Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008717.1 Hibiscus syriacus cultivar Beakdansim tig00111772_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3453450
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 16
Found at i:2816398 original size:2 final size:2
Alignment explanation
Indices: 2816391--2816421 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2816381 ATATTAAATC
2816391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2816422 AGTAGTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2817673 original size:19 final size:19
Alignment explanation
Indices: 2817630--2817680 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
2817620 AAATAACCAA
* *
2817630 CAAATTCACAACGCGATCT
1 CAAATTCGCAACGCGAACT
2817649 CAAATTCGCAACGCGAACT
1 CAAATTCGCAACGCGAACT
*
2817668 CCAATTTCGCAAC
1 -CAAATTCGCAAC
2817681 CCAGTTTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:2817678 original size:20 final size:20
Alignment explanation
Indices: 2817638--2817705 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
2817628 AACAAATTCA
* *
2817638 CAACGCGATCT-CAAATTCG
1 CAACGCGAACTCCAATTTCG
2817657 CAACGCGAACTCCAATTTCG
1 CAACGCGAACTCCAATTTCG
* **
2817677 CAAC-CCAGTTTCCAATTTCG
1 CAACGCGA-ACTCCAATTTCG
2817697 CAACGCGAA
1 CAACGCGAA
2817706 TATGTAAATC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 12 0.31
20 25 0.64
21 2 0.05
ACGTcount: A:0.31, C:0.34, G:0.15, T:0.21
Consensus pattern (20 bp):
CAACGCGAACTCCAATTTCG
Found at i:2817793 original size:24 final size:24
Alignment explanation
Indices: 2817766--2817819 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2817756 GTATTCGAAA
*
2817766 TTTGATTTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2817790 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2817814 TTTGAT
1 TTTGAT
2817820 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2820105 original size:18 final size:18
Alignment explanation
Indices: 2820082--2820122 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2820072 GCAAAAAAGG
2820082 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
2820100 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
*
2820118 CAATC
1 AAATC
2820123 GGCTTCACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:2820584 original size:25 final size:25
Alignment explanation
Indices: 2820546--2820595 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2820536 AAATCAATTA
*
2820546 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
2820571 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
2820596 GAAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:2821002 original size:18 final size:18
Alignment explanation
Indices: 2820981--2821017 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2820971 GTAATTGGAG
2820981 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2820999 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2821017 T
1 T
2821018 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:2821024 original size:24 final size:24
Alignment explanation
Indices: 2820973--2821025 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2820963 TTTCATATGT
* * *
2820973 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
2820997 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
2821021 AATTT
1 AATTT
2821026 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:2821996 original size:18 final size:18
Alignment explanation
Indices: 2821973--2822008 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2821963 AAGCAAAAGG
2821973 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
2821991 AAATCAAAATCCCAATCA
1 AAATCAAAATCACAATCA
2822009 TAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:2822499 original size:14 final size:14
Alignment explanation
Indices: 2822481--2822517 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2822471 ATCAAATCAA
2822481 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2822495 CCAAATCAACTTTT
1 ACAAATCAACTTTT
2822509 ACAAATCAA
1 ACAAATCAA
2822518 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2823761 original size:21 final size:21
Alignment explanation
Indices: 2823737--2823835 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
2823727 ATGGGTGAGA
* *
2823737 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAATGATGAGAGGGG
* *
2823758 CCTCTTGAATGGTGGGAGGGG
1 CCTCTTGAATGATGAGAGGGG
*
2823779 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAATGATGAGAGGGG
* *
2823800 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAATGATGA-GAGGGG
2823821 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
2823836 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.24
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGGG
Found at i:2823818 original size:42 final size:42
Alignment explanation
Indices: 2823737--2823835 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
2823727 ATGGGTGAGA
* * * * *
2823737 CCTCTTGAACGATGACAGGGGCCTCTTGAATGGTGGGAGGGG
1 CCTCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCG
* *
2823779 CTTCTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCG
1 CCTCTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGCG
2823821 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
2823836 TAGGTGCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 45 0.96
43 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.24
Consensus pattern (42 bp):
CCTCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCG
Found at i:2824916 original size:7 final size:7
Alignment explanation
Indices: 2824899--2824947 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
2824889 CCGTTGACCC
2824899 GACCTGTT
1 GACC-GTT
2824907 GACCGTT
1 GACCGTT
2824914 GACCGTT
1 GACCGTT
*
2824921 GACTTCCTTT
1 GA---CCGTT
2824931 GACCGTT
1 GACCGTT
2824938 GACCGTT
1 GACCGTT
2824945 GAC
1 GAC
2824948 TTCCTTTGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
7 26 0.72
8 4 0.11
10 6 0.17
ACGTcount: A:0.14, C:0.29, G:0.24, T:0.33
Consensus pattern (7 bp):
GACCGTT
Found at i:2824936 original size:24 final size:24
Alignment explanation
Indices: 2824905--2824958 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
2824895 ACCCGACCTG
2824905 TTGACCGTTGACCGTTGACTTCCT
1 TTGACCGTTGACCGTTGACTTCCT
2824929 TTGACCGTTGACCGTTGACTTCCT
1 TTGACCGTTGACCGTTGACTTCCT
2824953 TTGACC
1 TTGACC
2824959 AGAACTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.13, C:0.30, G:0.20, T:0.37
Consensus pattern (24 bp):
TTGACCGTTGACCGTTGACTTCCT
Found at i:2826468 original size:21 final size:21
Alignment explanation
Indices: 2826444--2826498 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
2826434 TAGAGCGGCA
2826444 ACCTCATCACGTAAAGTAGAT
1 ACCTCATCACGTAAAGTAGAT
2826465 ACCTCATCACGTAAAGTAGAT
1 ACCTCATCACGTAAAGTAGAT
*
2826486 ACCTCACCACGTA
1 ACCTCATCACGTA
2826499 GCGCACCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.29, G:0.13, T:0.22
Consensus pattern (21 bp):
ACCTCATCACGTAAAGTAGAT
Found at i:2826585 original size:65 final size:63
Alignment explanation
Indices: 2826501--2826624 Score: 142
Period size: 65 Copynumber: 1.9 Consensus size: 63
2826491 ACCACGTAGC
* * *
2826501 GCACCATTGTCATCGCGTAAAAAATCC-ACCTCACCACGTAAAGAGACCGAACCTCATCACGCCA
1 GCACCATTATCATCACGTAAAAAA-CCGACCTCACCACGTAAAG-CACCG-ACCTCATCACGCCA
2826565 T
63 T
* ** **
2826566 GCACCATTATCTTCACGTAAAGTACCGACCTCATGACGTAAAGCACCGACCTCATCACG
1 GCACCATTATCATCACGTAAAAAACCGACCTCACCACGTAAAGCACCGACCTCATCACG
2826625 TAACTCCCCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
63 11 0.22
64 6 0.12
65 33 0.66
ACGTcount: A:0.32, C:0.35, G:0.15, T:0.19
Consensus pattern (63 bp):
GCACCATTATCATCACGTAAAAAACCGACCTCACCACGTAAAGCACCGACCTCATCACGCCAT
Found at i:2826606 original size:21 final size:21
Alignment explanation
Indices: 2826578--2826627 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2826568 ACCATTATCT
*
2826578 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
2826599 TGACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
2826620 TCACGTAA
1 TCACGTAA
2826628 CTCCCCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:2828411 original size:19 final size:20
Alignment explanation
Indices: 2828366--2828403 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2828356 ATCACAATGA
*
2828366 GAAAATCGCGACGCGAAAAT
1 GAAAATCGCAACGCGAAAAT
2828386 GAAAATCGCAACGCGAAA
1 GAAAATCGCAACGCGAAA
2828404 CTAAAATCTC
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:0.47, C:0.21, G:0.24, T:0.08
Consensus pattern (20 bp):
GAAAATCGCAACGCGAAAAT
Found at i:2828471 original size:20 final size:20
Alignment explanation
Indices: 2828415--2828460 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2828405 TAAAATCTCT
2828415 TTGCGATTTTCATTTTCGCG
1 TTGCGATTTTCATTTTCGCG
*
2828435 TTGCGATTTTCATTTTCGTG
1 TTGCGATTTTCATTTTCGCG
2828455 TTGCGA
1 TTGCGA
2828461 ATTTATGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (20 bp):
TTGCGATTTTCATTTTCGCG
Found at i:2838251 original size:45 final size:45
Alignment explanation
Indices: 2838200--2838309 Score: 186
Period size: 45 Copynumber: 2.4 Consensus size: 45
2838190 ATGGAGACCT
2838200 TACCCTCCGAAGGGGAACCCAAACCAGAAAACAAGACGAGGATGA
1 TACCCTCCGAAGGGGAACCCAAACCAGAAAACAAGACGAGGATGA
* *
2838245 TACCCTCCAAAGGGGAACCCAAACCAGAAAACATGACGAGGATGA
1 TACCCTCCGAAGGGGAACCCAAACCAGAAAACAAGACGAGGATGA
2838290 TACCCTCCG-AGGAGGAACCC
1 TACCCTCCGAAGG-GGAACCC
2838310 GAGACTTCCA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 3 0.05
45 58 0.95
ACGTcount: A:0.39, C:0.29, G:0.24, T:0.08
Consensus pattern (45 bp):
TACCCTCCGAAGGGGAACCCAAACCAGAAAACAAGACGAGGATGA
Found at i:2840083 original size:6 final size:6
Alignment explanation
Indices: 2840072--2840156 Score: 125
Period size: 6 Copynumber: 14.2 Consensus size: 6
2840062 GACACGTATT
* * * *
2840072 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
2840120 ACCTCG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
2840157 GCCGAGCCGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.28, C:0.49, G:0.16, T:0.06
Consensus pattern (6 bp):
ACCACG
Found at i:2840164 original size:5 final size:5
Alignment explanation
Indices: 2840154--2840197 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
2840144 ACCACGACCA
* * * *
2840154 CGAGC CGAGC CGAGC CGTGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
2840198 ACGGACGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.20, C:0.34, G:0.41, T:0.05
Consensus pattern (5 bp):
CGAGC
Found at i:2846073 original size:6 final size:6
Alignment explanation
Indices: 2846058--2846106 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
2846048 GACACGTATT
* * *
2846058 ACCACG ACCTCG ACCTCG ACCTCG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2846106 A
1 A
2846107 GCCGAGCTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.29, C:0.49, G:0.16, T:0.06
Consensus pattern (6 bp):
ACCACG
Found at i:2846118 original size:5 final size:5
Alignment explanation
Indices: 2846104--2846167 Score: 74
Period size: 5 Copynumber: 12.8 Consensus size: 5
2846094 ACCACGACCA
* * * *
2846104 CGAGC CGAGC TGAGC CGAGC CGAGC CGAGC TGAGC CGTGC CGTGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
* *
2846154 CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAG
2846168 ACGAACGGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 52 1.00
ACGTcount: A:0.20, C:0.33, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:2850036 original size:22 final size:22
Alignment explanation
Indices: 2850011--2850061 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
2850001 AGAAAACCCT
2850011 TAAAATCAAACTTAGTTTCTTA
1 TAAAATCAAACTTAGTTTCTTA
2850033 TAAAATCAAACTTAGTTTCTTA
1 TAAAATCAAACTTAGTTTCTTA
2850055 TAAAATC
1 TAAAATC
2850062 TTTTATTTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (22 bp):
TAAAATCAAACTTAGTTTCTTA
Found at i:2850097 original size:39 final size:39
Alignment explanation
Indices: 2850054--2850716 Score: 586
Period size: 39 Copynumber: 17.3 Consensus size: 39
2850044 TTAGTTTCTT
* * **
2850054 ATAAAATCTTTTATTTCGAGAAAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* * *
2850093 ATAAAATCTTCTGTTTTGAGGGAAACTATCTTAAGCGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* * * *
2850132 ACAAAATCTTCTGTTTTGAGGGAAACTATCTCAAGAGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* *
2850171 ACAAAATCTTCTGTTTCGAGTGAAACTATCTCAAACGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* * *
2850210 ATAAAATATTTTATTTCGAGTGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* * *
2850249 ATAAAATATTTTGTTTTGAGTGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
2850288 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* * * *
2850327 ATAAAATCTTTTGTTTCAAGGGAAACTGTCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* * * * *
2850366 ATAAAATCTTCTGTTTCGAGGGAAATTGTCTTAAGGGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* * * ** * * * *
2850405 ACT---GTC-TCAAG---GGAGACAAAATTTGTTTCAAGGGAG
1 A-TAAAATCTTC-TGTTTCGAG-TGAAA-CTATCTCAAGCGAG
* * * ** *
2850441 A-CAAAT-TT-TGTTTCAAGGGAAACCGTCTCAAGGGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* * * *
2850477 ACAAAA--TT-TGTTTC-AGGGGAAACTGTCTCAAGGGAG
1 ATAAAATCTTCTGTTTCGA-GTGAAACTATCTCAAGCGAG
** * * * * *
2850513 ACCAAA--TT-TGTTTAGTGGGAAACTGTCTCAAGGGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* *
2850549 ACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
2850588 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* * *
2850627 ATAAAATCTTTTGTTTCAAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
* * * * *
2850666 ACAAAATCTTTTGTTTCAAGGGAAACTATCTCAACCGAG
1 ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
2850705 ATAAAATCTTCT
1 ATAAAATCTTCT
2850717 TTAAAAACAA
Statistics
Matches: 540, Mismatches: 67, Indels: 34
0.84 0.10 0.05
Matches are distributed among these distances:
34 3 0.01
35 5 0.01
36 91 0.17
37 11 0.02
38 4 0.01
39 425 0.79
40 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (39 bp):
ATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
Found at i:2850410 original size:15 final size:15
Alignment explanation
Indices: 2850392--2850421 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2850382 CGAGGGAAAT
*
2850392 TGTCTTAAGGGAGAC
1 TGTCTCAAGGGAGAC
2850407 TGTCTCAAGGGAGAC
1 TGTCTCAAGGGAGAC
2850422 AAAATTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (15 bp):
TGTCTCAAGGGAGAC
Found at i:2850437 original size:21 final size:21
Alignment explanation
Indices: 2850411--2850460 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
2850401 GGAGACTGTC
2850411 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
*
2850432 TCAAGGGAGACAAATTTTGTT
1 TCAAGGGAGACAAAATTTGTT
2850453 TCAAGGGA
1 TCAAGGGA
2850461 AACCGTCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:2850469 original size:57 final size:55
Alignment explanation
Indices: 2850335--2850496 Score: 181
Period size: 57 Copynumber: 2.9 Consensus size: 55
2850325 AGATAAAATC
* * *
2850335 TTTTGTTTCAAGGGAAACTGTCTCAAGCGAGATAAAATCTTCTGTTTCGA-GG-GAAA
1 TTTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA--TT-TGTTTCAAGGGAGAAA
*
2850391 --TTGTCTT-AAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAGACAAA
1 TTTTGT-TTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAG--AAA
* *
2850446 TTTTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTTTCAGGGGA
1 TTTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
2850497 AACTGTCTCA
Statistics
Matches: 91, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
51 7 0.08
52 4 0.04
53 1 0.01
54 29 0.32
55 5 0.05
56 2 0.02
57 43 0.47
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (55 bp):
TTTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAGAAA
Found at i:2850828 original size:39 final size:39
Alignment explanation
Indices: 2850783--2850905 Score: 110
Period size: 39 Copynumber: 3.2 Consensus size: 39
2850773 ACGAGACAAA
*
2850783 TCTTGTTTTAAGGAAAACAATCTTGAGTGAAATAAATAT
1 TCTTGTTTTAAGGAAAACAATATTGAGTGAAATAAATAT
* ** * * * * * *
2850822 TATTGTTTCGAGTAAAA-ATTGTCTCAGATGAGA-CAA-A-
1 TCTTGTTTTAAGGAAAACAATAT-TGAG-TGAAATAAATAT
2850859 TCTTGTTTTAAGGAAAACAATATTGAGTGAAATAAATAT
1 TCTTGTTTTAAGGAAAACAATATTGAGTGAAATAAATAT
2850898 TCTTGTTT
1 TCTTGTTT
2850906 CGAGTAAAAA
Statistics
Matches: 60, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
36 4 0.07
37 18 0.30
38 8 0.13
39 26 0.43
40 4 0.07
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (39 bp):
TCTTGTTTTAAGGAAAACAATATTGAGTGAAATAAATAT
Found at i:2850980 original size:75 final size:76
Alignment explanation
Indices: 2850719--2851047 Score: 382
Period size: 76 Copynumber: 4.3 Consensus size: 76
2850709 AATCTTCTTT
* * * *
2850719 AAAAACAATCTTGAGTGAAATTAAAT-GTCTTCTTTCGAGTAAAAACTGCCTC-AGACGAGACAA
1 AAAAACAATCTTGAGTGAAA-TAAATAGTCTTGTTTCGAGTAAAAATTGTCTCAAG-TGAGACAA
2850782 ATCTTGTTTTAAG
64 ATCTTGTTTTAAG
* * *
2850795 GAAAACAATCTTGAGTGAAATAAATATTATTGTTTCGAGTAAAAATTGTCTC-AGATGAGACAAA
1 AAAAACAATCTTGAGTGAAATAAATAGTCTTGTTTCGAGTAAAAATTGTCTCAAG-TGAGACAAA
2850859 TCTTGTTTTAAG
65 TCTTGTTTTAAG
* * * * *
2850871 GAAAACAATATTGAGTGAAATAAATATTCTTGTTTCGAGTAAAAATTATCTCAAGTTAGACAAAT
1 AAAAACAATCTTGAGTGAAATAAATAGTCTTGTTTCGAGTAAAAATTGTCTCAAGTGAGACAAAT
*
2850936 -ATGTTTTAAG
66 CTTGTTTTAAG
* * *
2850946 AAAAACAATCTTGAGTCAAATGAAAT-GTCTTGTTTTGAGTAAAAAAATGTCTCAAGTGAGACAA
1 AAAAACAATCTTGAGTGAAAT-AAATAGTCTTGTTTCGAGT-AAAAATTGTCTCAAGTGAGACAA
*
2851010 AGTC-TATTTTAAG
64 A-TCTTGTTTTAAG
** *
2851023 AAAAACAATCTCAAGTGAGATAAAT
1 AAAAACAATCTTGAGTGAAATAAAT
2851048 CCTCTGTATT
Statistics
Matches: 222, Mismatches: 25, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
75 44 0.20
76 150 0.68
77 28 0.13
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (76 bp):
AAAAACAATCTTGAGTGAAATAAATAGTCTTGTTTCGAGTAAAAATTGTCTCAAGTGAGACAAAT
CTTGTTTTAAG
Found at i:2856247 original size:18 final size:17
Alignment explanation
Indices: 2856224--2856258 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2856214 TAGGTTAGGG
2856224 TAGAAAGAATAGAAGAAA
1 TAGAAAG-ATAGAAGAAA
*
2856242 TAGAAAGGTAGAAGAAA
1 TAGAAAGATAGAAGAAA
2856259 GGATTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (17 bp):
TAGAAAGATAGAAGAAA
Found at i:2856480 original size:18 final size:17
Alignment explanation
Indices: 2856459--2856520 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
2856449 GCTTGCTTTC
2856459 TCTTTTTGAATTTCTTTT
1 TCTTTTTGAATTT-TTTT
*
2856477 TCTTTTCTGAATTTTTCT
1 TCTTTT-TGAATTTTTTT
**
2856495 TCTTTTTGTCTTTTATTT
1 TCTTTTTGAATTTT-TTT
2856513 TCTTTTTG
1 TCTTTTTG
2856521 CACTCCAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 6 0.16
18 25 0.66
19 7 0.18
ACGTcount: A:0.08, C:0.13, G:0.06, T:0.73
Consensus pattern (17 bp):
TCTTTTTGAATTTTTTT
Found at i:2858705 original size:16 final size:17
Alignment explanation
Indices: 2858684--2858720 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2858674 TCACTTTTCC
2858684 TTTG-TTTTTCTCTTTT
1 TTTGTTTTTTCTCTTTT
2858700 TTTGTTTTTTTCTCTTTT
1 TTTG-TTTTTTCTCTTTT
2858718 TTT
1 TTT
2858721 CTGATTAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
18 15 0.79
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (17 bp):
TTTGTTTTTTCTCTTTT
Found at i:2865839 original size:20 final size:20
Alignment explanation
Indices: 2865806--2865846 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
2865796 AACCAACTAG
2865806 AATTTAAAATATATAAACAA
1 AATTTAAAATATATAAACAA
2865826 AATTATAAAA-ATATAAACAA
1 AATT-TAAAATATATAAACAA
2865846 A
1 A
2865847 TATCAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (20 bp):
AATTTAAAATATATAAACAA
Found at i:2870316 original size:31 final size:31
Alignment explanation
Indices: 2870278--2870346 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2870268 GCACGCCCAA
** *
2870278 CTGCTGCAACGACCGGATCTAAGGGCAACAG
1 CTGCTGCAACGACCAAATCTAAGGACAACAG
*
2870309 CTGCTGCAACGACCAAATCTAAGGACAACGG
1 CTGCTGCAACGACCAAATCTAAGGACAACAG
2870340 CTGCTGC
1 CTGCTGC
2870347 TGCCACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.14
Consensus pattern (31 bp):
CTGCTGCAACGACCAAATCTAAGGACAACAG
Found at i:2872876 original size:461 final size:461
Alignment explanation
Indices: 2872014--2873398 Score: 2707
Period size: 461 Copynumber: 3.0 Consensus size: 461
2872004 TGATTCAAAA
2872014 GTTTTGAAATAATTGAAGCTGGCAATTATTAATACCGGAAGGTGAGCAATTCAAGATTAGGATAA
1 GTTTTGAAATAATTGAAGCTGGCAATTATTAATACCGGAAGGTGAGCAATTCAAGATTAGGATAA
2872079 TTCACATAAGGCTGTGTCCTATAGAAAAACTAGACTTTGTTTCTTTTCTTTAAATCCAATATGCG
66 TTCACATAAGGCTGTGTCCTATAGAAAAACTAGACTTTGTTTCTTTTCTTTAAATCCAATATGCG
*
2872144 ACTACTTACACTTAAAAAGGAGGTTTTAGTTGAGAAATCACACTAGAGAATTCATGTGAATCATC
131 ACTACTTACACTTAAAAAGGAGGTTTTAGTTGAAAAATCACACTAGAGAATTCATGTGAATCATC
2872209 TTTCTTCACTTTTATCATCCCACTAGGACCAAAAATAAAGCAAGTGCTTATATATAGAAACCTTG
196 TTTCTTCACTTTTATCATCCCACTAGGACCAAAAATAAAGCAAGTGCTTATATATAGAAACCTTG
2872274 GATGGCTCAAATTATAAGATAACTACAACACACCTGCCATGAAGTTGAAACAAGCGTCATCGTCT
261 GATGGCTCAAATTATAAGATAACTACAACACACCTGCCATGAAGTTGAAACAAGCGTCATCGTCT
2872339 TGGTTAAATGAATAAATATTTGAATGTAAACGGCAACCCGGTGATCTCCTGTCAGAAGTTCTATT
326 TGGTTAAATGAATAAATATTTGAATGTAAACGGCAACCCGGTGATCTCCTGTCAGAAGTTCTATT
2872404 CCCCGTAACAAACTCAAAATTCCGAAACAGTTATGTATTCAATACAAATTACTGAAGCAACAGAT
391 CCCCGTAACAAACTCAAAATTCCGAAACAGTTATGTATTCAATACAAATTACTGAAGCAACAGAT
2872469 ACTCAT
456 ACTCAT
2872475 GTTTTGAAATAATTGAAGCTGGCAATTATTAATACCGGAAGGTGAGCAATTCAAGATTAGGATAA
1 GTTTTGAAATAATTGAAGCTGGCAATTATTAATACCGGAAGGTGAGCAATTCAAGATTAGGATAA
2872540 TTCACATAAGGCTGTGTCCTATAGAAAAACTAGACTTTGTTTCTTTTCTTTAAATCCAATATGCG
66 TTCACATAAGGCTGTGTCCTATAGAAAAACTAGACTTTGTTTCTTTTCTTTAAATCCAATATGCG
2872605 ACTACTTACACTTAAAAAGGAGGTTTTAGTTGAAAAATCACACTAGAGAATTCATGTGAATCATC
131 ACTACTTACACTTAAAAAGGAGGTTTTAGTTGAAAAATCACACTAGAGAATTCATGTGAATCATC
2872670 TTTCTTCACTTTTATCATCCCACTAGGACCAAAAATAAAGCAAGTGCTTATATATAGAAACCTTG
196 TTTCTTCACTTTTATCATCCCACTAGGACCAAAAATAAAGCAAGTGCTTATATATAGAAACCTTG
*
2872735 GATGGCTCAAATTATAAGATAACTACAACACACCTGCCATGAAGTTGAAACAAGCGTCATTGTCT
261 GATGGCTCAAATTATAAGATAACTACAACACACCTGCCATGAAGTTGAAACAAGCGTCATCGTCT
2872800 TGGTTAAATGAATAAATATTTGAATGTAAACGGCAACCCGGTGATCTCCTGTCAGAAGTTCTATT
326 TGGTTAAATGAATAAATATTTGAATGTAAACGGCAACCCGGTGATCTCCTGTCAGAAGTTCTATT
2872865 CCCCGTAACAAACTCAAAATTCCGAAACAGTTATGTATTCAATACAAATTACTGAAGCAACAGAT
391 CCCCGTAACAAACTCAAAATTCCGAAACAGTTATGTATTCAATACAAATTACTGAAGCAACAGAT
2872930 ACTCAT
456 ACTCAT
2872936 GTTTTGAAATAATTGAAGCTGGCAATTATTAATACCGGAAGGTGAGCAATTCAAGATTAGGATAA
1 GTTTTGAAATAATTGAAGCTGGCAATTATTAATACCGGAAGGTGAGCAATTCAAGATTAGGATAA
2873001 TTCACATAAGGCTGTGTCCTATAGAAAAACTAGACTTTGTTTCTTTTCTTTAAATCCAATATGCG
66 TTCACATAAGGCTGTGTCCTATAGAAAAACTAGACTTTGTTTCTTTTCTTTAAATCCAATATGCG
*
2873066 ACTACTTACACTTAAAAAGGAGGTTTTAGTTGAAAAATCACACTAGAGAATTCATGAGAATCATC
131 ACTACTTACACTTAAAAAGGAGGTTTTAGTTGAAAAATCACACTAGAGAATTCATGTGAATCATC
* *
2873131 TTTCTTCACTTTTATCATCCCACTAGAACCCAAAATAAAGCAAGTGCTTATATATAGAAACCTTG
196 TTTCTTCACTTTTATCATCCCACTAGGACCAAAAATAAAGCAAGTGCTTATATATAGAAACCTTG
2873196 GATGGCTCAAATTATAAGATAACTACAACACACCTGCCATGAAGTTGAAACAAGCGTCATCGTCT
261 GATGGCTCAAATTATAAGATAACTACAACACACCTGCCATGAAGTTGAAACAAGCGTCATCGTCT
* *
2873261 TGGTTAAATGAATAAATATTTGAATGTAAACGGCAACCCAGTGATCTCCTGTCAGAAGTTCCATT
326 TGGTTAAATGAATAAATATTTGAATGTAAACGGCAACCCGGTGATCTCCTGTCAGAAGTTCTATT
2873326 CCCCGTAACAAACTCAAAATTCCGAAACAGTTATGTATTCAATACAAATTACTGAAGCAACAGAT
391 CCCCGTAACAAACTCAAAATTCCGAAACAGTTATGTATTCAATACAAATTACTGAAGCAACAGAT
2873391 ACTCAT
456 ACTCAT
2873397 GT
1 GT
2873399 AACTTTCAAG
Statistics
Matches: 916, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
461 916 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (461 bp):
GTTTTGAAATAATTGAAGCTGGCAATTATTAATACCGGAAGGTGAGCAATTCAAGATTAGGATAA
TTCACATAAGGCTGTGTCCTATAGAAAAACTAGACTTTGTTTCTTTTCTTTAAATCCAATATGCG
ACTACTTACACTTAAAAAGGAGGTTTTAGTTGAAAAATCACACTAGAGAATTCATGTGAATCATC
TTTCTTCACTTTTATCATCCCACTAGGACCAAAAATAAAGCAAGTGCTTATATATAGAAACCTTG
GATGGCTCAAATTATAAGATAACTACAACACACCTGCCATGAAGTTGAAACAAGCGTCATCGTCT
TGGTTAAATGAATAAATATTTGAATGTAAACGGCAACCCGGTGATCTCCTGTCAGAAGTTCTATT
CCCCGTAACAAACTCAAAATTCCGAAACAGTTATGTATTCAATACAAATTACTGAAGCAACAGAT
ACTCAT
Found at i:2874588 original size:3 final size:3
Alignment explanation
Indices: 2874580--2874611 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2874570 CAATCCAATG
2874580 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2874612 CAAATTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2877333 original size:140 final size:137
Alignment explanation
Indices: 2877076--2877340 Score: 354
Period size: 140 Copynumber: 1.9 Consensus size: 137
2877066 AGTGAACCCA
*
2877076 ATTTGTTGATGAATCTCCATACTTAGTTTCCAAGAAGTGCAAGATTAAAAAGTTTGAGGTCTCAG
1 ATTTGTTGATGAATCTCCATACTTAGTTTCCAAGAAGTGCAAGATAAAAAAGTTTGAGGTCTCAG
*
2877141 AATACAATTCCACCATCCCTTTTAGCTCTACGCACCTTGTTCCAACAAATGAAAGCCCAAGAAGC
66 AATACAATTCCACCATCCCTTTTAGCTCTACACACCTTGTTCCAACAAATGAAAGCCCAAGAAGC
2877206 GAACTCG
131 GAACTCG
* * * *
2877213 ATTTGTTGATGAATCTCCGTACTTAGTTTCTAAGAAGTGCGAGATAAAAAAAAAGCTTT-ATGTC
1 ATTTGTTGATGAATCTCCATACTTAGTTTCCAAGAAGTGCAAGAT---AAAAAAG-TTTGAGGTC
** * * * * *
2877277 TTGGAAT-CTCATTCCACCGTCCCTTTTAGCTCTACACACCTTGTTCTAAGAGATGAAAGCCCAA
62 TCAGAATAC-AATTCCACCATCCCTTTTAGCTCTACACACCTTGTTCCAACAAATGAAAGCCCAA
2877341 CATCTAGCAT
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
137 42 0.38
139 1 0.01
140 64 0.58
141 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (137 bp):
ATTTGTTGATGAATCTCCATACTTAGTTTCCAAGAAGTGCAAGATAAAAAAGTTTGAGGTCTCAG
AATACAATTCCACCATCCCTTTTAGCTCTACACACCTTGTTCCAACAAATGAAAGCCCAAGAAGC
GAACTCG
Found at i:2884129 original size:20 final size:20
Alignment explanation
Indices: 2884101--2884138 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2884091 AAGCTCACAT
*
2884101 AGGATCATATAGATGCATTA
1 AGGAGCATATAGATGCATTA
*
2884121 AGGAGCATATAGTTGCAT
1 AGGAGCATATAGATGCAT
2884139 GTGGTGGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (20 bp):
AGGAGCATATAGATGCATTA
Found at i:2893003 original size:21 final size:21
Alignment explanation
Indices: 2892977--2893030 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2892967 CCGTTGAACA
2892977 GGGGGAATCGGTACCCCCTAT
1 GGGGGAATCGGTACCCCCTAT
2892998 GGGGGAATCGGTACCCCCTAT
1 GGGGGAATCGGTACCCCCTAT
2893019 GGGGGAATCGGT
1 GGGGGAATCGGT
2893031 TCCCTTTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.24, G:0.39, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTAT
Found at i:2893492 original size:16 final size:17
Alignment explanation
Indices: 2893461--2893494 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
2893451 ATTTATCATT
2893461 TTAAAACACTCTTAAAAC
1 TTAAAACAC-CTTAAAAC
2893479 TTAAAACA-CTTAAAAC
1 TTAAAACACCTTAAAAC
2893495 ACAACTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (17 bp):
TTAAAACACCTTAAAAC
Found at i:2893760 original size:31 final size:27
Alignment explanation
Indices: 2893725--2893788 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 27
2893715 ATAAAACACA
2893725 CCAAACATATAAGTTCACACCATCCACAAAT
1 CCAAACATA-AA-TTCACA--ATCCACAAAT
2893756 CCAAAC--AAATTCACAATCCACAAAT
1 CCAAACATAAATTCACAATCCACAAAT
*
2893781 TCAAACAT
1 CCAAACAT
2893789 TCAAAATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
25 15 0.50
27 6 0.20
28 2 0.07
29 1 0.03
31 6 0.20
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (27 bp):
CCAAACATAAATTCACAATCCACAAAT
Found at i:2895356 original size:21 final size:20
Alignment explanation
Indices: 2895326--2895369 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2895316 AACACATTAA
2895326 TTTTGAAAATCAAAATTTTT
1 TTTTGAAAATCAAAATTTTT
**
2895346 TTTTCGAAAAT-TTAATTTTT
1 TTTT-GAAAATCAAAATTTTT
2895366 TTTT
1 TTTT
2895370 TTTTGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTGAAAATCAAAATTTTT
Found at i:2895764 original size:21 final size:20
Alignment explanation
Indices: 2895736--2895794 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
2895726 AACAGAACCC
2895736 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGG-ATCGATTCCCCT
** *
2895757 GTGGGGGGAATCGGTT-CCCT
1 CAGGGGGG-ATCGATTCCCCT
2895777 CAGGGGGGATCGATTCCC
1 CAGGGGGGATCGATTCCC
2895795 TCTGCACCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 6 0.20
20 12 0.40
21 12 0.40
ACGTcount: A:0.14, C:0.25, G:0.39, T:0.22
Consensus pattern (20 bp):
CAGGGGGGATCGATTCCCCT
Found at i:2895788 original size:19 final size:20
Alignment explanation
Indices: 2895736--2895796 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
2895726 AACAGAACCC
*
2895736 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATT-CCCT
** *
2895757 GTGGGGGGAATCGGTTCCCT
1 CAGGGGGGAATCGATTCCCT
2895777 CAGGGGGG-ATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
2895796 C
1 C
2895797 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
19 11 0.33
20 10 0.30
21 12 0.36
ACGTcount: A:0.13, C:0.26, G:0.38, T:0.23
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:2899635 original size:22 final size:21
Alignment explanation
Indices: 2899593--2899632 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2899583 GAGTTTATTT
*
2899593 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2899614 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2899633 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2901575 original size:21 final size:21
Alignment explanation
Indices: 2901549--2901602 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2901539 CCGTTGAACA
2901549 GGGGGAATCGGTACCCCCTAT
1 GGGGGAATCGGTACCCCCTAT
2901570 GGGGGAATCGGTACCCCCTAT
1 GGGGGAATCGGTACCCCCTAT
2901591 GGGGGAATCGGT
1 GGGGGAATCGGT
2901603 TCCCTCCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.24, G:0.39, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTAT
Found at i:2913408 original size:13 final size:12
Alignment explanation
Indices: 2913387--2913416 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2913377 AAAAGAATGG
2913387 AAAAATAAAATT
1 AAAAATAAAATT
2913399 AAAAATTAAAATT
1 AAAAA-TAAAATT
2913412 AAAAA
1 AAAAA
2913417 ACAAACAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATAAAATT
Found at i:2913925 original size:19 final size:18
Alignment explanation
Indices: 2913881--2913925 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2913871 AACAAAACTT
* *
2913881 AAAAAATTAAATAAAGAT
1 AAAAAATTAAATAAAAAG
2913899 AAATAAATTAAATAAAAAGG
1 AAA-AAATTAAATAAAAA-G
2913919 AAAAAAT
1 AAAAAAT
2913926 CATCGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 17 0.74
20 3 0.13
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (18 bp):
AAAAAATTAAATAAAAAG
Found at i:2914096 original size:17 final size:18
Alignment explanation
Indices: 2914068--2914103 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2914058 CAACAAGAGC
2914068 AAAAGCAAAATAAAAAAT
1 AAAAGCAAAATAAAAAAT
*
2914086 AAAAG-AAAATAGAAAAT
1 AAAAGCAAAATAAAAAAT
2914103 A
1 A
2914104 GAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (18 bp):
AAAAGCAAAATAAAAAAT
Found at i:2918749 original size:2 final size:2
Alignment explanation
Indices: 2918742--2918786 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2918732 AACATGAGGA
2918742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2918784 AT A
1 AT A
2918787 ATAAAATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2920977 original size:10 final size:8
Alignment explanation
Indices: 2920956--2921006 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
2920946 TTTTTTTTCA
2920956 AAAAAAAC
1 AAAAAAAC
*
2920964 AAAAAAGGC
1 AAAAAA-AC
2920973 AAAAAAAC
1 AAAAAAAC
2920981 AAAAAAAATGC
1 -AAAAAAA--C
2920992 AAAAAAAC
1 AAAAAAAC
2921000 AAAAAAA
1 AAAAAAA
2921007 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 15 0.41
9 14 0.38
10 7 0.19
11 1 0.03
ACGTcount: A:0.82, C:0.10, G:0.06, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:2920978 original size:17 final size:17
Alignment explanation
Indices: 2920956--2921005 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 17
2920946 TTTTTTTTCA
2920956 AAAAAAACAAAAAAGGC
1 AAAAAAACAAAAAAGGC
*
2920973 AAAAAAACAAAAAAAATGC
1 AAAAAAAC--AAAAAAGGC
2920992 AAAAAAACAAAAAA
1 AAAAAAACAAAAAA
2921006 AGCCAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 14 0.47
19 16 0.53
ACGTcount: A:0.82, C:0.10, G:0.06, T:0.02
Consensus pattern (17 bp):
AAAAAAACAAAAAAGGC
Found at i:2921012 original size:10 final size:9
Alignment explanation
Indices: 2920954--2921013 Score: 61
Period size: 9 Copynumber: 6.6 Consensus size: 9
2920944 AATTTTTTTT
*
2920954 CAAAAAAAA
1 CAAAAAAAG
*
2920963 CAAAAAAGG
1 CAAAAAAAG
2920972 CAAAAAAA-
1 CAAAAAAAG
2920980 CAAAAAAAATG
1 C-AAAAAAA-G
2920991 CAAAAAAA-
1 CAAAAAAAG
2920999 CAAAAAAAG
1 CAAAAAAAG
2921008 CCAAAA
1 -CAAAA
2921014 TTTAAAAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
8 9 0.21
9 21 0.49
10 12 0.28
11 1 0.02
ACGTcount: A:0.78, C:0.13, G:0.07, T:0.02
Consensus pattern (9 bp):
CAAAAAAAG
Found at i:2921013 original size:17 final size:17
Alignment explanation
Indices: 2920956--2921013 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 17
2920946 TTTTTTTTCA
*
2920956 AAAAAAACAAAAAAGGC
1 AAAAAAACAAAAAAAGC
2920973 AAAAAAACAAAAAAAATGC
1 AAAAAAAC-AAAAAAA-GC
2920992 AAAAAAACAAAAAAAGCC
1 AAAAAAACAAAAAAAG-C
2921010 AAAA
1 AAAA
2921014 TTTAAAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
17 9 0.24
18 18 0.49
19 10 0.27
ACGTcount: A:0.79, C:0.12, G:0.07, T:0.02
Consensus pattern (17 bp):
AAAAAAACAAAAAAAGC
Found at i:2926632 original size:100 final size:100
Alignment explanation
Indices: 2926502--2926693 Score: 269
Period size: 100 Copynumber: 1.9 Consensus size: 100
2926492 GGAAATTATT
* * *
2926502 TGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCGTGTGCTGTCTCGAGTCTAATATCCTT
1 TGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCGTATGCTGTCTCGAGTCCAATATCCTT
2926567 CGTCATGAAGTTGAAATTGACTCTGAATGAAATTG
66 CGTCATGAAGTTGAAATTGACTCTGAATGAAATTG
* * * * *
2926602 TGTTGACAATCAGCCGCCCCTTC-ATCGTGAAGTTGAGCTTATGTTGTCTTGGGTCCAATATCCT
1 TGTTGACAATCAGCCGCCCCTTCGCT-GTGAAGTTGAGCGTATGCTGTCTCGAGTCCAATATCCT
** *
2926666 TCGTTGTGAAGTTGAAATTGGCTCTGAA
65 TCGTCATGAAGTTGAAATTGACTCTGAA
2926694 ATTGTGAAGC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 1 0.01
100 79 0.99
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (100 bp):
TGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCGTATGCTGTCTCGAGTCCAATATCCTT
CGTCATGAAGTTGAAATTGACTCTGAATGAAATTG
Found at i:2927839 original size:7 final size:7
Alignment explanation
Indices: 2927823--2927872 Score: 66
Period size: 7 Copynumber: 6.9 Consensus size: 7
2927813 ACCCACCTTA
2927823 TTTTTC-
1 TTTTTCT
2927829 TTTTTCT
1 TTTTTCT
2927836 TTTTTCT
1 TTTTTCT
2927843 TTTTTCT
1 TTTTTCT
2927850 TTTGTTCT
1 TTT-TTCT
2927858 TTTTCCTCT
1 TTTT--TCT
2927867 TTTTTC
1 TTTTTC
2927873 AATTTAGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.15
7 20 0.50
8 7 0.17
9 7 0.17
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:2938608 original size:2 final size:2
Alignment explanation
Indices: 2938601--2938635 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2938591 CATGAGGAAA
*
2938601 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2938636 ATAATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2951748 original size:3 final size:3
Alignment explanation
Indices: 2951740--2951796 Score: 80
Period size: 3 Copynumber: 18.7 Consensus size: 3
2951730 GTCGAAAAAA
*
2951740 TAT TAT TAT TAT TAAT TAT TACT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
2951787 T-T TAT TAT TA
1 TAT TAT TAT TA
2951797 ACAATTGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2951778 original size:26 final size:23
Alignment explanation
Indices: 2951740--2951796 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 23
2951730 GTCGAAAAAA
*
2951740 TATTATTATTATTAATTATTACTTAT
1 TATTATTACTATT-ATTATTA-TT-T
2951766 TATTATTACTATTATTATTATTT
1 TATTATTACTATTATTATTATTT
2951789 TATTATTA
1 TATTATTA
2951797 ACAATTGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 9 0.30
24 2 0.07
25 7 0.23
26 12 0.40
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTATTACTATTATTATTATTT
Found at i:2951880 original size:3 final size:3
Alignment explanation
Indices: 2951874--2951902 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2951864 TTTATATTTA
2951874 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2951903 CTTTTATTTT
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:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2953269 original size:15 final size:15
Alignment explanation
Indices: 2953220--2953270 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
2953210 GTATTTTAGT
*
2953220 ATATGTGTATGTTTC
1 ATATGTGTATGTATC
* *
2953235 ATAT-TCTCATGTATT
1 ATATGTGT-ATGTATC
*
2953250 TTATGTGTATGTATC
1 ATATGTGTATGTATC
2953265 ATATGT
1 ATATGT
2953271 ATGTATTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
14 2 0.07
15 23 0.85
16 2 0.07
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (15 bp):
ATATGTGTATGTATC
Found at i:2959430 original size:24 final size:23
Alignment explanation
Indices: 2959368--2959431 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
2959358 TCCCCTTGAA
*
2959368 GTGCATCGATGCATCC-TACCGT
1 GTGCATCGATGCATCCTTAACGT
2959390 GT--ATCGATGCATCCCTTAACGT
1 GTGCATCGATGCAT-CCTTAACGT
2959412 GTGCATCGATGCACTCCTTA
1 GTGCATCGATGCA-TCCTTA
2959432 TGCATCGATG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 10 0.28
21 2 0.06
22 9 0.25
24 14 0.39
25 1 0.03
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTAACGT
Found at i:2963394 original size:24 final size:21
Alignment explanation
Indices: 2963345--2963418 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 21
2963335 TCTTGAAGTA
*
2963345 CATCGATGCATCCTACCGTGT
1 CATCGATGCATCCTAACGTGT
2963366 -ATCGATGCATCCCTTAACGTGT
1 CATCGATGCAT-CC-TAACGTGT
*
2963388 GCATCGATGCACTCCTTA--TG-
1 -CATCGATGCA-TCCTAACGTGT
2963408 CATCGATGCAT
1 CATCGATGCAT
2963419 TAATTGTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
18 1 0.02
19 10 0.22
20 10 0.22
21 4 0.09
22 7 0.15
23 2 0.04
24 11 0.24
25 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (21 bp):
CATCGATGCATCCTAACGTGT
Found at i:2970046 original size:20 final size:20
Alignment explanation
Indices: 2970017--2970059 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2970007 ATTCCACCAC
2970017 ATGCAACTATATGCTTCTAA
1 ATGCAACTATATGCTTCTAA
* * *
2970037 ATGCATCTATATGGTTTTAA
1 ATGCAACTATATGCTTCTAA
2970057 ATG
1 ATG
2970060 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGCAACTATATGCTTCTAA
Found at i:2971340 original size:10 final size:10
Alignment explanation
Indices: 2971325--2971389 Score: 73
Period size: 10 Copynumber: 6.5 Consensus size: 10
2971315 CAAAGAGAGA
2971325 AAAAAGAAAG
1 AAAAAGAAAG
2971335 AAAAAGAAAG
1 AAAAAGAAAG
2971345 AAAAAG-AAG
1 AAAAAGAAAG
2971354 CAAAAAGAAA-
1 -AAAAAGAAAG
*
2971364 AAACA-AAAG
1 AAAAAGAAAG
2971373 AAAAAGCAAAG
1 AAAAAG-AAAG
2971384 AGAAAA
1 A-AAAA
2971390 TAGAAGACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
8 3 0.06
9 11 0.23
10 22 0.47
11 7 0.15
12 4 0.09
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:2971342 original size:6 final size:6
Alignment explanation
Indices: 2971322--2971394 Score: 53
Period size: 6 Copynumber: 11.7 Consensus size: 6
2971312 AAACAAAGAG
*
2971322 AGAAAA A-AGAA AGAAAA AGAAAGA A-AAAGA AGCAAAA AGAAAA A-ACAAA
1 AGAAAA AGAAAA AGAAAA AGAAA-A AGAAA-A AG-AAAA AGAAAA AGA-AAA
*
2971371 AGAAAA AGCAAAG AGAAAA TAGAA
1 AGAAAA AG-AAAA AGAAAA -AGAA
2971395 GACAAGAAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
5 5 0.09
6 32 0.58
7 15 0.27
8 3 0.05
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.01
Consensus pattern (6 bp):
AGAAAA
Found at i:2971404 original size:25 final size:25
Alignment explanation
Indices: 2971331--2971405 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 25
2971321 GAGAAAAAAG
*
2971331 AAAGAAAAAGA-AAGAAAAAGAAGCAA
1 AAAGAAAAA-ACAA-AACAAGAAGCAA
* *
2971357 AAAGAAAAAACAAAAGAAAAAGCAA
1 AAAGAAAAAACAAAACAAGAAGCAA
* * * *
2971382 AGAGAAAATAGAAGACAAGAAGCA
1 AAAGAAAAAACAAAACAAGAAGCA
2971406 CATGTAAAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
25 29 0.73
26 11 0.28
ACGTcount: A:0.73, C:0.07, G:0.19, T:0.01
Consensus pattern (25 bp):
AAAGAAAAAACAAAACAAGAAGCAA
Found at i:2972743 original size:67 final size:67
Alignment explanation
Indices: 2972672--2972975 Score: 364
Period size: 67 Copynumber: 4.6 Consensus size: 67
2972662 ATTTTTTCTT
** * *
2972672 TGAAACAAAAATCTTTGAGTTTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCC
1 TGAAACACCAATCTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCC
2972737 CA
66 CA
* * *
2972739 TGAAACACCAACCTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTCCC
1 TGAAACACCAATCTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCC
2972804 CA
66 CA
* * *
2972806 TGAAACACCAACCTTTGAGATTATTTCCCTT-AAA-ATAAGTTTTGTCTCCCTTGAGACAATTTC
1 TGAAACACCAATCTTTGAGATTGTTTCCCTTGAAACA-AAATTTTGTCTCCCTTGAGACAATTTC
* *
2972869 TCT
65 CCA
* * * * * *
2972872 TGAAACACCCATCTTTGAGATCGTTTCCCTTGAAAC-GAATTTTGTCTCTCTTGAGACAACTTCT
1 TGAAACACCAATCTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCC
*
2972936 CT
66 CA
* * * *
2972938 TGAAGCATC-ATCTTTGAGTTTGTTTCTCTTGAAACAAA
1 TGAAACACCAATCTTTGAGATTGTTTCCCTTGAAACAAA
2972976 TCCCTAAAGA
Statistics
Matches: 208, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
65 24 0.12
66 89 0.43
67 95 0.46
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (67 bp):
TGAAACACCAATCTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCC
CA
Found at i:2972861 original size:66 final size:67
Alignment explanation
Indices: 2972684--2972975 Score: 358
Period size: 66 Copynumber: 4.4 Consensus size: 67
2972674 AAACAAAAAT
*
2972684 CTTTGAGTTTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCATGAAACACCA
1 CTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCATGAAACACCA
2972749 AC
66 AC
*
2972751 CTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTCCCCATGAAACACCA
1 CTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCATGAAACACCA
2972816 AC
66 AC
* * * * *
2972818 CTTTGAGATTATTTCCCTT-AAA-ATAAGTTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACC
1 CTTTGAGATTGTTTCCCTTGAAACA-AAATTTTGTCTCCCTTGAGACAGTTTCCCATGAAACACC
* *
2972881 CAT
65 AAC
* * * ** * * * *
2972884 CTTTGAGATCGTTTCCCTTGAAAC-GAATTTTGTCTCTCTTGAGACAACTTCTCTTGAAGCATC-
1 CTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCATGAAACACCA
*
2972947 AT
66 AC
* *
2972949 CTTTGAGTTTGTTTCTCTTGAAACAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAA
2972976 TCCCTAAAGA
Statistics
Matches: 199, Mismatches: 22, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
65 24 0.12
66 89 0.45
67 86 0.43
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (67 bp):
CTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCATGAAACACCA
AC
Found at i:2972889 original size:133 final size:133
Alignment explanation
Indices: 2972684--2972929 Score: 361
Period size: 133 Copynumber: 1.8 Consensus size: 133
2972674 AAACAAAAAT
* * *
2972684 CTTTGAGTTTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCATGAAACACCA
1 CTTTGAGATTATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCCCATGAAACACCA
*
2972749 ACCTTTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTCCCCATGAAACAC
66 ACCTTTGAGATCGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTCCCCATGAAACAC
2972814 CAAC
130 CAAC
* * *
2972818 CTTTGAGATTATTTCCCTT-AAA-ATAAGTTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACC
1 CTTTGAGATTATTTCCCTTGAAACA-AAATTTTGTCTCCCTTGAGACAATTTCCCATGAAACACC
* * * *
2972881 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
65 AACCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
2972930 ACTTCTCTTG
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
132 21 0.21
133 62 0.62
134 17 0.17
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.36
Consensus pattern (133 bp):
CTTTGAGATTATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCCCATGAAACACCA
ACCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTCCCCATGAAACACC
AAC
Found at i:2973109 original size:22 final size:22
Alignment explanation
Indices: 2973039--2973110 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
2973029 CCATACCTCC
*
2973039 TCATCACGTAGGAACCGTGTCA
1 TCATCACGTAGGAACCGTGTTA
* * * *
2973061 CCCTCA-G-ATG-ACCAGTCGTTC
1 TCATCACGTAGGAACC-GT-GTTA
2973082 TCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAACCGTGTTA
2973104 TCATCAC
1 TCATCAC
2973111 TAAAGATAAC
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
19 3 0.08
20 4 0.11
21 7 0.19
22 15 0.42
23 4 0.11
24 3 0.08
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (22 bp):
TCATCACGTAGGAACCGTGTTA
Found at i:2973326 original size:40 final size:42
Alignment explanation
Indices: 2973262--2973367 Score: 108
Period size: 43 Copynumber: 2.5 Consensus size: 42
2973252 GGCTAAGACG
* * * * *
2973262 TCCTCATCACGTAAGAACAATGTCATCC-A-CCGACCAGATC
1 TCCTCATCACGTAAGAGCAGTGTCACCCTAGACGACCAGAAC
* *
2973302 TCCTCATCACGTAGGAGCCGTGTCACCCTTAGACGACCAGAAC
1 TCCTCATCACGTAAGAGCAGTGTCACCC-TAGACGACCAGAAC
* *
2973345 TCTTCATCACGTATGAGCAGTGT
1 TCCTCATCACGTAAGAGCAGTGT
2973368 TGTCCCCAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
40 23 0.43
42 1 0.02
43 29 0.55
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (42 bp):
TCCTCATCACGTAAGAGCAGTGTCACCCTAGACGACCAGAAC
Found at i:2973555 original size:15 final size:15
Alignment explanation
Indices: 2973537--2973566 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2973527 ATTATTTATA
2973537 TTATTATTATTACAT
1 TTATTATTATTACAT
*
2973552 TTATTTTTATTACAT
1 TTATTATTATTACAT
2973567 ATTTTACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTATTATTACAT
Found at i:2973555 original size:24 final size:24
Alignment explanation
Indices: 2973528--2973576 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2973518 TACAAAAATA
*
2973528 TTATTTATATTA-TTATTATTACAT
1 TTATTTATATTACATATT-TTACAT
*
2973552 TTATTTTTATTACATATTTTACAT
1 TTATTTATATTACATATTTTACAT
2973576 T
1 T
2973577 GTTATTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATTTATATTACATATTTTACAT
Found at i:2974917 original size:35 final size:35
Alignment explanation
Indices: 2974871--2974950 Score: 160
Period size: 35 Copynumber: 2.3 Consensus size: 35
2974861 TTTTGGTCCT
2974871 TGTATTTTATTATATGTGTATGCTTCATATTCTCA
1 TGTATTTTATTATATGTGTATGCTTCATATTCTCA
2974906 TGTATTTTATTATATGTGTATGCTTCATATTCTCA
1 TGTATTTTATTATATGTGTATGCTTCATATTCTCA
2974941 TGTATTTTAT
1 TGTATTTTAT
2974951 GTGTATGTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.23, C:0.10, G:0.11, T:0.56
Consensus pattern (35 bp):
TGTATTTTATTATATGTGTATGCTTCATATTCTCA
Found at i:2974936 original size:20 final size:20
Alignment explanation
Indices: 2974878--2974936 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
2974868 CCTTGTATTT
2974878 TATTATATGTGTATGCTTCA
1 TATTATATGTGTATGCTTCA
*
2974898 TATTCTCA--TGTAT--TT--
1 TATTAT-ATGTGTATGCTTCA
2974913 TATTATATGTGTATGCTTCA
1 TATTATATGTGTATGCTTCA
2974933 TATT
1 TATT
2974937 CTCATGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 1 0.03
15 5 0.17
16 5 0.17
17 2 0.07
18 2 0.07
19 5 0.17
20 9 0.30
21 1 0.03
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (20 bp):
TATTATATGTGTATGCTTCA
Found at i:2976526 original size:20 final size:21
Alignment explanation
Indices: 2976503--2976541 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2976493 AAGCCTTTGT
2976503 ATTTAATAGTA-ATTTTCAAC
1 ATTTAATAGTATATTTTCAAC
* *
2976523 ATTTACTCGTATATTTTCA
1 ATTTAATAGTATATTTTCA
2976542 GGTTTCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTTAATAGTATATTTTCAAC
Found at i:2978263 original size:15 final size:15
Alignment explanation
Indices: 2978214--2978264 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
2978204 GTATTTTAAT
*
2978214 ATATGTGTATGTTTC
1 ATATGTGTATGTATC
* *
2978229 ATAT-TCTAATGTATT
1 ATATGTGT-ATGTATC
*
2978244 TTATGTGTATGTATC
1 ATATGTGTATGTATC
2978259 ATATGT
1 ATATGT
2978265 ATGTATTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
14 2 0.07
15 23 0.85
16 2 0.07
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (15 bp):
ATATGTGTATGTATC
Found at i:2978312 original size:20 final size:21
Alignment explanation
Indices: 2978289--2978327 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2978279 ATGTCTTTTT
*
2978289 ATTTAATTGTA-ATTTTCAAC
1 ATTTAATCGTATATTTTCAAC
*
2978309 ATTTACTCGTATATTTTCA
1 ATTTAATCGTATATTTTCA
2978328 GGCTTCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTAATCGTATATTTTCAAC
Found at i:2979539 original size:17 final size:16
Alignment explanation
Indices: 2979519--2979552 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2979509 TAAAAATATT
*
2979519 TAAAAAATGAAAAGAAA
1 TAAAAAAAGAAAA-AAA
2979536 TAAAAAAAGAAAAAAA
1 TAAAAAAAGAAAAAAA
2979552 T
1 T
2979553 TATATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
TAAAAAAAGAAAAAAA
Found at i:2988705 original size:37 final size:37
Alignment explanation
Indices: 2988663--2988755 Score: 109
Period size: 37 Copynumber: 2.5 Consensus size: 37
2988653 TAGAGACAAA
2988663 TTTTCT-TAAAAAAAAAATTTTATCTCACTTGAGATAG
1 TTTTCTCT-AAAAAAAAATTTTATCTCACTTGAGATAG
* * *
2988700 TTTTCTCTAAAAACAAATTTTGTCTCACTTGAGACA-
1 TTTTCTCTAAAAAAAAATTTTATCTCACTTGAGATAG
* * *
2988736 ATTTCTCTCAAAATAAATTT
1 TTTTCTCTAAAAAAAAATTT
2988756 CGTATCATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
36 17 0.35
37 31 0.63
38 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (37 bp):
TTTTCTCTAAAAAAAAATTTTATCTCACTTGAGATAG
Found at i:2988741 original size:36 final size:36
Alignment explanation
Indices: 2988634--2988771 Score: 125
Period size: 36 Copynumber: 3.8 Consensus size: 36
2988624 TGTTTTTCTG
* *
2988634 AAAACAAATTTCGTCTCGCTAGAGACAAATTT-TCTTAA
1 AAAACAAATTTCGTCTCACTTGAGAC-AATTTCTC-T-A
* ** * *
2988672 AAAAAAAATTTTATCTCACTTGAGATAGTTTTCTCTA
1 AAAACAAATTTCGTCTCACTTGAGACA-ATTTCTCTA
* *
2988709 AAAACAAATTTTGTCTCACTTGAGACAATTTCTCTC
1 AAAACAAATTTCGTCTCACTTGAGACAATTTCTCTA
* * *
2988745 AAAATAAATTTCGTATCATTTGAGACA
1 AAAACAAATTTCGTCTCACTTGAGACA
2988772 TTTTTCCTTT
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
36 30 0.37
37 26 0.32
38 24 0.29
39 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (36 bp):
AAAACAAATTTCGTCTCACTTGAGACAATTTCTCTA
Found at i:2989136 original size:21 final size:20
Alignment explanation
Indices: 2989112--2989153 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2989102 ACCTTTGAGA
*
2989112 TTGTTTCTCTTGAAACAAGTT
1 TTGTCTCTCTTGAAAC-AGTT
*
2989133 TTGTCTCTCTTGAGACAGTT
1 TTGTCTCTCTTGAAACAGTT
2989153 T
1 T
2989154 CTCTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (20 bp):
TTGTCTCTCTTGAAACAGTT
Found at i:2989154 original size:36 final size:36
Alignment explanation
Indices: 2989114--2989200 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
2989104 CTTTGAGATT
*
2989114 GTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
2989150 GTTTCTCTTGAAATAATTTTTGTCTCTCTTGAGATA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
2989186 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
2989201 TCATCTTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:2989260 original size:64 final size:65
Alignment explanation
Indices: 2989142--2989264 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 65
2989132 TTTGTCTCTC
* * * * *
2989142 TTGAGACAGTTTCTCTTGAAATAATTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATCATCT
1 TTGAGACAGTTTCCCTTGAAATAAATTTGGTCTCTCTTGAGACAGTTTCCCTTGAAACATCATCT
*
2989207 TTGAGATC-GTTTCCCTTGAAA-AAATTTGGTCTCTCTTGAGACGGTTTCCCTTGAAACA
1 TTGAGA-CAGTTTCCCTTGAAATAAATTTGGTCTCTCTTGAGACAGTTTCCCTTGAAACA
2989265 AATTTTGTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 32 0.63
65 18 0.35
66 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (65 bp):
TTGAGACAGTTTCCCTTGAAATAAATTTGGTCTCTCTTGAGACAGTTTCCCTTGAAACATCATCT
Found at i:2989260 original size:100 final size:101
Alignment explanation
Indices: 2989104--2989300 Score: 306
Period size: 100 Copynumber: 2.0 Consensus size: 101
2989094 TTGATAAAAC
* * * * * * *
2989104 CTTTGAGATTGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAATTT
1 CTTTGAGATCGTTTCCCTTGAAACAAATTTGGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
*
2989169 TTGTCTCTCTTGAGATAGTTTCTCTTGAAACATCAT
66 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCAT
*
2989205 CTTTGAGATCGTTTCCCTTGAAA-AAATTTGGTCTCTCTTGAGACGGTTTCCCTTGAAACAAATT
1 CTTTGAGATCGTTTCCCTTGAAACAAATTTGGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
2989269 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
66 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
2989301 AATCCCTAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
100 66 0.76
101 21 0.24
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (101 bp):
CTTTGAGATCGTTTCCCTTGAAACAAATTTGGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
TTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCAT
Found at i:2989275 original size:36 final size:35
Alignment explanation
Indices: 2989207--2989303 Score: 142
Period size: 36 Copynumber: 2.7 Consensus size: 35
2989197 AACATCATCT
2989207 TTGAGATCGTTTCCCTTGAAA-AAATTTGGTCTCTC
1 TTGAGA-CGTTTCCCTTGAAACAAATTTGGTCTCTC
*
2989242 TTGAGACGGTTTCCCTTGAAACAAATTTTGTCTCTC
1 TTGAGAC-GTTTCCCTTGAAACAAATTTGGTCTCTC
*
2989278 TTGAGACAGTTTCTCTTGAAACAAAT
1 TTGAGAC-GTTTCCCTTGAAACAAAT
2989304 CCCTAAAGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
34 1 0.02
35 19 0.33
36 37 0.65
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (35 bp):
TTGAGACGTTTCCCTTGAAACAAATTTGGTCTCTC
Found at i:2989469 original size:40 final size:41
Alignment explanation
Indices: 2989414--2989523 Score: 118
Period size: 43 Copynumber: 2.7 Consensus size: 41
2989404 TGGCATGTCA
** *
2989414 TCCTCATCGTGTAGGAATTGTGTCATCCACC-G-ACCAGCCG
1 TCCTCATCACGTAGGAACTGTGTCATCC-CCAGAACCAGCCG
* *
2989454 TCCTCATCACGTAGGAACCGTGTCA-CCCCTAGATAATCAGCCG
1 TCCTCATCACGTAGGAACTGTGTCATCCCC-AG--AACCAGCCG
2989497 TCCTCATCACGTAGGAACTGTGTCATC
1 TCCTCATCACGTAGGAACTGTGTCATC
2989524 TACCAATCAG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 22 0.38
43 31 0.53
44 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.25
Consensus pattern (41 bp):
TCCTCATCACGTAGGAACTGTGTCATCCCCAGAACCAGCCG
Found at i:2989763 original size:3 final size:3
Alignment explanation
Indices: 2989755--2989795 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
2989745 GGTCAAAAAA
*
2989755 TAT TAT TAT TAAT TAT TAA TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2989796 AGAATTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2991446 original size:5 final size:5
Alignment explanation
Indices: 2991433--2991470 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
2991423 CTCTTTTCAT
*
2991433 TTTTA TTTTG TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
2991471 CATCTTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:2995219 original size:12 final size:12
Alignment explanation
Indices: 2995202--2995230 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2995192 CCTGCAAGTT
2995202 GCCGCGTGAGCA
1 GCCGCGTGAGCA
2995214 GCCGCGTGAGCA
1 GCCGCGTGAGCA
2995226 GCCGC
1 GCCGC
2995231 CGAGTGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.38, G:0.41, T:0.07
Consensus pattern (12 bp):
GCCGCGTGAGCA
Found at i:2999449 original size:55 final size:55
Alignment explanation
Indices: 2999359--2999930 Score: 858
Period size: 55 Copynumber: 10.4 Consensus size: 55
2999349 ATTTATACAT
* * *
2999359 TTAGTATGAATTTCCT-AGTTTTTCACATGAAGTGCCCATACAGAAATTCATCCAC
1 TTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCCATACAGAAATTCATCCAC
* * * *
2999414 TTAGTATGAATTCCTTAAGTTTACACACAAGGTGCCCATACGGAAATTCATCCAC
1 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
* * * **
2999469 TTAGAATGAATTTCTTAAGTTTTCACATAAAGTGCCCATACAGAAATTCGTTTAC
1 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
* * ** *
2999524 TTAGTATGAATTTCTTAAGTTTACACACAAGGTGCCCATATGGAAATTCATCTAC
1 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
*
2999579 TTAGAATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
1 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
* ** *
2999634 TTAGTATGAATTTCTTAAGTTTACACACATGGTGCCCATACGGAAATTCATCCAC
1 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
2999689 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
1 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
* * *
2999744 TTAGTATGATTTTTTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATCCAC
1 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
* * *
2999799 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGTCCATAGAAAAATTCATCCAC
1 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
*
2999854 TTGGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
1 TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
*
2999909 TTAGAATGAATTTCTTAAGTTT
1 TTAGTATGAATTTCTTAAGTTT
2999931 TTGCACACTT
Statistics
Matches: 462, Mismatches: 54, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
55 460 1.00
56 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (55 bp):
TTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCCAC
Found at i:3002283 original size:2 final size:2
Alignment explanation
Indices: 3002276--3002306 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3002266 ATCTTTAATT
3002276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3002307 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3006454 original size:17 final size:18
Alignment explanation
Indices: 3006418--3006454 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3006408 TTATGAGGTG
3006418 AAAAATGACATTATTGTA
1 AAAAATGACATTATTGTA
3006436 AAAAATGTA-ATTATT-TA
1 AAAAATG-ACATTATTGTA
3006453 AA
1 AA
3006455 GTAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 13 0.72
19 1 0.06
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (18 bp):
AAAAATGACATTATTGTA
Found at i:3027018 original size:66 final size:67
Alignment explanation
Indices: 3026920--3027046 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 67
3026910 CCCAATTAAT
* *
3026920 TTCATCTCCCCAAACTTCCATATCCATTTACACTACACTCGTCTCCA-CTCACATCCCCACATCT
1 TTCATCTCCCCAAACTTCCATATCCATCTACACTACACTCATCTCCATC-CACATCCCCACATCT
3026984 ATC
65 ATC
** * * *
3026987 TTCATCTCCCC-GGCTTCCATCTCCATCTACACTACACTTATCTCCATCCACTTCCCCACA
1 TTCATCTCCCCAAACTTCCATATCCATCTACACTACACTCATCTCCATCCACATCCCCACA
3027047 ACAGTCTTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 40 0.77
67 12 0.23
ACGTcount: A:0.23, C:0.45, G:0.02, T:0.30
Consensus pattern (67 bp):
TTCATCTCCCCAAACTTCCATATCCATCTACACTACACTCATCTCCATCCACATCCCCACATCTA
TC
Found at i:3027850 original size:23 final size:23
Alignment explanation
Indices: 3027820--3027867 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3027810 ATACAATAAA
3027820 GTCTTTTCTTATCTCAAAGCTTG
1 GTCTTTTCTTATCTCAAAGCTTG
3027843 GTCTTTTCTTATCTCAAAGCTTG
1 GTCTTTTCTTATCTCAAAGCTTG
3027866 GT
1 GT
3027868 TTTGTTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.15, T:0.48
Consensus pattern (23 bp):
GTCTTTTCTTATCTCAAAGCTTG
Found at i:3029478 original size:6 final size:6
Alignment explanation
Indices: 3029467--3029628 Score: 225
Period size: 6 Copynumber: 27.0 Consensus size: 6
3029457 AGGTAAAGAT
* * * *
3029467 ACATAC ACATAC ACATAC ACATAC ACATGC ACATGC ACATGC ACATGC
1 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
* *
3029515 ACATGC ACATGC ACATCC ACATGC ACATGC ACATGC ACATCC ACATGC
1 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
* * * * *
3029563 ACATGC ACATGC ACATCC ACATAC ACATAC ACATAC ACATGC ACATAC
1 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
3029611 ACATGC ACATGC ACATGC
1 ACATGC ACATGC ACATGC
3029629 GTGTTGTCTT
Statistics
Matches: 146, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 146 1.00
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (6 bp):
ACATGC
Found at i:3031606 original size:13 final size:13
Alignment explanation
Indices: 3031588--3031612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3031578 CTTATTAGAG
3031588 AAAAAAGTTAAAA
1 AAAAAAGTTAAAA
3031601 AAAAAAGTTAAA
1 AAAAAAGTTAAA
3031613 TGGAAGGGAT
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAGTTAAAA
Found at i:3032356 original size:112 final size:112
Alignment explanation
Indices: 3032004--3032577 Score: 927
Period size: 112 Copynumber: 5.1 Consensus size: 112
3031994 TTGTTGGTTT
* * * *
3032004 GTGTCGATGCTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
3032069 GGTCTATAAATGGCAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
3032116 GTGTCGATACTTTATAAAAATATATCTATCCATAACAATATAACAGGT--AAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
3032179 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
3032226 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
3032291 GGTATATAAATGACAAAACAGGTAAAGCACTACCAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
3032338 GTGTCGATACTTTATAAAAATGTATTGATCCATAATAATATAACAGGTAAAAAAATGACAAAACT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
3032403 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
3032450 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGATAAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
** * *
3032515 CAATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
3032563 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
3032578 TATAAGTATC
Statistics
Matches: 433, Mismatches: 26, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
110 107 0.25
112 251 0.58
113 75 0.17
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:3032390 original size:222 final size:223
Alignment explanation
Indices: 3032004--3032577 Score: 927
Period size: 222 Copynumber: 2.6 Consensus size: 223
3031994 TTGTTGGTTT
* * * *
3032004 GTGTCGATGCTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
3032069 GGTCTATAAATGGCAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
3032134 AATATATCTATCCATAACAATATAACAGGT-AAAAATGACAAAACCGGTCTATAAATGACAAAAC
131 AATATATCTATCCATAACAATATAACAGGTAAAAAATGACAAAACCGGTCTATAAATGACAAAAC
3032198 AGGTAAAGCGCTACCGGATATATTGAAA
196 AGGTAAAGCGCTACCGGATATATTGAAA
3032226 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
3032291 GGTATATAAATGACAAAACAGGTAAAGCACTACCAGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* * *
3032356 AATGTAT-TGATCCATAATAATATAACAGGTAAAAAAATGACAAAACTGGTCTATAAATGACAAA
131 AATATATCT-ATCCATAACAATATAACAGGT-AAAAAATGACAAAACCGGTCTATAAATGACAAA
* *
3032420 ACAGGTAAAGCGCTACCGGATATGTTGATA
194 ACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
3032450 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGATAAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
** * *
3032515 CAATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
3032578 TATAAGTATC
Statistics
Matches: 325, Mismatches: 23, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
221 1 0.00
222 148 0.46
224 105 0.32
225 71 0.22
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.25
Consensus pattern (223 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
AATATATCTATCCATAACAATATAACAGGTAAAAAATGACAAAACCGGTCTATAAATGACAAAAC
AGGTAAAGCGCTACCGGATATATTGAAA
Found at i:3032861 original size:113 final size:112
Alignment explanation
Indices: 3032632--3032872 Score: 392
Period size: 113 Copynumber: 2.1 Consensus size: 112
3032622 GCGCTAATAA
* * * *
3032632 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
1 AGTGTCGATACTTTATAAAAATATATCGATCCATAACAATAAAACAGGTAAAAAAATGAAAAAAC
*
3032697 CGATCTATAAATGAAAAAACAAGTAAAGCGCTACCGGATATGTTGAT
66 CGATCTATAAATGAAAAAACAAGTAAAGCGCTACCAGATATGTTGAT
3032744 AGTGTCGATACTTTATAAAAATATATCGATCCATAACAATAAAACAGGTAAAAAAAATGAAAAAA
1 AGTGTCGATACTTTATAAAAATATATCGATCCATAACAATAAAACAGGT-AAAAAAATGAAAAAA
* * *
3032809 TCGGTCTATAAATGATAAAACAAGTAAAGCGCTACCAGATATGTTGAT
65 CCGATCTATAAATGAAAAAACAAGTAAAGCGCTACCAGATATGTTGAT
*
3032857 AGTGTCGAAACTTTAT
1 AGTGTCGATACTTTAT
3032873 TATAAGTATC
Statistics
Matches: 119, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
112 47 0.39
113 72 0.61
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (112 bp):
AGTGTCGATACTTTATAAAAATATATCGATCCATAACAATAAAACAGGTAAAAAAATGAAAAAAC
CGATCTATAAATGAAAAAACAAGTAAAGCGCTACCAGATATGTTGAT
Found at i:3032872 original size:295 final size:295
Alignment explanation
Indices: 3032335--3033054 Score: 1228
Period size: 295 Copynumber: 2.4 Consensus size: 295
3032325 AGATATATTG
* * *
3032335 AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAATAATATAACAGGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
3032400 ACTGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
* *
3032465 AAAAATGTATCGATCCATAACAATAAAACAGATAAAAAAAATGACAAAATCAATCTATAAATGAC
131 AAAAATATATCGATCCATAACAATAAAACAGATAAAAAAAATGAAAAAATCAATCTATAAATGAC
* * *
3032530 AAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGACACTT
196 AAAACAAGTAAAGCGCTACCAGATATGTTGATAGTGTCGAAACTTTATTATAAGTATCGACACTT
3032595 TT-AGAATTTAAAAGAGAATAAGTTATAGCGCTAAT
261 TTGA-AATTTAAAAGAGAATAAGTTATAGCGCTAAT
3032630 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
3032695 ACCGATCTATAAATGAAAAAACAAGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
* ** *
3032760 AAAAATATATCGATCCATAACAATAAAACAGGTAAAAAAAATGAAAAAATCGGTCTATAAATGAT
131 AAAAATATATCGATCCATAACAATAAAACAGATAAAAAAAATGAAAAAATCAATCTATAAATGAC
3032825 AAAACAAGTAAAGCGCTACCAGATATGTTGATAGTGTCGAAACTTTATTATAAGTATCGACACTT
196 AAAACAAGTAAAGCGCTACCAGATATGTTGATAGTGTCGAAACTTTATTATAAGTATCGACACTT
3032890 TTGAAATTTAAAAGAGAATAAGTTATAGCGCTAAT
261 TTGAAATTTAAAAGAGAATAAGTTATAGCGCTAAT
*
3032925 AAAATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
3032990 ATCGGTCT-TGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTA
66 ACCGGTCTAT-AAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTA
3033054 T
130 T
3033055 TATAAGTATC
Statistics
Matches: 400, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
294 1 0.00
295 398 1.00
296 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (295 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
AAAAATATATCGATCCATAACAATAAAACAGATAAAAAAAATGAAAAAATCAATCTATAAATGAC
AAAACAAGTAAAGCGCTACCAGATATGTTGATAGTGTCGAAACTTTATTATAAGTATCGACACTT
TTGAAATTTAAAAGAGAATAAGTTATAGCGCTAAT
Found at i:3033045 original size:407 final size:399
Alignment explanation
Indices: 3032117--3033054 Score: 879
Period size: 407 Copynumber: 2.3 Consensus size: 399
3032107 ATATTGAAAG
* * *
3032117 TGTCGATACTTTATAAAAATATATCTATCCATAACAATATAACAGGT-AAAA-ATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAATATGACAAAATCG
*
3032180 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
66 GTCT-TAAATGACAAAAC-GGTAAAGAGCTACCGGATAT-TTGAAAGTGTCGATACTTTATAAAA
* *
3032245 ATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTATATAAATGACAAAAC
128 ATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGATATATAAATGAAAAAAC
* * * *
3032310 AGGTAAAGCACTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATGTATTGATCCATAATA
193 AAGTAAAGCACTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACA
* * * *
3032375 ATATAACAGGTAAAAAAATGACAAAACTGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGA
258 ATAAAACAGGTAAAAAAATGAAAAAACTGGTCTATAAATGACAAAACAAGTAAAGCGCTACCAGA
*
3032440 TATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGATAAAAAAA
323 TATGTTGATAGTGTCGAAACTTTATAAAAATGTATCGATCCATAACAATAAAACAGATAAAAAAA
3032505 ATGACAAAATCAA
388 ATGACAAAA-CAA
* ** * * * * * * * * ***
3032518 --TCTATAAATGACAAAACAGGTA--AAGCGC-TACCGGATATGTTGATAGTGTCGATACTTTAT
1 TGTCGATACTTTATAAAA-ATGTATCAATC-CATAAC--A-AT-ATAACAG-GT--A-AAAATAT
* * * * * ** * ** * *
3032578 TATAAGTATCGACACTTTTAGAAT-TTAAAA-GAG-AATA-AGTTATAGCGCTA-AT-AAAGTGT
56 GACAA-AATCG---GTCTTA-AATGACAAAACG-GTAA-AGAGCTACCG-GATATTTGAAAGTGT
* *
3032637 CGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATC
113 CGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGATA
* * * *
3032702 TATAAATGAAAAAACAAGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATA
178 TATAAATGAAAAAACAAGTAAAGCACTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATA
*
3032767 TATCGATCCATAACAATAAAACAGGTAAAAAAAATGAAAAAA-TCGGTCTATAAATGATAAAACA
243 TATCGATCCATAACAATAAAACAGGT-AAAAAAATGAAAAAACT-GGTCTATAAATGACAAAACA
* * *
3032831 AGTAAAGCGCTACCAGATATGTTGATAGTGTCGAAACTTTATTATAA-GTATCGA-CACTTTTGA
306 AGTAAAGCGCTACCAGATATGTTGATAGTGTCGAAACTTTATAAAAATGTATCGATC-C--AT-A
* * * *** *
3032894 A-ATTTAAAAGAGA-ATAAGTTATAGCGCTAATAA-AA
367 ACA-ATAAAACAGATAAAAAAAAT-G-AC-AA-AACAA
*
3032929 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAATATGACAAAATCG
*
3032994 GTCTTGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 GTCTT-AAATGACAAAA-CGGTAAAGAGCTACCGGATAT-TTGAAAGTGTCGATACTTTAT
3033055 TATAAGTATC
Statistics
Matches: 406, Mismatches: 86, Indels: 84
0.70 0.15 0.15
Matches are distributed among these distances:
398 5 0.01
399 12 0.03
400 4 0.01
401 2 0.00
402 10 0.02
403 7 0.02
404 5 0.01
405 12 0.03
406 9 0.02
407 178 0.44
408 81 0.20
409 19 0.05
410 20 0.05
411 11 0.03
412 12 0.03
413 14 0.03
414 5 0.01
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (399 bp):
TGTCGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAATATGACAAAATCG
GTCTTAAATGACAAAACGGTAAAGAGCTACCGGATATTTGAAAGTGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGATATATAAATGAAAAAACAAG
TAAAGCACTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATA
AAACAGGTAAAAAAATGAAAAAACTGGTCTATAAATGACAAAACAAGTAAAGCGCTACCAGATAT
GTTGATAGTGTCGAAACTTTATAAAAATGTATCGATCCATAACAATAAAACAGATAAAAAAAATG
ACAAAACAA
Found at i:3033067 original size:182 final size:182
Alignment explanation
Indices: 3032746--3033195 Score: 715
Period size: 182 Copynumber: 2.5 Consensus size: 182
3032736 ATGTTGATAG
* * * *
3032746 TGTCGATACTTTATAAAAATATATCGATCCATAACAATAAAACAGGTAAAAAAAATGAAAAAATC
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAATATGACAAAATC
* ** *
3032811 GGTCTAT-AAATGATAAAACAAGTAAAGCGCTACCAGATATGTTGATAGTGTCGAAACTTTATTA
65 GGTCT-TGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGAAACTTTATTA
* *
3032875 TAAGTATCGACACTTTTGAAATTTAAAAGAGAATAAGTTATAGCG-CTAATAAAA
129 TAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCGTC-AATAAAA
3032929 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCG
* *
3032994 GTCTTGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTATA
66 GTCTTGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGAAACTTTATTATA
* *
3033059 AGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAATAAAG
131 AGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCGTCAATAAAA
3033111 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCG
* *
3033176 ATCTCGAAATGACAAAACCG
66 GTCTTGAAATGACAAAACCG
3033196 TTAGTGAAAA
Statistics
Matches: 249, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
181 1 0.00
182 202 0.81
183 46 0.18
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (182 bp):
TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCG
GTCTTGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGAAACTTTATTATA
AGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCGTCAATAAAA
Found at i:3033605 original size:23 final size:23
Alignment explanation
Indices: 3033576--3033623 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
3033566 AAATAGGTCA
*
3033576 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
3033599 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
3033622 AT
1 AT
3033624 TGTACTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:3034210 original size:32 final size:33
Alignment explanation
Indices: 3034172--3034249 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 33
3034162 TAAATGATTC
*
3034172 ATACATTTAAATATATAAATATATTTTTA-TTT
1 ATACATTTAAATATAAAAATATATTTTTAGTTT
* *
3034204 ATACATTTCAATACAAAAATATATTTTTAGTTT
1 ATACATTTAAATATAAAAATATATTTTTAGTTT
*
3034237 -TACAATTAAATAT
1 ATACATTTAAATAT
3034250 TTTTATTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 36 0.92
33 3 0.08
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.47
Consensus pattern (33 bp):
ATACATTTAAATATAAAAATATATTTTTAGTTT
Found at i:3035724 original size:60 final size:60
Alignment explanation
Indices: 3035636--3035758 Score: 178
Period size: 60 Copynumber: 2.0 Consensus size: 60
3035626 AAAGTACACG
* *
3035636 AATGATCTCCCGACTATAGGATGCTACTTTGTTGAGTCCTTCAACTATTAAAAGTTACAA
1 AATGATCTCCCGACTATAGGATGCTACTTTGTTGAGTCCCTCAACTAATAAAAGTTACAA
* *
3035696 AATGATC-CCCTGACTATAGGGA-GTTACTTTGTTGAGTCCCTCGACTAATAAAAGTTACAA
1 AATGATCTCCC-GACTATA-GGATGCTACTTTGTTGAGTCCCTCAACTAATAAAAGTTACAA
3035756 AAT
1 AAT
3035759 TATCACCCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
59 3 0.05
60 51 0.89
61 3 0.05
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (60 bp):
AATGATCTCCCGACTATAGGATGCTACTTTGTTGAGTCCCTCAACTAATAAAAGTTACAA
Found at i:3036827 original size:2 final size:2
Alignment explanation
Indices: 3036820--3036844 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3036810 TTCACCCCTA
3036820 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3036845 ATGATGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3042574 original size:29 final size:29
Alignment explanation
Indices: 3042542--3042599 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3042532 GAAAATAATG
* *
3042542 TAAC-AAAGAAAAGGAAAAGAAAAAGAAAA
1 TAACAAAAG-AAAGGAAAAAAAAAACAAAA
*
3042571 TAACAAAAGAAAGTAAAAAAAAAACAAAA
1 TAACAAAAGAAAGGAAAAAAAAAACAAAA
3042600 ACAAAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (29 bp):
TAACAAAAGAAAGGAAAAAAAAAACAAAA
Found at i:3043664 original size:16 final size:17
Alignment explanation
Indices: 3043643--3043687 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
3043633 AAACAAAAGT
3043643 TATTTAATATTATA-TA
1 TATTTAATATTATACTA
*
3043659 TATTTAA-ATTTTTACTA
1 TATTTAATA-TTATACTA
3043676 TATTTAATATTA
1 TATTTAATATTA
3043688 AATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 1 0.04
16 11 0.46
17 11 0.46
18 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTAATATTATACTA
Found at i:3044994 original size:15 final size:15
Alignment explanation
Indices: 3044974--3045021 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
3044964 ATATTTAGCT
*
3044974 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
3044989 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
3045004 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
3045019 GGG
1 GGG
3045022 TGGGTAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.06, C:0.17, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:3046559 original size:19 final size:17
Alignment explanation
Indices: 3046537--3046571 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
3046527 TTTTTCTACC
3046537 TTATTTACTTTTTCATTAA
1 TTATTTA-TTTTT-ATTAA
3046556 TTATTTATTTTTATTA
1 TTATTTATTTTTATTA
3046572 TTTTATTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTTATTTTTATTAA
Found at i:3048974 original size:69 final size:69
Alignment explanation
Indices: 3048851--3048987 Score: 184
Period size: 69 Copynumber: 2.0 Consensus size: 69
3048841 AATCCAACTA
* * * * * * * *
3048851 AGAAAAGCAATTTGAGAGCTTAGGAAACTTCTTGAGTTTATAGCATCCATCAAGAACAAGCTTTT
1 AGAAAAGCAATTTGAGAGCTCAGAAAACTTATTGAGTTTAAAACATCAAACAAGAACAAGCCTTT
3048916 CAAG
66 CAAG
**
3048920 AGAAAAGTTATTTGAGAGCTCAGAAAACTTATTGAGTTTAAAACATCAAACAAGAACAAGCCTTT
1 AGAAAAGCAATTTGAGAGCTCAGAAAACTTATTGAGTTTAAAACATCAAACAAGAACAAGCCTTT
3048985 CAA
66 CAA
3048988 ATGATATCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (69 bp):
AGAAAAGCAATTTGAGAGCTCAGAAAACTTATTGAGTTTAAAACATCAAACAAGAACAAGCCTTT
CAAG
Found at i:3049441 original size:138 final size:138
Alignment explanation
Indices: 3049037--3049801 Score: 867
Period size: 138 Copynumber: 5.6 Consensus size: 138
3049027 TTTCAGTCTC
* * *
3049037 TACAGTTAAGAATTTTGAGGTTAATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTCT-TACA
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCTTCCTTAAATT-TATACA
** * ** * *
3049101 A-TAAGAAAGGTGGAGCTTTTCAAGTGATAT-CAAATGAATGAGGCAAGATAGTTCAACCAAACT
65 ACT-AGAAAATTGAAGAGTTTCAAGAGAT-TCCAAATGATTGAGGCAAGATAGTTCAACCAAACT
* *
3049164 GTCACA-ACGTT
128 TTCACAGTCG-T
* * * *
3049175 TACAGTCAAGGATTTTGAGGTTGATGGCTCTTAATAGA-TACGGA--TTCTCTTAAATTTATGCA
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCTTC-CTTAAATTTATACA
* * *
3049237 ACCA-AAAAGTTGATGAGTTTCAAGGGATTCCAAATGATTGAGGCAAGATAGTTCAACCAAACTT
65 ACTAGAAAA-TTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGCAAGATAGTTCAACCAAACTT
3049301 TCACAGTCGT
129 TCACAGTCGT
* * * * *
3049311 TATAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGAATCTTTCTTGAATTTATGCAA
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTTATACAA
* *
3049376 CTAGAAAATTGAAGAGTTTCAAGAGATTCCAAATAATTGAGGTAAGATAGTT-AACCAAACTTTT
66 CTAGAAAATTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGCAAGATAGTTCAACCAAAC-TTT
*
3049440 CATAGTCGT
130 CACAGTCGT
* *
3049449 TACAGTCAAGCATTTTGATGTTGATGGCTCCTAATA-ACTTAGGGCTCTTCCTTAAATTCT-TAC
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGA-TTAGGGATCTTCCTTAAATT-TATAC
** ** *
3049512 AA-TCAGAAAGGTGAAGCTTTTCAAGTGATAT-CAAATGATTGAGGCAAGATAGTTCAACCAAAC
64 AACT-AGAAAATTGAAGAGTTTCAAGAGAT-TCCAAATGATTGAGGCAAGATAGTTCAACCAAAC
* *
3049575 TGTCACA-ACGTT
127 TTTCACAGTCG-T
* ** * * *
3049587 TACAGTCAAGGATTTTGAGGTTGATATCTCTTAATAGATTAGGGAT-TCCCCTTAAATTTACACA
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCT-TCCTTAAATTTATACA
* *
3049651 ACCAGAAAATTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGAAAGATAGTTCAACCAAACTTT
65 ACTAGAAAATTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGCAAGATAGTTCAACCAAACTTT
3049716 CACAGTCGT
130 CACAGTCGT
* * * *
3049725 TACAGTCAAACATTTTGAGGTTGATGGCTCCTAATAGATTAGGAATCTTTCTTAAATTTATGCAA
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTTATACAA
*
3049790 CTAGAAATTTGA
66 CTAGAAAATTGA
3049802 GAGCTTAGGA
Statistics
Matches: 527, Mismatches: 76, Indels: 48
0.81 0.12 0.07
Matches are distributed among these distances:
135 8 0.02
136 99 0.19
137 26 0.05
138 374 0.71
139 20 0.04
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (138 bp):
TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTTATACAA
CTAGAAAATTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGCAAGATAGTTCAACCAAACTTTC
ACAGTCGT
Found at i:3049853 original size:412 final size:408
Alignment explanation
Indices: 3049037--3049808 Score: 1235
Period size: 412 Copynumber: 1.9 Consensus size: 408
3049027 TTTCAGTCTC
*
3049037 TACAGTTAAGAATTTTGAGGTTAATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTCTTACAA
1 TACAGTCAAGAATTTTGAGGTTAATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTCTTACAA
*
3049102 TAAGAAAGGTGGAGCTTTTCAAGTGATATCAAATGAATGAGGCAAGATAGTTCAACCAAACTGTC
66 TAAGAAAGGTGAAGCTTTTCAAGTGATATCAAATGAATGAGGCAAGATAGTTCAACCAAACTGTC
* *
3049167 ACAACGTTTACAGTCAAGGATTTTGAGGTTGATGGCTCTTAATAGATACGGATTCTCTTAAATTT
131 ACAACGTTTACAGTCAAGGATTTTGAGGTTGATAGCTCTTAATAGATACGGATTCCCTTAAATTT
** * * *
3049232 ATGCAACCAAAAAGTTGATGAGTTTCAAGGGATTCCAAATGATTGAGGCAAGATAGTTCAACCAA
196 ACACAACCAAAAAGTTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGAAAGATAGTTCAACCAA
* *
3049297 ACTTTCACAGTCGTTATAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGAATCTTTC
261 ACTTTCACAGTCGTTACAGTCAAACATTTTGAGGTTGATGGCTCCTAATAGATTAGGAATCTTTC
* *
3049362 TTGAATTTATGCAACTAGAAAATTGAAGAGTTTCAAGAGATTCCAAATAATTGAGGTAAGATAGT
326 TTAAATTTATGCAACTAGAAAATTGAAGAGCTT-AAGAGA---CAAATAATTGAGGTAAGATAGT
* *
3049427 TAACCAAACTTTTCATAGTCGT
387 AAAACAAACTTTTCATAGTCGT
* * * *
3049449 TACAGTCAAGCATTTTGATGTTGATGGCTCCTAATA-ACTTAGGGCTCTTCCTTAAATTCTTACA
1 TACAGTCAAGAATTTTGAGGTTAATGGCTCCTAATAGA-TTAGGGATCTTCCTTAAATTCTTACA
* *
3049513 ATCAGAAAGGTGAAGCTTTTCAAGTGATATCAAATGATTGAGGCAAGATAGTTCAACCAAACTGT
65 ATAAGAAAGGTGAAGCTTTTCAAGTGATATCAAATGAATGAGGCAAGATAGTTCAACCAAACTGT
* *
3049578 CACAACGTTTACAGTCAAGGATTTTGAGGTTGATATCTCTTAATAGATTAGGGATTCCCCTTAAA
130 CACAACGTTTACAGTCAAGGATTTTGAGGTTGATAGCTCTTAATAGA-TACGGATT-CCCTTAAA
3049643 TTTACACAACCAGAAAA-TTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGAAAGATAGTTCAA
193 TTTACACAACCA-AAAAGTTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGAAAGATAGTTCAA
3049707 CCAAACTTTCACAGTCGTTACAGTCAAACATTTTGAGGTTGATGGCTCCTAATAGATTAGGAATC
257 CCAAACTTTCACAGTCGTTACAGTCAAACATTTTGAGGTTGATGGCTCCTAATAGATTAGGAATC
*
3049772 TTTCTTAAATTTATGCAACTAGAAATTTG-AGAGCTTA
322 TTTCTTAAATTTATGCAACTAGAAAATTGAAGAGCTTA
3049809 GGAAACTTCT
Statistics
Matches: 334, Mismatches: 22, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
411 1 0.00
412 165 0.49
413 13 0.04
414 151 0.45
415 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (408 bp):
TACAGTCAAGAATTTTGAGGTTAATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTCTTACAA
TAAGAAAGGTGAAGCTTTTCAAGTGATATCAAATGAATGAGGCAAGATAGTTCAACCAAACTGTC
ACAACGTTTACAGTCAAGGATTTTGAGGTTGATAGCTCTTAATAGATACGGATTCCCTTAAATTT
ACACAACCAAAAAGTTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGAAAGATAGTTCAACCAA
ACTTTCACAGTCGTTACAGTCAAACATTTTGAGGTTGATGGCTCCTAATAGATTAGGAATCTTTC
TTAAATTTATGCAACTAGAAAATTGAAGAGCTTAAGAGACAAATAATTGAGGTAAGATAGTAAAA
CAAACTTTTCATAGTCGT
Found at i:3050139 original size:138 final size:138
Alignment explanation
Indices: 3049966--3050786 Score: 911
Period size: 138 Copynumber: 6.0 Consensus size: 138
3049956 TTTCAGTCTC
* * *
3049966 TACAGTTAAGAATTTTGAGGTTAATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTCT-TACA
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCTTCCTTAAATT-TATACA
* ** * * *
3050030 ATAAGAAAGGTGAAGCTTTTCAAGTGATAT-CAAATGAATGAGGAAAGATAGTTCAACCAAACTG
65 ATAAGAAAGTTGAAGAGTTTCAAGAGAT-TCCAAATGATTGAGGAAAGATAGTTCAACCAAACTT
*
3050094 TCACA-ACGTT
129 TCACAGTCG-T
* * * *
3050104 TACAGTCAAGGATTTTGAGGTTGATGGCTCTTAATAGA-TACGGA--TTCTCTTAAATTTATGCA
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCTTC-CTTAAATTTATACA
* * * *
3050166 ACCAA-AAAGTTGATGAGTTTCAAGGGATTCCAAATGATTGAGGCAAGATAGTTCAACCAAACTT
65 A-TAAGAAAGTTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGAAAGATAGTTCAACCAAACTT
3050230 TCACAGTCGT
129 TCACAGTCGT
* * * * *
3050240 TATAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGAATCTTTCTTGAATTTATGCAA
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTTATACAA
* * *
3050305 CT-AGAAAATTGAAGAGTTTCAAGAGATTCCAAATAATTGAGGTAAGATAGTT-AACCAAACTTT
66 -TAAGAAAGTTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGAAAGATAGTTCAACCAAAC-TT
*
3050368 TCATAGTCGT
129 TCACAGTCGT
* *
3050378 TACAGTCAAGCATTTTGATGTTGATGGCTCCTAATA-ACTTAGGGCTCTTCCTTAAATTCT-TAC
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGA-TTAGGGATCTTCCTTAAATT-TATAC
* * ** * *
3050441 AATCAGAAAGGTGAAGCTTTTCAAGTGATAT-CAAATGATTGAGGCAAGATAGTTCAACCAAACT
64 AATAAGAAAGTTGAAGAGTTTCAAGAGAT-TCCAAATGATTGAGGAAAGATAGTTCAACCAAACT
* *
3050505 GTCACA-ACGTT
128 TTCACAGTCG-T
* * * *
3050516 TACAGTCAAGGATTTTGAGGTTGATGGCTCTTAATAGATTAGGGAT-TCCCCTTAAATTTACACA
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCT-TCCTTAAATTTATACA
** *
3050580 ACCAGAAAATTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGAAAGATAGTTCAACCAAACTTT
65 ATAAGAAAGTTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGAAAGATAGTTCAACCAAACTTT
3050645 CACAGTCGT
130 CACAGTCGT
* * * * *
3050654 TACAGTCAAACATTTTGAGGTTGATGGCTCCTAATAGATTAGGAATTTTTCTTAAATTTATGCAA
1 TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTTATACAA
* * * *
3050719 CT-AGAAAGTTGAAGAGTTTCTAGAGATGT-CAAATGATCGAGGCAAGGA-AGTTCAACCTAACT
66 -TAAGAAAGTTGAAGAGTTTCAAGAGAT-TCCAAATGATTGAGG-AAAGATAGTTCAACCAAACT
3050781 TTCACA
128 TTCACA
3050787 CCAAATGCTT
Statistics
Matches: 582, Mismatches: 76, Indels: 50
0.82 0.11 0.07
Matches are distributed among these distances:
135 5 0.01
136 102 0.18
137 29 0.05
138 425 0.73
139 21 0.04
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (138 bp):
TACAGTCAAGCATTTTGAGGTTGATGGCTCCTAATAGATTAGGGATCTTCCTTAAATTTATACAA
TAAGAAAGTTGAAGAGTTTCAAGAGATTCCAAATGATTGAGGAAAGATAGTTCAACCAAACTTTC
ACAGTCGT
Found at i:3052366 original size:90 final size:89
Alignment explanation
Indices: 3052266--3052432 Score: 307
Period size: 90 Copynumber: 1.9 Consensus size: 89
3052256 CCTGAATATT
3052266 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGGTAACT
1 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAGGGTAACT
3052331 TGAATATAAAAGGATTATTAAACTC
65 TGAATATAAAAGGATTATTAAACTC
3052356 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTT
1 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTT
**
3052421 GGCTATAAAAGG
66 GAATATAAAAGG
3052433 GAATGTTAGG
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 33 0.44
90 42 0.56
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (89 bp):
CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTT
GAATATAAAAGGATTATTAAACTC
Found at i:3061771 original size:3 final size:3
Alignment explanation
Indices: 3061757--3061821 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
3061747 TTAATATATC
* * * *
3061757 ATT ATA ATT ATT ATT AAT ATT ATC AAT ATT ATT ATT ATT AACTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -A-TT ATT
*
3061804 ATC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
3061822 CATTTACAGG
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
3 46 0.92
4 2 0.04
5 2 0.04
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Done.