Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 94 of 185
Found at i:29450739 original size:26 final size:27
Alignment explanation
Indices: 29450701--29450757 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
29450691 CTTAGTTTTA
*
29450701 TTTAATTTAGGCTATTCTTTA-TATAAT
1 TTTAATTTAGGCTATTC-ATACTATAAT
*
29450728 TTTAATTT-GGCTTTTCATACTATAAT
1 TTTAATTTAGGCTATTCATACTATAAT
29450754 TTTA
1 TTTA
29450758 GATTATTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 17 0.63
27 8 0.30
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.56
Consensus pattern (27 bp):
TTTAATTTAGGCTATTCATACTATAAT
Found at i:29461626 original size:19 final size:20
Alignment explanation
Indices: 29461602--29461649 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
29461592 TTTTAATAAT
29461602 AATAAATAGAAAAGAAAT-A
1 AATAAATAGAAAAGAAATCA
**
29461621 AATAAATA-CCAAGAAATCA
1 AATAAATAGAAAAGAAATCA
29461640 AAT-AATAGAA
1 AATAAATAGAA
29461650 GCTGTCAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.69, C:0.06, G:0.08, T:0.17
Consensus pattern (20 bp):
AATAAATAGAAAAGAAATCA
Found at i:29474208 original size:72 final size:72
Alignment explanation
Indices: 29474084--29474227 Score: 207
Period size: 72 Copynumber: 2.0 Consensus size: 72
29474074 GCAGTCTAAA
* * *
29474084 GGAAAGCCCTAGCGGCTATCATATGAATGGAACACCTTTGTGGCAGACCCTGAAGAAAGAAATGG
1 GGAAAGCCCTAGCAGCTATCATATGAAGGGAACACCTTTGTGGCAAACCCTGAAGAAAGAAATGG
29474149 TGAGTAT
66 TGAGTAT
* * * ** *
29474156 GGAAAGCCCTGGCAGCTATCATCTGACGGGAATGCCTTTGTGGCAAATCCTGAAGAAAGAAATGG
1 GGAAAGCCCTAGCAGCTATCATATGAAGGGAACACCTTTGTGGCAAACCCTGAAGAAAGAAATGG
29474221 TGAGTAT
66 TGAGTAT
29474228 AGCAAACCCT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (72 bp):
GGAAAGCCCTAGCAGCTATCATATGAAGGGAACACCTTTGTGGCAAACCCTGAAGAAAGAAATGG
TGAGTAT
Found at i:29485103 original size:40 final size:40
Alignment explanation
Indices: 29485059--29485320 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
29485049 GCTCCTCGTT
* *
29485059 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
29485099 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
29485139 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29485178 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29485217 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
29485256 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
29485297 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29485321 CATCATTCAA
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 126 0.62
40 64 0.32
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:29502198 original size:40 final size:40
Alignment explanation
Indices: 29502154--29502415 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
29502144 GCTCCTCGTT
* *
29502154 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
29502194 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
29502234 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29502273 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29502312 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
29502351 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
29502392 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29502416 CATCATTCAA
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 126 0.62
40 64 0.32
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:29505399 original size:20 final size:23
Alignment explanation
Indices: 29505368--29505412 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
29505358 TTGTTTGTAC
29505368 TTAAGTACATTTT-GTT-GCATT
1 TTAAGTACATTTTAGTTAGCATT
29505389 TTAAG-ACATTTTAGTTAGCATT
1 TTAAGTACATTTTAGTTAGCATT
29505411 TT
1 TT
29505413 TAATATTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 7 0.32
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (23 bp):
TTAAGTACATTTTAGTTAGCATT
Found at i:29520514 original size:31 final size:30
Alignment explanation
Indices: 29520476--29520549 Score: 132
Period size: 31 Copynumber: 2.5 Consensus size: 30
29520466 TAGTCCAACA
29520476 CATATATTTGGAAAAATTACCATTTTGCCC
1 CATATATTTGGAAAAATTACCATTTTGCCC
29520506 CTATATATTTGGAAAAATTACCATTTTGCCC
1 C-ATATATTTGGAAAAATTACCATTTTGCCC
29520537 C-TATATTTGGAAA
1 CATATATTTGGAAA
29520550 TTTACACAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
29 12 0.28
30 1 0.02
31 30 0.70
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (30 bp):
CATATATTTGGAAAAATTACCATTTTGCCC
Found at i:29531468 original size:30 final size:30
Alignment explanation
Indices: 29531434--29531494 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
29531424 CTAATGATTT
29531434 AGTACTGAATTTTGACGAATCTCAATTTCC
1 AGTACTGAATTTTGACGAATCTCAATTTCC
*
29531464 AGTACTGAATTTTGACGAATCTCGATTTCC
1 AGTACTGAATTTTGACGAATCTCAATTTCC
29531494 A
1 A
29531495 ACTAAGTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (30 bp):
AGTACTGAATTTTGACGAATCTCAATTTCC
Found at i:29532679 original size:25 final size:25
Alignment explanation
Indices: 29532651--29532730 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
29532641 AAAATTATTT
29532651 ACTTTACTTTTAACAGAAAAGTAAA
1 ACTTTACTTTTAACAGAAAAGTAAA
** * * **
29532676 ACTTT-CTCTCCAATAG-AAATTATTT
1 ACTTTACT-TTTAACAGAAAAGTA-AA
29532701 ACTTTACTTTTAACAGAAAAGTAAA
1 ACTTTACTTTTAACAGAAAAGTAAA
29532726 ACTTT
1 ACTTT
29532731 CTCTCCAATA
Statistics
Matches: 39, Mismatches: 12, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
24 7 0.18
25 25 0.64
26 7 0.18
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (25 bp):
ACTTTACTTTTAACAGAAAAGTAAA
Found at i:29532717 original size:50 final size:50
Alignment explanation
Indices: 29532642--29532744 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
29532632 GGACTCAAAA
29532642 AAATTATTTACTTTACTTTTAACAGAAAAGTAAAACTTTCTCTCCAATAG
1 AAATTATTTACTTTACTTTTAACAGAAAAGTAAAACTTTCTCTCCAATAG
29532692 AAATTATTTACTTTACTTTTAACAGAAAAGTAAAACTTTCTCTCCAATAG
1 AAATTATTTACTTTACTTTTAACAGAAAAGTAAAACTTTCTCTCCAATAG
29532742 AAA
1 AAA
29532745 CTGCTAGAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.37
Consensus pattern (50 bp):
AAATTATTTACTTTACTTTTAACAGAAAAGTAAAACTTTCTCTCCAATAG
Found at i:29532743 original size:25 final size:25
Alignment explanation
Indices: 29532665--29532744 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
29532655 TACTTTTAAC
29532665 AGAAAAGTAAAACTTTCTCTCCAAT
1 AGAAAAGTAAAACTTTCTCTCCAAT
* ** ** *
29532690 AG-AAATTATTTACTTTACT-TTTAAC
1 AGAAAAGTA-AAACTTT-CTCTCCAAT
29532715 AGAAAAGTAAAACTTTCTCTCCAAT
1 AGAAAAGTAAAACTTTCTCTCCAAT
29532740 AGAAA
1 AGAAA
29532745 CTGCTAGAAT
Statistics
Matches: 39, Mismatches: 12, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
24 7 0.18
25 25 0.64
26 7 0.18
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (25 bp):
AGAAAAGTAAAACTTTCTCTCCAAT
Found at i:29533171 original size:16 final size:16
Alignment explanation
Indices: 29533150--29533180 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29533140 AAACATCATA
*
29533150 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
29533166 AATTAAATAATTTTC
1 AATTAAATAATTTTC
29533181 TTAACCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:29534930 original size:261 final size:261
Alignment explanation
Indices: 29534462--29534988 Score: 1027
Period size: 261 Copynumber: 2.0 Consensus size: 261
29534452 CCAACCCATT
29534462 CCATAAATAGGGGAGAATCTATCAACAAATCAACTATTTCTTCAACCATACATCCCACAATTCCT
1 CCATAAATAGGGGAGAATCTATCAACAAATCAACTATTTCTTCAACCATACATCCCACAATTCCT
29534527 GGTCGACCATAGAAATGAGAAAATCAAGGGATTTTCATGCAATCTTCAAAAACCTCTCAAGCCCT
66 GGTCGACCATAGAAATGAGAAAATCAAGGGATTTTCATGCAATCTTCAAAAACCTCTCAAGCCCT
29534592 CCATCCACTATAAATACCACATTTCACTTCACTTTCCATCATACCTCAGCCATCATTCATCTCTC
131 CCATCCACTATAAATACCACATTTCACTTCACTTTCCATCATACCTCAGCCATCATTCATCTCTC
*
29534657 AGTTCACATTCTCTCATCTCCTTTCCTCTCCTTTTCACACAAAAAGCCATTCATTCTCCCCATTC
196 AGTTCACATTCTCTCATCTCCTTTCCTCTCCTTTTCACACAAAAAACCATTCATTCTCCCCATTC
29534722 C
261 C
29534723 CCATAAATAGGGGAGAATCTATCAACAAATCAACTATTTCTTCAACCATACATCCCACAATTCCT
1 CCATAAATAGGGGAGAATCTATCAACAAATCAACTATTTCTTCAACCATACATCCCACAATTCCT
29534788 GGTCGACCATAGAAATGAGAAAATCAAGGGATTTTCATGCAATCTTCAAAAACCTCTCAAGCCCT
66 GGTCGACCATAGAAATGAGAAAATCAAGGGATTTTCATGCAATCTTCAAAAACCTCTCAAGCCCT
29534853 CCATCCACTATAAATACCACATTTCACTTCACTTTCCATCATACCTCAGCCATCATTCATCTCTC
131 CCATCCACTATAAATACCACATTTCACTTCACTTTCCATCATACCTCAGCCATCATTCATCTCTC
* *
29534918 AGTTCGCATTCTCTCATCTCCTTTCCTCTCTTTTTCACACAAAAAACCATTCATTCTCCCCATTC
196 AGTTCACATTCTCTCATCTCCTTTCCTCTCCTTTTCACACAAAAAACCATTCATTCTCCCCATTC
29534983 C
261 C
29534984 CCATA
1 CCATA
29534989 GCTAGCAATA
Statistics
Matches: 263, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
261 263 1.00
ACGTcount: A:0.31, C:0.32, G:0.07, T:0.30
Consensus pattern (261 bp):
CCATAAATAGGGGAGAATCTATCAACAAATCAACTATTTCTTCAACCATACATCCCACAATTCCT
GGTCGACCATAGAAATGAGAAAATCAAGGGATTTTCATGCAATCTTCAAAAACCTCTCAAGCCCT
CCATCCACTATAAATACCACATTTCACTTCACTTTCCATCATACCTCAGCCATCATTCATCTCTC
AGTTCACATTCTCTCATCTCCTTTCCTCTCCTTTTCACACAAAAAACCATTCATTCTCCCCATTC
C
Found at i:29545821 original size:24 final size:24
Alignment explanation
Indices: 29545794--29545840 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
29545784 AGTCCTTACA
29545794 AACCCTAAACAAAAACCCTTAAAG
1 AACCCTAAACAAAAACCCTTAAAG
* *
29545818 AACCCTAAACCATAACCCTTAAA
1 AACCCTAAACAAAAACCCTTAAA
29545841 AGCCTAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.32, G:0.02, T:0.15
Consensus pattern (24 bp):
AACCCTAAACAAAAACCCTTAAAG
Found at i:29548525 original size:3 final size:3
Alignment explanation
Indices: 29548517--29548553 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
29548507 TGCCTATGGC
29548517 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29548554 AGGAAAGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29551777 original size:29 final size:29
Alignment explanation
Indices: 29551714--29551781 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
29551704 TAATCAACCA
29551714 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
29551743 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
29551772 CGCACACTTA
1 CGCACACTTA
29551782 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:29573773 original size:24 final size:27
Alignment explanation
Indices: 29573734--29573787 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
29573724 TTCTCCTAAA
29573734 TTTCAAATTTATTTG-ATTATTTAAT-T
1 TTTCAAATTTATTTGAATTA-TTAATAT
29573760 TTTC-AATTTA-TTGAATTATTAATAT
1 TTTCAAATTTATTTGAATTATTAATAT
29573785 TTT
1 TTT
29573788 ATGCAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.31
25 14 0.54
26 4 0.15
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTCAAATTTATTTGAATTATTAATAT
Found at i:29576082 original size:21 final size:22
Alignment explanation
Indices: 29576038--29576084 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
29576028 AAATTTAGTA
*
29576038 TATTTTAAATTTATTACAATAT
1 TATTTTAAATTTATAACAATAT
29576060 TATTTT-AATATTATAAC-ATAT
1 TATTTTAAAT-TTATAACAATAT
29576081 TATT
1 TATT
29576085 GTTCTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAAATTTATAACAATAT
Found at i:29583661 original size:88 final size:88
Alignment explanation
Indices: 29583445--29584061 Score: 880
Period size: 88 Copynumber: 7.0 Consensus size: 88
29583435 AACAGATCAG
* * * *
29583445 TGAAGATAGCAGATCTTGCCTTCCTACATTGATAGCGAAGCAGATCGAAGACA-AAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAGTCTTGCCT
* * *
29583509 CCATTGGTTGCAGTGGAGCTA-GT
66 CCCTCGGTTGTAGTGGAGC-AGGT
* *
29583532 TGAAGATAGCAGATCTTGCCTTCCTACATCAACAGCGAAGCAGATCGAAGACACAAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAGTCTTGCCT
*
29583597 CTCTCGGTTGTAGTGGAGCAGGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* * *
29583620 TGAAGATAGCAGATCTTGCCTTCCTGCACCGATAGCAAAGCAGATCGAAGACACAAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAGTCTTGCCT
* * *
29583685 CCATCGGTTGCAGTGGAGCTGGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* * * *
29583708 TGAAGATAGCAGATCTTGCCTTCCTGCATCAACAGTGAAGTAGATCGAAGACACAAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAGTCTTGCCT
*
29583773 CCCTTGGTTGTAGTGGAGCAGGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* * *
29583796 TGAAGATAGCAAATCTTGCCTTCTTGCATCGACAGCGAAGCAGATTGAAGACACAAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAGTCTTGCCT
*
29583861 CCCTCGGTTGTAGTAGAGCAGGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* * * * *
29583884 TGAAGATAGTAGATCTTGCATTCCTGCATCAACAGCGAAGCAGATCGAAGATACAAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAGTCTTGCCT
29583949 CCCTCGGTTGTAGTGGAGCAGGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* * * * *
29583972 TGAAGATAACAGATCTTGCTTTCCTGCATCGACAGTGAAGTAGATCGAAGGCACAA-TCCTTGCC
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAGT-CTTGCC
29584036 TCCCTCGGTTGTAGTGGAGCAGGT
65 TCCCTCGGTTGTAGTGGAGCAGGT
29584060 TG
1 TG
29584062 GAAACTACAA
Statistics
Matches: 472, Mismatches: 55, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
87 51 0.11
88 421 0.89
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (88 bp):
TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAGTCTTGCCT
CCCTCGGTTGTAGTGGAGCAGGT
Found at i:29585495 original size:21 final size:22
Alignment explanation
Indices: 29585451--29585497 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
29585441 AAATTTAGTA
*
29585451 TATTTTAAATTTATTACAATAT
1 TATTTTAAATTTATAACAATAT
29585473 TATTTT-AATATTATAAC-ATAT
1 TATTTTAAAT-TTATAACAATAT
29585494 TATT
1 TATT
29585498 GTTCTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAAATTTATAACAATAT
Found at i:29590720 original size:14 final size:14
Alignment explanation
Indices: 29590692--29590725 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29590682 ACATGTTTCA
*
29590692 TAATT-ATTTTCTT
1 TAATTAATTTTATT
29590705 TAATTAATTTTATT
1 TAATTAATTTTATT
29590719 TAATTAA
1 TAATTAA
29590726 GAGATCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TAATTAATTTTATT
Found at i:29594662 original size:44 final size:44
Alignment explanation
Indices: 29594596--29594683 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
29594586 AAAGTTCAGG
*
29594596 TAAAAGCATAATAAACAGATTCAGGTGAGTTGTAAGGGTTAAGA
1 TAAAAGCATAATAAACAAATTCAGGTGAGTTGTAAGGGTTAAGA
29594640 TAAAAGCATAATAAACAAATTCAGGTGAGTTGTAAGGGTTAAGA
1 TAAAAGCATAATAAACAAATTCAGGTGAGTTGTAAGGGTTAAGA
29594684 ATATCTCAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.25
Consensus pattern (44 bp):
TAAAAGCATAATAAACAAATTCAGGTGAGTTGTAAGGGTTAAGA
Found at i:29595332 original size:101 final size:101
Alignment explanation
Indices: 29595210--29595412 Score: 379
Period size: 101 Copynumber: 2.0 Consensus size: 101
29595200 AAAATCACCA
*
29595210 AAAATAGTAGAAATGGAATTAGAGAGTGAATGAGATATAAAATTAAATCTTATCGAGTCTATTTT
1 AAAATAGTAGAAATGGAATTAGAGAGTGAATGACATATAAAATTAAATCTTATCGAGTCTATTTT
29595275 CACATGAAAGAAACGATGTAGGAAAATGAATTATAT
66 CACATGAAAGAAACGATGTAGGAAAATGAATTATAT
*
29595311 AAAATAGTAGAAATGGGATTAGAGAGTGAATGACATATAAAATTAAATCTTATCGAGTCTATTTT
1 AAAATAGTAGAAATGGAATTAGAGAGTGAATGACATATAAAATTAAATCTTATCGAGTCTATTTT
*
29595376 CACATGAAAGAAACGATGTAGGCAAATGAATTATAT
66 CACATGAAAGAAACGATGTAGGAAAATGAATTATAT
29595412 A
1 A
29595413 TTACGAGATA
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.29
Consensus pattern (101 bp):
AAAATAGTAGAAATGGAATTAGAGAGTGAATGACATATAAAATTAAATCTTATCGAGTCTATTTT
CACATGAAAGAAACGATGTAGGAAAATGAATTATAT
Found at i:29602631 original size:25 final size:25
Alignment explanation
Indices: 29602594--29602641 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
29602584 ATGTGACTCT
*
29602594 GTATGTTTTCTTTGTGGCATATTTA
1 GTATGTTTCCTTTGTGGCATATTTA
29602619 GTATGTTTCCTTTGTGGCATATT
1 GTATGTTTCCTTTGTGGCATATT
29602642 CTATTTAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (25 bp):
GTATGTTTCCTTTGTGGCATATTTA
Found at i:29606164 original size:28 final size:27
Alignment explanation
Indices: 29606101--29606169 Score: 120
Period size: 27 Copynumber: 2.5 Consensus size: 27
29606091 ATATTAAGTC
*
29606101 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
29606128 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
29606156 CGCACACTTAGTGC
1 CGCACACTTAGTGC
29606170 CAATCTCATG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:29608869 original size:14 final size:14
Alignment explanation
Indices: 29608850--29608879 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29608840 TTTCATCCAA
*
29608850 ATTCACATATTCAC
1 ATTCACATATGCAC
29608864 ATTCACATATGCAC
1 ATTCACATATGCAC
29608878 AT
1 AT
29608880 AATTCAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (14 bp):
ATTCACATATGCAC
Found at i:29619544 original size:46 final size:45
Alignment explanation
Indices: 29619477--29619693 Score: 227
Period size: 36 Copynumber: 5.2 Consensus size: 45
29619467 TTTGAGTACT
* *
29619477 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
29619523 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
29619559 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
29619605 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * *
29619641 TCCGATCAAGTGACAAAGTGATAAGTGATAGCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
29619686 TCTGATCA
1 TCTGATCA
29619694 GGGACAAATG
Statistics
Matches: 142, Mismatches: 10, Indels: 39
0.74 0.05 0.20
Matches are distributed among these distances:
36 57 0.40
37 2 0.01
38 1 0.01
39 1 0.01
40 6 0.04
41 2 0.01
42 4 0.03
43 3 0.02
45 14 0.10
46 52 0.37
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:29619614 original size:82 final size:82
Alignment explanation
Indices: 29619477--29619693 Score: 382
Period size: 82 Copynumber: 2.7 Consensus size: 82
29619467 TTTGAGTACT
*
29619477 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
29619542 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
29619559 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
29619624 GATAAGTGCTATACTTA
66 GATAAGTGCTACACTTA
* * *
29619641 TCCGATCAAGTGACAAAGTGATAAGTGATAGC-TTAGCTACACTTATCTGATCA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCA
29619694 GGGACAAATG
Statistics
Matches: 130, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
81 21 0.16
82 109 0.84
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:29623764 original size:43 final size:43
Alignment explanation
Indices: 29623607--29623765 Score: 148
Period size: 43 Copynumber: 3.7 Consensus size: 43
29623597 TATGATTTAT
29623607 CATGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATT-AGA-TTA
* * * * * *
29623651 CGTGTAACACCAAGTCTGGGACATCGGCATCG-TA-TACGATTT
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATTA-GATTA
* * *
29623693 CGTGTAAGACC-CTGTCTGGGATAG-TGGCATCGATATTTGATTA
1 CATGTAAGACCAC-GTCTGGGA-CGTTGGCATCGATATTAGATTA
*
29623736 CATGTAAGGCCACGTCTGGGACGTTGGCAT
1 CATGTAAGACCACGTCTGGGACGTTGGCAT
29623766 TGTAAGAGCT
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
42 29 0.32
43 33 0.36
44 29 0.32
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATCGATATTAGATTA
Found at i:29624741 original size:31 final size:31
Alignment explanation
Indices: 29624698--29624758 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
29624688 TATAGGCTAT
29624698 TTTTAATATACTGGTTTTAGAATTTGTGTAG
1 TTTTAATATACTGGTTTTAGAATTTGTGTAG
*
29624729 TTTTGATATACTGGTTTTAGAATTTGTGTA
1 TTTTAATATACTGGTTTTAGAATTTGTGTA
29624759 TATATATAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.20, T:0.52
Consensus pattern (31 bp):
TTTTAATATACTGGTTTTAGAATTTGTGTAG
Found at i:29626077 original size:21 final size:22
Alignment explanation
Indices: 29626036--29626081 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
29626026 TTTTACACTC
*
29626036 AAACTAATATAAATAAGGCATGA
1 AAACTAATATAAATAAAGCAT-A
29626059 AAACT-ATAT-AATAAAGCATA
1 AAACTAATATAAATAAAGCATA
29626079 AAA
1 AAA
29626082 TCACATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 9 0.41
22 4 0.18
23 5 0.23
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.22
Consensus pattern (22 bp):
AAACTAATATAAATAAAGCATA
Found at i:29626947 original size:12 final size:12
Alignment explanation
Indices: 29626930--29626965 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
29626920 CTCAATCCAC
*
29626930 CATTTCATATTT
1 CATTTCACATTT
29626942 CATTTCACATTT
1 CATTTCACATTT
29626954 CATTTC-CATTT
1 CATTTCACATTT
29626965 C
1 C
29626966 TCATAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (12 bp):
CATTTCACATTT
Found at i:29629639 original size:15 final size:16
Alignment explanation
Indices: 29629619--29629650 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
29629609 ACTCTAAAAG
29629619 TTAAAAAAAT-ATTTT
1 TTAAAAAAATCATTTT
29629634 TTAAAAAAATCATTTT
1 TTAAAAAAATCATTTT
29629650 T
1 T
29629651 AGCCCTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAAAAATCATTTT
Found at i:29632319 original size:15 final size:16
Alignment explanation
Indices: 29632299--29632328 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29632289 GGCATCGACC
29632299 TCATATAAA-TATAAA
1 TCATATAAACTATAAA
29632314 TCATATAAACTATAA
1 TCATATAAACTATAA
29632329 TACGCTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
TCATATAAACTATAAA
Found at i:29633768 original size:21 final size:20
Alignment explanation
Indices: 29633735--29633778 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
29633725 AAATTTTTAT
*
29633735 AAAATTCTAAAATTTCTAAAA
1 AAAAATCTAAAA-TTCTAAAA
*
29633756 AAAAATCTTAAATTCTAAAA
1 AAAAATCTAAAATTCTAAAA
29633776 AAA
1 AAA
29633779 TGAGCTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATCTAAAATTCTAAAA
Found at i:29640024 original size:86 final size:87
Alignment explanation
Indices: 29639885--29640464 Score: 569
Period size: 86 Copynumber: 6.7 Consensus size: 87
29639875 GAAAATAAAA
* * *
29639885 AAATTAAAATTAAATAAAATCTATTTC-AGGAATTTATTCCCACCGTTCAACAGATTTTATTCCA
1 AAATTAAAATTAAATAAAATCTGTTTCGA-G-ATTTATTCCCTCCGTTTAACAGATTTTATTCCA
29639949 TTTTTTATTTTGTTTCCAAACGAG
64 TTTTTTATTTTGTTTCCAAACGAG
* * * * *
29639973 -TACTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCTCCGCTCAACAGATTTTATT-CTTT
1 AAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCTCCGTTTAACAGATTTTATTCCATT
*
29640036 TTTATATTTTATTTCCAAACGAG
66 TTT-TATTTTGTTTCCAAACGAG
* * * *
29640059 -TATTAAAATTAAATAAAATATGTTTCGGGATTTATT-CCTGCCGTTCAACAGATTTTATTCCAT
1 AAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCT-CCGTTTAACAGATTTTATTCCAT
* *
29640122 TTTTGATTTTGTTGCCAAACGAG
65 TTTTTATTTTGTTTCCAAACGAG
* * *
29640145 AAATTAAAAATTAAATAAAATCTATTTCGAGATTTATTCCCACCGTTTAACAGATTTTATTACAT
1 AAATT-AAAATTAAATAAAATCTGTTTCGAGATTTATTCCCTCCGTTTAACAGATTTTATTCCAT
* *
29640210 TTTTTATTTTGTTGCCAAATGAG
65 TTTTTATTTTGTTTCCAAACGAG
* * * *
29640233 AAATTATAATTAAAATTGAATAATCTGTTTCGGGATTTATTCCAGT-CGTTTAACATATTTTATT
1 AAATTAAAATT-AAA-T-AA-AATCTGTTTCGAGATTTATTCC-CTCCGTTTAACAGATTTTATT
* * * **
29640297 CGA-TTTTAAATTTGTTTCCAAAATAG
61 CCATTTTTTATTTTGTTTCCAAACGAG
* * * *
29640323 -AATT-AAATTGAAT-AATTTTGTTTCGAGATTTA-TCCCTGCCGTTTAACAGATTTTATTCGA-
1 AAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCT-CCGTTTAACAGATTTTATTCCAT
**
29640383 TTTCGATTTTGTTTCCAAACGAG
65 TTTTTATTTTGTTTCCAAACGAG
* * * * * *
29640406 AAGACTT--AATCAAAT-AATTCTGTTTCGGGATTTATTCCCGCCGCTTAACAAATTTTATT
1 AA-A-TTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCTCCGTTTAACAGATTTTATT
29640465 TTCATTTTGT
Statistics
Matches: 418, Mismatches: 56, Indels: 39
0.81 0.11 0.08
Matches are distributed among these distances:
81 1 0.00
82 3 0.01
83 53 0.13
84 2 0.00
85 50 0.12
86 120 0.29
87 40 0.10
88 84 0.20
89 7 0.02
90 20 0.05
91 38 0.09
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (87 bp):
AAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCTCCGTTTAACAGATTTTATTCCATT
TTTTATTTTGTTTCCAAACGAG
Found at i:29640349 original size:174 final size:174
Alignment explanation
Indices: 29639885--29640464 Score: 598
Period size: 174 Copynumber: 3.4 Consensus size: 174
29639875 GAAAATAAAA
* * *
29639885 AAATTAAAATT-AAATAA-AATCTATTTCAGGAATTTATTCCCA-CCGTTCAACAGATTTTATTC
1 AAATTATAATTAAAATAATAATCTGTTTC-GGGATTTATT-CCAGCCGTTCAACAGATTTTATTC
* * * *
29639947 CATTTTTTATTTTGTTTCCAAACGAGTACTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCC
64 CATTTTTAATTTTGTTTCCAAACGAGAAATTAAATTAAATAAAATCTGTTTCGAGATTTATTCCC
* * * * *
29640012 TCCGCTCAACAGATTTTATTCTTTTTTATATTTTATTTCCAAACGAG
129 ACCGTTTAACAGATTTTATTCATTTTT-TATTTTGTTTCCAAACGAG
* * * *
29640059 -TATTAAAATT-AAATAA-AATATGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTCCA
1 AAATTATAATTAAAATAATAATCTGTTTCGGGATTTATTCCAGCCGTTCAACAGATTTTATTCCA
* * *
29640121 TTTTTGATTTTGTTGCCAAACGAGAAATTAAAAATTAAATAAAATCTATTTCGAGATTTATTCCC
66 TTTTTAATTTTGTTTCCAAACGAGAAATT--AAATTAAATAAAATCTGTTTCGAGATTTATTCCC
* *
29640186 ACCGTTTAACAGATTTTATTACATTTTTTATTTTGTTGCCAAATGAG
129 ACCGTTTAACAGATTTTATT-CATTTTTTATTTTGTTTCCAAACGAG
* * *
29640233 AAATTATAATTAAAATTGAATAATCTGTTTCGGGATTTATTCCAGTCGTTTAACATATTTTATTC
1 AAATTATAATTAAAA-T-AATAATCTGTTTCGGGATTTATTCCAGCCGTTCAACAGATTTTATTC
* * ** * * *
29640298 GA-TTTTAAATTTGTTTCCAAAATAG-AATTAAATTGAAT-AATTTTGTTTCGAGATTTA-TCCC
64 CATTTTTAATTTTGTTTCCAAACGAGAAATTAAATTAAATAAAATCTGTTTCGAGATTTATTCCC
* **
29640359 TGCCGTTTAACAGATTTTATTCGA-TTTCGATTTTGTTTCCAAACGAG
129 -ACCGTTTAACAGATTTTATTC-ATTTTTTATTTTGTTTCCAAACGAG
* * * *
29640406 AAGACT-TAA-TCAAATAAT--TCTGTTTCGGGATTTATTCCCGCCGCTT-AACAAATTTTATT
1 AA-ATTATAATTAAAATAATAATCTGTTTCGGGATTTATTCCAGCCG-TTCAACAGATTTTATT
29640465 TTCATTTTGT
Statistics
Matches: 348, Mismatches: 45, Indels: 32
0.82 0.11 0.08
Matches are distributed among these distances:
168 35 0.10
169 2 0.01
170 3 0.01
171 3 0.01
172 59 0.17
173 52 0.15
174 104 0.30
175 22 0.06
176 3 0.01
177 5 0.01
178 20 0.06
179 40 0.11
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (174 bp):
AAATTATAATTAAAATAATAATCTGTTTCGGGATTTATTCCAGCCGTTCAACAGATTTTATTCCA
TTTTTAATTTTGTTTCCAAACGAGAAATTAAATTAAATAAAATCTGTTTCGAGATTTATTCCCAC
CGTTTAACAGATTTTATTCATTTTTTATTTTGTTTCCAAACGAG
Found at i:29651465 original size:18 final size:18
Alignment explanation
Indices: 29651442--29651477 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29651432 CAACCATTAC
29651442 AACCCATTTGGATGCTCA
1 AACCCATTTGGATGCTCA
29651460 AACCCATTTGGATGCTCA
1 AACCCATTTGGATGCTCA
29651478 CAGTGAGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
AACCCATTTGGATGCTCA
Found at i:29652027 original size:60 final size:61
Alignment explanation
Indices: 29651892--29652048 Score: 160
Period size: 60 Copynumber: 2.6 Consensus size: 61
29651882 TCCCCCCCCC
* * * *
29651892 CTGAACTTGGCAACTT-TTTCCACTTTAGGGCCTGAAACTTTTTTTTGGTCCATGTTAAGCC
1 CTGAACTTGGCAA-TTGTTCCCACATTAGGGCCTGAAACTTTTTTTTGGTCCAAGTTAAGCA
* * * * * *
29651953 CTAAACTTGACAATTGTTCCCACATTGGGGCTTG-AACTTTTTTTTTGTCCAAGTTAATCA
1 CTGAACTTGGCAATTGTTCCCACATTAGGGCCTGAAACTTTTTTTTGGTCCAAGTTAAGCA
* *
29652013 CTGAGCTTGGCAATTGTTCACGA-ATT-GGGCCTGAAA
1 CTGAACTTGGCAATTGTTC-CCACATTAGGGCCTGAAA
29652049 TTTAGGGTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
59 6 0.08
60 45 0.58
61 27 0.35
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (61 bp):
CTGAACTTGGCAATTGTTCCCACATTAGGGCCTGAAACTTTTTTTTGGTCCAAGTTAAGCA
Found at i:29652151 original size:58 final size:60
Alignment explanation
Indices: 29652058--29652204 Score: 183
Period size: 58 Copynumber: 2.5 Consensus size: 60
29652048 ATTTAGGGTT
* *
29652058 TTCAAGGACTAATTTGGACAAAGAAAAAAGGTTCAAG-CTCCAAAGTGGGAACAACTGCCAAG
1 TTCAAGGACTAACTTGGA-ACA-AAAAAAGGTTCAAGCCT-CAAAGTGGGAACAACTGCCAAG
* * * *
29652120 TTC-AGGACTAACTTGG-ATAAAAAAAGGTTCAAGCCTCAATGTTGGAACAATTGCCAAG
1 TTCAAGGACTAACTTGGAACAAAAAAAGGTTCAAGCCTCAAAGTGGGAACAACTGCCAAG
*
29652178 TTCAAGGCCTAACTTGGAACAAAAAAA
1 TTCAAGGACTAACTTGGAACAAAAAAA
29652205 AACTTTAAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
58 36 0.48
59 16 0.21
60 8 0.11
61 12 0.16
62 3 0.04
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (60 bp):
TTCAAGGACTAACTTGGAACAAAAAAAGGTTCAAGCCTCAAAGTGGGAACAACTGCCAAG
Found at i:29657407 original size:30 final size:30
Alignment explanation
Indices: 29657373--29657432 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
29657363 GGCCCGTTTT
* * *
29657373 TTAAATAAATACCAAAAATTTATTTTAAAA
1 TTAAAAAAAAACCAAAAATGTATTTTAAAA
**
29657403 TTAAAAAAAAATTAAAAATGTATTTTAAAA
1 TTAAAAAAAAACCAAAAATGTATTTTAAAA
29657433 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (30 bp):
TTAAAAAAAAACCAAAAATGTATTTTAAAA
Found at i:29657438 original size:11 final size:11
Alignment explanation
Indices: 29657424--29657484 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
29657414 TTAAAAATGT
29657424 ATTTTAAAAAA
1 ATTTTAAAAAA
29657435 ATTTT---AAA
1 ATTTTAAAAAA
29657443 A--TTAAAAAA
1 ATTTTAAAAAA
29657452 ATTTTTAAAAAAA
1 A-TTTT-AAAAAA
**
29657465 ATTTTAAAAGT
1 ATTTTAAAAAA
29657476 ATTTTAAAA
1 ATTTTAAAA
29657485 TTAAAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
6 2 0.05
8 4 0.10
9 4 0.10
11 18 0.44
12 6 0.15
13 7 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:29657439 original size:41 final size:40
Alignment explanation
Indices: 29657394--29657501 Score: 130
Period size: 41 Copynumber: 2.7 Consensus size: 40
29657384 CCAAAAATTT
**
29657394 ATTTTAAAATTAAAAAAAAATTAAAAATGTATTTTAAAAAA
1 ATTTTAAAATTAAAAAAAAATTAAAAA-AAATTTTAAAAAA
** **
29657435 ATTTTAAAATTAAAAAAATTTTTAAAAAAAATTTTAAAAGT
1 ATTTTAAAATTAAAAAAA-AATTAAAAAAAATTTTAAAAAA
29657476 ATTTTAAAATT--AAAAAAATTAAAAAA
1 ATTTTAAAATTAAAAAAAAATTAAAAAA
29657502 TTAAAATATT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
38 8 0.14
39 5 0.09
41 38 0.66
42 7 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (40 bp):
ATTTTAAAATTAAAAAAAAATTAAAAAAAATTTTAAAAAA
Found at i:29657449 original size:17 final size:17
Alignment explanation
Indices: 29657427--29657507 Score: 63
Period size: 17 Copynumber: 4.4 Consensus size: 17
29657417 AAAATGTATT
29657427 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
29657444 TTAAAAAAATTTTTAAAAAAAA
1 TTAAAAAAA-TTTT----AAAA
**
29657466 TTTTAAAAGTATTTTAAAA
1 --TTAAAAAAATTTTAAAA
**
29657485 TTAAAAAAATTAAAAAA
1 TTAAAAAAATTTTAAAA
29657502 TTAAAA
1 TTAAAA
29657508 TATTTATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
17 28 0.55
18 4 0.08
19 4 0.08
22 4 0.08
23 4 0.08
24 7 0.14
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:29657459 original size:29 final size:31
Alignment explanation
Indices: 29657410--29657473 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
29657400 AAATTAAAAA
**
29657410 AAAATTAAAAATGTATTTT-AAAAAAATTTT
1 AAAATTAAAAAAATATTTTAAAAAAAATTTT
29657440 AAAATTAAAAAAAT-TTTTAAAAAAAATTTT
1 AAAATTAAAAAAATATTTTAAAAAAAATTTT
29657470 AAAA
1 AAAA
29657474 GTATTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (31 bp):
AAAATTAAAAAAATATTTTAAAAAAAATTTT
Found at i:29657464 original size:13 final size:12
Alignment explanation
Indices: 29657444--29657473 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29657434 AATTTTAAAA
*
29657444 TTAAAAAAATTT
1 TTAAAAAAAATT
29657456 TTAAAAAAAATT
1 TTAAAAAAAATT
29657468 TTAAAA
1 TTAAAA
29657474 GTATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAAAAAAAATT
Found at i:29657885 original size:9 final size:9
Alignment explanation
Indices: 29657871--29657901 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29657861 GTTAAACGAA
29657871 TCGAGTTAT
1 TCGAGTTAT
*
29657880 TCGAGTTAA
1 TCGAGTTAT
29657889 TCGAGTTAT
1 TCGAGTTAT
29657898 TCGA
1 TCGA
29657902 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:29657972 original size:9 final size:9
Alignment explanation
Indices: 29657955--29657991 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
29657945 TGAGTTTTCA
29657955 AATTCGAAT
1 AATTCGAAT
*
29657964 AACTCGAAT
1 AATTCGAAT
29657973 AATTCGAAT
1 AATTCGAAT
29657982 AATTCGAAT
1 AATTCGAAT
29657991 A
1 A
29657992 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:29673331 original size:22 final size:21
Alignment explanation
Indices: 29673306--29673349 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
29673296 TGATAAACTT
29673306 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
29673328 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
29673349 T
1 T
29673350 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:29679405 original size:18 final size:19
Alignment explanation
Indices: 29679369--29679406 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
29679359 TTCTATAAAT
29679369 ATTTTCTACAACAATTAAAAG
1 ATTTTCTACAAC-A-TAAAAG
29679390 ATTTTCTACAAC-TAAAA
1 ATTTTCTACAACATAAAA
29679407 ATATTCTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (19 bp):
ATTTTCTACAACATAAAAG
Found at i:29695235 original size:20 final size:20
Alignment explanation
Indices: 29695210--29695249 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29695200 CGTAAAATGA
*
29695210 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
29695230 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
29695250 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:29695239 original size:34 final size:35
Alignment explanation
Indices: 29695195--29695261 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
29695185 CAGTAAAATA
*
29695195 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
29695229 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
29695262 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:29695265 original size:14 final size:15
Alignment explanation
Indices: 29695189--29695265 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
29695179 GATTGCCAGT
* *
29695189 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
29695203 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
29695217 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
29695237 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
29695252 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
29695266 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:29698721 original size:18 final size:17
Alignment explanation
Indices: 29698686--29698718 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29698676 TATTTTTGTA
29698686 AAACAATATTTATAAAC
1 AAACAATATTTATAAAC
29698703 AAACATATATTT-TAAA
1 AAACA-ATATTTATAAA
29698719 ACATTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
AAACAATATTTATAAAC
Found at i:29700433 original size:17 final size:16
Alignment explanation
Indices: 29700397--29700443 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
29700387 AATTTAGAAC
*
29700397 AATTTTTGAATTAGTG
1 AATTTTTGATTTAGTG
*
29700413 AATTTTGTGATTTATTG
1 AATTTT-TGATTTAGTG
29700430 AATTTTATGATTTA
1 AATTTT-TGATTTA
29700444 AAAAGAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (16 bp):
AATTTTTGATTTAGTG
Found at i:29701372 original size:46 final size:46
Alignment explanation
Indices: 29701302--29701486 Score: 298
Period size: 46 Copynumber: 4.0 Consensus size: 46
29701292 CATGGCAAAG
*
29701302 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
29701348 TGTGAAAAGCAGGTATGGTGTTTCAGTGAAGAAAATCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
29701394 TGTGACAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
29701440 TGTGAAAAGTAGGTATGGTATTTCTGTGAAGAAAACCATACCGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
29701486 T
1 T
29701487 ATAGCAATGT
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 127 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:29707809 original size:20 final size:20
Alignment explanation
Indices: 29707784--29707823 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29707774 ATCATATAAA
29707784 TTATAACTCATAATTATTTT
1 TTATAACTCATAATTATTTT
* **
29707804 TTATAATTTTTAATTATTTT
1 TTATAACTCATAATTATTTT
29707824 CCAAAATCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATAACTCATAATTATTTT
Found at i:29708318 original size:50 final size:50
Alignment explanation
Indices: 29708257--29708498 Score: 225
Period size: 50 Copynumber: 4.8 Consensus size: 50
29708247 TATCATTCGA
* * *
29708257 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTTCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACTTTCCGG
* * * *
29708307 TTCACGTAGTAGCCTGCACATGGTACTACACACGTGACCATTAA-TATCCGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA--AACTTTCCGG
* * * * * * *
29708358 TACATGTAGTATCCTGCACATAGTATTACACACGTGATCGAAGCTATCTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCAAACTTTCCGG
* * * * * *** * *
29708409 TACGCATAGTAGCCTGCATATAGTACTACACATGCGACCTTTCATTCCAG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACTTTCCGG
*
29708459 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
29708499 TCACTTTCAC
Statistics
Matches: 149, Mismatches: 39, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
50 75 0.50
51 70 0.47
52 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACTTTCCGG
Found at i:29708395 original size:101 final size:101
Alignment explanation
Indices: 29708254--29708495 Score: 292
Period size: 101 Copynumber: 2.4 Consensus size: 101
29708244 TATTATCATT
* * * *
29708254 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAACT-TTTCGGTTCACGTAGT
1 CGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCT-GGTACACATAGT
* *
29708317 AGCCTGCACATGGTACTACACACGTGACCATTAATATC
65 AGCCTGCACATAGTACTACACACGCGACCATTAAT-TC
* * * * * *
29708355 CGATACATGTAGTATCCTGCACATAGTATTACACACGTGATCGAAGCTATCTGGTACGCATAGTA
1 CGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCTGGTACACATAGTA
* * * *
29708420 GCCTGCATATAGTACTACACATGCGACCTTTCATTC
66 GCCTGCACATAGTACTACACACGCGACCATTAATTC
29708456 C-AGTACACGTAGTAGCCTACACATAGTACTACACACGTGA
1 CGA-TACACGTAGTAGCCTACACATAGTACTACACACGTGA
29708496 CCATCACTTT
Statistics
Matches: 119, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
100 1 0.01
101 74 0.62
102 42 0.35
103 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (101 bp):
CGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCTGGTACACATAGTA
GCCTGCACATAGTACTACACACGCGACCATTAATTC
Found at i:29717680 original size:23 final size:23
Alignment explanation
Indices: 29717654--29717697 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
29717644 GAAGGTGATG
29717654 GAGACAAAGATGAAGATGAAGCC
1 GAGACAAAGATGAAGATGAAGCC
* *
29717677 GAGATAGAGATGAAGATGAAG
1 GAGACAAAGATGAAGATGAAG
29717698 ACTACTGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.07, G:0.34, T:0.11
Consensus pattern (23 bp):
GAGACAAAGATGAAGATGAAGCC
Found at i:29735278 original size:43 final size:43
Alignment explanation
Indices: 29735211--29735348 Score: 138
Period size: 43 Copynumber: 3.3 Consensus size: 43
29735201 TGTGATTTTG
* *
29735211 TGTAAGACCATGTATGAGACATTGGCATCGATATGAGATTACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTACA
* * * *
29735254 TGTAAGACCATGTCTGGGATATTGGAACCG-TAT-ATGATT-CG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGA-GATTACA
* ** * **
29735295 TGTAAGACCCTGTCTGGGACAGAGGCATCGATATGTGACAACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTACA
29735338 TGTAAGACCAT
1 TGTAAGACCAT
29735349 ATCTAGGATA
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
41 26 0.35
42 12 0.16
43 36 0.49
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTACA
Found at i:29743783 original size:30 final size:30
Alignment explanation
Indices: 29743649--29744235 Score: 262
Period size: 31 Copynumber: 19.1 Consensus size: 30
29743639 CAACAATATA
* *
29743649 TATATTCATATACGAATCAAATTCGGA-AACT-
1 TATATTCATATACAAATC-AATT-TGACAA-TG
* * *
29743680 TATCTTCATATACAAATCAATTTCAATAATG
1 TATATTCATATACAAATCAATTT-GACAATG
** * *
29743711 TATAACCATATACAAATAAATTTCAGCAATG
1 TATATTCATATACAAATCAATTTGA-CAATG
* **
29743742 TATAATCATATATGAATCAATTTGACAACT-
1 TATATTCATATACAAATCAATTTGACAA-TG
* *
29743772 TATCTTCATATACAAATCAATTTCGATAATG
1 TATATTCATATACAAATCAATTT-GACAATG
** * *
29743803 TATAACCATATACAAATAAATTTCAGCAATG
1 TATATTCATATACAAATCAATTTGA-CAATG
** *
29743834 TATAATT-ATATATGAATCAATTTGGCAACT-
1 TAT-ATTCATATACAAATCAATTTGACAA-TG
* * * *
29743864 TATTTTCATATACAAATCAATTTCGATATTA
1 TATATTCATATACAAATCAATTT-GACAATG
** * *
29743895 TATAACCATATACAAATGAATTTCAACAATG
1 TATATTCATATACAAATCAATTT-GACAATG
* * * *
29743926 TTTAATT-ATATACGAATTAATTTGGCAACT-
1 TAT-ATTCATATACAAATCAATTTGACAA-TG
* * * *
29743956 TATCTTTATATACAAATCAATTTCGATAATA
1 TATATTCATATACAAATCAATTT-GACAATG
** * * *
29743987 TATAACCATATACAAATAAATTTCAGTAATG
1 TATATTCATATACAAATCAATTTGA-CAATG
* * * *
29744018 TATAATCATATACGAATCAATTCGGCAACT-
1 TATATTCATATACAAATCAATTTGACAA-TG
* * *
29744048 TATCTTCATATACATATCAATTTCGATAATG
1 TATATTCATATACAAATCAATTT-GACAATG
** * *
29744079 TATAACCATATACAAATAAATTTCAGCAATG
1 TATATTCATATACAAATCAATTTGA-CAATG
* *
29744110 TATAATT-ATATA-AGAATCAATTCGGCAACT-
1 TAT-ATTCATATACA-AATCAATTTGACAA-TG
* * *
29744140 TATCTTCATATACATATCAATTTCGATAATG
1 TATATTCATATACAAATCAATTT-GACAATG
** * *
29744171 TATAACCATATACAAATAAATTTCAGCAATG
1 TATATTCATATACAAATCAATTTGA-CAATG
* * * * *
29744202 TACAATT-ATATACGAATTAGTTTGGCAATG
1 TA-TATTCATATACAAATCAATTTGACAATG
29744232 TATA
1 TATA
29744236 AAACAATCAA
Statistics
Matches: 409, Mismatches: 115, Indels: 66
0.69 0.19 0.11
Matches are distributed among these distances:
29 7 0.02
30 123 0.30
31 275 0.67
32 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.36
Consensus pattern (30 bp):
TATATTCATATACAAATCAATTTGACAATG
Found at i:29743812 original size:92 final size:92
Alignment explanation
Indices: 29743629--29744229 Score: 907
Period size: 92 Copynumber: 6.5 Consensus size: 92
29743619 ATCCAATGCT
* * * * *
29743629 CAAATCAA-TTCAACAATATATATATTCATATACGAATCAAATTCGGAAACTTATCTTCATATAC
1 CAAATAAATTTCAGCAATGTATA-ATT-ATATACGAATC-AATTTGGCAACTTATCTTCATATAC
*
29743693 AAATCAATTTCAATAATGTATAACCATATA
63 AAATCAATTTCGATAATGTATAACCATATA
* * *
29743723 CAAATAAATTTCAGCAATGTATAATCATATATGAATCAATTTGACAACTTATCTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTTGGCAACTTATCTTCATATACAAA
29743788 TCAATTTCGATAATGTATAACCATATA
66 TCAATTTCGATAATGTATAACCATATA
* *
29743815 CAAATAAATTTCAGCAATGTATAATTATATATGAATCAATTTGGCAACTTATTTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTTGGCAACTTATCTTCATATACAAA
* *
29743880 TCAATTTCGATATTATATAACCATATA
66 TCAATTTCGATAATGTATAACCATATA
* * * * *
29743907 CAAATGAATTTCAACAATGTTTAATTATATACGAATTAATTTGGCAACTTATCTTTATATACAAA
1 CAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTTGGCAACTTATCTTCATATACAAA
*
29743972 TCAATTTCGATAATATATAACCATATA
66 TCAATTTCGATAATGTATAACCATATA
* * * *
29743999 CAAATAAATTTCAGTAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACATA
1 CAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTTGGCAACTTATCTTCATATACAAA
29744064 TCAATTTCGATAATGTATAACCATATA
66 TCAATTTCGATAATGTATAACCATATA
* * *
29744091 CAAATAAATTTCAGCAATGTATAATTATATAAGAATCAATTCGGCAACTTATCTTCATATACATA
1 CAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTTGGCAACTTATCTTCATATACAAA
29744156 TCAATTTCGATAATGTATAACCATATA
66 TCAATTTCGATAATGTATAACCATATA
* * *
29744183 CAAATAAATTTCAGCAATGTACAATTATATACGAATTAGTTTGGCAA
1 CAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTTGGCAA
29744230 TGTATAAAAC
Statistics
Matches: 466, Mismatches: 40, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
92 435 0.93
93 10 0.02
94 9 0.02
95 12 0.03
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (92 bp):
CAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTTGGCAACTTATCTTCATATACAAA
TCAATTTCGATAATGTATAACCATATA
Found at i:29753503 original size:18 final size:17
Alignment explanation
Indices: 29753459--29753503 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 17
29753449 TATTTCATGT
29753459 TAATTAATATGTTAAAAA
1 TAATTAATAT-TTAAAAA
29753477 T-A-TAATATTTAAAAA
1 TAATTAATATTTAAAAA
29753492 TAATTAAATATT
1 TAATT-AATATT
29753504 AAATACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.33
16 7 0.29
17 2 0.08
18 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TAATTAATATTTAAAAA
Found at i:29754792 original size:194 final size:194
Alignment explanation
Indices: 29754463--29754852 Score: 633
Period size: 194 Copynumber: 2.0 Consensus size: 194
29754453 ATTTGATACT
*
29754463 AATATTTTTACCAAGTAACCAATTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTATGGT
1 AATATTTTTACCAAGTAACCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTATGGT
*
29754528 CCCAAGTAAGCATCTATAATTTTTTTACTAGATTAGACATCAAAGACTCGTTGGACCACATGATG
66 CCCAAGTAAGCATCCATAATTTTTTTACTAGATTAGACATCAAAGACTCGTTGGACCACATGATG
* * *
29754593 CCATTTGGTTTAGGTACCAAATTGAACATTGAAATCAAACTCAGGTAGCAAATTAGGATGAATG
131 CCATTTGGTTTAGGTACCAAAGTGAACATTGAAACCAAACTCAGGTAGCAAATTAGGACGAATG
* *
29754657 AATATTTTT-CTCAAGTACCCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTTTGG
1 AATATTTTTAC-CAAGTAACCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTATGG
* *
29754721 TCCC-AGTTAAGTATCCAT-ATTCTTTTTACTAGATTAGACATCAAATACTCGTTGGACCACATG
65 TCCCAAG-TAAGCATCCATAATT-TTTTTACTAGATTAGACATCAAAGACTCGTTGGACCACATG
* *
29754784 ATGCCATTTGGTTTAGGTACCAAAGTGAGCATTGAAGCCAAACTCAGGTAGCAAATTAGGACGAA
128 ATGCCATTTGGTTTAGGTACCAAAGTGAACATTGAAACCAAACTCAGGTAGCAAATTAGGACGAA
29754849 TG
193 TG
29754851 AA
1 AA
29754853 AACTTAGGTA
Statistics
Matches: 182, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
193 6 0.03
194 176 0.97
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (194 bp):
AATATTTTTACCAAGTAACCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTATGGT
CCCAAGTAAGCATCCATAATTTTTTTACTAGATTAGACATCAAAGACTCGTTGGACCACATGATG
CCATTTGGTTTAGGTACCAAAGTGAACATTGAAACCAAACTCAGGTAGCAAATTAGGACGAATG
Found at i:29755154 original size:3 final size:3
Alignment explanation
Indices: 29755075--29755135 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
29755065 AATATTCTCT
29755075 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29755123 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
29755136 CATCATTAGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29755748 original size:39 final size:38
Alignment explanation
Indices: 29755686--29755762 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 38
29755676 ATAAATTAAT
* * *
29755686 TGTTATAATACATGATTTATCTCAGTTACATCCATATA
1 TGTTATAATACATAATATATCTCAATTACATCCATATA
* *
29755724 TGTTATATATTCATAATATATCTCAATTACATCGATATA
1 TGTTATA-ATACATAATATATCTCAATTACATCCATATA
29755763 AATATATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
38 7 0.21
39 26 0.79
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.43
Consensus pattern (38 bp):
TGTTATAATACATAATATATCTCAATTACATCCATATA
Found at i:29759663 original size:16 final size:16
Alignment explanation
Indices: 29759639--29759690 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
29759629 TGGTTCACTC
29759639 TAATGGAATAGAGTTG
1 TAATGGAATAGAGTTG
* *
29759655 TAATAGAATAAAGTTG
1 TAATGGAATAGAGTTG
*
29759671 TAATGGAATAGAGCTG
1 TAATGGAATAGAGTTG
29759687 TAAT
1 TAAT
29759691 CAGTAATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.31
Consensus pattern (16 bp):
TAATGGAATAGAGTTG
Found at i:29759986 original size:59 final size:61
Alignment explanation
Indices: 29759857--29759972 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
29759847 TTGTTATTAA
** * *
29759857 ATTTTAATAGGATTATTATTAAATATATAATTTAATAAAAATAAAAAAATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATATATAATTTAATAAAAATAAAAAAAAAATATAATCAT
29759918 ATTTTAATATAATTATTATTAAATA-A-AATTTAATAAAAATAAAAATAAAAATATA
1 ATTTTAATATAATTATTATTAAATATATAATTTAATAAAAATAAAAA-AAAAATATA
29759973 TAATTTAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 19 0.38
60 8 0.16
61 23 0.46
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.40
Consensus pattern (61 bp):
ATTTTAATATAATTATTATTAAATATATAATTTAATAAAAATAAAAAAAAAATATAATCAT
Found at i:29765456 original size:27 final size:27
Alignment explanation
Indices: 29765425--29765738 Score: 286
Period size: 27 Copynumber: 11.7 Consensus size: 27
29765415 ATTGGGCCTC
*
29765425 TAAAATTACTAAAATACCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
* * * *
29765452 TAAAATGACTAAAATACCCTTGTTGGG
1 TAAAATTACTGAAATACCCTCGATGGG
* * *
29765479 TACAATAACCGAAATACCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
*
29765506 TAAAATTA-TCGAAATACCC-CTGATAGG
1 TAAAATTACT-GAAATACCCTC-GATGGG
* *
29765533 TAAAATTATTGAAATACCCTCAATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
* *
29765560 TAAAATAACCGAAATACCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
**
29765587 TAAAATTACCAAAATACCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
* *
29765614 TAAAATTA-TAGAAATA-CCTTGATGGA
1 TAAAATTACT-GAAATACCCTCGATGGG
* *
29765640 TAAAATTA-TCAAAATA-CCTCCGAAGGG
1 TAAAATTACT-GAAATACCCT-CGATGGG
* *
29765667 TAAAATTACTGAAATACCC-CTAAAGGG
1 TAAAATTACTGAAATACCCTC-GATGGG
* *
29765694 TAAAATTA-TCGAAATACCCCCGAAGGG
1 TAAAATTACT-GAAATACCCTCGATGGG
29765721 TAAAATTA-TCGAAATACC
1 TAAAATTACT-GAAATACC
29765739 TTCAGGTTAA
Statistics
Matches: 243, Mismatches: 33, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
26 28 0.12
27 209 0.86
28 6 0.02
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (27 bp):
TAAAATTACTGAAATACCCTCGATGGG
Found at i:29765502 original size:54 final size:54
Alignment explanation
Indices: 29765436--29765738 Score: 328
Period size: 54 Copynumber: 5.6 Consensus size: 54
29765426 AAAATTACTA
* * * * * *
29765436 AAATACCCTCGATGGGTAAAATGACTAAAATACCCTTGTTGGGTACAATAACCG
1 AAATACCCTCGATGGGTAAAATTACTGAAATACCCTTGATGGGTAAAATTATCG
* * *
29765490 AAATACCCTCGATGGGTAAAATTA-TCGAAATACCCCTGATAGGTAAAATTATTG
1 AAATACCCTCGATGGGTAAAATTACT-GAAATACCCTTGATGGGTAAAATTATCG
* * * * * *
29765544 AAATACCCTCAATGGGTAAAATAACCGAAATACCCTCGATGGGTAAAATTACCA
1 AAATACCCTCGATGGGTAAAATTACTGAAATACCCTTGATGGGTAAAATTATCG
* *
29765598 AAATACCCTCGATGGGTAAAATTA-TAGAAATA-CCTTGATGGATAAAATTATCA
1 AAATACCCTCGATGGGTAAAATTACT-GAAATACCCTTGATGGGTAAAATTATCG
* * * *
29765651 AAATA-CCTCCGAAGGGTAAAATTACTGAAATACCCCTAAAGGGTAAAATTATCG
1 AAATACCCT-CGATGGGTAAAATTACTGAAATACCCTTGATGGGTAAAATTATCG
* *
29765705 AAATACCCCCGAAGGGTAAAATTA-TCGAAATACC
1 AAATACCCTCGATGGGTAAAATTACT-GAAATACC
29765739 TTCAGGTTAA
Statistics
Matches: 210, Mismatches: 31, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
52 3 0.01
53 45 0.21
54 160 0.76
55 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (54 bp):
AAATACCCTCGATGGGTAAAATTACTGAAATACCCTTGATGGGTAAAATTATCG
Found at i:29768156 original size:25 final size:24
Alignment explanation
Indices: 29768128--29768189 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
29768118 AATTTCATGT
**
29768128 AAAGCCTTTGTGGCAAATTTTCTGG
1 AAAGCCTTTGTGG-AAATCCTCTGG
* *
29768153 AAAGCATTTGTGGGAATCCTCTGG
1 AAAGCCTTTGTGGAAATCCTCTGG
29768177 AAAGCC-TTGTGGA
1 AAAGCCTTTGTGGA
29768190 GAGTCCTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 6 0.19
24 13 0.42
25 12 0.39
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (24 bp):
AAAGCCTTTGTGGAAATCCTCTGG
Found at i:29770842 original size:62 final size:58
Alignment explanation
Indices: 29770746--29770872 Score: 173
Period size: 62 Copynumber: 2.1 Consensus size: 58
29770736 CTCACTTTAA
* * *
29770746 TATTAAATTAGTATAATACTTATAAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATAGAATACTTATAAAGATAAATATTAAATTAAATTTAATATTAAATC
* *
29770804 TTATTAAATTAATAGAATATTTATTTACAAGATTAATATTAAATTAAATTTAATATTAAATC
1 -TATTAAATTAATAGAATACTTA--TA-AAGATAAATATTAAATTAAATTTAATATTAAATC
29770866 TATTAAA
1 TATTAAA
29770873 ATAAAATTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
59 19 0.32
61 9 0.15
62 32 0.53
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTATAAAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:29771602 original size:68 final size:66
Alignment explanation
Indices: 29771523--29771664 Score: 239
Period size: 68 Copynumber: 2.1 Consensus size: 66
29771513 TCAAGTTTGT
*
29771523 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAAATAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAAATAATAATTTGAT
29771588 AAA
64 AAA
*
29771591 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAAATAATAATTTGATAA
*
29771656 T
66 A
29771657 TTTACTAA
1 TTTACTAA
29771665 CAATTAGTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 26 0.37
67 1 0.01
68 44 0.62
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAAATAATAATTTGATAA
A
Found at i:29771678 original size:22 final size:23
Alignment explanation
Indices: 29771643--29771705 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
29771633 ATTAACAATT
*
29771643 AATAATTTGATAATTTTACT-AACA
1 AATAATTT--TAATTTTACTAAAAA
* * *
29771667 ATTAGTTTTAATTTTATTAAAAA
1 AATAATTTTAATTTTACTAAAAA
29771690 AATAATTTTAATTTTA
1 AATAATTTTAATTTTA
29771706 ATTTTAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 9 0.28
23 17 0.53
24 6 0.19
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
AATAATTTTAATTTTACTAAAAA
Found at i:29773513 original size:29 final size:29
Alignment explanation
Indices: 29773471--29773529 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
29773461 GTACTATTAT
*
29773471 CACAATACAATGTTATAGCTTTTTTCATA
1 CACAATACAATGTTATAACTTTTTTCATA
29773500 CACAATACAATGTTATAACTTTTTTCATA
1 CACAATACAATGTTATAACTTTTTTCATA
29773529 C
1 C
29773530 CAGGAATGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (29 bp):
CACAATACAATGTTATAACTTTTTTCATA
Found at i:29775058 original size:14 final size:14
Alignment explanation
Indices: 29775039--29775081 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
29775029 TTAAGAGAAT
29775039 TTTCTCTCTACAAC
1 TTTCTCTCTACAAC
* *
29775053 TTTCTCT-T-GAAT
1 TTTCTCTCTACAAC
29775065 TTTCTCTCTACAAC
1 TTTCTCTCTACAAC
29775079 TTT
1 TTT
29775082 AATAATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 12 0.52
ACGTcount: A:0.19, C:0.28, G:0.02, T:0.51
Consensus pattern (14 bp):
TTTCTCTCTACAAC
Found at i:29775649 original size:13 final size:15
Alignment explanation
Indices: 29775631--29775663 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
29775621 AATCTTAATT
29775631 TTAATT-AATTTTA-
1 TTAATTAAATTTTAC
29775644 TTAATTAAATTTTAC
1 TTAATTAAATTTTAC
29775659 TTAAT
1 TTAAT
29775664 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 7 0.39
15 5 0.28
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTAAATTTTAC
Found at i:29778099 original size:29 final size:28
Alignment explanation
Indices: 29778060--29778129 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 28
29778050 ATATAAAAGA
* *
29778060 AAAACCTTTGTGGAAAATCTCTGTATAG
1 AAAACCTTTGTGGAAAACCTCTGTAGAG
* *
29778088 AAAAGCCTTTGTGGCAAACCTCTTTAGAG
1 AAAA-CCTTTGTGGAAAACCTCTGTAGAG
29778117 AAAACCTTTGTGG
1 AAAACCTTTGTGG
29778130 TGACTTCTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 13 0.35
29 24 0.65
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (28 bp):
AAAACCTTTGTGGAAAACCTCTGTAGAG
Found at i:29778103 original size:55 final size:57
Alignment explanation
Indices: 29777994--29778103 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 57
29777984 GGCAAACCTC
* *
29777994 TATAAAAGGAAGAGCCTTTGTGAGAAATCTCTATAAAGGAAAAACCTTTGTGGCATA
1 TATAAAAGGAAAAACCTTTGTGAGAAATCTCTATAAAGGAAAAACCTTTGTGGCATA
* * *
29778051 TATAAAA-GAAAAACCTTTGTG-GAAAATCTCTGTATA-GAAAAGCCTTTGTGGCA
1 TATAAAAGGAAAAACCTTTGTGAG-AAATCTCTATAAAGGAAAAACCTTTGTGGCA
29778104 AACCTCTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 17 0.36
56 23 0.49
57 7 0.15
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (57 bp):
TATAAAAGGAAAAACCTTTGTGAGAAATCTCTATAAAGGAAAAACCTTTGTGGCATA
Found at i:29783772 original size:16 final size:16
Alignment explanation
Indices: 29783717--29783772 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
29783707 ATCTAACCAA
*
29783717 TATGTCATTGCGCATT
1 TATGTCATTACGCATT
* *
29783733 TATGTCATTACACAAT
1 TATGTCATTACGCATT
* * *
29783749 AATATCATTATGCATT
1 TATGTCATTACGCATT
29783765 TATGTCAT
1 TATGTCAT
29783773 CTAACCAATA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (16 bp):
TATGTCATTACGCATT
Found at i:29783789 original size:32 final size:32
Alignment explanation
Indices: 29783705--29783789 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
29783695 TCAACCCATT
*
29783705 TCATCTAACCAATATGTCATTGCGCATTTATG
1 TCATCTAACCAATATGTCATTACGCATTTATG
* *
29783737 TCAT-T-ACACAATAATATCATTATGCATTTATG
1 TCATCTAAC-CAAT-ATGTCATTACGCATTTATG
29783769 TCATCTAACCAATATGTCATT
1 TCATCTAACCAATATGTCATT
29783790 CAAAGACACC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 2 0.04
31 5 0.11
32 31 0.69
33 5 0.11
34 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (32 bp):
TCATCTAACCAATATGTCATTACGCATTTATG
Found at i:29784350 original size:40 final size:40
Alignment explanation
Indices: 29784296--29784527 Score: 233
Period size: 40 Copynumber: 5.8 Consensus size: 40
29784286 TATTCTTAGA
* *
29784296 GGTACCATAA-TAC-AATCAGGGGCACATATGTTCATTCAAA
1 GGTACCA-AAGTACAAAT-AGGGGCACATATGTGCATTCAAG
* ** *
29784336 GGTACCGAAGTACAAATAGGGGCATGTATGTGCATTCAGG
1 GGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAAG
* *
29784376 GGTACTAAAGTACAAATAGGGACACATATGTGCATTC-AG
1 GGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAAG
* * *
29784415 GGTATCAAAGTACAAATAGCGGCACGTATGTGCATTC-AG
1 GGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAAG
* * * * *
29784454 GAGTATCGAAGTACAAATACGGGCA-AGTATGTGCATTTAGG
1 G-GTACCAAAGTACAAATAGGGGCACA-TATGTGCATTCAAG
*
29784495 GGTACC-AAGTACAAATAGGGGCACGTATGTGCA
1 GGTACCAAAGTACAAATAGGGGCACATATGTGCA
29784528 CTCACACAAT
Statistics
Matches: 160, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
39 62 0.39
40 93 0.58
41 5 0.03
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.23
Consensus pattern (40 bp):
GGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAAG
Found at i:29784452 original size:79 final size:77
Alignment explanation
Indices: 29784315--29784527 Score: 259
Period size: 79 Copynumber: 2.7 Consensus size: 77
29784305 ATACAATCAG
* * * * *
29784315 GGGCACATATGTTCATTCAAAGGTACCGAAGTACAAATAGGGGCATGTATGTGCATTCAGGGGTA
1 GGGCACATATGTGCATTC-AGGGTA-CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGAGTA
29784380 -CTAAAGTACAAATA
64 TC-AAAGTACAAATA
*
29784394 GGGACACATATGTGCATTCAGGGTATCAAAGTACAAATAGCGGCACGTATGTGCATTCAGGAGTA
1 GGG-CACATATGTGCATTCAGGGTA-CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGAGTA
*
29784459 TCGAAGTACAAATA
64 TCAAAGTACAAATA
* *
29784473 CGGGCA-AGTATGTGCATTTAGGGGTACCAAGTACAAATAGGGGCACGTATGTGCA
1 -GGGCACA-TATGTGCATTCA-GGGTACAAAGTACAAATAGGGGCACGTATGTGCA
29784528 CTCACACAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 94 0.80
80 23 0.19
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (77 bp):
GGGCACATATGTGCATTCAGGGTACAAAGTACAAATAGGGGCACGTATGTGCATTCAGGAGTATC
AAAGTACAAATA
Found at i:29784943 original size:21 final size:20
Alignment explanation
Indices: 29784917--29784957 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29784907 CAATATATTC
29784917 TAAATTCAACACATTTACCCA
1 TAAATTCAA-ACATTTACCCA
* *
29784938 TAAATTCTAGCATTTACCCA
1 TAAATTCAAACATTTACCCA
29784958 ATTTAACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAATTCAAACATTTACCCA
Found at i:29790840 original size:21 final size:20
Alignment explanation
Indices: 29790790--29790840 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
29790780 GTTAAGTTTT
*
29790790 GTTAAATTTTAATTTATTTA
1 GTTAAATTTTAATTAATTTA
**
29790810 GTTATGTTTTCAATTAATTTA
1 GTTAAATTTT-AATTAATTTA
*
29790831 TTTAAATTTT
1 GTTAAATTTT
29790841 TGAAATCCCC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (20 bp):
GTTAAATTTTAATTAATTTA
Found at i:29791563 original size:21 final size:21
Alignment explanation
Indices: 29791539--29791600 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
29791529 GCCACATGGT
29791539 CATGTCCTTCAGTCACACGGG
1 CATGTCCTTCAGTCACACGGG
29791560 CATGTTCCTT-AGTCACACGGG
1 CATG-TCCTTCAGTCACACGGG
* *
29791581 CGTGTGCTTCAGTCACACGG
1 CATGTCCTTCAGTCACACGG
29791601 TCGTGTATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.11
21 28 0.76
22 5 0.14
ACGTcount: A:0.18, C:0.31, G:0.26, T:0.26
Consensus pattern (21 bp):
CATGTCCTTCAGTCACACGGG
Found at i:29791606 original size:21 final size:21
Alignment explanation
Indices: 29791531--29791602 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
29791521 ACAGTCTGGC
*
29791531 CACATGGTCATGTCCTTCAGT
1 CACACGGTCATGTCCTTCAGT
*
29791552 CACACGGGCATGTTCCTT-AGT
1 CACACGGTCATG-TCCTTCAGT
* * *
29791573 CACACGGGCGTGTGCTTCAGT
1 CACACGGTCATGTCCTTCAGT
29791594 CACACGGTC
1 CACACGGTC
29791603 GTGTATCTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
20 4 0.09
21 35 0.80
22 5 0.11
ACGTcount: A:0.18, C:0.31, G:0.25, T:0.26
Consensus pattern (21 bp):
CACACGGTCATGTCCTTCAGT
Found at i:29791774 original size:20 final size:20
Alignment explanation
Indices: 29791731--29791767 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
29791721 ATACTCTACA
29791731 TGTTTAAGCTGTTATATACG
1 TGTTTAAGCTGTTATATACG
29791751 TGTTTAAG-TGTTATATA
1 TGTTTAAGCTGTTATATA
29791768 ATGTGTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.49
Consensus pattern (20 bp):
TGTTTAAGCTGTTATATACG
Found at i:29793634 original size:30 final size:29
Alignment explanation
Indices: 29793451--29793745 Score: 171
Period size: 29 Copynumber: 10.3 Consensus size: 29
29793441 CAAAAAACGT
* * *
29793451 AAAAACCTTTGTGGTAAACCTCTGTAAAAAG
1 AAAAGCCTTTGTGGCAAATCTCTGT--AAAG
*
29793482 AAGAGCCTTTGTGGCAAATCTCTGTAAAGG
1 AAAAGCCTTTGTGGCAAATCTCTGTAAA-G
* * * * *
29793512 AAAAACCTTTATGGCGAACCTTTG-AATAG
1 AAAAGCCTTTGTGGCAAATCTCTGTAA-AG
* *
29793541 -AAAGCCTTTGTGG--AATATCT-AAAAG
1 AAAAGCCTTTGTGGCAAATCTCTGTAAAG
* * *
29793566 AAAAGCCTTTGAGGCAAACCTCTGTACAG
1 AAAAGCCTTTGTGGCAAATCTCTGTAAAG
* * *
29793595 AAAAACCTTTGTGGCAAATCTTTGTTAAGG
1 AAAAGCCTTTGTGGCAAATCTCTG-TAAAG
* *
29793625 AAAAGCCTTTGTGGGAAA-C-CTCTAAA-
1 AAAAGCCTTTGTGGCAAATCTCTGTAAAG
* * * *
29793651 CAGAGCCTTTGTGGC--ATATCT-AAAAG
1 AAAAGCCTTTGTGGCAAATCTCTGTAAAG
* * * * *
29793677 AAAAACCTTTCTGGAAAACCTCTGTATAG
1 AAAAGCCTTTGTGGCAAATCTCTGTAAAG
* * *
29793706 AAAAGCCTTTATGGCAAATCCCCGTAAAGG
1 AAAAGCCTTTGTGGCAAATCTCTGTAAA-G
*
29793736 AAAAACCTTT
1 AAAAGCCTTT
29793746 ATGGTGAACC
Statistics
Matches: 196, Mismatches: 53, Indels: 31
0.70 0.19 0.11
Matches are distributed among these distances:
24 1 0.01
25 5 0.03
26 42 0.21
27 3 0.02
28 21 0.11
29 54 0.28
30 49 0.25
31 21 0.11
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (29 bp):
AAAAGCCTTTGTGGCAAATCTCTGTAAAG
Found at i:29793696 original size:111 final size:112
Alignment explanation
Indices: 29793451--29793756 Score: 366
Period size: 111 Copynumber: 2.7 Consensus size: 112
29793441 CAAAAAACGT
* *
29793451 AAAAACCTTTGTGGTAAACCTCTGTAAAAAGAAGAGCCTTTGTGGCAAATCTCTGTAAAGGAAAA
1 AAAAACCTTTGTGGAAAACCTCTGTAAGAA-AA-A-CCTTTGTGGCAAATCTCTGTAAAGGAAAA
* *
29793516 ACCTTTATGGCGAACCTTTGAATAGAAAGCCTTTGTGGAATATCTAAAAG
63 ACCTTTATGGCGAACCTCTGAATACAAAGCCTTTGTGGAATATCTAAAAG
* * * * * *
29793566 AAAAGCCTTTGAGGCAAACCTCTGTACAGAAAAACCTTTGTGGCAAATCTTTGTTAAGGAAAAGC
1 AAAAACCTTTGTGGAAAACCTCTGTA-AGAAAAACCTTTGTGGCAAATCTCTGTAAAGGAAAAAC
* * *
29793631 CTTTGTGG-GAAACCTCT-AA-ACAGAGCCTTTGTGGCATATCTAAAAG
65 CTTTATGGCG-AACCTCTGAATACAAAGCCTTTGTGGAATATCTAAAAG
* * * * *
29793677 AAAAACCTTTCTGGAAAACCTCTGTATAGAAAAGCCTTTATGGCAAATCCCCGTAAAGGAAAAAC
1 AAAAACCTTTGTGGAAAACCTCTGTA-AGAAAAACCTTTGTGGCAAATCTCTGTAAAGGAAAAAC
*
29793742 CTTTATGGTGAACCT
65 CTTTATGGCGAACCT
29793757 TTGTAAAGAA
Statistics
Matches: 163, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
111 89 0.55
112 4 0.02
113 41 0.25
114 1 0.01
115 25 0.15
116 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (112 bp):
AAAAACCTTTGTGGAAAACCTCTGTAAGAAAAACCTTTGTGGCAAATCTCTGTAAAGGAAAAACC
TTTATGGCGAACCTCTGAATACAAAGCCTTTGTGGAATATCTAAAAG
Found at i:29793746 original size:30 final size:29
Alignment explanation
Indices: 29793673--29793767 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
29793663 GGCATATCTA
* *
29793673 AAAGAAAAACCTTTCTGGAAAACCTCTGT
1 AAAGAAAAACCTTTATGGAAAACCTCCGT
* * *
29793702 ATAGAAAAGCCTTTATGGCAAATCC-CCGT
1 AAAGAAAAACCTTTATGG-AAAACCTCCGT
** **
29793731 AAAGGAAAAACCTTTATGGTGAACCTTTGT
1 AAA-GAAAAACCTTTATGGAAAACCTCCGT
29793761 AAAGAAA
1 AAAGAAA
29793768 GCCCATTTGG
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 27 0.53
30 24 0.47
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (29 bp):
AAAGAAAAACCTTTATGGAAAACCTCCGT
Found at i:29799054 original size:19 final size:19
Alignment explanation
Indices: 29799032--29799068 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29799022 AATTTTTTGA
29799032 ATTTTTTATAATTTTAAAT
1 ATTTTTTATAATTTTAAAT
*
29799051 ATTTTTTATATTTTTAAA
1 ATTTTTTATAATTTTAAA
29799069 ATTATTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTTATAATTTTAAAT
Found at i:29802254 original size:25 final size:25
Alignment explanation
Indices: 29802216--29802263 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
29802206 ACCTGTACAT
*
29802216 GTATGCTCATATGAGCTCTAAATCA
1 GTATGCTCATATGAGCTATAAATCA
29802241 GTATGCTC-TAATGAGCTATAAAT
1 GTATGCTCAT-ATGAGCTATAAAT
29802264 GATAAGCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (25 bp):
GTATGCTCATATGAGCTATAAATCA
Found at i:29809699 original size:25 final size:25
Alignment explanation
Indices: 29809671--29809727 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
29809661 CTATAAACAA
**
29809671 TAAGCTCATACGAGTTGAATATCAG
1 TAAGCTCATACGAACTGAATATCAG
* *
29809696 TAAGCTCATGCGAACTGAATATCGG
1 TAAGCTCATACGAACTGAATATCAG
*
29809721 TATGCTC
1 TAAGCTC
29809728 TCTTGAGCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (25 bp):
TAAGCTCATACGAACTGAATATCAG
Found at i:29812689 original size:18 final size:18
Alignment explanation
Indices: 29812666--29812702 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29812656 AGTGTAAGAA
29812666 AACCGTTTTCAAATCGGG
1 AACCGTTTTCAAATCGGG
29812684 AACCGTTTTCAAATCGGG
1 AACCGTTTTCAAATCGGG
29812702 A
1 A
29812703 TTTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (18 bp):
AACCGTTTTCAAATCGGG
Found at i:29829256 original size:72 final size:72
Alignment explanation
Indices: 29829098--29829263 Score: 181
Period size: 72 Copynumber: 2.3 Consensus size: 72
29829088 TCTATTAAAG
* *
29829098 ATAAGAAGTGTT-GTAATGAGAAAATACATGTGTTGTATCATTCCATTCACTCGTATAGGTTATT
1 ATAAGAAGT-TTGGTAATGAGAAAATAAATGTGTTGCATCATTCCATTCACTCGTATAGGTTATT
29829162 CGATTACT
65 CGATTACT
* ** *** ** * *
29829170 ATAAGAAGTGTGGTAATGAGAAAATAAATGTGTTGCATTGTTTGTTTCACTTTTATAGGTTTTTT
1 ATAAGAAGTTTGGTAATGAGAAAATAAATGTGTTGCATCATTCCATTCACTCGTATAGGTTATTC
*
29829235 TATTACT
66 GATTACT
* *
29829242 ATGAGAAGTTTGGTAACGAGAA
1 ATAAGAAGTTTGGTAATGAGAA
29829264 GGTGATTGTC
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
71 1 0.01
72 76 0.99
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (72 bp):
ATAAGAAGTTTGGTAATGAGAAAATAAATGTGTTGCATCATTCCATTCACTCGTATAGGTTATTC
GATTACT
Found at i:29829539 original size:20 final size:20
Alignment explanation
Indices: 29829511--29829548 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29829501 TTGAAACCAA
*
29829511 TAATTATGTGTGTGTTTCAC
1 TAATCATGTGTGTGTTTCAC
29829531 TAATCATGTGTGTGTTTC
1 TAATCATGTGTGTGTTTC
29829549 GCTACAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.11, G:0.21, T:0.50
Consensus pattern (20 bp):
TAATCATGTGTGTGTTTCAC
Found at i:29832567 original size:33 final size:33
Alignment explanation
Indices: 29832530--29832641 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 33
29832520 ACCTATATTT
*
29832530 TGTGTTTACTATCGTAACAAACTTTCTTTGTTC
1 TGTGTTTACTATCGCAACAAACTTTCTTTGTTC
* * *
29832563 TGTGTTTACTATCGCAGCACACTTTCTCTGTTC
1 TGTGTTTACTATCGCAACAAACTTTCTTTGTTC
* ** *
29832596 TGTGTTTACTGTTC-CAACGGACTATCTTTGTTC
1 TGTGTTTACT-ATCGCAACAAACTTTCTTTGTTC
*
29832629 TATGTTTACTATC
1 TGTGTTTACTATC
29832642 CCTACGGACT
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
32 2 0.03
33 62 0.94
34 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.46
Consensus pattern (33 bp):
TGTGTTTACTATCGCAACAAACTTTCTTTGTTC
Found at i:29832649 original size:33 final size:32
Alignment explanation
Indices: 29832554--29832655 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 32
29832544 TAACAAACTT
* ** *
29832554 TCTTTGTTCTGTGTTTACTATCGCAGCACACTT
1 TCTTTGTTCTGTGTTTACTATCCCA-CGGACTA
* * *
29832587 TCTCTGTTCTGTGTTTACTGTTCCAACGGACTA
1 TCTTTGTTCTGTGTTTACT-ATCCCACGGACTA
*
29832620 TCTTTGTTCTATGTTTACTATCCCTACGGACTA
1 TCTTTGTTCTGTGTTTACTATCCC-ACGGACTA
29832653 TCT
1 TCT
29832656 CTGTGGATGC
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 3 0.05
33 50 0.89
34 3 0.05
ACGTcount: A:0.16, C:0.25, G:0.15, T:0.45
Consensus pattern (32 bp):
TCTTTGTTCTGTGTTTACTATCCCACGGACTA
Found at i:29843025 original size:30 final size:30
Alignment explanation
Indices: 29842980--29843046 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
29842970 ATTTCCCCGG
* * * *
29842980 GCATCAGCATTGACTATTGTATAGGTATCT
1 GCATCGGCATCGACTATTGCATAGGCATCT
*
29843010 GCATCGGCATCGACTATTGCATGGGCATCT
1 GCATCGGCATCGACTATTGCATAGGCATCT
*
29843040 GTATCGG
1 GCATCGG
29843047 TACCGTCATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
GCATCGGCATCGACTATTGCATAGGCATCT
Found at i:29846028 original size:9 final size:9
Alignment explanation
Indices: 29846002--29846043 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
29845992 ACAATTCTCA
29846002 CAAATTCTCT
1 CAAATT-TCT
29846012 CAAAATTTCT
1 C-AAATTTCT
29846022 CAAATTTCT
1 CAAATTTCT
29846031 CACAA-TTCT
1 CA-AATTTCT
29846040 CAAA
1 CAAA
29846044 AAGCTCTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.07
9 16 0.53
10 7 0.23
11 5 0.17
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (9 bp):
CAAATTTCT
Found at i:29849417 original size:46 final size:46
Alignment explanation
Indices: 29849342--29849456 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
29849332 CCACACTAAT
* * *
29849342 ATGTAGCCAAAGCTACCACTAATACGTAGCTGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
*
29849388 ATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
* *
29849434 ATGCAGCTGAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAT
29849457 CAATAACACT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
Found at i:29849454 original size:23 final size:23
Alignment explanation
Indices: 29849342--29849455 Score: 140
Period size: 23 Copynumber: 5.0 Consensus size: 23
29849332 CCACACTAAT
*
29849342 ATGTAGCCAAAGCTACCACT-AA
1 ATGTAGCCGAAGCTACCACTGAA
* * *
29849364 TACGTAGCTGTAGCTACCACTGAA
1 -ATGTAGCCGAAGCTACCACTGAA
*
29849388 ATGTAGCCGAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAA
*
29849411 ATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
* *
29849434 ATGCAGCTGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
29849456 TCAATAACAC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
23 75 0.97
24 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:29851790 original size:9 final size:9
Alignment explanation
Indices: 29851776--29851833 Score: 98
Period size: 9 Copynumber: 6.4 Consensus size: 9
29851766 TTTGGTTAAA
29851776 AATTAACCG
1 AATTAACCG
29851785 AATTAACCG
1 AATTAACCG
*
29851794 AATTAATCG
1 AATTAACCG
*
29851803 AATTACCCG
1 AATTAACCG
29851812 AATTAACCG
1 AATTAACCG
29851821 AATTAACCG
1 AATTAACCG
29851830 AATT
1 AATT
29851834 GAATCACTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:29851889 original size:11 final size:11
Alignment explanation
Indices: 29851873--29851897 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29851863 ACTTTTAGAC
29851873 TTTAGTTTTAG
1 TTTAGTTTTAG
29851884 TTTAGTTTTAG
1 TTTAGTTTTAG
29851895 TTT
1 TTT
29851898 TAGAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTAGTTTTAG
Found at i:29853127 original size:42 final size:42
Alignment explanation
Indices: 29853047--29853128 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
29853037 CGTTTTTTCT
* * **
29853047 ATGCCATAGTCCAATTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
29853089 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACA-TATGCACATAT
29853129 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:29853155 original size:47 final size:48
Alignment explanation
Indices: 29853088--29853180 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 48
29853078 TTTACATATT
* *
29853088 GATGCCATAGCCCAGCTATGGTCTTACACAG-TAGCACATATCACACC
1 GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACACC
* * * *
29853135 GATGCCATATCCCGGATATGGTCTTATACAGAAATCACATATCACA
1 GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACA
29853181 TGTTGTCATG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 27 0.69
48 12 0.31
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (48 bp):
GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACACC
Found at i:29855784 original size:23 final size:23
Alignment explanation
Indices: 29855758--29855876 Score: 150
Period size: 23 Copynumber: 5.2 Consensus size: 23
29855748 ATAAGTGCCA
29855758 CACTAATATGTAGCCGAAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
* * *
29855781 CACTAATACGTAGCTGTAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
* *
29855804 CACTAAAATATAGCCGAAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
** *
29855827 CACTGGTATGTAGCCGTAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
29855850 CACTGAA-ATGTAGCCGAAGCTAC
1 CACT-AATATGTAGCCGAAGCTAC
29855873 CACT
1 CACT
29855877 GATCAATAAC
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
23 79 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (23 bp):
CACTAATATGTAGCCGAAGCTAC
Found at i:29855877 original size:46 final size:46
Alignment explanation
Indices: 29855758--29855879 Score: 181
Period size: 46 Copynumber: 2.7 Consensus size: 46
29855748 ATAAGTGCCA
* * *
29855758 CACTAATATGTAGCCGAAGCTACCACTAATACGTAGCTGTAGCTAC
1 CACTAAAATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTAC
* * *
29855804 CACTAAAATATAGCCGAAGCTACCACTGGTATGTAGCCGTAGCTAC
1 CACTAAAATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTAC
*
29855850 CACTGAAATGTAGCCGAAGCTACCACTGAT
1 CACTAAAATGTAGCCGAAGCTACCACTGAT
29855880 CAATAACACT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (46 bp):
CACTAAAATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTAC
Found at i:29856131 original size:18 final size:17
Alignment explanation
Indices: 29856105--29856143 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
29856095 ATTTTCCTTC
29856105 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
29856122 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
29856140 CACA
1 CACA
29856144 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:29859509 original size:3 final size:3
Alignment explanation
Indices: 29859501--29859547 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
29859491 GAATCATGGA
*
29859501 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TAT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
29859548 ATTTTCATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:29861362 original size:3 final size:3
Alignment explanation
Indices: 29861356--29861384 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29861346 TTATTATTAT
29861356 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
29861385 TGGTATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:29864559 original size:6 final size:6
Alignment explanation
Indices: 29864548--29864584 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
29864538 TTTTTCAACC
* *
29864548 CCAAAT CCAAAT CCAAAT CCAAAC CCAAAC CCAAAT C
1 CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT C
29864585 TAATTCCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.41, G:0.00, T:0.11
Consensus pattern (6 bp):
CCAAAT
Found at i:29869123 original size:15 final size:16
Alignment explanation
Indices: 29869088--29869121 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
29869078 TCATTTGTTG
29869088 TTTAAAATTGTTATTA
1 TTTAAAATTGTTATTA
29869104 TTTAAATATTGTT-TTA
1 TTTAAA-ATTGTTATTA
29869120 TT
1 TT
29869122 AATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTAAAATTGTTATTA
Found at i:29869462 original size:27 final size:27
Alignment explanation
Indices: 29869404--29869466 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
29869394 TTAAATTATT
**
29869404 TATATTTTATAATTCAATATTTTTGTA
1 TATATTTTATAATTCAATATTTTAATA
29869431 TATATTTT-TAATTCAATATCATTTAATA
1 TATATTTTATAATTCAATAT--TTTAATA
29869459 -ATATTTTA
1 TATATTTTA
29869467 AACCCTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 11 0.35
27 15 0.48
28 5 0.16
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (27 bp):
TATATTTTATAATTCAATATTTTAATA
Found at i:29869702 original size:19 final size:19
Alignment explanation
Indices: 29869671--29869721 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
29869661 GTTTATGGTA
*
29869671 ATTA-AATAATATTTATTT
1 ATTATAATAATATTTATCT
*
29869689 ATTATAATAGTATTTATCT
1 ATTATAATAATATTTATCT
29869708 -TTATAATAAATATT
1 ATTATAAT-AATATT
29869722 AAATTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTATAATAATATTTATCT
Found at i:29869969 original size:162 final size:160
Alignment explanation
Indices: 29869801--29870114 Score: 431
Period size: 164 Copynumber: 1.9 Consensus size: 160
29869791 AATTTTGAAA
*
29869801 TTTAAACTA-ATTTCTTTAAAGATGAATAAA-A-ATATTATTTAAATTAAATTTTCTA-TGAAAG
1 TTTAAACTATATTTCTTTAAAGATAAATAAAGATATATT-TTTAAATTAAATTTTCTAGT-AAAG
* * *
29869862 TTTTAACTTTAAACTAAATATTAAAATTAGTAAATTTATAATTTATAATTTA-AATAAAAAATAT
64 TTTTAACTTTAAACTAAATATTAAAATTA-AAAATTT-TAATTCAGAATTTAGAAT-AAAAATAT
29869926 TAAAATTAAATTGTGTTATAGATTTTTATGAAAGGAT
126 TAAAATT-AATT-TGTTATAGATTTTTATGAAAGGAT
* * * *
29869963 TTTAAACTATATTTTTTTAATGATAAATAAAGATATATTTTTAAATTAAATTTTCTAGTAGATTT
1 TTTAAACTATATTTCTTTAAAGATAAATAAAGATATATTTTTAAATTAAATTTTCTAGTAAAGTT
*
29870028 TTAACTTTAAACTAAATATTAAAATTAAAAATTTTAATTCAGAATTTAGAATAAAAATATTGAAA
66 TTAACTTTAAACTAAATATTAAAATTAAAAATTTTAATTCAGAATTTAGAATAAAAATATTAAAA
* *
29870093 TTAATTTTTTATGGATTTTTAT
131 TTAATTTGTTATAGATTTTTAT
29870115 TAAAATTAAT
Statistics
Matches: 136, Mismatches: 11, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
160 14 0.10
161 4 0.03
162 35 0.26
163 27 0.20
164 50 0.37
165 6 0.04
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (160 bp):
TTTAAACTATATTTCTTTAAAGATAAATAAAGATATATTTTTAAATTAAATTTTCTAGTAAAGTT
TTAACTTTAAACTAAATATTAAAATTAAAAATTTTAATTCAGAATTTAGAATAAAAATATTAAAA
TTAATTTGTTATAGATTTTTATGAAAGGAT
Found at i:29870251 original size:13 final size:13
Alignment explanation
Indices: 29870220--29870252 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29870210 ATGATAGATA
*
29870220 TTAAATTTAAAAT
1 TTAAATATAAAAT
29870233 TT-AATATAAAAT
1 TTAAATATAAAAT
29870245 TTAAATAT
1 TTAAATAT
29870253 TATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAATATAAAAT
Found at i:29880212 original size:29 final size:29
Alignment explanation
Indices: 29880070--29880249 Score: 119
Period size: 29 Copynumber: 6.2 Consensus size: 29
29880060 AACCGTCCTA
* * *
29880070 TTTCATATTCGATGGTCAAAAGC-ATCGCT
1 TTTCATAATCGATGGTCGAAA-CTATCCCT
* * **
29880099 TTTCATAATCGATAGCCGAAGTTATCCCT
1 TTTCATAATCGATGGTCGAAACTATCCCT
* ** ** *
29880128 TTTCATATTTAATGGTCGTCACAATCCCT
1 TTTCATAATCGATGGTCGAAACTATCCCT
* ** * ** *
29880157 TTTCATGATTTATGATCGTCACCATCCCT
1 TTTCATAATCGATGGTCGAAACTATCCCT
*
29880186 TTTCATAATCGATAGTCGAAACTATCCCT
1 TTTCATAATCGATGGTCGAAACTATCCCT
* * * *
29880215 TTTCATATTCGATGGCCGGAGCTATCCCT
1 TTTCATAATCGATGGTCGAAACTATCCCT
29880244 TTTCAT
1 TTTCAT
29880250 TGGTCGATGA
Statistics
Matches: 115, Mismatches: 35, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
29 115 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (29 bp):
TTTCATAATCGATGGTCGAAACTATCCCT
Done.