Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_pilon, whole genome shotgun sequence
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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 37
Found at i:1328650 original size:89 final size:89
Alignment explanation
Indices: 1328493--1328671 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 89
1328483 ATTTCAAACT
*
1328493 TTCAACCAAAAGACAAAACAAAGACAAATATTAACTCACAGTGTTAAAGACACAGTTTAGCAGAA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTCACAGTGTTAAAGACACAGTTTAGCAGAA
1328558 TTGGCAGC-ACCGAATAAATTTAC
66 TTGGCAGCAACCGAATAAATTTAC
*
1328581 TTCAACCAAAAGA-AAAACCAAAAAGACAAATACTAACTTCACAGTGTT-AATA-ACAGTTTAGC
1 TTCAACCAAAAGACAAAA-C--AAAGACAAATACTAAC-TCACAGTGTTAAAGACACAGTTTAGC
*
1328643 AGTATTGGCAGCAACCGAATAAATTTAC
62 AGAATTGGCAGCAACCGAATAAATTTAC
1328671 T
1 T
1328672 AAGCATCTAA
Statistics
Matches: 83, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
87 4 0.05
88 14 0.17
89 21 0.25
90 34 0.41
91 10 0.12
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (89 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTCACAGTGTTAAAGACACAGTTTAGCAGAA
TTGGCAGCAACCGAATAAATTTAC
Found at i:1330313 original size:20 final size:19
Alignment explanation
Indices: 1330268--1330329 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
1330258 TCTTTTGGTT
1330268 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1330287 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
1330308 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
1330327 GAA
1 GAA
1330330 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.14
20 28 0.80
21 2 0.06
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1330331 original size:32 final size:32
Alignment explanation
Indices: 1330290--1330377 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
1330280 GCAACGAGAT
1330290 AATGAGAATCGCAACGCGGAAATGACTATCGC-
1 AATGAGAATCGCAACGC-GAAATGACTATCGCG
1330322 AATGAGAATCGCAACGCGAAA-GACTATCGCG
1 AATGAGAATCGCAACGCGAAATGACTATCGCG
*
1330353 ACGA-GAGAATCGCAACGTGAAATGA
1 A--ATGAGAATCGCAACGCGAAATGA
1330378 AAATTGCAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
30 9 0.18
31 5 0.10
32 34 0.67
33 3 0.06
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (32 bp):
AATGAGAATCGCAACGCGAAATGACTATCGCG
Found at i:1330388 original size:19 final size:19
Alignment explanation
Indices: 1330360--1330410 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1330350 GCGACGAGAG
*
1330360 AATCGCAACGTGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1330379 AATTGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1330398 AATCGCAATGCGA
1 AATCGCAACGCGA
1330411 TTTTGGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1331062 original size:20 final size:20
Alignment explanation
Indices: 1330977--1331070 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1330967 CGCTATGTAA
* *
1330977 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGATAGTCAGT
*
1330997 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
1331017 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGT
*
1331038 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1331058 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1331071 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1331089 original size:41 final size:41
Alignment explanation
Indices: 1330997--1331091 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
1330987 GAAAGTCAGA
* * * ** *
1330997 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
*
1331038 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
1331080 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1331092 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1331181 original size:21 final size:21
Alignment explanation
Indices: 1331141--1331181 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1331131 ACTGTAGACC
** *
1331141 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1331162 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1331182 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1333547 original size:31 final size:31
Alignment explanation
Indices: 1333512--1333570 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1333502 ATTTAGAAGT
*
1333512 TAATTTGATTAAATCTATCAAATTTAAGAAA
1 TAATTTGATCAAATCTATCAAATTTAAGAAA
* * *
1333543 TAATTTTATCAAATTTATCAAGTTTAAG
1 TAATTTGATCAAATCTATCAAATTTAAG
1333571 CGTGATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
TAATTTGATCAAATCTATCAAATTTAAGAAA
Found at i:1333786 original size:18 final size:19
Alignment explanation
Indices: 1333763--1333805 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1333753 TAAATTAATA
1333763 AAATTATAAAT-TTTCAAT
1 AAATTATAAATATTTCAAT
1333781 AAATTA-AAATATTTCAAT
1 AAATTATAAATATTTCAAT
*
1333799 GAATTAT
1 AAATTAT
1333806 TAAACATGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATTATAAATATTTCAAT
Found at i:1334953 original size:37 final size:37
Alignment explanation
Indices: 1334903--1334976 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
1334893 AGGACCAAGT
1334903 CACTGGAATGCAAAATAAAATGGAAGAGCAACAAGGG
1 CACTGGAATGCAAAATAAAATGGAAGAGCAACAAGGG
*
1334940 CACTGGAATGCAAAATAAAATGGAAGAGTAACAAGGG
1 CACTGGAATGCAAAATAAAATGGAAGAGCAACAAGGG
1334977 AGCATGGAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.49, C:0.12, G:0.27, T:0.12
Consensus pattern (37 bp):
CACTGGAATGCAAAATAAAATGGAAGAGCAACAAGGG
Found at i:1346395 original size:2 final size:2
Alignment explanation
Indices: 1346388--1346414 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1346378 TTAATCTTTG
1346388 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1346415 AATAACTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1355491 original size:172 final size:176
Alignment explanation
Indices: 1355247--1355594 Score: 491
Period size: 172 Copynumber: 2.0 Consensus size: 176
1355237 AATTTTAAAT
* *
1355247 ATATATATATATAACATATGGGCTCAGCCCAAACCATTAAAACCCAATTATTAATTTAAGATCCA
1 ATATATATATATAACATATGAGCTAAGCCCAAACCATTAAAACCCAA-TATT-ATTTAAGATCCA
1355312 ATAACTTTTAAACCTAAAT-AATATTAATTAATTTAAAAAATTATAT-AAATTTTTA-TTTATAA
64 ATAACTTTTAAACCTAAATCAAT-TTAATTAA-TTAAAAAATTATATGAAATTTTTATTTTATAA
* * *
1355374 TTATATATT-TATT-AATTAATTGTAAACTGTTTTTTTATTTAAAAATATTAA
127 TTATATATTAT-TTAAATTAATT-AAAACT-TTTTTTGAATTAAAAATATTAA
1355425 ATATATATATAT-ACATATGAGCTAAGCCCAAACCATTTAAAACCC-A-A-T-TTTAAGATCCAA
1 ATATATATATATAACATATGAGCTAAGCCCAAACCA-TTAAAACCCAATATTATTTAAGATCCAA
* *
1355485 TAACTTTTAAACCTAAATCAATTTAATTAATTAAAAATTTATCTGAAATTTTTATTTTATAATTA
65 TAACTTTTAAACCTAAATCAATTTAATTAATTAAAAAATTATATGAAATTTTTATTTTATAATTA
1355550 TATATTATTTAAATTAATTAAAACTTTTTTTGAATTAAAAATATT
130 TATATTATTTAAATTAATTAAAACTTTTTTTGAATTAAAAATATT
1355595 TAATTTTTAT
Statistics
Matches: 157, Mismatches: 7, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
171 12 0.08
172 65 0.41
173 26 0.17
174 10 0.06
175 1 0.01
177 22 0.14
178 21 0.13
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (176 bp):
ATATATATATATAACATATGAGCTAAGCCCAAACCATTAAAACCCAATATTATTTAAGATCCAAT
AACTTTTAAACCTAAATCAATTTAATTAATTAAAAAATTATATGAAATTTTTATTTTATAATTAT
ATATTATTTAAATTAATTAAAACTTTTTTTGAATTAAAAATATTAA
Found at i:1355637 original size:26 final size:26
Alignment explanation
Indices: 1355574--1355642 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
1355564 TAATTAAAAC
1355574 TTTTTTTG-AATTA-AAAATATTTAA
1 TTTTTTTGTAATTAGAAAATATTTAA
* *
1355598 TTTTTATATAAATTAGAAAAT-TTTAA
1 TTTTTTTGT-AATTAGAAAATATTTAA
*
1355624 TTTTTTTGTTAATTCGAAA
1 TTTTTTTG-TAATTAGAAA
1355643 TTAACTGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
24 6 0.17
26 24 0.67
27 6 0.17
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (26 bp):
TTTTTTTGTAATTAGAAAATATTTAA
Found at i:1362214 original size:30 final size:31
Alignment explanation
Indices: 1362178--1362237 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1362168 GGTGCATGAA
1362178 GCCCTCAAACCAAG-AAATTAAATCAATTAG
1 GCCCTCAAACCAAGAAAATTAAATCAATTAG
** *
1362208 GCCCTCAAACTGAGAAAATTGAATCAATTA
1 GCCCTCAAACCAAGAAAATTAAATCAATTA
1362238 ATTCTTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.22
Consensus pattern (31 bp):
GCCCTCAAACCAAGAAAATTAAATCAATTAG
Found at i:1368114 original size:2 final size:2
Alignment explanation
Indices: 1368107--1368133 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1368097 GAGGCGTCTT
1368107 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1368134 AAGTAGGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1377624 original size:21 final size:21
Alignment explanation
Indices: 1377598--1377642 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1377588 GATTTCTGGG
* *
1377598 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1377619 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1377640 CAA
1 CAA
1377643 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1379320 original size:149 final size:149
Alignment explanation
Indices: 1379134--1379437 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
1379124 GAGTCGAGGG
1379134 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
1379199 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
1379264 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
1379283 TCTATGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1379348 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
1379413 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1379432 TCTACG
1 TCTACG
1379438 GGGCACTTCG
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1379460 original size:23 final size:23
Alignment explanation
Indices: 1379416--1379460 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1379406 ATCATTATAT
*
1379416 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1379439 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1379461 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1383789 original size:2 final size:2
Alignment explanation
Indices: 1383782--1383809 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1383772 GAACATGTGA
1383782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1383810 GTCTAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1384463 original size:149 final size:149
Alignment explanation
Indices: 1384277--1384580 Score: 545
Period size: 149 Copynumber: 2.0 Consensus size: 149
1384267 GAGTCGAGGG
*
1384277 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGAAACAT
* * *
1384342 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATATATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
1384407 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
1384426 TCTATGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGAAACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGAAACAT
1384491 ACTTGATCCCTAGCATATATATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATATATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
1384556 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1384575 TCTACG
1 TCTACG
1384581 GGCACTTCGG
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGAAACAT
ACTTGATCCCTAGCATATATATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1384602 original size:22 final size:22
Alignment explanation
Indices: 1384559--1384602 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1384549 ATCATTATAT
*
1384559 GGCACTACGGTGCAATTCTACG
1 GGCACTACGGTGCAATTATACG
* *
1384581 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1384603 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.27
Consensus pattern (22 bp):
GGCACTACGGTGCAATTATACG
Found at i:1387126 original size:23 final size:24
Alignment explanation
Indices: 1387087--1387139 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
1387077 ACTTTTCAAC
1387087 CATTATTAGTGCAAACTATA-AAT-
1 CATTATTAGTGCAAACT-TACAATG
*
1387110 CATTATT-GTTGCCAACTTACAATG
1 CATTATTAG-TGCAAACTTACAATG
1387134 CATTAT
1 CATTAT
1387140 GAATCATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 3 0.12
23 17 0.65
24 6 0.23
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (24 bp):
CATTATTAGTGCAAACTTACAATG
Found at i:1389662 original size:2 final size:2
Alignment explanation
Indices: 1389655--1389679 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1389645 TATATTATTA
1389655 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1389680 CTTTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1398255 original size:19 final size:19
Alignment explanation
Indices: 1398231--1398269 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1398221 CGAATCAAAC
1398231 TAAATAAAAAAATTATTGT
1 TAAATAAAAAAATTATTGT
1398250 TAAATAAAAAAATTATTGT
1 TAAATAAAAAAATTATTGT
1398269 T
1 T
1398270 TTTACGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
TAAATAAAAAAATTATTGT
Found at i:1406280 original size:15 final size:16
Alignment explanation
Indices: 1406242--1406280 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1406232 ATCCTCATTA
*
1406242 TTTTAAACATTTTAAT
1 TTTTAAATATTTTAAT
1406258 TTTT-AATATTTT-AT
1 TTTTAAATATTTTAAT
1406272 TTTTAAATA
1 TTTTAAATA
1406281 AAATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 11 0.52
16 4 0.19
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAAATATTTTAAT
Found at i:1406299 original size:19 final size:20
Alignment explanation
Indices: 1406262--1406299 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1406252 TTTAATTTTT
*
1406262 AATATTTTATTTTTAAATAA
1 AATATTTTATTATTAAATAA
*
1406282 AATA-TTTATTATTGAATA
1 AATATTTTATTATTAAATA
1406300 TAATGGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AATATTTTATTATTAAATAA
Found at i:1408681 original size:29 final size:29
Alignment explanation
Indices: 1408648--1408703 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
1408638 CAAACTTGTA
1408648 GCATGT-AAACTATTAAAAAACAAATGATT
1 GCATGTGAAAC-ATTAAAAAACAAATGATT
1408677 GCATGTGAAACATTAAAAAACAAATGA
1 GCATGTGAAACATTAAAAAACAAATGA
1408704 CTGCCCTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.23
Consensus pattern (29 bp):
GCATGTGAAACATTAAAAAACAAATGATT
Found at i:1412092 original size:21 final size:21
Alignment explanation
Indices: 1412066--1412105 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1412056 TTTATCAATA
*
1412066 TTTAATGTGGATTGGATTTAG
1 TTTAATGTAGATTGGATTTAG
*
1412087 TTTAATTTAGATTGGATTT
1 TTTAATGTAGATTGGATTT
1412106 TGTATGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (21 bp):
TTTAATGTAGATTGGATTTAG
Found at i:1423534 original size:75 final size:75
Alignment explanation
Indices: 1423449--1423630 Score: 190
Period size: 75 Copynumber: 2.4 Consensus size: 75
1423439 ACTTAACGAT
* * * *
1423449 TAAAATAAAATATG-TGTTATCTATTATGTT-AAACTAACTACCAATATGTTTGAAGGTTACTAA
1 TAAAATAAAATA-GATGCTACCTATTACGTTAAAACTAA-TACCAATATGTTTAAAGGTTACTAA
1423512 TAATGTAAACCG
64 TAATGTAAACCG
* * **** *
1423524 TAAAATAAAATAGATGCTACCTATTACGTTAAAATTTATATTTGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGATGCTACCTATTACGTTAAAACTAATACCAATATGTTTAAAGGTTACTAATA
*
1423589 ATGTAAACGG
66 ATGTAAACCG
***
1423599 TAAAAT-AAATAGGCACTACCTATTACGTTAAA
1 TAAAATAAAATAGATGCTACCTATTACGTTAAA
1423631 CTACCTATCG
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
74 24 0.27
75 61 0.68
76 5 0.06
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (75 bp):
TAAAATAAAATAGATGCTACCTATTACGTTAAAACTAATACCAATATGTTTAAAGGTTACTAATA
ATGTAAACCG
Found at i:1423649 original size:74 final size:75
Alignment explanation
Indices: 1423495--1423651 Score: 208
Period size: 74 Copynumber: 2.1 Consensus size: 75
1423485 ACTACCAATA
* ** *
1423495 TGTTTGAAGGTTACTAATAATGTAAACCGTAAAATAAAATAGATGCTACCTATTACGTTAAAATT
1 TGTTTAAAGGTTACTAATAATGTAAACCGTAAAATAAAATAGACACTACCTATTACGTTAAAATA
* **
1423560 TATATTTGTT
66 CATATCGGTT
* * *
1423570 TGTTTAAAGGTTACTAATAATGTAAACGGTAAAAT-AAATAGGCACTACCTATTACGTTAAACTA
1 TGTTTAAAGGTTACTAATAATGTAAACCGTAAAATAAAATAGACACTACCTATTACGTTAAAATA
*
1423634 CCTATCGGTT
66 CATATCGGTT
1423644 TGTTTAAA
1 TGTTTAAA
1423652 CAATAAAATA
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 38 0.54
75 33 0.46
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (75 bp):
TGTTTAAAGGTTACTAATAATGTAAACCGTAAAATAAAATAGACACTACCTATTACGTTAAAATA
CATATCGGTT
Found at i:1423675 original size:52 final size:52
Alignment explanation
Indices: 1423605--1423703 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
1423595 ACGGTAAAAT
* * *
1423605 AAATAGGCACTACCTATTACGTTAAACTACCTATCGGTTTGTTTAAACAATA
1 AAATAGGCACTACATATTACGTTAAACTAACTATCAGTTTGTTTAAACAATA
** *
1423657 AAATAGGTGCTACATATTACGTTAAACTAACTATTAGTTTGTTTAAA
1 AAATAGGCACTACATATTACGTTAAACTAACTATCAGTTTGTTTAAA
1423704 TGTTAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (52 bp):
AAATAGGCACTACATATTACGTTAAACTAACTATCAGTTTGTTTAAACAATA
Found at i:1423675 original size:126 final size:127
Alignment explanation
Indices: 1423527--1423757 Score: 331
Period size: 126 Copynumber: 1.8 Consensus size: 127
1423517 TAAACCGTAA
* * * * *
1423527 AATAAAATAGATGCTACCTATTACGTTAAAATTTA-TATTTGTTTGTTTAAAGGTTACTAATAAT
1 AATAAAATAGATGCTACATATTACGTT-AAACTAACTATTAGTTTGTTTAAAGGTTAATAATAAT
1423591 GTAAACGGTAAAAT-AAATAGGCACTACCTATTACGTTAAACTACCTATCGGTTTGTTTAAAC
65 GTAAACGGTAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTATCGGTTTGTTTAAAC
* *
1423653 AATAAAATAGGTGCTACATATTACGTTAAACTAACTATTAGTTTGTTTAAATGTTAATAATAATG
1 AATAAAATAGATGCTACATATTACGTTAAACTAACTATTAGTTTGTTTAAAGGTTAATAATAATG
* ** * *
1423718 TAAATGGTAAAATAAAATAGGTGCTACGTATTATGTTAAA
66 TAAACGGTAAAATAAAATAGGCACTACCTATTACGTTAAA
1423758 TAGACGTTAC
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
125 5 0.05
126 64 0.70
127 22 0.24
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (127 bp):
AATAAAATAGATGCTACATATTACGTTAAACTAACTATTAGTTTGTTTAAAGGTTAATAATAATG
TAAACGGTAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTATCGGTTTGTTTAAAC
Found at i:1423826 original size:98 final size:98
Alignment explanation
Indices: 1423665--1423927 Score: 355
Period size: 98 Copynumber: 2.7 Consensus size: 98
1423655 TAAAATAGGT
* * * * *
1423665 GCTACATATTACGTTAAACTAACTATTAGTTTGTTTAAATGTTAATAATAATGTAAATGGTAAAA
1 GCTACCTATTACGTTAAACTAGCTATCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAA
* *
1423730 TAAAATAGGTGCTACGTATTATGTTAAATAGAC
66 TAAAATAGGCGCTACCTATTATGTTAAATAGAC
* * * *
1423763 GTTACCTATTACATTAAACTAGCTATCAGCTTGTTTAAAGGTTAATAATAATATAAACGGTAAAA
1 GCTACCTATTACGTTAAACTAGCTATCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAA
* *
1423828 TAAAATATGCGCTACCTATTATGTTAAATAGGC
66 TAAAATAGGCGCTACCTATTATGTTAAATAGAC
* * * * * *
1423861 GCTATCTATTACGTTAAACTAGCTATCTGTTTCTCTAAAGATTAATAATAATGTAAACGATAAAA
1 GCTACCTATTACGTTAAACTAGCTATCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAA
1423926 TA
66 TA
1423928 TATACAACTT
Statistics
Matches: 142, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
98 142 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (98 bp):
GCTACCTATTACGTTAAACTAGCTATCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAA
TAAAATAGGCGCTACCTATTATGTTAAATAGAC
Found at i:1423856 original size:23 final size:23
Alignment explanation
Indices: 1423830--1423878 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1423820 CGGTAAAATA
* *
1423830 AAATATGCGCTACCTATTATGTT
1 AAATAGGCGCTACCTATTACGTT
*
1423853 AAATAGGCGCTATCTATTACGTT
1 AAATAGGCGCTACCTATTACGTT
1423876 AAA
1 AAA
1423879 CTAGCTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (23 bp):
AAATAGGCGCTACCTATTACGTT
Found at i:1424727 original size:108 final size:108
Alignment explanation
Indices: 1424533--1424819 Score: 362
Period size: 108 Copynumber: 2.6 Consensus size: 108
1424523 TGATAATATT
* * ** * * * * * *
1424533 TATTTATAACAAAATAAGAAATTAAAATATTTTATTGTCGTC-GAATTTCGAAAGCCCAATTAGT
1 TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCAG-ATTTCTAAGGCCCAATCAGC
*
1424597 TTAAACTTTGGTAATATTTTAGG-TGCTAGCTAATATGTTGATAA
65 TTAAACTTTGGTAATATTTTAGGAT-CTACCTAATATGTTGATAA
* *
1424641 TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGTCCTATCAGCT
1 TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCAATCAGCT
*
1424706 TAAATTTTGGTAATATTTTAGGATCTACCTAATATGTTGATAA
66 TAAACTTTGGTAATATTTTAGGATCTACCTAATATGTTGATAA
* * * * *
1424749 TATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCATATTTCTAAGGCCCCATCAACT
1 TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCAATCAGC-
1424814 TTAAAC
65 TTAAAC
1424820 AGACGCTACC
Statistics
Matches: 155, Mismatches: 21, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
108 148 0.95
109 7 0.05
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (108 bp):
TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCAATCAGCT
TAAACTTTGGTAATATTTTAGGATCTACCTAATATGTTGATAA
Found at i:1430264 original size:34 final size:30
Alignment explanation
Indices: 1430226--1430294 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1430216 TTGATATAAC
1430226 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1430260 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1430289 AATTTA
1 AATTTA
1430295 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1430305 original size:29 final size:30
Alignment explanation
Indices: 1430235--1430294 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1430225 CAATTTAAGG
1430235 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1430266 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1430295 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1430526 original size:15 final size:15
Alignment explanation
Indices: 1430506--1430535 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1430496 TACCCCCAGG
1430506 GGTATCCATACCCCT
1 GGTATCCATACCCCT
*
1430521 GGTATCGATACCCCT
1 GGTATCCATACCCCT
1430536 TAGGGGTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.27
Consensus pattern (15 bp):
GGTATCCATACCCCT
Found at i:1430532 original size:33 final size:35
Alignment explanation
Indices: 1430488--1430558 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 35
1430478 TTGCTCGGAG
*
1430488 GGTATCTATACCCC-CAGGGGTATCCATA-CCCCT
1 GGTATCGATACCCCTCAGGGGTATCCATACCCCCT
* **
1430521 GGTATCGATACCCCTTAGGGGTATTTATACCCCCT
1 GGTATCGATACCCCTCAGGGGTATCCATACCCCCT
1430556 GGT
1 GGT
1430559 TGCAACGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 13 0.41
34 11 0.34
35 8 0.25
ACGTcount: A:0.20, C:0.31, G:0.21, T:0.28
Consensus pattern (35 bp):
GGTATCGATACCCCTCAGGGGTATCCATACCCCCT
Found at i:1430609 original size:21 final size:21
Alignment explanation
Indices: 1430585--1430627 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1430575 ATTTGAATTT
*
1430585 TATGAAGTAGTACCGATACCC
1 TATGAAGGAGTACCGATACCC
*
1430606 TATGAAGGATTACCGATACCC
1 TATGAAGGAGTACCGATACCC
1430627 T
1 T
1430628 CTATCGTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (21 bp):
TATGAAGGAGTACCGATACCC
Found at i:1431865 original size:19 final size:19
Alignment explanation
Indices: 1431829--1431865 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1431819 TGAAAATGAT
*
1431829 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
1431848 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
1431866 ATAAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:1433205 original size:29 final size:30
Alignment explanation
Indices: 1433135--1433194 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1433125 CAATTTAAGG
*
1433135 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTAGACTTGAATTGAATTTA
1433166 CAAAATGTTTTTAGACTT-AATTGAATTTA
1 CAAAATGTTTTTAGACTTGAATTGAATTTA
1433195 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTAGACTTGAATTGAATTTA
Found at i:1433420 original size:21 final size:21
Alignment explanation
Indices: 1433396--1433437 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1433386 ATTTGAATTT
*
1433396 TATGAAGTAGTACCGATACCC
1 TATGAAGGAGTACCGATACCC
* *
1433417 TATGAAGGGGTACTGATACCC
1 TATGAAGGAGTACCGATACCC
1433438 CCTATCGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (21 bp):
TATGAAGGAGTACCGATACCC
Found at i:1437674 original size:31 final size:30
Alignment explanation
Indices: 1437632--1437735 Score: 122
Period size: 31 Copynumber: 3.5 Consensus size: 30
1437622 AATATATGCA
1437632 AAAAGTTAAGATAAAAGTAAAATATATTTTT
1 AAAAGTTAAGATAAAA-TAAAATATATTTTT
*
1437663 AAAATTTAAGATAATAATAAAATATATTTTT
1 AAAAGTTAAGATAA-AATAAAATATATTTTT
* * *
1437694 -TAAGTTAAGGTAGAATAAAATATA-TTTT
1 AAAAGTTAAGATAAAATAAAATATATTTTT
* *
1437722 ATAAGCTAAGATAA
1 AAAAGTTAAGATAA
1437736 TAAATAGATA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.06
29 21 0.33
30 9 0.14
31 27 0.43
32 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.10, T:0.37
Consensus pattern (30 bp):
AAAAGTTAAGATAAAATAAAATATATTTTT
Found at i:1437711 original size:29 final size:29
Alignment explanation
Indices: 1437634--1437735 Score: 123
Period size: 29 Copynumber: 3.4 Consensus size: 29
1437624 TATATGCAAA
*
1437634 AAGTTAAGATAAAAGTAAAATATATTTTTAA
1 AAGTTAAGATAAAA-TAAAATATATTTTT-T
*
1437665 AATTTAAGATAATAATAAAATATATTTTTT
1 AAGTTAAGATAA-AATAAAATATATTTTTT
* * *
1437695 AAGTTAAGGTAGAATAAAATATATTTTAT
1 AAGTTAAGATAAAATAAAATATATTTTTT
*
1437724 AAGCTAAGATAA
1 AAGTTAAGATAA
1437736 TAAATAGATA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
29 25 0.41
30 9 0.15
31 25 0.41
32 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.37
Consensus pattern (29 bp):
AAGTTAAGATAAAATAAAATATATTTTTT
Found at i:1442270 original size:14 final size:15
Alignment explanation
Indices: 1442251--1442294 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
1442241 ATTTTCATTA
1442251 AAAAAAAT-AAAATT
1 AAAAAAATCAAAATT
1442265 AAAAAAATCAAAATT
1 AAAAAAATCAAAATT
1442280 AAAAAAATCAAAATT
1 AAAAAAATCAAAATT
1442295 TGAGATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAAAATCAAAATT
Found at i:1455398 original size:28 final size:28
Alignment explanation
Indices: 1455364--1455430 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
1455354 CATTTTACAC
* *
1455364 AAATAGCACCCTTTTAAAATAATTACCA
1 AAATAGCACCATTTCAAAATAATTACCA
*
1455392 AAATAGCACCATTTCAAATTAATTACCA
1 AAATAGCACCATTTCAAAATAATTACCA
*
1455420 GAATAGCACCA
1 AAATAGCACCA
1455431 AAACCGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.25
Consensus pattern (28 bp):
AAATAGCACCATTTCAAAATAATTACCA
Found at i:1455447 original size:29 final size:29
Alignment explanation
Indices: 1455408--1455487 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
1455398 CACCATTTCA
*
1455408 AATTAATTACCAGAATAGCACCAAAACCG
1 AATTATTTACCAGAATAGCACCAAAACCG
*
1455437 AATTATTTACCAGATTAGCACCAAAACCG
1 AATTATTTACCAGAATAGCACCAAAACCG
*
1455466 AATTATTTACCATAATAGCACC
1 AATTATTTACCAGAATAGCACC
1455488 GATCAACGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.24
Consensus pattern (29 bp):
AATTATTTACCAGAATAGCACCAAAACCG
Found at i:1466055 original size:25 final size:25
Alignment explanation
Indices: 1466022--1466074 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 25
1466012 AATCTAAACT
*
1466022 AAATATTAAGTATATTAAAA-AAAATA
1 AAATATTAA--ATATCAAAATAAAATA
1466048 AAAT-TTAAATATCAAAATAAAATA
1 AAATATTAAATATCAAAATAAAATA
1466072 AAA
1 AAA
1466075 GTAATAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 8 0.32
24 9 0.36
25 4 0.16
26 4 0.16
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (25 bp):
AAATATTAAATATCAAAATAAAATA
Found at i:1469151 original size:6 final size:6
Alignment explanation
Indices: 1469140--1469171 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1469130 GTTGCCCATT
1469140 GATGAA GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GA
1469172 AGAGCCATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16
Consensus pattern (6 bp):
GATGAA
Found at i:1470393 original size:48 final size:50
Alignment explanation
Indices: 1470310--1470455 Score: 197
Period size: 48 Copynumber: 2.9 Consensus size: 50
1470300 ACAAGACATT
* *
1470310 ACCAATATTTCAATCTATACATAACCGGGCATTCACTCTATTCAACCTATTA
1 ACCAATATTTCAA-CTA-ACATAATCGAGCATTCACTCTATTCAACCTATTA
* * *
1470362 ACCGATATTTTAA-T-ATATAATCGAGCATTCACTCTATTCAACCTATTA
1 ACCAATATTTCAACTAACATAATCGAGCATTCACTCTATTCAACCTATTA
1470410 ACCAATATTTCAATCTACACATAATCGAGCATTCACTCTATTCAAC
1 ACCAATATTTCAA-CTA-ACATAATCGAGCATTCACTCTATTCAAC
1470456 TTATCTATAC
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
48 42 0.51
50 2 0.02
52 38 0.46
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (50 bp):
ACCAATATTTCAACTAACATAATCGAGCATTCACTCTATTCAACCTATTA
Found at i:1470735 original size:21 final size:22
Alignment explanation
Indices: 1470700--1470740 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1470690 ACTATTTTAT
*
1470700 AAGTAAAAATCAAAGGAAATAA
1 AAGTAAAAATCAAAGAAAATAA
*
1470722 AAGTAAAACT-AAAGAAAAT
1 AAGTAAAAATCAAAGAAAAT
1470741 CAAACCTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (22 bp):
AAGTAAAAATCAAAGAAAATAA
Found at i:1481397 original size:16 final size:16
Alignment explanation
Indices: 1481376--1481406 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1481366 TCTAATTTTT
1481376 TTTTTGAGTTCAAGTC
1 TTTTTGAGTTCAAGTC
1481392 TTTTTGAGTTCAAGT
1 TTTTTGAGTTCAAGT
1481407 TTCAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTTTGAGTTCAAGTC
Found at i:1484228 original size:74 final size:75
Alignment explanation
Indices: 1484121--1484263 Score: 243
Period size: 74 Copynumber: 1.9 Consensus size: 75
1484111 TAAAAATCAT
*
1484121 CCGTATAATTTACCTAAGATTATTTATAATTTAAGATTAAAACTTTTAACTGAAGTTTTTACCGT
1 CCGTATAATTCACCTAAGATTATTTATAATTTAAGATTAAAACTTTTAACTGAAGTTTTTACCGT
1484186 TAAATGAACA
66 TAAATGAACA
* * *
1484196 CCGTGTAATTCACCTAA-ATTATTTATAGTTTAAGATTAAAACTTTTAACTGAAGTTTTTAGCGT
1 CCGTATAATTCACCTAAGATTATTTATAATTTAAGATTAAAACTTTTAACTGAAGTTTTTACCGT
1484260 TAAA
66 TAAA
1484264 CGGACTGGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
74 49 0.77
75 15 0.23
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (75 bp):
CCGTATAATTCACCTAAGATTATTTATAATTTAAGATTAAAACTTTTAACTGAAGTTTTTACCGT
TAAATGAACA
Found at i:1484689 original size:17 final size:17
Alignment explanation
Indices: 1484664--1484700 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1484654 ACTCGAATCG
1484664 AAAGCAACCTGAACCCA
1 AAAGCAACCTGAACCCA
* *
1484681 AAAGTAACCTGAACCGA
1 AAAGCAACCTGAACCCA
1484698 AAA
1 AAA
1484701 ATCAGAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.27, G:0.14, T:0.08
Consensus pattern (17 bp):
AAAGCAACCTGAACCCA
Found at i:1485844 original size:21 final size:20
Alignment explanation
Indices: 1485820--1485883 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1485810 AACTTTGAAA
1485820 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
1485841 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
1485855 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
1485876 AAATGTTT
1 AAATGTTT
1485884 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:1485858 original size:35 final size:36
Alignment explanation
Indices: 1485812--1485933 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
1485802 TGGTAACCAA
1485812 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
1485849 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
1485884 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
1485921 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
1485934 AATGGATAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:1490525 original size:37 final size:36
Alignment explanation
Indices: 1490426--1490544 Score: 152
Period size: 35 Copynumber: 3.3 Consensus size: 36
1490416 TGGTAACCAA
*
1490426 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAGATGTTT
* * *
1490463 CTTTG-AAAATGGTTTTCAAAATTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAGATGTTT
*
1490498 CTTTGAAAAATAATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-AGTTTTCAAAGTTTGGTAGATGTTT
*
1490535 -GTTGAAAAAT
1 CTTTGAAAAAT
1490545 GATAATGGGA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 33 0.45
36 14 0.19
37 26 0.36
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAGATGTTT
Found at i:1493592 original size:21 final size:20
Alignment explanation
Indices: 1493544--1493596 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
1493534 ACCGTGATTG
* *
1493544 CGGCCGTCGCGGTGCTATTG
1 CGGCCGTCGCGGCGCTATTA
* *
1493564 TGGTCGTCGCGGACGCTATTA
1 CGGCCGTCGCGG-CGCTATTA
1493585 CGGCCGTCGCGG
1 CGGCCGTCGCGG
1493597 GTAACTCGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.08, C:0.30, G:0.40, T:0.23
Consensus pattern (20 bp):
CGGCCGTCGCGGCGCTATTA
Found at i:1504776 original size:27 final size:26
Alignment explanation
Indices: 1504729--1504781 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1504719 CCCTCGAGCC
1504729 TCCATCCCCAAATCCTCCCCTCTCTCG
1 TCCATCCCCAAATCCTCCCCTC-CTCG
* *
1504756 TCCATTCCC-AATCTCTTCCCTCCTCG
1 TCCATCCCCAAATC-CTCCCCTCCTCG
1504782 CCGTTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.13, C:0.53, G:0.04, T:0.30
Consensus pattern (26 bp):
TCCATCCCCAAATCCTCCCCTCCTCG
Found at i:1509208 original size:24 final size:24
Alignment explanation
Indices: 1509176--1509225 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1509166 TTCTTTCGTT
1509176 TTCAATTGAGCTCAAATTTTAGGC
1 TTCAATTGAGCTCAAATTTTAGGC
1509200 TTCAATTGAGCTCAAATTTTAGGC
1 TTCAATTGAGCTCAAATTTTAGGC
1509224 TT
1 TT
1509226 TAATCAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (24 bp):
TTCAATTGAGCTCAAATTTTAGGC
Found at i:1509522 original size:20 final size:20
Alignment explanation
Indices: 1509497--1509582 Score: 95
Period size: 21 Copynumber: 4.3 Consensus size: 20
1509487 GTTCACCCCA
1509497 GTTTTCCCGGTTTTCAGCCG
1 GTTTTCCCGGTTTTCAGCCG
*
1509517 GTTTTCCCGATTTTCAGCCG
1 GTTTTCCCGGTTTTCAGCCG
**
1509537 GTTCACCCCGGTTTTCAGCCG
1 GTT-TTCCCGGTTTTCAGCCG
**
1509558 GTTCACCCCGGTTTTC--CCG
1 GTT-TTCCCGGTTTTCAGCCG
1509577 GTTTTC
1 GTTTTC
1509583 AGTCGGTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
18 1 0.02
19 6 0.10
20 22 0.37
21 30 0.51
ACGTcount: A:0.07, C:0.34, G:0.22, T:0.37
Consensus pattern (20 bp):
GTTTTCCCGGTTTTCAGCCG
Found at i:1509551 original size:21 final size:21
Alignment explanation
Indices: 1509502--1509573 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
1509492 CCCCAGTTTT
**
1509502 CCCGGTTTTCAGCCGGTT-TT
1 CCCGGTTTTCAGCCGGTTCAC
*
1509522 CCCGATTTTCAGCCGGTTCAC
1 CCCGGTTTTCAGCCGGTTCAC
1509543 CCCGGTTTTCAGCCGGTTCAC
1 CCCGGTTTTCAGCCGGTTCAC
1509564 CCCGGTTTTC
1 CCCGGTTTTC
1509574 CCGGTTTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.08, C:0.36, G:0.22, T:0.33
Consensus pattern (21 bp):
CCCGGTTTTCAGCCGGTTCAC
Found at i:1514632 original size:21 final size:21
Alignment explanation
Indices: 1514619--1514659 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1514609 AAATCCTATC
1514619 ATATAAACCCTAAACCCTAAT
1 ATATAAACCCTAAACCCTAAT
*
1514640 ATATAAACCCTAAACTCTAA
1 ATATAAACCCTAAACCCTAA
1514660 ACATTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (21 bp):
ATATAAACCCTAAACCCTAAT
Found at i:1514659 original size:56 final size:56
Alignment explanation
Indices: 1514565--1514695 Score: 181
Period size: 56 Copynumber: 2.3 Consensus size: 56
1514555 ACTTAAACCC
* * * * *
1514565 TAAACCCTTAACCCTTAACACATAAACCCTAAATTCTAAACTTTAAATCCTATCATA
1 TAAACCCTAAACCC-TAACACATAAACCCTAAACTCTAAACATTAAATCATATCACA
* * *
1514622 TAAACCCTAAACCCTAATATATAAACCCTAAACTCTAAACATTAAATCATTTCACA
1 TAAACCCTAAACCCTAACACATAAACCCTAAACTCTAAACATTAAATCATATCACA
1514678 TAAACCCTAAACCCTAAC
1 TAAACCCTAAACCCTAAC
1514696 CCTAAATCTT
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
56 52 0.80
57 13 0.20
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (56 bp):
TAAACCCTAAACCCTAACACATAAACCCTAAACTCTAAACATTAAATCATATCACA
Found at i:1514667 original size:21 final size:21
Alignment explanation
Indices: 1514608--1514667 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1514598 TTCTAAACTT
* *
1514608 TAAATCCTATCATATAAACCC
1 TAAACCCTAACATATAAACCC
*
1514629 TAAACCCTAATATATAAACCC
1 TAAACCCTAACATATAAACCC
*
1514650 TAAACTCTAAACAT-TAAA
1 TAAACCCT-AACATATAAA
1514668 TCATTTCACA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAACCCTAACATATAAACCC
Found at i:1514708 original size:41 final size:42
Alignment explanation
Indices: 1514643--1514744 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 42
1514633 CCCTAATATA
*
1514643 TAAACCCTAAACTCTAAACATTAAATCAT-TTCACATAAACCC
1 TAAACCCTAAACCCTAAACATTAAATCATATT-ACATAAACCC
*
1514685 TAAACCCT-AACCCTAAATC-TTAAATCATATTACATAAACTGC
1 TAAACCCTAAACCCTAAA-CATTAAATCATATTACATAAAC-CC
*
1514727 -AAACCCTAAACTCTAAAC
1 TAAACCCTAAACCCTAAAC
1514745 CCTAAACCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
41 33 0.62
42 20 0.38
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.25
Consensus pattern (42 bp):
TAAACCCTAAACCCTAAACATTAAATCATATTACATAAACCC
Found at i:1515167 original size:15 final size:14
Alignment explanation
Indices: 1515141--1515170 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1515131 TTTATTCATC
1515141 AATAATGTATTTTT
1 AATAATGTATTTTT
*
1515155 AATAATGTAATTTT
1 AATAATGTATTTTT
1515169 AA
1 AA
1515171 AAAATCTAAA
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:1516507 original size:18 final size:18
Alignment explanation
Indices: 1516484--1516527 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1516474 AAGAGACGGG
1516484 GAATGATGATGCTGTTTT
1 GAATGATGATGCTGTTTT
*
1516502 GAATGATGATGTTGTTTT
1 GAATGATGATGCTGTTTT
*
1516520 GCATGATG
1 GAATGATG
1516528 GCATGGCGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.43
Consensus pattern (18 bp):
GAATGATGATGCTGTTTT
Found at i:1520471 original size:21 final size:21
Alignment explanation
Indices: 1520447--1520488 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1520437 ATTCGCATCA
* *
1520447 ATACATACATTTTAATAATAT
1 ATACACACATCTTAATAATAT
1520468 ATACACACATCTTAATAATAT
1 ATACACACATCTTAATAATAT
1520489 GATAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (21 bp):
ATACACACATCTTAATAATAT
Found at i:1526062 original size:20 final size:20
Alignment explanation
Indices: 1526037--1526077 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1526027 ATCTATCAAG
**
1526037 TGATTTTAATGAATAAAAAA
1 TGATTTTAACAAATAAAAAA
1526057 TGATTTTAACAAATAAAAAA
1 TGATTTTAACAAATAAAAAA
1526077 T
1 T
1526078 ATTATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (20 bp):
TGATTTTAACAAATAAAAAA
Found at i:1526852 original size:2 final size:2
Alignment explanation
Indices: 1526845--1526887 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1526835 CCAAAAACAC
1526845 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1526886 TA
1 TA
1526888 ATTTTTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1527129 original size:16 final size:17
Alignment explanation
Indices: 1527097--1527132 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1527087 AGATATTAAA
*
1527097 ATTTGATAATTTATTTT
1 ATTTGATAATATATTTT
1527114 ATTTGATAA-ATATTTT
1 ATTTGATAATATATTTT
1527130 ATT
1 ATT
1527133 ACAAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
ATTTGATAATATATTTT
Found at i:1529535 original size:3 final size:3
Alignment explanation
Indices: 1529527--1529651 Score: 177
Period size: 3 Copynumber: 42.7 Consensus size: 3
1529517 TTATATAAAT
* *
1529527 TAA TAA TAA T-A TAA TGA TAA TAA TAA TAA TAA TGA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1529573 TAA TAA TGA TAA TAA TAA TAA TAA T-A TAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
1529618 TAA TGA TAA TAA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1529652 TGGATAAAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
2 8 0.07
3 98 0.90
4 3 0.03
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1530109 original size:119 final size:119
Alignment explanation
Indices: 1529807--1530326 Score: 797
Period size: 119 Copynumber: 4.5 Consensus size: 119
1529797 TTCTCCAGAT
* ** *
1529807 GAGTTCTTCTCATTACGAACT-TT-CTGCTGGGGATGA-GTTCCATCAAA-TGATGAATTCAAGC
1 GAGTTCTTCTCATTATGAACTCTTCCT-CTGGAAATGATGATCCATCAAATTGATGAATTCAAGC
*
1529868 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCCTT-CTTCTTCAGAT---
65 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT-CTTCCTTCTTCAGATGAC
* * *
1529920 GAGTTCTTCTC---ATGAAC-C-T--TCTGGTAATGTTGATCCATC-AAGTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATTCAAGCA
1529977 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
1530031 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATTCAAGCA
1530096 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
1530150 GAGTTCTTCTCATTATGAACTCTTCC-CTTGGAAATGATGATCCATCAAATTGATGAATTCAAAC
1 GAGTTCTTCTCATTATGAACTCTTCCTC-TGGAAATGATGATCCATCAAATTGATGAATTCAAGC
1530214 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
1530269 GAATTCTTCTCATTATGAACT-TTCCTCTGGAAATGATGATCCATCAAATTGATGAATT
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATT
1530327 TGAATCTTTG
Statistics
Matches: 379, Mismatches: 11, Indels: 29
0.90 0.03 0.07
Matches are distributed among these distances:
107 12 0.03
108 69 0.18
109 1 0.00
110 5 0.01
111 11 0.03
113 11 0.03
114 6 0.02
115 1 0.00
116 1 0.00
118 54 0.14
119 208 0.55
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (119 bp):
GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATTCAAGCA
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:1531082 original size:51 final size:52
Alignment explanation
Indices: 1530938--1531766 Score: 1455
Period size: 52 Copynumber: 16.1 Consensus size: 52
1530928 TCTAAACTCA
* *
1530938 ATGCT-TGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAA
1 ATGCTATG-TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
1530990 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531042 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
1531093 ATGCTATGTTCTGTCTAACCAGATCAGATACCTCAAAGAACACTTTCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
1531145 ATGCTATGTTCTGTCTAACCAGATCAGATACCTCAAAGAACACTTTCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
1531197 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531249 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
1531300 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
1531352 ATGATATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
1531403 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531455 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531506 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531557 ATGCTATGTTCT-TCTAACCAGATCAGATAACTC-AAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
1531607 ATGCTATATTCT-TCTAACCAGAT-AGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531657 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
1531708 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531760 ATGCTAT
1 ATGCTAT
1531767 TGAGCACATA
Statistics
Matches: 751, Mismatches: 19, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
49 9 0.01
50 78 0.10
51 310 0.41
52 352 0.47
53 2 0.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (52 bp):
ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:1531084 original size:103 final size:103
Alignment explanation
Indices: 1530938--1531766 Score: 1497
Period size: 103 Copynumber: 8.1 Consensus size: 103
1530928 TCTAAACTCA
* *
1530938 ATGCT-TGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGTTCT
1 ATGCTATG-TTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT
1531002 GTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
64 GTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531042 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
* * *
1531107 CTAACCAGATCAGATACCTCAAAGAACACTTTCAGAAG
66 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
1531145 ATGCTATGTTCTGTCTAACCAGATCAGATACCTCAAAGAACACTTTCAGAAGATGCTATGTTCTG
1 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG
1531210 TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
65 TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531249 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
1531314 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
66 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
1531352 ATGATATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
1531417 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
66 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531455 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-T
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
*
1531519 CTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
66 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
1531557 ATGCTATGTTCTTCTAACCAGATCAGATAACTC-AAGAACACTTCCAGAAGATGCTATATTCT-T
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
*
1531620 CTAACCAGAT-AGATAACTCAAAGAACACTTCCAGAAG
66 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531657 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
1531722 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
66 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1531760 ATGCTAT
1 ATGCTAT
1531767 TGAGCACATA
Statistics
Matches: 702, Mismatches: 18, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
100 60 0.09
101 67 0.10
102 81 0.12
103 385 0.55
104 107 0.15
105 2 0.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (103 bp):
ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT
CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:1532706 original size:6 final size:5
Alignment explanation
Indices: 1532689--1532749 Score: 60
Period size: 5 Copynumber: 13.0 Consensus size: 5
1532679 ACCTTGACCC
* *
1532689 CTTTT -TTTT -TTTC CTTTT CTTTT -TTTT CTTTT CTTTT TTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1532736 -TTTT -TTTCT CTTTT
1 CTTTT CTTT-T CTTTT
1532750 TTCTTCTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
4 18 0.38
5 27 0.56
6 3 0.06
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
CTTTT
Found at i:1532713 original size:15 final size:14
Alignment explanation
Indices: 1532689--1532749 Score: 81
Period size: 14 Copynumber: 4.4 Consensus size: 14
1532679 ACCTTGACCC
*
1532689 CTTTT-TTTTTTTC
1 CTTTTCTTTTTTTT
1532702 CTTTTCTTTTTTTT
1 CTTTTCTTTTTTTT
1532716 CTTTTCTTTTTTTTT
1 CTTTTC-TTTTTTTT
1532731 CTTTT-TTTTTTTCT
1 CTTTTCTTTTTTT-T
1532745 CTTTT
1 CTTTT
1532750 TTCTTCTTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
13 12 0.27
14 19 0.43
15 13 0.30
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
CTTTTCTTTTTTTT
Found at i:1532725 original size:29 final size:29
Alignment explanation
Indices: 1532693--1532749 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1532683 TGACCCCTTT
1532693 TTTTTTTTCCTTTTCTTTTTTT-TCTTTTC
1 TTTTTTTTCCTTTT-TTTTTTTCTCTTTTC
*
1532722 TTTTTTTTTCTTTTTTTTTTTCTCTTTT
1 TTTTTTTTCCTTTTTTTTTTTCTCTTTT
1532750 TTCTTCTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (29 bp):
TTTTTTTTCCTTTTTTTTTTTCTCTTTTC
Found at i:1532730 original size:24 final size:24
Alignment explanation
Indices: 1532703--1532757 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1532693 TTTTTTTTCC
1532703 TTTTCTTTTTTTTCTTT-TCTTTTT
1 TTTTCTTTTTTTT-TTTCTCTTTTT
1532727 TTTTCTTTTTTTTTTTCTCTTTTT
1 TTTTCTTTTTTTTTTTCTCTTTTT
*
1532751 TCTTCTT
1 TTTTCTT
1532758 CAAGCATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (24 bp):
TTTTCTTTTTTTTTTTCTCTTTTT
Found at i:1532750 original size:15 final size:15
Alignment explanation
Indices: 1532690--1532751 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 15
1532680 CCTTGACCCC
1532690 TTTTTTTTTTTC-CT
1 TTTTTTTTTTTCTCT
1532704 TTTCTTTTTTTTCT-T
1 TTT-TTTTTTTTCTCT
*
1532719 TTCTTTTTTTT-TC-
1 TTTTTTTTTTTCTCT
1532732 TTTTTTTTTTTCTCT
1 TTTTTTTTTTTCTCT
1532747 TTTTT
1 TTTTT
1532752 CTTCTTCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
13 11 0.27
14 13 0.32
15 17 0.41
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTTTCTCT
Found at i:1532751 original size:1 final size:1
Alignment explanation
Indices: 1532690--1532742 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
1532680 CCTTGACCCC
** * * * *
1532690 TTTTTTTTTTTCCTTTTCTTTTTTTTCTTTTCTTTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1532743 CTCTTTTTTC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:1543153 original size:18 final size:18
Alignment explanation
Indices: 1543130--1543164 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1543120 ATACTTGCAA
1543130 ATAAAACAT-ATAAATATT
1 ATAAAA-ATAATAAATATT
1543148 ATAAAAATAATAAATAT
1 ATAAAAATAATAAATAT
1543165 AAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATAATAAATATT
Found at i:1544789 original size:19 final size:20
Alignment explanation
Indices: 1544767--1544816 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1544757 CTCTGTATAT
*
1544767 TTTTTGTTTCTGTCTCT-TC
1 TTTTTGTTTCCGTCTCTGTC
1544786 TTTTTGTCTCTCCGTCTCTGTC
1 TTTTTGT-T-TCCGTCTCTGTC
1544808 TTTTT-TTTC
1 TTTTTGTTTC
1544817 AGGTGGGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 9 0.33
22 7 0.26
ACGTcount: A:0.00, C:0.24, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTTTGTTTCCGTCTCTGTC
Found at i:1545264 original size:3 final size:3
Alignment explanation
Indices: 1545256--1545388 Score: 214
Period size: 3 Copynumber: 44.7 Consensus size: 3
1545246 TAATATAAAT
* *
1545256 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1545304 TAA TAA TAA TAA TGA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1545351 TAT TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1545389 TGGATAAAAA
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 117 0.98
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1550309 original size:2 final size:2
Alignment explanation
Indices: 1550297--1550360 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
1550287 ACTTCAATAA
1550297 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1550338 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
1550361 ATATATATAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1550365 original size:2 final size:2
Alignment explanation
Indices: 1550360--1550397 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1550350 TCTCTCTCTC
1550360 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1550398 ATTACCAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1555492 original size:22 final size:23
Alignment explanation
Indices: 1555436--1555494 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1555426 TTCAAGTTCA
* * *
1555436 AACTCGAGTTCGAGCTTGAATTG
1 AACTCAAGTTTGAGCTTCAATTG
*
1555459 AGCTCAAGTTTGAGCTTCAATTG
1 AACTCAAGTTTGAGCTTCAATTG
1555482 AACT-AAGTTTGAG
1 AACTCAAGTTTGAG
1555495 AAGAGTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 9 0.29
23 22 0.71
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (23 bp):
AACTCAAGTTTGAGCTTCAATTG
Found at i:1557178 original size:17 final size:16
Alignment explanation
Indices: 1557158--1557189 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1557148 CCTTAAAAAA
1557158 ATATTTCTAGACTCAAG
1 ATATTTCTAG-CTCAAG
1557175 ATATTTCTAGCTCAA
1 ATATTTCTAGCTCAA
1557190 ATCGCATGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (16 bp):
ATATTTCTAGCTCAAG
Found at i:1569872 original size:34 final size:35
Alignment explanation
Indices: 1569798--1569872 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1569788 AAAACAGTCC
*
1569798 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
* *
1569833 TCAATTTCATTCTCAACCCTAAATTCCAAA-TAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
1569867 TCAATT
1 TCAATT
1569873 AATTCAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 10 0.27
35 27 0.73
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
Found at i:1570482 original size:23 final size:20
Alignment explanation
Indices: 1570440--1570485 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 20
1570430 AATTAATCAT
1570440 TTAACCAGATCTGACATATG
1 TTAACCAGATCTGACATATG
*
1570460 TTAACACATGATCATGATATATG
1 TTAAC-CA-GATC-TGACATATG
1570483 TTA
1 TTA
1570486 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 2 0.09
22 4 0.18
23 11 0.50
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
TTAACCAGATCTGACATATG
Found at i:1570501 original size:129 final size:130
Alignment explanation
Indices: 1570266--1570512 Score: 379
Period size: 129 Copynumber: 1.9 Consensus size: 130
1570256 TATTTATATA
* * ** *
1570266 ATCAATTTGGTCCTAAATTAAATAGAATTTAATTAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
1570331 TTAGCACATGATCATGACACGTGTCATTGGTGACGCATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1570396 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA-GATCTGACATATG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * * *
1570460 TTAACACATGATCATGATATATGTTATTGGTGACACCTGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
1570513 GAAGAAATTA
Statistics
Matches: 105, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
129 58 0.55
130 47 0.45
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1570997 original size:15 final size:16
Alignment explanation
Indices: 1570973--1571009 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1570963 TTTAATTTCT
1570973 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
1570987 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
1571003 TGATTCA
1 T-ATTCA
1571010 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:1573878 original size:4 final size:4
Alignment explanation
Indices: 1573869--1573895 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1573859 GCCTGCATAA
1573869 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
1573896 AACAGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1575355 original size:29 final size:29
Alignment explanation
Indices: 1575304--1575391 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
1575294 CTTCCTAGCA
* *
1575304 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACGCCGGGCGACCTTG
* * *
1575333 TAGGTCGCCATGCACGCCAGGCGACATGG
1 TAGGTCGCCATGCACGCCGGGCGACCTTG
*
1575362 TAGGTCGCCATGCACGCTGGGCGACCTTG
1 TAGGTCGCCATGCACGCCGGGCGACCTTG
1575391 T
1 T
1575392 CCTGCGCCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.19
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCGGGCGACCTTG
Found at i:1575425 original size:22 final size:23
Alignment explanation
Indices: 1575425--1575468 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1575415 TGCTCGCCTG
**
1575425 CGCCCTGCTCCCCGTTGCATGCT
1 CGCCCTGCTCCCCACTGCATGCT
1575448 CG-CCTGCTCCCCACTGCATGC
1 CGCCCTGCTCCCCACTGCATGC
1575469 AGGCGACCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.07, C:0.50, G:0.20, T:0.23
Consensus pattern (23 bp):
CGCCCTGCTCCCCACTGCATGCT
Found at i:1575425 original size:29 final size:29
Alignment explanation
Indices: 1575392--1575454 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
1575382 GCGACCTTGT
1575392 CCTGCGCCCTGCTCCCCATTGCATGCTCG
1 CCTGCGCCCTGCTCCCCATTGCATGCTCG
*
1575421 CCTGCGCCCTGCTCCCCGTTGCATGCTCG
1 CCTGCGCCCTGCTCCCCATTGCATGCTCG
1575450 CCTGC
1 CCTGC
1575455 TCCCCACTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.05, C:0.49, G:0.22, T:0.24
Consensus pattern (29 bp):
CCTGCGCCCTGCTCCCCATTGCATGCTCG
Found at i:1575534 original size:31 final size:31
Alignment explanation
Indices: 1575499--1575560 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1575489 CATGGCGCAT
*
1575499 GCAAAGCTTCATCTTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
*
1575530 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1575561 TAGAACACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Found at i:1576426 original size:29 final size:30
Alignment explanation
Indices: 1576393--1576460 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
1576383 CTTATAACAT
1576393 TTGTTATTAAGGATCCAA-TTTTTCAATAC
1 TTGTTATTAAGGATCCAATTTTTTCAATAC
* * * * * *
1576422 TTGTTATCAGGGGTCTAATTTTTTTAATAT
1 TTGTTATTAAGGATCCAATTTTTTCAATAC
1576452 TTGTTATTA
1 TTGTTATTA
1576461 GGGGCATACT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.51
Consensus pattern (30 bp):
TTGTTATTAAGGATCCAATTTTTTCAATAC
Found at i:1576549 original size:108 final size:109
Alignment explanation
Indices: 1576411--1576606 Score: 279
Period size: 108 Copynumber: 1.8 Consensus size: 109
1576401 AAGGATCCAA
* * * * *
1576411 TTTTTCAATACTTGTTATCAGGGGTCTAATTTTTTTAATATTTGTTATTAGGGGCATACTT-TTA
1 TTTTTCAATACTTGTTATCAGAGGTATAATTTTTTTAATATTTGTTATTAAGAGAAT-CTTCTTA
1576475 AAATTTAATTTTT-TTTAATATTTATTTGTTATTATGAGTTTAAT
65 AAATTTAATTTTTCTTTAATATTTATTTGTTATTATGAGTTTAAT
* * * *
1576519 TTTTTCAATACTTTTTATTAGAGGTATAATTTTTTTAATATTTTTTATTAAGAGAATGTTCTTAA
1 TTTTTCAATACTTGTTATCAGAGGTATAATTTTTTTAATATTTGTTATTAAGAGAATCTTCTTAA
*
1576584 AATTTACTTTTTCTTTAATATTT
66 AATTTAATTTTTCTTTAATATTT
1576607 GTTATTAGGA
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
107 2 0.03
108 64 0.84
109 10 0.13
ACGTcount: A:0.28, C:0.06, G:0.10, T:0.57
Consensus pattern (109 bp):
TTTTTCAATACTTGTTATCAGAGGTATAATTTTTTTAATATTTGTTATTAAGAGAATCTTCTTAA
AATTTAATTTTTCTTTAATATTTATTTGTTATTATGAGTTTAAT
Found at i:1593593 original size:25 final size:25
Alignment explanation
Indices: 1593537--1593599 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
1593527 TAATAATTAT
*
1593537 TTTAA-ATATTTTTATAATTTTTAAT
1 TTTAATATATTTTTAT-ATTTTTAAG
1593562 TTATAATATATTTTTAT-TTTTTAGAG
1 TT-TAATATATTTTTATATTTTTA-AG
*
1593588 TTTAATAAATTT
1 TTTAATATATTT
1593600 ACTCTTCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 17 0.52
26 6 0.18
27 10 0.30
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
TTTAATATATTTTTATATTTTTAAG
Found at i:1596965 original size:15 final size:15
Alignment explanation
Indices: 1596945--1596980 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1596935 TAATTATACG
1596945 TTTAATATTTTATAA
1 TTTAATATTTTATAA
1596960 TTTAATATTTTATAA
1 TTTAATATTTTATAA
*
1596975 ATTAAT
1 TTTAAT
1596981 TTAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATATTTTATAA
Found at i:1598952 original size:22 final size:21
Alignment explanation
Indices: 1598922--1598965 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1598912 TATATGTATA
1598922 TATTAATTATATTTTATTT-ATT
1 TATTAATTAT-TTTT-TTTCATT
*
1598944 TATTTATTATTTTTTTTCATT
1 TATTAATTATTTTTTTTCATT
1598965 T
1 T
1598966 TTCTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 8 0.40
22 9 0.45
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (21 bp):
TATTAATTATTTTTTTTCATT
Found at i:1599245 original size:21 final size:24
Alignment explanation
Indices: 1599186--1599259 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 24
1599176 CTATTTAGTA
* *
1599186 TTTATTA-TATTATACATAC-A-T
1 TTTATTATTTTTATATATACTATT
1599207 TTTA-TATTTTTATATATA-TATT
1 TTTATTATTTTTATATATACTATT
1599229 TTTATTATTTTT-T-TATACTATT
1 TTTATTATTTTTATATATACTATT
*
1599251 TAT-TTATTT
1 TTTATTATTT
1599260 CATTATATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 2 0.04
21 24 0.53
22 12 0.27
23 7 0.16
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTATTATTTTTATATATACTATT
Found at i:1603693 original size:16 final size:16
Alignment explanation
Indices: 1603660--1603739 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
1603650 AGATTCAATC
*
1603660 AAAACAAAAAGACAAAAA
1 AAAACAAAAA-A-GAAAA
1603678 AAAACAAAAAAGAAAA
1 AAAACAAAAAAGAAAA
* *
1603694 GAAGCAAAAAAG--AA
1 AAAACAAAAAAGAAAA
*
1603708 GAAA-AAAAAAGAACAA
1 AAAACAAAAAAGAA-AA
*
1603724 AAATC-AAAAAGAAAA
1 AAAACAAAAAAGAAAA
1603739 A
1 A
1603740 GGGACAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
13 7 0.13
14 5 0.10
15 3 0.06
16 26 0.50
17 1 0.02
18 10 0.19
ACGTcount: A:0.81, C:0.07, G:0.10, T:0.01
Consensus pattern (16 bp):
AAAACAAAAAAGAAAA
Found at i:1603693 original size:24 final size:23
Alignment explanation
Indices: 1603660--1603750 Score: 76
Period size: 23 Copynumber: 3.9 Consensus size: 23
1603650 AGATTCAATC
*
1603660 AAAACAAAAAG-ACAAAAAAAAA
1 AAAAAAAAAAGAACAAAAAAAAA
*
1603682 CAAAAAAGAAAAGAAGCAAAAAAGAA
1 -AAAAAA-AAAAGAA-CAAAAAAAAA
* **
1603708 GAAAAAAAAAGAACAAAAATCAA
1 AAAAAAAAAAGAACAAAAAAAAA
* * *
1603731 AAAGAAAAAGGGACAAAAAA
1 AAAAAAAAAAGAACAAAAAA
1603751 GCGCATGCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
23 28 0.51
24 12 0.22
25 6 0.11
26 9 0.16
ACGTcount: A:0.79, C:0.08, G:0.12, T:0.01
Consensus pattern (23 bp):
AAAAAAAAAAGAACAAAAAAAAA
Found at i:1604363 original size:22 final size:22
Alignment explanation
Indices: 1604338--1604392 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1604328 ATCACCCCAT
1604338 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
1604360 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGC
1604382 CAAACCTTTGA
1 CAAACCTTTGA
1604393 CCAACACAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:1605470 original size:106 final size:106
Alignment explanation
Indices: 1605342--1605638 Score: 461
Period size: 106 Copynumber: 2.8 Consensus size: 106
1605332 ATATCGTGCC
* * * *
1605342 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-TGACTGGTTGCCAACAAATAACTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* *
1605406 CAAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1605448 ACTCCAGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1605513 AATTTCAGAGCCAATGTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1605554 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1605619 AATTTCAGAGCCAATTTCAA
66 AATTTCAGAGCCAATTTCAA
1605639 ACTCAAGACA
Statistics
Matches: 173, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
106 172 0.99
107 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1605703 original size:85 final size:85
Alignment explanation
Indices: 1605554--1605723 Score: 295
Period size: 85 Copynumber: 2.0 Consensus size: 85
1605544 AGGATATTGG
* *
1605554 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1605619 AATTTCAGAGCCAATTTCAA
66 AATTTCAGAGCCAATTTCAA
**
1605639 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
1605704 AATTTCAGAGTCAATTTCAA
66 AATTTCAGAGCCAATTTCAA
1605724 CTTCACAGCG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (85 bp):
ACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAA
Found at i:1605780 original size:191 final size:191
Alignment explanation
Indices: 1605448--1605829 Score: 638
Period size: 191 Copynumber: 2.0 Consensus size: 191
1605438 AGGATATTGG
* *
1605448 ACTCCAGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCAAGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1605513 AATTTCAGAGCCAATGTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATGTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * *
1605578 TCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
131 TCACAACGAAGGGACCGCTAGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAA
* * * *
1605639 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1605704 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATGTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
1605769 TCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAA
131 TCACAACGAAGGGACCGCTAGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAA
1605830 CTTCACAGCG
Statistics
Matches: 177, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
191 177 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (191 bp):
ACTCAAGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATGTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACAACGAAGGGACCGCTAGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAA
Found at i:1605829 original size:106 final size:106
Alignment explanation
Indices: 1605639--1605922 Score: 505
Period size: 106 Copynumber: 2.7 Consensus size: 106
1605629 CCAATTTCAA
* * *
1605639 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1605704 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1605745 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1605810 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1605851 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1605916 AATTTCA
66 AATTTCA
1605923 CAGCGAATGA
Statistics
Matches: 169, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 169 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1605893 original size:212 final size:211
Alignment explanation
Indices: 1605639--1606558 Score: 1343
Period size: 212 Copynumber: 4.4 Consensus size: 211
1605629 CCAATTTCAA
* * *
1605639 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1605704 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAG-CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
1605769 TCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
130 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* *
1605834 ACAGCGAATGATATTGG
195 ACAACGAAGGATATTGG
1605851 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT--C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1605914 -----C----CAA--T----TTCACAGCGAATGATATTGGACTCGAGACAACGCAAGTTCAACTT
66 AATTTCAGAGCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
1605964 CACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCA
131 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
* *
1606029 CAGCGAAAGATATTGG
196 CAACGAAGGATATTGG
* * * *
1606045 ACTCCAGACAACGAAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAAGAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1606110 AATTTCGGAGCTAATTTCAACTTCACAGCGAAGGATATTGAACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGC-AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * * *
1606175 TCACGACGAAGGGACTGATGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
130 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
1606240 ACAACGAAGGATATTGG
195 ACAACGAAGGATATTGG
*
1606257 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1606322 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
66 AATTTCAGAG-CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
1606387 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTC
130 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
*
1606452 ACAACAAAGGATATTGG
195 ACAACGAAGGATATTGG
* * * * * * *
1606469 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1606534 GATTCCAGAGCCAATTTCAACTTCA
66 AATTTCAGAG-CAATTTCAACTTCA
1606559 TGATGGAGGA
Statistics
Matches: 638, Mismatches: 51, Indels: 38
0.88 0.07 0.05
Matches are distributed among these distances:
194 177 0.28
196 1 0.00
198 1 0.00
200 3 0.00
201 1 0.00
205 2 0.00
206 2 0.00
208 1 0.00
210 1 0.00
212 448 0.70
213 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (211 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
CAACGAAGGATATTGG
Found at i:1605980 original size:88 final size:88
Alignment explanation
Indices: 1605831--1606009 Score: 340
Period size: 88 Copynumber: 2.0 Consensus size: 88
1605821 CAATTTCAAC
1605831 TTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1605896 TTGTCAACAAACAACTTCCCAAT
66 TTGTCAACAAACAACTTCCCAAT
*
1605919 TTCACAGCGAATGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
*
1605984 TTGTCAACAAACAATTTCCCAAT
66 TTGTCAACAAACAACTTCCCAAT
1606007 TTC
1 TTC
1606010 GGAGCCAATT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (88 bp):
TTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
TTGTCAACAAACAACTTCCCAAT
Found at i:1606106 original size:106 final size:106
Alignment explanation
Indices: 1605919--1606558 Score: 1001
Period size: 106 Copynumber: 6.0 Consensus size: 106
1605909 ACTTCCCAAT
* *
1605919 TTCACAGCGAATGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
*
1605984 TTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAAC
66 TTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
* * *
1606025 TTCACAGCGAAAGATATTGGACTCCAGACAACGAAAGTTCAACTTCACGATGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * *
1606090 TTGTCAACAAAGAATTTCCCAATTTCGGAGCTAATTTCAAC
66 TTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
* * *
1606131 TTCACAGCGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGATGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * *
1606196 TTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAAC
66 TTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
*
1606237 TTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* *
1606302 TTGTTAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
66 TTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
* *
1606343 TTCACAGTGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
*
1606408 TTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAAC
66 TTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
* * * * * * *
1606449 TTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * *
1606514 TTGTCAACAAACAATTTCTCGATTCCAGAGCCAATTTCAAC
66 TTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
1606555 TTCA
1 TTCA
1606559 TGATGGAGGA
Statistics
Matches: 491, Mismatches: 43, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 491 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
TTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
Found at i:1606646 original size:34 final size:34
Alignment explanation
Indices: 1606603--1606697 Score: 113
Period size: 32 Copynumber: 2.9 Consensus size: 34
1606593 TACTTGGATT
1606603 TCAACTTCACGACGAAGGATATCCAATTCCAGGC
1 TCAACTTCACGACGAAGGATATCCAATTCCAGGC
* ** * **
1606637 TCAACTTCACGACGAAGG--GTCCACCTGCAGTT
1 TCAACTTCACGACGAAGGATATCCAATTCCAGGC
*
1606669 TCAACTTCACGACGAGGGATATCCAATTC
1 TCAACTTCACGACGAAGGATATCCAATTC
1606698 AAAGAAGAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
32 25 0.52
34 23 0.48
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (34 bp):
TCAACTTCACGACGAAGGATATCCAATTCCAGGC
Found at i:1607774 original size:15 final size:14
Alignment explanation
Indices: 1607754--1607799 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1607744 TATATGTATA
1607754 TATTTAATTATATTT
1 TATTTAATT-TATTT
1607769 TATTT-ATTTA-TT
1 TATTTAATTTATTT
1607781 TATTATAATTT-TTT
1 TATT-TAATTTATTT
1607795 TATTT
1 TATTT
1607800 TTCTTTGCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 6 0.21
13 4 0.14
14 13 0.46
15 5 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTAATTTATTT
Found at i:1607796 original size:22 final size:23
Alignment explanation
Indices: 1607754--1607799 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
1607744 TATATGTATA
1607754 TATTTAATTATATTTTATTTATT
1 TATTTAATTATATTTTATTTATT
1607777 TATTT-ATTATAATTTT-TTTATT
1 TATTTAATTAT-ATTTTATTTATT
1607799 T
1 T
1607800 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
TATTTAATTATATTTTATTTATT
Found at i:1608023 original size:18 final size:17
Alignment explanation
Indices: 1607990--1608023 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1607980 TTTTTTCATT
1607990 TATTTATATATTATTAC
1 TATTTATATATTATTAC
*
1608007 TATTTAGTATTTTATTA
1 TATTTA-TATATTATTA
1608024 TATATACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTTATATATTATTAC
Found at i:1608069 original size:21 final size:20
Alignment explanation
Indices: 1608043--1608100 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1608033 ACATTTTTAT
1608043 TTTTATATATATTTTTTATTA
1 TTTTAT-TATATTTTTTATTA
* *
1608064 TTTTATTTATACTATTTATTTA
1 TTTTA-TTATATTTTTTA-TTA
1608086 TTTTATTATATTTTT
1 TTTTATTATATTTTT
1608101 AATTTCTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTATATTTTTTATTA
Done.