Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 18 of 328
Found at i:5536991 original size:3 final size:3
Alignment explanation
Indices: 5536983--5537026 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5536973 GCCCAGATTT
5536983 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5537027 TCTCTTCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5539567 original size:3 final size:3
Alignment explanation
Indices: 5539561--5539607 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5539551 GAATAAGACA
5539561 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5539608 CAGATTTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5542125 original size:18 final size:18
Alignment explanation
Indices: 5542075--5542126 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
5542065 GGCGCACATC
* *
5542075 AATAAATATTTAAAAATTT
1 AATAAA-ATTTTAAAATTA
*
5542094 AA-AAATTTTCTAAAATTA
1 AATAAAATTT-TAAAATTA
5542112 AATAAAATTTTAAAA
1 AATAAAATTTTAAAA
5542127 ATTATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.11
18 16 0.59
19 8 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAAAATTTTAAAATTA
Found at i:5542852 original size:207 final size:211
Alignment explanation
Indices: 5542492--5542962 Score: 772
Period size: 207 Copynumber: 2.2 Consensus size: 211
5542482 TTTAATGCTG
* *
5542492 CATATTTCATCCAGATAAAGTATGTATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAA
1 CATACTTCATCCAGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAA
*
5542557 TTATAAAATAATATGTTACTTGGAAATTAACTATTATTGTAATGAGATACATGTTTTATTAGGTA
66 TTATAAAATAATATGTTACTTGGAAATTAACAATTATTGTAATGAGATACATGTTTTATTAGGTA
5542622 TAAGTATTTAAAATTTTATTTTTGTAATGTGATACAT-GTG-TA-ATATAT-ATATAATCATATT
131 TAAGTATTTAAAATTTTATTTTTGTAATGTGATACATCGTGATATATATATAATATAATCATATT
* * *
5542683 AGTGAATCTGTTAATG
196 ACTGAATCTGCTAATA
* *
5542699 CGTACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAA
1 CATACTTCATCCAGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAA
*
5542764 TTATAAAATAATATGTTATTTGGGAAA-TAACAATTATTGTAATGAGATACATGTTTTATTAGGT
66 TTATAAAATAATATGTTACTT-GGAAATTAACAATTATTGTAATGAGATACATGTTTTATTAGGT
*
5542828 ATAAGTATTTAAAATTTTATTTTTGTAATGTGATATATGCGTGTATATATATATAAATATAATCA
130 ATAAGTATTTAAAATTTTATTTTTGTAATGTGATACAT-CGTG-ATATATATAT-AATATAATCA
5542893 TATTACTGAATCTGCTAATA
192 TATTACTGAATCTGCTAATA
*
5542913 CATACTTCATCCTGATAAAGTATGCATTATTAAAATTAAATTAAAATATT
1 CATACTTCATCCAGATAAAGTATGCATTATTAAAATTAAATTAAAATATT
5542963 TTTTAAAAAC
Statistics
Matches: 244, Mismatches: 12, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
207 154 0.63
208 5 0.02
209 3 0.01
211 2 0.01
212 6 0.02
214 74 0.30
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (211 bp):
CATACTTCATCCAGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAA
TTATAAAATAATATGTTACTTGGAAATTAACAATTATTGTAATGAGATACATGTTTTATTAGGTA
TAAGTATTTAAAATTTTATTTTTGTAATGTGATACATCGTGATATATATATAATATAATCATATT
ACTGAATCTGCTAATA
Found at i:5543407 original size:31 final size:31
Alignment explanation
Indices: 5543372--5543460 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
5543362 ATATAAAATA
*
5543372 TTAGAT-TAATTTAT-ATTTTATATATAATTAT
1 TTAGATATAATTTATCATTATAT-TA-AATTAT
*
5543403 TTAGATATCATTTATCATTATATTAAATTAT
1 TTAGATATAATTTATCATTATATTAAATTAT
* * * *
5543434 TTAAATCTTATTTATTATTATATTAAA
1 TTAGATATAATTTATCATTATATTAAA
5543461 ATTTTAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 35 0.70
32 9 0.18
33 6 0.12
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.55
Consensus pattern (31 bp):
TTAGATATAATTTATCATTATATTAAATTAT
Found at i:5545607 original size:40 final size:40
Alignment explanation
Indices: 5545552--5545631 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
5545542 TGTAGAAAAA
5545552 GATTAAAAAAAAGAAAGAAAAACAAAAAAGAAACTATCAT
1 GATTAAAAAAAAGAAAGAAAAACAAAAAAGAAACTATCAT
*
5545592 GATTAAAAAAAAGAAAGAAAAACAAAAAAGAAGCTATCAT
1 GATTAAAAAAAAGAAAGAAAAACAAAAAAGAAACTATCAT
5545632 CCTTTCATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.69, C:0.07, G:0.11, T:0.12
Consensus pattern (40 bp):
GATTAAAAAAAAGAAAGAAAAACAAAAAAGAAACTATCAT
Found at i:5546166 original size:2 final size:2
Alignment explanation
Indices: 5546155--5546187 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5546145 TCACATAGAC
5546155 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5546188 TTAGTTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5546976 original size:21 final size:24
Alignment explanation
Indices: 5546939--5546985 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
5546929 ATTTGAAATG
5546939 TTTTATAATATTA-TTTTTTAAAA
1 TTTTATAATATTATTTTTTTAAAA
5546962 TTTTA-AATA-TATTTTTTTAAAA
1 TTTTATAATATTATTTTTTTAAAA
5546984 TT
1 TT
5546986 ATTTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 2 0.09
22 16 0.70
23 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTATAATATTATTTTTTTAAAA
Found at i:5547069 original size:28 final size:28
Alignment explanation
Indices: 5547003--5547073 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
5546993 AATAATATAA
5547003 AATA-TTTAAATGTATTATTAGTTTTAT
1 AATATTTTAAATGTATTATTAGTTTTAT
* ** * *
5547030 GACCTTTCAAATTTATTATTAGTTTTAT
1 AATATTTTAAATGTATTATTAGTTTTAT
5547058 AATATTTTAAATGTAT
1 AATATTTTAAATGTAT
5547074 ATTTTAGATA
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (28 bp):
AATATTTTAAATGTATTATTAGTTTTAT
Found at i:5549160 original size:23 final size:23
Alignment explanation
Indices: 5549132--5549177 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5549122 GCTAACATGT
5549132 TTGTTTTGGTTTAAGATGGGCCA
1 TTGTTTTGGTTTAAGATGGGCCA
5549155 TTGTTTTGGTTTAAGATGGGCCA
1 TTGTTTTGGTTTAAGATGGGCCA
5549178 CGTCTCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.09, G:0.30, T:0.43
Consensus pattern (23 bp):
TTGTTTTGGTTTAAGATGGGCCA
Found at i:5549903 original size:30 final size:30
Alignment explanation
Indices: 5549867--5549997 Score: 142
Period size: 30 Copynumber: 4.4 Consensus size: 30
5549857 GTCGTAGAGC
5549867 AGTTCATATCACCCGGACATGGGCGGTTCA
1 AGTTCATATCACCCGGACATGGGCGGTTCA
* * * *
5549897 AGTTC--ATCACTCGAAAATGGGCGGCTT-G
1 AGTTCATATCACCCGGACATGGGCGG-TTCA
** *
5549925 AGTTCATATCACTTGGACATGGGCGGTTCG
1 AGTTCATATCACCCGGACATGGGCGGTTCA
* *
5549955 AGTTCATATCACCCGGACATAGGCGATTCA
1 AGTTCATATCACCCGGACATGGGCGGTTCA
*
5549985 AGTTCATTTCACC
1 AGTTCATATCACC
5549998 GATATCAACC
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
28 21 0.25
29 4 0.05
30 59 0.70
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATGGGCGGTTCA
Found at i:5556574 original size:21 final size:21
Alignment explanation
Indices: 5556542--5556594 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
5556532 TTTTATATTA
5556542 TTAAAAAT-ATATTTAAAATT
1 TTAAAAATAATATTTAAAATT
*
5556562 TTAAAAATAATATTTAAATTT
1 TTAAAAATAATATTTAAAATT
5556583 TTAAAAA-AATAT
1 TTAAAAATAATAT
5556595 ATTTGAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAAAATAATATTTAAAATT
Found at i:5556631 original size:23 final size:26
Alignment explanation
Indices: 5556600--5556649 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
5556590 AATATATTTG
5556600 AAAGATAAAT-AA-AAAAACTTAAAA
1 AAAGATAAATAAATAAAAACTTAAAA
5556624 AAAG-TAAATAAATAAAAACTTAAAA
1 AAAGATAAATAAATAAAAACTTAAAA
5556649 A
1 A
5556650 GAAACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.21
24 6 0.25
25 13 0.54
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (26 bp):
AAAGATAAATAAATAAAAACTTAAAA
Found at i:5557612 original size:153 final size:154
Alignment explanation
Indices: 5557299--5557629 Score: 498
Period size: 153 Copynumber: 2.2 Consensus size: 154
5557289 ACCGCCCACT
* * *
5557299 ATAAAATCTAGATCCGAAAATTTTAAAAATACAAACAAATAGACAAAATTAGGGTTATTTACTAA
1 ATAAAATCAAGATCCGAAAATTTTAAAAATACAAACAAAGAGACAAAATTAAGGTTATTTACTAA
* * *
5557364 ATTAATATAAAAACAAAATAAAATAATACTTTTGAAACATTATGTACTAAAATATTGTAAAAGAA
66 ATTAATAT-AAAACAAAATAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAGAA
*
5557429 TAAAATAGGAAAATAGTATATTTTA
130 TAAAATAGGAAAATAATATATTTTA
*
5557454 A-AAAAT-AAGATCCGAAAATTTTAAAAATACAAACAAAGGGACAAAATTAAGGTTATTTACTAA
1 ATAAAATCAAGATCCGAAAATTTTAAAAATACAAACAAAGAGACAAAATTAAGGTTATTTACTAA
*
5557517 ATTAATAT-AAA-AAACTAAAAT-ATACATTTGAAACATTATGTACTAAAATAATATAAAA-AAT
66 ATTAATATAAAACAAAATAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAGAAT
5557578 AAAATAGGAAAATAATATATTTTA
131 AAAATAGGAAAATAATATATTTTA
* *
5557602 A-AAAAT-AAAATTCGAAAATTTTAAAAAT
1 ATAAAATCAAGATCCGAAAATTTTAAAAAT
5557630 TTTAAAAATA
Statistics
Matches: 165, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
148 52 0.32
149 34 0.21
150 9 0.05
151 3 0.02
153 61 0.37
154 5 0.03
155 1 0.01
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.29
Consensus pattern (154 bp):
ATAAAATCAAGATCCGAAAATTTTAAAAATACAAACAAAGAGACAAAATTAAGGTTATTTACTAA
ATTAATATAAAACAAAATAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAGAAT
AAAATAGGAAAATAATATATTTTA
Found at i:5558100 original size:28 final size:25
Alignment explanation
Indices: 5558045--5558106 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
5558035 TATTTTAGTG
5558045 CTTCTTGCTTCCCGAGTTGCTGCTT
1 CTTCTTGCTTCCCGAGTTGCTGCTT
*
5558070 CTTCTTGCTTCCCGAGTTGTTGCTT
1 CTTCTTGCTTCCCGAGTTGCTGCTT
5558095 CTTCTTGCTTCC
1 CTTCTTGCTTCC
5558107 AAAATTAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.03, C:0.32, G:0.18, T:0.47
Consensus pattern (25 bp):
CTTCTTGCTTCCCGAGTTGCTGCTT
Found at i:5564196 original size:20 final size:20
Alignment explanation
Indices: 5564171--5564208 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5564161 TATATATATT
* *
5564171 TATATATGCATGTATGCACC
1 TATATATACATATATGCACC
5564191 TATATATACATATATGCA
1 TATATATACATATATGCA
5564209 AAACAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
TATATATACATATATGCACC
Found at i:5566924 original size:27 final size:27
Alignment explanation
Indices: 5566894--5566950 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
5566884 ATACTGTTCC
* * *
5566894 AAACAAGGCTAAACCGATTAAAATAAA
1 AAACAAGGCAAAACCAATAAAAATAAA
* *
5566921 AAACTAGTCAAAACCAATAAAAATAAA
1 AAACAAGGCAAAACCAATAAAAATAAA
5566948 AAA
1 AAA
5566951 TGAGACAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.65, C:0.14, G:0.07, T:0.14
Consensus pattern (27 bp):
AAACAAGGCAAAACCAATAAAAATAAA
Found at i:5566959 original size:27 final size:27
Alignment explanation
Indices: 5566904--5566960 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
5566894 AAACAAGGCT
* * *
5566904 AAACCGATTAAAATAAAAAACTAGTCA
1 AAACCAATAAAAATAAAAAACTAGACA
5566931 AAACCAATAAAAATAAAAAA-TGAGACA
1 AAACCAATAAAAATAAAAAACT-AGACA
5566958 AAA
1 AAA
5566961 ATTAATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.67, C:0.12, G:0.07, T:0.14
Consensus pattern (27 bp):
AAACCAATAAAAATAAAAAACTAGACA
Found at i:5582678 original size:34 final size:33
Alignment explanation
Indices: 5582639--5582707 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 33
5582629 TCAACATTTA
5582639 AAAAACAAAACATTATCACAAAAGGTGAAAAACT
1 AAAAACAAAACATTATCACAAAAGGTG-AAAACT
* *
5582673 AAAAACAGAACATTATCACAGAAGGTGAAAACT
1 AAAAACAAAACATTATCACAAAAGGTGAAAACT
5582706 AA
1 AA
5582708 TACTTACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.14
Consensus pattern (33 bp):
AAAAACAAAACATTATCACAAAAGGTGAAAACT
Found at i:5584056 original size:14 final size:15
Alignment explanation
Indices: 5584037--5584068 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
5584027 ATACGATAAA
5584037 TTAATTAAT-AATGT
1 TTAATTAATAAATGT
5584051 TTAATTAATAAATGT
1 TTAATTAATAAATGT
5584066 TTA
1 TTA
5584069 CATAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTAATTAATAAATGT
Found at i:5595545 original size:24 final size:24
Alignment explanation
Indices: 5595518--5595566 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5595508 TGAAATTTAT
*
5595518 GATAATGAGATCGTATGAATAAAG
1 GATAATGAGATCATATGAATAAAG
5595542 GATAATGAGATCATATGAATAAAG
1 GATAATGAGATCATATGAATAAAG
5595566 G
1 G
5595567 GTTGATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.24
Consensus pattern (24 bp):
GATAATGAGATCATATGAATAAAG
Found at i:5603400 original size:19 final size:19
Alignment explanation
Indices: 5603376--5603415 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5603366 ACCATCTCAC
5603376 TTAACTCCCGTGATTTCTA
1 TTAACTCCCGTGATTTCTA
5603395 TTAACTCCCGTGATTTCTA
1 TTAACTCCCGTGATTTCTA
5603414 TT
1 TT
5603416 TGGTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (19 bp):
TTAACTCCCGTGATTTCTA
Found at i:5604432 original size:28 final size:29
Alignment explanation
Indices: 5604388--5604442 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
5604378 AATGCAAGGG
*
5604388 TAAAATTATATTTTGATAT-TTTAAAATT
1 TAAAATTATATTATGATATCTTTAAAATT
*
5604416 TAAAATT-TAATTATGATTTCTTTAAAA
1 TAAAATTAT-ATTATGATATCTTTAAAA
5604443 ATAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.04
28 15 0.65
29 7 0.30
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (29 bp):
TAAAATTATATTATGATATCTTTAAAATT
Found at i:5608357 original size:26 final size:26
Alignment explanation
Indices: 5608298--5608359 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
5608288 GAAATTTTTT
* *
5608298 AATACTTTAATAATTAATTAAATTAA
1 AATATTTTAAAAATTAATTAAATTAA
** *
5608324 TTTTTTTTAAAAATTAATTAAATTAA
1 AATATTTTAAAAATTAATTAAATTAA
5608350 AATATTTTAA
1 AATATTTTAA
5608360 TTAATTCAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATTTTAAAAATTAATTAAATTAA
Found at i:5611785 original size:31 final size:30
Alignment explanation
Indices: 5611750--5611808 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
5611740 ATTTGGGTAT
5611750 CAAATTAAAAAAGAATATCAAAT-CTAAATAC
1 CAAATTAAAAAA-AA-ATCAAATACTAAATAC
*
5611781 CAAATTAAAAAAAAATTAAATACTAAAT
1 CAAATTAAAAAAAAATCAAATACTAAAT
5611809 TAGAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.23
30 8 0.31
31 12 0.46
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.24
Consensus pattern (30 bp):
CAAATTAAAAAAAAATCAAATACTAAATAC
Found at i:5611796 original size:24 final size:25
Alignment explanation
Indices: 5611769--5611826 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
5611759 AAAGAATATC
5611769 AAATCTAAATACCAAATTA-AAAAA
1 AAATCTAAATACCAAATTAGAAAAA
*
5611793 AAAT-TAAATACTAAATTAGAAAAA
1 AAATCTAAATACCAAATTAGAAAAA
*
5611817 ATATC-AAATA
1 AAATCTAAATA
5611827 TCATTTAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.24
Consensus pattern (25 bp):
AAATCTAAATACCAAATTAGAAAAA
Found at i:5612888 original size:31 final size:33
Alignment explanation
Indices: 5612841--5612906 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
5612831 TAGTAAAAAT
5612841 AAAATTACACTTTAATT-TCCTTAAAA-TTATAAA
1 AAAATTACACTTTAATTAT--TTAAAACTTATAAA
5612874 AAAATTA-A-TTTAATTATTTAAAACTTATAAA
1 AAAATTACACTTTAATTATTTAAAACTTATAAA
5612905 AA
1 AA
5612907 TATAGACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
30 6 0.19
31 16 0.52
32 2 0.06
33 7 0.23
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAATTACACTTTAATTATTTAAAACTTATAAA
Found at i:5613801 original size:27 final size:27
Alignment explanation
Indices: 5613724--5613803 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
5613714 TTTTTGGGGA
* *
5613724 ATTTCCTAAAAAAAATCATTTTATATTATT
1 ATTTACTAAAAATAATCA-TTT-T-TTATT
** *
5613754 ATTTA-TTGAAATAGTCGATTTTTTATT
1 ATTTACTAAAAATAATC-ATTTTTTATT
5613781 ATTTACTAAAAATAATCATTTTT
1 ATTTACTAAAAATAATCATTTTT
5613804 CCCGAAAGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
27 16 0.40
28 9 0.22
29 10 0.25
30 5 0.12
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTTACTAAAAATAATCATTTTTTATT
Found at i:5614003 original size:20 final size:22
Alignment explanation
Indices: 5613968--5614009 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
5613958 CACAATAGTC
5613968 CTCTCACAATTCTCTCTAAATT
1 CTCTCACAATTCTCTCTAAATT
*
5613990 CTCTCA-AATT-TCTCTCAATT
1 CTCTCACAATTCTCTCTAAATT
5614010 TTTGTCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (22 bp):
CTCTCACAATTCTCTCTAAATT
Found at i:5614559 original size:52 final size:53
Alignment explanation
Indices: 5614502--5614672 Score: 190
Period size: 52 Copynumber: 3.2 Consensus size: 53
5614492 TACTTTACTT
*
5614502 TTTTTTTA-ATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTA
1 TTTTTTTATATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTA
* * ** *
5614554 TTTTTTTATATTTGA-TAAAATAAAAGTTCTTTTAATATT--TTAATTGTATTTTA
1 TTTTTTTATATTTTATTAAAATAAATGTTCTTTTAA-ATTAGCCAA-TAT-TTTTA
* * *
5614607 -CTTTTTAAATTTTATTAAAATAAATATTCTTTTAAATTAGCCAATATTTTTA
1 TTTTTTTATATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTA
5614659 TTATTTTTATATTT
1 TT-TTTTTATATTT
5614673 ATTTTTATAT
Statistics
Matches: 95, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
51 2 0.02
52 48 0.51
53 33 0.35
54 12 0.13
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (53 bp):
TTTTTTTATATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTA
Found at i:5614612 original size:53 final size:54
Alignment explanation
Indices: 5614464--5614641 Score: 170
Period size: 52 Copynumber: 3.3 Consensus size: 54
5614454 GAGTGCATTG
* * *
5614464 ATAAAAGTTGTTTTTAATATTTTAATTATACTTTACTTTTTTTTTAATTTTATTAAA
1 ATAAAAGTT-CTTTTAATATTTTAATTATATTTTAC-TTTTTTAT-ATTTTATTAAA
* ** * *
5614521 ATAAATGTTCTTTTAA-ATTAGGCAA-TAT-TTTTATTTTTTTATATTTGA-TAAA
1 ATAAAAGTTCTTTTAATATT--TTAATTATATTTTACTTTTTTATATTTTATTAAA
* *
5614573 ATAAAAGTTCTTTTAATATTTTAATTGTATTTTAC-TTTTTAAATTTTATTAAA
1 ATAAAAGTTCTTTTAATATTTTAATTATATTTTACTTTTTTATATTTTATTAAA
5614626 ATAAATA-TTCTTTTAA
1 ATAAA-AGTTCTTTTAA
5614642 ATTAGCCAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
51 2 0.02
52 32 0.32
53 31 0.31
54 8 0.08
55 7 0.07
56 9 0.09
57 10 0.10
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (54 bp):
ATAAAAGTTCTTTTAATATTTTAATTATATTTTACTTTTTTATATTTTATTAAA
Found at i:5614642 original size:105 final size:108
Alignment explanation
Indices: 5614464--5614672 Score: 325
Period size: 105 Copynumber: 1.9 Consensus size: 108
5614454 GAGTGCATTG
* * *
5614464 ATAAAAGTTGTTTTTAATATTTTAATTATACTTTACTTTTTTTTTAATTTTATTAAAATAAATGT
1 ATAAAAGTTGCTTTTAATATTTTAATTATACTTTAC--TTTTTTAAATTTTATTAAAATAAATAT
*
5614529 TCTTTTAAATTAGGCAATATTTTTATT-TTTTTATATTTGATAAA
64 TCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTGATAAA
* *
5614573 ATAAAAGTT-CTTTTAATATTTTAATTGTATTTTAC-TTTTTAAATTTTATTAAAATAAATATTC
1 ATAAAAGTTGCTTTTAATATTTTAATTATACTTTACTTTTTTAAATTTTATTAAAATAAATATTC
5614636 TTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
66 TTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
5614673 ATTTTTATAT
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
105 50 0.54
106 11 0.12
108 23 0.25
109 9 0.10
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (108 bp):
ATAAAAGTTGCTTTTAATATTTTAATTATACTTTACTTTTTTAAATTTTATTAAAATAAATATTC
TTTTAAATTAGCCAATATTTTTATTATTTTTATATTTGATAAA
Found at i:5616528 original size:17 final size:17
Alignment explanation
Indices: 5616493--5616527 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5616483 GTGCTCTCTA
5616493 TTCTTTTTCCTTTCTTT
1 TTCTTTTTCCTTTCTTT
*
5616510 TTCTTTTT-GTTTCTTT
1 TTCTTTTTCCTTTCTTT
5616526 TT
1 TT
5616528 TTCGTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (17 bp):
TTCTTTTTCCTTTCTTT
Found at i:5616724 original size:25 final size:24
Alignment explanation
Indices: 5616696--5616758 Score: 56
Period size: 25 Copynumber: 2.5 Consensus size: 24
5616686 AAATATCAAT
5616696 TTAATAAAAATAACATTAATAAATA
1 TTAATAAAAATAACA-TAATAAATA
* *
5616721 TTAAATGTAAAA-ACCATAATAAATA
1 TT-AAT-AAAAATAACATAATAAATA
* *
5616746 ATAATAATAATAA
1 TTAATAAAAATAA
5616759 TTTAATATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
23 3 0.10
24 4 0.14
25 12 0.41
26 6 0.21
27 4 0.14
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (24 bp):
TTAATAAAAATAACATAATAAATA
Found at i:5622461 original size:2 final size:2
Alignment explanation
Indices: 5622454--5622480 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5622444 ATTCAATGTG
5622454 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
5622481 ATAAATAATG
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:5623554 original size:31 final size:31
Alignment explanation
Indices: 5623519--5623577 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5623509 CTAATGACTT
5623519 TTAAATAAAAACTTCAAAATAATTCAGTAAA
1 TTAAATAAAAACTTCAAAATAATTCAGTAAA
* ***
5623550 TTAAATGAAAACTTTTGAATAATTCAGT
1 TTAAATAAAAACTTCAAAATAATTCAGT
5623578 GATTATTTTA
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:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (31 bp):
TTAAATAAAAACTTCAAAATAATTCAGTAAA
Found at i:5624709 original size:29 final size:30
Alignment explanation
Indices: 5624671--5624731 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
5624661 ATTCAAAATA
* *
5624671 TACAAGGACTAAAATTGA-CAATTTAAAAG
1 TACAAGGACTAAAATTAATCAAATTAAAAG
*
5624700 TACAATGACTAAAATTAATCAAATTAAAAG
1 TACAAGGACTAAAATTAATCAAATTAAAAG
5624730 TA
1 TA
5624732 TAGAAACTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (30 bp):
TACAAGGACTAAAATTAATCAAATTAAAAG
Found at i:5625630 original size:17 final size:17
Alignment explanation
Indices: 5625608--5625644 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
5625598 CTATTCATGA
*
5625608 TCAAAAGATACAATTGT
1 TCAAAAGATACAACTGT
5625625 TCAAAAGATACAACTGT
1 TCAAAAGATACAACTGT
5625642 TCA
1 TCA
5625645 TCAAGAGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (17 bp):
TCAAAAGATACAACTGT
Found at i:5629472 original size:29 final size:30
Alignment explanation
Indices: 5629418--5629478 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
5629408 GTAGTTTATG
* **
5629418 AAAATTATATTAAATCAAAATTTTATGCTT
1 AAAATTATATAAAATCAAAAAATTATGCTT
5629448 AAAATTATATAAAAT-AAAAAATTATGCTT
1 AAAATTATATAAAATCAAAAAATTATGCTT
5629477 AA
1 AA
5629479 TTTTGAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTATATAAAATCAAAAAATTATGCTT
Found at i:5629868 original size:16 final size:16
Alignment explanation
Indices: 5629847--5629889 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
5629837 GGTGGAAGAA
*
5629847 TTAAATTATAAAATTT
1 TTAAATTATAAAAATT
*
5629863 TTAAATTTTAAAAATT
1 TTAAATTATAAAAATT
*
5629879 TTAAAATATAA
1 TTAAATTATAA
5629890 TTTTATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTATAAAAATT
Found at i:5631648 original size:3 final size:3
Alignment explanation
Indices: 5631640--5631665 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5631630 GACAAAATAG
5631640 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5631666 AATTTAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5632425 original size:27 final size:26
Alignment explanation
Indices: 5632366--5632426 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
5632356 ATTAGTCTTC
* *
5632366 ATAT-TTTTATCAAAGATTAAAGAGA
1 ATATATTTTATCAAAGATCAAAAAGA
* *
5632391 GTAAATTTTATCAAAGATCAAAAAGAA
1 ATATATTTTATCAAAGATCAAAAAG-A
5632418 ATATATTTT
1 ATATATTTT
5632427 CATTAAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
25 2 0.07
26 18 0.64
27 8 0.29
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (26 bp):
ATATATTTTATCAAAGATCAAAAAGA
Found at i:5633551 original size:21 final size:21
Alignment explanation
Indices: 5633511--5633551 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5633501 TAGTTTTCTA
* **
5633511 ATTTTTTAGAATAATGATATC
1 ATTTTTTAAAATAAAAATATC
5633532 ATTTTTTAAAATAAAAATAT
1 ATTTTTTAAAATAAAAATAT
5633552 TTAATATTTT
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:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (21 bp):
ATTTTTTAAAATAAAAATATC
Found at i:5636149 original size:21 final size:20
Alignment explanation
Indices: 5636106--5636167 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
5636096 AAACCATGCC
*
5636106 AAAATTTTAA-AT-TTTTATA
1 AAAATTTTAACATATTGT-TA
5636125 AAAATTTTTAACATATTGTTA
1 AAAA-TTTTAACATATTGTTA
* *
5636146 AAAATTTTAATATATTTTTA
1 AAAATTTTAACATATTGTTA
5636166 AA
1 AA
5636168 GCATTTGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.11
20 22 0.59
21 8 0.22
22 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
AAAATTTTAACATATTGTTA
Found at i:5638524 original size:12 final size:12
Alignment explanation
Indices: 5638497--5638536 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
5638487 TTTTTGGCCG
5638497 ATTGTTATCA--
1 ATTGTTATCAGC
5638507 ATTGTTATCAGC
1 ATTGTTATCAGC
5638519 ATTGTTATCAGC
1 ATTGTTATCAGC
5638531 ATTGTT
1 ATTGTT
5638537 GCTAGTGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.36
12 18 0.64
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (12 bp):
ATTGTTATCAGC
Found at i:5639093 original size:16 final size:17
Alignment explanation
Indices: 5639054--5639093 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5639044 AAGTGTCACG
*
5639054 AAAAT-TAA-AAAATTA
1 AAAATATAACAAAACTA
5639069 AAAATATAACAAAACTA
1 AAAATATAACAAAACTA
5639086 AAAA-ATAA
1 AAAATATAA
5639094 TTTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 7 0.32
17 10 0.45
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAATATAACAAAACTA
Found at i:5639104 original size:17 final size:17
Alignment explanation
Indices: 5639079--5639144 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 17
5639069 AAAATATAAC
5639079 AAAACTAAAAAATAATTT
1 AAAACTAAAAAAT-ATTT
*
5639097 AAAA-TAAAAAAT-CTT
1 AAAACTAAAAAATATTT
5639112 AAAACTCAAAAAATTATTT
1 AAAACT-AAAAAA-TATTT
5639131 AAAAAACTAAAAAA
1 --AAAACTAAAAAA
5639145 AATCATAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
15 6 0.15
16 1 0.03
17 14 0.35
18 5 0.12
19 2 0.05
20 6 0.15
21 6 0.15
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAACTAAAAAATATTT
Found at i:5639106 original size:34 final size:35
Alignment explanation
Indices: 5639062--5639134 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
5639052 CGAAAATTAA
5639062 AAAATTAAAAATATAACAAAACT-AAAAAATAATTT
1 AAAATTAAAAA-ATAACAAAACTCAAAAAATAATTT
*** *
5639097 AAAA-TAAAAAATCTTAAAACTCAAAAAATTATTT
1 AAAATTAAAAAATAACAAAACTCAAAAAATAATTT
5639131 AAAA
1 AAAA
5639135 AACTAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 8 0.24
34 21 0.64
35 4 0.12
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (35 bp):
AAAATTAAAAAATAACAAAACTCAAAAAATAATTT
Found at i:5658368 original size:90 final size:90
Alignment explanation
Indices: 5658195--5658369 Score: 307
Period size: 89 Copynumber: 2.0 Consensus size: 90
5658185 AGTCATTGAA
*
5658195 CAATTAGTCGTCACCCATCTTTGCTACTCCTGCTTCGACCATGATACCAATCATCAGTTATTTTT
1 CAATTAATCGTCACCCATCTTTGCTACTCCTGCTTCGACCATGATACCAATCATCAGTTATTTTT
5658260 TCGAAATAATAAAGTTTTTTCATCC
66 TCGAAATAATAAAGTTTTTTCATCC
* * *
5658285 CAATTAATCGTCACCCGTCTTTGCTA-TCCTGCTTCGGCCATGATACCAATCATCAGTTGTTTTT
1 CAATTAATCGTCACCCATCTTTGCTACTCCTGCTTCGACCATGATACCAATCATCAGTTATTTTT
5658349 TCGAAATAATAAAGTTTTTTC
66 TCGAAATAATAAAGTTTTTTC
5658370 GTCCAAGTGT
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 57 0.70
90 24 0.30
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (90 bp):
CAATTAATCGTCACCCATCTTTGCTACTCCTGCTTCGACCATGATACCAATCATCAGTTATTTTT
TCGAAATAATAAAGTTTTTTCATCC
Found at i:5659325 original size:46 final size:46
Alignment explanation
Indices: 5659265--5659583 Score: 428
Period size: 46 Copynumber: 6.9 Consensus size: 46
5659255 TTTGACATGA
* * * * * *
5659265 TGCCATAGTGTCTTTAAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
* * *
5659311 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
5659357 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
5659403 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
5659449 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* * * *
5659495 TGCCTTGGTATCTTTCAATCATGGTCTTA-TACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACT-CATTTCATATCACGT
5659541 TGCCATGGTATCTTTCAACCATGGTCTTACAT-ATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTCATATCA
5659584 GAGAGCACAC
Statistics
Matches: 251, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
45 4 0.02
46 246 0.98
48 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:5661680 original size:11 final size:11
Alignment explanation
Indices: 5661664--5661711 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
5661654 CTTTATATAC
5661664 TAATAAAATAA
1 TAATAAAATAA
*
5661675 TAATAAAATATCT
1 TAATAAAATA--A
* *
5661688 TATTAAAATAT
1 TAATAAAATAA
5661699 TAATAAAATAA
1 TAATAAAATAA
5661710 TA
1 TA
5661712 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:5671088 original size:149 final size:150
Alignment explanation
Indices: 5670649--5671203 Score: 773
Period size: 149 Copynumber: 3.7 Consensus size: 150
5670639 CACATTTTGT
*
5670649 AATCATAAATTCCCAAGATTTTGAAATTCATGTTTT-TCT-ATACATTTCAAATACATAATCAAA
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTCT-TAATACATTTCAAATACATAATCAAA
* * * * *
5670712 GTTCAACCATAACTAATTTGTC-TTTTCATAGCTCATAGTTAATATAACAAATAAAAATCCAAAT
65 GTTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATAAAAATCCAAAT
5670776 TCAGCTTTTCATAGCTTATAA
130 TCAGCTTTTCATAGCTTATAA
* *
5670797 AATCATAAATTCTTAAGATTTTGAAATAT-ATGTTTTTCTTAATGCATTTCAAATACATAATCAA
1 AATCATAAATTCCTAAGATTTTGAAAT-TCATG-TTTTCTTAATACATTTCAAATACATAATCAA
* * *
5670861 AGTTCAACCTTCACTAATTTGGCCTTTTCATAGCTCAAAATTAATA-AACAAATCAAAAATCCAA
64 AGTTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAAT-AAAAATCCAA
5670925 ATTCAGCTTTTCATAGCTTATAA
128 ATTCAGCTTTTCATAGCTTATAA
* * * *
5670948 AATCATAAATTCCTAAGATTTCGAAATTCTTGTTTTCTT-ATGCATTTCAAATACATGATCAAAG
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTCTTAATACATTTCAAATACATAATCAAAG
* *
5671012 TTCAACCTTAACCAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAATATCCAAAT
66 TTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAAT-AAAAATCCAAAT
* * * *
5671076 TTAACTTCTCATACCTTATAA
130 TCAGCTTTTCATAGCTTATAA
* * * *
5671097 AATCATAAATTTCTAAGATTTTGAAATTCATGTTTTTTTAATATATTTCAAATACATAGTCAAAG
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTCTTAATACATTTCAAATACATAATCAAAG
*
5671162 TTCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCA
66 TTCAACCTTAACT-AATTTGGCTTTTTCATAGCTCAAAATCA
5671204 TAAATTTCAA
Statistics
Matches: 365, Mismatches: 31, Indels: 18
0.88 0.07 0.04
Matches are distributed among these distances:
148 42 0.12
149 125 0.34
150 91 0.25
151 95 0.26
152 12 0.03
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (150 bp):
AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTCTTAATACATTTCAAATACATAATCAAAG
TTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATAAAAATCCAAATT
CAGCTTTTCATAGCTTATAA
Found at i:5671496 original size:258 final size:257
Alignment explanation
Indices: 5670954--5671695 Score: 1159
Period size: 258 Copynumber: 2.9 Consensus size: 257
5670944 ATAAAATCAT
* * * * *
5670954 AAATTCCTAAGATTTCGAAATTCT-TGTTTTCTTATGCATTTC-AAATACATGATCAAAGTTCAA
1 AAATTCCTAAGCTTTCGAAATT-TGTGTTTTCTAATACATTTCAAAATTCATAATCAAAGTTCAA
* * * *
5671017 CCTTAACCAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAATATCCAAATTTAAC
65 CCTTAACAAATTT-GC-TTTTCATAGCTCAAAATTAATATAACAAATGAAAAATCCAAATTTAGC
* *
5671081 TTCTCATACCTTATAAAATCATAAATTTCTAAGATTTTGAAATTCATGTTTTTTTAATATATTTC
128 TTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATG-TTTTTT-ATACATTTC
*
5671146 AAATACATAGTCAAAGTTCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCATAAATTT
191 AAATACATAATCAAAGTTCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCATAAATTT
5671211 CA
256 CA
5671213 AAATTCCTAAGCTTTCGAAATTTGTGTTTTCTAATACATTTCAAAATTCATAATCAAAGTTCAAC
1 AAATTCCTAAGCTTTCGAAATTTGTGTTTTCTAATACATTTCAAAATTCATAATCAAAGTTCAAC
5671278 CTTAACAAATTTGCTTTTCATAGCTCAAAATTAATATAACAAATGAAAAATCCAAATTTAGCTTC
66 CTTAACAAATTTGCTTTTCATAGCTCAAAATTAATATAACAAATGAAAAATCCAAATTTAGCTTC
* * * * *
5671343 TCATACCTTATAAAATCCTAAATTCCTAATATTTTGACATTCATGTTTTCTTCTACAATTCAAAT
131 TCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTT-TTATACATTTCAAAT
*
5671408 ACAGAATCAAAGTTCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCATAAATTTCA
195 ACATAATCAAAGTTCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCATAAATTTCA
5671471 AAATTCCTAAGCTTTCGAAATTTGTGTTTTCTAATACATTTCAAAATTCATAATCAAAGTTCAAC
1 AAATTCCTAAGCTTTCGAAATTTGTGTTTTCTAATACATTTCAAAATTCATAATCAAAGTTCAAC
*
5671536 CTTAACAAATTTGCTTTTCATAGCTCAAAATTAATATAACAAATGAAAAATCCAAATCTAGCTTC
66 CTTAACAAATTTGCTTTTCATAGCTCAAAATTAATATAACAAATGAAAAATCCAAATTTAGCTTC
* * * *
5671601 TCATACCTTATAAAATCATAAATTCCTAAGCTTTCGAAATTTAT-TTATTTTATACTTTTTCAAA
131 TCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTT-TTTTATAC-ATTTCAAA
* *
5671665 TACATAATCAAAATTCAAACTTAACTAAATT
194 TACATAATCAAAGTTCAACCTTAACTAAATT
5671696 AAACTTTAGT
Statistics
Matches: 446, Mismatches: 31, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
257 7 0.02
258 285 0.64
259 123 0.28
260 31 0.07
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (257 bp):
AAATTCCTAAGCTTTCGAAATTTGTGTTTTCTAATACATTTCAAAATTCATAATCAAAGTTCAAC
CTTAACAAATTTGCTTTTCATAGCTCAAAATTAATATAACAAATGAAAAATCCAAATTTAGCTTC
TCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTATACATTTCAAATA
CATAATCAAAGTTCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCATAAATTTCA
Found at i:5674030 original size:22 final size:23
Alignment explanation
Indices: 5673987--5674030 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5673977 TTGAGCAGTT
* *
5673987 CTTTTTCTTTTATGTTCTTTCAA
1 CTTTTCCTTTTATGTTCCTTCAA
*
5674010 CTTTTCCTTTT-TTTTCCTTCA
1 CTTTTCCTTTTATGTTCCTTCA
5674031 TTTTCCATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.66
Consensus pattern (23 bp):
CTTTTCCTTTTATGTTCCTTCAA
Found at i:5675266 original size:26 final size:26
Alignment explanation
Indices: 5675218--5675267 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5675208 TTTTAAGCAT
*
5675218 GTAAAATTATAAAATTTTAAAAAGTA
1 GTAAAATTATAAAATTCTAAAAAGTA
*
5675244 GTAAAA-TATTAAAATTCTCAAAAG
1 GTAAAATTA-TAAAATTCTAAAAAG
5675268 AAACTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (26 bp):
GTAAAATTATAAAATTCTAAAAAGTA
Found at i:5691242 original size:25 final size:25
Alignment explanation
Indices: 5691214--5691263 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5691204 AGAACATGTA
5691214 TAAGTTAGATTTAATTCCTATTTTT
1 TAAGTTAGATTTAATTCCTATTTTT
5691239 TAAGTTAGATTTAATTCCTATTTTT
1 TAAGTTAGATTTAATTCCTATTTTT
5691264 AATAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (25 bp):
TAAGTTAGATTTAATTCCTATTTTT
Found at i:5699077 original size:16 final size:16
Alignment explanation
Indices: 5699043--5699077 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5699033 ATTTTTCATG
*
5699043 TATTTTTATAATATCT
1 TATTTTTATAAAATCT
*
5699059 TATTTTTATAAAATTT
1 TATTTTTATAAAATCT
5699075 TAT
1 TAT
5699078 AATATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTTTATAAAATCT
Found at i:5702681 original size:6 final size:6
Alignment explanation
Indices: 5702649--5702699 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
5702639 AGGGGTTACG
* * * * *
5702649 GGTTCG GGTT-T GGGTCT GGTACT GGTTCA GGTTCT GGTTCT GGTTAT
1 GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT
5702696 GGTT
1 GGTT
5702700 ATGGGAGTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
5 3 0.08
6 33 0.92
ACGTcount: A:0.06, C:0.12, G:0.39, T:0.43
Consensus pattern (6 bp):
GGTTCT
Found at i:5705346 original size:15 final size:15
Alignment explanation
Indices: 5705301--5705347 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
5705291 TCATGTTTAT
*
5705301 ACTTTTATTTTAGTC
1 ACTTATATTTTAGTC
*
5705316 ACCTA-ACTTTTAAGTC
1 ACTTATA-TTTT-AGTC
5705332 ACTTATATTTTAGTC
1 ACTTATATTTTAGTC
5705347 A
1 A
5705348 TCCAATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
14 1 0.04
15 12 0.46
16 12 0.46
17 1 0.04
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (15 bp):
ACTTATATTTTAGTC
Found at i:5707281 original size:19 final size:19
Alignment explanation
Indices: 5707251--5707306 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
5707241 AATACATTTA
5707251 AAAACATAAAAACAAATATT
1 AAAAC-TAAAAACAAATATT
5707271 AAAACTAAAAACAAATATT
1 AAAACTAAAAACAAATATT
5707290 AAAAC-AAGAAACAAATA
1 AAAACTAA-AAACAAATA
5707307 ACAATTGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 2 0.06
19 28 0.80
20 5 0.14
ACGTcount: A:0.71, C:0.11, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAACTAAAAACAAATATT
Found at i:5716066 original size:15 final size:15
Alignment explanation
Indices: 5716043--5716075 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5716033 GACAAACTTA
*
5716043 ATACGTTCATGTAAC
1 ATACATTCATGTAAC
5716058 ATACATTCATGTAAC
1 ATACATTCATGTAAC
5716073 ATA
1 ATA
5716076 TTGTCTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (15 bp):
ATACATTCATGTAAC
Found at i:5717256 original size:22 final size:24
Alignment explanation
Indices: 5717220--5717265 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
5717210 TTCAGATTAG
5717220 TAAATTTAGAATTAAAATTACAAT
1 TAAATTTAGAATTAAAATTACAAT
5717244 TAAA-TTA-AATTAAAATTACAAT
1 TAAATTTAGAATTAAAATTACAAT
5717266 ATTTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 15 0.68
23 3 0.14
24 4 0.18
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (24 bp):
TAAATTTAGAATTAAAATTACAAT
Found at i:5717977 original size:33 final size:33
Alignment explanation
Indices: 5717935--5718004 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5717925 AAGAGATGGG
5717935 TCAATTTTTGAAGAGAGCTTCATCCGTAGTTCC
1 TCAATTTTTGAAGAGAGCTTCATCCGTAGTTCC
* *
5717968 TCAATTTTTGAAGAGAGTTTCATCCGTGGTTCC
1 TCAATTTTTGAAGAGAGCTTCATCCGTAGTTCC
5718001 -CAAT
1 TCAAT
5718005 CTCCATGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 4 0.11
33 31 0.89
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (33 bp):
TCAATTTTTGAAGAGAGCTTCATCCGTAGTTCC
Found at i:5720967 original size:44 final size:45
Alignment explanation
Indices: 5720877--5721005 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
5720867 GACAGAACGA
*
5720877 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
5720923 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
5720967 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5721006 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:5732981 original size:59 final size:59
Alignment explanation
Indices: 5732916--5733032 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 59
5732906 TTTATTTTCT
5732916 AAATGAAAATTAAAACTATAATTTGTTAATTTTAAAAAATCTAAATTACTAATTGAGTA
1 AAATGAAAATTAAAACTATAATTTGTTAATTTTAAAAAATCTAAATTACTAATTGAGTA
*
5732975 AAATGAAAATTAAAACTATAATTTGTTAATTTTAAAAAATTTAAATTACTAATTGAGT
1 AAATGAAAATTAAAACTATAATTTGTTAATTTTAAAAAATCTAAATTACTAATTGAGT
5733033 TTTAATTCGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.38
Consensus pattern (59 bp):
AAATGAAAATTAAAACTATAATTTGTTAATTTTAAAAAATCTAAATTACTAATTGAGTA
Found at i:5733035 original size:28 final size:28
Alignment explanation
Indices: 5732945--5733037 Score: 73
Period size: 30 Copynumber: 3.2 Consensus size: 28
5732935 AATTTGTTAA
*
5732945 TTTTAAAAAATCTAAATTACTAATTGAG
1 TTTTAAAAAATTTAAATTACTAATTGAG
** * * *
5732973 -TAAAATGAAAATTAAAACTA-TAATTTGTTAA
1 TTTTAA--AAAATTTAAATTACTAA-TTG--AG
5733004 TTTTAAAAAATTTAAATTACTAATTGAG
1 TTTTAAAAAATTTAAATTACTAATTGAG
5733032 TTTTAA
1 TTTTAA
5733038 TTCGATTGGT
Statistics
Matches: 47, Mismatches: 11, Indels: 14
0.65 0.15 0.19
Matches are distributed among these distances:
27 3 0.06
28 10 0.21
29 13 0.28
30 14 0.30
31 4 0.09
32 3 0.06
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.41
Consensus pattern (28 bp):
TTTTAAAAAATTTAAATTACTAATTGAG
Found at i:5744461 original size:17 final size:17
Alignment explanation
Indices: 5744435--5744475 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5744425 AAAACCAAAT
*
5744435 CAGTTTATTAGAAATAA
1 CAGTTCATTAGAAATAA
*
5744452 CAGTTCATTAGACATAA
1 CAGTTCATTAGAAATAA
*
5744469 CAATTCA
1 CAGTTCA
5744476 CACACACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (17 bp):
CAGTTCATTAGAAATAA
Found at i:5747825 original size:6 final size:7
Alignment explanation
Indices: 5747799--5747824 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5747789 TATTACTCTT
5747799 TTTTTTC
1 TTTTTTC
5747806 TTTTTTC
1 TTTTTTC
5747813 TTTTTTC
1 TTTTTTC
5747820 TTTTT
1 TTTTT
5747825 CATCACGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:5755327 original size:19 final size:19
Alignment explanation
Indices: 5755303--5755342 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5755293 CCATCCCATA
5755303 ATCTACCCAAATGCTTTCT
1 ATCTACCCAAATGCTTTCT
5755322 ATCTACCCAAATGCTTTCT
1 ATCTACCCAAATGCTTTCT
5755341 AT
1 AT
5755343 TAACTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.05, T:0.38
Consensus pattern (19 bp):
ATCTACCCAAATGCTTTCT
Found at i:5758191 original size:23 final size:23
Alignment explanation
Indices: 5758141--5758197 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
5758131 AATATTTAAT
*
5758141 AATAAATGTTTTATAATATAGAA
1 AATAAATATTTTATAATATAGAA
* *
5758164 TATAAATATTTTAATTATATA-AA
1 AATAAATATTTT-ATAATATAGAA
*
5758187 AATAAGTATTT
1 AATAAATATTT
5758198 ATTTAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (23 bp):
AATAAATATTTTATAATATAGAA
Found at i:5759748 original size:163 final size:164
Alignment explanation
Indices: 5759545--5759844 Score: 417
Period size: 163 Copynumber: 1.8 Consensus size: 164
5759535 ATCTTGTATT
* * * *
5759545 AGCATCTTTAGTTGTTTGTTTAGCTATATACAAGTCCGGATCGAAAACTT-GTGTTATAAAGTCG
1 AGCATCTTTAGTTGATTGTATAGCTATATACAAATCCGGATCGAAAA-TTCATGTTATAAAGTCG
* * *
5759609 TATATTAGTTGCTCGAAAACTCTGATGTA-GTGAAAGGAAAAGAAATTTCTCCAGTGATCGATCA
65 TATAGTAGTTGCTCGAAAACTCCGATGTATGTG-AAGGAAAAGAAATTTCTCCAGTGATCAATCA
*
5759673 TGCATCGTTTTAATCCGGGAAAGATGCATCGTTTTA
129 TACATCGTTTTAATCCGGGAAAGATGCATCGTTTTA
**
5759709 AGCATCTTTAGTT-ATTGTATAGCTATATACAAATCCGGATCGAAAATTCATGTTATAAAGTTTT
1 AGCATCTTTAGTTGATTGTATAGCTATATACAAATCCGGATCGAAAATTCATGTTATAAAGTCGT
* * * * * *
5759773 ATAGTAGTTGCTTGAAAACTCCGATTTATTTGTAGGAAAAGAAATTTCTCCGGTGATCAATCTTA
66 ATAGTAGTTGCTCGAAAACTCCGATGTATGTGAAGGAAAAGAAATTTCTCCAGTGATCAATCATA
5759838 CATCGTT
131 CATCGTT
5759845 CTAAAGCAAG
Statistics
Matches: 118, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
162 2 0.02
163 101 0.86
164 15 0.13
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (164 bp):
AGCATCTTTAGTTGATTGTATAGCTATATACAAATCCGGATCGAAAATTCATGTTATAAAGTCGT
ATAGTAGTTGCTCGAAAACTCCGATGTATGTGAAGGAAAAGAAATTTCTCCAGTGATCAATCATA
CATCGTTTTAATCCGGGAAAGATGCATCGTTTTA
Found at i:5759961 original size:199 final size:199
Alignment explanation
Indices: 5759707--5760126 Score: 682
Period size: 199 Copynumber: 2.1 Consensus size: 199
5759697 TGCATCGTTT
* *
5759707 TAAGCATCTTTAGTT-ATTGTATAGCTATATACAAATCCGGATCGAAAATTCATGTTATAAAGTT
1 TAAGCATCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACTCATGTTATAAAGTT
* * * *
5759771 TTATAGTAGTTGCTTGAAAACTCCGATTTATTTGTAGGAAAAGAAATTTCTCCGGTGATCAATCT
66 GTATAGTAGTTGCTTGAAAACTCCGATTTATTTGAAGGAAAAGAAATTTCTCAGGTGATCAATAT
* *
5759836 TACATCGTTCTAAAGCAAGTTTTTTAA-TTCGGGAAGACGATGGAAAGATGCTAATGGTAACATC
131 CACATCGTTCTAAAGCAAG-TTTTTAATTTCGGGAAGACGACGGAAAGATGCTAATGGTAACATC
5759900 TTGTA
195 TTGTA
*
5759905 TAAGCATCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACTCATGTTATGAAGTT
1 TAAGCATCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACTCATGTTATAAAGTT
* *
5759970 GTATATTAGTTGCTTGAAAACTCCGATTTATTTGAAGGAAAAGAAATTTCTCAGGTGATCGATAT
66 GTATAGTAGTTGCTTGAAAACTCCGATTTATTTGAAGGAAAAGAAATTTCTCAGGTGATCAATAT
* * *
5760035 CACATCGTTTTAAAGCAAGTTTTTAATTTGGGGAAGACGACGGGAAGATGCTAATGGTAACATCT
131 CACATCGTTCTAAAGCAAGTTTTTAATTTCGGGAAGACGACGGAAAGATGCTAATGGTAACATCT
5760100 TGTA
196 TGTA
*
5760104 TAAGTATCTTTAGTTGTTTGTAT
1 TAAGCATCTTTAGTTGTTTGTAT
5760127 CGGTGTTGAA
Statistics
Matches: 205, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
198 22 0.11
199 183 0.89
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (199 bp):
TAAGCATCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACTCATGTTATAAAGTT
GTATAGTAGTTGCTTGAAAACTCCGATTTATTTGAAGGAAAAGAAATTTCTCAGGTGATCAATAT
CACATCGTTCTAAAGCAAGTTTTTAATTTCGGGAAGACGACGGAAAGATGCTAATGGTAACATCT
TGTA
Found at i:5760043 original size:362 final size:364
Alignment explanation
Indices: 5759369--5760047 Score: 978
Period size: 362 Copynumber: 1.9 Consensus size: 364
5759359 AAAGATGCTA
* * * *
5759369 ATATACAAATCCGGATCGAAAACTTGTGCTAGTAAGTCGTATATTTGTTGCTCGAAAACTCTGAT
1 ATATACAAATCCGGATCGAAAACTTATGCTAGTAAGTCGTATAGTAGTTGCTCGAAAACTCCGAT
* * *
5759434 TTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGATCATACATCGTTGTAAAGCTAGTTTTCTTA
66 TTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCAATCATACATCGTTCTAAAGCAAGTTTTCTTA
* * * *
5759499 ATCCGGGGAAGACGATTGAAAGATGTTAATGTTAACATCTTGTATTAGCATCTTTAGTTGTTTGT
131 ATCCGGGGAAGACGATGGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGT
* * **
5759564 TTAGCTATATACAAGTCCGGATCGAAAACTTGTGTTATAAAGTCGTATATTAGTTGCTCGAAAAC
196 ATAGCTATATACAAATCCGGATCGAAAACTCATGTTATAAAGTCGTATATTAGTTGCTCGAAAAC
* *
5759629 TCTGATGTAGTGAAAGGAAAAGAAATTTCTCCAGTGATCGATCATGCATCGTTTTAATCCGGGAA
261 TCCGATGTAGTGAAAGGAAAAGAAATTTCTCCAGTGATCGATCATACATCGTTTTAATCCGGGAA
5759694 AGATGCATCGTTTTAAGCATCTTTAGTTATTGTATAGCT
326 AGATGCATCGTTTTAAGCATCTTTAGTTATTGTATAGCT
* ** *
5759733 ATATACAAATCCGGATCGAAAA-TTCATGTTA-TAAAGTTTTATAGTAGTTGCTTGAAAACTCCG
1 ATATACAAATCCGGATCGAAAACTT-ATGCTAGT-AAGTCGTATAGTAGTTGCTCGAAAACTCCG
* * *
5759796 ATTTATTTG-TAGGAAAAGAAATTTCTCCGGTGATCAATCTTACATCGTTCTAAAGCAAGTTTT-
64 ATTTA-GTGAAAGGAAAAGAAATTTCTCCGGTGATCAATCATACATCGTTCTAAAGCAAGTTTTC
*
5759859 TTAATTC-GGGAAGACGATGGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTT
128 TTAATCCGGGGAAGACGATGGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTT
* * *
5759923 TGTATAGCTATATACAAATCCGGATCGAAAACTCATGTTATGAAGTTGTATATTAGTTGCTTGAA
193 TGTATAGCTATATACAAATCCGGATCGAAAACTCATGTTATAAAGTCGTATATTAGTTGCTCGAA
* *
5759988 AACTCCGATTTATTTG-AAGGAAAAGAAATTTCT-CAGGTGATCGAT-ATCACATCGTTTTAA
258 AACTCCGATGTA-GTGAAAGGAAAAGAAATTTCTCCA-GTGATCGATCAT-ACATCGTTTTAA
5760048 AGCAAGTTTT
Statistics
Matches: 279, Mismatches: 30, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
361 4 0.01
362 158 0.57
363 11 0.04
364 104 0.37
365 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (364 bp):
ATATACAAATCCGGATCGAAAACTTATGCTAGTAAGTCGTATAGTAGTTGCTCGAAAACTCCGAT
TTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCAATCATACATCGTTCTAAAGCAAGTTTTCTTA
ATCCGGGGAAGACGATGGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGT
ATAGCTATATACAAATCCGGATCGAAAACTCATGTTATAAAGTCGTATATTAGTTGCTCGAAAAC
TCCGATGTAGTGAAAGGAAAAGAAATTTCTCCAGTGATCGATCATACATCGTTTTAATCCGGGAA
AGATGCATCGTTTTAAGCATCTTTAGTTATTGTATAGCT
Found at i:5762117 original size:131 final size:131
Alignment explanation
Indices: 5761902--5762146 Score: 339
Period size: 131 Copynumber: 1.9 Consensus size: 131
5761892 TTTAAATTAC
* * * ** *
5761902 TTAAATTATTTAAGTTGTAAAACTCAAGTATGATTCTAATTTGAAAAATTAATTATTAATTTAAA
1 TTAAATTATTCAAGTTATAAAACTCAAGTATGACTCTAATTAAAAAAATAAATTATTAATTTAAA
5761967 TTAATTAAAAAAAACTGAATAACTCCCTTCAATTAATTTGAAAGTTGAATTTTATCGATTTATTT
66 TTAATTAAAAAAAACTGAATAACTCCCTTCAATTAATTTGAAAGTTGAATTTTATCGATTTATTT
5762032 T
131 T
* *
5762033 TTAAATTATTCAAGTTATAAAACTGAAGTATTACTCTAATTAAAAAAAATAAATTATTAATTTAA
1 TTAAATTATTCAAGTTATAAAACTCAAGTATGACTCTAATT-AAAAAAATAAATTATTAATTTAA
* ** ** * *
5762098 GTTAATT-AAAAAAACTGAATTTCTCTTTTCGATTACTTTGAAAGTTGAA
65 ATTAATTAAAAAAAACTGAATAACTCCCTTCAATTAATTTGAAAGTTGAA
5762147 AATTTTAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
131 72 0.73
132 26 0.27
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (131 bp):
TTAAATTATTCAAGTTATAAAACTCAAGTATGACTCTAATTAAAAAAATAAATTATTAATTTAAA
TTAATTAAAAAAAACTGAATAACTCCCTTCAATTAATTTGAAAGTTGAATTTTATCGATTTATTT
T
Found at i:5767576 original size:18 final size:17
Alignment explanation
Indices: 5767553--5767610 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
5767543 TTGGAGTCAA
5767553 ATTTTTTGAACTTCCACT
1 ATTTTTTGAACTT-CACT
* * *
5767571 A-TTTTTGGA-GTCA-A
1 ATTTTTTGAACTTCACT
5767585 ATTTTTTGAACTTTCACT
1 ATTTTTTGAAC-TTCACT
5767603 ATTTTTTG
1 ATTTTTTG
5767611 TAAAAACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
14 1 0.03
15 9 0.30
16 1 0.03
17 10 0.33
18 9 0.30
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.53
Consensus pattern (17 bp):
ATTTTTTGAACTTCACT
Found at i:5767592 original size:15 final size:15
Alignment explanation
Indices: 5767541--5767592 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5767531 CAGCTGATAA
5767541 TTTTGGAGTCAAATT
1 TTTTGGAGTCAAATT
* * * *
5767556 TTTTGAACTTCCACTAT
1 TTTTGGA-GTCAAAT-T
5767573 TTTTGGAGTCAAATT
1 TTTTGGAGTCAAATT
5767588 TTTTG
1 TTTTG
5767593 AACTTTCACT
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 12 0.44
16 8 0.30
17 7 0.26
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (15 bp):
TTTTGGAGTCAAATT
Found at i:5767610 original size:33 final size:32
Alignment explanation
Indices: 5767541--5767608 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
5767531 CAGCTGATAA
5767541 TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
1 TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
*
5767573 TTTTGGAGTCAAATTTTTTGAACTTTCACTAT
1 TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
5767605 TTTT
1 TTTT
5767609 TGTAAAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (32 bp):
TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
Found at i:5769309 original size:29 final size:29
Alignment explanation
Indices: 5769273--5769332 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
5769263 TCTTGTCTTG
*
5769273 TTCATAACATTTTTGTATTAAGATTGTAC
1 TTCATAACATTTTTGTATCAAGATTGTAC
*
5769302 TTCATAACATTTTTGTATCATGATTGTAC
1 TTCATAACATTTTTGTATCAAGATTGTAC
5769331 TT
1 TT
5769333 AATTATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (29 bp):
TTCATAACATTTTTGTATCAAGATTGTAC
Found at i:5771838 original size:181 final size:180
Alignment explanation
Indices: 5771534--5771898 Score: 651
Period size: 181 Copynumber: 2.0 Consensus size: 180
5771524 ATCACAAACC
5771534 TCTCCTAAATCAAGGAGATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAAT
1 TCTCCTAAATCAAGGAGATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAAT
*
5771599 ATAATGAAATCAAAGCGTGACTCAGAGCCAACTAATTGACGAAAACAGATTCTAAAGCACACCAA
66 ATAATGAAATCAAAGCGTGACTCAGAGCCAACTAATTGACAAAAACAGATTCTAAAGCACACCAA
*
5771664 GAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTCAATTAGTAAGCCACCT
131 GAAAGACTATTCTTCATTTTTGTGCTGTTCTTGTC-ATTAGTAAGCCACCT
*
5771715 TCTCCTAAATCAA-GACGATTGAAATAAGAAAGACACTAATTACTGATCTCCAGGCAGGCAGGAA
1 TCTCCTAAATCAAGGA-GATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAA
* **
5771779 TATAATGAAATCAAAGGGTGACTCAGAGCTGACTAATTGACAAAAACAGATTCTAAAGCACACCA
65 TATAATGAAATCAAAGCGTGACTCAGAGCCAACTAATTGACAAAAACAGATTCTAAAGCACACCA
5771844 AGAAAGACTATTCTTCATTTTTGTGCTGTTCTTGTCATTAGTAAGCCACCT
130 AGAAAGACTATTCTTCATTTTTGTGCTGTTCTTGTCATTAGTAAGCCACCT
5771895 TCTC
1 TCTC
5771899 TAAGGCATTC
Statistics
Matches: 177, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
180 21 0.12
181 156 0.88
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (180 bp):
TCTCCTAAATCAAGGAGATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAAT
ATAATGAAATCAAAGCGTGACTCAGAGCCAACTAATTGACAAAAACAGATTCTAAAGCACACCAA
GAAAGACTATTCTTCATTTTTGTGCTGTTCTTGTCATTAGTAAGCCACCT
Found at i:5781971 original size:31 final size:31
Alignment explanation
Indices: 5781936--5782003 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
5781926 TCCTCACGAA
5781936 AAACATTAAATTCATTAAAATTTTATACCGC
1 AAACATTAAATTCATTAAAATTTTATACCGC
5781967 AAACATTAAATTCATTAAAATTTTATACCGC
1 AAACATTAAATTCATTAAAATTTTATACCGC
5781998 AAACAT
1 AAACAT
5782004 ATTATTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (31 bp):
AAACATTAAATTCATTAAAATTTTATACCGC
Found at i:5783098 original size:20 final size:21
Alignment explanation
Indices: 5783070--5783110 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5783060 TTGGACTAAA
5783070 AAATAA-TTTAAAAAATTATT
1 AAATAATTTTAAAAAATTATT
*
5783090 AAATTATTTTAAAAAATTATT
1 AAATAATTTTAAAAAATTATT
5783111 TAAGTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATAATTTTAAAAAATTATT
Found at i:5783102 original size:21 final size:22
Alignment explanation
Indices: 5783076--5783119 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
5783066 TAAAAAATAA
5783076 TTTAAAAAATTA-TTAAATTAT
1 TTTAAAAAATTATTTAAATTAT
*
5783097 TTTAAAAAATTATTTAAGTTAT
1 TTTAAAAAATTATTTAAATTAT
5783119 T
1 T
5783120 AGGCATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAAAAAATTATTTAAATTAT
Found at i:5794994 original size:19 final size:19
Alignment explanation
Indices: 5794958--5795017 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
5794948 AGAAATAGTT
* *
5794958 TAATTGAATAATATACATTA
1 TAATT-AATATTACACATTA
*
5794978 TAATTAATATTACACATTG
1 TAATTAATATTACACATTA
*
5794997 TAATTAATATTACACAATA
1 TAATTAATATTACACATTA
5795016 TA
1 TA
5795018 TTATTATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.86
20 5 0.14
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (19 bp):
TAATTAATATTACACATTA
Found at i:5796133 original size:39 final size:39
Alignment explanation
Indices: 5796090--5796224 Score: 114
Period size: 39 Copynumber: 3.4 Consensus size: 39
5796080 ACCAATATGG
*
5796090 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAATTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAATTGA
* * * *
5796129 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAATTGA
* * * * *
5796167 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATA-ATTGA
*
5796208 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5796225 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAATTGA
Found at i:5797763 original size:17 final size:17
Alignment explanation
Indices: 5797741--5797775 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5797731 GAATGCTCTC
*
5797741 TGTTTCTTATTCTTCTT
1 TGTTTCTTATTATTCTT
*
5797758 TGTTTCTTTTTATTCTT
1 TGTTTCTTATTATTCTT
5797775 T
1 T
5797776 TTCTTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTTTCTTATTATTCTT
Found at i:5797845 original size:13 final size:13
Alignment explanation
Indices: 5797805--5797838 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5797795 ACATATATAT
* *
5797805 ATAATATTATTTA
1 ATAATAATAGTTA
5797818 ATAATAATAGTTA
1 ATAATAATAGTTA
5797831 ATAATAAT
1 ATAATAAT
5797839 TTATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
ATAATAATAGTTA
Found at i:5801670 original size:15 final size:15
Alignment explanation
Indices: 5801650--5801679 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5801640 GTAGTTTAAT
5801650 TCAGTAACTAAATTA
1 TCAGTAACTAAATTA
5801665 TCAGTAACTAAATTA
1 TCAGTAACTAAATTA
5801680 ATTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
TCAGTAACTAAATTA
Found at i:5805515 original size:29 final size:29
Alignment explanation
Indices: 5805476--5805534 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
5805466 GACCTAAACT
5805476 TTAAAATATAAAA-AGTAAAAATTTAAATTC
1 TTAAAATATAAAATA-TAAAAA-TTAAATTC
5805506 TTAAAA-ATAAAATATAAAAATTAAATTC
1 TTAAAATATAAAATATAAAAATTAAATTC
5805534 T
1 T
5805535 AACTTTATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 9 0.32
29 12 0.43
30 7 0.25
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (29 bp):
TTAAAATATAAAATATAAAAATTAAATTC
Found at i:5807848 original size:44 final size:45
Alignment explanation
Indices: 5807789--5807875 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 45
5807779 ATGAATTATT
*
5807789 CTGTCTCCAATGCCATA-TATAATATGGACTTACATGGCTCAATC
1 CTGTCTCCAAAGCCATATTATAATATGGACTTACATGGCTCAATC
*
5807833 CTGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 CTGTCTCCAAAGCCATA-TTATAATATGGACTTACATGGCTCA
5807876 TTTCTGTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 16 0.41
46 23 0.59
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (45 bp):
CTGTCTCCAAAGCCATATTATAATATGGACTTACATGGCTCAATC
Found at i:5812858 original size:2 final size:2
Alignment explanation
Indices: 5812851--5812879 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5812841 ATTCATGTAT
5812851 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5812880 TTGATGCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5813740 original size:134 final size:133
Alignment explanation
Indices: 5813518--5813854 Score: 357
Period size: 134 Copynumber: 2.5 Consensus size: 133
5813508 TAGATGTTTG
* * *
5813518 GCAATTCAGGAAATCGTACCCTATCGTGCTGGGTTGCAATTTCCTGTTTGTTCGAAACAATCGAA
1 GCAATTCAGGAAATCGTACCCTATCGTGCTGGGTTGCAATTTCCTGTTTGCTCAAAATAATCGAA
* * * **** *
5813583 TAT-TCCTTCGGTGTTCCACTCATGTCTTT-TAAAAAATTTTA-TTA-AAACGAAAGAGATGTTC
66 TATCTCTTTAGATGTTCCACTCATGT-TTTCTAAAAAAAAAAACTTATAAA-G---GAAATGTTC
5813644 GATATTTA
126 GATATTTA
* * * *
5813652 GCAATTCATGAAATCGTGCCCTAACGTGTTGGGTTGCAATTT-CTCGTTTGCTCAAAATAATCGA
1 GCAATTCAGGAAATCGTACCCTATCGTGCTGGGTTGCAATTTCCT-GTTTGCTCAAAATAATCGA
* * *
5813716 ATGTCTCTTTAGAAT-TT-CATTCATGTTTTCTAAAAAAAAAAACTTATAAAGGAAATGTTCGGT
65 ATATCTCTTTAG-ATGTTCCACTCATGTTTTCTAAAAAAAAAAACTTATAAAGGAAATGTTCGAT
5813779 ATTTA
129 ATTTA
* * * *
5813784 GCAGTTC-GGGAATAGTACCCTATCGTGCTGGGTTGCAATTTCCTATTTGCTCAAAATAATCGAA
1 GCAATTCAGGAAATCGTACCCTATCGTGCTGGGTTGCAATTTCCTGTTTGCTCAAAATAATCGAA
5813848 TATCTCT
66 TATCTCT
5813855 CCGGAATTTC
Statistics
Matches: 169, Mismatches: 27, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
131 53 0.31
132 23 0.14
133 5 0.03
134 73 0.43
135 11 0.07
136 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (133 bp):
GCAATTCAGGAAATCGTACCCTATCGTGCTGGGTTGCAATTTCCTGTTTGCTCAAAATAATCGAA
TATCTCTTTAGATGTTCCACTCATGTTTTCTAAAAAAAAAAACTTATAAAGGAAATGTTCGATAT
TTA
Found at i:5819291 original size:24 final size:24
Alignment explanation
Indices: 5819260--5819310 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
5819250 GAACTTAAAT
5819260 CTTTCTTTTAAAAATACAACATGA
1 CTTTCTTTTAAAAATACAACATGA
*
5819284 CTTTCTTTTAAAAATACAACGTGA
1 CTTTCTTTTAAAAATACAACATGA
5819308 CTT
1 CTT
5819311 ACCATTATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (24 bp):
CTTTCTTTTAAAAATACAACATGA
Found at i:5823679 original size:23 final size:23
Alignment explanation
Indices: 5823653--5823700 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5823643 TTGTCTTTTA
**
5823653 TGGTAAAATTGGATTGAGTTGGG
1 TGGTAAAATTGGACCGAGTTGGG
*
5823676 TGGTCAAATTGGACCGAGTTGGG
1 TGGTAAAATTGGACCGAGTTGGG
5823699 TG
1 TG
5823701 TGGGCAGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.06, G:0.40, T:0.31
Consensus pattern (23 bp):
TGGTAAAATTGGACCGAGTTGGG
Found at i:5826881 original size:21 final size:21
Alignment explanation
Indices: 5826857--5826897 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5826847 AAATAGTTTG
*
5826857 GTCAACAGAAAATAACTTATA
1 GTCAACAAAAAATAACTTATA
* *
5826878 GTCAAGAAAAAATAAGTTAT
1 GTCAACAAAAAATAACTTAT
5826898 TTTTCCTGTA
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:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (21 bp):
GTCAACAAAAAATAACTTATA
Found at i:5827188 original size:13 final size:14
Alignment explanation
Indices: 5827172--5827213 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
5827162 TTTCAATTTT
5827172 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
5827185 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
5827200 ATTTTAAATAATAT
1 ATTTT-AATAATAT
5827214 TATTGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:5827198 original size:16 final size:16
Alignment explanation
Indices: 5827176--5827212 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
5827166 AATTTTATTT
5827176 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
5827193 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
5827208 TAATA
1 TAATA
5827213 TTATTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:5827284 original size:15 final size:15
Alignment explanation
Indices: 5827234--5827284 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 15
5827224 ATTCAATATT
5827234 AATAT-TTAATAATA
1 AATATATTAATAATA
*
5827248 AATATTTATTACAATTATA
1 AATA--TATT--AATAATA
5827267 AATATATTAATAATA
1 AATATATTAATAATA
5827282 AAT
1 AAT
5827285 GTTTTGTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 1 0.03
17 6 0.20
19 10 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:5827694 original size:32 final size:33
Alignment explanation
Indices: 5827658--5827729 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
5827648 AAATTTTATG
5827658 AAATATTTTA-A-AGAAATC-TACTAAATAACAGA
1 AAATATTTTACACAG-AATCAT-CTAAATAACAGA
* *
5827690 AAATATTTTACACAGATTCATCTAAATACCAGA
1 AAATATTTTACACAGAATCATCTAAATAACAGA
5827723 AAATATT
1 AAATATT
5827730 AGCTTTTCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 10 0.29
33 22 0.63
34 3 0.09
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (33 bp):
AAATATTTTACACAGAATCATCTAAATAACAGA
Found at i:5828057 original size:90 final size:90
Alignment explanation
Indices: 5827904--5828072 Score: 320
Period size: 90 Copynumber: 1.9 Consensus size: 90
5827894 TGAACTAGAG
5827904 GCTTGAACTAGACAACTATTCTCACATTAGAGCTTGAATTTTTGTTTGTCCAAATTAATCATTGA
1 GCTTGAACTAGACAACTATTCTCACATTAGAGCTTGAATTTTTGTTTGTCCAAATTAATCATTGA
5827969 ACTTGATAATTGTTTCCACACAGAA
66 ACTTGATAATTGTTTCCACACAGAA
*
5827994 GCTTGAACTAGACAACTATTCTCACATTGGAGCTTGAATTTTTGTTTGTCCAAATTAATCATTGA
1 GCTTGAACTAGACAACTATTCTCACATTAGAGCTTGAATTTTTGTTTGTCCAAATTAATCATTGA
*
5828059 GCTTGATAATTGTT
66 ACTTGATAATTGTT
5828073 CCTGCATTGG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 77 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (90 bp):
GCTTGAACTAGACAACTATTCTCACATTAGAGCTTGAATTTTTGTTTGTCCAAATTAATCATTGA
ACTTGATAATTGTTTCCACACAGAA
Found at i:5831704 original size:3 final size:3
Alignment explanation
Indices: 5831696--5831727 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5831686 TCCTTCTTTC
5831696 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
5831728 AGCCTTTTCT
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:5832713 original size:18 final size:17
Alignment explanation
Indices: 5832690--5832724 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5832680 GGCTTGGTTG
5832690 CCTCAGGATCATCTATCT
1 CCTCAGGATCATC-ATCT
*
5832708 CCTCAGGCTCATCATCT
1 CCTCAGGATCATCATCT
5832725 AACCATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.37, G:0.11, T:0.31
Consensus pattern (17 bp):
CCTCAGGATCATCATCT
Found at i:5835037 original size:31 final size:32
Alignment explanation
Indices: 5834999--5835119 Score: 135
Period size: 31 Copynumber: 3.9 Consensus size: 32
5834989 GAATAATTAT
* *
5834999 TAAACTATTTGACAA-TTTTCATTTAAGTCAC
1 TAAACTATTTGAAAAGATTTCATTTAAGTCAC
* *
5835030 TAAACTATTT-AAAAGATTTCATTGAATTCAC
1 TAAACTATTTGAAAAGATTTCATTTAAGTCAC
* * *
5835061 TAAATTATTTGAAAA-TTTTCATTTAAGACAC
1 TAAACTATTTGAAAAGATTTCATTTAAGTCAC
*
5835092 TGAACTATTTG-AAAGATTTCA-TTAAGTC
1 TAAACTATTTGAAAAGATTTCATTTAAGTC
5835120 GCTATTAAGT
Statistics
Matches: 74, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
30 12 0.16
31 58 0.78
32 4 0.05
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (32 bp):
TAAACTATTTGAAAAGATTTCATTTAAGTCAC
Found at i:5835998 original size:58 final size:60
Alignment explanation
Indices: 5835930--5836061 Score: 157
Period size: 58 Copynumber: 2.3 Consensus size: 60
5835920 GTTAATGTTA
* * *
5835930 ATATAATTTAAAATTTTAATTTATTATTATAATTT-TT-TGAAAAATATTTTTCT-TATTT
1 ATATATTTTAAAATTTTAATATATTATTATAATTTCTTGTCAAAAATATTTTT-TATATTT
* * * *
5835988 ATATATTTT--AATTTTTATATATTATTATTATTTCTTGTCAACAATATTTTTTATTTTT
1 ATATATTTTAAAATTTTAATATATTATTATAATTTCTTGTCAAAAATATTTTTTATATTT
5836046 ATATATTTTAAAATTT
1 ATATATTTTAAAATTT
5836062 ATTTTTTTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
56 21 0.34
57 3 0.05
58 33 0.53
60 5 0.08
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (60 bp):
ATATATTTTAAAATTTTAATATATTATTATAATTTCTTGTCAAAAATATTTTTTATATTT
Found at i:5836918 original size:9 final size:9
Alignment explanation
Indices: 5836896--5837029 Score: 50
Period size: 9 Copynumber: 14.8 Consensus size: 9
5836886 TTATTTTCCC
*
5836896 ATAAAAAAT
1 ATAAAAATT
5836905 A-AAAAATT
1 ATAAAAATT
*
5836913 ATAAAAAGTC
1 ATAAAAA-TT
*
5836923 AGAAAAATT
1 ATAAAAATT
5836932 ATTAAAATATT
1 A-TAAAA-ATT
*
5836943 -TATAAAGTT
1 ATA-AAAATT
*
5836952 ATTAAAA-T
1 ATAAAAATT
*
5836960 -TAATAATT
1 ATAAAAATT
*
5836968 AATAAAACTT
1 -ATAAAAATT
*
5836978 ATAAATATT
1 ATAAAAATT
5836987 AT-AAAA-T
1 ATAAAAATT
5836994 ATAATAAATCT
1 ATAA-AAAT-T
*
5837005 A-ATAAATT
1 ATAAAAATT
5837013 -TCAATAAATT
1 AT-AA-AAATT
5837023 ATAAAAA
1 ATAAAAA
5837030 ATTTATAAGA
Statistics
Matches: 91, Mismatches: 17, Indels: 34
0.64 0.12 0.24
Matches are distributed among these distances:
7 7 0.08
8 14 0.15
9 35 0.38
10 29 0.32
11 6 0.07
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:5837009 original size:19 final size:17
Alignment explanation
Indices: 5836944--5837028 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 17
5836934 TAAAATATTT
*
5836944 ATAAAGTTATTAAAATTA
1 ATAAA-TTAATAAAATTA
5836962 AT-AATTAATAAAACTT-
1 ATAAATTAATAAAA-TTA
*
5836978 ATAAATATTATAAAATATA
1 ATAAAT-TAATAAAAT-TA
*
5836997 ATAAATCTAATAAATTTCA
1 ATAAAT-TAATAAAATT-A
5837016 ATAAATT-ATAAAA
1 ATAAATTAATAAAA
5837029 AATTTATAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
16 10 0.18
17 13 0.24
18 12 0.22
19 20 0.36
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (17 bp):
ATAAATTAATAAAATTA
Found at i:5837328 original size:23 final size:23
Alignment explanation
Indices: 5837298--5837348 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
5837288 TACTATTTCA
5837298 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
5837321 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
5837344 TATTT
1 TATTT
5837349 GAAATATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (23 bp):
TATTTAAGCTTTATTCACCAAAG
Found at i:5838055 original size:42 final size:42
Alignment explanation
Indices: 5837992--5838106 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
5837982 CTTCGTTTTC
** * *
5837992 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCAGATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGAT-A
* *
5838035 T-GATGCCATAGGCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATA
5838076 TCGATGCCATAGCCCAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
5838107 GAATCACATA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.03
42 62 0.95
43 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATA
Found at i:5838214 original size:31 final size:31
Alignment explanation
Indices: 5838171--5838350 Score: 299
Period size: 31 Copynumber: 5.8 Consensus size: 31
5838161 CTTGTCACTT
*
5838171 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5838202 GTAGCC-AGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
5838233 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5838264 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5838295 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
5838326 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
5838351 TGTTATTTGT
Statistics
Matches: 140, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
30 1 0.01
31 139 0.99
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:5838424 original size:50 final size:51
Alignment explanation
Indices: 5838326--5838454 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
5838316 CACTGATCAG
* * *
5838326 GTAGCCGAAGCTACCACTTTTCACTTGTTATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
* *
5838377 GTAGCCGAAGCTATTACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
5838427 GTAGCCAAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
5838455 TGCTATGGTC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 46 0.66
51 24 0.34
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:5843972 original size:27 final size:25
Alignment explanation
Indices: 5843906--5844095 Score: 121
Period size: 27 Copynumber: 7.6 Consensus size: 25
5843896 TTTTGAACAG
* * * *
5843906 TTTTATTATTATATATTTTAAGTTT
1 TTTTAATATTATTTATTTTAAATTA
* *
5843931 TTTTCATATGGTATTTGTTTTAAATTA
1 TTTTAATAT--TATTTATTTTAAATTA
5843958 TTTTACCATATTATTTATTTT-AATTCA
1 TTTTA--ATATTATTTATTTTAAATT-A
*
5843985 TTTT-GTATTA-TTATTTTAAATTA
1 TTTTAATATTATTTATTTTAAATTA
* *
5844008 TTTTATATATTATTTACTTTAAATTGC
1 TTTTA-ATATTATTTATTTTAAATT-A
*
5844035 TTTATAA-ATTATTTATTTCAAATTA
1 TTT-TAATATTATTTATTTTAAATTA
* *
5844060 ATTT-ATA--CTTTATTTTAAA--A
1 TTTTAATATTATTTATTTTAAATTA
5844080 -TTTATATATTATTTAT
1 TTTTA-ATATTATTTAT
5844096 CTTGAACCAT
Statistics
Matches: 130, Mismatches: 19, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
19 3 0.02
20 1 0.01
21 3 0.02
22 10 0.08
23 18 0.14
24 11 0.08
25 14 0.11
26 30 0.23
27 34 0.26
28 2 0.02
29 4 0.03
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (25 bp):
TTTTAATATTATTTATTTTAAATTA
Found at i:5843978 original size:54 final size:49
Alignment explanation
Indices: 5843948--5844064 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 49
5843938 ATGGTATTTG
*
5843948 TTTTAAATTATTTTACCATATTATTTATTTTAATTCATTTTGTATTATTA
1 TTTTAAATTATTTTA-CATATTATTTATTTTAATTCATTTTATATTATTA
* * *
5843998 TTTTAAATTATTTTATATATTATTTACTTTAAATTGC-TTTATAAATTATTTA
1 TTTTAAATTATTTTACATATTATTTA-TTTTAATT-CATTT-TATATTA-TTA
* *
5844050 TTTCAAATTAATTTA
1 TTTTAAATTATTTTA
5844065 TACTTTATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
49 10 0.18
50 25 0.44
51 6 0.11
52 16 0.28
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (49 bp):
TTTTAAATTATTTTACATATTATTTATTTTAATTCATTTTATATTATTA
Found at i:5844001 original size:23 final size:23
Alignment explanation
Indices: 5843906--5844092 Score: 94
Period size: 26 Copynumber: 7.5 Consensus size: 23
5843896 TTTTGAACAG
* *
5843906 TTTTATTATTATATATTTTAAGTTT
1 TTTTA-TATTAT-TATTTTAAATTA
*
5843931 TTTTCATATGGTATTTGTTTTAAATTA
1 TTTT-ATAT--TA-TTATTTTAAATTA
5843958 TTTTACCATATTATTTATTTT-AATTCA
1 TTTT---ATATTA-TTATTTTAAATT-A
*
5843985 TTTTGTATTATTATTTTAAATTA
1 TTTTATATTATTATTTTAAATTA
* *
5844008 TTTTATATATTATTTACTTTAAATTGC
1 -TTT-TATATTA-TTATTTTAAATT-A
* *
5844035 TTTATAAATTATTTATTTCAAATTA
1 TTT-TATATTA-TTATTTTAAATTA
* *
5844060 ATTTATACT-TTATTTTAAA--A
1 TTTTATATTATTATTTTAAATTA
5844080 TTTATATATTATT
1 TTT-TATATTATT
5844093 TATCTTGAAC
Statistics
Matches: 130, Mismatches: 18, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
20 3 0.02
21 5 0.04
22 11 0.08
23 8 0.06
24 16 0.12
25 15 0.12
26 37 0.28
27 29 0.22
28 1 0.01
29 5 0.04
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (23 bp):
TTTTATATTATTATTTTAAATTA
Found at i:5844029 original size:76 final size:75
Alignment explanation
Indices: 5843907--5844094 Score: 170
Period size: 76 Copynumber: 2.5 Consensus size: 75
5843897 TTTGAACAGT
* * ** ** * *
5843907 TTTATTATTATATATTTTAAGTTTTTTTCATATGGTATTTGTTTTAAATTATTTTACCATATTAT
1 TTTA-TATTAT-TATTTTAAATTATTTT-ATATATTATTTACTTTAAATTACTTTA-CAAATTAT
* *
5843972 TTATTT-TAATTCAT
62 TTATTTCAAATT-AA
* * *
5843986 TTTGTATTATTATTTTAAATTATTTTATATATTATTTACTTTAAATTGCTTTATAAATTATTTAT
1 TTTATATTATTATTTTAAATTATTTTATATATTATTTACTTTAAATTACTTTACAAATTATTTAT
5844051 TTCAAATTAA
66 TTCAAATTAA
*
5844061 TTTATACT-TTATTTTAAA--A-TTTATATATTATTTA
1 TTTATATTATTATTTTAAATTATTTTATATATTATTTA
5844095 TCTTGAACCA
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
71 15 0.16
72 1 0.01
74 10 0.11
75 19 0.20
76 25 0.27
77 14 0.15
78 6 0.06
79 3 0.03
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (75 bp):
TTTATATTATTATTTTAAATTATTTTATATATTATTTACTTTAAATTACTTTACAAATTATTTAT
TTCAAATTAA
Found at i:5844031 original size:26 final size:25
Alignment explanation
Indices: 5843949--5844095 Score: 107
Period size: 26 Copynumber: 6.0 Consensus size: 25
5843939 TGGTATTTGT
*
5843949 TTTAAATTATTTTACCATATTATTTA
1 TTTAAATTATTTTA-TATATTATTTA
* *
5843975 TTTTAATTCA-TTT-TGTATTA-TTA
1 TTTAAATT-ATTTTATATATTATTTA
5843998 TTTTAAATTATTTTATATATTATTTA
1 -TTTAAATTATTTTATATATTATTTA
** *
5844024 CTTTAAATTGCTTTATAAATTATTTA
1 -TTTAAATTATTTTATATATTATTTA
*
5844050 TTTCAAATTAATTTATACT-TTA--T-
1 TTT-AAATTATTTTATA-TATTATTTA
5844073 TTTAAA--A-TTTATATATTATTTA
1 TTTAAATTATTTTATATATTATTTA
5844095 T
1 T
5844096 CTTGAACCAT
Statistics
Matches: 98, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
18 1 0.01
19 9 0.09
20 1 0.01
21 1 0.01
22 4 0.04
23 7 0.07
24 16 0.16
25 9 0.09
26 49 0.50
27 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (25 bp):
TTTAAATTATTTTATATATTATTTA
Found at i:5847687 original size:3 final size:3
Alignment explanation
Indices: 5847673--5847709 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
5847663 AAGAATGTGG
5847673 AGA AGCA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
5847710 GCTTTAGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5849706 original size:26 final size:27
Alignment explanation
Indices: 5849677--5849739 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
5849667 TATTTAGCAA
5849677 TGCTTTTGAAAAA-TACTTTTAAAAAG
1 TGCTTTTGAAAAAGTACTTTTAAAAAG
* * *
5849703 TGC-TGTGAAAAAGTACTTTTGAGAAG
1 TGCTTTTGAAAAAGTACTTTTAAAAAG
*
5849729 TACTTTTGAAA
1 TGCTTTTGAAA
5849740 CTTTGAGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 8 0.27
26 16 0.53
27 6 0.20
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (27 bp):
TGCTTTTGAAAAAGTACTTTTAAAAAG
Found at i:5849729 original size:13 final size:13
Alignment explanation
Indices: 5849713--5849737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5849703 TGCTGTGAAA
5849713 AAGTACTTTTGAG
1 AAGTACTTTTGAG
5849726 AAGTACTTTTGA
1 AAGTACTTTTGA
5849738 AACTTTGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
AAGTACTTTTGAG
Found at i:5857401 original size:22 final size:22
Alignment explanation
Indices: 5857376--5857428 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
5857366 ATTATAAGGA
5857376 TTATAATAAGTATAAATTTTAC
1 TTATAATAAGTATAAATTTTAC
5857398 TTATAATAAGTATAAATTTTAC
1 TTATAATAAGTATAAATTTTAC
5857420 TTATAATAA
1 TTATAATAA
5857429 ATTTTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
TTATAATAAGTATAAATTTTAC
Found at i:5858172 original size:15 final size:15
Alignment explanation
Indices: 5858152--5858181 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5858142 CATTTTATTT
*
5858152 ATATTAGGATAATTA
1 ATATTAAGATAATTA
5858167 ATATTAAGATAATTA
1 ATATTAAGATAATTA
5858182 TTAGAATTAT
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:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:5859650 original size:21 final size:21
Alignment explanation
Indices: 5859626--5859707 Score: 101
Period size: 21 Copynumber: 3.8 Consensus size: 21
5859616 GACACATAAA
*
5859626 GTGCTTAAAACGACACACGAG
1 GTGCCTAAAACGACACACGAG
* *
5859647 GTGCCTGATACGACACACGAG
1 GTGCCTAAAACGACACACGAG
* *
5859668 GTGCCTGATACGACACACGAG
1 GTGCCTAAAACGACACACGAG
5859689 GTGCCTGAAATACGACACA
1 GTGCCT-AAA-ACGACACA
5859708 TAAAGTGCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 45 0.83
22 1 0.02
23 8 0.15
ACGTcount: A:0.33, C:0.27, G:0.26, T:0.15
Consensus pattern (21 bp):
GTGCCTAAAACGACACACGAG
Done.