Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold84
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: 4163231
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 246351 characters in sequence are not A, C, G, or T
File 4 of 11
Found at i:1508144 original size:41 final size:40
Alignment explanation
Indices: 1508022--1508147 Score: 112
Period size: 40 Copynumber: 3.1 Consensus size: 40
1508012 ATTTTACTAG
* * * *
1508022 ATTCAAGGTTACCGGAGT-GTAAACAAGGCACGCATGTGCA
1 ATTCAAGGGTACCGAAGTAG-AAACAGGGCACGTATGTGCA
* * * * * *
1508062 TTTCAGGGGTGCCGAAGTATAATA-GGGGCACATATGTGCA
1 ATTCAAGGGTACCGAAGTAGAA-ACAGGGCACGTATGTGCA
*
1508102 ATTCAAGGGTACCGAAGTAGAAACATGGGCACGTATGCGCA
1 ATTCAAGGGTACCGAAGTAGAAACA-GGGCACGTATGTGCA
1508143 ATTCA
1 ATTCA
1508148 GGGAATAATT
Statistics
Matches: 65, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
39 1 0.02
40 45 0.69
41 19 0.29
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (40 bp):
ATTCAAGGGTACCGAAGTAGAAACAGGGCACGTATGTGCA
Found at i:1512450 original size:3 final size:3
Alignment explanation
Indices: 1512442--1512473 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1512432 CTCTATGGGA
1512442 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1512474 GGGGTCCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1513398 original size:8 final size:8
Alignment explanation
Indices: 1513375--1513412 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
1513365 ATAAAATATT
1513375 AATAATTA
1 AATAATTA
*
1513383 AATAAATTG
1 AAT-AATTA
1513392 AATAATTA
1 AATAATTA
1513400 AATAATTA
1 AATAATTA
1513408 AATAA
1 AATAA
1513413 AATTCAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (8 bp):
AATAATTA
Found at i:1513423 original size:25 final size:25
Alignment explanation
Indices: 1513375--1513423 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1513365 ATAAAATATT
*
1513375 AATAATTAAATAAATTGAATAATTA
1 AATAATTAAATAAATTCAATAATTA
1513400 AATAATTAAATAAAATTCAA-AATT
1 AATAATTAAAT-AAATTCAATAATT
1513424 TAAGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AATAATTAAATAAATTCAATAATTA
Found at i:1514219 original size:16 final size:15
Alignment explanation
Indices: 1514194--1514227 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1514184 AAAGTTGATA
*
1514194 ATAATTAATATATATT
1 ATAATAAATATA-ATT
1514210 ATAATAAATATAATT
1 ATAATAAATATAATT
1514225 ATA
1 ATA
1514228 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:1518274 original size:23 final size:23
Alignment explanation
Indices: 1518216--1518268 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
1518206 TTTGAACCCA
1518216 TAAGTGGGTAATTGGGAGTTCCT
1 TAAGTGGGTAATTGGGAGTTCCT
1518239 TAAGTGGGTAATTGGGAGTTCCT
1 TAAGTGGGTAATTGGGAGTTCCT
1518262 TAAGTGG
1 TAAGTGG
1518269 AAAATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.08, G:0.36, T:0.34
Consensus pattern (23 bp):
TAAGTGGGTAATTGGGAGTTCCT
Found at i:1532093 original size:25 final size:25
Alignment explanation
Indices: 1532065--1532117 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1532055 TGTAGCTACG
*
1532065 TACCACCCCAAAGCTCGTAGGAGCT
1 TACCAACCCAAAGCTCGTAGGAGCT
** * *
1532090 TACCAATTCATAGCTCGTATGAGCT
1 TACCAACCCAAAGCTCGTAGGAGCT
1532115 TAC
1 TAC
1532118 TGATTTACAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (25 bp):
TACCAACCCAAAGCTCGTAGGAGCT
Found at i:1536414 original size:15 final size:16
Alignment explanation
Indices: 1536385--1536414 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1536375 CAAACATGCT
1536385 TTAACACATTATCAAA
1 TTAACACATTATCAAA
1536401 TTAACACA-TATCAA
1 TTAACACATTATCAA
1536415 CAAAGACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:1537579 original size:25 final size:24
Alignment explanation
Indices: 1537542--1537673 Score: 90
Period size: 25 Copynumber: 5.4 Consensus size: 24
1537532 ACGAGCTGTG
* * *
1537542 AATCAGTATGCTCTCACGAGCTAT
1 AATCGGTAAGCTCTCACGAGCTAC
* * *
1537566 ATATCGGTAAGCTCAT-ATGAGTTGAG
1 A-ATCGGTAAGCTC-TCACGAGCT-AC
* * *
1537592 AATCGGTAAGCTCTCACAAGGTGC
1 AATCGGTAAGCTCTCACGAGCTAC
* *
1537616 AATCGGTAAGCT-TATATGAGCTA-
1 AATCGGTAAGCTCT-CACGAGCTAC
1537639 AGACTCGGTAAGCTCTCACGAGCTAC
1 A-A-TCGGTAAGCTCTCACGAGCTAC
1537665 AATCGGTAA
1 AATCGGTAA
1537674 TCCCTAATGA
Statistics
Matches: 82, Mismatches: 17, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
23 2 0.02
24 26 0.32
25 49 0.60
26 5 0.06
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (24 bp):
AATCGGTAAGCTCTCACGAGCTAC
Found at i:1537633 original size:49 final size:49
Alignment explanation
Indices: 1537541--1537673 Score: 158
Period size: 49 Copynumber: 2.7 Consensus size: 49
1537531 CACGAGCTGT
* * * * * *
1537541 GAATCAGTATGCTCTCACGAGCTATATATCGGTAAGCTCATATGAGTTGA
1 GAATCGGTAAGCTCTCACAAGCTACA-ATCGGTAAGCTCATATGAGCTAA
* * *
1537591 GAATCGGTAAGCTCTCACAAGGTGCAATCGGTAAGCTTATATGAGCTAA
1 GAATCGGTAAGCTCTCACAAGCTACAATCGGTAAGCTCATATGAGCTAA
* *
1537640 GACTCGGTAAGCTCTCACGAGCTACAATCGGTAA
1 GAATCGGTAAGCTCTCACAAGCTACAATCGGTAA
1537674 TCCCTAATGA
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
49 50 0.71
50 20 0.29
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (49 bp):
GAATCGGTAAGCTCTCACAAGCTACAATCGGTAAGCTCATATGAGCTAA
Found at i:1545010 original size:12 final size:12
Alignment explanation
Indices: 1544993--1545018 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1544983 ATCCACACTC
1544993 CCGTGTGCTAGG
1 CCGTGTGCTAGG
1545005 CCGTGTGCTAGG
1 CCGTGTGCTAGG
1545017 CC
1 CC
1545019 ATGTAACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.31, G:0.38, T:0.23
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:1546314 original size:25 final size:25
Alignment explanation
Indices: 1546280--1546353 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
1546270 TCATGTACAT
* * *
1546280 GTATGCTCATACGAGCTGTGAATCG
1 GTATGATCATACGAGCTATAAATCG
**
1546305 GTATGATCATTTGAGCTATAAATCG
1 GTATGATCATACGAGCTATAAATCG
*
1546330 GTATGCTC-TCACGAGCTATAAATC
1 GTATGATCAT-ACGAGCTATAAATC
1546354 AGTAACCCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 1 0.03
25 39 0.98
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (25 bp):
GTATGATCATACGAGCTATAAATCG
Found at i:1547884 original size:16 final size:16
Alignment explanation
Indices: 1547839--1547884 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1547829 CTATAGACCT
*
1547839 TGAAACTATAAGAATG
1 TGAAACTATAGGAATG
*
1547855 TGAAAAT-TATGGAATG
1 TGAAACTATA-GGAATG
1547871 TGAAACTATAGGAA
1 TGAAACTATAGGAA
1547885 ACTTTTGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (16 bp):
TGAAACTATAGGAATG
Found at i:1553522 original size:94 final size:94
Alignment explanation
Indices: 1553350--1553523 Score: 294
Period size: 94 Copynumber: 1.9 Consensus size: 94
1553340 CTGATGAAAC
* * *
1553350 TTCAAAACAAGTTTAGGAACCTCTTAATCATGTAAAAATCTATTTATTAACACTTTGAAATCACA
1 TTCAAAACAAGTTTAAGAACCTCTTAATCATGTAAAAATCTATTGATTAACACTTTAAAATCACA
**
1553415 TTTTTACTTGAAAATCTGAAATTCATCAT
66 TTTTTACACGAAAATCTGAAATTCATCAT
*
1553444 TTCAAAACAAGTTTAAGAACCTCTTAATCATGTAAAAATTTATTGATTAACACTTTAAAATCACA
1 TTCAAAACAAGTTTAAGAACCTCTTAATCATGTAAAAATCTATTGATTAACACTTTAAAATCACA
1553509 TTTTTACACGAAAAT
66 TTTTTACACGAAAAT
1553524 ATTTAACGAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
94 74 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (94 bp):
TTCAAAACAAGTTTAAGAACCTCTTAATCATGTAAAAATCTATTGATTAACACTTTAAAATCACA
TTTTTACACGAAAATCTGAAATTCATCAT
Found at i:1559095 original size:23 final size:22
Alignment explanation
Indices: 1559064--1559107 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1559054 TTCTTGTCTT
1559064 TTCTATTTCATCTTGTTTAATTG
1 TTCTATTTCATC-TGTTTAATTG
* *
1559087 TTCTGTTTCGTCTGTTTAATT
1 TTCTATTTCATCTGTTTAATT
1559108 ATTTTACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.61
Consensus pattern (22 bp):
TTCTATTTCATCTGTTTAATTG
Found at i:1571322 original size:14 final size:14
Alignment explanation
Indices: 1571305--1571334 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1571295 GAGACATGAA
*
1571305 AACAAAGACCTCAC
1 AACAAAAACCTCAC
1571319 AACAAAAACCTCAC
1 AACAAAAACCTCAC
1571333 AA
1 AA
1571335 ATATCTCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.33, G:0.03, T:0.07
Consensus pattern (14 bp):
AACAAAAACCTCAC
Found at i:1571709 original size:18 final size:17
Alignment explanation
Indices: 1571670--1571714 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1571660 TCACAACACC
*
1571670 TTTTTTATTAATTCACG
1 TTTTTTTTTAATTCACG
*
1571687 ATTTTTTTTCAATTCAC-
1 -TTTTTTTTTAATTCACG
1571704 TTTTTTTTTAA
1 TTTTTTTTTAA
1571715 AATTTCGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
18 14 0.58
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTTTTTAATTCACG
Found at i:1571759 original size:14 final size:14
Alignment explanation
Indices: 1571750--1571784 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1571740 AATTTCAGAA
1571750 TTTTTTTTTCAAAC
1 TTTTTTTTTCAAAC
*
1571764 TCTTTTTTTCAAAC
1 TTTTTTTTTCAAAC
1571778 TTTTTTT
1 TTTTTTT
1571785 ACGTACCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTTTTTCAAAC
Found at i:1582943 original size:56 final size:56
Alignment explanation
Indices: 1582876--1582995 Score: 161
Period size: 56 Copynumber: 2.1 Consensus size: 56
1582866 CAGTAATAGT
* * * *
1582876 ACAGTGTGGGCCTTAGCCTGA-TACAGTAACAATGTGGGCATTAGCCCAATATAGAA
1 ACAGTGTGGGCCTTAGCC-CATTACAGTAACAATGTGGGCATTAACCCAAAACAGAA
* *
1582932 ACAGTGTGGGCCTTAGCCCATTACAGTAACAGTGTGGGCCTTAACCCAAAACAGAA
1 ACAGTGTGGGCCTTAGCCCATTACAGTAACAATGTGGGCATTAACCCAAAACAGAA
*
1582988 ATAGTGTG
1 ACAGTGTG
1582996 ATAATGAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 1 0.02
56 55 0.98
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (56 bp):
ACAGTGTGGGCCTTAGCCCATTACAGTAACAATGTGGGCATTAACCCAAAACAGAA
Found at i:1582985 original size:28 final size:28
Alignment explanation
Indices: 1582876--1582995 Score: 141
Period size: 28 Copynumber: 4.3 Consensus size: 28
1582866 CAGTAATAGT
** *
1582876 ACAGTGTGGGCCTTAGCCTGATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGAA
* * *
1582904 ACAATGTGGGCATTAGCCCAATATAGAA
1 ACAGTGTGGGCCTTAGCCCAATACAGAA
* *
1582932 ACAGTGTGGGCCTTAGCCCATTACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGAA
* *
1582960 ACAGTGTGGGCCTTAACCCAAAACAGAA
1 ACAGTGTGGGCCTTAGCCCAATACAGAA
*
1582988 ATAGTGTG
1 ACAGTGTG
1582996 ATAATGAAAC
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 76 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAGAA
Found at i:1583348 original size:27 final size:27
Alignment explanation
Indices: 1583318--1583997 Score: 732
Period size: 27 Copynumber: 25.2 Consensus size: 27
1583308 GGTATAATGG
* *
1583318 TCATTTTACCATAT-GAGGGTACTTCGA
1 TCATTTTACCCT-TCGAGGGTATTTCGA
* *
1583345 TCATTTTACCCTGT-GGGGGTATTTCGG
1 TCATTTTACCCT-TCGAGGGTATTTCGA
*
1583372 TCATTTTACCCTTCGAGGGTATTT-AA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
1583398 GTCATTTTACCCTTC-AGAGGTATTTCAA
1 -TCATTTTACCCTTCGAG-GGTATTTCGA
* * *
1583426 TCATTTTACCCTTTGGGGGTATTTTGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
1583453 TCATTTTACCCTTCGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
1583480 TCATTCTACCCTTCGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
1583507 TCATTTTACCCTTTGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
** *
1583534 TCATTTTACTTTTCAAGGGTATTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
1583560 GTCATTTTATCCTTCAAGGGTATTTC-A
1 -TCATTTTACCCTTCGAGGGTATTTCGA
* *
1583587 GTCATTTTACCCTTCGGGGGTATTTCTA
1 -TCATTTTACCCTTCGAGGGTATTTCGA
* *
1583615 TCATTTTACCCTTCGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * * *
1583642 TCATTTTACCCTTTGACGATATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
1583669 TCATTTTACCCTACGGGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
1583696 TCATTTTACCTTTCGAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
1583723 TCATTTTACCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
1583750 TCATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
1583777 TCATTTTACCCTTCGAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
1583804 TCATTTTACCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
1583831 TTATTTTACCCTTTG-GAGGTATTTCGG
1 TCATTTTACCCTTCGAG-GGTATTTCGA
* *
1583858 TTATTTTACCCTTC-ATGGGTATTTCGG
1 TCATTTTACCCTTCGA-GGGTATTTCGA
* * * *
1583885 CCATTTTATCCTTCGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
1583912 TCATTTT-CCCTTCTAGGATATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
1583938 TCATTTTACCTTTCGAGGGTATTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
1583964 GTCATTTTACCCTTCGAGGCTATTTCGG
1 -TCATTTTACCCTTCGAGGGTATTTCGA
1583992 TCATTT
1 TCATTT
1583998 GCCTACGAAT
Statistics
Matches: 563, Mismatches: 76, Indels: 28
0.84 0.11 0.04
Matches are distributed among these distances:
26 26 0.05
27 532 0.94
28 5 0.01
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCGA
Found at i:1583429 original size:81 final size:80
Alignment explanation
Indices: 1583317--1583997 Score: 812
Period size: 81 Copynumber: 8.4 Consensus size: 80
1583307 GGGTATAATG
* * * *
1583317 GTCATTTTACCATAT-GAGGGTACTTCGATCATTTTACCCTGTGGGGGTATTTCGGTCATTTTAC
1 GTCATTTTACCCT-TCGAGGGTATTTCGGTCATTTTACCCT-TGGGGGTATTTCGATCATTTTAC
*
1583381 CCTTCGAGGGTATTTAA
64 CCTTCGAGGGTATTTCA
** *
1583398 GTCATTTTACCCTTC-AGAGGTATTTCAATCATTTTACCCTTTGGGGGTATTTTGATCATTTTAC
1 GTCATTTTACCCTTCGAG-GGTATTTCGGTCATTTTACCC-TTGGGGGTATTTCGATCATTTTAC
* *
1583462 CCTTCGGGGGTATTTCG
64 CCTTCGAGGGTATTTCA
* * * * * *
1583479 GTCATTCTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTTGAGGGTATTTTGGTCATTTTACT
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCC-TTGGGGGTATTTCGATCATTTTACC
* *
1583544 TTTCAAGGGTATTTCA
65 CTTCGAGGGTATTTCA
* * * *
1583560 GTCATTTTATCCTTCAAGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCTATCATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTT-GGGGGTATTTCGATCATTTTACC
**
1583625 CTTCGAGGGTATTTTG
65 CTTCGAGGGTATTTCA
* * * * *
1583641 GTCATTTTACCCTTTGACGATATTTCGGTCATTTTACCCTACGGGGGTATTTCAATCATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCT-TGGGGGTATTTCGATCATTTTACC
*
1583706 TTTCGAGGGTATTTCA
65 CTTCGAGGGTATTTCA
* *
1583722 ATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTT-GGGGGTATTTCGATCATTTTACC
1583787 CTTCGAGGGTATTTCA
65 CTTCGAGGGTATTTCA
* * * * *
1583803 ATCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTTGGAGGTATTTCGGTTATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCC-TTGGGGGTATTTCGATCATTTTACC
*
1583868 CTTC-ATGGGTATTTCG
65 CTTCGA-GGGTATTTCA
* * * ** * *
1583884 GCCATTTTATCCTTCGGGGGTATTTCGGTCATTTT-CCCTTCTAGGATATTTCGGTCATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTT-GGGGGTATTTCGATCATTTTACC
*
1583948 TTTCGAGGGTATTTCA
65 CTTCGAGGGTATTTCA
*
1583964 GTCATTTTACCCTTCGAGGCTATTTCGGTCATTT
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTT
1583998 GCCTACGAAT
Statistics
Matches: 515, Mismatches: 74, Indels: 23
0.84 0.12 0.04
Matches are distributed among these distances:
79 2 0.00
80 69 0.13
81 439 0.85
82 5 0.01
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.43
Consensus pattern (80 bp):
GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTGGGGGTATTTCGATCATTTTACCC
TTCGAGGGTATTTCA
Found at i:1594875 original size:22 final size:23
Alignment explanation
Indices: 1594834--1594888 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
1594824 AAATTCCCTA
* *
1594834 AAATTATTTTTTTTA-ATTTTAG
1 AAATTATTTTTATCATATTTTAG
*
1594856 AAATTATTTTTATCATTTTTTAG
1 AAATTATTTTTATCATATTTTAG
1594879 -AATATATTTT
1 AAAT-TATTTT
1594889 AACATTCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
AAATTATTTTTATCATATTTTAG
Found at i:1594889 original size:22 final size:23
Alignment explanation
Indices: 1594850--1594894 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1594840 TTTTTTTTAA
*
1594850 TTTTAGAAATTATTTTTATCATT
1 TTTTAGAAATTATTTTTAACATT
1594873 TTTTAG-AA-TATATTTTAACATT
1 TTTTAGAAATTAT-TTTTAACATT
1594895 CTATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 11 0.55
23 6 0.30
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTTAGAAATTATTTTTAACATT
Found at i:1596720 original size:16 final size:17
Alignment explanation
Indices: 1596699--1596732 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1596689 AATAAGAGGG
*
1596699 GCAAAAGTGT-AATTTT
1 GCAAAAGTATGAATTTT
1596715 GCAAAAGTATGAATTTT
1 GCAAAAGTATGAATTTT
1596732 G
1 G
1596733 GACTGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (17 bp):
GCAAAAGTATGAATTTT
Found at i:1600530 original size:13 final size:13
Alignment explanation
Indices: 1600512--1600536 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1600502 TAATGGTTTC
1600512 AAAAATCCCAATA
1 AAAAATCCCAATA
1600525 AAAAATCCCAAT
1 AAAAATCCCAAT
1600537 CAGATAGAAA
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:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATCCCAATA
Found at i:1601810 original size:32 final size:32
Alignment explanation
Indices: 1601774--1601837 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1601764 GTAAGTGTAA
1601774 CGAGGAATATGCGCAAATGTACACAATCGTTC
1 CGAGGAATATGCGCAAATGTACACAATCGTTC
1601806 CGAGGAATATGCGCAAATGTACACAATCGTTC
1 CGAGGAATATGCGCAAATGTACACAATCGTTC
1601838 AAGTAATAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (32 bp):
CGAGGAATATGCGCAAATGTACACAATCGTTC
Found at i:1608680 original size:16 final size:17
Alignment explanation
Indices: 1608653--1608684 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1608643 AGTATAGGGT
1608653 TAAAATTGTAAATTTGC
1 TAAAATTGTAAATTTGC
1608670 TAAAA-TGTAAATTTG
1 TAAAATTGTAAATTTG
1608685 GGTTAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (17 bp):
TAAAATTGTAAATTTGC
Found at i:1618620 original size:18 final size:18
Alignment explanation
Indices: 1618597--1618632 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1618587 AAACCATAGA
1618597 ATTCTTT-TGAATCTGATT
1 ATTCTTTGTG-ATCTGATT
1618615 ATTCTTTGTGATCTGATT
1 ATTCTTTGTGATCTGATT
1618633 TTTTAATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (18 bp):
ATTCTTTGTGATCTGATT
Found at i:1622380 original size:23 final size:23
Alignment explanation
Indices: 1622350--1622398 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1622340 TTTAGCTAGC
1622350 TTTTATAGACGATTTGTGAAAGA
1 TTTTATAGACGATTTGTGAAAGA
1622373 TTTTATAGACGATTTGTGAAAGA
1 TTTTATAGACGATTTGTGAAAGA
1622396 TTT
1 TTT
1622399 CTCTACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (23 bp):
TTTTATAGACGATTTGTGAAAGA
Found at i:1634890 original size:13 final size:13
Alignment explanation
Indices: 1634874--1634906 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1634864 GTTTTACTTT
*
1634874 TTAATTTTCTTAG
1 TTAATTTACTTAG
1634887 TTAATTTACTTAG
1 TTAATTTACTTAG
1634900 TTAATTT
1 TTAATTT
1634907 CTAGTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (13 bp):
TTAATTTACTTAG
Found at i:1634907 original size:25 final size:24
Alignment explanation
Indices: 1634866--1634912 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1634856 CATTGGAAGT
*
1634866 TTTACTTTTTAATTTTCTTAGTTAA
1 TTTACTTGTTAATTTTC-TAGTTAA
1634891 TTTACTTAGTTAA-TTTCTAGTT
1 TTTACTT-GTTAATTTTCTAGTT
1634913 TTTAAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 11 0.55
26 4 0.20
ACGTcount: A:0.23, C:0.09, G:0.06, T:0.62
Consensus pattern (24 bp):
TTTACTTGTTAATTTTCTAGTTAA
Found at i:1635819 original size:39 final size:36
Alignment explanation
Indices: 1635730--1635819 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 36
1635720 AGTTTAAGTC
* *
1635730 TTTAATTATGTCATAACTTGAACATCATTAATATGT
1 TTTAATTATGTCATAACTTAAACATCATTAATAGGT
* *
1635766 TTTAATTATATCATAA-TCTAAACATCTTTAATAAAGGTT
1 TTTAATTATGTCATAACT-TAAACATCATTAAT--AGG-T
1635805 TTTAATTATGTCATA
1 TTTAATTATGTCATA
1635820 GTGTAGGACA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
35 1 0.02
36 27 0.60
38 2 0.04
39 15 0.33
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (36 bp):
TTTAATTATGTCATAACTTAAACATCATTAATAGGT
Found at i:1644228 original size:23 final size:24
Alignment explanation
Indices: 1644190--1644234 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
1644180 ACAAAAAGAA
1644190 AAAATTGAAAAAGAAAAAGAAAAG
1 AAAATTGAAAAAGAAAAAGAAAAG
1644214 AAAATTG-AAAAGAAAAAGAAA
1 AAAATTGAAAAAGAAAAAGAAA
1644235 GCAAGAGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (24 bp):
AAAATTGAAAAAGAAAAAGAAAAG
Found at i:1644246 original size:23 final size:23
Alignment explanation
Indices: 1644198--1644247 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1644188 AAAAAATTGA
**
1644198 AAAAGAAAAAGAAAAGAAAATTG
1 AAAAGAAAAAGAAAAGAAAAGGG
*
1644221 AAAAGAAAAAG-AAAGCAAGAGGG
1 AAAAGAAAAAGAAAAG-AAAAGGG
1644244 AAAA
1 AAAA
1644248 ACGAGGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (23 bp):
AAAAGAAAAAGAAAAGAAAAGGG
Found at i:1647424 original size:38 final size:38
Alignment explanation
Indices: 1647346--1647424 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
1647336 AGTTTAAGTC
* * *
1647346 TTTAATTATGTCATAATTTGAACATCATTAAAATGAGT
1 TTTAATTATGCCATAATCTGAACATCATTAAAACGAGT
*
1647384 TTTAATTATGCCATAATCTGAACATCTTTAATAACG-GT
1 TTTAATTATGCCATAATCTGAACATCATTAA-AACGAGT
1647422 TTT
1 TTT
1647425 TAGTTATGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 33 0.92
39 3 0.08
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.43
Consensus pattern (38 bp):
TTTAATTATGCCATAATCTGAACATCATTAAAACGAGT
Found at i:1647525 original size:27 final size:26
Alignment explanation
Indices: 1647463--1647526 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
1647453 AATATATATT
* **
1647463 TTAAAT-ATGTCTTAGTTTAGACATC
1 TTAAATCATGTCTTAGTTCAGACAAA
*
1647488 TTTAATACATGTCGTTAGTTCAGACAAA
1 TTAAAT-CATGTC-TTAGTTCAGACAAA
1647516 TTAAATCATGT
1 TTAAATCATGT
1647527 TTAAACTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 5 0.16
27 10 0.32
28 16 0.52
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (26 bp):
TTAAATCATGTCTTAGTTCAGACAAA
Found at i:1656698 original size:45 final size:45
Alignment explanation
Indices: 1656635--1656815 Score: 335
Period size: 45 Copynumber: 4.0 Consensus size: 45
1656625 CTGCTAAGTA
1656635 AGAGAGGAGTGGGTGAGCTCATTGCGAACTCAATGAATAATTAGG
1 AGAGAGGAGTGGGTGAGCTCATTGCGAACTCAATGAATAATTAGG
1656680 AGAGAGGAGTGGGTGAGCTCATTGCGAACTCAATGAATAATTAGG
1 AGAGAGGAGTGGGTGAGCTCATTGCGAACTCAATGAATAATTAGG
1656725 AGAGAGGAGTGGGTGAGCTCATTGCGAACTCAATGAATAATTAGG
1 AGAGAGGAGTGGGTGAGCTCATTGCGAACTCAATGAATAATTAGG
* * *
1656770 AGAGAGGAGTGGGTGAGCTTATTGCGAACTCAGTGAATAATCAGG
1 AGAGAGGAGTGGGTGAGCTCATTGCGAACTCAATGAATAATTAGG
1656815 A
1 A
1656816 ATTAGAGGAG
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.33, C:0.11, G:0.34, T:0.22
Consensus pattern (45 bp):
AGAGAGGAGTGGGTGAGCTCATTGCGAACTCAATGAATAATTAGG
Found at i:1659073 original size:17 final size:18
Alignment explanation
Indices: 1659028--1659078 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
1659018 TTAATAAAAT
*
1659028 AAAATAAAAGATTAATATA
1 AAAATAAAACA-TAATATA
*
1659047 ATAATGAAAACATAATA-A
1 AAAAT-AAAACATAATATA
1659065 AAAATAAAACATAA
1 AAAATAAAACATAA
1659079 GTGAATATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 9 0.32
18 5 0.18
19 9 0.32
20 5 0.18
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (18 bp):
AAAATAAAACATAATATA
Found at i:1672558 original size:17 final size:17
Alignment explanation
Indices: 1672533--1672572 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1672523 TGAGGTGGAG
*
1672533 GTTGTGATGGAAAATAA
1 GTTGCGATGGAAAATAA
* *
1672550 GTTGCGATGGTAATTAA
1 GTTGCGATGGAAAATAA
1672567 GTTGCG
1 GTTGCG
1672573 GTGCTGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.33
Consensus pattern (17 bp):
GTTGCGATGGAAAATAA
Found at i:1680336 original size:62 final size:62
Alignment explanation
Indices: 1680265--1680388 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
1680255 CGAGACGCGG
1680265 TGAGTATAGTGATGATACTGATGTCATTGCAGCTAGCTTCTTTATTGATTCTGTTTCGTACT
1 TGAGTATAGTGATGATACTGATGTCATTGCAGCTAGCTTCTTTATTGATTCTGTTTCGTACT
1680327 TGAGTATAGTGATGATACTGATGTCATTGCAGCTAGCTTCTTTATTGATTCTGTTTCGTACT
1 TGAGTATAGTGATGATACTGATGTCATTGCAGCTAGCTTCTTTATTGATTCTGTTTCGTACT
1680389 ATGCTCTCAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (62 bp):
TGAGTATAGTGATGATACTGATGTCATTGCAGCTAGCTTCTTTATTGATTCTGTTTCGTACT
Found at i:1687407 original size:23 final size:23
Alignment explanation
Indices: 1687367--1687772 Score: 551
Period size: 23 Copynumber: 17.5 Consensus size: 23
1687357 TCTACCCTGT
* *
1687367 TTGGACAGCTTTTATACATCAAA
1 TTGGACAGCATTTATACACCAAA
* * *
1687390 TCGGATAGCATTTATACACCCAA
1 TTGGACAGCATTTATACACCAAA
* *
1687413 TTGGACAGCATATATATACCAAA
1 TTGGACAGCATTTATACACCAAA
*
1687436 TTGGACAGCATATATACACCAAA
1 TTGGACAGCATTTATACACCAAA
*
1687459 TTGGATAGCATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
1687482 TTGGACAGCATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
* *
1687505 TTGGACAGCATATATACACTAAA
1 TTGGACAGCATTTATACACCAAA
*
1687528 TTGGACAGCAGTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
1687551 TTGGACAGCATTTTATACACCAAA
1 TTGGACAGCA-TTTATACACCAAA
* *
1687575 TTGGACAGCATTTTATACACTATA
1 TTGGACAGCA-TTTATACACCAAA
* *
1687599 TTGGATAACATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
* * *
1687622 TTGGACAGCATATATACACTAAT
1 TTGGACAGCATTTATACACCAAA
1687645 TTGGACAGCATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
*
1687668 TTGGACAGCATTTTACACACCAAA
1 TTGGACAGCA-TTTATACACCAAA
* *
1687692 TTGGACAGCATATATACACTAAA
1 TTGGACAGCATTTATACACCAAA
*
1687715 TTGGATAGCATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
* *
1687738 GTGGACAGCATTTTATGCACCAAA
1 TTGGACAGCA-TTTATACACCAAA
1687762 TTGGACAGCAT
1 TTGGACAGCAT
1687773 ATAATATACC
Statistics
Matches: 335, Mismatches: 45, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
23 250 0.75
24 85 0.25
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (23 bp):
TTGGACAGCATTTATACACCAAA
Found at i:1687630 original size:117 final size:115
Alignment explanation
Indices: 1687367--1687772 Score: 562
Period size: 117 Copynumber: 3.5 Consensus size: 115
1687357 TCTACCCTGT
* * * * * * * *
1687367 TTGGACAGCTTTTATACATCAAATCGGATAGCATTTATACACCCAATTGGACAGCATATATATAC
1 TTGGATAGCATTTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCAT-TATACAC
* * *
1687432 CAAATTGGACAGCA-TATATACACCAAATTGGATAGCATTTATACACCAAA
65 CAAATTGGACAGCATTTTATACACCAAATTGGACAGCATTTATACACTAAA
* *
1687482 TTGGACAGCATTTATACACCAAATTGGACAGCATATATACACTAAATTGGACAGCAGTTATACAC
1 TTGGATAGCATTTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCA-TTATACAC
*
1687547 CAAATTGGACAGCATTTTATACACCAAATTGGACAGCATTTTATACACTATA
65 CAAATTGGACAGCATTTTATACACCAAATTGGACAGCA-TTTATACACTAAA
* * *
1687599 TTGGATAACATTTATACACCAAATTGGACAGCATATATACACTAATTTGGACAGCATTTATACAC
1 TTGGATAGCATTTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCA-TTATACAC
* *
1687664 CAAATTGGACAGCATTTTACACACCAAATTGGACAGCATATATACACTAAA
65 CAAATTGGACAGCATTTTATACACCAAATTGGACAGCATTTATACACTAAA
* * *
1687715 TTGGATAGCATTTATACACCAAAGTGGACAGCATTTTATGCACCAAATTGGACAGCAT
1 TTGGATAGCATTTATACACCAAATTGGACAGCA-TATATACACCAAATTGGACAGCAT
1687773 ATAATATACC
Statistics
Matches: 262, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
115 69 0.26
116 65 0.25
117 128 0.49
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (115 bp):
TTGGATAGCATTTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCATTATACACC
AAATTGGACAGCATTTTATACACCAAATTGGACAGCATTTATACACTAAA
Found at i:1688821 original size:43 final size:43
Alignment explanation
Indices: 1688751--1688864 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
1688741 ATATCGTACA
* * *
1688751 ATGCCAACGTCCTAGACGTGGTTTTACATGTAATCACATA-ATG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACA-AGATG
*
1688794 ATGCC-ACTGTCCCAGACAG-GGTCTTACATGTAAACACAAGTTG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAAACACAAGATG
1688837 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
1688865 CAATAACACA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
42 4 0.06
43 55 0.89
44 3 0.05
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACAAGATG
Found at i:1694385 original size:14 final size:14
Alignment explanation
Indices: 1694366--1694417 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
1694356 TGACATGTTC
1694366 TTCTTTCTTTTTCT
1 TTCTTTCTTTTTCT
*
1694380 TTCTTTCTTTTTAT
1 TTCTTTCTTTTTCT
* *
1694394 TTTTTTC-TTCTCT
1 TTCTTTCTTTTTCT
1694407 TTCTTCTCTTT
1 TTCTT-TCTTT
1694418 ACTCCTTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 8 0.26
14 21 0.68
15 2 0.06
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (14 bp):
TTCTTTCTTTTTCT
Found at i:1698424 original size:377 final size:377
Alignment explanation
Indices: 1697730--1698483 Score: 1508
Period size: 377 Copynumber: 2.0 Consensus size: 377
1697720 TGACATAAGT
1697730 AAACTCGCATATAACATAAGTAAAATTCGTCCTTACAAGTAAGTTCTTTAACTCAACAAGCCTTT
1 AAACTCGCATATAACATAAGTAAAATTCGTCCTTACAAGTAAGTTCTTTAACTCAACAAGCCTTT
1697795 TATTTTCTCATATTACATCTCTACTATGAACTTACCATTTTACTACATATTCTCACCTGTTTCAT
66 TATTTTCTCATATTACATCTCTACTATGAACTTACCATTTTACTACATATTCTCACCTGTTTCAT
1697860 TTGCATAATACGTAAGACATAAGCATGTACATCAACTGTAGCCACAAGCTAGTGCATTTAAACAT
131 TTGCATAATACGTAAGACATAAGCATGTACATCAACTGTAGCCACAAGCTAGTGCATTTAAACAT
1697925 AACTCTTTTAAAATCAACTACATGTTAAACCATTTCATGATAAATTACATACTTTGATTCTTACC
196 AACTCTTTTAAAATCAACTACATGTTAAACCATTTCATGATAAATTACATACTTTGATTCTTACC
1697990 ACTCTTTCATGCACGTAAACATCTTTCCATCTGGTCACTTACCATTTCAATGCATATCTTTAGAA
261 ACTCTTTCATGCACGTAAACATCTTTCCATCTGGTCACTTACCATTTCAATGCATATCTTTAGAA
1698055 CTAACATAATACAATACAACCAATAGTTTGCCACAAGCCTAAGCATCATCAA
326 CTAACATAATACAATACAACCAATAGTTTGCCACAAGCCTAAGCATCATCAA
1698107 AAACTCGCATATAACATAAGTAAAATTCGTCCTTACAAGTAAGTTCTTTAACTCAACAAGCCTTT
1 AAACTCGCATATAACATAAGTAAAATTCGTCCTTACAAGTAAGTTCTTTAACTCAACAAGCCTTT
1698172 TATTTTCTCATATTACATCTCTACTATGAACTTACCATTTTACTACATATTCTCACCTGTTTCAT
66 TATTTTCTCATATTACATCTCTACTATGAACTTACCATTTTACTACATATTCTCACCTGTTTCAT
1698237 TTGCATAATACGTAAGACATAAGCATGTACATCAACTGTAGCCACAAGCTAGTGCATTTAAACAT
131 TTGCATAATACGTAAGACATAAGCATGTACATCAACTGTAGCCACAAGCTAGTGCATTTAAACAT
1698302 AACTCTTTTAAAATCAACTACATGTTAAACCATTTCATGATAAATTACATACTTTGATTCTTACC
196 AACTCTTTTAAAATCAACTACATGTTAAACCATTTCATGATAAATTACATACTTTGATTCTTACC
1698367 ACTCTTTCATGCACGTAAACATCTTTCCATCTGGTCACTTACCATTTCAATGCATATCTTTAGAA
261 ACTCTTTCATGCACGTAAACATCTTTCCATCTGGTCACTTACCATTTCAATGCATATCTTTAGAA
1698432 CTAACATAATACAATACAACCAATAGTTTGCCACAAGCCTAAGCATCATCAA
326 CTAACATAATACAATACAACCAATAGTTTGCCACAAGCCTAAGCATCATCAA
1698484 TAACACATGT
Statistics
Matches: 377, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
377 377 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (377 bp):
AAACTCGCATATAACATAAGTAAAATTCGTCCTTACAAGTAAGTTCTTTAACTCAACAAGCCTTT
TATTTTCTCATATTACATCTCTACTATGAACTTACCATTTTACTACATATTCTCACCTGTTTCAT
TTGCATAATACGTAAGACATAAGCATGTACATCAACTGTAGCCACAAGCTAGTGCATTTAAACAT
AACTCTTTTAAAATCAACTACATGTTAAACCATTTCATGATAAATTACATACTTTGATTCTTACC
ACTCTTTCATGCACGTAAACATCTTTCCATCTGGTCACTTACCATTTCAATGCATATCTTTAGAA
CTAACATAATACAATACAACCAATAGTTTGCCACAAGCCTAAGCATCATCAA
Found at i:1710529 original size:21 final size:21
Alignment explanation
Indices: 1710503--1710546 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1710493 TAGTAGTGTC
*
1710503 TGTCGAGCATTTTTCTCCCTT
1 TGTCGAGCAGTTTTCTCCCTT
1710524 TGTCGAGCAGTTTTCTCCCTT
1 TGTCGAGCAGTTTTCTCCCTT
1710545 TG
1 TG
1710547 GGAGAATCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.27, G:0.18, T:0.45
Consensus pattern (21 bp):
TGTCGAGCAGTTTTCTCCCTT
Found at i:1718858 original size:41 final size:41
Alignment explanation
Indices: 1718814--1719132 Score: 302
Period size: 41 Copynumber: 7.8 Consensus size: 41
1718804 ACTAGAGTGT
* * ** *
1718814 AAACAGGGGCACATATGTGCTATTCAGGGGTACTGGAGTAT
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACTAAAGTAC
*
1718855 AAACAGGGGCACGTATGTGCAATTCAAGGGTAAC-AAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGT-ACTAAAGTAC
* *
1718896 AAATAGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACTAAAGTAC
* * * **
1718937 -AACTAGGTGCATGTATGTGCAATTCAAGGGTACCGAAGTAC
1 AAAC-AGGGGCACGTATGTGCAATTCAGGGGTACTAAAGTAC
* * *
1718978 AAATAGGGGCACCTATGTGCAATTCAGGGGTA-TCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACT-AAAGTAC
* * * **
1719019 AAATAGGGGCACGTATGTCCAATTTAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACTAAAGTAC
** * * * * *
1719060 AATTATGGGCACCTATATGCAATTCAGGGGTAACAAAAATAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGT-ACTAAAGTAC
* * *
1719102 AAATAGGGGCATGTATGTGCAATTCAAGGGT
1 AAACAGGGGCACGTATGTGCAATTCAGGGGT
1719133 TAACTAACTA
Statistics
Matches: 233, Mismatches: 38, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
40 4 0.02
41 193 0.83
42 36 0.15
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (41 bp):
AAACAGGGGCACGTATGTGCAATTCAGGGGTACTAAAGTAC
Found at i:1718953 original size:82 final size:82
Alignment explanation
Indices: 1718818--1719132 Score: 405
Period size: 82 Copynumber: 3.8 Consensus size: 82
1718808 GAGTGTAAAC
* * *** * *
1718818 AGGGGCACATATGTGCTATTCAGGGGTACTGGAGTATAAACAGGGGCACGTATGTGCAATTCAAG
1 AGGGGCACCTATGTGCAATTCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATTCAAG
* *
1718883 GGTAACAAAGTACAAAT
66 GGTACCGAAGTACAAAT
* * * *
1718900 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAACTAGGTGCATGTATGTGCAATTCAAG
1 AGGGGCACCTATGTGCAATTCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATTCAAG
1718965 GGTACCGAAGTACAAAT
66 GGTACCGAAGTACAAAT
* * * * *
1718982 AGGGGCACCTATGTGCAATTCAGGGGTATCGAAGTACAAATAGGGGCACGTATGTCCAATTTAGG
1 AGGGGCACCTATGTGCAATTCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATTCAAG
*
1719047 GGTACCGAAGTACAATT
66 GGTACCGAAGTACAAAT
* * * * *
1719064 ATGGGCACCTATATGCAATTCAGGGGTAACAAAAATACAAATAGGGGCATGTATGTGCAATTCAA
1 AGGGGCACCTATGTGCAATTCAGGGGT-ACCAAAGTACAAATAGGGGCACGTATGTGCAATTCAA
1719129 GGGT
65 GGGT
1719133 TAACTAACTA
Statistics
Matches: 200, Mismatches: 32, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
82 167 0.83
83 33 0.17
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (82 bp):
AGGGGCACCTATGTGCAATTCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATTCAAG
GGTACCGAAGTACAAAT
Found at i:1719017 original size:123 final size:123
Alignment explanation
Indices: 1718820--1719132 Score: 403
Period size: 123 Copynumber: 2.5 Consensus size: 123
1718810 GTGTAAACAG
* * * * * *
1718820 GGGCACATATGTGCTATTCAGGGGTACTGGAGTATAAACAGGGGCACGTATGTGCAATTCAAGGG
1 GGGCACCTATGTGCAATTCAGGGGTACAGAAGTACAAATAGGGGCACGTATGTGCAATTCAAGGG
*
1718885 TAACAAAGTACAAATAGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAACTA-
66 TAACAAAGTACAAATAGGGGCACGTATGTCCAATTCAGGGGTACCAAAGTACAACTAT
** * * * *
1718942 GGTGCATGTATGTGCAATTCAAGGGTACCGAAGTACAAATAGGGGCACCTATGTGCAATTCAGGG
1 GG-GCACCTATGTGCAATTCAGGGGTACAGAAGTACAAATAGGGGCACGTATGTGCAATTCAAGG
* * * * *
1719007 GTATCGAAGTACAAATAGGGGCACGTATGTCCAATTTAGGGGTACCGAAGTACAATTAT
65 GTAACAAAGTACAAATAGGGGCACGTATGTCCAATTCAGGGGTACCAAAGTACAACTAT
* * * *
1719066 GGGCACCTATATGCAATTCAGGGGTAACAAAAATACAAATAGGGGCATGTATGTGCAATTCAAGG
1 GGGCACCTATGTGCAATTCAGGGGT-ACAGAAGTACAAATAGGGGCACGTATGTGCAATTCAAGG
1719131 GT
65 GT
1719133 TAACTAACTA
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
122 2 0.01
123 123 0.76
124 37 0.23
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (123 bp):
GGGCACCTATGTGCAATTCAGGGGTACAGAAGTACAAATAGGGGCACGTATGTGCAATTCAAGGG
TAACAAAGTACAAATAGGGGCACGTATGTCCAATTCAGGGGTACCAAAGTACAACTAT
Found at i:1719062 original size:21 final size:21
Alignment explanation
Indices: 1718964--1719063 Score: 71
Period size: 21 Copynumber: 4.9 Consensus size: 21
1718954 TGCAATTCAA
*
1718964 GGGTACCGAAGTACAA-ATAG
1 GGGTACCGAAGTACAATTTAG
* * * * *
1718984 GGGCACCTATGTGCAATTCAG
1 GGGTACCGAAGTACAATTTAG
* *
1719005 GGGTATCGAAGTACAA-ATAG
1 GGGTACCGAAGTACAATTTAG
* * *
1719025 GGGCA-CGTATGTCCAATTTAG
1 GGGTACCG-AAGTACAATTTAG
1719046 GGGTACCGAAGTACAATT
1 GGGTACCGAAGTACAATT
1719064 ATGGGCACCT
Statistics
Matches: 56, Mismatches: 20, Indels: 7
0.67 0.24 0.08
Matches are distributed among these distances:
19 2 0.04
20 24 0.43
21 28 0.50
22 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (21 bp):
GGGTACCGAAGTACAATTTAG
Found at i:1723919 original size:50 final size:50
Alignment explanation
Indices: 1723865--1724003 Score: 188
Period size: 50 Copynumber: 2.8 Consensus size: 50
1723855 TTCTCATATA
* * * * *
1723865 GGTGCCCATGCCATGTCCCAAATATGGTCTTACGGGGGACCTCCCATCTC
1 GGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCCCATCTC
* * *
1723915 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTT
1 GGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCCCATCTC
* *
1723965 AGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 GGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGA
1724004 TCTCATCCTC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 80 1.00
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.24
Consensus pattern (50 bp):
GGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCCCATCTC
Found at i:1725041 original size:8 final size:8
Alignment explanation
Indices: 1725028--1725052 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1725018 GTAGAACTCA
1725028 ACTTTTAC
1 ACTTTTAC
1725036 ACTTTTAC
1 ACTTTTAC
1725044 ACTTTTAC
1 ACTTTTAC
1725052 A
1 A
1725053 ATTTAGTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (8 bp):
ACTTTTAC
Found at i:1726052 original size:4 final size:4
Alignment explanation
Indices: 1726043--1726871 Score: 1658
Period size: 4 Copynumber: 207.2 Consensus size: 4
1726033 TTATTAAATC
1726043 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726091 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726139 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726187 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726235 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726283 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726331 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726379 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726427 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726475 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726523 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726571 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726619 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726667 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726715 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726763 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726811 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1726859 TGTA TGTA TGTA T
1 TGTA TGTA TGTA T
1726872 ATTTTATTTT
Statistics
Matches: 825, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 825 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:1727057 original size:10 final size:10
Alignment explanation
Indices: 1727042--1727070 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1727032 CGAATAATTA
1727042 TATATGTATC
1 TATATGTATC
1727052 TATATGTATC
1 TATATGTATC
1727062 TATATGTAT
1 TATATGTAT
1727071 ATGTTCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (10 bp):
TATATGTATC
Found at i:1727852 original size:42 final size:42
Alignment explanation
Indices: 1727805--1727978 Score: 233
Period size: 42 Copynumber: 4.2 Consensus size: 42
1727795 TTAGTGCCTG
*
1727805 GCAGGCTTAGTGCCAGTGAAACAATATCAGACTTTACGTCTA
1 GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTA
* * * *
1727847 GCAGGCTTAATGTCGGTGAAATAATTTCAGACTTTACGTCTA
1 GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTA
*
1727889 GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACATCTA
1 GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTA
** * * * *
1727931 GTTGGCTTAATGCCAGTGAAAC-ATTTTAGACTATATGTCTA
1 GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTA
1727972 GCAGGCT
1 GCAGGCT
1727979 AACTGTCGAT
Statistics
Matches: 113, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 19 0.17
42 94 0.83
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (42 bp):
GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTA
Found at i:1734641 original size:13 final size:13
Alignment explanation
Indices: 1734625--1734659 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1734615 ACAACTCTAT
1734625 AAATATTTAATAA
1 AAATATTTAATAA
1734638 AAATATTTAATAA
1 AAATATTTAATAA
1734651 AAATATTTA
1 AAATATTTA
1734660 TGGGCTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATATTTAATAA
Found at i:1741216 original size:2 final size:2
Alignment explanation
Indices: 1741209--1741243 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1741199 TACGCTAGAA
*
1741209 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1741244 GATCAGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1744194 original size:3 final size:3
Alignment explanation
Indices: 1744186--1744257 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
1744176 CTTTACAGCC
*
1744186 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1744234 ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
1744258 TTCTNNNNNN
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1746706 original size:9 final size:9
Alignment explanation
Indices: 1746688--1746761 Score: 67
Period size: 9 Copynumber: 8.2 Consensus size: 9
1746678 CTCTACAGCC
*
1746688 ATTATCATT
1 ATTATTATT
1746697 ATTATTATT
1 ATTATTATT
*
1746706 ATTATTATA
1 ATTATTATT
*
1746715 ATTATTCTT
1 ATTATTATT
*
1746724 ATTCTTATT
1 ATTATTATT
* * *
1746733 CTTAATCTT
1 ATTATTATT
*
1746742 ATTCTTATT
1 ATTATTATT
*
1746751 ATTCTTATT
1 ATTATTATT
1746760 AT
1 AT
1746762 CTTCTTTGAA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTATTATT
Found at i:1746711 original size:6 final size:6
Alignment explanation
Indices: 1746688--1746761 Score: 67
Period size: 6 Copynumber: 12.3 Consensus size: 6
1746678 CTCTACAGCC
* * * * *
1746688 ATTATC ATTATT ATTATT ATTATT ATAATT ATTCTT ATTCTT ATTCTT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* * * *
1746736 AATCTT ATTCTT ATTATT CTTATT AT
1 ATTATT ATTATT ATTATT ATTATT AT
1746762 CTTCTTTGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (6 bp):
ATTATT
Found at i:1755942 original size:9 final size:9
Alignment explanation
Indices: 1755928--1755976 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
1755918 TTTGGTTAAA
1755928 AATTAACCG
1 AATTAACCG
1755937 AATTAACCG
1 AATTAACCG
*
1755946 AATTAATCG
1 AATTAACCG
*
1755955 AATTACCCG
1 AATTAACCG
*
1755964 AATTACCCG
1 AATTAACCG
1755973 AATT
1 AATT
1755977 GAATCACTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:1755959 original size:27 final size:28
Alignment explanation
Indices: 1755928--1755981 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
1755918 TTTGGTTAAA
1755928 AATTAACCGAATTAACCGAATT-AATCG
1 AATTAACCGAATTAACCGAATTGAATCG
* *
1755955 AATTACCCGAATTACCCGAATTGAATC
1 AATTAACCGAATTAACCGAATTGAATC
1755982 ACTACATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (28 bp):
AATTAACCGAATTAACCGAATTGAATCG
Found at i:1756006 original size:17 final size:17
Alignment explanation
Indices: 1755984--1756047 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
1755974 ATTGAATCAC
1755984 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
1756001 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
1756021 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
1756038 TACATAATTA
1 TACATAATTA
1756048 TTGAAATTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
17 18 0.51
18 4 0.11
19 5 0.14
20 8 0.23
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:1756273 original size:39 final size:39
Alignment explanation
Indices: 1756181--1756297 Score: 202
Period size: 38 Copynumber: 3.0 Consensus size: 39
1756171 TACTAAGAGT
*
1756181 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1756219 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTT-GGGTAATTGGG
1756259 T-GACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1756297 T
1 T
1756298 TGGGTAATTG
Statistics
Matches: 76, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
38 39 0.51
39 26 0.34
40 11 0.14
ACGTcount: A:0.17, C:0.03, G:0.30, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:1756296 original size:13 final size:13
Alignment explanation
Indices: 1756278--1756315 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1756268 TTTTAGTTTT
1756278 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
1756291 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
*
1756304 ATTGAGTTGGGT
1 ATTGGGTTGGGT
1756316 TGGATAATTT
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:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:1758486 original size:26 final size:26
Alignment explanation
Indices: 1758446--1758495 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1758436 AAAATATTAT
* *
1758446 CCAAAGTTCCTAAATCAAAATCCAAA
1 CCAAAGTCCCAAAATCAAAATCCAAA
* *
1758472 CCAAAGTCCCAAAATTAAAGTCCA
1 CCAAAGTCCCAAAATCAAAATCCA
1758496 TATAGCATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.48, C:0.28, G:0.06, T:0.18
Consensus pattern (26 bp):
CCAAAGTCCCAAAATCAAAATCCAAA
Found at i:1765335 original size:3 final size:3
Alignment explanation
Indices: 1765327--1765361 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1765317 AGCTTCAATA
*
1765327 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT AAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1765362 AGTCGATGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:1766858 original size:54 final size:54
Alignment explanation
Indices: 1766768--1766928 Score: 155
Period size: 54 Copynumber: 3.0 Consensus size: 54
1766758 TGAACAAAGG
* * ** * *
1766768 GACACACAGCCATGTCCCAGCCCGTGT-CTTAAACCGTGTAACTCACTGATTTAG-
1 GACACACAACCATGTCGCAAACCGTGTGC-TAGACCGTGTAACTCACTGACTT-GC
* * * * **
1766822 GTCACACGATCGTGTCGCAAACCGTGTGCTAGACCGTGTAACTCTTTGACTTGC
1 GACACACAACCATGTCGCAAACCGTGTGCTAGACCGTGTAACTCACTGACTTGC
** *
1766876 GACACACAACCATGTCGCAGGCCGTGTGCTAGACCATGTAACTCACTGACTTG
1 GACACACAACCATGTCGCAAACCGTGTGCTAGACCGTGTAACTCACTGACTTG
1766929 AAATAATAAG
Statistics
Matches: 84, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
53 1 0.01
54 82 0.98
55 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (54 bp):
GACACACAACCATGTCGCAAACCGTGTGCTAGACCGTGTAACTCACTGACTTGC
Found at i:1769513 original size:15 final size:15
Alignment explanation
Indices: 1769493--1769523 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1769483 AAACCTATAG
*
1769493 AAATTAAATACAACT
1 AAATTAAATAAAACT
1769508 AAATTAAATAAAACT
1 AAATTAAATAAAACT
1769523 A
1 A
1769524 GTGGAATTAG
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:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATTAAATAAAACT
Found at i:1778012 original size:36 final size:37
Alignment explanation
Indices: 1777931--1778013 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 37
1777921 ACATTATAAA
* * *
1777931 CACTTTCACATGGCATGAATAATATACCCACATATAT
1 CACTTTCACATGGCATGAACAACACACCCACATATAT
* * *
1777968 -ACTGTCACATGGGATGAACAACACACCCTCATAT-T
1 CACTTTCACATGGCATGAACAACACACCCACATATAT
1778003 CACTTTCACAT
1 CACTTTCACAT
1778014 CAATCATCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 1 0.03
36 37 0.97
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (37 bp):
CACTTTCACATGGCATGAACAACACACCCACATATAT
Found at i:1782250 original size:13 final size:11
Alignment explanation
Indices: 1782218--1782247 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1782208 TTGATTAATC
1782218 AAATATATTAA
1 AAATATATTAA
1782229 AAATATATTAA
1 AAATATATTAA
1782240 AAATATAT
1 AAATATAT
1782248 ATTGAGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATATATTAA
Found at i:1782456 original size:17 final size:17
Alignment explanation
Indices: 1782434--1782480 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1782424 NNNNNNNAGT
*
1782434 TATTAAAATAATATTTA
1 TATTAAAATAATATTAA
1782451 TATTAATAATAA-ATTAA
1 TATTAA-AATAATATTAA
*
1782468 TAATATAAATAAT
1 TATTA-AAATAAT
1782481 TAAAATGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATTAAAATAATATTAA
Found at i:1783220 original size:229 final size:230
Alignment explanation
Indices: 1782819--1783281 Score: 894
Period size: 229 Copynumber: 2.0 Consensus size: 230
1782809 AACCGATTTG
1782819 AACACATTAAAATTGAATCGATTGATTTTCTTTAATAAAATCAATAAAATCAAACTTACATTAAT
1 AACACATTAAAATTGAATCGATTGATTTTCTTTAATAAAATCAATAAAATCAAACTTACATTAAT
1782884 TTGTTTAGTTTTTCAGTTAAACAACTCAAATTTTAAATAATTAAAATATAAAGATATTTATTATA
66 TTGTTTAGTTTTTCAGTTAAACAACTCAAATTTTAAATAATTAAAATATAAAGATATTTATTATA
1782949 TTTTTTTAAAATAATTAAAAAGTAATATGATATAAAGTCCGTTTCTTTTAGTAAATTCGGTTTTG
131 TTTTTTTAAAATAATTAAAAAGTAATATGATATAAAGTCCGTTTCTTTTAGTAAATTCGGTTTTG
*
1783014 TGATTTAAAAATTAGAAAACAACTAATAACACAA-
196 TGATTTAAAAATTAGAAAACAACTAATAAAACAAT
1783048 AACACATTAAAATTGAATCGATTGATTTTCTTTAATAAAATCAATAAAATCAAACTTACATTAAT
1 AACACATTAAAATTGAATCGATTGATTTTCTTTAATAAAATCAATAAAATCAAACTTACATTAAT
1783113 TTGTTTAGTTTTTCAGTTAAACAACTCAAATTTTAAATAATTAAAATATAAAGATATTTATTATA
66 TTGTTTAGTTTTTCAGTTAAACAACTCAAATTTTAAATAATTAAAATATAAAGATATTTATTATA
1783178 TTTTTTTAAAATTAATTAAAAA-TAATATGATATAAAGTCCGTTTCTTTTAGTAAATTCGGTTTT
131 TTTTTTTAAAA-TAATTAAAAAGTAATATGATATAAAGTCCGTTTCTTTTAGTAAATTCGGTTTT
1783242 GTGATTTAAAAATTAGAAAACAACTAATAAAACAAT
195 GTGATTTAAAAATTAGAAAACAACTAATAAAACAAT
1783278 AACA
1 AACA
1783282 GATGACAAAT
Statistics
Matches: 231, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
229 217 0.94
230 14 0.06
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (230 bp):
AACACATTAAAATTGAATCGATTGATTTTCTTTAATAAAATCAATAAAATCAAACTTACATTAAT
TTGTTTAGTTTTTCAGTTAAACAACTCAAATTTTAAATAATTAAAATATAAAGATATTTATTATA
TTTTTTTAAAATAATTAAAAAGTAATATGATATAAAGTCCGTTTCTTTTAGTAAATTCGGTTTTG
TGATTTAAAAATTAGAAAACAACTAATAAAACAAT
Found at i:1784953 original size:22 final size:22
Alignment explanation
Indices: 1784928--1784969 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1784918 TTGAATTTAA
1784928 AATTTATTACACA-TATTAATCC
1 AATTTATTA-ACATTATTAATCC
1784950 AATTTATTAACATTATTAAT
1 AATTTATTAACATTATTAAT
1784970 TTTTTAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTATTAACATTATTAATCC
Found at i:1796592 original size:22 final size:22
Alignment explanation
Indices: 1796567--1796610 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1796557 ACAAGTTCCC
*
1796567 ATGGAGACTTAGGTTGAGTTAA
1 ATGGACACTTAGGTTGAGTTAA
*
1796589 ATGGACACTTCGGTTGAGTTAA
1 ATGGACACTTAGGTTGAGTTAA
1796611 GAAGAATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (22 bp):
ATGGACACTTAGGTTGAGTTAA
Found at i:1797625 original size:32 final size:32
Alignment explanation
Indices: 1797586--1797662 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
1797576 TAGATAGGAA
1797586 AGCCTTTGTGGCAAGTACTGGATATAAATG-AT
1 AGCCTTTGTGGCAAGTACTGGATATAAA-GAAT
* *
1797618 AGTCTTTGTGGCCAGTACTGGATATAAAGAAT
1 AGCCTTTGTGGCAAGTACTGGATATAAAGAAT
*
1797650 AGCCTTTATGGCA
1 AGCCTTTGTGGCA
1797663 CAACTCTGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (32 bp):
AGCCTTTGTGGCAAGTACTGGATATAAAGAAT
Found at i:1797686 original size:61 final size:61
Alignment explanation
Indices: 1797621--1797751 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 61
1797611 AAATGATAGT
** * * * * *
1797621 CTTTGTGGCCAGTACTGGATATAAAGAATAGCCTTTATGGCACAACTCTGGACAAGAAAGC
1 CTTTGTGGCCAGTACTAAATATAAAGAACAACCTTTATGGAAAAACTCTAGACAAGAAAGC
* * ** * *
1797682 CTTTGTGGCGAGTACTAAATGTAAAGGCCAACCTTTGTGGAAAAACTCTAGACAAGATAGC
1 CTTTGTGGCCAGTACTAAATATAAAGAACAACCTTTATGGAAAAACTCTAGACAAGAAAGC
1797743 CTTTGTGGC
1 CTTTGTGGC
1797752 AGCCTATGTT
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (61 bp):
CTTTGTGGCCAGTACTAAATATAAAGAACAACCTTTATGGAAAAACTCTAGACAAGAAAGC
Found at i:1797718 original size:93 final size:93
Alignment explanation
Indices: 1797519--1797721 Score: 219
Period size: 93 Copynumber: 2.2 Consensus size: 93
1797509 TCACTAGGAG
* ** * * * * *
1797519 AAGGAAAACCTTTGTGGTGAGTACCT-AATATAAAGGATAGCCTTTGTGGAACAACTCTAGATAG
1 AAGGACAACCTTTGTGGCCAGTA-CTGGATATAAAGAATAGCCTTTATGGAACAACTCTAGACAA
**
1797583 GAAAGCCTTTGTGGCAAGTACTGGATATA
65 GAAAGCCTTTGTGGCAAGTACTAAATATA
* * ** * *
1797612 AATGATAGTCTTTGTGGCCAGTACTGGATATAAAGAATAGCCTTTATGGCACAACTCTGGACAAG
1 AAGGACAACCTTTGTGGCCAGTACTGGATATAAAGAATAGCCTTTATGGAACAACTCTAGACAAG
* *
1797677 AAAGCCTTTGTGGCGAGTACTAAATGTA
66 AAAGCCTTTGTGGCAAGTACTAAATATA
*
1797705 AAGGCCAACCTTTGTGG
1 AAGGACAACCTTTGTGG
1797722 AAAAACTCTA
Statistics
Matches: 87, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
92 2 0.02
93 85 0.98
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (93 bp):
AAGGACAACCTTTGTGGCCAGTACTGGATATAAAGAATAGCCTTTATGGAACAACTCTAGACAAG
AAAGCCTTTGTGGCAAGTACTAAATATA
Found at i:1805432 original size:43 final size:41
Alignment explanation
Indices: 1805384--1805482 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
1805374 TCCTAGATAT
** * *
1805384 GGTCTTACATGTTATAATATTTCGATGCCACTGTCCCAGACAG
1 GGTCTTACATGAAATAATATAT-GATG-CAATGTCCCAGACAG
* *
1805427 GGTCTTACACT-AAATCATATATGATGCAATGTCCCAGACAT
1 GGTCTTACA-TGAAATAATATATGATGCAATGTCCCAGACAG
1805468 GGTCTTACATGAAAT
1 GGTCTTACATGAAAT
1805483 CACACCTCAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
40 1 0.02
41 26 0.54
42 4 0.08
43 16 0.33
44 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (41 bp):
GGTCTTACATGAAATAATATATGATGCAATGTCCCAGACAG
Found at i:1823791 original size:6 final size:6
Alignment explanation
Indices: 1823737--1823782 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
1823727 CCTTTCGAGC
* *
1823737 TTTTGT TTTTGT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1823783 TTTCATTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.11, C:0.00, G:0.04, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:1828035 original size:10 final size:10
Alignment explanation
Indices: 1828012--1828057 Score: 74
Period size: 10 Copynumber: 4.5 Consensus size: 10
1828002 TATATTCCGA
1828012 CACATATCAAT
1 CACATAT-AAT
1828023 CACATATAAT
1 CACATATAAT
1828033 CACATATAAT
1 CACATATAAT
*
1828043 TACATATAAT
1 CACATATAAT
1828053 CACAT
1 CACAT
1828058 TTAGTCACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (10 bp):
CACATATAAT
Found at i:1832531 original size:9 final size:9
Alignment explanation
Indices: 1832513--1832597 Score: 91
Period size: 9 Copynumber: 9.4 Consensus size: 9
1832503 GTAGTGATTC
*
1832513 AATTTGGTT
1 AATTCGGTT
*
1832522 AATTCTGTT
1 AATTCGGTT
1832531 AATTCTGG-T
1 AATTC-GGTT
*
1832540 AATTCAGTT
1 AATTCGGTT
*
1832549 AATTCGGGT
1 AATTCGGTT
* *
1832558 AATCCGATT
1 AATTCGGTT
1832567 AATTCGGTT
1 AATTCGGTT
*
1832576 AATTCGGGT
1 AATTCGGTT
1832585 AATTCGGTT
1 AATTCGGTT
1832594 AATT
1 AATT
1832598 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
8 1 0.02
9 59 0.97
10 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:1836312 original size:15 final size:15
Alignment explanation
Indices: 1836292--1836322 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1836282 AAGTTTAATG
1836292 AAGAATTAAACTCAA
1 AAGAATTAAACTCAA
*
1836307 AAGAATTTAACTCAA
1 AAGAATTAAACTCAA
1836322 A
1 A
1836323 CTAGAACTAA
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:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (15 bp):
AAGAATTAAACTCAA
Found at i:1853600 original size:104 final size:103
Alignment explanation
Indices: 1853463--1853653 Score: 301
Period size: 103 Copynumber: 1.8 Consensus size: 103
1853453 ATGCAATGCC
* * *
1853463 TACACCACTTTATAATTTAGGGGATGTAGGACTTAGATTAAGGGCTACTTAGTATTTCTTTTGAT
1 TACACCACTTTATAATTTAGGGGATGGAGGACTTAGATTAA-GGCTACTTAGCATTGCTTTTGAT
1853528 AAGTGATTTTGAGAAGAATGTTTCTTAAAAGTTAGTGCT
65 AAGTGATTTTGAGAAGAATGTTTCTTAAAAGTTAGTGCT
* * * *
1853567 TACACCACTTTATAATTTAGTGGATGGATGACTTAGATTAAGGTTAGTTAGCATTGCTTTTGATA
1 TACACCACTTTATAATTTAGGGGATGGAGGACTTAGATTAAGGCTACTTAGCATTGCTTTTGATA
*
1853632 GGTGATTTTGAGAAGAATGTTT
66 AGTGATTTTGAGAAGAATGTTT
1853654 TTGTAAAGTT
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
103 41 0.52
104 38 0.48
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (103 bp):
TACACCACTTTATAATTTAGGGGATGGAGGACTTAGATTAAGGCTACTTAGCATTGCTTTTGATA
AGTGATTTTGAGAAGAATGTTTCTTAAAAGTTAGTGCT
Found at i:1857502 original size:13 final size:13
Alignment explanation
Indices: 1857484--1857536 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
1857474 AATGGCAGCG
*
1857484 GAAAAATAGAGAA
1 GAAAAATAAAGAA
1857497 GAAAAATAAAGAA
1 GAAAAATAAAGAA
* * *
1857510 TAAAGAGAAAGAA
1 GAAAAATAAAGAA
*
1857523 CGAAAAAAAAAGAA
1 -GAAAAATAAAGAA
1857537 ACGTGAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 22 0.69
14 10 0.31
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.06
Consensus pattern (13 bp):
GAAAAATAAAGAA
Found at i:1865103 original size:6 final size:6
Alignment explanation
Indices: 1865092--1865119 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1865082 TTCAATTCCA
1865092 TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1865120 CGCTCTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTGT
Found at i:1866675 original size:190 final size:190
Alignment explanation
Indices: 1866348--1866718 Score: 564
Period size: 190 Copynumber: 2.0 Consensus size: 190
1866338 CTATACTTGC
* *
1866348 CATTATATCAAAAGTTATTTTACTAATTATACCAAGGTGAGCTAAAGGATAGTGTGATCTTGCTC
1 CATTATACCAAAAGTAATTTTACTAATTATACCAAGGTGAGCTAAAGGATAGTGTGATCTTGCTC
* *
1866413 CGACCCGCTTCCAACCTTTACGAGCTTCCGAGTACTATAAAACAGAGGAAAGAAAAAACGAGTAA
66 CAACCCGCTTCCAACCTTTACGAGCTTCCGAGTACTATAAAACAAAGGAAAGAAAAAACGAGTAA
* *
1866478 ACATTTAATGCTTAATGAGTTTGTATAACAG-AAATCAACTTACCATTCATACCGAGTAAG
131 ACATTTAATGCTTAATAAGTTCGTAT-ACAGAAAATCAACTTACCATTCATACCGAGTAAG
*
1866538 CATTATACCAAAAGTAATTTTACTAATTATACCAAGGTGAGCTGAAGGATAGTGTGATCTTGCTC
1 CATTATACCAAAAGTAATTTTACTAATTATACCAAGGTGAGCTAAAGGATAGTGTGATCTTGCTC
** * * **
1866603 CAACCCGCTTTTAACCTTTACGAGCTTCTGAGTACTATAAAATAAAGGAAAGAAAAATTGAGTAA
66 CAACCCGCTTCCAACCTTTACGAGCTTCCGAGTACTATAAAACAAAGGAAAGAAAAAACGAGTAA
* * ** *
1866668 GCATTTAATGCTTAGTAAGTTCGTATATTGAAAATTAACTTACCATTCATA
131 ACATTTAATGCTTAATAAGTTCGTATACAGAAAATCAACTTACCATTCATA
1866719 TTCATCTAAA
Statistics
Matches: 162, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
189 2 0.01
190 160 0.99
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (190 bp):
CATTATACCAAAAGTAATTTTACTAATTATACCAAGGTGAGCTAAAGGATAGTGTGATCTTGCTC
CAACCCGCTTCCAACCTTTACGAGCTTCCGAGTACTATAAAACAAAGGAAAGAAAAAACGAGTAA
ACATTTAATGCTTAATAAGTTCGTATACAGAAAATCAACTTACCATTCATACCGAGTAAG
Found at i:1880655 original size:17 final size:19
Alignment explanation
Indices: 1880633--1880667 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1880623 GTTCTGAATG
1880633 CAATC-TTCA-TCACATCA
1 CAATCTTTCACTCACATCA
1880650 CAATCTTTCACTCACATC
1 CAATCTTTCACTCACATC
1880668 TGATAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.31
Consensus pattern (19 bp):
CAATCTTTCACTCACATCA
Found at i:1883974 original size:14 final size:14
Alignment explanation
Indices: 1883955--1883981 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1883945 CAAAACATCT
1883955 AAAACTACTGATCA
1 AAAACTACTGATCA
1883969 AAAACTACTGATC
1 AAAACTACTGATC
1883982 TTCGACGAGC
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:0.22, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAACTACTGATCA
Found at i:1884859 original size:25 final size:26
Alignment explanation
Indices: 1884818--1884868 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1884808 AAATATATAA
1884818 ATTCAATTCACTAAATACTTC-TATT
1 ATTCAATTCACTAAATACTTCATATT
* * *
1884843 ATTCAATTCAGTCAATATTTCATATT
1 ATTCAATTCACTAAATACTTCATATT
1884869 TTTGCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTCAATTCACTAAATACTTCATATT
Found at i:1887323 original size:19 final size:20
Alignment explanation
Indices: 1887286--1887328 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1887276 ATATATGAAA
1887286 ATTTAGAATTTTTATAAA-T
1 ATTTAGAATTTTTATAAATT
1887305 ATTTAGAATTTTTGA-AAATT
1 ATTTAGAATTTTT-ATAAATT
1887325 ATTT
1 ATTT
1887329 TGATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
ATTTAGAATTTTTATAAATT
Found at i:1888490 original size:19 final size:18
Alignment explanation
Indices: 1888466--1888502 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
1888456 AATCGGTCAG
1888466 ATTAAAAAATTATTAAAAA
1 ATTAAAAAATT-TTAAAAA
1888485 ATTAAAAAATTTTAAAAA
1 ATTAAAAAATTTTAAAAA
1888503 TCCTGATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTAAAAAATTTTAAAAA
Found at i:1888825 original size:22 final size:20
Alignment explanation
Indices: 1888784--1888828 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
1888774 TCATCAAAAC
1888784 TCATCTCATTTGATAATTCT
1 TCATCTCATTTGATAATTCT
*
1888804 TCATCTTCATTTGGGTAATTCT
1 TCATC-TCATTT-GATAATTCT
1888826 TCA
1 TCA
1888829 CCATCAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 6 0.27
22 11 0.50
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (20 bp):
TCATCTCATTTGATAATTCT
Found at i:1903075 original size:27 final size:27
Alignment explanation
Indices: 1903044--1903109 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1903034 ATCGGGACAG
* *
1903044 TAAACACGGGGTAGTCCATTGGGAAAA
1 TAAACATGGGGTAATCCATTGGGAAAA
* *
1903071 TAAACATGGGGTAATTCATTGGGATAA
1 TAAACATGGGGTAATCCATTGGGAAAA
*
1903098 TAATCATGGGGT
1 TAAACATGGGGT
1903110 TACTTTGGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.26
Consensus pattern (27 bp):
TAAACATGGGGTAATCCATTGGGAAAA
Found at i:1912624 original size:13 final size:13
Alignment explanation
Indices: 1912608--1912639 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1912598 ACACATATTT
1912608 AAAACATAACTTG
1 AAAACATAACTTG
*
1912621 AAAACATATCTTG
1 AAAACATAACTTG
1912634 AAAACA
1 AAAACA
1912640 GAGTATCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.22
Consensus pattern (13 bp):
AAAACATAACTTG
Found at i:1914977 original size:52 final size:50
Alignment explanation
Indices: 1914913--1915029 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 50
1914903 AAATGAACAA
* *
1914913 AAGTTACTTAATGCAAGAC-TTAATTTAATGATGTAGACTTAAACTAACATGG
1 AAGTTACATAATGCAAGACATT-ATTT-ATGATGCAGACTTAAACTAACAT-G
* * * * * *
1914965 GAGTTACATAATGCATGTCATTATTTATGATGCATACTTTAACTAGCATG
1 AAGTTACATAATGCAAGACATTATTTATGATGCAGACTTAAACTAACATG
1915015 AAGTTACATAATGCA
1 AAGTTACATAATGCA
1915030 TAACTTTATT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
50 15 0.27
51 19 0.35
52 19 0.35
53 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (50 bp):
AAGTTACATAATGCAAGACATTATTTATGATGCAGACTTAAACTAACATG
Found at i:1915039 original size:50 final size:52
Alignment explanation
Indices: 1914913--1915044 Score: 135
Period size: 50 Copynumber: 2.6 Consensus size: 52
1914903 AAATGAACAA
* * *
1914913 AAGTTACTTAATGCA-AGACTTAATTTAATGATGTAGACTTAAACTAACATGG
1 AAGTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGG
* ** * * * *
1914965 GAGTTACATAATGCATGTCATTATTT-ATGATGCATACTTTAACTAGCAT-G
1 AAGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGG
*
1915015 AAGTTACATAATGCATAACTTTATTAAATG
1 AAGTTACATAATGCATAACTTTATTTAATG
1915045 TAAAACACAC
Statistics
Matches: 63, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
50 22 0.35
51 22 0.35
52 19 0.30
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (52 bp):
AAGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGG
Found at i:1917750 original size:18 final size:17
Alignment explanation
Indices: 1917716--1917750 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1917706 TTCCAACACT
*
1917716 TTTTTTTTCAATTTTCA
1 TTTTTTTTCAATCTTCA
1917733 TTTTTTTTCAATACTTCA
1 TTTTTTTTCAAT-CTTCA
1917751 AATTTCAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTTTTCAATCTTCA
Found at i:1917805 original size:11 final size:12
Alignment explanation
Indices: 1917780--1917804 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1917770 CGAATACAAC
1917780 TTGAATTTTTTT
1 TTGAATTTTTTT
1917792 TTGAATTTTTTT
1 TTGAATTTTTTT
1917804 T
1 T
1917805 GCACTTCATG
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTGAATTTTTTT
Found at i:1933024 original size:721 final size:721
Alignment explanation
Indices: 1931642--1933085 Score: 2888
Period size: 721 Copynumber: 2.0 Consensus size: 721
1931632 AAGAGGAGGA
1931642 CGTCGTTTGTGTTGAAGTTGTGAACGAGATGGCCGAGGAAAAAAATACTGAGATAGAAGCTACTG
1 CGTCGTTTGTGTTGAAGTTGTGAACGAGATGGCCGAGGAAAAAAATACTGAGATAGAAGCTACTG
1931707 AGAAAGAATCTGTTGAGGATATTGTCAATGCATTCAAGCTTATGGATACAACTAAAGATGATTTG
66 AGAAAGAATCTGTTGAGGATATTGTCAATGCATTCAAGCTTATGGATACAACTAAAGATGATTTG
1931772 GAGCTAGACCGGAGGAAGCTGCAGAGGTAACAAGTGAGGAGCACCACAATTCGTTGGCTATAGTG
131 GAGCTAGACCGGAGGAAGCTGCAGAGGTAACAAGTGAGGAGCACCACAATTCGTTGGCTATAGTG
1931837 GTCTATATTAGACCACTCAAGGTGACCCTTCCTACACAAAAAGTAGTCGATGATGCCGAGGCAGA
196 GTCTATATTAGACCACTCAAGGTGACCCTTCCTACACAAAAAGTAGTCGATGATGCCGAGGCAGA
1931902 AGAACTTGAGGAGGAATCTGAGGACCGAGCAAATCCTAAAGAAAGGAAGAGAAATCACTCCAAAG
261 AGAACTTGAGGAGGAATCTGAGGACCGAGCAAATCCTAAAGAAAGGAAGAGAAATCACTCCAAAG
1931967 ATAAAAAGTGCAAGAAGGATGAGAAAAAGAGGAGGAAGAAGAAACACCGTGCAGCCACATTGATG
326 ATAAAAAGTGCAAGAAGGATGAGAAAAAGAGGAGGAAGAAGAAACACCGTGCAGCCACATTGATG
1932032 GCCGAGGAAAACTGAGTTAATTTATTTTAAGTTTTAGTTGTAGTATTCATGCATTGCATGTAGCT
391 GCCGAGGAAAACTGAGTTAATTTATTTTAAGTTTTAGTTGTAGTATTCATGCATTGCATGTAGCT
1932097 GTAATTTTCATTTTGTTAGTGAACATTGCCGTTGCATTGTTCTTGTCATCACATTTAAATCTTAG
456 GTAATTTTCATTTTGTTAGTGAACATTGCCGTTGCATTGTTCTTGTCATCACATTTAAATCTTAG
1932162 TGCATTGAGGACAATGCGAACTTTAAGTTTGGGAGAATGCATATGGAGATTGGAAATACACCCAT
521 TGCATTGAGGACAATGCGAACTTTAAGTTTGGGAGAATGCATATGGAGATTGGAAATACACCCAT
1932227 ATTTCAATTTTTTTTAATGAAGCATACAAGGTTTATTTGTGGTTAATACAAATGTGTTGAAAGCT
586 ATTTCAATTTTTTTTAATGAAGCATACAAGGTTTATTTGTGGTTAATACAAATGTGTTGAAAGCT
1932292 TTTTTTGTTACATTCGATGTTTAATTCTTGAATCAAGTCAACTATCAATGAATGAGTTGGATAAA
651 TTTTTTGTTACATTCGATGTTTAATTCTTGAATCAAGTCAACTATCAATGAATGAGTTGGATAAA
1932357 TTTGAC
716 TTTGAC
1932363 CGTCGTTTGTGTTGAAGTTGTGAACGAGATGGCCGAGGAAAAAAATACTGAGATAGAAGCTACTG
1 CGTCGTTTGTGTTGAAGTTGTGAACGAGATGGCCGAGGAAAAAAATACTGAGATAGAAGCTACTG
1932428 AGAAAGAATCTGTTGAGGATATTGTCAATGCATTCAAGCTTATGGATACAACTAAAGATGATTTG
66 AGAAAGAATCTGTTGAGGATATTGTCAATGCATTCAAGCTTATGGATACAACTAAAGATGATTTG
1932493 GAGCTAGACCGGAGGAAGCTGCAGAGGTAACAAGTGAGGAGCACCACAATTCGTTGGCTATAGTG
131 GAGCTAGACCGGAGGAAGCTGCAGAGGTAACAAGTGAGGAGCACCACAATTCGTTGGCTATAGTG
1932558 GTCTATATTAGACCACTCAAGGTGACCCTTCCTACACAAAAAGTAGTCGATGATGCCGAGGCAGA
196 GTCTATATTAGACCACTCAAGGTGACCCTTCCTACACAAAAAGTAGTCGATGATGCCGAGGCAGA
1932623 AGAACTTGAGGAGGAATCTGAGGACCGAGCAAATCCTAAAGAAAGGAAGAGAAATCACTCCAAAG
261 AGAACTTGAGGAGGAATCTGAGGACCGAGCAAATCCTAAAGAAAGGAAGAGAAATCACTCCAAAG
1932688 ATAAAAAGTGCAAGAAGGATGAGAAAAAGAGGAGGAAGAAGAAACACCGTGCAGCCACATTGATG
326 ATAAAAAGTGCAAGAAGGATGAGAAAAAGAGGAGGAAGAAGAAACACCGTGCAGCCACATTGATG
1932753 GCCGAGGAAAACTGAGTTAATTTATTTTAAGTTTTAGTTGTAGTATTCATGCATTGCATGTAGCT
391 GCCGAGGAAAACTGAGTTAATTTATTTTAAGTTTTAGTTGTAGTATTCATGCATTGCATGTAGCT
1932818 GTAATTTTCATTTTGTTAGTGAACATTGCCGTTGCATTGTTCTTGTCATCACATTTAAATCTTAG
456 GTAATTTTCATTTTGTTAGTGAACATTGCCGTTGCATTGTTCTTGTCATCACATTTAAATCTTAG
1932883 TGCATTGAGGACAATGCGAACTTTAAGTTTGGGAGAATGCATATGGAGATTGGAAATACACCCAT
521 TGCATTGAGGACAATGCGAACTTTAAGTTTGGGAGAATGCATATGGAGATTGGAAATACACCCAT
1932948 ATTTCAATTTTTTTTAATGAAGCATACAAGGTTTATTTGTGGTTAATACAAATGTGTTGAAAGCT
586 ATTTCAATTTTTTTTAATGAAGCATACAAGGTTTATTTGTGGTTAATACAAATGTGTTGAAAGCT
1933013 TTTTTTGTTACATTCGATGTTTAATTCTTGAATCAAGTCAACTATCAATGAATGAGTTGGATAAA
651 TTTTTTGTTACATTCGATGTTTAATTCTTGAATCAAGTCAACTATCAATGAATGAGTTGGATAAA
1933078 TTTGAC
716 TTTGAC
1933084 CG
1 CG
1933086 AATGTTGTAT
Statistics
Matches: 723, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
721 723 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (721 bp):
CGTCGTTTGTGTTGAAGTTGTGAACGAGATGGCCGAGGAAAAAAATACTGAGATAGAAGCTACTG
AGAAAGAATCTGTTGAGGATATTGTCAATGCATTCAAGCTTATGGATACAACTAAAGATGATTTG
GAGCTAGACCGGAGGAAGCTGCAGAGGTAACAAGTGAGGAGCACCACAATTCGTTGGCTATAGTG
GTCTATATTAGACCACTCAAGGTGACCCTTCCTACACAAAAAGTAGTCGATGATGCCGAGGCAGA
AGAACTTGAGGAGGAATCTGAGGACCGAGCAAATCCTAAAGAAAGGAAGAGAAATCACTCCAAAG
ATAAAAAGTGCAAGAAGGATGAGAAAAAGAGGAGGAAGAAGAAACACCGTGCAGCCACATTGATG
GCCGAGGAAAACTGAGTTAATTTATTTTAAGTTTTAGTTGTAGTATTCATGCATTGCATGTAGCT
GTAATTTTCATTTTGTTAGTGAACATTGCCGTTGCATTGTTCTTGTCATCACATTTAAATCTTAG
TGCATTGAGGACAATGCGAACTTTAAGTTTGGGAGAATGCATATGGAGATTGGAAATACACCCAT
ATTTCAATTTTTTTTAATGAAGCATACAAGGTTTATTTGTGGTTAATACAAATGTGTTGAAAGCT
TTTTTTGTTACATTCGATGTTTAATTCTTGAATCAAGTCAACTATCAATGAATGAGTTGGATAAA
TTTGAC
Found at i:1936042 original size:104 final size:104
Alignment explanation
Indices: 1935856--1936077 Score: 336
Period size: 104 Copynumber: 2.1 Consensus size: 104
1935846 GTTAGTTTCC
* * * *
1935856 ATTATTAAGGCTCACTGATTTAAGATAGCAACCTTCGATTATTTGAGTTAGCTGATTTAATATCC
1 ATTATTAAGGCTCACTAATTTAAGATAGCAACCTCCGATTATTTAAGTTAGCTGATTTAAGATCC
* *
1935921 CAACTCCTAACAGCTCGCTGACGTACGTTCACAACGAAT
66 CAACTCCTAACAACTCGCTGACCTACGTTCACAACGAAT
* * *
1935960 ATTACTAAGGCTCACTAATTTAAGATCGCAACCTCCGATTATTTAAGTTAGCTGATTTAAGATCG
1 ATTATTAAGGCTCACTAATTTAAGATAGCAACCTCCGATTATTTAAGTTAGCTGATTTAAGATCC
* *
1936025 CAACTCCTAACAACTCGCTGACCTACGTTCACAGCTAAT
66 CAACTCCTAACAACTCGCTGACCTACGTTCACAACGAAT
*
1936064 GTTATTAAGGCTCA
1 ATTATTAAGGCTCA
1936078 TTGACCTACA
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (104 bp):
ATTATTAAGGCTCACTAATTTAAGATAGCAACCTCCGATTATTTAAGTTAGCTGATTTAAGATCC
CAACTCCTAACAACTCGCTGACCTACGTTCACAACGAAT
Found at i:1936092 original size:36 final size:36
Alignment explanation
Indices: 1936043--1936117 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
1936033 AACAACTCGC
* * *
1936043 TGACCTACGTTCACAGCTAATGTTATTAAGGCTCAT
1 TGACCTACATTCACAACTAATGTTACTAAGGCTCAT
* * *
1936079 TGACCTACATTCACAACTGATTTTACTAAGGCTCGT
1 TGACCTACATTCACAACTAATGTTACTAAGGCTCAT
1936115 TGA
1 TGA
1936118 TTTAAGATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (36 bp):
TGACCTACATTCACAACTAATGTTACTAAGGCTCAT
Found at i:1939435 original size:21 final size:20
Alignment explanation
Indices: 1939411--1939450 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1939401 AAAGTATCAA
1939411 TAATATTATATACTTTTGAAG
1 TAATATTATA-ACTTTTGAAG
* *
1939432 TAATTTTATAATTTTTGAA
1 TAATATTATAACTTTTGAA
1939451 TATTTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (20 bp):
TAATATTATAACTTTTGAAG
Found at i:1939457 original size:18 final size:21
Alignment explanation
Indices: 1939411--1939466 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 21
1939401 AAAGTATCAA
*
1939411 TAATATTAT-ATACTTTTGAAG
1 TAATTTTATAATA-TTTTGAAG
1939432 TAATTTTATAAT-TTTTGAA-
1 TAATTTTATAATATTTTGAAG
1939451 T-ATTTTATAATATTTT
1 TAATTTTATAATATTTT
1939467 TGTATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 10 0.31
19 5 0.16
20 7 0.22
21 8 0.25
22 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
TAATTTTATAATATTTTGAAG
Found at i:1939467 original size:20 final size:19
Alignment explanation
Indices: 1939424--1939486 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
1939414 TATTATATAC
1939424 TTTTGAAGTAATTTTAT-AAT
1 TTTTGAA-T-ATTTTATAAAT
1939444 TTTTGAATATTTTATAATAT
1 TTTTGAATATTTTATAA-AT
* *
1939464 TTTTGTATTTTTTTATAAAT
1 TTTTG-AATATTTTATAAAT
1939484 TTT
1 TTT
1939487 AATAAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 7 0.18
19 2 0.05
20 19 0.50
21 10 0.26
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.63
Consensus pattern (19 bp):
TTTTGAATATTTTATAAAT
Found at i:1939527 original size:49 final size:48
Alignment explanation
Indices: 1939433--1939527 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 48
1939423 CTTTTGAAGT
* *
1939433 AATTTTATAATTTTTGAATATTTTATAATATTTTTGTATTTTTTTATA
1 AATTTTATAAATTTTGAATATTTTATAATATTTTTGTAATTTTTTATA
*
1939481 AATTTTAATAAATTTTGAAT-TTTTATATTTATATTTTG-AATTTTTTA
1 AATTTT-ATAAATTTTGAATATTTTATA-ATAT-TTTTGTAATTTTTTA
1939528 ATTATATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
48 13 0.32
49 23 0.56
50 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (48 bp):
AATTTTATAAATTTTGAATATTTTATAATATTTTTGTAATTTTTTATA
Found at i:1939532 original size:20 final size:20
Alignment explanation
Indices: 1939483--1939539 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
1939473 TTTTTATAAA
*
1939483 TTTTAA-TAAATTTTGAATT
1 TTTTAATTATATTTTGAATT
*
1939502 TTTATATTTATATTTTGAATT
1 TTT-TAATTATATTTTGAATT
*
1939523 TTTTAATTATATATTGA
1 TTTTAATTATATTTTGA
1939540 TAAATTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.09
20 14 0.44
21 15 0.47
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTAATTATATTTTGAATT
Found at i:1943658 original size:76 final size:76
Alignment explanation
Indices: 1943577--1943925 Score: 635
Period size: 76 Copynumber: 4.6 Consensus size: 76
1943567 TTTTTGTGTA
1943577 TATATATATTAAAAATGAGATTCACTTGATTATATTTAAAACTTAATTTAAATATAAGACCCACT
1 TATATATATTAAAAATGAGATTCACTTGATTATATTTAAAACTTAATTTAAATATAAGACCCACT
1943642 TTAAATATAAC
66 TTAAATATAAC
1943653 TATATATATTAAAAATGAGATTCACTTGATTATATTTAAAACTTAATTTAAATATAAGACCCACT
1 TATATATATTAAAAATGAGATTCACTTGATTATATTTAAAACTTAATTTAAATATAAGACCCACT
1943718 TTAAATATAAC
66 TTAAATATAAC
1943729 TATATATATTAAAAATGAGATTCACTTGATTATATTTAAAACTTAATTTAAATATAAGACCCACT
1 TATATATATTAAAAATGAGATTCACTTGATTATATTTAAAACTTAATTTAAATATAAGACCCACT
1943794 TTAAATATAAC
66 TTAAATATAAC
*
1943805 TATATATATTAAAAATGAGATTCACTTGATTATATTTAAAACTTAATTTAAATATAAGATCCACT
1 TATATATATTAAAAATGAGATTCACTTGATTATATTTAAAACTTAATTTAAATATAAGACCCACT
1943870 TTAAATATAAC
66 TTAAATATAAC
* * * * * *
1943881 TATATGTATTAAAAATGGGACTGACTTAATCATATTTAAAACTTA
1 TATATATATTAAAAATGAGATTCACTTGATTATATTTAAAACTTA
1943926 GGGTCTGTTT
Statistics
Matches: 266, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 266 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (76 bp):
TATATATATTAAAAATGAGATTCACTTGATTATATTTAAAACTTAATTTAAATATAAGACCCACT
TTAAATATAAC
Found at i:1944508 original size:34 final size:35
Alignment explanation
Indices: 1944449--1944515 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
1944439 CAAACACCAG
*
1944449 AAAATATTTTCCAGTAAACCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAACCATTTTACAGAAAAGT
* * *
1944484 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAACCATTTTACAGAAAA
1944516 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAACCATTTTACAGAAAAGT
Found at i:1954157 original size:56 final size:56
Alignment explanation
Indices: 1954066--1954174 Score: 200
Period size: 56 Copynumber: 1.9 Consensus size: 56
1954056 TGGAATAGTG
* *
1954066 ATTAGAGACAACGAAGGATGAGTATTGGGTTCAAAAGTGGTAATAAACAGAAATGT
1 ATTAAAGACAACGAAAGATGAGTATTGGGTTCAAAAGTGGTAATAAACAGAAATGT
1954122 ATTAAAGACAACGAAAGATGAGTATTGGGTTCAAAAGTGGTAATAAACAGAAA
1 ATTAAAGACAACGAAAGATGAGTATTGGGTTCAAAAGTGGTAATAAACAGAAA
1954175 CGTACCTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.22
Consensus pattern (56 bp):
ATTAAAGACAACGAAAGATGAGTATTGGGTTCAAAAGTGGTAATAAACAGAAATGT
Found at i:1955116 original size:17 final size:16
Alignment explanation
Indices: 1955094--1955129 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1955084 GACTAGTTTT
1955094 AAATATAATTAAAAATA
1 AAATAT-ATTAAAAATA
*
1955111 AAATATTTTAAAAATA
1 AAATATATTAAAAATA
1955127 AAA
1 AAA
1955130 AAAATTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATATATTAAAAATA
Found at i:1956490 original size:27 final size:26
Alignment explanation
Indices: 1956455--1956516 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
1956445 GTATGTGTAT
*
1956455 ATATATATATATATATGAAAATA-AAAA
1 ATATATATAGAT-TAT-AAAATATAAAA
* *
1956482 ATGTATATAGATTATAGAATATAAAA
1 ATATATATAGATTATAAAATATAAAA
1956508 ATATATATA
1 ATATATATA
1956517 AGTATGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 15 0.50
27 10 0.33
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (26 bp):
ATATATATAGATTATAAAATATAAAA
Found at i:1958192 original size:40 final size:42
Alignment explanation
Indices: 1958074--1958634 Score: 328
Period size: 44 Copynumber: 13.2 Consensus size: 42
1958064 GCAACTTCAA
* * * * *
1958074 GGAGATAGGATTAGTAGCTTCAGTCTGCTGCACTACTGCTTAG
1 GGAGATAAGATT-GTGGCTTTAATCTGCTCCACTACTGCTTAG
* * * *
1958117 AGAGATAAGACTTGAT-GC---GATCTACTCTACTACTGCTTAG
1 GGAGATAAGA-TTG-TGGCTTTAATCTGCTCCACTACTGCTTAG
* **
1958157 GGAGATAAGATATGTGGCTTTAATCTGCTCCACTGCAACTTTAG
1 GGAGATAAGAT-TGTGGCTTTAATCTGCTCCACTACTGC-TTAG
* *** **
1958201 GGAGATATGATTGGTTTTTTTTCTCTGCTCCACTACTGCTTAG
1 GGAGATAAGATT-GTGGCTTTAATCTGCTCCACTACTGCTTAG
*
1958244 GGAGATAAGACTTGAT-GC---GATCTGCTCCACTACTGCTTAG
1 GGAGATAAGA-TTG-TGGCTTTAATCTGCTCCACTACTGCTTAG
* * * * **
1958284 GGAGATAAGATCTGTGGTTTTAATCAGCTCTACTGCAACTTCAG
1 GGAGATAAGAT-TGTGGCTTTAATCTGCTCCACTACTGCTT-AG
* * ** ** *
1958328 AGAGATAGGATTGATTTCTTTTGTCTGCTGCACTACTGCTTAG
1 GGAGATAAGATTG-TGGCTTTAATCTGCTCCACTACTGCTTAG
1958371 GGAGATAAGACTTGAT-GC---AATCTGCTCCACTACTGCTTAG
1 GGAGATAAGA-TTG-TGGCTTTAATCTGCTCCACTACTGCTTAG
* * * **
1958411 GGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAG
1 GGAGATAAGAT-TGTGGCTTTAATCTGCTCCACTACTGCTT-AG
* * * * * *
1958455 AGAGATAGGATTAGTAGCTTCAGTCTGCTGCACTACTGCTTAG
1 GGAGATAAGATT-GTGGCTTTAATCTGCTCCACTACTGCTTAG
*
1958498 AGAGATAAGACTTGAT-GC---AATCTGCTCCACTACTGCTTAG
1 GGAGATAAGA-TTG-TGGCTTTAATCTGCTCCACTACTGCTTAG
* * * **
1958538 GGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAG
1 GGAGATAAGAT-TGTGGCTTTAATCTGCTCCACTACTGCTT-AG
** *
1958582 GGAGATAAGATTGGTTTCTTCT-GTCTGCTCCACTACTGCTTAG
1 GGAGATAAGATT-GTGGCTT-TAATCTGCTCCACTACTGCTTAG
*
1958625 GAAGATAAGA
1 GGAGATAAGA
1958635 CCTGCTATCT
Statistics
Matches: 394, Mismatches: 88, Indels: 72
0.71 0.16 0.13
Matches are distributed among these distances:
39 8 0.02
40 127 0.32
43 124 0.31
44 134 0.34
45 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (42 bp):
GGAGATAAGATTGTGGCTTTAATCTGCTCCACTACTGCTTAG
Found at i:1958228 original size:127 final size:127
Alignment explanation
Indices: 1958046--1958635 Score: 869
Period size: 127 Copynumber: 4.6 Consensus size: 127
1958036 ATGATTCATC
* ** *
1958046 GTTTTAATCCGCTCCACTGCAACTTCA-AGGAGATAGGATTAGTAGCTTCAGTCTGCTGCACTAC
1 GTTTTAATCCGCTCCACTGCAACTTCAGA-GAGATAGGATTGGTTTCTTCTGTCTGCTGCACTAC
* * * *
1958110 TGCTTAGAGAGATAAGACTTGATGCGATCTACTCTACTACTGCTTAGGGAGATAAGATATGTG
65 TGCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
* * * * * * * * *
1958173 GCTTTAATCTGCTCCACTGCAACTTTAGGGAGATATGATTGGTTTTTTTTCTCTGCTCCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTGCACTACT
* *
1958238 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
66 GCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
* * * *
1958300 GTTTTAATCAGCTCTACTGCAACTTCAGAGAGATAGGATTGATTTCTTTTGTCTGCTGCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTGCACTACT
*
1958365 GCTTAGGGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
66 GCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
* ** *
1958427 GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTAGTAGCTTCAGTCTGCTGCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTGCACTACT
1958492 GCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
66 GCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
* * *
1958554 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTGTCTGCTCCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTGCACTACT
1958619 GCTTAG-GAAGATAAGAC
66 GCTTAGAG-AGATAAGAC
1958636 CTGCTATCTT
Statistics
Matches: 417, Mismatches: 44, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
126 1 0.00
127 416 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (127 bp):
GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTGCACTACT
GCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
Found at i:1958500 original size:43 final size:41
Alignment explanation
Indices: 1958075--1958634 Score: 249
Period size: 40 Copynumber: 13.2 Consensus size: 41
1958065 CAACTTCAAG
* * *
1958075 GAGATAGGATTAGTAGCTTCAGTCTGCTGCACTACTGCTTAGA
1 GAGATAAGATT-GTAG-TTCAATCTGCTCCACTACTGCTTAGA
* * * * *
1958118 GAGATAAGACTTG-A-TGCGATCTACTCTACTACTGCTTAGG
1 GAGATAAGA-TTGTAGTTCAATCTGCTCCACTACTGCTTAGA
* * * ** *
1958158 GAGATAAGATATGTGGCTTTAATCTGCTCCACTGCAACTTTAGG
1 GAGATAAGAT-TGTAG-TTCAATCTGCTCCACTACTGC-TTAGA
* ** *** *
1958202 GAGATATGATTGGTTTTTTTTCTCTGCTCCACTACTGCTTAGG
1 GAGATAAGATT-G-TAGTTCAATCTGCTCCACTACTGCTTAGA
* * *
1958245 GAGATAAGACTTG-A-TGCGATCTGCTCCACTACTGCTTAGG
1 GAGATAAGA-TTGTAGTTCAATCTGCTCCACTACTGCTTAGA
* * * * * **
1958285 GAGATAAGATCTGTGGTTTTAATCAGCTCTACTGCAACTTCAGA
1 GAGATAAGAT-TGTAG-TTCAATCTGCTCCACTACTGCTT-AGA
* * ** * *
1958329 GAGATAGGATTG-ATTTCTTTTGTCTGCTGCACTACTGCTTAGG
1 GAGATAAGATTGTAGTTC---AATCTGCTCCACTACTGCTTAGA
* *
1958372 GAGATAAGACTTG-A-TGCAATCTGCTCCACTACTGCTTAGG
1 GAGATAAGA-TTGTAGTTCAATCTGCTCCACTACTGCTTAGA
* * * * **
1958412 GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGA
1 GAGATAAGAT-TGTAG-TTCAATCTGCTCCACTACTGCTT-AGA
* * *
1958456 GAGATAGGATTAGTAGCTTCAGTCTGCTGCACTACTGCTTAGA
1 GAGATAAGATT-GTAG-TTCAATCTGCTCCACTACTGCTTAGA
* *
1958499 GAGATAAGACTTG-A-TGCAATCTGCTCCACTACTGCTTAGG
1 GAGATAAGA-TTGTAGTTCAATCTGCTCCACTACTGCTTAGA
* * * * ** *
1958539 GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
1 GAGATAAGAT-TGTAG-TTCAATCTGCTCCACTACTGCTT-AGA
** **
1958583 GAGATAAGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAG-
1 GAGATAAGATT-G-TAGTTCAATCTGCTCCACTACTGCTTAGA
1958625 GAAGATAAGA
1 G-AGATAAGA
1958635 CCTGCTATCT
Statistics
Matches: 386, Mismatches: 98, Indels: 66
0.70 0.18 0.12
Matches are distributed among these distances:
39 4 0.01
40 127 0.33
41 2 0.01
42 3 0.01
43 124 0.32
44 124 0.32
45 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (41 bp):
GAGATAAGATTGTAGTTCAATCTGCTCCACTACTGCTTAGA
Found at i:1958612 original size:87 final size:86
Alignment explanation
Indices: 1958263--1958634 Score: 278
Period size: 87 Copynumber: 4.4 Consensus size: 86
1958253 ACTTGATGCG
* * * *
1958263 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCAGCTCTACTGCAACTTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCAATCTGCTCCACTACAACTT-AG
* * **
1958328 AGAGATAGGATTGATTTCTTTT
65 AGAGATAAGATTGGTTTCTTCA
* * * * ** *
1958350 GTCTGCTGCACTACTGCTTAGGGAGATAAGA-CT-T-GATGCAATCTGCTCCACTACTGCTTAGG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCAATCTGCTCCACTACAACTTAGA
*
1958412 GAGATAAGATCTGTGGTT-TT-A
66 GAGATAAGAT-TG-GTTTCTTCA
* * ** * * * * * * **
1958433 ATCCGCTCCACTGCAACTTCAGAGAGATAGGAT-TAGTAGCTTCAGTCTGCTGCACTACTGCTTA
1 ATCTGCTCCACTACTGCTT-AGGGAGATAAGATCT-GTGGTTTCAATCTGCTCCACTACAACTTA
* *
1958497 GAGAGATAAGACTT-G---ATGCA
64 GAGAGATAAGA-TTGGTTTCTTCA
* * *
1958517 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCAATCTGCTCCACTACAACTT-AG
* *
1958582 GGAGATAAGATTGGTTTCTTCT
65 AGAGATAAGATTGGTTTCTTCA
* *
1958604 GTCTGCTCCACTACTGCTTAGGAAGATAAGA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGA
1958635 CCTGCTATCT
Statistics
Matches: 219, Mismatches: 50, Indels: 32
0.73 0.17 0.11
Matches are distributed among these distances:
83 57 0.26
84 61 0.28
85 4 0.02
86 3 0.01
87 93 0.42
88 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (86 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCAATCTGCTCCACTACAACTTAGA
GAGATAAGATTGGTTTCTTCA
Found at i:1958859 original size:90 final size:90
Alignment explanation
Indices: 1958623--1959767 Score: 586
Period size: 90 Copynumber: 12.6 Consensus size: 90
1958613 ACTACTGCTT
* * * * *
1958623 AGGAAGA-TAAGACCTGCTATCTTTGATCTACTTCGCTACCAATATAGGAAGACAAGACTTGCTA
1 AGGAAGACT-AGACTTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTA
*
1958687 TCTTCAGTCTACTTCGCTGCCAATAC
65 TCTTCAGTCTACTTCACTGCCAATAC
*
1958713 AGGAAGAC-AAACTTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGA-TCTGCTA
1 AGGAAGACTAGACTTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGACT-TGCTA
* * ***
1958776 TCTTTAGTCTACTTCGCTATTAATAC
65 TCTTCAGTCTACTTCACTGCCAATAC
* * *
1958802 AGGAAGACTAGACTTGCTATCTTCGATCTACTTAACAGCCAATACAGGAAGATAAGA-TCTGCTA
1 AGGAAGACTAGACTTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGACT-TGCTA
* *
1958866 TCTTCAGTCTACTTCATTGTCAATAC
65 TCTTCAGTCTACTTCACTGCCAATAC
*
1958892 AGGAAGATTAGACTTGCTATCTTC-AGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTA
1 AGGAAGACTAGACTTGCTATCTTCGA-TCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTA
*
1958956 TTTTC-GATCTACTTCACTGCCAATAC
65 TCTTCAG-TCTACTTCACTGCCAATAC
* * *
1958982 AGGAAAACAAGA-TCTGCTATCTTC-AGTCTACTTCGCTGCCAATACAGGAAGACAAGACTTGCT
1 AGGAAGACTAGACT-TGCTATCTTCGA-TCTACTTCACTGCCAATACAGGAAGACAAGACTTGCT
* *
1959045 ATCTTC-GATCTACTTTACTACCAATAC
64 ATCTTCAG-TCTACTTCACTGCCAATAC
* * * ** * * * *
1959072 AGGAAGA-TAAGA-TCTGTTATCTTC-AGTCTAATT-AATTACAGTGTCGGGGA-ACAAGATTCA
1 AGGAAGACT-AGACT-TGCTATCTTCGA-TCTACTTCACTGCCAAT-ACAGGAAGACAAG----A
* * * **
1959132 CCGTTG-TAGCTTCAATCT-GTTCCACTGTACC--GCC
58 -C-TTGCTATCTTCAGTCTACTT-CACTG--CCAATAC
* * * ** * *
1959166 AGAGAAG--TAGGATTTGCAGTTACGGCTTCAATCTTTTTAATTG-CAATGTA-ATGGAAG-CAA
1 AG-GAAGACTA-GACTTGC---TA--TCTTCGATCTACTTCACTGCCAA--TACA-GGAAGACAA
* * ***
1959226 GA-TTCGTCATTGTAGCTTCAATCTA-TTCCACTG-CACCGC
56 GACTT-G-C----TATCTTCAGTCTACTT-CACTGCCAATAC
* * * * * * * *
1959265 TTGGAA-AGTAAGATTCATTG-T-T-TTCGATTTGC-TC-C-ACCACTGCTTAGG--GATAAGA-
1 -AGGAAGACT-AGA--C-TTGCTATCTTCGATCTACTTCACTGCCAATAC--AGGAAGACAAGAC
* ** * ***
1959320 TCTGCAATCTTCAACCTAC-TCAATGCTGCT-C
59 T-TGCTATCTTCAGTCTACTTCACTGCCAATAC
* * * * * *
1959351 AGGGAGA-TAAGGCTGGTGC--T-TTCGATCTGCTTTACTGCCAGTATAGGAAGACAAGA-TCTG
1 AGGAAGACT-AGACT--TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGACT-TG
*
1959411 CTATCTTCAGTCTACTTCGCTGCCAATAC
62 CTATCTTCAGTCTACTTCACTGCCAATAC
* * * * *
1959440 AGGAAGACAAGACTTGCTATCTTTGATCTACTTCGCTGCCAATACAGAAAGAAAAGA-TCTGCTA
1 AGGAAGACTAGACTTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGACT-TGCTA
* ** *
1959504 TCTTC-GATCCACTTTGCTGCCAATAT
65 TCTTCAG-TCTACTTCACTGCCAATAC
* ** *
1959530 AGGAAGACAAGA-TCTGCTATCTTCGATCTACTTCGGTGCCAATACAGGAAGACAAGA-TCTACT
1 AGGAAGACTAGACT-TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGACT-TGCT
* * *
1959593 ATCTTTAGTCTACTTCGCTGCCAATAT
64 ATCTTCAGTCTACTTCACTGCCAATAC
* * *
1959620 AGGAAGACAAGACTTGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGA-TCTGTTA
1 AGGAAGACTAGACTTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGACT-TGCTA
1959684 TCTTCAGTCTACTTCACTGCCAATAC
65 TCTTCAGTCTACTTCACTGCCAATAC
* * ** *
1959710 AGGAAGACAAGACTTGCTATCTTCAATCTACTTTGCTGCCAAATACAGGAAGATAAGA
1 AGGAAGACTAGACTTGCTATCTTCGATCTACTTCACTGCC-AATACAGGAAGACAAGA
1959768 TCTGTAATGT
Statistics
Matches: 844, Mismatches: 133, Indels: 155
0.75 0.12 0.14
Matches are distributed among these distances:
82 1 0.00
83 1 0.00
84 12 0.01
85 11 0.01
86 7 0.01
87 41 0.05
88 7 0.01
89 103 0.12
90 523 0.62
91 22 0.03
92 6 0.01
93 11 0.01
94 24 0.03
95 14 0.02
96 3 0.00
97 3 0.00
99 16 0.02
100 34 0.04
101 2 0.00
103 3 0.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (90 bp):
AGGAAGACTAGACTTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTAT
CTTCAGTCTACTTCACTGCCAATAC
Found at i:1958936 original size:135 final size:136
Alignment explanation
Indices: 1958623--1959767 Score: 658
Period size: 135 Copynumber: 8.4 Consensus size: 136
1958613 ACTACTGCTT
* * * * *
1958623 AGGAAGATAAGACCTGCTATCTT-TGATCTACTTCGCTACCAATATAGGAAGACAAGACTTGCTA
1 AGGAAGACAAGACTTGCTATCTTCAGATCTACTTCACTACCAATACAGGAAGACAAGACTTGCTA
*
1958687 TCTTC-AGTCTACTTCGCTGCCAATACAGGAAGACAA-A-CTTGCTATCTTC-GATCTACTTCAC
66 TCTTCGA-TCTACTTCACTGCCAATACAGGAAGACAAGATC-TGCTATCTTCAG-TCTACTTCAC
1958748 TGCCAATAC
128 TGCCAATAC
* * ** *
1958757 AGGAAGACAAGA-TCTGCTATCTTTAG-TCTACTTCGCTATTAATACAGGAAGACTAGACTTGCT
1 AGGAAGACAAGACT-TGCTATCTTCAGATCTACTTCACTACCAATACAGGAAGACAAGACTTGCT
* * * *
1958820 ATCTTCGATCTACTTAACAGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTACTTCATTG
65 ATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCACTG
*
1958885 TCAATAC
130 CCAATAC
** *
1958892 AGGAAGATTAGACTTGCTATCTTCAG-TCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTA
1 AGGAAGACAAGACTTGCTATCTTCAGATCTACTTCACTACCAATACAGGAAGACAAGACTTGCTA
* * *
1958956 TTTTCGATCTACTTCACTGCCAATACAGGAAAACAAGATCTGCTATCTTCAGTCTACTTCGCTGC
66 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCACTGC
1959021 CAATAC
131 CAATAC
* * *
1959027 AGGAAGACAAGACTTGCTATCTTC-GATCTACTTTACTACCAATACAGGAAGATAAGA-TCTGTT
1 AGGAAGACAAGACTTGCTATCTTCAGATCTACTTCACTACCAATACAGGAAGACAAGACT-TGCT
* * ** * * * * * *
1959090 ATCTTC-AGTCTAATT-AATTACAGTGTCGGGGA-ACAAGATTCACCGTTG-TAGCTTCAATCT-
65 ATCTTCGA-TCTACTTCACTGCCAAT-ACAGGAAGACAAGA-T---C--TGCTATCTTCAGTCTA
* **
1959150 GTTCCACTGTACC--GCC
122 CTT-CACTG--CCAATAC
* * * * * * * **
1959166 AGAGAAG-TAGGATTTGCAGTTACGGCTTCA-ATCT-TTTTAATTGCAATGTA-ATGGAAG-CAA
1 AG-GAAGACAAGACTTGC---TA--TCTTCAGATCTACTTCACTACCAA--TACA-GGAAGACAA
* * *** * *
1959226 GA-TTCGTCATTGTAGCTTCAATCTA-TTCCACTG-CACCGCTTGGAA-AGTAAGATTCATTG-T
57 GACTT-G-C----TATCTTCGATCTACTT-CACTGCCAATAC-AGGAAGA-CAAGA-TC--TGCT
* * ** *
1959286 -T-TTCGATTTGCTCCACCACTG-C--T-T
110 ATCTTC-A-GT-CTACTTCACTGCCAATAC
* * * * * *** * * *
1959310 AGG--GATAAGA-TCTGCAATCTTCA-ACCTAC-TCAATGCTGCT-CAGGGAGATAAGGCTGGTG
1 AGGAAGACAAGACT-TGCTATCTTCAGATCTACTTCACTACCAATACAGGAAGACAAGACT--TG
* * * * *
1959369 C--T-TTCGATCTGCTTTACTGCCAGTATAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGC
63 CTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCAC
1959431 TGCCAATAC
128 TGCCAATAC
* * * * *
1959440 AGGAAGACAAGACTTGCTATCTT-TGATCTACTTCGCTGCCAATACAGAAAGAAAAGA-TCTGCT
1 AGGAAGACAAGACTTGCTATCTTCAGATCTACTTCACTACCAATACAGGAAGACAAGACT-TGCT
* ** * **
1959503 ATCTTCGATCCACTTTGCTGCCAATATAGGAAGACAAGATCTGCTATCTTC-GATCTACTTCGGT
65 ATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAG-TCTACTTCACT
1959567 GCCAATAC
129 GCCAATAC
* * * * *
1959575 AGGAAGACAAGA-TCTACTATCTTTAG-TCTACTTCGCTGCCAATATAGGAAGACAAGACTTGCT
1 AGGAAGACAAGACT-TGCTATCTTCAGATCTACTTCACTACCAATACAGGAAGACAAGACTTGCT
* *
1959638 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCAGTCTACTTCACTG
65 ATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCACTG
1959703 CCAATAC
130 CCAATAC
** * *
1959710 AGGAAGACAAGACTTGCTATCTTCA-ATCTACTTTGCTGCCAAATACAGGAAGATAAGA
1 AGGAAGACAAGACTTGCTATCTTCAGATCTACTTCACTACC-AATACAGGAAGACAAGA
1959768 TCTGTAATGT
Statistics
Matches: 789, Mismatches: 142, Indels: 158
0.72 0.13 0.15
Matches are distributed among these distances:
126 9 0.01
127 3 0.00
128 4 0.01
129 23 0.03
130 8 0.01
132 22 0.03
133 8 0.01
134 114 0.14
135 433 0.55
136 24 0.03
137 13 0.02
138 4 0.01
139 25 0.03
140 6 0.01
141 4 0.01
142 9 0.01
143 10 0.01
144 17 0.02
145 11 0.01
146 1 0.00
147 6 0.01
148 10 0.01
149 16 0.02
150 9 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (136 bp):
AGGAAGACAAGACTTGCTATCTTCAGATCTACTTCACTACCAATACAGGAAGACAAGACTTGCTA
TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCACTGC
CAATAC
Found at i:1959093 original size:45 final size:46
Alignment explanation
Indices: 1958623--1959101 Score: 567
Period size: 45 Copynumber: 10.7 Consensus size: 46
1958613 ACTACTGCTT
* * * * * *
1958623 AGGAAGATAAGACCTGCTATCTTTGA-TCTACTTCGCTACCAATAT
1 AGGAAGACAAGACTTGCTATCTTCGAGTCTACTTCACTGCCAATAC
*
1958668 AGGAAGACAAGACTTGCTATCTTC-AGTCTACTTCGCTGCCAATAC
1 AGGAAGACAAGACTTGCTATCTTCGAGTCTACTTCACTGCCAATAC
1958713 AGGAAGACAA-ACTTGCTATCTTCGA-TCTACTTCACTGCCAATAC
1 AGGAAGACAAGACTTGCTATCTTCGAGTCTACTTCACTGCCAATAC
* * ***
1958757 AGGAAGACAAGA-TCTGCTATCTT-TAGTCTACTTCGCTATTAATAC
1 AGGAAGACAAGACT-TGCTATCTTCGAGTCTACTTCACTGCCAATAC
* * *
1958802 AGGAAGACTAGACTTGCTATCTTCGA-TCTACTTAACAGCCAATAC
1 AGGAAGACAAGACTTGCTATCTTCGAGTCTACTTCACTGCCAATAC
* * *
1958847 AGGAAGATAAGA-TCTGCTATCTTC-AGTCTACTTCATTGTCAATAC
1 AGGAAGACAAGACT-TGCTATCTTCGAGTCTACTTCACTGCCAATAC
**
1958892 AGGAAGATTAGACTTGCTATCTTC-AGTCTACTTCACTGCCAATAC
1 AGGAAGACAAGACTTGCTATCTTCGAGTCTACTTCACTGCCAATAC
*
1958937 AGGAAGACAAGACTTGCTATTTTCGA-TCTACTTCACTGCCAATAC
1 AGGAAGACAAGACTTGCTATCTTCGAGTCTACTTCACTGCCAATAC
* *
1958982 AGGAAAACAAGA-TCTGCTATCTTC-AGTCTACTTCGCTGCCAATAC
1 AGGAAGACAAGACT-TGCTATCTTCGAGTCTACTTCACTGCCAATAC
* *
1959027 AGGAAGACAAGACTTGCTATCTTCGA-TCTACTTTACTACCAATAC
1 AGGAAGACAAGACTTGCTATCTTCGAGTCTACTTCACTGCCAATAC
* *
1959072 AGGAAGATAAGA-TCTGTTATCTTC-AGTCTA
1 AGGAAGACAAGACT-TGCTATCTTCGAGTCTA
1959102 ATTAATTACA
Statistics
Matches: 377, Mismatches: 40, Indels: 34
0.84 0.09 0.08
Matches are distributed among these distances:
44 50 0.13
45 321 0.85
46 6 0.02
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (46 bp):
AGGAAGACAAGACTTGCTATCTTCGAGTCTACTTCACTGCCAATAC
Done.