Score: 258
Period size: 32 Copynumber: 9.7 Consensus size: 32
1389762 ATCTTTTCTC
1389772 TAAGTCCACAACTCCGTGGCACCTTCTTCTTT
1 TAAGTCCACAACTCCGTGGCACCTTCTTCTTT
* *
1389804 TAAGTCCACAACTTCGTGGCACCTTCTCCTTT
1 TAAGTCCACAACTCCGTGGCACCTTCTTCTTT
*
1389836 TAAGTCCACAACTCCGTGGCACCTTTTTCTTT
1 TAAGTCCACAACTCCGTGGCACCTTCTTCTTT
** * *
1389868 TAAGTCCATGACTCTGTGGCACTCTTTTTCCTTT
1 TAAGTCCACAACTCCGTGGCAC-CTTCTT-CTTT
* * **
1389902 TAAGTTCACTACTCTATGGCA-C--C--CTTT
1 TAAGTCCACAACTCCGTGGCACCTTCTTCTTT
* *
1389929 TAAGTCTACAACTCCGTGGCACCTTTTTCTTT
1 TAAGTCCACAACTCCGTGGCACCTTCTTCTTT
* *
1389961 TCAAAGCCCACAACTCCGTGGCATCTT-TTCCTTTT
1 T--AAGTCCACAACTCCGTGGCACCTTCTT-C-TTT
*
1389996 TAAGTCCACAACTTCGTGGCA-C--C--CTTT
1 TAAGTCCACAACTCCGTGGCACCTTCTTCTTT
* *
1390023 TAAGTCCATAACTCCGTGACA-C--C--CTTT
1 TAAGTCCACAACTCCGTGGCACCTTCTTCTTT
*
1390050 TAAGTCCATAACTCCTGTGGCACC
1 TAAGTCCACAACTCC-GTGGCACC
1390074 CCCTTTTAAA
Statistics
Matches: 228, Mismatches: 28, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
27 62 0.27
28 7 0.03
29 1 0.00
32 85 0.37
33 26 0.11
34 43 0.19
35 4 0.02
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (32 bp):
TAAGTCCACAACTCCGTGGCACCTTCTTCTTT
Found at i:1389855 original size:94 final size:89
Alignment explanation
Indices: 1389489--1390073 Score: 310
Period size: 94 Copynumber: 6.5 Consensus size: 89
1389479 AGAATGTAAT
* * * *
1389489 AACTCCGTGGCA-CATTT-T-TAAGTCCACAACTCTGTGACA-C--C-T-TTTTAAGTTCACAAC
1 AACTCCGTGGCACCTTTTCTCTAAGTCCACAACTCCGTGGCACCTTCTTCTTTTAAGTCCACAAC
* * * * *
1389546 TCCATGGCATCCTTTAAAGTCCAT
66 TTCGTGGCACCCTTTTAAGTCCAC
* ** * * * ** * *
1389570 GACTCAATGGCA-TTTCTTCTCCAAGTCCACGACTTAGTGGCATCTTTTTCTTTTTTAAGTCCAC
1 AACTCCGTGGCACCTT-TTCTCTAAGTCCACAACTCCGTGGCACCTTCTTC--TTTTAAGTCCAC
* *
1389634 AACTCCATGGCACCCTTTTAAGTCCAC
63 AACTTCGTGGCACCCTTTTAAGTCCAC
* * * * ** * *
1389661 AACTCCGTGGCATCC---T-TCAAAGTCCACGACTCAGTGGCATC-TCTTC-TCCATGTCCACGA
1 AACTCCGTGGCA-CCTTTTCTCTAAGTCCACAACTCCGTGGCACCTTCTTCTTTTAAGTCCACAA
* * * *
1389720 CTTAGTGGTATCCTTTTTTTTCCAAGTCCAT
65 CTTCGTGGCA-CC---CTTTT--AAGTCCAC
* ** *
1389751 GACTTAGTGGCATCTTTTCTCTAAGTCCACAACTCCGTGGCACCTTCTTCTTTTAAGTCCACAAC
1 AACTCCGTGGCACCTTTTCTCTAAGTCCACAACTCCGTGGCACCTTCTTCTTTTAAGTCCACAAC
1389816 TTCGTGGCACCTTCTCCTTTTAAGTCCAC
66 TTCGTGGCA----C-CCTTTTAAGTCCAC
* ** * * *
1389845 AACTCCGTGGCACCTTTTTCTTTTAAGTCCATGACTCTGTGGCACTCTTTTTCCTTTTAAGTTCA
1 AACTCCGTGGCACC-TTTTC-TCTAAGTCCACAACTCCGTGGCAC-CTTCTT-CTTTTAAGTCCA
* * *
1389910 CTAC-TCTATGGCACCCTTTTAAGTCTAC
62 CAACTTC-GTGGCACCCTTTTAAGTCCAC
* * *
1389938 AACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCATCTT-TTCCTTTTTAAGTC
1 AACTCCGTGGCACC-TTTTC---TCTAAGTCCACAACTCCGTGGCACCTTCTT-C-TTTTAAGTC
*
1390002 CACAACTTCGTGGCACCCTTTTAAGTCCAT
60 CACAACTTCGTGGCACCCTTTTAAGTCCAC
* * *
1390032 AACTCCGTGACACC-CTT-T-TAAGTCCATAACTCCTGTGGCACC
1 AACTCCGTGGCACCTTTTCTCTAAGTCCACAACTCC-GTGGCACC
1390074 CCCTTTTAAA
Statistics
Matches: 387, Mismatches: 79, Indels: 69
0.72 0.15 0.13
Matches are distributed among these distances:
81 10 0.03
82 2 0.01
83 1 0.00
84 31 0.08
85 3 0.01
87 16 0.04
88 36 0.09
89 2 0.01
90 16 0.04
91 44 0.11
92 3 0.01
93 58 0.15
94 70 0.18
95 42 0.11
96 24 0.06
97 7 0.02
98 21 0.05
99 1 0.00
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.35
Consensus pattern (89 bp):
AACTCCGTGGCACCTTTTCTCTAAGTCCACAACTCCGTGGCACCTTCTTCTTTTAAGTCCACAAC
TTCGTGGCACCCTTTTAAGTCCAC
Found at i:1389942 original size:27 final size:27
Alignment explanation
Indices: 1389897--1390074 Score: 70
Period size: 27 Copynumber: 6.1 Consensus size: 27
1389887 CACTCTTTTT
* *
1389897 CCTTTTAAGTTCACTACTCTATGGCAC
1 CCTTTTAAGTTCACAACTCCATGGCAC
*
1389924 CCTTTTAAG-TCTACAACTCCGTGGCAC
1 CCTTTTAAGTTC-ACAACTCCATGGCAC
** *
1389951 CTTTTTCTTTTCAAAGCCCACAACTCCGTGGCATC
1 C-----CTTTT--AAGTTCACAACTCCATGGCA-C
* * *
1389986 TTTTCCTTTTTAAGTCCACAACTTCGTGGCAC
1 ----CC-TTTTAAGTTCACAACTCCATGGCAC
* * * *
1390018 CCTTTTAAGTCCATAACTCCGTGACAC
1 CCTTTTAAGTTCACAACTCCATGGCAC
* * *
1390045 CCTTTTAAGTCCATAACTCCTGTGGCAC
1 CCTTTTAAGTTCACAACTCC-ATGGCAC
1390073 CC
1 CC
1390075 CCTTTTAAAG
Statistics
Matches: 125, Mismatches: 10, Indels: 31
0.75 0.06 0.19
Matches are distributed among these distances:
26 2 0.02
27 64 0.51
28 10 0.08
32 6 0.05
33 18 0.14
34 18 0.14
35 6 0.05
39 1 0.01
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (27 bp):
CCTTTTAAGTTCACAACTCCATGGCAC
Found at i:1390216 original size:52 final size:52
Alignment explanation
Indices: 1390128--1390801 Score: 530
Period size: 52 Copynumber: 13.4 Consensus size: 52
1390118 ATTATCATTA
* * ** *
1390128 GCCTTGAATCAGCACT-TTAGCATCTTTTTCATCTTTAAGTCCAATATCGCTT
1 GCCTTGAATCAGCA-TATTGGCACCTTTACCATCTTTAAGTCCAATATCGCTG
* * *
1390180 GCCTTGAATCAGCATATTAGCACCTTTACCACCTTTAAGTCTAATATCGCTG
1 GCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATATCGCTG
* * * *
1390232 ACCTTGAATCAGCATATTGGCACCTTTACCATCTTCAAGCCCAATGTCGCTG
1 GCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATATCGCTG
* *
1390284 GCCTTGAATCAGCACATT---ACC---A-C-T-TTTAAGTCCAATATCGCTA
1 GCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATATCGCTG
* * * *
1390327 GCCTTGAATCAGTATATTGGCGCC-TTAGTCATCTTTAAGTCCAATGTCGCTG
1 GCCTTGAATCAGCATATTGGCACCTTTA-CCATCTTTAAGTCCAATATCGCTG
*
1390379 GCCTTGAATCAGCACATTGGCACCTTTA--AGTC--TAA-T---AT-T-GCTG
1 GCCTTGAATCAGCATATTGGCACCTTTACCA-TCTTTAAGTCCAATATCGCTG
* * * *
1390422 GCTTTGAATCAGCATATTGGCACTTTTACCACCTTTAAGTCCAATGTCGCTG
1 GCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATATCGCTG
* * * * *
1390474 CCCTTGAATCAGCACATTGGCACGTTTACCATCTTTAAGTCCAATGTCACTG
1 GCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATATCGCTG
* * * *
1390526 GCCTTGAATTAGCACATTGGCACCTTT---ATCTTTAAGTCCAATGTTGCTG
1 GCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATATCGCTG
* * **
1390575 GCCTTGAATCAGCACATTGGTACC-TT--CATCTTTAAGTCTGATATCGCTG
1 GCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATATCGCTG
* * * * * *
1390624 GCCTTGAATCAGCATAATGGCATCTTTAACAT-TCCTAAGCCCAATGTCGCTG
1 GCCTTGAATCAGCATATTGGCACCTTTACCATCT-TTAAGTCCAATATCGCTG
* * * * * * *
1390676 GCCTTGAATCAACACATTGGCA--TTCTTCTCATCTTCAAGTCTAATGTCGTTG
1 GCCTTGAATCAGCATATTGGCACCTT-TAC-CATCTTTAAGTCCAATATCGCTG
* * * * * * *
1390728 GCCGTGAATCAGCACATT-G-ACATTCTTCGCATTTTTAGGCCCAATATCGCTG
1 GCCTTGAATCAGCATATTGGCACCTT-TAC-CATCTTTAAGTCCAATATCGCTG
* *
1390780 GCCTGGAATCAGTATATTGGCA
1 GCCTTGAATCAGCATATTGGCA
1390802 TTTTTATCAT
Statistics
Matches: 507, Mismatches: 81, Indels: 66
0.78 0.12 0.10
Matches are distributed among these distances:
43 60 0.12
44 3 0.01
45 4 0.01
46 6 0.01
47 1 0.00
48 4 0.01
49 86 0.17
50 9 0.02
51 8 0.02
52 320 0.63
53 5 0.01
54 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (52 bp):
GCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATATCGCTG
Found at i:1390322 original size:95 final size:95
Alignment explanation
Indices: 1390205--1390693 Score: 502
Period size: 95 Copynumber: 5.0 Consensus size: 95
1390195 ATTAGCACCT
* * *
1390205 TTACCACCTTTAAGTCTAATATCGCTGACCTTGAATCAGCATATTGGCACCTTTACCATCTTCAA
1 TTACCACTTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAA
*
1390270 GCCCAATGTCGCTGGCCTTGAATCAGCACA
66 GTCCAATGTCGCTGGCCTTGAATCAGCACA
* * * * *
1390300 TTACCACTTTTAAGTCCAATATCGCTAGCCTTGAATCAGTATATTGGCGCC-TTAGTCATCTTTA
1 TTACCACTTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA-CCATCTTTA
1390364 AGTCCAATGTCGCTGGCCTTGAATCAGCACA
65 AGTCCAATGTCGCTGGCCTTGAATCAGCACA
** * * * * *
1390395 TTGGCACCTTTAAGTCTAATATTGCTGGCTTTGAATCAGCATATTGGCACTTTTACCACCTTTAA
1 TTACCACTTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAA
*
1390460 GTCCAATGTCGCTGCCCTTGAATCAGCACA
66 GTCCAATGTCGCTGGCCTTGAATCAGCACA
* * * * * *
1390490 TTGGCACGTTTACCATCTTTAAGTCCAATGTCACTGGCCTTGAATTAGCACATTGGCACCTTT--
1 TT---AC---CA-C-T-TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAC
*
1390553 -ATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACA
57 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
* * * * *
1390591 TTGGTACCTTCATCTTTAAGTCTGATATCGCTGGCCTTGAATCAGCATAATGGCATCTTTAACAT
1 -T--TACC-AC-T-TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCAT
* * *
1390656 -TCCTAAGCCCAATGTCGCTGGCCTTGAATCAACACA
60 CT-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
1390692 TT
1 TT
1390694 GGCATTCTTC
Statistics
Matches: 324, Mismatches: 51, Indels: 35
0.79 0.12 0.09
Matches are distributed among these distances:
94 3 0.01
95 162 0.50
96 3 0.01
98 43 0.13
100 2 0.01
101 70 0.22
102 2 0.01
104 39 0.12
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (95 bp):
TTACCACTTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAA
GTCCAATGTCGCTGGCCTTGAATCAGCACA
Found at i:1390451 original size:147 final size:146
Alignment explanation
Indices: 1390161--1390801 Score: 493
Period size: 147 Copynumber: 4.3 Consensus size: 146
1390151 CTTTTTCATC
* * * * *
1390161 TTTAAGTCCAATATCGCTTGCCTTGAATCAGCATATTAGCACCTTTACCACCTTTAAGTCTAATA
1 TTTAAGTCCAATATCGC-TGCCTTGAATCAGCATATTGGCA-CTTTAACATCTTTAAGTCCAATG
* * * * *
1390226 TCGCTGACCTTGAATCAGCATATTGGCACCTTTACCATCTTCAAGCCCAATGTCGCTGGCCTTGA
64 TCGCTGGCCTTGAATCAGCACATTGGCACC--T--C-T-TT-AAGTCCAATATTGCTGGCCTTGA
1390291 ATCAG--CA----CA--TTACCACT
122 ATCAGCACATTGGCACCTTACCACT
* * * *
1390308 TTTAAGTCCAATATCGCTAGCCTTGAATCAGTATATTGGCGCCTTAGTCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCT-GCCTTGAATCAGCATATTGGCACTTTA-ACATCTTTAAGTCCAATG
* *
1390373 TCGCTGGCCTTGAATCAGCACATTGGCA-C-CTTTAAGTCTAATATTGCTGGCTTTGAATCAGCA
64 TCGCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCA
* * *
1390436 TATTGGCACTTTTACCACC
129 CATTGGCAC-CTTACCACT
* * *
1390455 TTTAAGTCCAATGTCGCTGCCCTTGAATCAGCACATTGGCACGTTTACCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTG-CCTTGAATCAGCATATTGGCAC-TTTAACATCTTTAAGTCCAATG
* * *
1390520 TCACTGGCCTTGAATTAGCACATTGGCACCTTTATCTTTAAGTCCAATGTTGCTGGCCTTGAATC
64 TCGCTGGCCTTGAATCAGCACATTGGCACC----TCTTTAAGTCCAATATTGCTGGCCTTGAATC
*
1390585 AGCACATTGGTACCTT--CA-T
125 AGCACATTGGCACCTTACCACT
** * * *
1390604 CTTTAAGTCTGATATCGCTGGCCTTGAATCAGCATAATGGCATCTTTAACAT-TCCTAAGCCCAA
1 -TTTAAGTCCAATATCGCT-GCCTTGAATCAGCATATTGGCA-CTTTAACATCT-TTAAGTCCAA
* * * * * *
1390668 TGTCGCTGGCCTTGAATCAACACATTGGCATTCTTCTCATCTTCAAGTCTAATGTCGTTGGCCGT
62 TGTCGCTGGCCTTGAATCAGCACATTGGCA--C--CTC-T-TT-AAGTCCAATATTGCTGGCCTT
* * *
1390733 GAATCAGCACATTGACATTCTT-CGCATT
120 GAATCAGCACATTGGCA-CCTTAC-CACT
* * * *
1390761 TTTAGGCCCAATATCGCTGGCCTGGAATCAGTATATTGGCA
1 TTTAAGTCCAATATCGCT-GCCTTGAATCAGCATATTGGCA
1390802 TTTTTATCAT
Statistics
Matches: 403, Mismatches: 57, Indels: 59
0.78 0.11 0.11
Matches are distributed among these distances:
138 23 0.06
139 2 0.00
140 2 0.00
141 1 0.00
144 2 0.00
146 7 0.02
147 162 0.40
148 4 0.01
149 1 0.00
150 80 0.20
151 3 0.01
152 5 0.01
153 70 0.17
154 4 0.01
156 36 0.09
157 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (146 bp):
TTTAAGTCCAATATCGCTGCCTTGAATCAGCATATTGGCACTTTAACATCTTTAAGTCCAATGTC
GCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACA
TTGGCACCTTACCACT
Found at i:1397216 original size:20 final size:20
Alignment explanation
Indices: 1397193--1397267 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
1397183 AAGTACCCAT
1397193 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1397213 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1397233 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
1397253 ATGCATCGATACATT
1 ATGTATCGATACATT
1397268 CTATCTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1402410 original size:38 final size:39
Alignment explanation
Indices: 1402345--1402420 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 39
1402335 ATGAAGAAGT
* *
1402345 AAAAAAATAAAAAATAAAAGCAGAAACAACA-AAAAAAC
1 AAAAAAATAAAAAATAAAAGCAAAAACAAAATAAAAAAC
*
1402383 AAAAAAATAAAAAA-AAAGTGCAAAAACAAAATAAAAAA
1 AAAAAAATAAAAAATAAA-AGCAAAAACAAAATAAAAAA
1402421 AGGGACAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 3 0.09
38 24 0.73
39 6 0.18
ACGTcount: A:0.80, C:0.08, G:0.05, T:0.07
Consensus pattern (39 bp):
AAAAAAATAAAAAATAAAAGCAAAAACAAAATAAAAAAC
Found at i:1403688 original size:32 final size:34
Alignment explanation
Indices: 1403654--1403717 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
1403644 CTTACAAATC
*
1403654 TTTT-TACAAAAGTCCACAACTTATTGGCATTCT
1 TTTTCTACAAAAGTCCACAACTTAGTGGCATTCT
* * *
1403687 TTTTCTCCCAAAGTCCACGACTTAGTGGCAT
1 TTTTCTACAAAAGTCCACAACTTAGTGGCAT
1403718 CTCTACTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 4 0.15
34 22 0.85
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (34 bp):
TTTTCTACAAAAGTCCACAACTTAGTGGCATTCT
Found at i:1403787 original size:54 final size:54
Alignment explanation
Indices: 1403726--1404093 Score: 204
Period size: 59 Copynumber: 6.4 Consensus size: 54
1403716 ATCTCTACTC
*
1403726 TAAGTCCACAACTCCATGGCACCTTTTTAAGTCCACAACTTCGTTGCACCTTTT
1 TAAGTCCACAACTCCATGGCACCTTTTTAAGTCCACAACTTCGTGGCACCTTTT
* * *
1403780 TAAGTCCACAACTCCATGGCACCTTTTTCCTTTAAATCAACAACTTCGTGGCATCC-TTC
1 TAAGTCCACAACTCCATGGCACC---TT--TTTAAGTCCACAACTTCGTGGCA-CCTTTT
* * * ** * *
1403839 AAAGTCAACGACT-CAGTGGCATCTCTTCTCCAAGTCCACGAC-TCAATGGCATCCTTTTCCTTT
1 TAAGTCCACAACTCCA-TGGCA-C-CTT-TTTAAGTCCACAACTTC-GTGGCA-CC---T--TTT
* * * *
1403902 TCAAGTCCACAACTACGTGGCACCTTTTTAAGTCCACAACTCCGTGACACCTTTT
1 T-AAGTCCACAACTCCATGGCACCTTTTTAAGTCCACAACTTCGTGGCACCTTTT
* * ** * *
1403957 TAAATCCATAACTCTGTGGTACCTTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTT
1 TAAGTCCACAACTCCATGGCACCTTTTTAAGTCCACAACTTCGTGGCACC---TT--TT
* * ** * * *
1404016 TAAATCCACAACTCCGTGGCATCC-TTCGAAGTCCACGACTTAGTGGCATCTCTTCTC
1 TAAGTCCACAACTCCATGGCA-CCTTTTTAAGTCCACAACTTCGTGGCA-C-CTT-TT
*
1404073 TAAGTCCACAACTCCGTGGCA
1 TAAGTCCACAACTCCATGGCA
1404094 TTTTTTCCTT
Statistics
Matches: 247, Mismatches: 40, Indels: 51
0.73 0.12 0.15
Matches are distributed among these distances:
54 66 0.27
55 4 0.02
56 2 0.01
57 45 0.18
58 6 0.02
59 76 0.31
60 8 0.03
61 17 0.07
62 4 0.02
63 3 0.01
64 15 0.06
65 1 0.00
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.31
Consensus pattern (54 bp):
TAAGTCCACAACTCCATGGCACCTTTTTAAGTCCACAACTTCGTGGCACCTTTT
Found at i:1403814 original size:32 final size:31
Alignment explanation
Indices: 1403726--1404264 Score: 269
Period size: 27 Copynumber: 17.9 Consensus size: 31
1403716 ATCTCTACTC
*
1403726 TAAGTCCACAACTCCATGGCACC--TT--TT
1 TAAGTCCACAACTCCGTGGCACCTTTTCCTT
* *
1403753 TAAGTCCACAACTTCGTTGCACC--TT--TT
1 TAAGTCCACAACTCCGTGGCACCTTTTCCTT
*
1403780 TAAGTCCACAACTCCATGGCACCTTTTTCCTT
1 TAAGTCCACAACTCCGTGGCACC-TTTTCCTT
* * *
1403812 TAAATCAACAACTTCGTGGCA-----TCCTT
1 TAAGTCCACAACTCCGTGGCACCTTTTCCTT
* * * * * * *
1403838 CAAAGTCAACGACTCAGTGGCATCTCTT-CTC
1 -TAAGTCCACAACTCCGTGGCACCTTTTCCTT
* * **
1403869 CAAGTCCACGACTCAATGGCATCCTTTTCCTTT
1 TAAGTCCACAACTCCGTGGCA-CCTTTTCC-TT
*
1403902 TCAAGTCCACAACTACGTGGCACC--TT--TT
1 T-AAGTCCACAACTCCGTGGCACCTTTTCCTT
*
1403930 TAAGTCCACAACTCCGTGACACC--TT--TT
1 TAAGTCCACAACTCCGTGGCACCTTTTCCTT
* * * *
1403957 TAAATCCATAACTCTGTGGTACC--TT--TT
1 TAAGTCCACAACTCCGTGGCACCTTTTCCTT
1403984 TAAGTCCACAACTCCGTGGCACCTTTTTCCTT
1 TAAGTCCACAACTCCGTGGCACC-TTTTCCTT
*
1404016 TAAATCCACAACTCCGTGGCA-----TCCTT
1 TAAGTCCACAACTCCGTGGCACCTTTTCCTT
* * ** * * *
1404042 CGAAGTCCACGACTTAGTGGCATCTCTT-CTC
1 -TAAGTCCACAACTCCGTGGCACCTTTTCCTT
**
1404073 TAAGTCCACAACTCCGTGGCATTTTTTCCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTCC-TT
* * * *
1404105 TAAATCCATAACTTCGTGGCACATTTTCCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTCC-TT
*
1404137 TAAGTCCACAACTTCGTGGCACCCTTTTTCCTTT
1 TAAGTCCACAACTCCGTGGCA-CC-TTTTCC-TT
* * * *
1404171 TAAGTCTACAACTTCATGGCACCTTTTTCTTT
1 TAAGTCCACAACTCCGTGGCACC-TTTTCCTT
* *
1404203 TCAAAGCCCACAACTCCGTGGCATCTTTTCCTTT
1 T--AAGTCCACAACTCCGTGGCACCTTTTCC-TT
* * *
1404237 TAACTCTACAACTTCGTGGCACCCTTTT
1 TAAGTCCACAACTCCGTGGCA-CCTTTT
1404265 AAGTCTATAA
Statistics
Matches: 404, Mismatches: 74, Indels: 62
0.75 0.14 0.11
Matches are distributed among these distances:
26 10 0.02
27 141 0.35
28 3 0.01
30 43 0.11
31 11 0.03
32 110 0.27
33 22 0.05
34 64 0.16
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.34
Consensus pattern (31 bp):
TAAGTCCACAACTCCGTGGCACCTTTTCCTT
Found at i:1403836 original size:26 final size:27
Alignment explanation
Indices: 1403807--1403894 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 27
1403797 GGCACCTTTT
*
1403807 TCCTTTAAA-TCAACAACTTC-GTGGCA
1 TCCTTCAAAGTCAACAAC-TCAGTGGCA
*
1403833 TCCTTCAAAGTCAACGACTCAGTGGCA
1 TCCTTCAAAGTCAACAACTCAGTGGCA
* * * *
1403860 TCTCTTCTCCAAGTCCACGACTCAATGGCA
1 TC-C-T-TCAAAGTCAACAACTCAGTGGCA
1403890 TCCTT
1 TCCTT
1403895 TTCCTTTTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
26 10 0.19
27 16 0.31
28 2 0.04
29 2 0.04
30 22 0.42
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (27 bp):
TCCTTCAAAGTCAACAACTCAGTGGCA
Found at i:1404037 original size:177 final size:167
Alignment explanation
Indices: 1403697--1404093 Score: 406
Period size: 177 Copynumber: 2.3 Consensus size: 167
1403687 TTTTCTCCCA
* * * *
1403697 AAGTCCACGACTTAGTGGCATCTCTACTCTAAGTCCACAACTCCATGGCACCTTTTTAAGTCCAC
1 AAGTCCACGACTCAATGGCATCTCTTCTCTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCAC
* * *
1403762 AACTTCGTTGCACCTTTTTAAGTCCACAACTCCATGGCACCTTTTTCCTTTAAATCAACAACTTC
66 AACTCCGTTGCACCTTTTTAAATCCACAACTCCATGGCACC--TTT-CTTTAAATCAACAACTCC
*
1403827 GTGGCATCCTTCAAAGTCAACGACTCAGTGGCATCTCTTCTCC
128 GTGGCATCCTTCAAAGTCAACAACTCAGTGGCATC-C-T-TCC
* * *
1403870 AAGTCCACGACTCAATGGCATCCTTTTCCTTTTCAAGTCCACAACTACGTGGCACCTTTTTAAGT
1 AAGTCCACGACTCAATGGCAT-CTCTT-C-TCT-AAGTCCACAACTCCGTGGCACCTTTTTAAGT
* ** * * *
1403935 CCACAACTCCG-TGACACCTTTTTAAATCCATAACTCTGTGGTACC-TT-TTTAAGTCCACAACT
62 CCACAACTCCGTTG-CACCTTTTTAAATCCACAACTCCATGGCACCTTTCTTTAAATCAACAACT
* * * *
1403997 CCGTGGCACCTTTTTCCTTTAAA-TCCACAACTCCGTGGCATCCTTCG
126 CCGTGGCA------TCCTTCAAAGTCAACAACTCAGTGGCATCCTTCC
* *
1404044 AAGTCCACGACTTAGTGGCATCTCTTCTCTAAGTCCACAACTCCGTGGCA
1 AAGTCCACGACTCAATGGCATCTCTTCTCTAAGTCCACAACTCCGTGGCA
1404094 TTTTTTCCTT
Statistics
Matches: 187, Mismatches: 26, Indels: 25
0.79 0.11 0.11
Matches are distributed among these distances:
170 19 0.10
171 2 0.01
172 21 0.11
173 23 0.12
174 26 0.14
175 2 0.01
176 5 0.03
177 81 0.43
178 8 0.04
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.31
Consensus pattern (167 bp):
AAGTCCACGACTCAATGGCATCTCTTCTCTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCAC
AACTCCGTTGCACCTTTTTAAATCCACAACTCCATGGCACCTTTCTTTAAATCAACAACTCCGTG
GCATCCTTCAAAGTCAACAACTCAGTGGCATCCTTCC
Found at i:1404080 original size:204 final size:202
Alignment explanation
Indices: 1403726--1404131 Score: 589
Period size: 204 Copynumber: 2.0 Consensus size: 202
1403716 ATCTCTACTC
* * *
1403726 TAAGTCCACAACTCCATGGCACCTTTTTAAGTCCACAACTTCGTTGCACCTTTTTAAGTCCACAA
1 TAAGTCCACAACTCCATGACACCTTTTTAAATCCACAACTTCGTGGCACCTTTTTAAGTCCACAA
*
1403791 CTCCATGGCACCTTTTTCCTTTAAATCAACAACTTCGTGGCATCCTTCAAAGTCAACGACTCAGT
66 CTCCATGGCACCTTTTTCCTTTAAATCAACAACTCCGTGGCATCCTTCAAAGTCAACGACTCAGT
* *
1403856 GGCATCTCTTCTCCAAGTCCACGACTCAATGGCATCCTTTTCCTTTTCAAGTCCACAACTACGTG
131 GGCATCTCTTCTCCAAGTCCACAACTCAATGGCAT-CTTTTCCTTTT-AAATCCACAACTACGTG
*
1403921 GCACCTTTT
194 GCACATTTT
* * *
1403930 TAAGTCCACAACTCCGTGACACCTTTTTAAATCCATAAC-TCTGTGGTACCTTTTTAAGTCCACA
1 TAAGTCCACAACTCCATGACACCTTTTTAAATCCACAACTTC-GTGGCACCTTTTTAAGTCCACA
* * * * *
1403994 ACTCCGTGGCACCTTTTTCCTTTAAATCCACAACTCCGTGGCATCCTTCGAAGTCCACGACTTAG
65 ACTCCATGGCACCTTTTTCCTTTAAATCAACAACTCCGTGGCATCCTTCAAAGTCAACGACTCAG
* ** * * *
1404059 TGGCATCTCTTCTCTAAGTCCACAACTCCGTGGCATTTTTTCCTTTTAAATCCATAACTTCGTGG
130 TGGCATCTCTTCTCCAAGTCCACAACTCAATGGCATCTTTTCCTTTTAAATCCACAACTACGTGG
1404124 CACATTTT
195 CACATTTT
1404132 CCTTTTAAGT
Statistics
Matches: 180, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
202 22 0.12
203 12 0.07
204 146 0.81
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.33
Consensus pattern (202 bp):
TAAGTCCACAACTCCATGACACCTTTTTAAATCCACAACTTCGTGGCACCTTTTTAAGTCCACAA
CTCCATGGCACCTTTTTCCTTTAAATCAACAACTCCGTGGCATCCTTCAAAGTCAACGACTCAGT
GGCATCTCTTCTCCAAGTCCACAACTCAATGGCATCTTTTCCTTTTAAATCCACAACTACGTGGC
ACATTTT
Found at i:1404171 original size:34 final size:33
Alignment explanation
Indices: 1403981--1404264 Score: 236
Period size: 32 Copynumber: 8.9 Consensus size: 33
1403971 TGTGGTACCT
*
1403981 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCC
1 TTTTAAGTCCACAACTTCGTGGCACCTTTTTCC
* *
1404014 -TTTAAATCCACAACTCCGTGGCA------TCC
1 TTTTAAGTCCACAACTTCGTGGCACCTTTTTCC
** * * * *
1404040 TTCGAAGTCCACGACTTAGTGGCATC-TCTT-C
1 TTTTAAGTCCACAACTTCGTGGCACCTTTTTCC
* * *
1404071 -TCTAAGTCCACAACTCCGTGGCA-TTTTTTCC
1 TTTTAAGTCCACAACTTCGTGGCACCTTTTTCC
* * *
1404102 TTTTAAATCCATAACTTCGTGGCA-CATTTTCC
1 TTTTAAGTCCACAACTTCGTGGCACCTTTTTCC
1404134 TTTTAAGTCCACAACTTCGTGGCACCCTTTTTCC
1 TTTTAAGTCCACAACTTCGTGGCA-CCTTTTTCC
* *
1404168 TTTTAAGTCTACAACTTCATGGCACCTTTTT-C
1 TTTTAAGTCCACAACTTCGTGGCACCTTTTTCC
* * *
1404200 TTTTCAAAGCCCACAACTCCGTGGCATC-TTTTCC
1 TTTT--AAGTCCACAACTTCGTGGCACCTTTTTCC
* * *
1404234 TTTTAACTCTACAACTTCGTGGCACCCTTTT
1 TTTTAAGTCCACAACTTCGTGGCACCTTTTT
1404265 AAGTCTATAA
Statistics
Matches: 202, Mismatches: 34, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.01
27 17 0.08
30 22 0.11
31 2 0.01
32 92 0.46
33 15 0.07
34 51 0.25
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.37
Consensus pattern (33 bp):
TTTTAAGTCCACAACTTCGTGGCACCTTTTTCC
Found at i:1404259 original size:66 final size:64
Alignment explanation
Indices: 1403981--1404264 Score: 231
Period size: 66 Copynumber: 4.5 Consensus size: 64
1403971 TGTGGTACCT
* * * * **
1403981 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTAAATCCACAACTCCGTGGCA-----TCC
1 TTTTAAATCTACAACTTCGTGGCACCTTTTTCTTTTAAGCCCACAACTCCGTGGCATCTTTTCC
** * * * * * * * * *
1404040 TTCGAAGTCCACGACTTAGTGGCATC-TCTTC-TCTAAGTCCACAACTCCGTGGCATTTTTTCC
1 TTTTAAATCTACAACTTCGTGGCACCTTTTTCTTTTAAGCCCACAACTCCGTGGCATCTTTTCC
* * * * * * *
1404102 TTTTAAATCCATAACTTCGTGGCACATTTTCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTTC
1 TTTTAAATCTACAACTTCGTGGCACCTTTTTCTTTTAAGCCCACAACTCCGTGGCA-TC-TTTTC
1404167 C
64 C
* *
1404168 TTTTAAGTCTACAACTTCATGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCATCTTTTC
1 TTTTAAATCTACAACTTCGTGGCACCTTTTTCTTTT--AAGCCCACAACTCCGTGGCATCTTTTC
1404233 C
64 C
* *
1404234 TTTTAACTCTACAACTTCGTGGCACCCTTTT
1 TTTTAAATCTACAACTTCGTGGCACCTTTTT
1404265 AAGTCTATAA
Statistics
Matches: 179, Mismatches: 35, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
57 21 0.12
58 4 0.02
59 20 0.11
62 21 0.12
63 3 0.02
64 21 0.12
66 70 0.39
67 1 0.01
68 18 0.10
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.37
Consensus pattern (64 bp):
TTTTAAATCTACAACTTCGTGGCACCTTTTTCTTTTAAGCCCACAACTCCGTGGCATCTTTTCC
Found at i:1404263 original size:27 final size:27
Alignment explanation
Indices: 1404232--1404285 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1404222 GGCATCTTTT
* *
1404232 CCTTTTAACTCTACAACTTCGTGGCAC
1 CCTTTTAACTCTACAACTCCATGGCAC
* *
1404259 CCTTTTAAGTCTATAACTCCATGGCAC
1 CCTTTTAACTCTACAACTCCATGGCAC
1404286 TCCCTTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.24, C:0.31, G:0.11, T:0.33
Consensus pattern (27 bp):
CCTTTTAACTCTACAACTCCATGGCAC
Found at i:1404391 original size:52 final size:51
Alignment explanation
Indices: 1404324--1405114 Score: 542
Period size: 52 Copynumber: 15.8 Consensus size: 51
1404314 GCAACCCTTC
* * * *
1404324 TAAGCCCAATATTGCTGGCCTTGAATCAGCACATTGGCATCTTTTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCCATCTT
* * * *
1404376 TAAGTCCAATATTGCTTGCCTTGAATCAGCATATTGGCACCTTTACCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCCATCTT
* * * *
1404428 TAAGTCCAATATCGTTGGCCTTAAATCAGCATATTGGCACCTTTACCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCCATCTT
* * *
1404480 TAAG-CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCCATCTT
* *
1404531 TAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCCATCTT
* * * * * *
1404583 CAAGCCCAATGTCGTTGGCCTTAAATCAGCACATTGGCA------C--C--
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTCCATCTT
* *
1404624 TAAGTCCAGTATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGT-CATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTT-TCCATCTT
* * * * *
1404676 TAAGTCCAATGTCGCTGGCTTTGAATAAGCACATTAGCA------C--CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTCCATCTT
* * *
1404719 TAAGTCCAATATCG-TGGCCTTCAATTAGCATATTGGCACTTTTACCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTT-CCATCTT
* * * * * * *
1404770 TAAGTCCAATGTCGCTAGCCTTGAAACAGCACATTGGCACCTTTGCTATTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCCATCTT
* * * * *
1404822 TAAGTCTAATGTCGCTGGCCTTTAATCAGCACATTGGCAC-CTT-CATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTCCATCTT
* ** * *
1404871 TAAGTCCAATGTCATTGGCCTTGAATCAGCACATTGGCAC-CTT-CATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTCCATCTT
* * * * ** *
1404920 TAAGTCCGATATCGTTGGCCTTGAATCAACATATTGGTATCTTTAACAT-TCC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCCATCT-T
** * ** * * *
1404972 TAAACCCAATGTCATTAGCCTTGAATCAGCACATTAGCA-TTCTTCTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTT-TTC-CATCTT
* * * * * * * *
1405024 CAAGTCTAATGTTGCTGG-CTGTGAATCAGTATGTTGACA-TTCTTCGCATATT
1 TAAGTCCAATATCGCTGGCCT-TGAATCAGCATATTGGCACTT-TTC-CATCTT
* * * *
1405076 TAAGCCCAATATCGATGGCTTTGAATCAGTATATTGGCA
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1405115 TATTTATCAT
Statistics
Matches: 600, Mismatches: 107, Indels: 64
0.78 0.14 0.08
Matches are distributed among these distances:
41 31 0.05
42 19 0.03
43 17 0.03
45 2 0.00
48 1 0.00
49 83 0.14
50 5 0.01
51 72 0.12
52 364 0.61
53 6 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (51 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTCCATCTT
Found at i:1404525 original size:103 final size:104
Alignment explanation
Indices: 1404319--1404956 Score: 560
Period size: 103 Copynumber: 6.4 Consensus size: 104
1404309 TGGTGGCAAC
* * * * * ** *
1404319 CCTTCTAAGCCCAATATTGCTGGCCTTGAATCAGCACATTGGCATCTTTTTCATCTTTAAGTCCA
1 CCTT-TAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGCCCA
* * *
1404384 ATATTGCTTGCCTTGAATCAGCATATTGGCACCTTTACCA
65 ATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCA
* *
1404424 CCTTTAAGTCCAATATCGTTGGCCTTAAATCAGCATATTGGCACCTTTACCACCTTTAAG-CCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGCCCAA
1404488 TATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCA
66 TATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCA
*
1404527 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTCAAGCCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGCCCAA
* * *
1404592 TGTCGTTGGCCTTAAATCAGCACATTGG---------CA
66 TATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCA
* * * ** *
1404622 CC--TAAGTCCAGTATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGCCCAA
* ** * *
1404685 TGTCGCTGG-CTT---T--G-A-ATAAGCA-CATTAGCA
66 TATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCA
* * * * *
1404715 CCTTTAAGTCCAATATCG-TGGCCTTCAATTAGCATATTGGCACTTTTACCACCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGCCCAA
* * * * *
1404779 TGTCGCTAGCCTTGAAA-CAGCACATTGGCACCTTTGCTA
66 TATCGCTGGCCTT-AAATCAGCATATTGGCACCTTTACCA
** * * * * *
1404818 TTTTTAAGTCTAATGTCGCTGGCCTTTAATCAGCACATTGGCACC-TT--CATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGCCCAA
* ** * *
1404880 TGTCATTGGCCTTGAATCAGCACATTGGCACC-TT--CA
66 TATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCA
* * * * *
1404916 TCTTTAAGTCCGATATCGTTGGCCTTGAATCAACATATTGG
1 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGG
1404957 TATCTTTAAC
Statistics
Matches: 445, Mismatches: 65, Indels: 53
0.79 0.12 0.09
Matches are distributed among these distances:
85 3 0.01
86 1 0.00
87 1 0.00
89 1 0.00
92 3 0.01
93 66 0.15
94 47 0.11
95 20 0.04
98 34 0.08
100 5 0.01
101 40 0.09
102 5 0.01
103 117 0.26
104 98 0.22
105 4 0.01
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (104 bp):
CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGCCCAA
TATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCA
Found at i:1404611 original size:155 final size:153
Alignment explanation
Indices: 1404319--1404956 Score: 645
Period size: 155 Copynumber: 4.3 Consensus size: 153
1404309 TGGTGGCAAC
* * * * **
1404319 CCTTCTAAGCCCAATATTGCTGGCCTTGAATCAGCACATTGGCATCTTTTTCATCTTTAAGTCCA
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGCCATCTTTAAGTCCA
* * * *
1404384 ATATTGCTTGCCTTGAATCAGCATATTGGCACCTTTACCACCTTTAAGTCCAATATCGTTGGCCT
65 ATATCGCTGGCCTTGAATCAGCACATTGGCACC-TTACCATCTTTAAGTCCAATATCGTTGGCCT
*
1404449 TAAATCAGCATATTGGCACCTTTACCA
129 TAAATCAGCACATTGGCACC-TTA-CA
* * *
1404476 CCTTTAAG-CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCACCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGCCATCTTTAAGTCCAA
* * * * *
1404540 TATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTCAAGCCCAATGTCGTTGGCCTT
66 TATCGCTGGCCTTGAATCAGCACATTGGCACC-TTACCATCTTTAAGTCCAATATCGTTGGCCTT
1404605 AAATCAGCACATTGG-------CA
130 AAATCAGCACATTGGCACCTTACA
* * *
1404622 CC--TAAGTCCAGTATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGCCATCTTTAAGTCCAA
* * * * *
1404685 TGTCGCTGGCTTTGAATAAGCACATT---AGC--A-C--CTTTAAGTCCAATATCG-TGGCCTTC
66 TATCGCTGGCCTTGAATCAGCACATTGGCACCTTACCATCTTTAAGTCCAATATCGTTGGCCTTA
* * *
1404741 AATTAGCATATTGGCACTTTTACCA
131 AATCAGCACATTGGCAC-CTTA-CA
* * * * * * *
1404766 CCTTTAAGTCCAATGTCGCTAGCCTTGAAACAGCACATTGGCACCTTTGCTATTTTTAAGTCTAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGCCATCTTTAAGTCCAA
* * * * *
1404831 TGTCGCTGGCCTTTAATCAGCACATTGGCACCTT--CATCTTTAAGTCCAATGTCATTGGCCTTG
66 TATCGCTGGCCTTGAATCAGCACATTGGCACCTTACCATCTTTAAGTCCAATATCGTTGGCCTTA
1404894 AATCAGCACATTGGCACCTT-CA
131 AATCAGCACATTGGCACCTTACA
* * * *
1404916 TCTTTAAGTCCGATATCGTTGGCCTTGAATCAACATATTGG
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
1404957 TATCTTTAAC
Statistics
Matches: 402, Mismatches: 59, Indels: 47
0.79 0.12 0.09
Matches are distributed among these distances:
135 19 0.05
136 14 0.03
138 1 0.00
139 1 0.00
142 2 0.00
144 8 0.02
145 71 0.18
146 80 0.20
149 2 0.00
150 36 0.09
152 17 0.04
153 22 0.05
155 121 0.30
156 4 0.01
157 4 0.01
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (153 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGCCATCTTTAAGTCCAA
TATCGCTGGCCTTGAATCAGCACATTGGCACCTTACCATCTTTAAGTCCAATATCGTTGGCCTTA
AATCAGCACATTGGCACCTTACA
Found at i:1404651 original size:93 final size:93
Alignment explanation
Indices: 1404531--1404912 Score: 387
Period size: 93 Copynumber: 4.0 Consensus size: 93
1404521 TTACCACCTT
* *
1404531 TAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTCAAGCCCAATGTC
1 TAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATGTC
*
1404596 GTTGGCCTTAAATCAGCACATTGGCACC
66 GCTGGCCTTAAATCAGCACATTGGCACC
* * * **
1404624 TAAGTCCAGTATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTC
1 TAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATGTC
* * * *
1404689 GCTGGCTTTGAATAAGCACATTAGCACC
66 GCTGGCCTTAAATCAGCACATTGGCACC
* * * *
1404717 TTTAAGTCCAATATCG-TGGCCTTCAATTAGCATATTGGCACTTTTACCACCTTTAAGTCCAATG
1 --TAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATG
*
1404781 TCGCTAGCCTTGAAA-CAGCACATTGGCACCTTTGC
64 TCGCTGGCCTT-AAATCAGCACATTGGCA-C----C
* * * *
1404816 TATTTTTAAGTCTAATGTCGCTGGCCTTTAATCAGCACATTGGCACC-TT--CATCTTTAAGTCC
1 ------TAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGTCC
** *
1404878 AATGTCATTGGCCTTGAATCAGCACATTGGCACC
60 AATGTCGCTGGCCTTAAATCAGCACATTGGCACC
1404912 T
1 T
1404913 TCATCTTTAA
Statistics
Matches: 239, Mismatches: 36, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
90 1 0.00
93 81 0.34
94 61 0.26
95 16 0.07
96 1 0.00
99 1 0.00
100 3 0.01
101 37 0.15
103 16 0.07
104 22 0.09
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (93 bp):
TAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTACCATCTTTAAGTCCAATGTC
GCTGGCCTTAAATCAGCACATTGGCACC
Found at i:1404808 original size:239 final size:245
Alignment explanation
Indices: 1404376--1404863 Score: 641
Period size: 239 Copynumber: 2.0 Consensus size: 245
1404366 TTTTCATCTT
* *
1404376 TAAGTCCAATATTGCTTGCCTTGAATCAGCATATTGGCACCTTTACCACCTTTAAGTCCAATATC
1 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCACCTTTAAGTCCAATATC
* ** *
1404441 GTTGGCCTTAAATCAGCATATTGGCACCTTTACCACCTTTAAGCCAATATCGCTGGCCTTAAATC
66 GCTGGCCTT--AT-AGCATATAAGCACCATTACCACCTTTAAGCCAATATCGCTGGCCTTAAATC
* *
1404506 AGCATATTGGCACCTTTACCACCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCAC
128 AGCATATTGGCACCTTTACCACCTTTAAGTCCAATATCGCTAGCCTTAAATCAGCACATTGGCAC
*
1404571 CTTTACCATCTTCAAGCCCAATGTCGTTGGCCTTAAATCAGCACATTGGCACC
193 CTTTACCATCTTCAAGCCCAATGTCGCTGGCCTTAAATCAGCACATTGGCACC
* ** * *
1404624 TAAGTCCAGTATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTC
1 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCACCTTTAAGTCCAATATC
* * *
1404689 GCTGG-CTT-T-G-A-ATAAGCA-CATTAGCACCTTTAAGTCCAATATCG-TGGCCTTCAATTAG
66 GCTGGCCTTATAGCATATAAGCACCATTACCACCTTTAAG-CCAATATCGCTGGCCTTAAATCAG
* *
1404747 CATATTGGCACTTTTACCACCTTTAAGTCCAATGTCGCTAGCCTTGAAA-CAGCACATTGGCACC
130 CATATTGGCACCTTTACCACCTTTAAGTCCAATATCGCTAGCCTT-AAATCAGCACATTGGCACC
* * * * * * *
1404811 TTTGCTATTTTTAAGTCTAATGTCGCTGGCCTTTAATCAGCACATTGGCACC
194 TTTACCATCTTCAAGCCCAATGTCGCTGGCCTTAAATCAGCACATTGGCACC
1404863 T
1 T
1404864 TCATCTTTAA
Statistics
Matches: 212, Mismatches: 26, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
239 127 0.60
240 17 0.08
241 1 0.00
242 1 0.00
244 1 0.00
247 3 0.01
248 62 0.29
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.32
Consensus pattern (245 bp):
TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCACCTTTAAGTCCAATATC
GCTGGCCTTATAGCATATAAGCACCATTACCACCTTTAAGCCAATATCGCTGGCCTTAAATCAGC
ATATTGGCACCTTTACCACCTTTAAGTCCAATATCGCTAGCCTTAAATCAGCACATTGGCACCTT
TACCATCTTCAAGCCCAATGTCGCTGGCCTTAAATCAGCACATTGGCACC
Found at i:1404892 original size:101 final size:102
Alignment explanation
Indices: 1404717--1405006 Score: 279
Period size: 101 Copynumber: 2.9 Consensus size: 102
1404707 CATTAGCACC
* * *
1404717 TTTAAGTCCAATATCGTGGCCTTCAATTAGCATATTGGCACTTTTACCACCTTTAAGTCCAATGT
1 TTTAAGTCCAATATCGTGGCCTTCAATCAGCACATTGGCACTCTTA-CACCTTTAAGTCCAATGT
*
1404782 CGCTAGCCTTGAAACAGCACATTGGCACCTTTGCTATT
65 CACTAGCCTTGAAACAGCACATTGGCACCTTTGCTATT
* * * *
1404820 TTTAAGTCTAATGTCGCTGGCCTTTAATCAGCACATTGGCAC-CTT-CATCTTTAAGTCCAATGT
1 TTTAAGTCCAATATCG-TGGCCTTCAATCAGCACATTGGCACTCTTACACCTTTAAGTCCAATGT
* * * *
1404883 CATTGGCCTTGAATCAGCACATTGGCACC-TT-C-ATC
65 CACTAGCCTTGAAACAGCACATTGGCACCTTTGCTATT
* * * * * * **
1404918 TTTAAGTCCGATATCGTTGGCCTTGAATCAACATATTGGTA-TCTTTA-ACATTCCTAAACCCAA
1 TTTAAGTCCAATATCG-TGGCCTTCAATCAGCACATTGGCACTC-TTACACCTT--TAAGTCCAA
* *
1404981 TGTCATTAGCCTTGAATCAGCACATT
62 TGTCACTAGCCTTGAAACAGCACATT
1405007 AGCATTCTTC
Statistics
Matches: 156, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
98 36 0.23
99 6 0.04
100 2 0.01
101 74 0.47
103 16 0.10
104 22 0.14
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (102 bp):
TTTAAGTCCAATATCGTGGCCTTCAATCAGCACATTGGCACTCTTACACCTTTAAGTCCAATGTC
ACTAGCCTTGAAACAGCACATTGGCACCTTTGCTATT
Found at i:1405171 original size:61 final size:61
Alignment explanation
Indices: 1405074--1405199 Score: 166
Period size: 61 Copynumber: 2.1 Consensus size: 61
1405064 TCTTCGCATA
** * *
1405074 TTTAAGCCCAATATCGATGGCTTTGAATCAGTATATTGGCATATTTATCA-TTTTTCTCATC
1 TTTAAGCCCAATATCGATGGCCCTGAATCAGCATATTGGCATATTTATCACTCTTT-TCATC
* *
1405135 TTTAAGCCCAATATC-ACTGGCCCTGAATTAGCATATTGGCATCTTTATCACTCTTTTCATC
1 TTTAAGCCCAATATCGA-TGGCCCTGAATCAGCATATTGGCATATTTATCACTCTTTTCATC
1405196 TTTA
1 TTTA
1405200 TGAACTTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 1 0.02
61 52 0.91
62 4 0.07
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (61 bp):
TTTAAGCCCAATATCGATGGCCCTGAATCAGCATATTGGCATATTTATCACTCTTTTCATC
Found at i:1411908 original size:21 final size:21
Alignment explanation
Indices: 1411884--1411923 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1411874 TAACAACATT
1411884 TTCTCCCCCATTTAA-AACTCA
1 TTCTCCCCC-TTTAATAACTCA
*
1411905 TTCTCCTCCTTTAATAACT
1 TTCTCCCCCTTTAATAACT
1411924 TCTCCCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (21 bp):
TTCTCCCCCTTTAATAACTCA
Done.