Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 318 of 318
Found at i:100400919 original size:20 final size:20
Alignment explanation
Indices: 100400894--100400943 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
100400884 TGGCTTAAAA
100400894 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
100400914 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
100400931 GTGGTAGTGGATT
1 TTGGTAGTGGATT
100400944 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:100415559 original size:43 final size:42
Alignment explanation
Indices: 100415511--100415603 Score: 150
Period size: 43 Copynumber: 2.2 Consensus size: 42
100415501 ATTTTAGAAA
100415511 TATTTTTATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTT-TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
* *
100415554 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTT-TTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
100415597 TATTTTT
1 TATTTTT
100415604 CCAATTAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 1 0.02
43 45 0.96
44 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (42 bp):
TATTTTTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
Found at i:100420364 original size:30 final size:31
Alignment explanation
Indices: 100420330--100420393 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
100420320 ACTTAACAAG
*
100420330 CAAATACCTCTAAAA-CAATAACAAAATTAA
1 CAAATACCTCTAAAATAAATAACAAAATTAA
* *
100420360 CAAATGCCTTTAAAATAAATAACAAAATTAA
1 CAAATACCTCTAAAATAAATAACAAAATTAA
100420391 CAA
1 CAA
100420394 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.59, C:0.17, G:0.02, T:0.22
Consensus pattern (31 bp):
CAAATACCTCTAAAATAAATAACAAAATTAA
Found at i:100426455 original size:18 final size:18
Alignment explanation
Indices: 100426432--100426467 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
100426422 ATAAATAAAT
*
100426432 AAGGTTGGATCGTACTAA
1 AAGGTTAGATCGTACTAA
100426450 AAGGTTAGATCGTACTAA
1 AAGGTTAGATCGTACTAA
100426468 CATATTCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (18 bp):
AAGGTTAGATCGTACTAA
Found at i:100438547 original size:24 final size:23
Alignment explanation
Indices: 100438520--100438564 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
100438510 ATTTATAAAA
**
100438520 TTTTAATTTTTAAAAGAAATTATT
1 TTTTAATAATTAAAA-AAATTATT
*
100438544 TTTTTATAATTAAAAAAATTA
1 TTTTAATAATTAAAAAAATTA
100438565 AGTCTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTTAATAATTAAAAAAATTATT
Found at i:100439378 original size:30 final size:29
Alignment explanation
Indices: 100439342--100439408 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
100439332 TATCTTTGTA
100439342 ATTTTTAGAA-AATAAAATAAAATTTTTATT
1 ATTTTTA-AAGAATAAAATAAAA-TTTTATT
*
100439372 ATTTTTAAAGAATAAAATATAATTTTATT
1 ATTTTTAAAGAATAAAATAAAATTTTATT
*
100439401 ATTATTAA
1 ATTTTTAA
100439409 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 16 0.47
30 18 0.53
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (29 bp):
ATTTTTAAAGAATAAAATAAAATTTTATT
Found at i:100443016 original size:56 final size:56
Alignment explanation
Indices: 100442954--100443073 Score: 177
Period size: 56 Copynumber: 2.1 Consensus size: 56
100442944 ATCCATACGA
* * *
100442954 ACTCTTACCTAGAAGAAAATCCATACAAACTCGTTCTTGAAAGATAATTTAAGTGG
1 ACTCTTACCTAGAAGAAAATCCATACAAACTCGTACTTGAAAGATAATTCAAGTAG
* * * *
100443010 ACTCTTACCTGGATGAAGATCCATACAAACTCGTACTTGAAAGATAATTCATGTAG
1 ACTCTTACCTAGAAGAAAATCCATACAAACTCGTACTTGAAAGATAATTCAAGTAG
100443066 ACTCTTAC
1 ACTCTTAC
100443074 ATGTAAATTC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (56 bp):
ACTCTTACCTAGAAGAAAATCCATACAAACTCGTACTTGAAAGATAATTCAAGTAG
Found at i:100446383 original size:19 final size:19
Alignment explanation
Indices: 100446359--100446398 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
100446349 CTTGATTTCA
100446359 AATGCATGGGAAAGAAAAC
1 AATGCATGGGAAAGAAAAC
100446378 AATGCATGGGAAAGAAAAC
1 AATGCATGGGAAAGAAAAC
100446397 AA
1 AA
100446399 CTCCCACTTC
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:0.55, C:0.10, G:0.25, T:0.10
Consensus pattern (19 bp):
AATGCATGGGAAAGAAAAC
Found at i:100452940 original size:24 final size:24
Alignment explanation
Indices: 100452913--100452961 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
100452903 ATGTAATTTA
100452913 AAATT-TTAAAAATAATAAAAATAT
1 AAATTATT-AAAATAATAAAAATAT
*
100452937 AAATTATTAAAATAATAAAATTAT
1 AAATTATTAAAATAATAAAAATAT
100452961 A
1 A
100452962 TTTTTACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATTATTAAAATAATAAAAATAT
Found at i:100453839 original size:16 final size:16
Alignment explanation
Indices: 100453811--100453848 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
100453801 TGGAATTGAA
100453811 TTTTTT-TACAAAATT
1 TTTTTTGTACAAAATT
*
100453826 TTTTTTGTAGAAAATT
1 TTTTTTGTACAAAATT
100453842 TTTTTTG
1 TTTTTTG
100453849 GGCTAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (16 bp):
TTTTTTGTACAAAATT
Found at i:100456550 original size:21 final size:21
Alignment explanation
Indices: 100456510--100456548 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
100456500 TTATATGCAC
100456510 ATTTTAATTATTTTTTAAAAT
1 ATTTTAATTATTTTTTAAAAT
100456531 ATTTT-ATT-TTTTTTAAAA
1 ATTTTAATTATTTTTTAAAA
100456549 AAGTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTAATTATTTTTTAAAAT
Found at i:100457234 original size:15 final size:12
Alignment explanation
Indices: 100457194--100457224 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
100457184 TAAGGTAAAA
100457194 TAATAATGGTAT
1 TAATAATGGTAT
100457206 TAATAATGGTAT
1 TAATAATGGTAT
100457218 TAATAAT
1 TAATAAT
100457225 CGGGTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (12 bp):
TAATAATGGTAT
Found at i:100465036 original size:372 final size:373
Alignment explanation
Indices: 100464328--100465048 Score: 1068
Period size: 372 Copynumber: 1.9 Consensus size: 373
100464318 AATTGAGCAT
* * *
100464328 TATTATCGGTTTGATATATTCATTGCTGGTATCGATTCATTGCTAACAAAAATGAATTCTCGCTT
1 TATTATAGGTTTGATATATTCATTGCTGGTATCAATTAATTGCTAACAAAAATGAATTCTCGCTT
* *
100464393 TAATGATGAAGTAGTGGAGTTACTTGTTCTTAGCTCCGCATTGGATCCACGCGATAATTACAAAG
66 TAATGACGAAGTAGTGGAGTTACTTGTTCTTAGCTCCGCATTGGATCCACGCGATAATCACAAAG
* *
100464458 CTTTTTCGTGTAGAAGATATTTGCAAGCCTATAAATGATTTTTATCCAAACAATTTTACAAAGTA
131 CTTTTTCGTGTAGAAGATATCTGCAAGCCTATAAATGATTTTTATCCAAACAATTTTACAAAGCA
*
100464523 AAAAAAGCTACATATGAAAATTCCATTAGAGCATTTTCAACTTAATGCTCATCAAAGCACAGAGT
196 AAAAAAGCTACATATGAAAATTCAATTAGAGCATTTTCAACTTAATGCTCATCAAAGCACAGAGT
* * * * * * *
100464588 TGCAGAAAGCTTCTACAGTTGTCGAGTTGTGTTAAGTGCTAGCTAAGACAAATAAGTCAAGTATT
261 TGCAGAAAACTTCTACAATTGACGAGTTGTGTCAAGTACTAACTAAGACAAATAACTCAAGTATT
*
100464653 TATCCTCTTCTTGATAGAATTATTTGTCTTGTGCACTCTTCTCATGTC
326 TATCATCTTCTTGATAGAATTATTTGTCTTGTGCACTCTTCTCATGTC
* * * *
100464701 TATTATAGGTTTGATATATTTATTGTTGGTATCAATTAATTGTTAACAGAAATGAATTCTCGCTT
1 TATTATAGGTTTGATATATTCATTGCTGGTATCAATTAATTGCTAACAAAAATGAATTCTCGCTT
* * *
100464766 TAATGACGAGGTAGTGGAGTTACTTGTTCTTAGCTTCGCTTTGGATCCACGCGATAATCACAAAG
66 TAATGACGAAGTAGTGGAGTTACTTGTTCTTAGCTCCGCATTGGATCCACGCGATAATCACAAAG
* ** * * * ***
100464831 CTTTTT-GTGTGGAAGATATCTGCAAGTTTATGAATGATTTTTATCTAAATAATTTTATGGAGCA
131 CTTTTTCGTGTAGAAGATATCTGCAAGCCTATAAATGATTTTTATCCAAACAATTTTACAAAGCA
* * * *
100464895 AGATAAGCTACATATGAAGATTCAATTGGAGCATTTTCAACTTAATGCTCATCAAAGCACAGAGT
196 AAAAAAGCTACATATGAAAATTCAATTAGAGCATTTTCAACTTAATGCTCATCAAAGCACAGAGT
* * *
100464960 TGTAGAAAACTTCTACAATT-ACGGAGTTGTGTCAAGTACTAACTAAGACAAATAACTTAAGTGT
261 TGCAGAAAACTTCTACAATTGAC-GAGTTGTGTCAAGTACTAACTAAGACAAATAACTCAAGTAT
100465024 TTATCATCTTCTTGATAGAATTATT
325 TTATCATCTTCTTGATAGAATTATT
100465049 CATCTCGTAC
Statistics
Matches: 308, Mismatches: 39, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
371 1 0.00
372 183 0.59
373 124 0.40
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (373 bp):
TATTATAGGTTTGATATATTCATTGCTGGTATCAATTAATTGCTAACAAAAATGAATTCTCGCTT
TAATGACGAAGTAGTGGAGTTACTTGTTCTTAGCTCCGCATTGGATCCACGCGATAATCACAAAG
CTTTTTCGTGTAGAAGATATCTGCAAGCCTATAAATGATTTTTATCCAAACAATTTTACAAAGCA
AAAAAAGCTACATATGAAAATTCAATTAGAGCATTTTCAACTTAATGCTCATCAAAGCACAGAGT
TGCAGAAAACTTCTACAATTGACGAGTTGTGTCAAGTACTAACTAAGACAAATAACTCAAGTATT
TATCATCTTCTTGATAGAATTATTTGTCTTGTGCACTCTTCTCATGTC
Found at i:100465767 original size:19 final size:21
Alignment explanation
Indices: 100465743--100465781 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
100465733 CAATTTATTT
*
100465743 TTATATTTG-ATA-AATATAA
1 TTATATATGCATACAATATAA
100465762 TTATATATGCATACAATATA
1 TTATATATGCATACAATATA
100465782 TATAACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
TTATATATGCATACAATATAA
Found at i:100465879 original size:30 final size:29
Alignment explanation
Indices: 100465831--100465914 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
100465821 AATTTGTAAG
*
100465831 AATTGTATC-AAATCAAAATTTCATATATAA
1 AATTGTA-CAAAATCAAAA-TCCATATATAA
* *
100465861 AATTGTACAAAATTAAAATCCATGTATAA
1 AATTGTACAAAATCAAAATCCATATATAA
* *
100465890 AACTGTACATTAGATCAAAATCCAT
1 AATTGTACA--AAATCAAAATCCAT
100465915 GTGTTAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 18 0.40
30 15 0.33
31 12 0.27
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AATTGTACAAAATCAAAATCCATATATAA
Found at i:100465889 original size:29 final size:30
Alignment explanation
Indices: 100465840--100465916 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
100465830 GAATTGTATC
* * *
100465840 AAATCAAAATTTCATATATAAAATTGTACA-
1 AAATCAAAA-TCCATGTATAAAACTGTACAT
*
100465870 AAATTAAAATCCATGTATAAAACTGTACATT
1 AAATCAAAATCCATGTATAAAACTGTACA-T
*
100465901 AGATCAAAATCCATGT
1 AAATCAAAATCCATGT
100465917 GTTAATAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 17 0.44
30 8 0.21
31 14 0.36
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.31
Consensus pattern (30 bp):
AAATCAAAATCCATGTATAAAACTGTACAT
Found at i:100479372 original size:36 final size:36
Alignment explanation
Indices: 100479325--100479398 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
100479315 CAACTTTCCC
100479325 ACCTTTTATCATGATTGCTATGTTCATGGGAAAGTA
1 ACCTTTTATCATGATTGCTATGTTCATGGGAAAGTA
100479361 ACCTTTTATCATGATTGCTATGTTCATGGGAAAGTA
1 ACCTTTTATCATGATTGCTATGTTCATGGGAAAGTA
100479397 AC
1 AC
100479399 TCCCAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (36 bp):
ACCTTTTATCATGATTGCTATGTTCATGGGAAAGTA
Found at i:100479804 original size:26 final size:26
Alignment explanation
Indices: 100479775--100479838 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
100479765 ATAATTCAAC
100479775 TATTCTTTTATTTTACTTTCAAAAAA
1 TATTCTTTTATTTTACTTTCAAAAAA
*
100479801 TATTCTTTTATTTTACTTTCAAAAAG
1 TATTCTTTTATTTTACTTTCAAAAAA
*
100479827 TATTATTTTATT
1 TATTCTTTTATT
100479839 AATATTCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (26 bp):
TATTCTTTTATTTTACTTTCAAAAAA
Found at i:100481072 original size:162 final size:160
Alignment explanation
Indices: 100480728--100481043 Score: 391
Period size: 160 Copynumber: 2.0 Consensus size: 160
100480718 GGCAAATTAT
* * * * *
100480728 CACAGTTATAATGGTAAAACCAAAGAAAAAGTGCTAGCAATGGTACATAATGTTAAGCACCCAAG
1 CACAATTATAAAGGTAAAACCAAAGAAAAAGTGATAGCAACGGTACAAAATGTTAAGCACCCAAG
* * * * *
100480793 CAAGAACCAATATACTAGGCAAGAAACCTAATTTGAATATCGAGCCACAGAAAACTAAAGACTTA
66 CAAGAACAAATAGACTAGGCAAGAAACCTAATTCGAACATCAAGCCACAGAAAACTAAAGACTTA
* ** * *
100480858 ACTAATGATCAGTGAGACCAGTTAAATTAT
131 ACTAATGAACAGAAAGACCAGTTAAATCAC
* * * * *
100480888 CACAGTTATAATGGTAAAACCAAAGTAAAAGTGATAGCTACGGTACAAAATGTTAAGCATCCAAG
1 CACAATTATAAAGGTAAAACCAAAGAAAAAGTGATAGCAACGGTACAAAATGTTAAGCACCCAAG
* * *
100480953 CAAGAACAAATAGACTATAGGCAAGAAGCCTCATTCGAACATCAAGCCACAGAAAACTAATGACT
66 CAAGAACAAATAGAC--TAGGCAAGAAACCTAATTCGAACATCAAGCCACAGAAAACTAAAGACT
100481018 TAACTAATGAAC-GAAAAGACCAGTTA
129 TAACTAATGAACAG-AAAGACCAGTTA
100481044 CTCCCCGTAA
Statistics
Matches: 136, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
160 72 0.53
161 1 0.01
162 63 0.46
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.20
Consensus pattern (160 bp):
CACAATTATAAAGGTAAAACCAAAGAAAAAGTGATAGCAACGGTACAAAATGTTAAGCACCCAAG
CAAGAACAAATAGACTAGGCAAGAAACCTAATTCGAACATCAAGCCACAGAAAACTAAAGACTTA
ACTAATGAACAGAAAGACCAGTTAAATCAC
Found at i:100490270 original size:15 final size:15
Alignment explanation
Indices: 100490250--100490283 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
100490240 CTTCAATGGC
100490250 AGAAG-AAGAAGAGAA
1 AGAAGAAAGAA-AGAA
100490265 AGAAGAAAGAAAGAA
1 AGAAGAAAGAAAGAA
100490280 AGAA
1 AGAA
100490284 ATGTCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
AGAAGAAAGAAAGAA
Found at i:100505753 original size:30 final size:30
Alignment explanation
Indices: 100505719--100505781 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
100505709 ATTTATTTTA
100505719 TTGTTAATTTTCTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTCTTATTATTTTAGAA-GCAT
*
100505749 TTGTTAATTTTTTTATTATTTTAGAAGCAT
1 TTGTTAATTTTCTTATTATTTTAGAAGCAT
100505779 TTG
1 TTG
100505782 CTTCTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAGAAGCAT
Found at i:100507490 original size:53 final size:53
Alignment explanation
Indices: 100507409--100507564 Score: 210
Period size: 53 Copynumber: 3.0 Consensus size: 53
100507399 GACGAAAAAT
* *
100507409 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* *
100507461 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATTGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * *
100507514 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTA
100507565 TGATATGTGA
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
51 4 0.04
52 11 0.12
53 78 0.84
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
Found at i:100507586 original size:46 final size:48
Alignment explanation
Indices: 100507464--100507609 Score: 118
Period size: 53 Copynumber: 3.0 Consensus size: 48
100507454 CGGTGCAATG
* * ** *
100507464 TGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATT-GGTATAA
1 TGATAATGTGAATCCGTATAAGACCATGGCAAGGATATGGC-TTCGG--T-A
* * **
100507515 TGTGATAATGTGATTCCGTATAAGACCATGTCTGGGATATGGCTTCGGTA
1 --TGATAATGTGAATCCGTATAAGACCATGGCAAGGATATGGCTTCGGTA
* *
100507565 TGAT-ATGTGAAT-CGTGTAAGACCATGGCAAGGCTATGGCTTCGGT
1 TGATAATGTGAATCCGTATAAGACCATGGCAAGGATATGGCTTCGGT
100507610 GTGTGATGCG
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
46 28 0.34
47 7 0.09
48 4 0.05
50 1 0.01
51 1 0.01
52 2 0.02
53 39 0.48
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (48 bp):
TGATAATGTGAATCCGTATAAGACCATGGCAAGGATATGGCTTCGGTA
Found at i:100509615 original size:18 final size:17
Alignment explanation
Indices: 100509575--100509628 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
100509565 AATATTATTA
*
100509575 TATTT-ATAATAATTTTT
1 TATTTAATAATAA-ATTT
* *
100509592 TATTTAATATTTAATTT
1 TATTTAATAATAAATTT
100509609 TATTTTAATAATAAATTT
1 TA-TTTAATAATAAATTT
100509627 TA
1 TA
100509629 AATAATATTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 10 0.33
18 20 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTAATAATAAATTT
Found at i:100509660 original size:59 final size:62
Alignment explanation
Indices: 100509596--100509815 Score: 179
Period size: 62 Copynumber: 3.5 Consensus size: 62
100509586 ATTTTTTATT
*
100509596 TAATATTTAATTT-TATTTTAATAATAAATTTTAAATAATATTCTTCATATATTATTGAAAAATA
1 TAATATTCAATTTATATTTTAATAATAAATTTTAAATAATATTCTTCATATATTATTG---AATA
* * * * * * * *
100509660 TACATATTTAATTATCTATATCTAATCATATAATAATT-AATAA-ATTATT-AT-T-TTAATAAA
1 TA-ATATTCAATT-TATAT-TTTAATAATA-AAT-TTTAAATAATATTCTTCATATATTATTGAA
100509720 TTA
61 -TA
100509723 TTTAATATTCAATTT-TATTTTAATAATAAATTTTAAATAATATTCTTCATATATTATTGAA-A
1 --TAATATTCAATTTATATTTTAATAATAAATTTTAAATAATATTCTTCATATATTATTGAATA
100509785 -AATATTCAATATTAATATTTTAATAATAAAT
1 TAATATTCAAT-TT-ATATTTTAATAATAAAT
100509816 ATTTTATAGT
Statistics
Matches: 126, Mismatches: 13, Indels: 36
0.72 0.07 0.21
Matches are distributed among these distances:
59 12 0.10
60 10 0.08
61 13 0.10
62 24 0.19
63 4 0.03
64 17 0.13
65 16 0.13
66 2 0.02
67 5 0.04
68 13 0.10
69 8 0.06
70 2 0.02
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (62 bp):
TAATATTCAATTTATATTTTAATAATAAATTTTAAATAATATTCTTCATATATTATTGAATA
Found at i:100509742 original size:17 final size:17
Alignment explanation
Indices: 100509720--100509767 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
100509710 TTTTAATAAA
100509720 TTATTTAATATTCAATT
1 TTATTTAATATTCAATT
* *
100509737 TTATTTTAATAATAAATT
1 TTA-TTTAATATTCAATT
**
100509755 TTAAATAATATTC
1 TTATTTAATATTC
100509768 TTCATATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTTAATATTCAATT
Found at i:100509746 original size:18 final size:18
Alignment explanation
Indices: 100509697--100509757 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
100509687 ATATAATAAT
100509697 TAATAAATTATTA-TTT--
1 TAATAAATT-TTATTTTAA
100509713 TAATAAA--TTA-TTTAA
1 TAATAAATTTTATTTTAA
* *
100509728 TATTCAATTTTATTTTAA
1 TAATAAATTTTATTTTAA
100509746 TAATAAATTTTA
1 TAATAAATTTTA
100509758 AATAATATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
15 5 0.14
16 7 0.19
17 3 0.08
18 15 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATAAATTTTATTTTAA
Found at i:100511375 original size:20 final size:20
Alignment explanation
Indices: 100511350--100511389 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
100511340 TTACTTAGAG
*
100511350 TATATTTTAAAATTTAAAAT
1 TATATTCTAAAATTTAAAAT
*
100511370 TATATTCTATAATTTAAAAT
1 TATATTCTAAAATTTAAAAT
100511390 AAACAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATTCTAAAATTTAAAAT
Found at i:100541928 original size:38 final size:38
Alignment explanation
Indices: 100541880--100541955 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
100541870 CTACATGATG
100541880 ATTTATTTAATGTAGCGTGATCTTATTTTAATTTGTTT
1 ATTTATTTAATGTAGCGTGATCTTATTTTAATTTGTTT
*
100541918 ATTTATTTAATGTAGGGTGATCTTATTTTAATTTGTTT
1 ATTTATTTAATGTAGCGTGATCTTATTTTAATTTGTTT
100541956 TGGTTTAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.24, C:0.04, G:0.14, T:0.58
Consensus pattern (38 bp):
ATTTATTTAATGTAGCGTGATCTTATTTTAATTTGTTT
Found at i:100542403 original size:20 final size:19
Alignment explanation
Indices: 100542353--100542403 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
100542343 TAAACCATTT
*
100542353 TAAAA-TTTAAAAATATCA
1 TAAAATTTTAAAAAAATCA
*
100542371 TAAAATTTATAAAAAAATTA
1 TAAAATTT-TAAAAAAATCA
100542391 TAAAATGTTTAAA
1 TAAAAT-TTTAAA
100542404 TTATAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.18
19 2 0.07
20 19 0.68
21 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAAATTTTAAAAAAATCA
Found at i:100556821 original size:30 final size:30
Alignment explanation
Indices: 100556780--100556838 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
100556770 AGTCGACCGC
*
100556780 TGCTAGCTGTTCTCAAACAAAAATGGGGGT
1 TGCTAGCTGTTCCCAAACAAAAATGGGGGT
* * *
100556810 TGCTGGCTGTTCCCAAAGAGAAATGGGGG
1 TGCTAGCTGTTCCCAAACAAAAATGGGGG
100556839 CTGCAGGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (30 bp):
TGCTAGCTGTTCCCAAACAAAAATGGGGGT
Found at i:100557955 original size:40 final size:40
Alignment explanation
Indices: 100557906--100558042 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
100557896 AACACACCAG
* *
100557906 TTTGGCACCCAGTGCCTCATCGGATAATTTGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAATCTGAAGTAATAA
* * *
100557946 TTTGACACCCAGTGTCTCATCGGCTAA-CCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGATAATCTGAAGTAATAA
*
100557983 -TTGACACCCAGTGCCTCATCGAATTAATCCT-AAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGA-TAAT-CTGAAGTAATAA
* *
100558023 ATTGACACCCAGTGTCTCAT
1 TTTGACACCCAGTGCCTCAT
100558043 TGACTCAAAG
Statistics
Matches: 81, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
36 20 0.25
37 5 0.06
38 5 0.06
39 7 0.09
40 26 0.32
41 18 0.22
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAATCTGAAGTAATAA
Found at i:100557994 original size:36 final size:37
Alignment explanation
Indices: 100557911--100558042 Score: 131
Period size: 41 Copynumber: 3.4 Consensus size: 37
100557901 ACCAGTTTGG
**
100557911 CACCCAGTGCCTCATCGGATAATTTGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGGATAATCCGAAGT-A-AA-TTGA
* *
100557951 CACCCAGTGTCTCATCGGCTAA-CCGAAGTAAATTGA
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAAATTGA
* *
100557987 CACCCAGTGCCTCATCGAATTAATCCTAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATCCGAAG---TAAATTGA
*
100558028 CACCCAGTGTCTCAT
1 CACCCAGTGCCTCAT
100558043 TGACTCAAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
36 20 0.26
37 5 0.06
38 6 0.08
39 5 0.06
40 20 0.26
41 22 0.28
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGATAATCCGAAGTAAATTGA
Found at i:100559080 original size:19 final size:20
Alignment explanation
Indices: 100559056--100559094 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
100559046 ATTAATAAGC
100559056 AATACATAT-TTTATTATTA
1 AATACATATGTTTATTATTA
100559075 AATACATATGTTTATTATTA
1 AATACATATGTTTATTATTA
100559095 TTACACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
AATACATATGTTTATTATTA
Found at i:100586786 original size:9 final size:9
Alignment explanation
Indices: 100586772--100586817 Score: 92
Period size: 9 Copynumber: 5.1 Consensus size: 9
100586762 TGAGTATTCG
100586772 AATTCGAAT
1 AATTCGAAT
100586781 AATTCGAAT
1 AATTCGAAT
100586790 AATTCGAAT
1 AATTCGAAT
100586799 AATTCGAAT
1 AATTCGAAT
100586808 AATTCGAAT
1 AATTCGAAT
100586817 A
1 A
100586818 TCAAACTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:100591310 original size:13 final size:13
Alignment explanation
Indices: 100591292--100591323 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
100591282 TTTCCAGCAA
100591292 TTATGAATTTATT
1 TTATGAATTTATT
100591305 TTATGAATTTATT
1 TTATGAATTTATT
*
100591318 TGATGA
1 TTATGA
100591324 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:100591531 original size:50 final size:50
Alignment explanation
Indices: 100591418--100591659 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
100591408 ATTTGGGTAA
* * *
100591418 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
100591474 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
100591524 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
100591574 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
100591624 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
100591660 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:100591607 original size:100 final size:103
Alignment explanation
Indices: 100591418--100591667 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
100591408 ATTTGGGTAA
100591418 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
100591483 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
100591524 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
100591586 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
100591624 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
100591668 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:100594246 original size:13 final size:14
Alignment explanation
Indices: 100594223--100594251 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
100594213 TAAAAGTATT
100594223 TAAAAATTAAAAAA
1 TAAAAATTAAAAAA
100594237 TAAAAA-TAAAAAA
1 TAAAAATTAAAAAA
100594250 TA
1 TA
100594252 TATATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAAATTAAAAAA
Found at i:100595516 original size:15 final size:14
Alignment explanation
Indices: 100595497--100595539 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
100595487 TAATTTTTTT
100595497 TCTAATTTTAAAAA
1 TCTAATTTTAAAAA
*
100595511 TACTAA-TATAAAAA
1 T-CTAATTTTAAAAA
100595525 TCTAATATTTAAAAA
1 TCTAAT-TTTAAAAA
100595540 AAATCCGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 4 0.17
14 9 0.38
15 11 0.46
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
TCTAATTTTAAAAA
Found at i:100595812 original size:16 final size:16
Alignment explanation
Indices: 100595791--100595821 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
100595781 TAGACATACA
*
100595791 ATTTTAATAATTTTAT
1 ATTTTAAAAATTTTAT
100595807 ATTTTAAAAATTTTA
1 ATTTTAAAAATTTTA
100595822 AAATATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTAAAAATTTTAT
Found at i:100595831 original size:2 final size:2
Alignment explanation
Indices: 100595824--100595858 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
100595814 AAATTTTAAA
100595824 AT AT AT AT 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 AT AT AT AT A
100595859 AACTTGCCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:100612037 original size:15 final size:15
Alignment explanation
Indices: 100612017--100612048 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
100612007 TCAAAATTTG
*
100612017 AAAATAATAATAAAA
1 AAAATAAAAATAAAA
100612032 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
100612047 AA
1 AA
100612049 GAGTAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATAAAAATAAAA
Found at i:100612373 original size:3 final size:3
Alignment explanation
Indices: 100612355--100612455 Score: 105
Period size: 3 Copynumber: 33.3 Consensus size: 3
100612345 AGGTATAAAT
* * * * * * *
100612355 ATA ATG ATA GTA ATA ATA ATA GTA GTA ATA ATA CTA ACA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
100612403 A-A GATA ATA ATA GTAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA -ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
100612449 ATA ATA A
1 ATA ATA A
100612456 AATTAACAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
2 1 0.01
3 77 0.95
4 3 0.04
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:100617514 original size:17 final size:16
Alignment explanation
Indices: 100617494--100617532 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
100617484 ATTAGAAATA
100617494 TTTTGTAATTATATTAT
1 TTTTGTAATT-TATTAT
*
100617511 TTTTTTAATTTATTAT
1 TTTTGTAATTTATTAT
100617527 TGTTTG
1 T-TTTG
100617533 AGAAAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (16 bp):
TTTTGTAATTTATTAT
Found at i:100622072 original size:21 final size:21
Alignment explanation
Indices: 100622046--100622086 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
100622036 AGACGAGCAA
* *
100622046 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
100622067 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
100622087 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:100637048 original size:2 final size:2
Alignment explanation
Indices: 100637041--100637065 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
100637031 AAGGTTTTCT
100637041 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
100637066 GTTATTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:100648783 original size:21 final size:21
Alignment explanation
Indices: 100648733--100648783 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
100648723 TTAAAAGAAG
100648733 AAATAAAATGGAATTAGAAAA
1 AAATAAAATGGAATTAGAAAA
*
100648754 CAATGAAAATCGGAA-TA-AAAA
1 AAAT-AAAAT-GGAATTAGAAAA
100648775 TAAATAAAA
1 -AAATAAAA
100648784 AAAAGGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 11 0.44
22 10 0.40
23 4 0.16
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.18
Consensus pattern (21 bp):
AAATAAAATGGAATTAGAAAA
Found at i:100657520 original size:31 final size:31
Alignment explanation
Indices: 100657485--100657553 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
100657475 ATACAAAATG
*
100657485 GTTACTGAACTATTTGAAAGTTTTCATTTAA
1 GTTACTGAACTATTTAAAAGTTTTCATTTAA
* *
100657516 GTTACTGAATTATTTAAAAGTTTTTATTTAA
1 GTTACTGAACTATTTAAAAGTTTTCATTTAA
100657547 GTTACTG
1 GTTACTG
100657554 GGTTGTTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (31 bp):
GTTACTGAACTATTTAAAAGTTTTCATTTAA
Found at i:100659197 original size:15 final size:16
Alignment explanation
Indices: 100659170--100659200 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
100659160 AGAAATCGAC
100659170 AGAAAATAAAGAAAAG
1 AGAAAATAAAGAAAAG
100659186 AGAAAA-AAAGAAAAG
1 AGAAAATAAAGAAAAG
100659201 GAAGCGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (16 bp):
AGAAAATAAAGAAAAG
Found at i:100665707 original size:20 final size:20
Alignment explanation
Indices: 100665674--100665713 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
100665664 CCCTTGCAGT
* *
100665674 CTAAATTTTTCAAATTTTTC
1 CTAAAATTTCCAAATTTTTC
100665694 CTAAAATTTCCAAATTTTTC
1 CTAAAATTTCCAAATTTTTC
100665714 TGATATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (20 bp):
CTAAAATTTCCAAATTTTTC
Found at i:100670139 original size:43 final size:42
Alignment explanation
Indices: 100670091--100670177 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 42
100670081 TATTCCCCTT
100670091 TGACTTGATTTGTGGAATCAGTTTTAGTTAAGCCTGTCAATTC
1 TGACTTGATTTGTGGAATCAGTTTTAGTTAAG-CTGTCAATTC
*
100670134 TGACTTGATTTGTGGAATCAGTTTTAGTTTAGCTGTCAATTC
1 TGACTTGATTTGTGGAATCAGTTTTAGTTAAGCTGTCAATTC
100670176 TG
1 TG
100670178 CCATTACTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 12 0.28
43 31 0.72
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.44
Consensus pattern (42 bp):
TGACTTGATTTGTGGAATCAGTTTTAGTTAAGCTGTCAATTC
Found at i:100672322 original size:27 final size:27
Alignment explanation
Indices: 100672284--100672340 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
100672274 AATGGCGTGT
100672284 CAATAGGAGTTTTCAGAGACTCATTTG
1 CAATAGGAGTTTTCAGAGACTCATTTG
100672311 CAATAGGAGTTTTCAGAGACTCATTTG
1 CAATAGGAGTTTTCAGAGACTCATTTG
100672338 CAA
1 CAA
100672341 ACTGGTACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (27 bp):
CAATAGGAGTTTTCAGAGACTCATTTG
Found at i:100673114 original size:7 final size:6
Alignment explanation
Indices: 100673093--100673122 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
100673083 ATATCTCTCT
100673093 CCCTCTC CCCTCC CCCTCC CCCTCC CCCTC
1 CCCTC-C CCCTCC CCCTCC CCCTCC CCCTC
100673123 TCTCTCTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (6 bp):
CCCTCC
Found at i:100673116 original size:12 final size:13
Alignment explanation
Indices: 100673093--100673124 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
100673083 ATATCTCTCT
100673093 CCCTCTCCCCTCC
1 CCCTCTCCCCTCC
100673106 CCCTC-CCCCTCC
1 CCCTCTCCCCTCC
100673118 CCCTCTC
1 CCCTCTC
100673125 TCTCTCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.00, C:0.78, G:0.00, T:0.22
Consensus pattern (13 bp):
CCCTCTCCCCTCC
Found at i:100673941 original size:17 final size:16
Alignment explanation
Indices: 100673919--100673965 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
100673909 GTTATGCCAA
*
100673919 TTGGCGAACTCTTTGCT
1 TTGGCGAACTCTTTG-G
*
100673936 TTGGCGAGA-TCTATGG
1 TTGGCGA-ACTCTTTGG
100673952 TTGGCGAACTCTTT
1 TTGGCGAACTCTTT
100673966 TGTTAAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.04
16 11 0.44
17 12 0.48
18 1 0.04
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (16 bp):
TTGGCGAACTCTTTGG
Found at i:100674125 original size:34 final size:35
Alignment explanation
Indices: 100674081--100674147 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
100674071 CAGTAAAATA
* * *
100674081 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACAGGAAAATATTTTAC
*
100674115 TTTTCTGTAAAATGACTTACAGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACAGGAAAATATTTT
100674148 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACAGGAAAATATTTTAC
Found at i:100674134 original size:20 final size:20
Alignment explanation
Indices: 100674096--100674134 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
100674086 CGTAAAATGA
**
100674096 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
100674116 TTTCTGTAAAATGACTTAC
1 TTTCTGGAAAATGACTTAC
100674135 AGGAAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:100687103 original size:16 final size:16
Alignment explanation
Indices: 100687082--100687121 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
100687072 TTGGGATGAC
* *
100687082 AATATTTATTTAGATA
1 AATATTTAATTAAATA
100687098 AATATTTAATTAAATA
1 AATATTTAATTAAATA
100687114 AA-ATTTAA
1 AATATTTAA
100687122 ATAGATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AATATTTAATTAAATA
Found at i:100687119 original size:27 final size:28
Alignment explanation
Indices: 100687089--100687142 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
100687079 GACAATATTT
* *
100687089 ATTTAGATAAATATTTAATTA-AATAAA
1 ATTTAAATAAATAATTAATTATAATAAA
*
100687116 ATTTAAATAGATAATTAATTATAATAA
1 ATTTAAATAAATAATTAATTATAATAA
100687143 TAGGTACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (28 bp):
ATTTAAATAAATAATTAATTATAATAAA
Found at i:100687129 original size:15 final size:16
Alignment explanation
Indices: 100687082--100687129 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
100687072 TTGGGATGAC
**
100687082 AATATTTATTTAGATA
1 AATATTTAAATAGATA
* *
100687098 AATATTTAATTAAATA
1 AATATTTAAATAGATA
100687114 AA-ATTTAAATAGATA
1 AATATTTAAATAGATA
100687129 A
1 A
100687130 TTAATTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
AATATTTAAATAGATA
Found at i:100692858 original size:13 final size:13
Alignment explanation
Indices: 100692840--100692864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100692830 AAAAATTCAA
100692840 AACACGAAAAATC
1 AACACGAAAAATC
100692853 AACACGAAAAAT
1 AACACGAAAAAT
100692865 TAAAATATTA
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:0.64, C:0.20, G:0.08, T:0.08
Consensus pattern (13 bp):
AACACGAAAAATC
Found at i:100697990 original size:3 final size:3
Alignment explanation
Indices: 100697982--100698012 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
100697972 AACACCCAGG
100697982 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
100698013 CTCCTCCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:100702679 original size:31 final size:32
Alignment explanation
Indices: 100702623--100702684 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
100702613 AAATTACAAC
100702623 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
100702655 AGTAATTGAATCCTAAT-AAAACTCTTTAAA
1 AGTAATTGAATCCTAATAAAAACTCTTTAAA
100702685 ATTATTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (32 bp):
AGTAATTGAATCCTAATAAAAACTCTTTAAAG
Found at i:100705081 original size:17 final size:17
Alignment explanation
Indices: 100705045--100705082 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
100705035 TTGTATAAAT
*
100705045 TGTGAATTATATTTATA
1 TGTGAATTATATTGATA
100705062 TGTGAATTAATATTGA-A
1 TGTGAATT-ATATTGATA
100705079 TGTG
1 TGTG
100705083 GAAGGAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (17 bp):
TGTGAATTATATTGATA
Found at i:100705334 original size:23 final size:23
Alignment explanation
Indices: 100705307--100705404 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
100705297 AGTGTTATTG
100705307 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
100705330 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
100705353 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
100705375 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
100705398 ATCAGTG
1 ATCAGTG
100705405 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:100705373 original size:45 final size:45
Alignment explanation
Indices: 100705309--100705397 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
100705299 TGTTATTGAT
* *
100705309 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
100705354 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
100705398 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:100712705 original size:23 final size:23
Alignment explanation
Indices: 100712678--100712775 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
100712668 AGTGTTATTG
100712678 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
100712701 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
100712724 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
100712746 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
100712769 ATCAGTG
1 ATCAGTG
100712776 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:100712744 original size:45 final size:45
Alignment explanation
Indices: 100712680--100712768 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
100712670 TGTTATTGAT
* *
100712680 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
100712725 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
100712769 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Done.