Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 42 of 185
Found at i:12435908 original size:27 final size:27
Alignment explanation
Indices: 12435878--12436008 Score: 131
Period size: 27 Copynumber: 4.9 Consensus size: 27
12435868 CTATTATTTT
* * * *
12435878 ATATTATGCCACAAAGGCATTCCTTTA
1 ATATTACGCCACAAAGGCTTTTCTTTC
12435905 ATATTACGCCACAAAGGCTTTTCTTTC
1 ATATTACGCCACAAAGGCTTTTCTTTC
* * *
12435932 ATTTTGCGCCATAAAGGCTTTTCTTTC
1 ATATTACGCCACAAAGGCTTTTCTTTC
* * * *
12435959 ATATTATG-C-CATATGCTTTTCTTTT
1 ATATTACGCCACAAAGGCTTTTCTTTC
* *
12435984 ATATTACACCACAAAGGTTTTTCTT
1 ATATTACGCCACAAAGGCTTTTCTT
12436009 ATCTGATGTG
Statistics
Matches: 83, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
25 18 0.22
26 2 0.02
27 63 0.76
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (27 bp):
ATATTACGCCACAAAGGCTTTTCTTTC
Found at i:12436000 original size:52 final size:54
Alignment explanation
Indices: 12435874--12436008 Score: 139
Period size: 52 Copynumber: 2.5 Consensus size: 54
12435864 AATTCTATTA
* * *
12435874 TTTTATATTATGCCACAAAGGCATTCCTTTAATATTACGCCACAAAGGCTTTTC
1 TTTTATATTACGCCACAAAGGCTTTTCTTTAATATTACGCCACAAAGGCTTTTC
* * * * * * * *
12435928 TTTCATTTTGCGCCATAAAGGCTTTTCTTTCATATTATG-C-CATATGCTTTTC
1 TTTTATATTACGCCACAAAGGCTTTTCTTTAATATTACGCCACAAAGGCTTTTC
* *
12435980 TTTTATATTACACCACAAAGGTTTTTCTT
1 TTTTATATTACGCCACAAAGGCTTTTCTT
12436009 ATCTGATGTG
Statistics
Matches: 64, Mismatches: 17, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
52 33 0.52
53 1 0.02
54 30 0.47
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (54 bp):
TTTTATATTACGCCACAAAGGCTTTTCTTTAATATTACGCCACAAAGGCTTTTC
Found at i:12442805 original size:13 final size:13
Alignment explanation
Indices: 12442772--12442817 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
12442762 CCTGCTTTAA
12442772 ATTTTGTTA-TTT
1 ATTTTGTTATTTT
12442784 A--TT-TTATTTT
1 ATTTTGTTATTTT
12442794 ATTTTGTTATTTT
1 ATTTTGTTATTTT
*
12442807 ATTTTATTATT
1 ATTTTGTTATT
12442818 AATTTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
9 3 0.10
10 6 0.21
12 3 0.10
13 17 0.59
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (13 bp):
ATTTTGTTATTTT
Found at i:12450408 original size:20 final size:20
Alignment explanation
Indices: 12450380--12450433 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
12450370 AATACTATGA
* *
12450380 ACCACTCCATTTACTTTCTT
1 ACCATTCCATTTACTTACTT
12450400 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
* *
12450420 TCCATTTCATTTAC
1 ACCATTCCATTTAC
12450434 CTAGCATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.46
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:12453631 original size:18 final size:19
Alignment explanation
Indices: 12453576--12453620 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
12453566 TACAAAAAAA
*
12453576 AAAAAT-CAAAATATTTTT
1 AAAAATCCAAAATATTTAT
12453594 AAAAATCCAAAATATTTAT
1 AAAAATCCAAAATATTTAT
12453613 AAAAATCC
1 AAAAATCC
12453621 CATAATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATCCAAAATATTTAT
Found at i:12453681 original size:20 final size:21
Alignment explanation
Indices: 12453636--12453694 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
12453626 TTTATATTTT
*
12453636 TAAAAAATTATAAAAATTTCA
1 TAAAAAATTATAAAAATATCA
*
12453657 -AAAAAAATATAAATAATAT-A
1 TAAAAAATTATAAA-AATATCA
12453677 TAAAAAAGTTA-AAAAATA
1 TAAAAAA-TTATAAAAATA
12453695 AAAATTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 17 0.53
21 13 0.41
22 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAAAATTATAAAAATATCA
Found at i:12453729 original size:17 final size:16
Alignment explanation
Indices: 12453691--12453723 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12453681 AAAGTTAAAA
*
12453691 AATAAAAATTTTCTAG
1 AATAAAAATTTTATAG
12453707 AATAAAAATTTTATAG
1 AATAAAAATTTTATAG
12453723 A
1 A
12453724 CTTAAATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (16 bp):
AATAAAAATTTTATAG
Found at i:12454261 original size:27 final size:27
Alignment explanation
Indices: 12454231--12454309 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
12454221 ATTCCATCCG
* * *
12454231 GAGTACGCCACAAAGGCTATTCTTTTA
1 GAGTTCGCCACAAAGGCTTTTCTTTCA
* * *
12454258 GAGTTTGCCACAAAGGATTTTCTTCCA
1 GAGTTCGCCACAAAGGCTTTTCTTTCA
* *
12454285 TAGTTCGCCACAATGGCTTTTCTTT
1 GAGTTCGCCACAAAGGCTTTTCTTT
12454310 ACCGACATGT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (27 bp):
GAGTTCGCCACAAAGGCTTTTCTTTCA
Found at i:12456050 original size:27 final size:27
Alignment explanation
Indices: 12456015--12456093 Score: 92
Period size: 26 Copynumber: 2.9 Consensus size: 27
12456005 CCTTCATGAT
12456015 TCACACACAAAGACGTTCCTTTCATAATG
1 TCAC-CACAAAGACGTTCCTTTCATAA-G
12456044 T-ACCACAAATGA-GTTCCTTTCAT-AG
1 TCACCACAAA-GACGTTCCTTTCATAAG
* *
12456069 TCACCACAAAGGCTTTCCTTTCATA
1 TCACCACAAAGACGTTCCTTTCATA
12456094 TTGCTCTACA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
25 3 0.07
26 19 0.43
27 17 0.39
28 4 0.09
29 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (27 bp):
TCACCACAAAGACGTTCCTTTCATAAG
Found at i:12456089 original size:53 final size:52
Alignment explanation
Indices: 12456015--12456142 Score: 132
Period size: 53 Copynumber: 2.4 Consensus size: 52
12456005 CCTTCATGAT
* *
12456015 TCACACACAAAGACGTTCCTTTCATAATG-TACCACAAATGAGTTCCTTTCATAG
1 TCAC-CACAAAGGC-TTCCTTTCATAATGCT-CCACAAAGGAGTTCCTTTCATAG
* * * * *
12456069 TCACCACAAAGGCTTTCCTTTCATATTGCTCTACAAAGGATTTTCTTTCATAT
1 TCACCACAAAGGC-TTCCTTTCATAATGCTCCACAAAGGAGTTCCTTTCATAG
*
12456122 TGCGCCACAAAGGCTTCCTTT
1 T-CACCACAAAGGCTTCCTTT
12456143 ATCTATCGTG
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
53 47 0.75
54 16 0.25
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.34
Consensus pattern (52 bp):
TCACCACAAAGGCTTCCTTTCATAATGCTCCACAAAGGAGTTCCTTTCATAG
Found at i:12456116 original size:27 final size:27
Alignment explanation
Indices: 12456030--12456142 Score: 104
Period size: 27 Copynumber: 4.3 Consensus size: 27
12456020 CACAAAGACG
* ** * *
12456030 TTCCTTTCATAATGTACCACAAATGAG
1 TTCCTTTCATATTGCGCCACAAAGGAT
* * *
12456057 TTCCTTTCATAGT-CACCACAAAGGCT
1 TTCCTTTCATATTGCGCCACAAAGGAT
* *
12456083 TTCCTTTCATATTGCTCTACAAAGGAT
1 TTCCTTTCATATTGCGCCACAAAGGAT
* *
12456110 TTTCTTTCATATTGCGCCACAAAGG-C
1 TTCCTTTCATATTGCGCCACAAAGGAT
12456136 TTCCTTT
1 TTCCTTT
12456143 ATCTATCGTG
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
26 27 0.38
27 44 0.62
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.37
Consensus pattern (27 bp):
TTCCTTTCATATTGCGCCACAAAGGAT
Found at i:12457535 original size:55 final size:58
Alignment explanation
Indices: 12457471--12457618 Score: 160
Period size: 57 Copynumber: 2.6 Consensus size: 58
12457461 ACAAAAACAT
* * *
12457471 CCTTTTAATAAAGATAGCCACAAAGGCTTCC-TTTAACA-TAGTAGCCAC-AAGGCTG
1 CCTTTTAATAGAGATAGCCACAAAGGCTTCCTTTTAACAGAAATAGCCACAAAGGCTG
* * * * * *
12457526 CCTTTTAATAGAGATAGCTAAAAAGGTTTCCTTTTAACAGAAATAGGCACAAATGCTT
1 CCTTTTAATAGAGATAGCCACAAAGGCTTCCTTTTAACAGAAATAGCCACAAAGGCTG
* * *
12457584 CC-TTTAACAGAGATAGCCACAAAGGATTCTTTTTA
1 CCTTTTAATAGAGATAGCCACAAAGGCTTCCTTTTA
12457619 TAGAGATCAC
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
55 27 0.36
56 7 0.09
57 35 0.46
58 7 0.09
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (58 bp):
CCTTTTAATAGAGATAGCCACAAAGGCTTCCTTTTAACAGAAATAGCCACAAAGGCTG
Found at i:12457558 original size:84 final size:85
Alignment explanation
Indices: 12457470--12457678 Score: 239
Period size: 84 Copynumber: 2.5 Consensus size: 85
12457460 CACAAAAACA
* * *
12457470 TCCTTTTAATAAAGATAGCCACAAAGGCTTCCTTTAACATAG-TAGCCAC-AAGGCTGCCTTTTA
1 TCCTTTTAACAAAGATAGCCACAAAGGCTTCCTTTAACAGAGATAGCCACAAAGGAT-CCTTTTA
*
12457533 ATAGAGAT-AGCTAAAAAGGTT
65 ATAGAGATCA-CCAAAAAGGTT
* * * *
12457554 TCCTTTTAACAGAA-ATAGGCACAAATGCTTCCTTTAACAGAGATAGCCACAAAGGATTCTTTTT
1 TCCTTTTAACA-AAGATAGCCACAAAGGCTTCCTTTAACAGAGATAGCCACAAAGGATCCTTTTA
* *
12457618 ATAGAGATCACCATAAAGTTT
65 ATAGAGATCACCAAAAAGGTT
** *
12457639 TCC-TTTAACAAAGATAGCCATGAAGGCTTCCTTTTACAGA
1 TCCTTTTAACAAAGATAGCCACAAAGGCTTCCTTTAACAGA
12457679 ATCTGCCATA
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
83 2 0.02
84 64 0.61
85 33 0.31
86 6 0.06
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (85 bp):
TCCTTTTAACAAAGATAGCCACAAAGGCTTCCTTTAACAGAGATAGCCACAAAGGATCCTTTTAA
TAGAGATCACCAAAAAGGTT
Found at i:12457599 original size:28 final size:29
Alignment explanation
Indices: 12457470--12457678 Score: 173
Period size: 28 Copynumber: 7.4 Consensus size: 29
12457460 CACAAAAACA
* *
12457470 TCCTTTTAATAAAGATAGCCACAAAGGCT
1 TCCTTTTAACAGAGATAGCCACAAAGGCT
*
12457499 TCC-TTTAACATAG-TAGCCAC-AAGGCT
1 TCCTTTTAACAGAGATAGCCACAAAGGCT
* * * * *
12457525 GCCTTTTAATAGAGATAGCTAAAAAGGTT
1 TCCTTTTAACAGAGATAGCCACAAAGGCT
* * *
12457554 TCCTTTTAACAGAAATAGGCACAAATGCT
1 TCCTTTTAACAGAGATAGCCACAAAGGCT
*
12457583 TCC-TTTAACAGAGATAGCCACAAAGGAT
1 TCCTTTTAACAGAGATAGCCACAAAGGCT
* * * **
12457611 T-CTTTTTATAGAGATCA-CCATAAAGTTT
1 TCCTTTTAACAGAGAT-AGCCACAAAGGCT
* **
12457639 TCC-TTTAACAAAGATAGCCATGAAGGCT
1 TCCTTTTAACAGAGATAGCCACAAAGGCT
12457667 TCCTTTT-ACAGA
1 TCCTTTTAACAGA
12457679 ATCTGCCATA
Statistics
Matches: 140, Mismatches: 32, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
26 8 0.06
27 17 0.12
28 78 0.56
29 37 0.26
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (29 bp):
TCCTTTTAACAGAGATAGCCACAAAGGCT
Found at i:12457674 original size:56 final size:56
Alignment explanation
Indices: 12457582--12457691 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 56
12457572 GCACAAATGC
* * *
12457582 TTCCTTTAACAGAGATAGCCACAAAGGATTCTTTTTATAGAGATC-ACCATAAAGTT
1 TTCCTTTAACAAAGATAGCCACAAAGGATTCCTTTTACAGA-ATCTACCATAAAGTT
** * *
12457638 TTCCTTTAACAAAGATAGCCATGAAGGCTTCCTTTTACAGAATCTGCCATAAAG
1 TTCCTTTAACAAAGATAGCCACAAAGGATTCCTTTTACAGAATCTACCATAAAG
12457692 GCACTTATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
55 3 0.07
56 43 0.93
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31
Consensus pattern (56 bp):
TTCCTTTAACAAAGATAGCCACAAAGGATTCCTTTTACAGAATCTACCATAAAGTT
Found at i:12466516 original size:51 final size:51
Alignment explanation
Indices: 12466347--12466546 Score: 219
Period size: 51 Copynumber: 3.9 Consensus size: 51
12466337 TGAAAGTGAA
*
12466347 AGTGATGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAA-
1 AGTGATGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAAT
* * * * *
12466398 A--GATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT
1 AGTGAT-GATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT
* * * *
12466448 AGCT-TTGATCACGTGTGTAGTACTATGTGCAGGCAACTACGTGTATCGAAT
1 AG-TGATGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT
* * * *
12466499 AGTGATGGTCACATGTGTAGTACTATGTGTAGGCTACTATGTGAACCG
1 AGTGATGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
12466547 GTATCATTAA
Statistics
Matches: 120, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
49 5 0.04
50 38 0.32
51 76 0.63
52 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (51 bp):
AGTGATGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT
Found at i:12466578 original size:101 final size:101
Alignment explanation
Indices: 12466361--12466557 Score: 247
Period size: 101 Copynumber: 2.0 Consensus size: 101
12466351 ATGATCACGT
* *
12466361 GTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGATAGGTCGCATGTGTAGTACTATGTG
1 GTGTAGTACTATGTGCAGGCAACTACGTGTACCAGAAAGATAGGTCACATGTGTAGTACTATGTG
* * * **
12466426 CAGGCTACTATGCGTACCGGATAGCTTTGATCACGT
66 CAGGCTACTATGCGAACCGGATAGCATTAATCACAA
*
12466462 GTGTAGTACTATGTGCAGGCAACTACGTGTATC-GAATAG-TGATGGTCACATGTGTAGTACTAT
1 GTGTAGTACTATGTGCAGGCAACTACGTGTACCAGAA-AGAT-A-GGTCACATGTGTAGTACTAT
* * *
12466525 GTGTAGGCTACTATGTGAACCGG-TATCATTAAT
63 GTGCAGGCTACTATGCGAACCGGATAGCATTAAT
12466558 TATAAGGTGG
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
100 4 0.05
101 41 0.49
102 39 0.46
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (101 bp):
GTGTAGTACTATGTGCAGGCAACTACGTGTACCAGAAAGATAGGTCACATGTGTAGTACTATGTG
CAGGCTACTATGCGAACCGGATAGCATTAATCACAA
Found at i:12471938 original size:51 final size:50
Alignment explanation
Indices: 12471819--12471939 Score: 134
Period size: 50 Copynumber: 2.4 Consensus size: 50
12471809 AAAGTGATGG
* * *
12471819 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGATAGG
1 TCACGTGTGTAGTACTATGTACAGGCTACTACGCGTACCAGAAAGATAGA
* * * * * * * *
12471869 TCGCATGTGTAGTACTATGTACCGGCTACTATGCGTACCGGATAGCTTTGA
1 TCACGTGTGTAGTACTATGTACAGGCTACTACGCGTACCAGAAAG-ATAGA
12471920 TCACGTGTGTAGTACTATGT
1 TCACGTGTGTAGTACTATGT
12471940 GTAGGCAACT
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
50 37 0.65
51 20 0.35
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTACAGGCTACTACGCGTACCAGAAAGATAGA
Found at i:12472011 original size:102 final size:101
Alignment explanation
Indices: 12471819--12472011 Score: 255
Period size: 101 Copynumber: 1.9 Consensus size: 101
12471809 AAAGTGATGG
* * *
12471819 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCAACTACGTGAACCAGAAAGATAGGTCACATGTGTAGTAC
* *
12471884 TATGTACCGGCTACTATGCGTACCGGATAGCTTTGA
66 TATGTACAGGCTACTATGCGAACCGGATAGCTTTGA
* *
12471920 TCACGTGTGTAGTACTATGTGTAGGCAACTACGTGAATC-GAATAG-TGACGGTCACATGTGTAG
1 TCACGTGTGTAGTACTATGTGCAGGCAACTACGTGAACCAGAA-AGAT-A-GGTCACATGTGTAG
** *
12471983 TACTATGTGTAGGCTACTATGTGAACCGG
63 TACTATGTACAGGCTACTATGCGAACCGG
12472012 TATCATTAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
100 4 0.05
101 38 0.48
102 37 0.47
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCAACTACGTGAACCAGAAAGATAGGTCACATGTGTAGTAC
TATGTACAGGCTACTATGCGAACCGGATAGCTTTGA
Found at i:12472274 original size:37 final size:38
Alignment explanation
Indices: 12472205--12472277 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
12472195 ATGTGTGGAA
* * **
12472205 TTGAATTGAATATTTACTTGAAAATGGCAAAGTGAATT
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
*
12472243 TTGAATTGAATAGTGA-TTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAA
12472278 ATTATGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 16 0.53
38 14 0.47
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (38 bp):
TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
Found at i:12477922 original size:26 final size:26
Alignment explanation
Indices: 12477890--12477947 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
12477880 TATTTTATAA
12477890 ATTTCATTATTGAAATGGTATATTAT
1 ATTTCATTATTGAAATGGTATATTAT
12477916 ATTTCATTATTGAAATGGTATATTAT
1 ATTTCATTATTGAAATGGTATATTAT
*
12477942 GTTTCA
1 ATTTCA
12477948 AATTATCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (26 bp):
ATTTCATTATTGAAATGGTATATTAT
Found at i:12478911 original size:10 final size:10
Alignment explanation
Indices: 12478896--12478942 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
12478886 TAACATGTTG
12478896 AATTTTAATT
1 AATTTTAATT
12478906 AATTTTATAATT
1 AA-TTT-TAATT
*
12478918 AATTTTGATT
1 AATTTTAATT
*
12478928 AATTTTGATT
1 AATTTTAATT
12478938 -ATTTT
1 AATTTT
12478943 CGACAGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.15
10 16 0.47
11 6 0.18
12 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (10 bp):
AATTTTAATT
Found at i:12479087 original size:22 final size:22
Alignment explanation
Indices: 12479061--12479105 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12479051 ATTACGTGTA
*
12479061 TTAATTCATAATATAAT-TAATT
1 TTAATT-ATAATACAATCTAATT
*
12479083 TTAATTTTAATACAATCTAATT
1 TTAATTATAATACAATCTAATT
12479105 T
1 T
12479106 GGGTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAATTATAATACAATCTAATT
Found at i:12485640 original size:229 final size:229
Alignment explanation
Indices: 12485239--12485693 Score: 784
Period size: 229 Copynumber: 2.0 Consensus size: 229
12485229 CTAGTGTTTG
12485239 CCAACATCAATGCGTCATAGGCGTACTCAAAGGGTTCTTATACTTAGTCTAGTTCTAACACTATA
1 CCAACATCAATGCGTCATAGGCGTACTCAAAGGGTTCTTATACTTAGTCTAGTTCTAACACTATA
* * *
12485304 CATATTCAAAACTTATCTCGTTTGTCTTATTTCCCTAAATAGTATCTAGACACCAAAGCTTCATC
66 CATATTCAAAACTTATCTCGTTCGTCTTATTTCCCTAAAAAATATCTAGACACCAAAGCTTCATC
* *
12485369 GGGCGAGGTGTTACAATAGCATAACACGCATTCTATTTTCAACATTCACTCATACAATTACATAA
131 GGACGAGGTGTTACAACAGCATAACACGCATTCTATTTTCAACATTCACTCATACAATTACATAA
* *
12485434 CCATCATACTATACTTTTCTAGCTTTGGCATTTT
196 CCAACATACTATAATTTTCTAGCTTTGGCATTTT
* * *
12485468 CCAACATCAATGCGTCATAGGCGTGCTCAGAGGGTTTTTATACTTAGTCTAGTTCTAACACTATA
1 CCAACATCAATGCGTCATAGGCGTACTCAAAGGGTTCTTATACTTAGTCTAGTTCTAACACTATA
* *
12485533 CATATTCAAAAGTTATCTCGTTCGTCTTATTTCCCTAAAAAATATCTAGACACTAAAGCTTCATC
66 CATATTCAAAACTTATCTCGTTCGTCTTATTTCCCTAAAAAATATCTAGACACCAAAGCTTCATC
* *
12485598 GGACGGGGTGTTACAACAGCATAACACGCATTCTATTTTCAACATTCACTCATACAGTTACATAA
131 GGACGAGGTGTTACAACAGCATAACACGCATTCTATTTTCAACATTCACTCATACAATTACATAA
12485663 CCAACATACTATAATTTTCTAGCTTTGGCAT
196 CCAACATACTATAATTTTCTAGCTTTGGCAT
12485694 CATTATTCAA
Statistics
Matches: 212, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
229 212 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (229 bp):
CCAACATCAATGCGTCATAGGCGTACTCAAAGGGTTCTTATACTTAGTCTAGTTCTAACACTATA
CATATTCAAAACTTATCTCGTTCGTCTTATTTCCCTAAAAAATATCTAGACACCAAAGCTTCATC
GGACGAGGTGTTACAACAGCATAACACGCATTCTATTTTCAACATTCACTCATACAATTACATAA
CCAACATACTATAATTTTCTAGCTTTGGCATTTT
Found at i:12492113 original size:13 final size:15
Alignment explanation
Indices: 12492094--12492134 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 15
12492084 CCTATAGGGG
12492094 ACACATGGCTGTG-T
1 ACACATGGCTGTGTT
12492108 -CACATGGCCGTGTGTT
1 ACACATGG-C-TGTGTT
12492124 ACACATGGCTG
1 ACACATGGCTG
12492135 GGACAAACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 7 0.30
14 1 0.04
15 6 0.26
16 2 0.09
17 7 0.30
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (15 bp):
ACACATGGCTGTGTT
Found at i:12504512 original size:27 final size:28
Alignment explanation
Indices: 12504465--12504588 Score: 191
Period size: 27 Copynumber: 4.5 Consensus size: 28
12504455 TAAATTGTGC
12504465 AGCAC-AAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
12504492 AGCACTAAGTGTGCGAG-TTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
12504519 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
12504547 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
12504574 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12504589 GACTTAATAT
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
27 55 0.60
28 37 0.40
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:12504531 original size:55 final size:55
Alignment explanation
Indices: 12504465--12504588 Score: 205
Period size: 55 Copynumber: 2.3 Consensus size: 55
12504455 TAAATTGTGC
*
12504465 AGCAC-AAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATAT
* *
12504519 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATAT
*
12504574 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12504589 GACTTAATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
54 5 0.08
55 60 0.92
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATAT
Found at i:12513607 original size:18 final size:19
Alignment explanation
Indices: 12513584--12513619 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12513574 TCCCTTAATG
12513584 ATTAGATTCTCAA-AATCC
1 ATTAGATTCTCAATAATCC
*
12513602 ATTAGATTGTCAATAATC
1 ATTAGATTCTCAATAATC
12513620 GTAGCAGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (19 bp):
ATTAGATTCTCAATAATCC
Found at i:12528421 original size:40 final size:39
Alignment explanation
Indices: 12528354--12528483 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
12528344 GGACTAAGAT
* *
12528354 CCGAAGGCCTTTGTGCGAGA-TACTAAATCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGA-ATTACTAAATCCGGGTTATGTC
**
12528394 CCGAAGGCATTCGTGCGAATTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATT-GTGCGAATTACTAAATCCGGGTTATGTC
* * *
12528434 CCGAAGGCATTGTGTGAGTTACTAAATCCGGGCTATGTC
1 CCGAAGGCATTGTGCGAATTACTAAATCCGGGTTATGTC
12528473 CCGAAGGCATT
1 CCGAAGGCATT
12528484 TGAACGAGGA
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 38 0.48
40 41 0.52
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAATTACTAAATCCGGGTTATGTC
Found at i:12528503 original size:79 final size:79
Alignment explanation
Indices: 12528354--12528518 Score: 179
Period size: 79 Copynumber: 2.1 Consensus size: 79
12528344 GGACTAAGAT
* * ** ** *
12528354 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAATTGTTA
1 CCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAAGAGCTA
**
12528419 AATCCGGGTTATGTC
66 AATCC-GGTTAAATC
* * * * *
12528434 CCGAAGG-CATTGTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAAGAGCTA
*
12528498 TATCCGGTTAAATC
66 AATCCGGTTAAATC
12528512 CCGAAGG
1 CCGAAGG
12528519 TACGTGATTT
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
78 14 0.20
79 49 0.70
80 7 0.10
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAAGAGCTA
AATCCGGTTAAATC
Found at i:12536354 original size:14 final size:15
Alignment explanation
Indices: 12536335--12536367 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12536325 TATAATAAGA
12536335 AAAGAAAT-AAAAAT
1 AAAGAAATCAAAAAT
12536349 AAAGAAATCGAAAAAT
1 AAAGAAATC-AAAAAT
12536365 AAA
1 AAA
12536368 TTAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
16 9 0.53
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAGAAATCAAAAAT
Found at i:12546548 original size:21 final size:20
Alignment explanation
Indices: 12546522--12546587 Score: 89
Period size: 20 Copynumber: 3.2 Consensus size: 20
12546512 TACGGGATTT
12546522 ACACTTCGGGTGTCCCTGTTC
1 ACACTTC-GGTGTCCCTGTTC
* *
12546543 ACACTTCGGTGCCCCTATAT-
1 ACACTTCGGTGTCCCTGT-TC
12546563 ACACTTCGGTGTCCCTGTTC
1 ACACTTCGGTGTCCCTGTTC
12546583 ACACT
1 ACACT
12546588 ATGGTGCCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.77
21 8 0.21
ACGTcount: A:0.15, C:0.35, G:0.18, T:0.32
Consensus pattern (20 bp):
ACACTTCGGTGTCCCTGTTC
Found at i:12546558 original size:20 final size:20
Alignment explanation
Indices: 12546522--12546596 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
12546512 TACGGGATTT
*
12546522 ACACTTCGGGTGTCCCTGTTC
1 ACACTTC-GGTGCCCCTGTTC
*
12546543 ACACTTCGGTGCCCCTATAT-
1 ACACTTCGGTGCCCCTGT-TC
*
12546563 ACACTTCGGTGTCCCTGTTC
1 ACACTTCGGTGCCCCTGTTC
12546583 ACACTAT-GGTGCCC
1 ACACT-TCGGTGCCC
12546597 TTATTTGCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.02
20 36 0.78
21 9 0.20
ACGTcount: A:0.15, C:0.35, G:0.20, T:0.31
Consensus pattern (20 bp):
ACACTTCGGTGCCCCTGTTC
Found at i:12548266 original size:111 final size:111
Alignment explanation
Indices: 12548072--12548289 Score: 337
Period size: 111 Copynumber: 2.0 Consensus size: 111
12548062 CGACCTAGCG
* *
12548072 CACGGGCGTGTGGTTTGGCCATGTGACCAAACTCAGAGAGTTACACGGGTGACGACACGGGTAAG
1 CACGGGCGTGTGGTTTGGCCATGTGACCAAACTCAGAGAGTTACACGGGTAACGACACGGATAAG
* *
12548137 GACAGAAGCTAGGACATGAACGTGTGTCCTTATTTCGATTGTGGCA
66 GACACAAGCTAGGACATGAACGTGTGTCCTTACTTCGATTGTGGCA
* * * *
12548183 CACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAGAGTTACACGGGTAAGGACTCGGATGAG
1 CACGGGCGTGTGGTTTGGCCATGTGACCAAACTCAGAGAGTTACACGGGTAACGACACGGATAAG
* * *
12548248 GACACAAGTTGGGACATGAATGTGTGTCCTTACTTCGATTGT
66 GACACAAGCTAGGACATGAACGTGTGTCCTTACTTCGATTGT
12548290 TACACGGCCT
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 96 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (111 bp):
CACGGGCGTGTGGTTTGGCCATGTGACCAAACTCAGAGAGTTACACGGGTAACGACACGGATAAG
GACACAAGCTAGGACATGAACGTGTGTCCTTACTTCGATTGTGGCA
Found at i:12550251 original size:26 final size:25
Alignment explanation
Indices: 12550191--12550265 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
12550181 TGAGGTCAGG
*
12550191 CGAGCTGGTGTTTGTAGTAGGACTGG
1 CGAGCTGGTGTTTGTAGTAGG-CTGA
* * *
12550217 TGAGTTGGTATTTGTAGTAGGCTTGA
1 CGAGCTGGTGTTTGTAGTAGGC-TGA
*
12550243 CGAGCTGGTGTTCGTCAGTAGGC
1 CGAGCTGGTGTTTGT-AGTAGGC
12550266 CAGACAAGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
25 1 0.03
26 31 0.79
27 7 0.18
ACGTcount: A:0.16, C:0.12, G:0.39, T:0.33
Consensus pattern (25 bp):
CGAGCTGGTGTTTGTAGTAGGCTGA
Found at i:12556900 original size:40 final size:40
Alignment explanation
Indices: 12556863--12557043 Score: 190
Period size: 40 Copynumber: 4.5 Consensus size: 40
12556853 GCTACTCGTT
* * *
12556863 CAAACGCCTTTGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
12556903 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
12556943 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
12556982 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
12557023 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
12557044 TGGACATCAT
Statistics
Matches: 117, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.27
40 71 0.61
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:12556963 original size:79 final size:80
Alignment explanation
Indices: 12556863--12557043 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
12556853 GCTACTCGTT
* * * * *
12556863 CAAACGCCTTTGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAA-GCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCACACAAATGCCTTC-GGATCTTAACCC
* *
12556926 GGATTTAGTAAC-TCGCA
63 GGATATAGTAACTTAGCA
* **
12556943 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACACAAATGCCTTCGGATCTTAGTCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATTAGTAACTCACACAAATGCCTTCGGATCTTAACCCGG
* *
12557007 ATATGGTCACTTAGCA
65 ATATAGTAACTTAGCA
12557023 CAAAGCCTTCGGGACTTAGCC
1 CAAAGCCTTCGGGACTTAGCC
12557044 TGGACATCAT
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
78 3 0.04
79 53 0.63
80 28 0.33
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATTAGTAACTCACACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:12556984 original size:39 final size:40
Alignment explanation
Indices: 12556891--12556994 Score: 156
Period size: 39 Copynumber: 2.6 Consensus size: 40
12556881 AGCCCGGTTA
* *
12556891 TAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
*
12556931 TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
* *
12556970 TAGTATCTCACACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
12556995 ATCTTAGTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 34 0.58
40 25 0.42
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
Found at i:12565468 original size:15 final size:15
Alignment explanation
Indices: 12565450--12565500 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
12565440 ATGGCCGTGT
12565450 GTCACACACGGCTAA
1 GTCACACACGGCTAA
* * **
12565465 GTCACACGC-CCGTGT
1 GTCACACACGGC-TAA
12565480 GTCACACACGGCTAA
1 GTCACACACGGCTAA
12565495 GTCACA
1 GTCACA
12565501 TGCCTGTGTG
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.27, C:0.35, G:0.22, T:0.16
Consensus pattern (15 bp):
GTCACACACGGCTAA
Found at i:12565480 original size:30 final size:30
Alignment explanation
Indices: 12565444--12565513 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
12565434 TGTCGCATGG
12565444 CCGTGTGTCACACACGGCTAAGTCACACGC
1 CCGTGTGTCACACACGGCTAAGTCACACGC
*
12565474 CCGTGTGTCACACACGGCTAAGTCACATGC
1 CCGTGTGTCACACACGGCTAAGTCACACGC
*
12565504 CTGTGTGTCA
1 CCGTGTGTCA
12565514 GGCCGTATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.21
Consensus pattern (30 bp):
CCGTGTGTCACACACGGCTAAGTCACACGC
Found at i:12569906 original size:27 final size:27
Alignment explanation
Indices: 12569873--12570147 Score: 195
Period size: 27 Copynumber: 10.2 Consensus size: 27
12569863 CCCAATATTT
* * *
12569873 GTAAAATGACCGTAATACCCCTGTAGG
1 GTAAAATGATCGAAATACCCCTATAGG
* **
12569900 GTAAAATGATCGAAATACCCTCGA-ACA
1 GTAAAATGATCGAAATACCC-CTATAGG
* *
12569927 GTAAAATGATTGAAATACCCCCGA-AGG
1 GTAAAATGATCGAAATA-CCCCTATAGG
*
12569954 GTAAAATGATCGAAATA-CCCTCAAAGG
1 GTAAAATGATCGAAATACCCCT-ATAGG
* * *
12569981 GTAAAATGACCAAAATA-CCCTCAAAGG
1 GTAAAATGATCGAAATACCCCT-ATAGG
*
12570008 GTAAAATGATCGAAAAATCCCC-ATAGG
1 GTAAAATGATCGAAATA-CCCCTATAGG
* * * * * *
12570035 GCAAAATGGTCGTAATGCCCCTGTAGA
1 GTAAAATGATCGAAATACCCCTATAGG
* * *
12570062 GTAAAATGATTGTAATACCCTTATAGG
1 GTAAAATGATCGAAATACCCCTATAGG
* *
12570089 GTTAAATGA-CTGAAATACCCCTATAAG
1 GTAAAATGATC-GAAATACCCCTATAGG
* * *
12570116 GTAAAAT-ATCCGTAATGCCCCTAGAGG
1 GTAAAATGAT-CGAAATACCCCTATAGG
12570143 GTAAA
1 GTAAA
12570148 TGACTATTTT
Statistics
Matches: 197, Mismatches: 41, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
25 3 0.02
26 6 0.03
27 180 0.91
28 5 0.03
29 3 0.02
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (27 bp):
GTAAAATGATCGAAATACCCCTATAGG
Found at i:12570110 original size:54 final size:54
Alignment explanation
Indices: 12569873--12570122 Score: 220
Period size: 54 Copynumber: 4.6 Consensus size: 54
12569863 CCCAATATTT
* * **
12569873 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATCGAAATACCCTCGA-ACA
1 GTAAAATGACTGAAATACCCCTGTAGGGTAAAATGATCGAAATACCCTC-ATAGG
* * * *
12569927 GTAAAATGATTGAAATACCCCCGAAGGGTAAAATGATCGAAATACCCTCAAAGG
1 GTAAAATGACTGAAATACCCCTGTAGGGTAAAATGATCGAAATACCCTCATAGG
** ** *
12569981 GTAAAATGACCAAAATA-CCCTCAAAGGGTAAAATGATCGAAAAATCCC-CATAGG
1 GTAAAATGACTGAAATACCCCT-GTAGGGTAAAATGATCGAAATA-CCCTCATAGG
* * * * * * * *
12570035 GCAAAATG-GTCGTAATGCCCCTGTAGAGTAAAATGATTGTAATACCCTTATAGG
1 GTAAAATGACT-GAAATACCCCTGTAGGGTAAAATGATCGAAATACCCTCATAGG
* * *
12570089 GTTAAATGACTGAAATACCCCTATAAGGTAAAAT
1 GTAAAATGACTGAAATACCCCTGTAGGGTAAAAT
12570123 ATCCGTAATG
Statistics
Matches: 154, Mismatches: 35, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
53 7 0.05
54 139 0.90
55 8 0.05
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (54 bp):
GTAAAATGACTGAAATACCCCTGTAGGGTAAAATGATCGAAATACCCTCATAGG
Found at i:12570241 original size:24 final size:24
Alignment explanation
Indices: 12570170--12570266 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
12570160 CCCTCGAGTG
* *
12570170 TAAATGATTGATTTGTCTGTGATG
1 TAAATGACTGATTTGTCTGTGATT
** *
12570194 TAAATGAGGGATTTATCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
*
12570218 TAAATGACTAATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
*** * *
12570242 GGTATAACTGATTTGTCTATGATT
1 TAAATGACTGATTTGTCTGTGATT
12570266 T
1 T
12570267 GTATTACTGA
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:12570270 original size:24 final size:24
Alignment explanation
Indices: 12570228--12570278 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
12570218 TAAATGACTA
*
12570228 ATTTGTCTGTGATTGGTATAACTG
1 ATTTGTCTATGATTGGTATAACTG
* *
12570252 ATTTGTCTATGATTTGTATTACTG
1 ATTTGTCTATGATTGGTATAACTG
12570276 ATT
1 ATT
12570279 CTGAGCATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.51
Consensus pattern (24 bp):
ATTTGTCTATGATTGGTATAACTG
Found at i:12570491 original size:32 final size:32
Alignment explanation
Indices: 12570450--12570619 Score: 195
Period size: 32 Copynumber: 5.4 Consensus size: 32
12570440 GCTGCGATAC
**
12570450 TACTGATGGCTTTGTGTTGATCATATTA-TCGT
1 TACTGATGGCTTTGTGCCGATCATATTACT-GT
12570482 TACTGATGGCTTTGTGCCGATCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
12570514 TACTAATGGCTTTGTGCCGATCATATTACCG-
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * * * *
12570545 CACTGATAG-TTGTGTGCCGGTCATATCACTGC
1 TACTGATGGCTT-TGTGCCGATCATATTACTGT
*
12570577 TACTGATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
12570608 TACTTATGGCTT
1 TACTGATGGCTT
12570620 GTAGCCATTC
Statistics
Matches: 118, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.02
31 33 0.28
32 80 0.68
33 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACTGT
Found at i:12570586 original size:63 final size:64
Alignment explanation
Indices: 12570449--12570605 Score: 201
Period size: 63 Copynumber: 2.5 Consensus size: 64
12570439 TGCTGCGATA
** * * * *
12570449 CTACTGATGGCTTTGTGTTGATCATATTATCGTTACTGATGGCTTTGTGCCGATCATATTACTG
1 CTACTGATGGCTTTGTGCCGATCATATTACCGTCACTGATAGCTTTGTGCCGATCATATCACTG
* * *
12570513 TTACTAATGGCTTTGTGCCGATCATATTACCG-CACTGATAG-TTGTGTGCCGGTCATATCACTG
1 CTACTGATGGCTTTGTGCCGATCATATTACCGTCACTGATAGCTT-TGTGCCGATCATATCACTG
*
12570576 CTACTGATGGCTTTGTGCCAATCATATTAC
1 CTACTGATGGCTTTGTGCCGATCATATTAC
12570606 TGTACTTATG
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
62 2 0.03
63 51 0.64
64 27 0.34
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (64 bp):
CTACTGATGGCTTTGTGCCGATCATATTACCGTCACTGATAGCTTTGTGCCGATCATATCACTG
Found at i:12570967 original size:32 final size:33
Alignment explanation
Indices: 12570907--12570968 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
12570897 GATACTGTAA
* *
12570907 TGGGCTAAGGCCCACACTACACTTTTACTGTTT
1 TGGGCTAAAGCCCACACTACACTGTTACTGTTT
*
12570940 TGGGCTAAAG-CCACACTATACTGTTACTG
1 TGGGCTAAAGCCCACACTACACTGTTACTG
12570969 GATAGGGCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (33 bp):
TGGGCTAAAGCCCACACTACACTGTTACTGTTT
Found at i:12570977 original size:32 final size:33
Alignment explanation
Indices: 12570908--12570977 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 33
12570898 ATACTGTAAT
* * ** *
12570908 GGGCTAAGGCCCACACTACACTTTTACTGTTTT
1 GGGCTAAAGCCCACACTACACTGTTACTGGATA
*
12570941 GGGCTAAAG-CCACACTATACTGTTACTGGATA
1 GGGCTAAAGCCCACACTACACTGTTACTGGATA
12570973 GGGCT
1 GGGCT
12570978 CAGGCCCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
32 23 0.74
33 8 0.26
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (33 bp):
GGGCTAAAGCCCACACTACACTGTTACTGGATA
Found at i:12575931 original size:28 final size:28
Alignment explanation
Indices: 12575891--12575947 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
12575881 GAACTTTGAG
12575891 TATGTGAACCTCAAATCTAAGTGGACAA
1 TATGTGAACCTCAAATCTAAGTGGACAA
12575919 TATGTGAACCTCAAATCTAAGTGGACAA
1 TATGTGAACCTCAAATCTAAGTGGACAA
12575947 T
1 T
12575948 CCCTTAGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (28 bp):
TATGTGAACCTCAAATCTAAGTGGACAA
Found at i:12592100 original size:20 final size:20
Alignment explanation
Indices: 12592048--12592100 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
12592038 ACATTTGTGC
*
12592048 CTCTATTTGCACTTTGGTGT
1 CTCTATTTGCACTTTGATGT
* *
12592068 CTCTACTTACACTTTGATGT
1 CTCTATTTGCACTTTGATGT
*
12592088 CTCTGTTTGCACT
1 CTCTATTTGCACT
12592101 ACAGTGCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.13, C:0.25, G:0.15, T:0.47
Consensus pattern (20 bp):
CTCTATTTGCACTTTGATGT
Found at i:12609120 original size:5 final size:5
Alignment explanation
Indices: 12609106--12609156 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
12609096 TAAATATACA
*
12609106 ATAT- ATATG ATATG ATATG ATATG ATATG ATATG ATATG -TA-C ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
12609153 ATAT
1 ATAT
12609157 ATGTATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
4 8 0.19
5 34 0.81
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:12611186 original size:33 final size:33
Alignment explanation
Indices: 12611134--12611262 Score: 125
Period size: 33 Copynumber: 3.7 Consensus size: 33
12611124 TTTAAAAGCA
*
12611134 TTTGTTAATTTGT-TATTATTTTAGAGACATTTG
1 TTTGTTAAGTTGTAT-TTATTTTAGAGACATTTG
** **
12611167 TTTGTTAAGTTGTATTTATTTTAGTTTATTTTTAAAG
1 TTTGTTAAGTTGTATTTATTTTAG-AGACATTT---G
* *
12611204 CATTTGTTAATTTGTTTTTATTTTAGAGACATTTG
1 --TTTGTTAAGTTGTATTTATTTTAGAGACATTTG
12611239 TTTGTTAAGTTGTATTTATTTTAG
1 TTTGTTAAGTTGTATTTATTTTAG
12611263 TGTTATTTAA
Statistics
Matches: 76, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
33 43 0.57
34 5 0.07
35 1 0.01
37 1 0.01
38 4 0.05
39 22 0.29
ACGTcount: A:0.23, C:0.02, G:0.15, T:0.60
Consensus pattern (33 bp):
TTTGTTAAGTTGTATTTATTTTAGAGACATTTG
Found at i:12611204 original size:72 final size:73
Alignment explanation
Indices: 12611120--12611270 Score: 277
Period size: 72 Copynumber: 2.1 Consensus size: 73
12611110 AATTTTGTTA
12611120 TTATTTTAAAAGCATTTGTTAATTTGTTATTATTTTAGAGACATTTGTTTGTTAAGTTGTATTTA
1 TTATTTTAAAAGCATTTGTTAATTTGTTATTATTTTAGAGACATTTGTTTGTTAAGTTGTATTTA
12611185 TTTTAGT-
66 TTTTAGTG
* *
12611192 TTATTTTTAAAGCATTTGTTAATTTGTTTTTATTTTAGAGACATTTGTTTGTTAAGTTGTATTTA
1 TTATTTTAAAAGCATTTGTTAATTTGTTATTATTTTAGAGACATTTGTTTGTTAAGTTGTATTTA
12611257 TTTTAGTG
66 TTTTAGTG
12611265 TTATTT
1 TTATTT
12611271 AAGTCTACAT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 70 0.92
73 6 0.08
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.59
Consensus pattern (73 bp):
TTATTTTAAAAGCATTTGTTAATTTGTTATTATTTTAGAGACATTTGTTTGTTAAGTTGTATTTA
TTTTAGTG
Found at i:12611356 original size:18 final size:18
Alignment explanation
Indices: 12611321--12611358 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12611311 GAAATATTTA
*
12611321 TTTTGATATTTTTAATAT
1 TTTTGATATTTATAATAT
12611339 TTTTGATATATTAT-ATAT
1 TTTTGATAT-TTATAATAT
12611357 TT
1 TT
12611359 AAAAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTGATATTTATAATAT
Found at i:12618189 original size:2 final size:2
Alignment explanation
Indices: 12618182--12618212 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12618172 AGTCATATGC
12618182 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
12618213 AACATATCCT
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:12626635 original size:32 final size:31
Alignment explanation
Indices: 12626582--12626641 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12626572 CATGTACTTA
* *
12626582 TATAAAAAAAATTATATACATATATATAGAT
1 TATAAAAAAAATAATACACATATATATAGAT
12626613 TATAAAAAAAATAATTACACATATATATA
1 TATAAAAAAAATAA-TACACATATATATA
12626642 AACAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (31 bp):
TATAAAAAAAATAATACACATATATATAGAT
Found at i:12626658 original size:27 final size:25
Alignment explanation
Indices: 12626613--12626663 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
12626603 ATATATAGAT
*
12626613 TATAAAAAAAATAATTACACATATA
1 TATAAAAAAAATAACTACACATATA
*
12626638 TATAAACAAATAATAACTACATATAT
1 TATAAA-AAA-AATAACTACACATAT
12626664 TAAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (25 bp):
TATAAAAAAAATAACTACACATATA
Found at i:12626659 original size:25 final size:24
Alignment explanation
Indices: 12626613--12626668 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
12626603 ATATATAGAT
*
12626613 TATA-AAAAAAATAATTACACATA
1 TATATAAAAAAATAATAACACATA
*
12626636 TATATAAACAAATAATAACTACATA
1 TATATAAAAAAATAATAAC-ACATA
12626661 TAT-TAAAA
1 TATATAAAA
12626669 TTAATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.14
24 16 0.57
25 8 0.29
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (24 bp):
TATATAAAAAAATAATAACACATA
Found at i:12626824 original size:17 final size:17
Alignment explanation
Indices: 12626802--12626836 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12626792 TAGGAAATAA
* *
12626802 AAAATGTATATGTATAT
1 AAAATGTAAATATATAT
12626819 AAAATGTAAATATATAT
1 AAAATGTAAATATATAT
12626836 A
1 A
12626837 TAAGTTATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (17 bp):
AAAATGTAAATATATAT
Found at i:12626964 original size:3 final size:3
Alignment explanation
Indices: 12626956--12626994 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
12626946 GTATATATAG
* * *
12626956 TAA TAA TAA TAA TGA TAA TAA TAA CAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12626995 CTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:12627342 original size:23 final size:22
Alignment explanation
Indices: 12627299--12627356 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
12627289 AAAGGGTATC
* *
12627299 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
12627320 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
12627343 TTCATATCATATCT
1 TACAAATCATATCT
12627357 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:12627359 original size:19 final size:19
Alignment explanation
Indices: 12627327--12627382 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
12627317 GATTACAAAA
12627327 TCATATC-T-TCTAAGATT
1 TCATATCATATCTAAGATT
12627344 TCATATCATATCTAAGATT
1 TCATATCATATCTAAGATT
*
12627363 GCATATATCATATCTAAGAT
1 TC--ATATCATATCTAAGAT
12627383 CATATCTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.21
18 1 0.03
19 10 0.29
21 16 0.47
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (19 bp):
TCATATCATATCTAAGATT
Found at i:12627402 original size:14 final size:12
Alignment explanation
Indices: 12627369--12627394 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12627359 GATTGCATAT
12627369 ATCATATCTAAG
1 ATCATATCTAAG
12627381 ATCATATCTAAG
1 ATCATATCTAAG
12627393 AT
1 AT
12627395 TGCATATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:12630144 original size:33 final size:32
Alignment explanation
Indices: 12630097--12630194 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
12630087 TACGCGGTTC
* * *
12630097 TGTGAAATGGTAACAAATATCAGCCTTTCATTT
1 TGTGAAATGATAACAAATATCA-ACTTTAATTT
12630130 TGTGAAATGATAACAAAT-TACAACTTTAATTT
1 TGTGAAATGATAACAAATAT-CAACTTTAATTT
* *
12630162 TGTAAAATGATAACAAATATCAACTTCAATTT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
12630194 T
1 T
12630195 TTTTAAATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
32 38 0.66
33 20 0.34
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (32 bp):
TGTGAAATGATAACAAATATCAACTTTAATTT
Found at i:12635070 original size:17 final size:18
Alignment explanation
Indices: 12635009--12635070 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
12634999 AAACTAAATC
12635009 AAAATCTAA-TAAAACCT
1 AAAATCTAATTAAAACCT
** *
12635026 AATAAGAT-TTTAAAACCT
1 AA-AATCTAATTAAAACCT
*
12635044 AAAATTTAATTAAAACCT
1 AAAATCTAATTAAAACCT
12635062 -AAATCTAAT
1 AAAATCTAAT
12635071 AATACTTAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
17 13 0.37
18 22 0.63
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATCTAATTAAAACCT
Found at i:12635584 original size:17 final size:17
Alignment explanation
Indices: 12635564--12635610 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
12635554 GAATTCGCCA
* *
12635564 TTTGGCGAACTCTAGGT
1 TTTGGCAAACTCTAGGG
12635581 TTTGGCAAACTCTAGGG
1 TTTGGCAAACTCTAGGG
*
12635598 ATTGGCAAACTCT
1 TTTGGCAAACTCT
12635611 TCTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (17 bp):
TTTGGCAAACTCTAGGG
Found at i:12640567 original size:72 final size:72
Alignment explanation
Indices: 12640412--12640567 Score: 168
Period size: 72 Copynumber: 2.2 Consensus size: 72
12640402 AAGGTTGAGG
* * * *
12640412 GTGTCGTGACATACCCATAAAGATGGCTGCAGTGGAGTATACTAGTTGCTACGTCACGACATAGG
1 GTGTCGTGACATACCCATAAAGATGGCTGCAGAGGAGCATACTAGTTGCTACGTCACGACACAAG
12640477 CGTTGGT
66 CGTTGGT
* * ** * * * * * *
12640484 GTTTCATGACATACCTTTGAAGATGGCTGTAGAGGAGCATATTGGTTGCTATGTCATGACACAAG
1 GTGTCGTGACATACCCATAAAGATGGCTGCAGAGGAGCATACTAGTTGCTACGTCACGACACAAG
*
12640549 TGTTGGT
66 CGTTGGT
*
12640556 GTGTCGCGACAT
1 GTGTCGTGACAT
12640568 CGACTCTATG
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (72 bp):
GTGTCGTGACATACCCATAAAGATGGCTGCAGAGGAGCATACTAGTTGCTACGTCACGACACAAG
CGTTGGT
Found at i:12647434 original size:22 final size:22
Alignment explanation
Indices: 12647402--12647445 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12647392 TATATAAAAA
12647402 GAGCTTAAATACAAATGAGTTT
1 GAGCTTAAATACAAATGAGTTT
* *
12647424 GAGCTTGAATACTAATGAGTTT
1 GAGCTTAAATACAAATGAGTTT
12647446 AATTGAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (22 bp):
GAGCTTAAATACAAATGAGTTT
Found at i:12657739 original size:9 final size:9
Alignment explanation
Indices: 12657725--12657780 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
12657715 AAATAAAAAC
12657725 ATTATTAAA
1 ATTATTAAA
12657734 ATTATTAAA
1 ATTATTAAA
12657743 A-TATTAAA
1 ATTATTAAA
12657751 ATTTTATATAAA
1 A--TTAT-TAAA
* *
12657763 CTTATAAAA
1 ATTATTAAA
12657772 ATTA-TAAA
1 ATTATTAAA
12657780 A
1 A
12657781 AATTACAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 12 0.31
9 16 0.41
10 4 0.10
11 3 0.08
12 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (9 bp):
ATTATTAAA
Found at i:12657776 original size:19 final size:18
Alignment explanation
Indices: 12657711--12657857 Score: 90
Period size: 19 Copynumber: 7.8 Consensus size: 18
12657701 AAAATGTAAA
12657711 ATAAAAA-TA-AAAACATT
1 ATAAAAATTATAAAAC-TT
*
12657728 ATTAAAATTATTAAAA--T
1 ATAAAAATTA-TAAAACTT
*
12657745 ATTAAAATTTTATATAAACTT
1 A-TAAAA-ATTATA-AAACTT
*
12657766 ATAAAAATTATAAAAAATT
1 ATAAAAATTAT-AAAACTT
* *
12657785 ACAAAAA-AATAATAACTT
1 ATAAAAATTATAA-AACTT
*
12657803 ATAAATATTATAAATACTT
1 ATAAAAATTATAAA-ACTT
12657822 AT-AAAATTATAATAAACTAT
1 ATAAAAATTAT-A-AAACT-T
12657842 ATAAATAATTATAAAA
1 ATAAA-AATTATAAAA
12657858 GATAAAGATA
Statistics
Matches: 101, Mismatches: 12, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
17 10 0.10
18 27 0.27
19 35 0.35
20 18 0.18
21 5 0.05
22 6 0.06
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAAATTATAAAACTT
Found at i:12657780 original size:37 final size:37
Alignment explanation
Indices: 12657721--12657857 Score: 118
Period size: 37 Copynumber: 3.6 Consensus size: 37
12657711 ATAAAAATAA
* *
12657721 AAACATTATTAAAATTATTAAAATATTA-AAATTTTATAT
1 AAAC-TTATAAAAATTA-TAAAATATTACAAA-ATTATAT
* **
12657760 AAACTTATAAAAATTATAAAAAATTACAAAAAAATA-
1 AAACTTATAAAAATTATAAAATATTACAAAATTATAT
* *
12657796 ATAACTTATAAATATTAT-AAATACTTATAAAATTATAAT
1 A-AACTTATAAAAATTATAAAATA-TTACAAAATTAT-AT
12657835 AAACTATATAAATAATTATAAAA
1 AAACT-TATAAA-AATTATAAAA
12657858 GATAAAGATA
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
36 5 0.06
37 36 0.46
38 19 0.24
39 11 0.14
40 5 0.06
41 3 0.04
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (37 bp):
AAACTTATAAAAATTATAAAATATTACAAAATTATAT
Found at i:12657781 original size:9 final size:9
Alignment explanation
Indices: 12657711--12658067 Score: 82
Period size: 10 Copynumber: 37.9 Consensus size: 9
12657701 AAAATGTAAA
12657711 ATAAAAA-T
1 ATAAAAATT
12657719 A-AAAACATT
1 ATAAAA-ATT
*
12657728 ATTAAAATT
1 ATAAAAATT
12657737 ATTAAAATATT
1 A-TAAAA-ATT
**
12657748 A-AAATTTT
1 ATAAAAATT
*
12657756 ATATAAACTT
1 ATA-AAAATT
12657766 ATAAAAATT
1 ATAAAAATT
12657775 ATAAAAAATT
1 AT-AAAAATT
* *
12657785 ACAAAAA-A
1 ATAAAAATT
*
12657793 ATAATAACTT
1 ATAA-AAATT
*
12657803 ATAAATATT
1 ATAAAAATT
*
12657812 ATAAATACTT
1 ATAAA-AATT
12657822 AT-AAAATT
1 ATAAAAATT
12657830 ATAATAAACTAT
1 ATAA-AAA-T-T
12657842 ATAAATAATT
1 ATAAA-AATT
12657852 ATAAAAGA-T
1 ATAAAA-ATT
12657861 A-AAGATAATT
1 ATAA-A-AATT
12657871 -TAAATAATT
1 ATAAA-AATT
*
12657880 -T-AAATTT
1 ATAAAAATT
**
12657887 ATTTAAATAT
1 ATAAAAAT-T
12657897 ATAAAAATT
1 ATAAAAATT
*
12657906 ATTAAAAA-A
1 A-TAAAAATT
* **
12657915 ACAAAAAAA
1 ATAAAAATT
*
12657924 ATGGATAATATT
1 AT--A-AAAATT
12657936 ATAAAAACTCT
1 ATAAAAA-T-T
12657947 A-AAAAATT
1 ATAAAAATT
*
12657955 ATCAATAATT
1 AT-AAAAATT
*
12657965 ATAAAACTT
1 ATAAAAATT
**
12657974 ATAAACACAGC
1 ATAAA-A-ATT
12657985 ATAAAAACTT
1 ATAAAAA-TT
12657995 ATTTAAAAA--
1 A--TAAAAATT
12658004 ATCAAAAAGTT
1 AT-AAAAA-TT
* *
12658015 CTAATAATT
1 ATAAAAATT
12658024 ATAAAAA-T
1 ATAAAAATT
*
12658032 ATATAAAATC
1 ATA-AAAATT
12658042 AT-AAAA-T
1 ATAAAAATT
12658049 ATTAAAAATAT
1 A-TAAAAAT-T
12658060 ATAAAAAT
1 ATAAAAAT
12658068 CCATTTATAG
Statistics
Matches: 258, Mismatches: 43, Indels: 94
0.65 0.11 0.24
Matches are distributed among these distances:
7 9 0.03
8 39 0.15
9 86 0.33
10 88 0.34
11 18 0.07
12 18 0.07
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:12657907 original size:19 final size:19
Alignment explanation
Indices: 12657824--12657908 Score: 52
Period size: 19 Copynumber: 4.5 Consensus size: 19
12657814 AAATACTTAT
*
12657824 AAAATTATAATAAACTATATA
1 AAAATTAT-TTAAA-TATATA
*
12657845 AATAATTA--TAAA-AGATA
1 AA-AATTATTTAAATATATA
* * *
12657862 AAGATAATTTAAATA-ATTT
1 AAAATTATTTAAATATA-TA
*
12657881 AAATTTATTTAAATATATA
1 AAAATTATTTAAATATATA
12657900 AAAATTATT
1 AAAATTATT
12657909 AAAAAAACAA
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
16 3 0.06
17 6 0.12
18 5 0.10
19 27 0.55
20 1 0.02
21 2 0.04
22 5 0.10
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAATTATTTAAATATATA
Found at i:12658038 original size:10 final size:10
Alignment explanation
Indices: 12658023--12658067 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
12658013 TTCTAATAAT
12658023 TATAAAAATA
1 TATAAAAATA
12658033 TAT-AAAAT-
1 TATAAAAATA
*
12658041 CAT-AAAATA
1 TATAAAAATA
12658050 T-TAAAAATA
1 TATAAAAATA
12658059 TATAAAAAT
1 TATAAAAAT
12658068 CCATTTATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 8 0.27
9 12 0.40
10 10 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
TATAAAAATA
Found at i:12658585 original size:30 final size:30
Alignment explanation
Indices: 12658551--12658618 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
12658541 ATTATTCTTT
* *
12658551 AAATTTT-TATAATTTATTAGATTTTTATGA
1 AAATTTTATATAATTTATAAG-TTTTTATAA
*
12658581 AAATTTTATATTATTTATAAGTTTTTATAA
1 AAATTTTATATAATTTATAAGTTTTTATAA
*
12658611 AAAATTTA
1 AAATTTTA
12658619 AATATGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 22 0.67
31 11 0.33
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (30 bp):
AAATTTTATATAATTTATAAGTTTTTATAA
Found at i:12658734 original size:9 final size:9
Alignment explanation
Indices: 12658537--12658734 Score: 52
Period size: 9 Copynumber: 20.9 Consensus size: 9
12658527 ATAATTTTTA
*
12658537 TTTTATTAT
1 TTTTATAAT
12658546 TCTTTA-AAT
1 T-TTTATAAT
12658555 TTTTATAAT
1 TTTTATAAT
*
12658564 TTATTA-GAT
1 TT-TTATAAT
*
12658573 TTTTATGAAAA
1 TTTTAT--AAT
12658584 TTTTAT-AT
1 TTTTATAAT
12658592 TATTTATAAGT
1 T-TTTATAA-T
*
12658603 TTTTATAAAAA
1 TTTTAT--AAT
*
12658614 ATTTA-AAT
1 TTTTATAAT
* *
12658622 ATGTTAAATAT
1 -TTTTATA-AT
12658633 GTTTTAT-AT
1 -TTTTATAAT
12658642 GTTTTATTAA-
1 -TTTTA-TAAT
12658652 TTTTATAAT
1 TTTTATAAT
12658661 TTATTA-AA-
1 TT-TTATAAT
**
12658669 AATTATAAT
1 TTTTATAAT
*
12658678 TGTTTATCAT
1 T-TTTATAAT
*
12658688 ATTTATAAGT
1 TTTTATAA-T
12658698 TTTTATGAATT
1 TTTTAT-AA-T
* *
12658709 TTTTACAAG
1 TTTTATAAT
*
12658718 TCTTATAAT
1 TTTTATAAT
12658727 TTTTATAA
1 TTTTATAA
12658735 ATTTATACCA
Statistics
Matches: 138, Mismatches: 28, Indels: 46
0.65 0.13 0.22
Matches are distributed among these distances:
7 3 0.02
8 16 0.12
9 57 0.41
10 32 0.23
11 28 0.20
12 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (9 bp):
TTTTATAAT
Found at i:12667856 original size:31 final size:31
Alignment explanation
Indices: 12667807--12667867 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
12667797 TTAGTATAAT
*
12667807 TATATACATGAAACTTTTATTATAATTTAAA
1 TATATACAAGAAACTTTTATTATAATTTAAA
* * * *
12667838 TATATATAAGAAATTTTTATTTTGATTTAA
1 TATATACAAGAAACTTTTATTATAATTTAA
12667868 TTATGCACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (31 bp):
TATATACAAGAAACTTTTATTATAATTTAAA
Found at i:12668463 original size:32 final size:32
Alignment explanation
Indices: 12668423--12668484 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
12668413 TTTTTTTAAG
* * **
12668423 TTAAATTTAGTCTTTAATTTTTTTTAAAAAAT
1 TTAAATTTAATCATTAACCTTTTTTAAAAAAT
12668455 TTAAATTTAATCATTAACCTTTTTTAAAAA
1 TTAAATTTAATCATTAACCTTTTTTAAAAA
12668485 GAGTCGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (32 bp):
TTAAATTTAATCATTAACCTTTTTTAAAAAAT
Found at i:12671772 original size:13 final size:13
Alignment explanation
Indices: 12671754--12671781 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12671744 TATTGCATTA
12671754 TTTGTTTCGGTTC
1 TTTGTTTCGGTTC
12671767 TTTGTTTCGGTTC
1 TTTGTTTCGGTTC
12671780 TT
1 TT
12671782 GCCTGTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.21, T:0.64
Consensus pattern (13 bp):
TTTGTTTCGGTTC
Found at i:12673636 original size:13 final size:13
Alignment explanation
Indices: 12673618--12673643 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12673608 TCTAAATCAG
12673618 AATTATTTTTGAA
1 AATTATTTTTGAA
12673631 AATTATTTTTGAA
1 AATTATTTTTGAA
12673644 CTCAAAAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
AATTATTTTTGAA
Found at i:12676859 original size:91 final size:91
Alignment explanation
Indices: 12676712--12676919 Score: 344
Period size: 91 Copynumber: 2.3 Consensus size: 91
12676702 TTGATTTTAG
* *
12676712 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
12676777 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
12676804 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
12676869 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
*
12676895 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
12676920 GTTATAATTA
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 93 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:12676888 original size:26 final size:28
Alignment explanation
Indices: 12676834--12676894 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
12676824 TATTATCAAG
* *
12676834 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
12676862 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
12676888 AATTATA
1 AATTATA
12676895 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:12676894 original size:44 final size:43
Alignment explanation
Indices: 12676752--12676894 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
12676742 GAATTTTATG
* *
12676752 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
12676796 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
12676843 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
12676887 AAATTATA
1 AAATTATA
12676895 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:12676968 original size:16 final size:16
Alignment explanation
Indices: 12676949--12676991 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
12676939 TTATTAAATC
12676949 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
12676965 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
12676980 AT-TATGTTAATT
1 ATATATTTTAATT
12676992 TATCTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:12677009 original size:59 final size:59
Alignment explanation
Indices: 12676946--12677134 Score: 190
Period size: 59 Copynumber: 3.2 Consensus size: 59
12676936 AATTTATTAA
*
12676946 ATCATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATCTTTTATAGT
1 ATCATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
* * * * * * *
12677005 ATCATATATTATGATTTGAGTAA-ATTCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-
1 ATCATATATT-TTAATT-A-TAATA-T-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAG
*
12677065 A
59 T
*
12677066 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
12677125 ATCATATATT
1 ATCATATATT
12677135 ATGAAATGAG
Statistics
Matches: 99, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
57 8 0.08
58 10 0.10
59 29 0.29
60 16 0.16
61 18 0.18
62 10 0.10
63 8 0.08
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (59 bp):
ATCATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
Found at i:12677062 original size:120 final size:120
Alignment explanation
Indices: 12676938--12677227 Score: 526
Period size: 120 Copynumber: 2.4 Consensus size: 120
12676928 TATTTTAAAA
* *
12676938 TTTATTAAATCATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATCTTTTATA
1 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATA
**
12677003 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
66 GTATCATATATTATGAAATGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
12677058 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATA
1 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATA
12677123 GTATCATATATTATGAAATGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
66 GTATCATATATTATGAAATGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
* *
12677178 TTTATTAAATTATATATTTCAATTATATTATATTTAATAATAATTATGTT
1 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
12677228 TAAATATGAT
Statistics
Matches: 164, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 164 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATA
GTATCATATATTATGAAATGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
Found at i:12677095 original size:15 final size:15
Alignment explanation
Indices: 12677060--12677111 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
12677050 TTAAGAATTT
*
12677060 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12677074 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12677088 TATTTAATAATAAT-
1 TATTTAATTATAATA
12677102 TATGTTAATT
1 TAT-TTAATT
12677112 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:12677193 original size:61 final size:61
Alignment explanation
Indices: 12677008--12677195 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
12676998 TTATAGTATC
**
12677008 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGAAATGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
12677069 ATATATT-T-TAATTA-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGAAATGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
12677127 C
61 T
12677128 ATATATTATGAAATGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGAAATGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
12677189 ATATATT
1 ATATATT
12677196 TCAATTATAT
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
57 11 0.12
58 8 0.08
59 19 0.20
60 10 0.11
61 28 0.29
62 8 0.08
63 11 0.12
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (61 bp):
ATATATTATGAAATGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:12677452 original size:45 final size:44
Alignment explanation
Indices: 12677369--12677459 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 44
12677359 ACCTCTATTC
*
12677369 CATTCAACCAAACACAAGATTACTCTTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
* * *
12677413 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCTATTA
1 CATTCAACCAAACACA-AGA-TTACTATTACGCCTCTATTCCATTA
12677458 CA
1 CA
12677460 CATCTATTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.39
45 24 0.59
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
Found at i:12677457 original size:16 final size:16
Alignment explanation
Indices: 12677436--12677484 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
12677426 AATTGATTTG
12677436 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
* *
12677452 CTATTACACATCTATT
1 CTATTACGCCTCTATT
* *
12677468 CCATTACGGCTCTATT
1 CTATTACGCCTCTATT
12677484 C
1 C
12677485 CAATACAGCG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.41
Consensus pattern (16 bp):
CTATTACGCCTCTATT
Found at i:12679249 original size:14 final size:15
Alignment explanation
Indices: 12679230--12679263 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12679220 TACAGAATAC
*
12679230 AATAAA-ATATTAAA
1 AATAAATATATAAAA
12679244 AATAAATATATAAAA
1 AATAAATATATAAAA
12679259 AATAA
1 AATAA
12679264 GACAGTGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAATATATAAAA
Found at i:12684718 original size:25 final size:24
Alignment explanation
Indices: 12684658--12684711 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
12684648 AAGCTCATAT
* *
12684658 GAGCCAATTTCGGGAAGTTCAAGC
1 GAGCCAATATCGGGAAGTTCAAGA
12684682 GAGCCAATATCGGGAAGTTTC-AGA
1 GAGCCAATATCGGGAAG-TTCAAGA
12684706 GAGCCA
1 GAGCCA
12684712 TTAATCGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (24 bp):
GAGCCAATATCGGGAAGTTCAAGA
Found at i:12684781 original size:25 final size:24
Alignment explanation
Indices: 12684724--12684781 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
12684714 AATCGTAAAA
*
12684724 CTCATAAGAGCCATAAACGGGAAG
1 CTCATAAGAACCATAAACGGGAAG
** *
12684748 CTCGCAAGAACCATATAATGGGAAG
1 CTCATAAGAACCATA-AACGGGAAG
12684773 CTCATAAGA
1 CTCATAAGA
12684782 GCCAAATATC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (24 bp):
CTCATAAGAACCATAAACGGGAAG
Found at i:12692731 original size:6 final size:6
Alignment explanation
Indices: 12692720--12692765 Score: 56
Period size: 6 Copynumber: 7.0 Consensus size: 6
12692710 GCATCAAGCT
12692720 ACCTCC ACCTCC ACCTCC ACCGATCC ACCTCC ACCGGTCC ACCTCC
1 ACCTCC ACCTCC ACCTCC ACC--TCC ACCTCC ACC--TCC ACCTCC
12692766 GGTCCTGCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 24 0.67
8 12 0.33
ACGTcount: A:0.17, C:0.61, G:0.07, T:0.15
Consensus pattern (6 bp):
ACCTCC
Found at i:12692748 original size:14 final size:13
Alignment explanation
Indices: 12692720--12692765 Score: 67
Period size: 14 Copynumber: 3.5 Consensus size: 13
12692710 GCATCAAGCT
12692720 ACCTCCACC-TCC
1 ACCTCCACCGTCC
12692732 ACCTCCACCGATCC
1 ACCTCCACCG-TCC
12692746 ACCTCCACCGGTCC
1 ACCTCCACC-GTCC
12692760 ACCTCC
1 ACCTCC
12692766 GGTCCTGCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 9 0.29
14 21 0.68
15 1 0.03
ACGTcount: A:0.17, C:0.61, G:0.07, T:0.15
Consensus pattern (13 bp):
ACCTCCACCGTCC
Found at i:12694044 original size:32 final size:32
Alignment explanation
Indices: 12694003--12694067 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
12693993 CAATGAGAGT
12694003 ATGGATCAATTTTGATATTGTTATCCTTTAAA
1 ATGGATCAATTTTGATATTGTTATCCTTTAAA
*
12694035 ATGGATCAATTTTGATGTTGTTATCCTTTAAA
1 ATGGATCAATTTTGATATTGTTATCCTTTAAA
12694067 A
1 A
12694068 GCATAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (32 bp):
ATGGATCAATTTTGATATTGTTATCCTTTAAA
Found at i:12694238 original size:25 final size:25
Alignment explanation
Indices: 12694204--12694255 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
12694194 CTTTTTTAAG
*
12694204 AATTGATTGTTTGTAATTAAATTCA
1 AATTAATTGTTTGTAATTAAATTCA
12694229 AATTAATTGTTTGTAATTAAATTCA
1 AATTAATTGTTTGTAATTAAATTCA
12694254 AA
1 AA
12694256 CAAGTAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (25 bp):
AATTAATTGTTTGTAATTAAATTCA
Found at i:12703865 original size:25 final size:25
Alignment explanation
Indices: 12703837--12703889 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
12703827 TTTATTAAAC
* **
12703837 TTATTATTTATTATTATATTTAATT
1 TTATTATTAATTAAAATATTTAATT
12703862 TTATTATTAATTAAAATATTTAATT
1 TTATTATTAATTAAAATATTTAATT
12703887 TTA
1 TTA
12703890 GAAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATTATTAATTAAAATATTTAATT
Found at i:12703930 original size:19 final size:18
Alignment explanation
Indices: 12703894--12703932 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12703884 ATTTTAGAAA
*
12703894 ATATTTTTATTGATATTT
1 ATATTTTTATTAATATTT
*
12703912 ATATTTTTTTTAATAATTT
1 ATATTTTTATTAAT-ATTT
12703931 AT
1 AT
12703933 GTAAACTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
ATATTTTTATTAATATTT
Found at i:12708331 original size:30 final size:30
Alignment explanation
Indices: 12708297--12708353 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
12708287 TACATCAGAG
*
12708297 TAGTGGTAGTAGTTGTGTTTAGTAAAAAAT
1 TAGTGGTAGTAGTTGCGTTTAGTAAAAAAT
*
12708327 TAGTGGTAGTAGTTGCGTTTGGTAAAA
1 TAGTGGTAGTAGTTGCGTTTAGTAAAA
12708354 TAATAGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.39
Consensus pattern (30 bp):
TAGTGGTAGTAGTTGCGTTTAGTAAAAAAT
Found at i:12710135 original size:14 final size:14
Alignment explanation
Indices: 12710104--12710152 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
12710094 AGGAAAGAAA
12710104 AAAGAA-AAGGGA-
1 AAAGAAGAAGGGAG
12710116 AGAAGAAGAAGGGAG
1 A-AAGAAGAAGGGAG
* *
12710131 AAAGAAAAAGAGAG
1 AAAGAAGAAGGGAG
12710145 AAA-AAGAA
1 AAAGAAGAA
12710153 AGAAAAAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 1 0.03
13 9 0.29
14 20 0.65
15 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAGGGAG
Found at i:12710146 original size:10 final size:10
Alignment explanation
Indices: 12710129--12710160 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
12710119 AGAAGAAGGG
12710129 AGAAAGAAAA
1 AGAAAGAAAA
*
12710139 AGAGAGAAAA
1 AGAAAGAAAA
12710149 AGAAAGAAAA
1 AGAAAGAAAA
12710159 AG
1 AG
12710161 GAAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
AGAAAGAAAA
Found at i:12710567 original size:3 final size:3
Alignment explanation
Indices: 12710559--12710583 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12710549 TATTTTTTAA
12710559 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
12710584 TTTTAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12710728 original size:20 final size:20
Alignment explanation
Indices: 12710703--12710740 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12710693 AAAAATATTC
12710703 AAAAATCCTCGTATTTTAAT
1 AAAAATCCTCGTATTTTAAT
* *
12710723 AAAAATTCTCGTGTTTTA
1 AAAAATCCTCGTATTTTA
12710741 TTAGAATCTC
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:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAAATCCTCGTATTTTAAT
Found at i:12710903 original size:17 final size:17
Alignment explanation
Indices: 12710857--12710905 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
12710847 TAAAGAAAAA
*
12710857 TCGTGTTTCAAAATTTT
1 TCGTGTTTCAAAATTTC
*
12710874 TCATGTCTTCAAAATTTC
1 TCGTGT-TTCAAAATTTC
12710892 TCGTGTTTCAAAAT
1 TCGTGTTTCAAAAT
12710906 AATGATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (17 bp):
TCGTGTTTCAAAATTTC
Found at i:12710985 original size:16 final size:16
Alignment explanation
Indices: 12710964--12711037 Score: 69
Period size: 17 Copynumber: 4.5 Consensus size: 16
12710954 TCTTTAAAAA
12710964 AAAAATTTCGTGTTTC
1 AAAAATTTCGTGTTTC
** *
12710980 AAAAATTCTCGTGAATA
1 AAAAATT-TCGTGTTTC
*
12710997 AAAAAATTCGTGTTTTC
1 AAAAATTTCGTG-TTTC
*
12711014 AAAAATTCCGGTGTTT-
1 AAAAATTTC-GTGTTTC
12711030 AAAAATTT
1 AAAAATTT
12711038 TTTCGTGTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
16 19 0.42
17 23 0.51
18 3 0.07
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:12711075 original size:18 final size:19
Alignment explanation
Indices: 12711045--12711302 Score: 120
Period size: 17 Copynumber: 13.9 Consensus size: 19
12711035 TTTTTTCGTG
12711045 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
12711064 TTCTT-GTG-TTTC-AAAAA
1 TT-TTCGTGTTTTCAAAAAA
12711081 TTTTCGTGTTTTCAAAATTTTCATA
1 TTTTCGTGTTTTCAAAA-----A-A
12711106 TTTTCGTGTTTTCAAAAAAA
1 TTTTCGTGTTTTC-AAAAAA
* *
12711126 TTATCGTGTTTTTTAAAAAAA
1 TTTTCGTG--TTTTCAAAAAA
** *
12711147 AATTCATG-TTT-AAAAAA
1 TTTTCGTGTTTTCAAAAAA
* *
12711164 --TTCATGTTTTC--GAAA
1 TTTTCGTGTTTTCAAAAAA
* *
12711179 TTTTTGTGTTTTC-AAAAT
1 TTTTCGTGTTTTCAAAAAA
12711197 TTTTCGTG---TCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
* * * *
12711213 TTCTCATG-TAT-AGAAAA
1 TTTTCGTGTTTTCAAAAAA
* *
12711230 TTTCCTTGTTTTCAAAACAA
1 TTTTCGTGTTTTCAAAA-AA
*
12711250 -TTCCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
* *
12711268 ATTTCGTG-TTTC-GAAAA
1 TTTTCGTGTTTTCAAAAAA
*
12711285 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
12711303 TTATCATTGT
Statistics
Matches: 185, Mismatches: 27, Indels: 54
0.70 0.10 0.20
Matches are distributed among these distances:
15 11 0.06
16 15 0.08
17 45 0.24
18 33 0.18
19 35 0.19
20 12 0.06
21 11 0.06
22 4 0.02
24 1 0.01
25 14 0.08
26 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (19 bp):
TTTTCGTGTTTTCAAAAAA
Found at i:12711081 original size:17 final size:18
Alignment explanation
Indices: 12711045--12711304 Score: 94
Period size: 18 Copynumber: 14.1 Consensus size: 18
12711035 TTTTTTCGTG
12711045 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
12711064 TTCTT-GTG-TTTCAAAAA
1 TT-TTCGTGTTTTCAAAAA
12711081 TTTTCGTGTTTTCAAAATTTTCATA
1 TTTTCGTGTTTTC-AAA-----A-A
12711106 TTTTCGTGTTTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
* *
12711126 TTATCGTGTTTTTTAAAAAAA
1 TTTTCGTG--TTTT-CAAAAA
** *
12711147 AATTCATG-TTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
12711163 -ATTCATGTTTTC-GAAA
1 TTTTCGTGTTTTCAAAAA
* *
12711179 TTTTTGTGTTTTCAAAAT
1 TTTTCGTGTTTTCAAAAA
12711197 TTTTCGTG---TCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* * *
12711213 TTCTCATG-TAT-AGAAAA
1 TTTTCGTGTTTTCA-AAAA
* *
12711230 TTTCCTTGTTTTCAAAACA
1 TTTTCGTGTTTTCAAAA-A
* *
12711249 ATTCCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
12711268 ATTTCGTG-TTTCGAAAA
1 TTTTCGTGTTTTCAAAAA
*
12711285 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
12711303 TT
1 TT
12711305 ATCATTGTGT
Statistics
Matches: 186, Mismatches: 28, Indels: 55
0.69 0.10 0.20
Matches are distributed among these distances:
15 9 0.05
16 24 0.13
17 38 0.20
18 39 0.21
19 29 0.16
20 14 0.08
21 10 0.05
22 4 0.02
24 1 0.01
25 14 0.08
26 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:12711085 original size:44 final size:43
Alignment explanation
Indices: 12711003--12711093 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 43
12710993 AATAAAAAAA
12711003 TTCGTGTTTTCAAAAATTCCGGTGTTTAAAAATTTTTTCGTGTT
1 TTCGTGTTTTCAAAAATTCCGGTGTTTAAAAA-TTTTTCGTGTT
**
12711047 TTCGTGTTTTCAAAAAATTCTTGTGTTTCAAAAA-TTTTCGTGTT
1 TTCGTGTTTTC-AAAAATTCCGGTGTTT-AAAAATTTTTCGTGTT
12711091 TTC
1 TTC
12711094 AAAATTTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 24 0.56
45 14 0.33
46 5 0.12
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (43 bp):
TTCGTGTTTTCAAAAATTCCGGTGTTTAAAAATTTTTCGTGTT
Found at i:12711102 original size:45 final size:44
Alignment explanation
Indices: 12711009--12711103 Score: 104
Period size: 45 Copynumber: 2.1 Consensus size: 44
12710999 AAAATTCGTG
***
12711009 TTTTC-AAAAATTCCGGTGTTTAAAAATTTTTTCGTGTTTTCGTG
1 TTTTCAAAAAATTCCGGTGTTTAAAAA-TTTTTCGTGTTTTCAAA
**
12711053 TTTTCAAAAAATTCTTGTGTTTCAAAAA-TTTTCGTGTTTTCAAAA
1 TTTTCAAAAAATTCCGGTGTTT-AAAAATTTTTCGTGTTTTC-AAA
12711098 TTTTCA
1 TTTTCA
12711104 TATTTTCGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
44 18 0.42
45 20 0.47
46 5 0.12
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (44 bp):
TTTTCAAAAAATTCCGGTGTTTAAAAATTTTTCGTGTTTTCAAA
Found at i:12711125 original size:62 final size:62
Alignment explanation
Indices: 12710996--12711136 Score: 164
Period size: 61 Copynumber: 2.3 Consensus size: 62
12710986 TCTCGTGAAT
* * *
12710996 AAAAAAATTCGTGT-TTTCAAAAATTCCGGTGTTTAAAAATTTTTTCGTGTTTTCGTGTTTTC
1 AAAAAAATTCTTGTGTTTCAAAAATTCCGGTGTTTAAAAA-TTTTTCATATTTTCGTGTTTTC
* *
12711058 -AAAAAATTCTTGTGTTTCAAAAATTTTC-GTGTTTTCAAAA-TTTTCATATTTTCGTGTTTTC
1 AAAAAAATTCTTGTGTTTCAAAAA-TTCCGGTG-TTTAAAAATTTTTCATATTTTCGTGTTTTC
* *
12711119 AAAAAAATTATCGTGTTT
1 AAAAAAATTCTTGTGTTT
12711137 TTTAAAAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
61 31 0.46
62 27 0.40
63 10 0.15
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.48
Consensus pattern (62 bp):
AAAAAAATTCTTGTGTTTCAAAAATTCCGGTGTTTAAAAATTTTTCATATTTTCGTGTTTTC
Found at i:12711156 original size:21 final size:22
Alignment explanation
Indices: 12711114--12711157 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12711104 TATTTTCGTG
* * *
12711114 TTTTCAAAAAAATTATCGTGTT
1 TTTTAAAAAAAAATATCATGTT
12711136 TTTTAAAAAAAAAT-TCATGTT
1 TTTTAAAAAAAAATATCATGTT
12711157 T
1 T
12711158 AAAAAATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTAAAAAAAAATATCATGTT
Found at i:12711180 original size:15 final size:15
Alignment explanation
Indices: 12711143--12711172 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12711133 GTTTTTTAAA
12711143 AAAAAATTCATGTTT
1 AAAAAATTCATGTTT
12711158 AAAAAATTCATGTTT
1 AAAAAATTCATGTTT
12711173 TCGAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
AAAAAATTCATGTTT
Found at i:12714503 original size:20 final size:20
Alignment explanation
Indices: 12714478--12714544 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
12714468 TTCTACAGGA
12714478 TTTGCACTTCGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* *
12714498 TTTGCACTTCGATGTCCCTG
1 TTTGCACTTCGGTGCCCCTG
* *
12714518 TTCGCACTACGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
12714538 TTATGCA
1 TT-TGCA
12714545 TATATGATGC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 36 0.92
21 3 0.08
ACGTcount: A:0.10, C:0.33, G:0.22, T:0.34
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:12715236 original size:29 final size:25
Alignment explanation
Indices: 12715177--12715228 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
12715167 AGCGGTTAAT
12715177 TTACTTCTTACGAGATTACTAAGCA
1 TTACTTCTTACGAGATTACTAAGCA
* *
12715202 TTACTTTTTACGAGCTTACTAAGCA
1 TTACTTCTTACGAGATTACTAAGCA
12715227 TT
1 TT
12715229 CATTACTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (25 bp):
TTACTTCTTACGAGATTACTAAGCA
Found at i:12719252 original size:46 final size:46
Alignment explanation
Indices: 12719137--12719354 Score: 233
Period size: 46 Copynumber: 4.6 Consensus size: 46
12719127 CTTCAAGAAG
* *
12719137 ATAAGATTCGC-GTCCTTCAGCTTTAATCTACTACAACACTAGGGAA
1 ATAAGATTCGCTG-CCTTCAGCTTTAATCTACTACAACGCCAGGGAA
* * *
12719183 A-AAGATTCGTTGCCTTCAGCTTTAATCTACTGCAATGCCAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAA
* * * *
12719228 ATAAGATTCGCTGCCTTCAACTTTAATCTATTCCATTGCAATGCCAAGGAAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTA---C--TACAACGCC-AGGGAA
* * *
12719280 AAAAGATTCACTGCCTTCAGCTTTAATCTACTACAACGCTAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAA
* *
12719326 ATAATATTTGCTGCCTTCAGCTTTAATCT
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT
12719355 GTTCCACTGC
Statistics
Matches: 145, Mismatches: 19, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
45 38 0.26
46 58 0.40
47 6 0.04
49 2 0.01
51 9 0.06
52 32 0.22
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (46 bp):
ATAAGATTCGCTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAA
Found at i:12719308 original size:98 final size:97
Alignment explanation
Indices: 12719181--12719385 Score: 286
Period size: 98 Copynumber: 2.1 Consensus size: 97
12719171 AACACTAGGG
** * *
12719181 AAAAAGATTCGTTGCCTTCAGCTTTAATCTACTGCAATGCCAGGGAAATAAGATTCGCTGCCTTC
1 AAAAAGATTCACTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
12719246 AACTTTAATCTATTCCATTGCAATG-CCAAGGAA
66 AACTTTAATCTATTCCACTGCAACGCCCAA--AA
* * *
12719279 AAAAAGATTCACTGCCTTCAGCTTTAATCTACTACAACGCTAGGGAAATAATATTTGCTGCCTTC
1 AAAAAGATTCACTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
12719344 AGCTTTAATCTGTTCCACTGCAACGCCCAAAA
66 AACTTTAATCTATTCCACTGCAACGCCCAAAA
12719376 AAAAAGATTC
1 AAAAAGATTC
12719386 GCCATAATAA
Statistics
Matches: 95, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
97 12 0.13
98 79 0.83
99 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (97 bp):
AAAAAGATTCACTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAAATAAGATTCGCTGCCTTC
AACTTTAATCTATTCCACTGCAACGCCCAAAA
Found at i:12724151 original size:45 final size:44
Alignment explanation
Indices: 12724064--12724157 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
12724054 TTCAATCCGC
* *
12724064 ATTTCACAGCTTTGTAATGCCATCTCTAATTCTTCTATTCTTCNT
1 ATTTCACAGCTTTGTAATGCCATCTCTAATTCTTCCACTCTTC-T
* * *
12724109 ATTTCACAGTTTTGTAATGGCATTTCTAATTCTTCCACTCTTCT
1 ATTTCACAGCTTTGTAATGCCATCTCTAATTCTTCCACTCTTCT
12724153 -TTTCA
1 ATTTCA
12724158 TTTCCTCGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 5 0.11
44 1 0.02
45 38 0.86
ACGTcount: A:0.20, C:0.23, G:0.07, T:0.48
Consensus pattern (44 bp):
ATTTCACAGCTTTGTAATGCCATCTCTAATTCTTCCACTCTTCT
Found at i:12730373 original size:20 final size:20
Alignment explanation
Indices: 12730350--12730387 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12730340 TTTCATCATC
12730350 TATTTTATAATAA-TATTAGT
1 TATTTTA-AATAACTATTAGT
12730370 TATTTTAAATAACTATTA
1 TATTTTAAATAACTATTA
12730388 TCCTCAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTTAAATAACTATTAGT
Found at i:12731744 original size:46 final size:46
Alignment explanation
Indices: 12731643--12731745 Score: 145
Period size: 46 Copynumber: 2.2 Consensus size: 46
12731633 ATAATATCTT
* * *
12731643 ATAATATCCCATTAGAAATCAAATTGTTAAGAGATAATATCCCATA
1 ATAATATCCTATTAGAAATCAAATTGCTAAAAGATAATATCCCATA
* *
12731689 ATAATATCCTATTATG-ATTCAAATTGCTAAAAGATGATATCCCATA
1 ATAATATCCTATTA-GAAATCAAATTGCTAAAAGATAATATCCCATA
12731735 ATAATATCCTA
1 ATAATATCCTA
12731746 ACACCCCCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 50 0.98
47 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.33
Consensus pattern (46 bp):
ATAATATCCTATTAGAAATCAAATTGCTAAAAGATAATATCCCATA
Done.