Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 111 of 143
Found at i:33761606 original size:16 final size:14
Alignment explanation
Indices: 33761579--33761609 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
33761569 AAATGATCAC
33761579 TTCTCTCATTTTTT
1 TTCTCTCATTTTTT
33761593 TTCTCTCATTTTTT
1 TTCTCTCATTTTTT
33761607 TTC
1 TTC
33761610 AATCAAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCTCTCATTTTTT
Found at i:33780976 original size:2 final size:2
Alignment explanation
Indices: 33780969--33780996 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33780959 GTTTTGGAGT
33780969 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
33780997 TGATGGGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33784640 original size:25 final size:23
Alignment explanation
Indices: 33784610--33784656 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
33784600 AGTTGAATCC
33784610 AAATTAAATTCTAAAAAGATAATTA
1 AAATTAAA-TCTAAAAA-ATAATTA
*
33784635 AAATTAAATCTAAACAATAATT
1 AAATTAAATCTAAAAAATAATT
33784657 CTCTAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (23 bp):
AAATTAAATCTAAAAAATAATTA
Found at i:33787603 original size:11 final size:11
Alignment explanation
Indices: 33787570--33787607 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
33787560 TACAAAAAAA
33787570 ATAAACATATT
1 ATAAACATATT
*
33787581 ATATATCATATT
1 ATA-AACATATT
33787593 ATAAACATATT
1 ATAAACATATT
33787604 ATAA
1 ATAA
33787608 TATACTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (11 bp):
ATAAACATATT
Found at i:33787913 original size:17 final size:17
Alignment explanation
Indices: 33787884--33787917 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
33787874 TTTAGATTAG
33787884 TTTTTATTTAAAAATAA
1 TTTTTATTTAAAAATAA
33787901 TTTTT-TTTAAAAATAA
1 TTTTTATTTAAAAATAA
33787917 T
1 T
33787918 GCTAAATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTATTTAAAAATAA
Found at i:33793151 original size:3 final size:3
Alignment explanation
Indices: 33793143--33793209 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
33793133 CTCGCCCGGA
33793143 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
33793191 TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC T
33793210 CCGGTGGAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:33796777 original size:3 final size:3
Alignment explanation
Indices: 33796769--33796806 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
33796759 TCCACCAATA
33796769 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
33796807 AATATAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:33803375 original size:31 final size:31
Alignment explanation
Indices: 33803313--33803379 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
33803303 AAAATATAAC
* **
33803313 AATTTGACTTTTTTTAAAAGGGTGATTGTCA
1 AATTTGACTTTTTTTAAAAGAGTGAGGGTCA
* *
33803344 AATTTGACTTTTTTTTAAAGATTGAGGGTCA
1 AATTTGACTTTTTTTAAAAGAGTGAGGGTCA
33803375 AATTT
1 AATTT
33803380 AGTTAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.46
Consensus pattern (31 bp):
AATTTGACTTTTTTTAAAAGAGTGAGGGTCA
Found at i:33807445 original size:58 final size:58
Alignment explanation
Indices: 33807364--33807794 Score: 627
Period size: 58 Copynumber: 7.4 Consensus size: 58
33807354 TTTAACTTTC
* *
33807364 GGGGGTAAAAAT-GTAATTTTTGGTGAAATCGAAGTCGAAAATGGGATTTTAGGAAA-TTT
1 GGGGGT-AAAATGGTAATTTTTGGTGAAATCGAGGT-TAAAATGGGATTTT-GGAAAGTTT
*
33807423 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGGATTTTGGAAAGTTT
* * * *
33807481 GAGGGTAAAACGGTAATTTTTGGTGAAATCGAGGTTAAAACTGGGATTTTAGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAA-TGGGATTTTGGAAAGTTT
* *
33807540 GAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGGATTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGGATTTTGGAAAGTTT
* * *
33807598 GGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAATGGGATTTTGGAAATTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGGATTTTGGAAAGTTT
* * *
33807656 GGGGGTAAAATGGTAATTTTTGGTGAAATTGAGGTTAAAACGGGATTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGGATTTTGGAAAGTTT
* *
33807714 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGGATTTTGGAAAGTTT
33807772 GGGGGTAAAATGGTAATTTTTGG
1 GGGGGTAAAATGGTAATTTTTGG
33807795 ACAGTCTAGG
Statistics
Matches: 339, Mismatches: 26, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
57 22 0.06
58 228 0.67
59 89 0.26
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGGATTTTGGAAAGTTT
Found at i:33826508 original size:33 final size:33
Alignment explanation
Indices: 33826458--33826524 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
33826448 TTGTGTTCAT
* *
33826458 TGTCTCGATGGATTATCTCTGTTCCATGTTTAC
1 TGTCCCGATGGACTATCTCTGTTCCATGTTTAC
* *
33826491 TGTCCCGATGGACTATCTTTGTTCCGTGTTTAC
1 TGTCCCGATGGACTATCTCTGTTCCATGTTTAC
33826524 T
1 T
33826525 ATCCAAGGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
TGTCCCGATGGACTATCTCTGTTCCATGTTTAC
Found at i:33826870 original size:57 final size:57
Alignment explanation
Indices: 33826666--33826861 Score: 185
Period size: 57 Copynumber: 3.4 Consensus size: 57
33826656 GCTGTCATAG
* ** * * * * * * * *
33826666 CGTCTTTCATCTATGGTCTTAAACCGTTTACCTTATACCTTATACCTTGCCGTCATGG
1 CGTCTTTCATCCATGGTCTTATGCCATATACCTT-TACCGTGTACCATGCTGCCATGA
* ** **
33826724 CGTCTTTCATCCATGGTGTTGCGCCATATACCTTTATTGTGTACCATGCTGCCATGA
1 CGTCTTTCATCCATGGTCTTATGCCATATACCTTTACCGTGTACCATGCTGCCATGA
* * * * *
33826781 CATCTTTCACCCATGATCTTATGCCATATACCTTTACCGTGTACCATGTTGTCATGA
1 CGTCTTTCATCCATGGTCTTATGCCATATACCTTTACCGTGTACCATGCTGCCATGA
*
33826838 TGTCTTTCATCCATGGTCTTATGC
1 CGTCTTTCATCCATGGTCTTATGC
33826862 TACGTACCTC
Statistics
Matches: 109, Mismatches: 29, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
57 82 0.75
58 27 0.25
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.39
Consensus pattern (57 bp):
CGTCTTTCATCCATGGTCTTATGCCATATACCTTTACCGTGTACCATGCTGCCATGA
Found at i:33832112 original size:28 final size:28
Alignment explanation
Indices: 33832072--33832132 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
33832062 AAACCAAGAA
*
33832072 TCAAATTAGTTCAA-CTCCAAGTTCTTAG
1 TCAAATCAGTTCAACCT-CAAGTTCTTAG
*
33832100 TCAAATCAGTTCAACCTCAAGTTCTTTG
1 TCAAATCAGTTCAACCTCAAGTTCTTAG
33832128 TCAAA
1 TCAAA
33832133 AGAAAAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (28 bp):
TCAAATCAGTTCAACCTCAAGTTCTTAG
Found at i:33832131 original size:114 final size:112
Alignment explanation
Indices: 33831925--33832143 Score: 348
Period size: 113 Copynumber: 1.9 Consensus size: 112
33831915 TCTAAATCTT
* *
33831925 TATCTCTTCTTGCAAAAAAAAAAAAAAAAAAGCATCAAATCAGTTCAACTCCAAGTTCTTAGTTA
1 TATCTCTTCTTGCAAAAAAAAAAAAAAAAAAGAATCAAATCAGTTCAACTCCAAGTTCTTAGTAA
*
33831990 ATCAGTTCAACCTCAAGTTCTTTGTCAAAATAAAAAAATACATTCTA
66 ATCAGTTCAACCTCAAGTTCTTTGTCAAAAGAAAAAAATACATTCTA
* ** *
33832037 TATCTCTTCTTGCAAGAAAAACAAAAAACCAAGAATCAAATTAGTTCAACTCCAAGTTCTTAGTC
1 TATCTCTTCTTGCAA-AAAAAAAAAAAAAAAAGAATCAAATCAGTTCAACTCCAAGTTCTTAGT-
*
33832102 AAATCAGTTCAACCTCAAGTTCTTTGTCAAAAGAAAAGAATA
64 AAATCAGTTCAACCTCAAGTTCTTTGTCAAAAGAAAAAAATA
33832144 TATAAAAAAA
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
112 15 0.15
113 43 0.44
114 39 0.40
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (112 bp):
TATCTCTTCTTGCAAAAAAAAAAAAAAAAAAGAATCAAATCAGTTCAACTCCAAGTTCTTAGTAA
ATCAGTTCAACCTCAAGTTCTTTGTCAAAAGAAAAAAATACATTCTA
Found at i:33832461 original size:16 final size:16
Alignment explanation
Indices: 33832442--33832480 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
33832432 ACTAATGATA
33832442 AAATTTAAT-ATTAATT
1 AAATTTAATGA-TAATT
*
33832458 AAATTTTATGATAATT
1 AAATTTAATGATAATT
33832474 AAATTTA
1 AAATTTA
33832481 CCTTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
AAATTTAATGATAATT
Found at i:33833029 original size:24 final size:23
Alignment explanation
Indices: 33833002--33833059 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
33832992 AAGATGTTCG
* **
33833002 TGAACATGTTCAATTATATTTTCA
1 TGAACATGTTCAATTA-AGTTAAA
* *
33833026 TGAACATATTCGATTAAGTTAAA
1 TGAACATGTTCAATTAAGTTAAA
33833049 TGAACATGTTC
1 TGAACATGTTC
33833060 GTGAACATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (23 bp):
TGAACATGTTCAATTAAGTTAAA
Found at i:33834723 original size:15 final size:15
Alignment explanation
Indices: 33834686--33834726 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
33834676 GTATAATTCT
*
33834686 TATTTTGTTGTTA-A
1 TATTTTGTTATTATA
33834700 -ATTTT-TTATTATA
1 TATTTTGTTATTATA
33834713 TATTTTGTTATTAT
1 TATTTTGTTATTAT
33834727 CTTGACCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 5 0.22
13 6 0.26
14 5 0.22
15 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (15 bp):
TATTTTGTTATTATA
Found at i:33842710 original size:32 final size:29
Alignment explanation
Indices: 33842659--33842749 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 29
33842649 CCGTCCATAT
*
33842659 TATT-TTTTATTTTTTTTAAAAAATATTTA
1 TATTATTTTATTTTTATTAAAAAAT-TTTA
*
33842688 TATTATTTTATTTTAATATTAAATAATTTTA
1 TATTATTTTATTTT--TATTAAAAAATTTTA
* * * **
33842719 TATAATTTT-TATTTATTGAAATTTTTTA
1 TATTATTTTATTTTTATTAAAAAATTTTA
33842747 TAT
1 TAT
33842750 AGTCATCTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
28 14 0.27
29 4 0.08
30 12 0.24
31 12 0.24
32 9 0.18
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (29 bp):
TATTATTTTATTTTTATTAAAAAATTTTA
Found at i:33850609 original size:12 final size:12
Alignment explanation
Indices: 33850592--33850625 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
33850582 CTTTCAACTC
33850592 TGAAATTATCAT
1 TGAAATTATCAT
* *
33850604 TGAAATTGTCCT
1 TGAAATTATCAT
33850616 TGAAATTATC
1 TGAAATTATC
33850626 TGAAATGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (12 bp):
TGAAATTATCAT
Found at i:33851714 original size:12 final size:12
Alignment explanation
Indices: 33851697--33851730 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
33851687 CTTTCAACTC
33851697 TGAAATTATCAT
1 TGAAATTATCAT
* *
33851709 TGAAATTGTCCT
1 TGAAATTATCAT
33851721 TGAAATTATC
1 TGAAATTATC
33851731 TGAAGTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (12 bp):
TGAAATTATCAT
Found at i:33853023 original size:793 final size:790
Alignment explanation
Indices: 33851177--33853061 Score: 2902
Period size: 792 Copynumber: 2.4 Consensus size: 790
33851167 TTTAATATAA
* * *
33851177 AAGTGGTATCAA-AGTTAGGTTCGTGTTGACGTCATAATGGCAAATATGATTCAACCGCAGATTC
1 AAGTGGTAT-AAGAGCTAGGTTCGTGTAGACGTCATAATGGCAAACATGATTCAA-CGCAGATTC
* *
33851241 CGAAATTAACAAAGGTAAATTATGGCAATTAGAGCATCCAAATGAAGGCTTTGCTCGGTTCTCAA
64 CGAAATTAACAAAGGCAAATTATGGCAATTGGAGCATCCAAATGAAGGCTTTGCTCGGTTCTCAA
* * *
33851306 GACTGTTAGGATGTTGTC-AAAGAATGATATGTCGAGCCC-AAACCGCAGCAGCTGAAGCAACTT
129 AACTGTT-GGATGTTGTCGAAA-AAGGATATGTCGAGCCCGAAAACGCAGCAGCTGAAGCAACTT
* * *
33851369 TGACAAATGAAGAAAAAAATAGTATTGAAGAAAGCTCGTAAAAAAGATAAGAGGGTGTTGTTCTT
192 TGACAAACGAAG-AAAAAAGAGTATTGAAGGAAGCTCGTAAAAAAGATAAGAGGGTGTTGTTCTT
*
33851434 TATTTTTCAAGGTGTTGATGAATCAACCTTTGAAAAAATTTCAATGGCATCCTGGGCCTGCTGGG
256 TATTTTTCAAGGTGTTGATGAATCAACCTTTGAAAAAATTTCAATGGCATCCTAGGCCTGCTGGG
* * * * *
33851499 TGCCTTTTCGTTTTGGTCGTTGACGGTGTATTTCCCGATCCAAATGCATATAGCGAGAGAACAGA
321 CGCCTCTCCGTTTTGGCCGTTGACGGTGTATTTCCCAATCCAAATGCATATAGCGAGAGAACAGA
**
33851564 TCCAAGCCTTTAGTTGGAAATGGATATGGTTAAACTTCTTGGTGTTACTTTGCTTGATTATATTA
386 TCCAAGCCTTTAGTTGGAAATGGATATGGTTAAACTTCTTGGTGTTACTTTGCTTGATTATACCA
33851629 GTCCTTGCAGCGGCTGACTCCATTGCTACAATTGTCAAGGATCTCAACACATATGAACCTTTCAA
451 GTCCTTGCAGCGGCTGACTCCATTGCTACAATTGTCAAGGATCTCAACACATATGAACCTTTCAA
* * *
33851694 CTCTGAAATTATCATTGAAATTGTCCTTGAAATTATCTGAAGTGAAACTAAAACATTTTGATTTT
516 CTCTGAAATTATCATTGAAATTGTCCATGAAATTATCTGAAATGAAACTAAAACATATTGATTTT
*
33851759 CAGATTTAAAATTTTCGAAAATGAAGTTTTGAATTTTTATTTTTATTTTTATACTGAAAATTTAG
581 CAGATTTAAAATTTTCGAAAATGAAGTTTTGAATTTATATTTTTATTTTTATACTGAAAATTTAG
* * *
33851824 ATAATAATACAAAATTTAATATAAAATGTGAGTGAGGAGTAAAAAAATTAGCAGTAGCTAGTAGA
646 ATAATAATACAAAATTTAATATAAAATGTGAGTGAGGAGTAAAAAAACTAGCAGCAACTAGTAGA
* *
33851889 GTAAAAGAGAGATATTTGTATTGTGATTTGTGTGTAATAATTTTTTTTATTTTAGTTAGTAATTT
711 GTAAAAGAGAGATATTTGTATTGTGATTTATGTGTAATAAATTTTTTTATTTTAGTTAGTAATTT
*
33851954 TATCCATCTTCCAAC
776 TATCCAGCTTCCAAC
* * * * * * * **
33851969 AAGTAGTATCAGAGCTAGATTCATGTCGACGTCATAATGACAAACATGATTTAACTGCAGAACCC
1 AAGTGGTATAAGAGCTAGGTTCGTGTAGACGTCATAATGGCAAACATGATTCAAC-GCAGATTCC
* * *
33852034 GAAATTAATAAAGGCAAATTATGGCAATTGGAGCATCCAAATGAAGGCTTTGCCCGATTCTCAAA
65 GAAATTAACAAAGGCAAATTATGGCAATTGGAGCATCCAAATGAAGGCTTTGCTCGGTTCTCAAA
* * * ***
33852099 ACTGTTGGGATGTTGTCGAAGAAGGATATGTCAAGCCCGAAAATGCAGCAGCTGAAGTGGCTTTG
130 ACTGTT-GGATGTTGTCGAAAAAGGATATGTCGAGCCCGAAAACGCAGCAGCTGAAGCAACTTTG
* * * *
33852164 ACAAACGAAGAAAAAAGAGTGTTGAAGGAAGCTTGTAAAAAAGATAAGAGGGCGCTGTTCTTTAT
194 ACAAACGAAGAAAAAAGAGTATTGAAGGAAGCTCGTAAAAAAGATAAGAGGGTGTTGTTCTTTAT
* * * *
33852229 TTTTCAAGGTGTTGATGAATCATCCTTTGAAAAAAATTCAATGGCATTCTAGGCCTGTTGGGCG-
259 TTTTCAAGGTGTTGATGAATCAACCTTTGAAAAAATTTCAATGGCATCCTAGGCCTGCTGGGCGC
*
33852293 CTGCTCCGTTTTGGCCGTTGACGGTGTATTTCCCAATCCAAATGCATATAGTGAGAGAACAGATC
324 CT-CTCCGTTTTGGCCGTTGACGGTGTATTTCCCAATCCAAATGCATATAGCGAGAGAACAGATC
*
33852358 CGAGCCTTTAGTTGGAAATGGATATGGTTAAACTTCTTGGTGTTACTTTGCTTGATTATACCAGT
388 CAAGCCTTTAGTTGGAAATGGATATGGTTAAACTTCTTGGTGTTACTTTGCTTGATTATACCAGT
* * **
33852423 CCTTGCAGCGGCTGGCT-CATATGTTACAATTGTCAAGGATCTCAGTACATATGAACCTTTCAAC
453 CCTTGCAGCGGCTGACTCCAT-TGCTACAATTGTCAAGGATCTCAACACATATGAACCTTTCAAC
*
33852487 TCTGAAATTATCATTGAAATTGTCCATGAAATTATCTGAAATGAAGCTAAAACATATTGATTTTC
517 TCTGAAATTATCATTGAAATTGTCCATGAAATTATCTGAAATGAAACTAAAACATATTGATTTTC
* * *
33852552 ATATTTAAAGTTTTTGAAAATGAAGTTTTGAATTTAATATTTTTATTTTTATACTGAAAATTTAG
582 AGATTTAAAATTTTCGAAAATGAAGTTTTGAATTT-ATATTTTTATTTTTATACTGAAAATTTAG
* *
33852617 ATAATAATACAAAGTTTAATATAAAATGTGAGTGAGTAGTAAAAAAAAACTAGCAGCAACTAGTA
646 ATAATAATACAAAATTTAATATAAAATGTGAGTGAGGAGT--AAAAAAACTAGCAGCAACTAGTA
33852682 GAGTAAAA-AGAGATATTTGTATTGTGATTTATGTGTAATAAATTTTTTT-TTTTAGTTAGTAAT
709 GAGTAAAAGAGAGATATTTGTATTGTGATTTATGTGTAATAAATTTTTTTATTTTAGTTAGTAAT
*
33852745 TTTATCCCGCTTCCAAC
774 TTTATCCAGCTTCCAAC
* * *
33852762 AAGTGGTATAAGAGCTAGGTTCGTGTAGACATCATAATGGTAAACATGATTGAATCGCAGATTCC
1 AAGTGGTATAAGAGCTAGGTTCGTGTAGACGTCATAATGGCAAACATGATTCAA-CGCAGATTCC
33852827 GAAATTAACAAAGGCAAATTATGGCAATTGGAGCATCCAAATGAAGGCTTTGCTCGGTTCTCAAA
65 GAAATTAACAAAGGCAAATTATGGCAATTGGAGCATCCAAATGAAGGCTTTGCTCGGTTCTCAAA
* * *
33852892 ACTATTGGAATGTTGTCGAAAAAGGATATGTCGAGCCCGAAAACGGAGCAGTTGAAGCAACTTTG
130 ACTGTTGG-ATGTTGTCGAAAAAGGATATGTCGAGCCCGAAAACGCAGCAGCTGAAGCAACTTTG
* *
33852957 ACAAACAAAGAAAAAAGAGTATTGAAGGAAGCTCGTATAAAAGATAAGAGGGTGTTGTTCTTTAT
194 ACAAACGAAGAAAAAAGAGTATTGAAGGAAGCTCGTAAAAAAGATAAGAGGGTGTTGTTCTTTAT
*
33853022 TTTTCAAGGTGTTGATGAATCAACATTTGAAAAAATTTCA
259 TTTTCAAGGTGTTGATGAATCAACCTTTGAAAAAATTTCA
33853062 GATGCGAAGA
Statistics
Matches: 982, Mismatches: 100, Indels: 21
0.89 0.09 0.02
Matches are distributed among these distances:
791 7 0.01
792 517 0.53
793 390 0.40
794 40 0.04
795 28 0.03
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (790 bp):
AAGTGGTATAAGAGCTAGGTTCGTGTAGACGTCATAATGGCAAACATGATTCAACGCAGATTCCG
AAATTAACAAAGGCAAATTATGGCAATTGGAGCATCCAAATGAAGGCTTTGCTCGGTTCTCAAAA
CTGTTGGATGTTGTCGAAAAAGGATATGTCGAGCCCGAAAACGCAGCAGCTGAAGCAACTTTGAC
AAACGAAGAAAAAAGAGTATTGAAGGAAGCTCGTAAAAAAGATAAGAGGGTGTTGTTCTTTATTT
TTCAAGGTGTTGATGAATCAACCTTTGAAAAAATTTCAATGGCATCCTAGGCCTGCTGGGCGCCT
CTCCGTTTTGGCCGTTGACGGTGTATTTCCCAATCCAAATGCATATAGCGAGAGAACAGATCCAA
GCCTTTAGTTGGAAATGGATATGGTTAAACTTCTTGGTGTTACTTTGCTTGATTATACCAGTCCT
TGCAGCGGCTGACTCCATTGCTACAATTGTCAAGGATCTCAACACATATGAACCTTTCAACTCTG
AAATTATCATTGAAATTGTCCATGAAATTATCTGAAATGAAACTAAAACATATTGATTTTCAGAT
TTAAAATTTTCGAAAATGAAGTTTTGAATTTATATTTTTATTTTTATACTGAAAATTTAGATAAT
AATACAAAATTTAATATAAAATGTGAGTGAGGAGTAAAAAAACTAGCAGCAACTAGTAGAGTAAA
AGAGAGATATTTGTATTGTGATTTATGTGTAATAAATTTTTTTATTTTAGTTAGTAATTTTATCC
AGCTTCCAAC
Found at i:33857016 original size:12 final size:12
Alignment explanation
Indices: 33856999--33857026 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
33856989 AGATTAATTT
33856999 GCAAGGTGGATA
1 GCAAGGTGGATA
33857011 GCAAGGTGGATA
1 GCAAGGTGGATA
33857023 GCAA
1 GCAA
33857027 ATTGTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.39, T:0.14
Consensus pattern (12 bp):
GCAAGGTGGATA
Found at i:33859593 original size:31 final size:31
Alignment explanation
Indices: 33859556--33859617 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
33859546 ATCCAATTAC
* *
33859556 TTAAATAAAAACTTTT-GAATAGTTCAGTGAT
1 TTAAATAAAAA-TTTTCGAAGAGTTAAGTGAT
33859587 TTAAATAAAAATTTTCGAAGAGTTAAGTGAT
1 TTAAATAAAAATTTTCGAAGAGTTAAGTGAT
33859618 CATTTTATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (31 bp):
TTAAATAAAAATTTTCGAAGAGTTAAGTGAT
Found at i:33865047 original size:29 final size:29
Alignment explanation
Indices: 33865001--33865057 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
33864991 CTGAAAATTG
* *
33865001 AATCAAATTTTATATATAAAATTGCACAA
1 AATCAAAATTTATATATAAAATTACACAA
* *
33865030 AATCAAAATTTATCTATAATATTACACA
1 AATCAAAATTTATATATAAAATTACACA
33865058 TTAGATCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (29 bp):
AATCAAAATTTATATATAAAATTACACAA
Found at i:33875991 original size:41 final size:40
Alignment explanation
Indices: 33875927--33876032 Score: 126
Period size: 41 Copynumber: 2.6 Consensus size: 40
33875917 GCTTATTGGA
* *
33875927 AAACGTCGCTATTG-TCTAACCTTTAACGACGC-TTTTCCAT
1 AAACGCCGCTAATGCTCTAACCTTT-A-GACGCATTTTCCAT
*
33875967 AAACGCCGCTAATGCTCTAACCTTTAGAGGCATTTTTCCAT
1 AAACGCCGCTAATGCTCTAACCTTTAGACGCA-TTTTCCAT
* *
33876008 AAACGCCGCTAATGCTTTGACCTTT
1 AAACGCCGCTAATGCTCTAACCTTT
33876033 TGTGGCGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
39 4 0.07
40 13 0.22
41 41 0.71
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (40 bp):
AAACGCCGCTAATGCTCTAACCTTTAGACGCATTTTCCAT
Found at i:33876053 original size:41 final size:40
Alignment explanation
Indices: 33875962--33876074 Score: 102
Period size: 41 Copynumber: 2.8 Consensus size: 40
33875952 ACGACGCTTT
* * * *
33875962 TCCATAAACGCCGCTAATGCTCTAACCTTTAGAGGCATTTT
1 TCCAAAAACGCCGCTAATGCT-TTACCTTTTGAGGCATTTA
* * *
33876003 TCCATAAACGCCGCTAATGCTTTGACCTTTTGTGGCGTTTA
1 TCCAAAAACGCCGCTAATGCTTT-ACCTTTTGAGGCATTTA
** *
33876044 TGGAAAAACGCAC-CTAATACTTTACCTTTTG
1 TCCAAAAACGC-CGCTAATGCTTTACCTTTTG
33876075 CAGTGTTTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
40 9 0.15
41 51 0.84
42 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (40 bp):
TCCAAAAACGCCGCTAATGCTTTACCTTTTGAGGCATTTA
Found at i:33880315 original size:29 final size:30
Alignment explanation
Indices: 33880280--33880338 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
33880270 TATAGTTTAA
33880280 TGTGCAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* * *
33880309 TGTGCAATTTTATACTTGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
33880339 GATCTAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:33884246 original size:29 final size:29
Alignment explanation
Indices: 33884200--33884256 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
33884190 CTGAAAATTG
* *
33884200 AATCAAATTTTATATATAAAATTGCACAA
1 AATCAAAATTTATATATAAAATTACACAA
* *
33884229 AATCAAAATTTATTTATAATATTACACA
1 AATCAAAATTTATATATAAAATTACACA
33884257 TTAGATCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.37
Consensus pattern (29 bp):
AATCAAAATTTATATATAAAATTACACAA
Found at i:33886847 original size:16 final size:16
Alignment explanation
Indices: 33886826--33886856 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33886816 TTATGATTAA
33886826 TTATATTAATTTTATT
1 TTATATTAATTTTATT
*
33886842 TTATATTATTTTTAT
1 TTATATTAATTTTAT
33886857 GAGTTTTGAA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATTAATTTTATT
Found at i:33895344 original size:16 final size:16
Alignment explanation
Indices: 33895320--33895371 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
33895310 AAAATATAAG
* *
33895320 ATTACTTTTATGGGTA
1 ATTATTTTTATGGATA
*
33895336 ATTATTTTTTTGGATA
1 ATTATTTTTATGGATA
33895352 A--A-TTTTATGGATA
1 ATTATTTTTATGGATA
33895365 ATTATTT
1 ATTATTT
33895372 GGTACATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 11 0.38
14 1 0.03
15 1 0.03
16 16 0.55
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (16 bp):
ATTATTTTTATGGATA
Found at i:33898501 original size:44 final size:44
Alignment explanation
Indices: 33898438--33898525 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
33898428 ATAATTGTAA
* * * *
33898438 TTTAAGTTGTAATTATTTTTAAATTTGTAATTATCACAACTTCT
1 TTTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCT
* *
33898482 TTTAAATTATAATTATTTTTACATGTATAATTATCACAATTTCT
1 TTTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCT
33898526 ATTTTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (44 bp):
TTTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCT
Found at i:33921526 original size:22 final size:23
Alignment explanation
Indices: 33921487--33921529 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
33921477 AATATCAACT
33921487 TAAATTTTTAAATAAAATAAAAA
1 TAAATTTTTAAATAAAATAAAAA
*
33921510 TAAATTTTT-AATTAAATAAA
1 TAAATTTTTAAATAAAATAAA
33921530 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATTTTTAAATAAAATAAAAA
Found at i:33921528 original size:16 final size:17
Alignment explanation
Indices: 33921507--33921543 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
33921497 AATAAAATAA
33921507 AAATAAATTT-TTAATT
1 AAATAAATTTATTAATT
33921523 AAATAAATTTAATTAATT
1 AAATAAATTT-ATTAATT
33921541 AAA
1 AAA
33921544 AATTTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATTTATTAATT
Found at i:33921728 original size:13 final size:13
Alignment explanation
Indices: 33921710--33921737 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33921700 AAATTTCAAT
33921710 ATTCAAAAATTAA
1 ATTCAAAAATTAA
33921723 ATTCAAAAATTAA
1 ATTCAAAAATTAA
33921736 AT
1 AT
33921738 CTGAGTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTCAAAAATTAA
Found at i:33922028 original size:24 final size:23
Alignment explanation
Indices: 33921979--33922037 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
33921969 TACTATTAAA
33921979 AAAATAA-CAAAATTTAAAAAAC
1 AAAATAATCAAAATTTAAAAAAC
* * *
33922001 AAAATAATCATAAATTTCAAATAT
1 AAAATAATCA-AAATTTAAAAAAC
*
33922025 AAAATAATTAAAA
1 AAAATAATCAAAA
33922038 CGTAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 7 0.23
23 5 0.16
24 19 0.61
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAATAATCAAAATTTAAAAAAC
Found at i:33937069 original size:21 final size:21
Alignment explanation
Indices: 33937038--33937078 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
33937028 TTTTTTAAAA
33937038 AAATCGAAATAGATAAAAAATG
1 AAATCGAAATA-ATAAAAAATG
*
33937060 AAAT-GAAATAATAGAAAAT
1 AAATCGAAATAATAAAAAAT
33937079 TGTTGGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (21 bp):
AAATCGAAATAATAAAAAATG
Found at i:33956067 original size:59 final size:59
Alignment explanation
Indices: 33955915--33956069 Score: 143
Period size: 59 Copynumber: 2.6 Consensus size: 59
33955905 TTTTAGGGGT
* * * * * * *
33955915 AAAATGGTAATTTTTTGTGAAATCGGGGCTAAAAATGGAATTTGGAAAGTTTGTGGAAT
1 AAAATGGTAAATTTTGGTGAAATCGAGGTTAAAAATGAAATTTGGAAAGTTCGTGGAAC
** * * * *
33955974 AAAATGGTAAATTTTGGCAAAAACAAGGTCAAAAATGAAATTTTGGAAAGTTC--GGAGGC
1 AAAATGGTAAATTTTGGTGAAATCGAGGTTAAAAATGAAA-TTTGGAAAGTTCGTGGA-AC
* *
33956033 AAAACGGTAAGTTTTGGTGAAATCGAGGTTAAAAATG
1 AAAATGGTAAATTTTGGTGAAATCGAGGTTAAAAATG
33956070 GGATTTACGA
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
58 3 0.04
59 60 0.81
60 11 0.15
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28
Consensus pattern (59 bp):
AAAATGGTAAATTTTGGTGAAATCGAGGTTAAAAATGAAATTTGGAAAGTTCGTGGAAC
Found at i:33956114 original size:30 final size:30
Alignment explanation
Indices: 33956079--33956229 Score: 155
Period size: 30 Copynumber: 5.0 Consensus size: 30
33956069 GGGATTTACG
* * *
33956079 AAAGTTTGAGGGTAAAAATGGTAATTTTTG-
1 AAAGTTTGAGGGTCAAAAT-ATAATTTTGGA
*
33956109 AAAGTTTCG-GGGTCAAAATATAATTTTAGA
1 AAAGTTT-GAGGGTCAAAATATAATTTTGGA
* *
33956139 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
1 AAAGTTTGAGGGTCAAAATATAATTTTGGA
* *
33956169 AAAGTTTTAGGGTTAAAATATAATTTTGGA
1 AAAGTTTGAGGGTCAAAATATAATTTTGGA
* *
33956199 AAAGTTTTG-GTGTTAAAATATAATTTATGGA
1 AAAG-TTTGAGGGTCAAAATATAATTT-TGGA
33956230 CAATTTAGGG
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
29 8 0.08
30 90 0.85
31 8 0.08
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (30 bp):
AAAGTTTGAGGGTCAAAATATAATTTTGGA
Found at i:33956206 original size:60 final size:60
Alignment explanation
Indices: 33956079--33956229 Score: 180
Period size: 60 Copynumber: 2.5 Consensus size: 60
33956069 GGGATTTACG
* * *
33956079 AAAGTTTGAGGGTAAAAATGGTAATTTTTG-AAAGTTTCGGGGTCAAAATATAATTTTAGA
1 AAAGTTTTAGGGTAAAAAT-GTAATTTTGGAAAAGTTTCAGGGTCAAAATATAATTTTAGA
* * * *
33956139 AAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATATAATTTTGGA
1 AAAGTTTTAGGGTAAAAATGTAATTTTGGAAAAGTTTCAGGGTCAAAATATAATTTTAGA
* *
33956199 AAAGTTTT-GGTGTTAAAATATAATTTATGGA
1 AAAGTTTTAGG-GTAAAAATGTAATTT-TGGA
33956230 CAATTTAGGG
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 11 0.14
60 64 0.81
61 4 0.05
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (60 bp):
AAAGTTTTAGGGTAAAAATGTAATTTTGGAAAAGTTTCAGGGTCAAAATATAATTTTAGA
Found at i:33958116 original size:25 final size:25
Alignment explanation
Indices: 33958078--33958156 Score: 95
Period size: 25 Copynumber: 3.0 Consensus size: 25
33958068 AATTTGTTTT
*
33958078 ATAATTTAAATTTAAGGTAAATTTAA
1 ATAA-TTAAATTTAAGATAAATTTAA
33958104 ATAATTAAATTTAAGATAAATTTAA
1 ATAATTAAATTTAAGATAAATTTAA
* * *
33958129 ATTCAAATAAATTTAAAATCAATTTAA
1 A-T-AATTAAATTTAAGATAAATTTAA
33958156 A
1 A
33958157 CTCTTAATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
25 21 0.45
26 5 0.11
27 21 0.45
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (25 bp):
ATAATTAAATTTAAGATAAATTTAA
Found at i:33958138 original size:16 final size:16
Alignment explanation
Indices: 33958095--33958150 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
33958085 AAATTTAAGG
*
33958095 TAAATTTAAAT-AA-T
1 TAAATTCAAATAAATT
*
33958109 TAAATTTAAGATAAATT
1 TAAATTCAA-ATAAATT
33958126 TAAATTCAAATAAATT
1 TAAATTCAAATAAATT
*
33958142 TAAAATCAA
1 TAAATTCAA
33958151 TTTAAACTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 9 0.24
15 2 0.05
16 17 0.46
17 9 0.24
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAATTCAAATAAATT
Found at i:33958618 original size:68 final size:68
Alignment explanation
Indices: 33958502--33958902 Score: 685
Period size: 68 Copynumber: 5.9 Consensus size: 68
33958492 GAAAATGATC
* * *
33958502 TTGCTCTTATTTCAATTCCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
33958567 ACG
66 ACG
* * *
33958570 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
*
33958635 ACA
66 ACG
* * *
33958638 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
*
33958703 ACA
66 ACG
*
33958706 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
33958771 ACG
66 ACG
*
33958774 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
33958839 ACG
66 ACG
33958842 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAG
33958903 ATAAAGACGT
Statistics
Matches: 318, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 318 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (68 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
ACG
Found at i:33958932 original size:242 final size:242
Alignment explanation
Indices: 33958645--33959142 Score: 908
Period size: 242 Copynumber: 2.1 Consensus size: 242
33958635 ACATTGCTCT
*
33958645 TACTTCAATTTC-AGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACGACATTG
1 TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
* *
33958709 CTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATGACG
66 CTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGACGACA
* *
33958774 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
131 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATG
33958839 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
196 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
33958886 TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
1 TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
* * *
33958951 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACGACA
66 CTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGACGACA
33959016 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATG
131 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATG
*
33959081 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTT
196 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
33959128 TACTTCAATTTCAAG
1 TACTTCAATTTCAAG
33959143 GGGATGACGT
Statistics
Matches: 247, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
241 12 0.05
242 235 0.95
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (242 bp):
TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
CTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGACGACA
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATG
ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
Found at i:33958935 original size:174 final size:174
Alignment explanation
Indices: 33958713--33959076 Score: 631
Period size: 174 Copynumber: 2.1 Consensus size: 174
33958703 ACATTGCTCT
* *
33958713 TACTTCAATTTC-AGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTCAAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGACGACATTG
* * *
33958777 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
66 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGACGACA
*
33958842 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
131 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTC
* *
33958886 TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
1 TACTTCAATTTCAAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGACGACATTG
* *
33958951 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACGACA
66 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGACGACA
33959016 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTC
131 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTC
33959060 TACTTCAATTTCAAGAG
1 TACTTCAATTTCAAGAG
33959077 GATGACGTTG
Statistics
Matches: 180, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
173 12 0.07
174 168 0.93
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (174 bp):
TACTTCAATTTCAAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGACGACATTG
CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGACGACA
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTC
Found at i:33958979 original size:68 final size:68
Alignment explanation
Indices: 33958886--33959351 Score: 725
Period size: 68 Copynumber: 6.8 Consensus size: 68
33958876 TTATCCACTC
33958886 TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
1 TACTTCAATTTC-AGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
33958951 CTCT
65 CTCT
*
33958955 TACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACGACATTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTGC
33959020 TCT
66 TCT
* * * *
33959023 TACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTGC
33959088 TCT
66 TCT
* * *
33959091 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGGGGATGACGTTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTGC
33959156 TCT
66 TCT
**
33959159 TACTTCAATTTCAGAGATAAAGACGTGTTATCCGTTTTACTTCAATTTCAAGAGGACGACATTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTGC
33959224 TCT
66 TCT
* * * * * * **
33959227 TACTTCAATTTCAGAGATAAAGACATATTATCCACTCTACTTCAACTTCAAGAGGATGACGTCAC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTGC
33959292 TCT
66 TCT
* * *
33959295 TACTTCAATTTCAGAGATGAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGA
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTTTACTTCAATTTCAAGAGGA
33959352 TAGGAAATAA
Statistics
Matches: 366, Mismatches: 30, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
68 334 0.91
69 32 0.09
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (68 bp):
TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTGC
TCT
Found at i:33959151 original size:310 final size:310
Alignment explanation
Indices: 33958577--33959212 Score: 1220
Period size: 310 Copynumber: 2.1 Consensus size: 310
33958567 ACGTTGCTCT
*
33958577 TACTTCAATTTC-AGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACGACATTG
1 TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
33958641 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACGACA
66 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACGACA
33958706 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATG
131 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATG
33958771 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
196 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
33958836 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
261 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
33958886 TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
1 TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
33958951 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACGACA
66 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACGACA
33959016 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATG
131 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATG
*
33959081 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGGGG
196 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
** *
33959146 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGTTT
261 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
33959196 TACTTCAATTTCAAGAG
1 TACTTCAATTTCAAGAG
33959213 GACGACATTG
Statistics
Matches: 321, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
309 12 0.04
310 309 0.96
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (310 bp):
TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACGACATTG
CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGACGACA
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATG
ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
Found at i:33959158 original size:204 final size:204
Alignment explanation
Indices: 33958881--33959352 Score: 820
Period size: 204 Copynumber: 2.3 Consensus size: 204
33958871 ACGTGTTATC
*
33958881 CACTC-TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGACG
1 CACTCTTACTTCAATTTC-AGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGATG
33958945 ACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGG
65 ACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGG
* *
33959010 ACGACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAG
130 ACGACATTGCTCTTACTTCAATTTCAGAGATAAAGACATATTATCCACTCTACTTCAACTTCAAG
33959075 AGGATGACGT
195 AGGATGACGT
** *
33959085 TGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGGGGATGA
1 CACTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGATGA
* *
33959150 CGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGTTTTACTTCAATTTCAAGAGGA
66 CATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGA
33959215 CGACATTGCTCTTACTTCAATTTCAGAGATAAAGACATATTATCCACTCTACTTCAACTTCAAGA
131 CGACATTGCTCTTACTTCAATTTCAGAGATAAAGACATATTATCCACTCTACTTCAACTTCAAGA
33959280 GGATGACGT
196 GGATGACGT
* * *
33959289 CACTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGAT
1 CACTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTTTACTTCAATTTCAAGAGGAT
33959353 AGGAAATAAT
Statistics
Matches: 252, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
204 218 0.87
205 34 0.13
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (204 bp):
CACTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGAGGATGA
CATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGCTTTACTTCAATTTCAAGAGGA
CGACATTGCTCTTACTTCAATTTCAGAGATAAAGACATATTATCCACTCTACTTCAACTTCAAGA
GGATGACGT
Found at i:33971306 original size:31 final size:30
Alignment explanation
Indices: 33971198--33971371 Score: 197
Period size: 30 Copynumber: 5.7 Consensus size: 30
33971188 TTTAAGGAAG
* *
33971198 TTTGAGGGTAAAAATGGTAATTTTTG-AAAGT
1 TTTG-GGGTTAAAAT-GTAATTTTGGAAAAGT
* * * * *
33971229 TTCGAGGTCAAAATATAATTTTAGAAAAGT
1 TTTGGGGTTAAAATGTAATTTTGGAAAAGT
*
33971259 TTTAGGGTTAAAATGTAATTTTGGAAAAGT
1 TTTGGGGTTAAAATGTAATTTTGGAAAAGT
* *
33971289 TTCGGGGTTAAAAATGTAATTATGGAAAAGT
1 TTTGGGGTT-AAAATGTAATTTTGGAAAAGT
*
33971320 TTTGGGGTTAAAATGCAATTTTGGAAAAGT
1 TTTGGGGTTAAAATGTAATTTTGGAAAAGT
* *
33971350 TTTGGGGTCAAAATATAATTTT
1 TTTGGGGTTAAAATGTAATTTT
33971372 TGGACAATTT
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.07
30 82 0.68
31 31 0.26
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTGGGGTTAAAATGTAATTTTGGAAAAGT
Found at i:33971317 original size:61 final size:61
Alignment explanation
Indices: 33971170--33971362 Score: 205
Period size: 61 Copynumber: 3.2 Consensus size: 61
33971160 TTTGGTGAAA
* * * * * *
33971170 TCGGGGTTAAAAATGGGATTTAAGG--AAGTTTGAGGGTAAAAATGGTAATTTTTG-AAAGTT
1 TCGGGGTTAAAAAT-GTAATTATGGAAAAGTTTTAGGGTTAAAAT-GTAATTTTGGAAAAGTT
* * * * *
33971230 TCGAGG-TCAAAATATAATTTTAGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTT
1 TCGGGGTTAAAAATGTAATTATGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTT
* *
33971290 TCGGGGTTAAAAATGTAATTATGGAAAAGTTTTGGGGTTAAAATGCAATTTTGGAAAAGTT
1 TCGGGGTTAAAAATGTAATTATGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTT
* *
33971351 TTGGGGTCAAAA
1 TCGGGGTTAAAA
33971363 TATAATTTTT
Statistics
Matches: 109, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
58 4 0.04
59 15 0.14
60 32 0.29
61 58 0.53
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (61 bp):
TCGGGGTTAAAAATGTAATTATGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTT
Found at i:33973238 original size:6 final size:6
Alignment explanation
Indices: 33973222--33973304 Score: 68
Period size: 6 Copynumber: 14.0 Consensus size: 6
33973212 TTAAATTTGT
**
33973222 TTTATAA TTTAAA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
*
33973272 TTTAAGA --TAAA TTTAAA TTCAAA --TAAA TTTAAA
1 TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
33973305 ATCAATTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
4 4 0.06
5 6 0.10
6 41 0.66
7 5 0.08
8 6 0.10
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:33973270 original size:25 final size:25
Alignment explanation
Indices: 33973231--33973315 Score: 102
Period size: 25 Copynumber: 3.4 Consensus size: 25
33973221 TTTTATAATT
*
33973231 TAAATTTAAAT--TTAAATTTAAGG
1 TAAATTTAAATAATTAAATTTAAGA
33973254 TAAATTTAAATAATTAAATTTAAGA
1 TAAATTTAAATAATTAAATTTAAGA
* *
33973279 TAAATTTAAATTCAAATAAATTTAAAA
1 TAAATTTAAA-T-AATTAAATTTAAGA
*
33973306 TCAATTTAAA
1 TAAATTTAAA
33973316 CTCTTAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
23 11 0.20
25 21 0.39
26 1 0.02
27 21 0.39
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
TAAATTTAAATAATTAAATTTAAGA
Found at i:33977452 original size:7 final size:7
Alignment explanation
Indices: 33977440--33977466 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
33977430 TTCCTTAGTG
33977440 TGCAGAC
1 TGCAGAC
33977447 TGCAGAC
1 TGCAGAC
33977454 TGCAGAC
1 TGCAGAC
33977461 TGCAGA
1 TGCAGA
33977467 GTAGGCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (7 bp):
TGCAGAC
Found at i:33977643 original size:15 final size:15
Alignment explanation
Indices: 33977596--33977644 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
33977586 TAAACTACTC
33977596 ATTTT-GTCACTT-A
1 ATTTTAGTCACTTCA
*
33977609 ATTTTTAGACACTTTC-
1 A-TTTTAGTCAC-TTCA
33977625 ATTTTAGTCACTTCA
1 ATTTTAGTCACTTCA
33977640 ATTTT
1 ATTTT
33977645 TTTTTTTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.03
14 7 0.24
15 18 0.62
16 3 0.10
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.53
Consensus pattern (15 bp):
ATTTTAGTCACTTCA
Found at i:33978115 original size:4 final size:4
Alignment explanation
Indices: 33978106--33978138 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
33978096 TGGAAGATAA
33978106 AATT AATT AATT AATT AATT AATT AAATT AATT
1 AATT AATT AATT AATT AATT AATT -AATT AATT
33978139 GAAATAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:33978123 original size:12 final size:13
Alignment explanation
Indices: 33978105--33978148 Score: 63
Period size: 12 Copynumber: 3.4 Consensus size: 13
33978095 ATGGAAGATA
33978105 AAATTAATTAATT
1 AAATTAATTAATT
33978118 -AATTAATTAATT
1 AAATTAATTAATT
*
33978130 AAATTAATTGAAAT
1 AAATTAATT-AATT
33978144 AAATT
1 AAATT
33978149 TTTTTTTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 12 0.43
13 8 0.29
14 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:33981128 original size:228 final size:228
Alignment explanation
Indices: 33980717--33982053 Score: 1446
Period size: 228 Copynumber: 5.9 Consensus size: 228
33980707 CAGGTGCAAA
* * * * ** * * *
33980717 GTGGATTCCTTCTGGATATTGTAGTCTGCAAGGGTCCTCCCATCTTCAAGTTGCTTCCCAGCAAA
1 GTGGACTCCTTCTGGATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGCTGCTTACCAGCAAA
* * * * * *
33980782 AATCAGCCTCTGCTGGTCTGGTGGGATTCCTTCCTTATCCTGGATCTTGGCCTTCACATTATCAA
66 GATCAGCCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGAATCTTGGCCTTAACATTGTCAA
* * * * * * * * * * * *
33980847 TCGTGTCTGAGCTTTCAACTTCCAGGGTGATGGTCTTTCCAGTCAGGGTCTTCACGAAAATTTGC
131 TGGTATCAGAACTCTCCACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCTTGACAAAAATTTGC
* * *
33980912 ATCCCACCACGGAGACGGAGCACCAAGTGGAGG
196 ATACCACCACGCAGACGGAGCACCAAGTGGAGT
* * * ** *
33980945 GTGGACTCCTTCTGGATGTTGTAATCTGCAAGGGTCCTCCCATCCTCTAGCTGCTTACCAGCAAA
1 GTGGACTCCTTCTGGATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGCTGCTTACCAGCAAA
* * * * * * *
33981010 TATCAGCCTCTGCTGGTCTGGAGGGATACCTTCCTTATCTTGAATTTTGGCCTTAACATTATCAA
66 GATCAGCCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGAATCTTGGCCTTAACATTGTCAA
* * * * * * * * * * *
33981075 TTGTGTCAGAGCTCTCAACTTCCAGGGTGATGGTCTTCCCGGTAAGTGTCTTCACAAAAATCTGC
131 TGGTATCAGAACTCTCCACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCTTGACAAAAATTTGC
* *
33981140 ATACCACCACGAAGACGGAGCACCAAGTGGAGG
196 ATACCACCACGCAGACGGAGCACCAAGTGGAGT
* * *
33981173 GTGGACTCCTTCTGGATGTTATAGTCAGCCAGGGTACGGCCATCCTCAAGTTGCTTACCAGCAAA
1 GTGGACTCCTTCTGGATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGCTGCTTACCAGCAAA
* * * *
33981238 TATCAGCCTCTGTTGGTCTGG-GGGAATTCCC-TCCTTGTCCTGAATTTTCGCCTTAACATTGTC
66 GATCAGCCTCTGCTGGTCTGGTGGG-A-TCCCTTCCTTGTCCTGAATCTTGGCCTTAACATTGTC
* * * * * ** *
33981301 AATGGTATCTGAACTCTCTACCTCCAATGTAATGGTCTTCCCAGTCAAAGTCTTAACAAAAATTT
129 AATGGTATCAGAACTCTCCACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCTTGACAAAAATTT
* * * * *
33981366 GCATTCCTCCACGGAGGCGAAGCACCAAGTGGAGT
194 GCATACCACCACGCAGACGGAGCACCAAGTGGAGT
* * * * *
33981401 GTGGACTCCTTCTGGATGTTGTAATCAGCCAA-TGTGCGGCCATCCTCAAGTTGCTTACCAGCGA
1 GTGGACTCCTTCTGGATGTTGTAGTCAG-CAAGGGTACGGCCATCCTCAAGCTGCTTACCAGCAA
* * *
33981465 AGATCAGCCTCTGCTGGTCTGG-GGGTATGCCTTCCTTGTCCTGAATCTTAGCCTTGACATTGTC
65 AGATCAGCCTCTGCTGGTCTGGTGGG-ATCCCTTCCTTGTCCTGAATCTTGGCCTTAACATTGTC
** * *
33981529 AACAGTATCAGAACTCTCCACCTCCAATGTGATGGTCTTCCCGGTGAGGGTCTTGACAAAAATTT
129 AATGGTATCAGAACTCTCCACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCTTGACAAAAATTT
* * * *
33981594 GCATACCACCCCTCA-ATCGGAGGACCAAATGGAGT
194 GCATACCACCACGCAGA-CGGAGCACCAAGTGGAGT
* * * * *
33981629 GTGGATTCCTTCTGAATGTTGTAGTCAGCAAGGGTACGGCCATCCTCCAGCTGTTTCCCAGCAAA
1 GTGGACTCCTTCTGGATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGCTGCTTACCAGCAAA
* * * * * * *
33981694 GATAAGCCTCTGTTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTAGACTTGACATTGTCAA
66 GATCAGCCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGAATCTTGGCCTTAACATTGTCAA
* * *
33981759 TGGTATCTGAACTCTCCACCTCCAATGTGATGGTCTTCCCGGTGAGGGTCTTGACAAAAATTTGC
131 TGGTATCAGAACTCTCCACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCTTGACAAAAATTTGC
* * * *
33981824 ATACCACCCCTCA-ATCGGAGGACCAAATGGAGT
196 ATACCACCACGCAGA-CGGAGCACCAAGTGGAGT
* * * *
33981857 GTGGATTCCTTCTGAATGTTGTAGTCAGCAAGGGTACGGCCATCCTCCAGCTGTTTACCAGCAAA
1 GTGGACTCCTTCTGGATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGCTGCTTACCAGCAAA
* * * * * *
33981922 GATAAGCCTCTGTTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTTACATTGTCGA
66 GATCAGCCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGAATCTTGGCCTTAACATTGTCAA
* * *
33981987 TGGTATCAGAACTTTCCACCT-CAAGGGTGATGGTCTTGCCAGTGAGGGTCTTGACGAAAATTTG
131 TGGTATCAGAACTCTCCACCTCCAA-GGTGATGGTCTTCCCAGTGAGGGTCTTGACAAAAATTTG
33982051 CAT
195 CAT
33982054 CTATTTTGAT
Statistics
Matches: 978, Mismatches: 123, Indels: 16
0.88 0.11 0.01
Matches are distributed among these distances:
227 12 0.01
228 958 0.98
229 8 0.01
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.29
Consensus pattern (228 bp):
GTGGACTCCTTCTGGATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGCTGCTTACCAGCAAA
GATCAGCCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGAATCTTGGCCTTAACATTGTCAA
TGGTATCAGAACTCTCCACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCTTGACAAAAATTTGC
ATACCACCACGCAGACGGAGCACCAAGTGGAGT
Found at i:33982022 original size:684 final size:684
Alignment explanation
Indices: 33980756--33982053 Score: 1620
Period size: 684 Copynumber: 1.9 Consensus size: 684
33980746 AAGGGTCCTC
* * *
33980756 CCATCTTCAAGTTGCTTCCCAGCAAAAATCAGCCTCTGCTGGTCTGGTGGGATTCCTTCCTTATC
1 CCATCCTCAAGTTGCTTACCAGCAAAAATCAGCCTCTGCTGGTCTGGTGGGATGCCTTCCTTATC
* * * * * * * * *
33980821 CTGGATCTTGGCCTTCACATTATCAATCGTGTCTGAGCTTTCAACTTCCAGGGTGATGGTCTTTC
66 CTGAATCTTAGCCTTCACATTATCAATCGTATCAGAACTCTCAACCTCCAAGGTGATGGTCTTCC
* * * *
33980886 CAGTCAGGGTCTTCACGAAAATTTGCATCCCACCACGGAGACGGAGCACCAAGTGGAGGGTGGAC
131 CAGTCAGGGTCTTCACAAAAATTTGCATACCACCACGCAGACGGAGCACCAAATGGAGGGTGGAC
* * * * * * *
33980951 TCCTTCTGGATGTTGTAATCTGCAAGGGTCCTCCCATCCTCTAGCTGCTTACCAGCAAATATCAG
196 TCCTTCTGAATGTTGTAATCAGCAAGGGTACGCCCATCCTCCAGCTGCTTACCAGCAAAGATAAG
* * * * *
33981016 CCTCTGCTGGTCTGGAGGGATACCTTCCTTATCTTGAATTTTGGCCTTAACATTATCAATTGTGT
261 CCTCTGCTGGTCTGGAGGGATACCTTCCTTATCTTGAATCTTAGACTTAACATTATCAATGGTAT
* * * *
33981081 CAGAGCTCTCAACTTCCAGGGTGATGGTCTTCCCGGTAAGTGTCTTCACAAAAATCTGCATACCA
326 CAGAACTCTCAACCTCCAAGGTGATGGTCTTCCCGGTAAGGGTCTTCACAAAAATCTGCATACCA
* * * *
33981146 CCACGAAGACGGAGCACCAAGTGGAGGGTGGACTCCTTCTGGATGTTATAGTCAGCCAGGGTACG
391 CCACCAAGACGGAGCACCAAATGGAGGGTGGACTCCTTCTGAATGTTATAGTCAGCAAGGGTACG
* * *
33981211 GCCATCCTCAAGTTGCTTACCAGCAAATATCAGCCTCTGTTGGTCTGGGGGAATTCCCTCCTTGT
456 GCCATCCTCAAGCTGCTTACCAGCAAAGATAAGCCTCTGTTGGTCTGGGGGAATTCCCTCCTTGT
* * * *
33981276 CCTGAATTTTCGCCTTAACATTGTCAATGGTATCTGAACTCTCTACCTCCAATGTAATGGTCTTC
521 CCTGAATCTTCGCCTTAACATTGTCAATGGTATCAGAACTCTCCACCTCCAAGGTAATGGTCTTC
33981341 CCAGTCAAAGTCTTAACAAAAATTTGCATTCCTCCACGGAGGCGAAGCACCAAGTGGAGTGTGGA
586 CCAGTCAAAGTCTTAACAAAAATTTGCATTCCTCCACGGAGGCGAAGCACCAAGTGGAGTGTGGA
33981406 CTCCTTCTGGATGTTGTAATCAGCCAATGTGCGG
651 CTCCTTCTGGATGTTGTAATCAGCCAATGTGCGG
* * *
33981440 CCATCCTCAAGTTGCTTACCAGCGAAGATCAGCCTCTGCTGGTCTGG-GGGTATGCCTTCCTTGT
1 CCATCCTCAAGTTGCTTACCAGCAAAAATCAGCCTCTGCTGGTCTGGTGGG-ATGCCTTCCTTAT
* * * *
33981504 CCTGAATCTTAGCCTTGACATTGTCAA-CAGTATCAGAACTCTCCACCTCCAATGTGATGGTCTT
65 CCTGAATCTTAGCCTTCACATTATCAATC-GTATCAGAACTCTCAACCTCCAAGGTGATGGTCTT
* * * * * * *
33981568 CCCGGTGAGGGTCTTGACAAAAATTTGCATACCACCCCTCA-ATCGGAGGACCAAATGGAGTGTG
129 CCCAGTCAGGGTCTTCACAAAAATTTGCATACCACCACGCAGA-CGGAGCACCAAATGGAGGGTG
* * * * *
33981632 GATTCCTTCTGAATGTTGTAGTCAGCAAGGGTACGGCCATCCTCCAGCTGTTTCCCAGCAAAGAT
193 GACTCCTTCTGAATGTTGTAATCAGCAAGGGTACGCCCATCCTCCAGCTGCTTACCAGCAAAGAT
* * * * * * *
33981697 AAGCCTCTGTTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTAGACTTGACATTGTCAATGG
258 AAGCCTCTGCTGGTCTGGAGGGATACCTTCCTTATCTTGAATCTTAGACTTAACATTATCAATGG
* * * * * *
33981762 TATCTGAACTCTCCACCTCCAATGTGATGGTCTTCCCGGTGAGGGTCTTGACAAAAATTTGCATA
323 TATCAGAACTCTCAACCTCCAAGGTGATGGTCTTCCCGGTAAGGGTCTTCACAAAAATCTGCATA
* * * * * *
33981827 CCACCCCTCAA-TCGGAGGACCAAATGGAGTGTGGATTCCTTCTGAATGTTGTAGTCAGCAAGGG
388 CCACCAC-CAAGACGGAGCACCAAATGGAGGGTGGACTCCTTCTGAATGTTATAGTCAGCAAGGG
* *
33981891 TACGGCCATCCTCCAGCTGTTTACCAGCAAAGATAAGCCTCTGTTGGTCTGGTGGG-A-TCCCTT
452 TACGGCCATCCTCAAGCTGCTTACCAGCAAAGATAAGCCTCTGTTGGTCTGG-GGGAATTCCC-T
* * * * * * *
33981954 CCTTGTCTTGGATCTTGGCCTTTACATTGTCGATGGTATCAGAACTTTCCACCT-CAAGGGTGAT
515 CCTTGTCCTGAATCTTCGCCTTAACATTGTCAATGGTATCAGAACTCTCCACCTCCAA-GGTAAT
* * ** * *
33982018 GGTCTTGCCAGTGAGGGTCTTGACGAAAATTTGCAT
579 GGTCTTCCCAGTCAAAGTCTTAACAAAAATTTGCAT
33982054 CTATTTTGAT
Statistics
Matches: 511, Mismatches: 96, Indels: 14
0.82 0.15 0.02
Matches are distributed among these distances:
683 12 0.02
684 494 0.97
685 5 0.01
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (684 bp):
CCATCCTCAAGTTGCTTACCAGCAAAAATCAGCCTCTGCTGGTCTGGTGGGATGCCTTCCTTATC
CTGAATCTTAGCCTTCACATTATCAATCGTATCAGAACTCTCAACCTCCAAGGTGATGGTCTTCC
CAGTCAGGGTCTTCACAAAAATTTGCATACCACCACGCAGACGGAGCACCAAATGGAGGGTGGAC
TCCTTCTGAATGTTGTAATCAGCAAGGGTACGCCCATCCTCCAGCTGCTTACCAGCAAAGATAAG
CCTCTGCTGGTCTGGAGGGATACCTTCCTTATCTTGAATCTTAGACTTAACATTATCAATGGTAT
CAGAACTCTCAACCTCCAAGGTGATGGTCTTCCCGGTAAGGGTCTTCACAAAAATCTGCATACCA
CCACCAAGACGGAGCACCAAATGGAGGGTGGACTCCTTCTGAATGTTATAGTCAGCAAGGGTACG
GCCATCCTCAAGCTGCTTACCAGCAAAGATAAGCCTCTGTTGGTCTGGGGGAATTCCCTCCTTGT
CCTGAATCTTCGCCTTAACATTGTCAATGGTATCAGAACTCTCCACCTCCAAGGTAATGGTCTTC
CCAGTCAAAGTCTTAACAAAAATTTGCATTCCTCCACGGAGGCGAAGCACCAAGTGGAGTGTGGA
CTCCTTCTGGATGTTGTAATCAGCCAATGTGCGG
Found at i:33988380 original size:59 final size:59
Alignment explanation
Indices: 33988231--33988406 Score: 205
Period size: 59 Copynumber: 2.9 Consensus size: 59
33988221 TTTTTCTAAT
* * * *
33988231 ATTATATATTATAATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTGA
1 ATTATTTATTAT--TTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAA
* * *
33988294 ATTAATTATTA--TTTCATTAAATTATATTTAATAATAATTATGTTAAAATATAATTAA
1 ATTATTTATTATTTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
* *
33988351 ATTATTTATTATTTTTTATTAAATTATATTTAATAATAATTTTATTAAAATTTAAT
1 ATTATTTATTATTTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAAT
33988407 AACAATAACT
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
57 20 0.20
58 17 0.17
59 48 0.49
60 4 0.04
63 9 0.09
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (59 bp):
ATTATTTATTATTTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
Found at i:33988591 original size:16 final size:16
Alignment explanation
Indices: 33988564--33988631 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
33988554 AATTACTGAC
*
33988564 TACAACCCTATTCCAT
1 TACAACTCTATTCCAT
* *
33988580 TACAATTTTATTCCAT
1 TACAACTCTATTCCAT
33988596 TACAACTCTATTCCAT
1 TACAACTCTATTCCAT
* *
33988612 TACAGCTCTATTTCAT
1 TACAACTCTATTCCAT
33988628 TACA
1 TACA
33988632 GCGAACCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.31, C:0.28, G:0.01, T:0.40
Consensus pattern (16 bp):
TACAACTCTATTCCAT
Found at i:33989146 original size:29 final size:27
Alignment explanation
Indices: 33989058--33989146 Score: 65
Period size: 29 Copynumber: 3.1 Consensus size: 27
33989048 AAATAAACAT
* *
33989058 TATAATTTATAAAAAATTTATTTTTACAA
1 TATAAATTAT-AAAATTTTATTTTTA-AA
* * *
33989087 AAT-AA-TATAAAATTATATAATTTAAA
1 TATAAATTATAAAATTTTAT-TTTTAAA
33989113 GTATAAATTATGAAAATTTTATTTTTATAA
1 -TATAAATTAT-AAAATTTTATTTTTA-AA
33989143 TATA
1 TATA
33989147 TTATAACATG
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
26 10 0.22
27 9 0.20
28 3 0.07
29 13 0.28
30 11 0.24
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (27 bp):
TATAAATTATAAAATTTTATTTTTAAA
Found at i:33991180 original size:20 final size:18
Alignment explanation
Indices: 33991146--33991182 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
33991136 TTGTCTTTTT
33991146 ATTTAATTTTTTTTAAAA
1 ATTTAATTTTTTTTAAAA
33991164 ATTTATATTTTTATTTAAA
1 ATTTA-ATTTTT-TTTAAA
33991183 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTAATTTTTTTTAAAA
Found at i:33991205 original size:30 final size:30
Alignment explanation
Indices: 33991140--33991205 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
33991130 TGAGTCTTGT
*
33991140 CTTTTTATTTAATTTTTTTTAAAAATTTAT
1 CTTTTTATTTAATTTTTTTTAAAAATTTAC
*
33991170 ATTTTTATTTAAATTTATTTTT-AAAATTT-C
1 CTTTTTATTT-AATTT-TTTTTAAAAATTTAC
33991200 CTTTTT
1 CTTTTT
33991206 TGTTTTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 14 0.45
31 12 0.39
32 5 0.16
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (30 bp):
CTTTTTATTTAATTTTTTTTAAAAATTTAC
Found at i:34006256 original size:20 final size:20
Alignment explanation
Indices: 34006203--34006256 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 20
34006193 TTTTTTCTAC
34006203 TTAATACTATTAATTTGGTAA
1 TTAAT-CTATTAATTTGGTAA
* **
34006224 -TAA-CTAATAATTTTTTAA
1 TTAATCTATTAATTTGGTAA
34006242 TTAATCTATTAATTT
1 TTAATCTATTAATTT
34006257 CTTAGATACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 12 0.44
19 3 0.11
20 12 0.44
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (20 bp):
TTAATCTATTAATTTGGTAA
Found at i:34006572 original size:33 final size:35
Alignment explanation
Indices: 34006500--34006572 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
34006490 TCCGCATAAG
34006500 GGGGCTTGTACATGCATGGGTGATTCACATATGCAA
1 GGGGCTTGTACATGCATGGGTGATTCACA-ATGCAA
*
34006536 GGGGCTTGTACGTGCAATGGG-G-TTCAC-ATGCAA
1 GGGGCTTGTACATGC-ATGGGTGATTCACAATGCAA
34006569 GGGG
1 GGGG
34006573 GTTCGCATGC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
33 10 0.29
35 5 0.14
36 15 0.43
37 5 0.14
ACGTcount: A:0.22, C:0.16, G:0.37, T:0.25
Consensus pattern (35 bp):
GGGGCTTGTACATGCATGGGTGATTCACAATGCAA
Found at i:34006573 original size:16 final size:16
Alignment explanation
Indices: 34006548--34006582 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34006538 GGCTTGTACG
*
34006548 TGCAATGGGGTTCACA
1 TGCAAGGGGGTTCACA
*
34006564 TGCAAGGGGGTTCGCA
1 TGCAAGGGGGTTCACA
34006580 TGC
1 TGC
34006583 GGACTGCTTA
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:0.20, C:0.20, G:0.37, T:0.23
Consensus pattern (16 bp):
TGCAAGGGGGTTCACA
Found at i:34009525 original size:126 final size:126
Alignment explanation
Indices: 34009343--34009745 Score: 477
Period size: 126 Copynumber: 3.2 Consensus size: 126
34009333 TTTGTTTCCG
* * * * * * *
34009343 AACTATACTAATATTC-AAAAATGAAAATAAAATGCCAAGAAAAAAGAGATTTCTGACCTAAGTT
1 AACTATACTAATATCCAAAAAATGAAAATAAAATGCGAGGGAAAGAGAGATTCCTGACCTGAGTT
* * * * * *
34009407 AATACTTCTTTACCTTACTACCTTCAAGTTTTTAGTTCGGCAACAGTGGAGTGCAAAAATA
66 AAAACTTCCTTCCCTTACTACCTTCGAGTTCTTAGTTCGGCAACAATGGAGTGCAAAAATA
*
34009468 AACTATACTAATATCCAAAAAATGAAAATAAAATGCGAGGGAAAGAGATATTCCTGACCTGAGTT
1 AACTATACTAATATCCAAAAAATGAAAATAAAATGCGAGGGAAAGAGAGATTCCTGACCTGAGTT
* * * *
34009533 AAAACTTCCTTCCCTTACTACTTTCGAGATCTTAGTTTGGCAACAATGGAGAGCAAAAATAA
66 AAAACTTCCTTCCCTTACTACCTTCGAGTTCTTAGTTCGGCAACAATGGAGTGCAAAAAT-A
*
34009595 AAC-ATACTAATATCCAAAAAAAAAATGAAAATAAAATGAGAGGGAAAGAGAGATTCCTGACCTG
1 AACTATACTAATATCC----AAAAAATGAAAATAAAATGCGAGGGAAAGAGAGATTCCTGACCTG
* * * * * * * *
34009659 AGGTAAAACTCCCTTCCCTTTCTATCTTCGGGTTCTTAGTTCGGAAACATTAGAGTGCAAAAATA
62 AGTTAAAACTTCCTTCCCTTACTACCTTCGAGTTCTTAGTTCGGCAACAATGGAGTGCAAAAATA
* * *
34009724 AACTTTATTAATATCGAAAAAA
1 AACTATACTAATATCCAAAAAA
34009746 ATGAGAGGGA
Statistics
Matches: 236, Mismatches: 35, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
125 15 0.06
126 109 0.46
127 4 0.02
129 4 0.02
130 104 0.44
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (126 bp):
AACTATACTAATATCCAAAAAATGAAAATAAAATGCGAGGGAAAGAGAGATTCCTGACCTGAGTT
AAAACTTCCTTCCCTTACTACCTTCGAGTTCTTAGTTCGGCAACAATGGAGTGCAAAAATA
Found at i:34009746 original size:130 final size:128
Alignment explanation
Indices: 34009359--34009746 Score: 451
Period size: 130 Copynumber: 3.0 Consensus size: 128
34009349 ACTAATATTC
* * * * * * * * *
34009359 AAAAATGAAAATAAAATGCCAAGAAAAAAGAGATTTCTGACCTAAGTTAATACTTCTTTACCTTA
1 AAAAATGAAAATAAAATGCGAGGGAAAGAGAGATTCCTGACCTGAGTTAAAACTTCCTTCCCTTA
* * * *
34009424 CTACCTTCAAGTTTTTAGTTCGGCAACAGTGGAGTGCAAAAATAAACTATACTAATATC---CA
66 CTA-CTTCGAGTTCTTAGTTCGGCAACAATGGAGTGCAAAAATAAACTATACTAATATCAAAAA
*
34009485 AAAAATGAAAATAAAATGCGAGGGAAAGAGATATTCCTGACCTGAGTTAAAACTTCCTTCCCTTA
1 AAAAATGAAAATAAAATGCGAGGGAAAGAGAGATTCCTGACCTGAGTTAAAACTTCCTTCCCTTA
* * *
34009550 CTACTTTCGAGATCTTAGTTTGGCAACAATGGAGAGCAAAAATAAAAC-ATACTAATATCCAAAA
66 CTAC-TTCGAGTTCTTAGTTCGGCAACAATGGAGTGCAAAAAT-AAACTATACTAATAT-CAAAA
34009614 A
128 A
* * * *
34009615 AAAAATGAAAATAAAATGAGAGGGAAAGAGAGATTCCTGACCTGAGGTAAAACTCCCTTCCCTTT
1 AAAAATGAAAATAAAATGCGAGGGAAAGAGAGATTCCTGACCTGAGTTAAAACTTCCTTCCCTTA
* * * * * * *
34009680 CTATCTTCGGGTTCTTAGTTCGGAAACATTAGAGTGCAAAAATAAACTTTATTAATATCGAAAA
66 CTA-CTTCGAGTTCTTAGTTCGGCAACAATGGAGTGCAAAAATAAACTATACTAATATCAAAAA
34009744 AAA
1 AAA
34009747 TGAGAGGGAA
Statistics
Matches: 222, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
125 1 0.00
126 100 0.45
127 5 0.02
129 12 0.05
130 103 0.46
131 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (128 bp):
AAAAATGAAAATAAAATGCGAGGGAAAGAGAGATTCCTGACCTGAGTTAAAACTTCCTTCCCTTA
CTACTTCGAGTTCTTAGTTCGGCAACAATGGAGTGCAAAAATAAACTATACTAATATCAAAAA
Found at i:34013035 original size:20 final size:20
Alignment explanation
Indices: 34013012--34013050 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34013002 TTTTTAATTG
34013012 ACTTTAATACATTTTATTAC
1 ACTTTAATACATTTTATTAC
**
34013032 ACTTTAATTTATTTTATTA
1 ACTTTAATACATTTTATTA
34013051 TAATGCACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
ACTTTAATACATTTTATTAC
Found at i:34016145 original size:19 final size:19
Alignment explanation
Indices: 34016117--34016160 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
34016107 GGAAGAGAAT
34016117 GAAAAATAAAGAAAA-AAAA
1 GAAAAATAAA-AAAATAAAA
* *
34016136 GAAAATTAAAAAAATAAAG
1 GAAAAATAAAAAAATAAAA
34016155 GAAAAA
1 GAAAAA
34016161 ATTAAACTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (19 bp):
GAAAAATAAAAAAATAAAA
Found at i:34018145 original size:22 final size:22
Alignment explanation
Indices: 34018117--34018162 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
34018107 CTTAAATTTT
34018117 AAAAGTTACAAAATGATTATTG
1 AAAAGTTACAAAATGATTATTG
34018139 AAAAGTTACAAAATGATTATTG
1 AAAAGTTACAAAATGATTATTG
34018161 AA
1 AA
34018163 TTATTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (22 bp):
AAAAGTTACAAAATGATTATTG
Found at i:34019944 original size:59 final size:59
Alignment explanation
Indices: 34019875--34019996 Score: 235
Period size: 59 Copynumber: 2.1 Consensus size: 59
34019865 CAACTCAATT
*
34019875 ATAAACTTAGTATAAATAAATATATATTTTTCATTAATTGCATTTATGTTCATATCTAA
1 ATAAACTTAGTATAAATAAATATATATTTTTCATTAATTGCATTCATGTTCATATCTAA
34019934 ATAAACTTAGTATAAATAAATATATATTTTTCATTAATTGCATTCATGTTCATATCTAA
1 ATAAACTTAGTATAAATAAATATATATTTTTCATTAATTGCATTCATGTTCATATCTAA
34019993 ATAA
1 ATAA
34019997 TTACAAACAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (59 bp):
ATAAACTTAGTATAAATAAATATATATTTTTCATTAATTGCATTCATGTTCATATCTAA
Found at i:34033115 original size:30 final size:30
Alignment explanation
Indices: 34033081--34033168 Score: 167
Period size: 30 Copynumber: 2.9 Consensus size: 30
34033071 CTAGGACCAC
34033081 CACCAGCTTTTGGAGGAGGTGGTGGAGGAG
1 CACCAGCTTTTGGAGGAGGTGGTGGAGGAG
34033111 CACCAGCTTTTGGAGGAGGTGGTGGAGGAG
1 CACCAGCTTTTGGAGGAGGTGGTGGAGGAG
*
34033141 CACCAGCTTTTGGAGGAGGGGGTGGAGG
1 CACCAGCTTTTGGAGGAGGTGGTGGAGG
34033169 GACTGCATTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.19, C:0.14, G:0.48, T:0.19
Consensus pattern (30 bp):
CACCAGCTTTTGGAGGAGGTGGTGGAGGAG
Found at i:34033189 original size:60 final size:60
Alignment explanation
Indices: 34033081--34033200 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
34033071 CTAGGACCAC
* *
34033081 CACCAGCTTTTGGAGGAGGTGGTGGAGGAGCACCAGCTTTTGGAGGAGGTGGTGGAGGAG
1 CACCAGCTTTTGGAGGAGGGGGTGGAGGAGCACCAGCTTGTGGAGGAGGTGGTGGAGGAG
*
34033141 CACCAGCTTTTGGAGGAGGGGGTGGAGG-G-A-CTGCATTGGTGGAGGGAGGTGGTGGAGGAG
1 CACCAGCTTTTGGAGGAGGGGGTGGAGGAGCACCAGC-TT-GTGGA-GGAGGTGGTGGAGGAG
34033201 GAGGAGCAGC
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
57 3 0.06
58 3 0.06
59 5 0.09
60 43 0.80
ACGTcount: A:0.19, C:0.12, G:0.50, T:0.19
Consensus pattern (60 bp):
CACCAGCTTTTGGAGGAGGGGGTGGAGGAGCACCAGCTTGTGGAGGAGGTGGTGGAGGAG
Found at i:34033779 original size:15 final size:15
Alignment explanation
Indices: 34033755--34033789 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34033745 GTCTCTCCTT
*
34033755 CTTCTTCTCCTTCTC
1 CTTCTACTCCTTCTC
*
34033770 CTTCTACTCCTTCTT
1 CTTCTACTCCTTCTC
34033785 CTTCT
1 CTTCT
34033790 TCATAATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.54
Consensus pattern (15 bp):
CTTCTACTCCTTCTC
Found at i:34033791 original size:9 final size:9
Alignment explanation
Indices: 34033748--34033791 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
34033738 GTGATCAGTC
34033748 TCTCCTTCT
1 TCTCCTTCT
* *
34033757 TCTTCTCCT
1 TCTCCTTCT
34033766 TCTCCTTCT
1 TCTCCTTCT
*
34033775 ACTCCTTCT
1 TCTCCTTCT
*
34033784 TCTTCTTC
1 TCTCCTTC
34033792 ATAATCATCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.02, C:0.43, G:0.00, T:0.55
Consensus pattern (9 bp):
TCTCCTTCT
Found at i:34040871 original size:21 final size:21
Alignment explanation
Indices: 34040841--34040886 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
34040831 TGTGAATGTG
* *
34040841 ATTA-TTAAATGTTTTTAATT
1 ATTATTTAAATATTATTAATT
34040861 ATTATTTAAATATTATTAATT
1 ATTATTTAAATATTATTAATT
34040882 ATTAT
1 ATTAT
34040887 ATATTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTATTTAAATATTATTAATT
Found at i:34049323 original size:22 final size:21
Alignment explanation
Indices: 34049286--34049326 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
34049276 ATATAGCTAT
*
34049286 ATAAAAAATTTAAATATTAAA
1 ATAAAAAATATAAATATTAAA
34049307 ATAAAACAATATAAATATTA
1 ATAAAA-AATATAAATATTA
34049327 TTTTAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAAAAATATAAATATTAAA
Found at i:34050124 original size:31 final size:30
Alignment explanation
Indices: 34050073--34050164 Score: 114
Period size: 29 Copynumber: 3.1 Consensus size: 30
34050063 AACGGGCAAG
34050073 TAAATTTACAAATTGATCACTTAATTATTTA
1 TAAATTTACAAATTGATCACTTAATT-TTTA
* * * *
34050104 TAAACTTACAATTTGGTCACTTAA-TTTCA
1 TAAATTTACAAATTGATCACTTAATTTTTA
* *
34050133 TAAATTTACAAGTTGATCACTCAATTTTTA
1 TAAATTTACAAATTGATCACTTAATTTTTA
34050163 TA
1 TA
34050165 CCATTACTCC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 23 0.45
30 7 0.14
31 21 0.41
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.43
Consensus pattern (30 bp):
TAAATTTACAAATTGATCACTTAATTTTTA
Found at i:34055496 original size:30 final size:30
Alignment explanation
Indices: 34055429--34055498 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
34055419 TGTATTATTG
34055429 CATATATTTT-TATTATTATTAACTTCAAA
1 CATATATTTTATATTATTATTAACTTCAAA
* * * *
34055458 TATTTATTTTATATTATTTTTAAACTT-ATA
1 CATATATTTTATATTATTATT-AACTTCAAA
34055488 CATATATTTTA
1 CATATATTTTA
34055499 ATACTATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 8 0.24
30 20 0.61
31 5 0.15
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (30 bp):
CATATATTTTATATTATTATTAACTTCAAA
Found at i:34061281 original size:31 final size:32
Alignment explanation
Indices: 34061243--34061302 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
34061233 TTACTTAAAA
34061243 AAGTACACATAAAAGACTTCTTAT-TATAGAG
1 AAGTACACATAAAAGACTTCTTATATATAGAG
* *
34061274 AAGTACACATAGAAGGCTTCTTATATATA
1 AAGTACACATAAAAGACTTCTTATATATA
34061303 TTATCAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (32 bp):
AAGTACACATAAAAGACTTCTTATATATAGAG
Found at i:34070584 original size:17 final size:17
Alignment explanation
Indices: 34070562--34070600 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
34070552 AGGTTGAAAA
* *
34070562 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
34070579 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
34070596 CTTGT
1 CTTGT
34070601 CATGGTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:34080401 original size:29 final size:29
Alignment explanation
Indices: 34080345--34080402 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
34080335 ATTATTTAAA
* *
34080345 ATATAGAAATTATTAAATTTTATAAAAAG
1 ATATAGAAAATATTAAAATTTATAAAAAG
*
34080374 ATATAGAAAATATTAAAAATTTAGAAAAA
1 ATATAGAAAATATT-AAAATTTATAAAAA
34080403 AAAAGTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (29 bp):
ATATAGAAAATATTAAAATTTATAAAAAG
Found at i:34080440 original size:19 final size:17
Alignment explanation
Indices: 34080416--34080454 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
34080406 AGTATAAAAC
*
34080416 ATTATTAGAATGATAGAAA
1 ATTATTAAAAT-AT-GAAA
34080435 ATTATTAAAATATGAAA
1 ATTATTAAAATATGAAA
34080452 ATT
1 ATT
34080455 TTTATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (17 bp):
ATTATTAAAATATGAAA
Found at i:34080554 original size:9 final size:10
Alignment explanation
Indices: 34080533--34080574 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
34080523 GTTGTGGTGG
*
34080533 AAAATAATAA
1 AAAATTATAA
34080543 AAAATTATAA
1 AAAATTATAA
*
34080553 AAAAATATAA
1 AAAATTATAA
34080563 AAAATTA-AA
1 AAAATTATAA
34080572 AAA
1 AAA
34080575 TTTAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 5 0.17
10 24 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAATTATAA
Found at i:34080562 original size:20 final size:20
Alignment explanation
Indices: 34080533--34080574 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
34080523 GTTGTGGTGG
34080533 AAAATAATAAAAAATTATAAA
1 AAAATAATAAAAAATTA-AAA
34080554 AAAAT-ATAAAAAATTAAAA
1 AAAATAATAAAAAATTAAAA
34080573 AA
1 AA
34080575 TTTAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAATAAAAAATTAAAA
Found at i:34080887 original size:22 final size:21
Alignment explanation
Indices: 34080847--34080888 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34080837 TTTTATTTGT
34080847 ATTTTTATATTTTATAATAAA
1 ATTTTTATATTTTATAATAAA
34080868 ATTTTTATGTATTTTA-AATAA
1 ATTTTTA--TATTTTATAATAA
34080889 TTTTCTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTTTATATTTTATAATAAA
Found at i:34080903 original size:21 final size:22
Alignment explanation
Indices: 34080848--34080909 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
34080838 TTTATTTGTA
34080848 TTTT-TATATTTTATAATAAAAT
1 TTTTATATATTTTATAAT-AAAT
*
34080870 TTTTATGTATTTTA-AAT-AAT
1 TTTTATATATTTTATAATAAAT
*
34080890 TTTCTATATATTTTTTAATA
1 TTT-TATATATTTTATAATA
34080910 TTTTTGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 6 0.18
21 9 0.27
22 10 0.30
23 8 0.24
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTATATATTTTATAATAAAT
Found at i:34082637 original size:13 final size:13
Alignment explanation
Indices: 34082619--34082643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34082609 ATTTCGATCA
34082619 TATTTTCTTTTTT
1 TATTTTCTTTTTT
34082632 TATTTTCTTTTT
1 TATTTTCTTTTT
34082644 ATATATACAT
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:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (13 bp):
TATTTTCTTTTTT
Found at i:34088328 original size:13 final size:12
Alignment explanation
Indices: 34088305--34088334 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
34088295 ATTTGGTTTT
34088305 GAAAAAAAAAAA
1 GAAAAAAAAAAA
34088317 GAAAAAAGAAAAA
1 GAAAAAA-AAAAA
34088330 GAAAA
1 GAAAA
34088335 TATATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:34098787 original size:15 final size:16
Alignment explanation
Indices: 34098769--34098805 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
34098759 CCAATTAGTC
34098769 CAAAAAA-AATTTTAT
1 CAAAAAATAATTTTAT
*
34098784 CAAAAAATATTTTTAT
1 CAAAAAATAATTTTAT
34098800 -AAAAAA
1 CAAAAAA
34098806 CTCAATTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
CAAAAAATAATTTTAT
Found at i:34099540 original size:30 final size:30
Alignment explanation
Indices: 34099476--34099540 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
34099466 TTCGTGAACA
*** **
34099476 TTAAACAAACGAACATGAACATTCATAATT
1 TTAAACAAACGAACATGAACACAAATAAGC
*
34099506 TTAAATAAACGAACATGAACACAAATAAGC
1 TTAAACAAACGAACATGAACACAAATAAGC
34099536 TTAAA
1 TTAAA
34099541 AATAAACAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (30 bp):
TTAAACAAACGAACATGAACACAAATAAGC
Found at i:34110276 original size:30 final size:26
Alignment explanation
Indices: 34110257--34110307 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 26
34110247 ATAAATATTG
34110257 GATTAATTTAATTTTTTAT-TAAATA
1 GATTAATTTAATTTTTTATATAAATA
34110282 GATTAATTTAATTTTTATAATATAAA
1 GATTAATTTAATTTTT-T-ATATAAA
34110308 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 16 0.70
26 1 0.04
27 2 0.09
28 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
GATTAATTTAATTTTTTATATAAATA
Found at i:34110465 original size:21 final size:20
Alignment explanation
Indices: 34110441--34110484 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
34110431 CATAATTATG
34110441 TTAAACAATAAATGAAAAATT
1 TTAAACAATAAATG-AAAATT
* *
34110462 TTAAACAGTAAATGATAATT
1 TTAAACAATAAATGAAAATT
34110482 TTA
1 TTA
34110485 TTTTAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (20 bp):
TTAAACAATAAATGAAAATT
Found at i:34121616 original size:14 final size:14
Alignment explanation
Indices: 34121557--34121629 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
34121547 GATTTTTATT
34121557 TATT-TATTATTAA
1 TATTATATTATTAA
*
34121570 T-TAATATTA-TAA
1 TATTATATTATTAA
* * *
34121582 TATAATAATATAAA
1 TATTATATTATTAA
34121596 TTATTAT-TTAATTAA
1 -TATTATATT-ATTAA
*
34121611 TATTATATTATTAT
1 TATTATATTATTAA
34121625 TATTA
1 TATTA
34121630 ACTAATATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
12 5 0.11
13 13 0.28
14 18 0.38
15 11 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTATATTATTAA
Found at i:34129288 original size:13 final size:13
Alignment explanation
Indices: 34129233--34129289 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
34129223 TTTTTATATA
*
34129233 TTTTTATAATTTT
1 TTTTTAAAATTTT
34129246 TTATTT-AAATTTT
1 TT-TTTAAAATTTT
* *
34129259 TTTTTCGAACTTATT
1 TTTTT-AAAATT-TT
34129274 TTTTTAAAATTTT
1 TTTTTAAAATTTT
34129287 TTT
1 TTT
34129290 CTAGATTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 3 0.08
13 15 0.42
14 11 0.31
15 7 0.19
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTTAAAATTTT
Found at i:34132899 original size:17 final size:17
Alignment explanation
Indices: 34132845--34132899 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
34132835 TTTGTTACTA
34132845 TTATTTTATTGTT-ATT
1 TTATTTTATTGTTAATT
*
34132861 GTT-TTAATATTGTATAACTT
1 -TTATT-TTATTGT-TAA-TT
34132881 TTATTTTATTGTTAATT
1 TTATTTTATTGTTAATT
34132898 TT
1 TT
34132900 GTTATTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
16 2 0.06
17 12 0.39
18 4 0.13
19 9 0.29
20 4 0.13
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (17 bp):
TTATTTTATTGTTAATT
Found at i:34150155 original size:58 final size:56
Alignment explanation
Indices: 34150065--34150179 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 56
34150055 TTTTATTATA
* *
34150065 ATATTTTATTATTTCAGTTTGTTATTTAGTTTAAAAAATATTAGATATCTTTTTGGAC
1 ATATTTTATTACTTCAGTTTATTATTTAGTTT--AAAATATTAGATATCTTTTTGGAC
* * *
34150123 ATATTTTATTGCTTCAGTTTATTATTTAGTTTAAAGTATTAGATGTCTTTTTGGAC
1 ATATTTTATTACTTCAGTTTATTATTTAGTTTAAAATATTAGATATCTTTTTGGAC
34150179 A
1 A
34150180 GCTAAGCTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
56 23 0.44
58 29 0.56
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (56 bp):
ATATTTTATTACTTCAGTTTATTATTTAGTTTAAAATATTAGATATCTTTTTGGAC
Found at i:34154581 original size:18 final size:18
Alignment explanation
Indices: 34154558--34154599 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
34154548 AGGATGTTTT
34154558 TTATTT-CTAAAAATAAGA
1 TTATTTACT-AAAATAAGA
* *
34154576 TTATTTAGTGAAATAAGA
1 TTATTTACTAAAATAAGA
34154594 TTATTT
1 TTATTT
34154600 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (18 bp):
TTATTTACTAAAATAAGA
Found at i:34156002 original size:26 final size:26
Alignment explanation
Indices: 34155944--34156004 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
34155934 GTTACTTTTT
* * * *
34155944 TTAGGGTTAGGGTTTTTTAATTAGGG
1 TTAGGTTTAGGGTTTTTAAAATAGGA
*
34155970 TTAAGGTTTATGGTTTTTAAAATAGGA
1 TT-AGGTTTAGGGTTTTTAAAATAGGA
34155997 TTAGGTTT
1 TTAGGTTT
34156005 TTTTAGATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.48
Consensus pattern (26 bp):
TTAGGTTTAGGGTTTTTAAAATAGGA
Found at i:34156064 original size:16 final size:16
Alignment explanation
Indices: 34156026--34156074 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
34156016 AAGGTTTAAG
*
34156026 ATTTTTATATATTATTTT
1 ATTTTT-TATAAT-TTTT
34156044 A-TTTTTATAATTTTT
1 ATTTTTTATAATTTTT
*
34156059 ATTTTTTCTAATTTTT
1 ATTTTTTATAATTTTT
34156075 TGAGACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 4 0.14
18 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTTTATAATTTTT
Found at i:34160252 original size:16 final size:16
Alignment explanation
Indices: 34160228--34160265 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
34160218 CTTTAGAGAT
*
34160228 TACGAGGTCCGATGAC
1 TACGTGGTCCGATGAC
34160244 TACGTGGTCCGATGAC
1 TACGTGGTCCGATGAC
34160260 TACGTG
1 TACGTG
34160266 TCATCGTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.24
Consensus pattern (16 bp):
TACGTGGTCCGATGAC
Found at i:34160297 original size:68 final size:68
Alignment explanation
Indices: 34160181--34160317 Score: 222
Period size: 68 Copynumber: 2.0 Consensus size: 68
34160171 AAATGAGAAA
* *
34160181 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTAGAGATTACGAGGTCCGATGACTA
1 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTAGAGATTACGAGATCCGATAACTA
34160246 CGT
66 CGT
* *
34160249 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTTTACG-GATTATGAGATCCGATAACT
1 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTA-GAGATTACGAGATCCGATAACT
34160313 ACGT
65 ACGT
34160317 G
1 G
34160318 TCATCGTGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 63 0.98
69 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (68 bp):
GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTAGAGATTACGAGATCCGATAACTA
CGT
Found at i:34160329 original size:52 final size:52
Alignment explanation
Indices: 34160249--34160434 Score: 255
Period size: 52 Copynumber: 3.6 Consensus size: 52
34160239 ATGACTACGT
*
34160249 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGA
1 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCATTTACGGATTATGA
* * *
34160301 GATCCGATAACTACGTGTCATCGTGAGTATATGAATCATTTACGGATTATAA
1 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCATTTACGGATTATGA
* * * * * ** *
34160353 GGTCCAATGACTACGTGTCATCGTGAGTGTATGATTCCTCTACGGAACAAGA
1 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCATTTACGGATTATGA
*
34160405 GGTCCGATGACTATGTGTCATCGTGAGTAT
1 GGTCCGATGACTACGTGTCATCGTGAGTAT
34160435 TAAGTGTAAT
Statistics
Matches: 116, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 116 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (52 bp):
GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCATTTACGGATTATGA
Found at i:34162356 original size:63 final size:61
Alignment explanation
Indices: 34162255--34162436 Score: 221
Period size: 67 Copynumber: 2.9 Consensus size: 61
34162245 TTTTGGTTTG
* * *
34162255 TTATTTATTTATTTATTT-ATTTATAATAATAAATAAATAATAAAACAAAATTAATATTATT
1 TTATTTATTTATTTATTTCA-TAAAAATAATAAATAAATAATAAAATAAAATTAATATTATT
34162316 TTACATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAATAAAATTAATATTA
1 TT--ATTTATTTATTTAT-TTCAT-AAA-AAT-AATAAATAAATAATAAAATAAAATTAATATTA
34162381 TT
60 TT
34162383 TTA--TATTTATTTATGTTCATAAAAATAAT-AATAAATAA-ATAAATAAAATTAATA
1 TTATTTATTTATTTAT-TTCATAAAAATAATAAATAAATAATA-AAATAAAATTAATA
34162437 AGAAAAATGG
Statistics
Matches: 109, Mismatches: 4, Indels: 18
0.83 0.03 0.14
Matches are distributed among these distances:
58 1 0.01
59 23 0.21
60 3 0.03
61 5 0.05
62 3 0.03
63 30 0.28
64 3 0.03
65 3 0.03
66 3 0.03
67 35 0.32
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (61 bp):
TTATTTATTTATTTATTTCATAAAAATAATAAATAAATAATAAAATAAAATTAATATTATT
Found at i:34162363 original size:67 final size:63
Alignment explanation
Indices: 34162255--34162430 Score: 234
Period size: 63 Copynumber: 2.7 Consensus size: 63
34162245 TTTTGGTTTG
**
34162255 TTATTTATTTATTTATTT-AT-TTATAATAATAAATAAATAATAAAACAAAATTAATATTATT
1 TTATTTATTTATTTATTTCATAAAATAATAATAAATAAATAATAAAACAAAATTAATATTATT
*
34162316 TTACATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAATAAAATTAATATTA
1 TT--ATTTATTTATTTAT-TTCATAAAATAAT-AATAAATAAATAATAAAACAAAATTAATATTA
34162381 TT
62 TT
34162383 TTA--TATTTATTTATGTTCATAAAAATAATAATAAATAAATAAATAAAA
1 TTATTTATTTATTTAT-TTCAT-AAAATAATAATAAATAAAT-AATAAAA
34162431 TTAATAAGAA
Statistics
Matches: 103, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
61 2 0.02
63 41 0.40
64 17 0.17
65 3 0.03
66 5 0.05
67 35 0.34
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (63 bp):
TTATTTATTTATTTATTTCATAAAATAATAATAAATAAATAATAAAACAAAATTAATATTATT
Found at i:34163151 original size:80 final size:80
Alignment explanation
Indices: 34162963--34164413 Score: 2365
Period size: 80 Copynumber: 18.2 Consensus size: 80
34162953 ATAACTTTAG
* * * * *
34162963 GGGTAAAAGATTAGATTGT-TTCAA-CTTGCCCCATGGTCGAGGTAAGAGATCTGATGGTCTTCA
1 GGGTAAAAGATTGGATT-TCTTCAATC-TGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCA
*
34163026 ATC-TGCCCTTTGGTTA
64 ATCTTGCCCTCTGGTTA
*
34163042 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
34163107 CTTGCCTTCTAGTTA
66 CTTGCCCTCTGGTTA
*
34163122 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTTTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
34163187 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* * * * *
34163202 TGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATTGGGGTAGAAGATCGGATGGTCTTTAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
34163267 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
34163282 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
34163347 CTT-CCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
34163361 GGGTAAAAGATTAGATTTCTTCAATCTGCCTCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
34163426 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* * *
34163441 GGGTAAAAGATTGGATTTCTTTAATCTGCCCCATGATCAGGGTAGAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
34163506 CTT-CTCTCTAGTTA
66 CTTGCCCTCTGGTTA
*
34163520 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
34163585 CTT-TCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
34163599 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCAGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
34163664 CTTGTCCTCTAGTTA
66 CTTGCCCTCTGGTTA
* *
34163679 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATAATCGGGGTAAAAGATTGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
34163744 TTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
34163759 GGGTAAAAGATTGGATTTCTTCAATTTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTTAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
34163824 CTTGCCCTCTAGTTA
66 CTTGCCCTCTGGTTA
*
34163839 GGGTAAAAGATTGGATTTCTTTAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
34163904 CTTGCCCTCTAGTTT
66 CTTGCCCTCTGGTTA
* *
34163919 GGGTAAAAGATTGGATTTCTTCAATTTGCCCCATGATCGAGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
34163984 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
34163999 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGAGTAAAAGATCGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
34164064 CTTGCCCTCTAGTTA
66 CTTGCCCTCTGGTTA
* *
34164079 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTTAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
34164144 CTTGCACTCTGGTTA
66 CTTGCCCTCTGGTTA
34164159 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
34164224 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
*
34164239 GGGTAAAAGATTGGATTTCTTCAATCTGCCACATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
34164304 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* * *
34164319 GGGTAAAAGATTGGATTTCTTCAATTTGCCCCATGATCGGGGTAAAAGATCTGATGGTTTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
34164384 CTTGCCCTTTGGTGA
66 CTTGCCCTCTGGTTA
34164399 GGGTAAAAGATTGGA
1 GGGTAAAAGATTGGA
34164414 GGTTGTAATT
Statistics
Matches: 1283, Mismatches: 84, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
78 1 0.00
79 282 0.22
80 1000 0.78
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (80 bp):
GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
CTTGCCCTCTGGTTA
Found at i:34164553 original size:50 final size:50
Alignment explanation
Indices: 34164499--34164644 Score: 168
Period size: 50 Copynumber: 2.9 Consensus size: 50
34164489 TTTAAATGAC
* * *
34164499 TGAGATTTGCCATTACAGCTTCATTCTGCCCCTCTACAACTTTAGGTGTA
1 TGAGATTTGCCATTACAGCTTCAATCTGCACCTCCACAACTTTAGGTGTA
* * * * *
34164549 TGAGATTTGACATTGCGGTTTCAATCTGCACCTCCACAGCTTTAGGTGTA
1 TGAGATTTGCCATTACAGCTTCAATCTGCACCTCCACAACTTTAGGTGTA
* * **
34164599 TGAGATTTACCA-TAGCAGTTTCAATCTGCACCTCCACCGCTTTAGG
1 TGAGATTTGCCATTA-CAGCTTCAATCTGCACCTCCACAACTTTAGG
34164645 GGTAAAAGAT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 1 0.01
50 81 0.99
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (50 bp):
TGAGATTTGCCATTACAGCTTCAATCTGCACCTCCACAACTTTAGGTGTA
Found at i:34165578 original size:6 final size:6
Alignment explanation
Indices: 34165569--34165626 Score: 53
Period size: 6 Copynumber: 8.8 Consensus size: 6
34165559 CGACCTCCCT
* *
34165569 TTTTTC TTTTTC TTTTCTTC TTTTTC CTTTTC TTTGTCTT TTTTTC TTTTTTC
1 TTTTTC TTTTTC -TTT-TTC TTTTTC TTTTTC TTT-T-TC TTTTTC -TTTTTC
34165622 TTTTT
1 TTTTT
34165627 TTAATTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 22 0.51
7 14 0.33
8 7 0.16
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:34165593 original size:21 final size:20
Alignment explanation
Indices: 34165567--34165625 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
34165557 CTCGACCTCC
34165567 CTTTTTTCTTTTTCTTTTCT
1 CTTTTTTCTTTTTCTTTTCT
*
34165587 -TCTTTTTCCTTTTCTTTGTCT
1 CT-TTTTTCTTTTTCTTT-TCT
34165608 -TTTTTTCTTTTTTCTTTT
1 CTTTTTTC-TTTTTCTTTT
34165626 TTTAATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.03
20 21 0.62
21 12 0.35
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (20 bp):
CTTTTTTCTTTTTCTTTTCT
Found at i:34165599 original size:26 final size:26
Alignment explanation
Indices: 34165570--34165625 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
34165560 GACCTCCCTT
*
34165570 TTTTCTTTTTCTTTTCTTCTTTTTCC
1 TTTTCTTTGTCTTTTCTTCTTTTTCC
* *
34165596 TTTTCTTTGTCTTTTTTTCTTTTTTC
1 TTTTCTTTGTCTTTTCTTCTTTTTCC
34165622 TTTT
1 TTTT
34165626 TTTAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTTCTTTGTCTTTTCTTCTTTTTCC
Found at i:34165625 original size:15 final size:14
Alignment explanation
Indices: 34165568--34165628 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 14
34165558 TCGACCTCCC
34165568 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
*
34165582 TTTCTTCTTTTTC-
1 TTTTTTCTTTTTCT
* *
34165595 -CTTTTCTTTGTCT
1 TTTTTTCTTTTTCT
34165608 TTTTTTCTTTTTTCT
1 TTTTTTC-TTTTTCT
34165623 TTTTTT
1 TTTTTT
34165629 AATTTTTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 9 0.24
14 17 0.45
15 12 0.32
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTTTTCTTTTTCT
Found at i:34165628 original size:8 final size:8
Alignment explanation
Indices: 34165575--34165646 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 8
34165565 CCCTTTTTTC
34165575 TTTTTCTT
1 TTTTTCTT
*
34165583 TTCTTCTT
1 TTTTTCTT
34165591 TTTCCTT-TT
1 TTT--TTCTT
*
34165600 CTTTGTCTT
1 -TTTTTCTT
34165609 TTTTTC-T
1 TTTTTCTT
34165616 TTTTTCTT
1 TTTTTCTT
*
34165624 TTTTTAATT
1 TTTTT-CTT
34165633 TTTTATCTT
1 TTTT-TCTT
34165642 TTTTT
1 TTTTT
34165647 TTGAAATTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
7 7 0.14
8 22 0.43
9 16 0.31
10 6 0.12
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:34165636 original size:26 final size:25
Alignment explanation
Indices: 34165570--34165645 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
34165560 GACCTCCCTT
* * *
34165570 TTTTCTTTTTCTTTTCTTCTTTTTCC
1 TTTTC-TTTACTTTTTTTCTTTTTTC
*
34165596 TTTTCTTTGTCTTTTTTTCTTTTTTC
1 TTTTCTTT-ACTTTTTTTCTTTTTTC
*
34165622 TTTT-TTTAATTTTTTATCTTTTTT
1 TTTTCTTTACTTTTTT-TCTTTTTT
34165646 TTTGAAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
24 6 0.14
25 14 0.32
26 24 0.55
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.80
Consensus pattern (25 bp):
TTTTCTTTACTTTTTTTCTTTTTTC
Found at i:34165642 original size:33 final size:33
Alignment explanation
Indices: 34165575--34165646 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
34165565 CCCTTTTTTC
*
34165575 TTTTTCTTTTCTTCTTTTTCCTTTTCTTTGTCTT
1 TTTTTCTTTTCTTCTTTTT-CTTTTCTTTATCTT
*
34165609 TTTTTCTTTT-TTCTTTTT-TTAATTTTTTATCTT
1 TTTTTCTTTTCTTCTTTTTCTT--TTCTTTATCTT
34165642 TTTTT
1 TTTTT
34165647 TTGAAATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 2 0.06
33 22 0.65
34 10 0.29
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (33 bp):
TTTTTCTTTTCTTCTTTTTCTTTTCTTTATCTT
Found at i:34170727 original size:63 final size:61
Alignment explanation
Indices: 34170626--34170796 Score: 206
Period size: 67 Copynumber: 2.7 Consensus size: 61
34170616 TTTTGGTTTG
* *
34170626 TTATTTATTTATTTATTT-ATTTATAATAATAAATAAATAATAAAACAAAATTAATATTATT
1 TTATTTATTTATTTATTTCA-TAAAAATAATAAATAAATAATAAAACAAAATTAATATTATT
*
34170687 TTACATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAATAAAATTAATATTA
1 TT--ATTTATTTATTTAT-TTCAT-AAA-AAT-AATAAATAAATAATAAAACAAAATTAATATTA
34170752 TT
60 TT
34170754 TTA--TATTTATTTATGTTCATAAAAATAAT-AATAAATAAATAAA
1 TTATTTATTTATTTAT-TTCATAAAAATAATAAATAAAT-AATAAA
34170797 TAAATAAAAA
Statistics
Matches: 98, Mismatches: 4, Indels: 17
0.82 0.03 0.14
Matches are distributed among these distances:
59 7 0.07
60 9 0.09
61 5 0.05
62 3 0.03
63 30 0.31
64 3 0.03
65 3 0.03
66 3 0.03
67 35 0.36
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (61 bp):
TTATTTATTTATTTATTTCATAAAAATAATAAATAAATAATAAAACAAAATTAATATTATT
Found at i:34170734 original size:67 final size:63
Alignment explanation
Indices: 34170626--34170800 Score: 232
Period size: 63 Copynumber: 2.7 Consensus size: 63
34170616 TTTTGGTTTG
**
34170626 TTATTTATTTATTTATTT-AT-TTATAATAATAAATAAATAATAAAACAAAATTAATATTATT
1 TTATTTATTTATTTATTTCATAAAATAATAATAAATAAATAATAAAACAAAATTAATATTATT
*
34170687 TTACATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAATAAAATTAATATTA
1 TT--ATTTATTTATTTAT-TTCATAAAATAAT-AATAAATAAATAATAAAACAAAATTAATATTA
34170752 TT
62 TT
34170754 TTA--TATTTATTTATGTTCATAAAAATAATAATAAATAAATAAATAAA
1 TTATTTATTTATTTAT-TTCAT-AAAATAATAATAAATAAAT-AATAAA
34170801 TAAAAATAAT
Statistics
Matches: 102, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
61 2 0.02
63 41 0.40
64 16 0.16
65 3 0.03
66 5 0.05
67 35 0.34
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (63 bp):
TTATTTATTTATTTATTTCATAAAATAATAATAAATAAATAATAAAACAAAATTAATATTATT
Found at i:34170802 original size:63 final size:64
Alignment explanation
Indices: 34170648--34170811 Score: 235
Period size: 63 Copynumber: 2.5 Consensus size: 64
34170638 TTATTTATTT
*
34170648 ATAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCATAA
1 ATAATAATAAATAAATAATAAAATAAAATTAATATTATTTTA-A-TTATTTATTTATATTCATAA
34170713 A
64 A
*
34170714 ATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTT-A-TATTTATTTATGTTCATAAA
1 ATAAT-AATAAATAAATAATAAAATAAAATTAATATTATTTTAATTATTTATTTATATTCAT-AA
34170777 A
64 A
*
34170778 ATAATAATAAATAAATAA-ATAAATAAAAATAATA
1 ATAATAATAAATAAATAATA-AAATAAAATTAATA
34170812 AGAAAAATGA
Statistics
Matches: 92, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
62 1 0.01
63 42 0.46
64 8 0.09
65 1 0.01
66 5 0.05
67 35 0.38
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (64 bp):
ATAATAATAAATAAATAATAAAATAAAATTAATATTATTTTAATTATTTATTTATATTCATAAA
Found at i:34170819 original size:22 final size:23
Alignment explanation
Indices: 34170776--34170824 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
34170766 ATGTTCATAA
* *
34170776 AAATAATAATAAATAAATAAAT-
1 AAATAAAAATAAATAAAAAAATG
34170798 AAATAAAAAT-AATAAGAAAAATG
1 AAATAAAAATAAATAA-AAAAATG
34170821 AAAT
1 AAAT
34170825 TGGGTTTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 14 0.61
23 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (23 bp):
AAATAAAAATAAATAAAAAAATG
Found at i:34172055 original size:1 final size:1
Alignment explanation
Indices: 34172049--34172073 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
34172039 GTGTGTGTGT
34172049 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
34172074 CGGGTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:34172472 original size:16 final size:16
Alignment explanation
Indices: 34172421--34172474 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
34172411 ACAACCATAT
*
34172421 AACAATAACAAAATAAC
1 AACAATAAC-AAACAAC
*
34172438 AAC-ATAAC-AACAATA
1 AACAATAACAAACAA-C
34172453 AACAATAACAAACAAC
1 AACAATAACAAACAAC
34172469 AACAAT
1 AACAAT
34172475 TTTGTCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.13
15 3 0.10
16 16 0.52
17 8 0.26
ACGTcount: A:0.69, C:0.20, G:0.00, T:0.11
Consensus pattern (16 bp):
AACAATAACAAACAAC
Found at i:34174988 original size:58 final size:58
Alignment explanation
Indices: 34174877--34174988 Score: 183
Period size: 58 Copynumber: 1.9 Consensus size: 58
34174867 ACCTATCAAC
*
34174877 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTTAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTCAAAAACACTTAT
34174935 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTATC-TTCCT-AAATAACAC
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATT-TCATTCCTCAAA-AACAC
34174989 CCATAAACAA
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
57 3 0.06
58 46 0.90
59 2 0.04
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.31
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTCAAAAACACTTAT
Done.