Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 79 of 213
Found at i:21683323 original size:30 final size:30
Alignment explanation
Indices: 21683289--21683347 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
21683279 GCATCACAAA
21683289 ATGTTAAAATT-T-ATTAATAATATATTTTTT
1 ATGTT-AAATTATAATTAA-AATATATTTTTT
21683319 ATGTTAAATTATAAATTAAAATATATTTT
1 ATGTTAAATTAT-AATTAAAATATATTTT
21683348 AAAAACATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 5 0.19
30 6 0.23
31 10 0.38
32 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (30 bp):
ATGTTAAATTATAATTAAAATATATTTTTT
Found at i:21685606 original size:23 final size:23
Alignment explanation
Indices: 21685574--21685617 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21685564 GCTACCATTT
21685574 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
21685597 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
21685618 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:21685610 original size:13 final size:11
Alignment explanation
Indices: 21685578--21685620 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
21685568 CCATTTTCTA
*
21685578 AATAAAATAAT
1 AATAAAATATT
21685589 AAT-AAATATCT
1 AATAAAATAT-T
21685600 AAGTAAAATATT
1 AA-TAAAATATT
21685612 AATAAAATA
1 AATAAAATA
21685621 ATTTTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:21688158 original size:29 final size:29
Alignment explanation
Indices: 21688126--21688183 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
21688116 AATCTCGATC
21688126 ACCATCCTTTAAGAACAATAAAAAATTAT
1 ACCATCCTTTAAGAACAATAAAAAATTAT
21688155 ACCATCCTTTAAGAACAATAAAAAATTAT
1 ACCATCCTTTAAGAACAATAAAAAATTAT
21688184 CTCAATAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (29 bp):
ACCATCCTTTAAGAACAATAAAAAATTAT
Found at i:21690001 original size:50 final size:50
Alignment explanation
Indices: 21689830--21690000 Score: 225
Period size: 50 Copynumber: 3.4 Consensus size: 50
21689820 TATCCCATAT
** * * * *
21689830 ATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
** * *
21689880 ATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCTTGTTCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* *
21689930 ACGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
*
21689980 ATGGTCTTACATTGGACCTCT
1 ATGGTCTTACATGGGACCTCT
21690001 TTACCCAAAT
Statistics
Matches: 103, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 103 1.00
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
Found at i:21692903 original size:37 final size:37
Alignment explanation
Indices: 21692861--21692958 Score: 135
Period size: 37 Copynumber: 2.6 Consensus size: 37
21692851 CATATTGAGA
* *
21692861 TCTGATTTGCATGTTAAA-CATGCCATATTTTTTATAT
1 TCTGATTTGCATG-TAAAGCATGCCATATTTCTGATAT
* *
21692898 TCTGATTCGCATGTAAAGCATGTCATATTTCTGATAT
1 TCTGATTTGCATGTAAAGCATGCCATATTTCTGATAT
*
21692935 TCTGATTTGCTTGTAAAGCATGCC
1 TCTGATTTGCATGTAAAGCATGCC
21692959 TACTGAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
36 4 0.08
37 49 0.92
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (37 bp):
TCTGATTTGCATGTAAAGCATGCCATATTTCTGATAT
Found at i:21693558 original size:25 final size:25
Alignment explanation
Indices: 21693517--21693575 Score: 100
Period size: 25 Copynumber: 2.3 Consensus size: 25
21693507 GTTTAATTAT
*
21693517 TTTGGACTTTGGTTTTGGACATGGAC
1 TTTGGA-TTTGGATTTGGACATGGAC
21693543 TTTGGATTTGGATTTGGACATGGAC
1 TTTGGATTTGGATTTGGACATGGAC
21693568 TTTGGATT
1 TTTGGATT
21693576 ATTTTTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 26 0.81
26 6 0.19
ACGTcount: A:0.17, C:0.08, G:0.31, T:0.44
Consensus pattern (25 bp):
TTTGGATTTGGATTTGGACATGGAC
Found at i:21693560 original size:19 final size:19
Alignment explanation
Indices: 21693517--21693575 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
21693507 GTTTAATTAT
*
21693517 TTTGGACTTTGGTTTTGGA
1 TTTGGACTTTGGATTTGGA
**
21693536 CATGGACTTTGGATTTGGA
1 TTTGGACTTTGGATTTGGA
*
21693555 TTTGGAC-ATGGACTTTGGA
1 TTTGGACTTTGGA-TTTGGA
21693574 TT
1 TT
21693576 ATTTTTGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 4 0.12
19 29 0.88
ACGTcount: A:0.17, C:0.08, G:0.31, T:0.44
Consensus pattern (19 bp):
TTTGGACTTTGGATTTGGA
Found at i:21695702 original size:74 final size:74
Alignment explanation
Indices: 21695545--21695735 Score: 208
Period size: 74 Copynumber: 2.6 Consensus size: 74
21695535 AAATCGATAG
* * * * * * *
21695545 ATATAATGATGTTCCCTGCACTAGTAAGATAAACTGACGAAAGTTGCACCTAGCGCTAGTCGGAT
1 ATATAATGGTGTGCCCAGCACTAGTAAGAT-AATTGATGAAACTTGCACCTAGCGCTAGTCGGAA
21695610 AAACCGAAAA
65 AAACCGAAAA
* *
21695620 ATATAATGGTGTGCCCAGCACTAGTAAGATAATTGATGAAACTTGC-GCTCAGCAG-TAGTCGTA
1 ATATAATGGTGTGCCCAGCACTAGTAAGATAATTGATGAAACTTGCACCT-AGC-GCTAGTCGGA
21695683 AAAACC-AAAA
64 AAAACCGAAAA
* * *
21695693 ACTATAATGGTGTGCCCAACACTAGTCAGAAAAATTGATGAAA
1 A-TATAATGGTGTGCCCAGCACTAGTAAG-ATAATTGATGAAA
21695736 GTTTTGCCAA
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
73 7 0.07
74 53 0.53
75 40 0.40
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (74 bp):
ATATAATGGTGTGCCCAGCACTAGTAAGATAATTGATGAAACTTGCACCTAGCGCTAGTCGGAAA
AACCGAAAA
Found at i:21695774 original size:75 final size:74
Alignment explanation
Indices: 21695600--21695781 Score: 215
Period size: 75 Copynumber: 2.4 Consensus size: 74
21695590 GCACCTAGCG
* * *
21695600 CTAGTCGGATAAACCGAAAAATATAATGGTGTGCCCAGCACTAGTAAGATAATTGATGAAACTTG
1 CTAGTCGTATAAACCGAAAAATATAATGGTGTGCCCAACACTAGTAAGAAAATTGATGAAACTTG
*
21695665 CGCTCAGCA
66 CGCTCAACA
* * * *
21695674 GTAGTCGTAAAAACC-AAAAACTATAATGGTGTGCCCAACACTAGTCAGAAAAATTGATGAAAGT
1 CTAGTCGTATAAACCGAAAAA-TATAATGGTGTGCCCAACACTAGTAAG-AAAATTGATGAAACT
**
21695738 TTTGC-CAAACA
64 TGCGCTC-AACA
* *
21695749 CTAGTCGTATCAACCGACAAATATAATGGTGTG
1 CTAGTCGTATAAACCGAAAAATATAATGGTGTG
21695782 TCCAGCAGTA
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
73 5 0.06
74 38 0.42
75 43 0.48
76 4 0.04
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (74 bp):
CTAGTCGTATAAACCGAAAAATATAATGGTGTGCCCAACACTAGTAAGAAAATTGATGAAACTTG
CGCTCAACA
Found at i:21697173 original size:38 final size:38
Alignment explanation
Indices: 21697122--21697198 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
21697112 CAGTAACTTG
* *
21697122 ATCAATGGTTTATTTTCCTAATAAGCCCCTTGTTTGAT
1 ATCAATGGCTTATTTGCCTAATAAGCCCCTTGTTTGAT
21697160 ATCAATGGCTTATTTGCCTAATAAGCCCCTTGTTTGAT
1 ATCAATGGCTTATTTGCCTAATAAGCCCCTTGTTTGAT
21697198 A
1 A
21697199 GTCACTTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (38 bp):
ATCAATGGCTTATTTGCCTAATAAGCCCCTTGTTTGAT
Found at i:21702287 original size:192 final size:192
Alignment explanation
Indices: 21701960--21702346 Score: 774
Period size: 192 Copynumber: 2.0 Consensus size: 192
21701950 CATAATTCTA
21701960 AAGTTTATATGACTTTCAATATAAGTAACTTATACTAGATTCAACCACAGACCAGAAGACTATTA
1 AAGTTTATATGACTTTCAATATAAGTAACTTATACTAGATTCAACCACAGACCAGAAGACTATTA
21702025 CTCAAATTATCATTATCCTAGGTACATGTCATGACACAAAAAGAAATACTTCACCAACATTGAGT
66 CTCAAATTATCATTATCCTAGGTACATGTCATGACACAAAAAGAAATACTTCACCAACATTGAGT
21702090 TCGAGATTTGTCGTGGATGCTGAGTCATTGAACAAAAGTAAGTACCTAACCAACATTCAAAG
131 TCGAGATTTGTCGTGGATGCTGAGTCATTGAACAAAAGTAAGTACCTAACCAACATTCAAAG
21702152 AAGTTTATATGACTTTCAATATAAGTAACTTATACTAGATTCAACCACAGACCAGAAGACTATTA
1 AAGTTTATATGACTTTCAATATAAGTAACTTATACTAGATTCAACCACAGACCAGAAGACTATTA
21702217 CTCAAATTATCATTATCCTAGGTACATGTCATGACACAAAAAGAAATACTTCACCAACATTGAGT
66 CTCAAATTATCATTATCCTAGGTACATGTCATGACACAAAAAGAAATACTTCACCAACATTGAGT
21702282 TCGAGATTTGTCGTGGATGCTGAGTCATTGAACAAAAGTAAGTACCTAACCAACATTCAAAG
131 TCGAGATTTGTCGTGGATGCTGAGTCATTGAACAAAAGTAAGTACCTAACCAACATTCAAAG
21702344 AAG
1 AAG
21702347 GGTTCAAAAA
Statistics
Matches: 195, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
192 195 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (192 bp):
AAGTTTATATGACTTTCAATATAAGTAACTTATACTAGATTCAACCACAGACCAGAAGACTATTA
CTCAAATTATCATTATCCTAGGTACATGTCATGACACAAAAAGAAATACTTCACCAACATTGAGT
TCGAGATTTGTCGTGGATGCTGAGTCATTGAACAAAAGTAAGTACCTAACCAACATTCAAAG
Found at i:21702394 original size:18 final size:18
Alignment explanation
Indices: 21702373--21702409 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
21702363 AAACTCATTC
*
21702373 ATTTAAAGAATTACACTA
1 ATTTAAAGAATCACACTA
21702391 ATTTAAAGAATCACACTA
1 ATTTAAAGAATCACACTA
21702409 A
1 A
21702410 CACCTAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (18 bp):
ATTTAAAGAATCACACTA
Found at i:21702814 original size:40 final size:39
Alignment explanation
Indices: 21702688--21702823 Score: 118
Period size: 40 Copynumber: 3.5 Consensus size: 39
21702678 AAAAGTTGCA
* * *
21702688 CCCAGCGCTAGTTAGATAAATCGAAAAATATAATGGTGTG
1 CCCAGCACTAGTTAGATAAACCG-ACAATATAATGGTGTG
* * * * *
21702728 CCTAACACTAGTAAGATAAACTGAC--GA-AA-GGTGTG
1 CCCAGCACTAGTTAGATAAACCGACAATATAATGGTGTG
* * *
21702763 CCTAGCGCTAGTTGGATAAACCGAGCAATATAATGGTGTG
1 CCCAGCACTAGTTAGATAAACCGA-CAATATAATGGTGTG
*
21702803 CCCAGCACTAGTCAGATAAAC
1 CCCAGCACTAGTTAGATAAAC
21702824 TAACGAAAGT
Statistics
Matches: 73, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
35 25 0.34
36 3 0.04
37 1 0.01
38 1 0.01
39 3 0.04
40 40 0.55
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (39 bp):
CCCAGCACTAGTTAGATAAACCGACAATATAATGGTGTG
Found at i:21702830 original size:75 final size:75
Alignment explanation
Indices: 21702639--21702858 Score: 278
Period size: 75 Copynumber: 2.9 Consensus size: 75
21702629 TAATTTGACG
* * ** ** *
21702639 AATATAATGATGTGCCTATCACTAGTCAGATAAACTGATAAAAGTTGCACCCAGCGCTAGTTAGA
1 AATATAATGGTGTGCCTAACACTAGTCAGATAAACTGACGAAAGTTGTGCCCAGCGCTAGTTGGA
*
21702704 TAAATCGAAA
66 TAAACCGAAA
* * *
21702714 AATATAATGGTGTGCCTAACACTAGTAAGATAAACTGACGAAAGGTGTGCCTAGCGCTAGTTGGA
1 AATATAATGGTGTGCCTAACACTAGTCAGATAAACTGACGAAAGTTGTGCCCAGCGCTAGTTGGA
**
21702779 TAAACCGAGC
66 TAAACCGAAA
* * * * *
21702789 AATATAATGGTGTGCCCAGCACTAGTCAGATAAACTAACGAAAGTTATGCCCAGTGCTAGTTGGA
1 AATATAATGGTGTGCCTAACACTAGTCAGATAAACTGACGAAAGTTGTGCCCAGCGCTAGTTGGA
21702854 TAAAC
66 TAAAC
21702859 ATATAAATAG
Statistics
Matches: 124, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 124 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (75 bp):
AATATAATGGTGTGCCTAACACTAGTCAGATAAACTGACGAAAGTTGTGCCCAGCGCTAGTTGGA
TAAACCGAAA
Found at i:21704479 original size:16 final size:16
Alignment explanation
Indices: 21704458--21704527 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
21704448 TTTGGTTCGC
* * *
21704458 TGTATTGGATTAGAAG
1 TGTAATGGAATAGAGG
* *
21704474 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
21704490 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
21704506 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
21704522 TGTAAT
1 TGTAAT
21704528 AGCAAATCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:21704509 original size:32 final size:32
Alignment explanation
Indices: 21704458--21704527 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
21704448 TTTGGTTCGC
* * * *
21704458 TGTATTGGATTAGAAGTGTATTGGATTAGAGG
1 TGTAATGGAATAGAAGTGTAATGGAATAGAGG
*
21704490 TGTAATGGAATAGATGTGTAATGGAATAGAGG
1 TGTAATGGAATAGAAGTGTAATGGAATAGAGG
21704522 TGTAAT
1 TGTAAT
21704528 AGCAAATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.34
Consensus pattern (32 bp):
TGTAATGGAATAGAAGTGTAATGGAATAGAGG
Found at i:21704611 original size:39 final size:43
Alignment explanation
Indices: 21704506--21704615 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
21704496 GGAATAGATG
21704506 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
21704551 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
21704591 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
21704616 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:21704782 original size:18 final size:17
Alignment explanation
Indices: 21704761--21704795 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21704751 TTATTATTAA
*
21704761 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
21704779 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
21704796 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:21704849 original size:157 final size:157
Alignment explanation
Indices: 21704648--21704964 Score: 598
Period size: 157 Copynumber: 2.0 Consensus size: 157
21704638 CAGAATACCC
*
21704648 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
21704713 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
21704778 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
21704805 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
21704870 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
21704935 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
21704962 TTA
1 TTA
21704965 ATATTCTCAT
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:21704935 original size:16 final size:16
Alignment explanation
Indices: 21704898--21704939 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
21704888 TTAATCATAT
*
21704898 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
21704914 TT-AAATATATTATAA
1 TTAAAATATATTATAA
21704929 TTAAAATATAT
1 TTAAAATATAT
21704940 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:21704946 original size:14 final size:15
Alignment explanation
Indices: 21704907--21704948 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21704897 TTTAAACATA
*
21704907 ATTATTATTAAATAT
1 ATTATAATTAAATAT
21704922 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
21704936 A-TATAATTTAATA
1 ATTATAATTAAATA
21704949 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:21704998 original size:61 final size:61
Alignment explanation
Indices: 21704933--21705120 Score: 201
Period size: 61 Copynumber: 3.1 Consensus size: 61
21704923 TTATAATTAA
*
21704933 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTCATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * *
21704994 AATATATAATACT-ATAAAA-T-AT-A-AATTAACATAGTTATTAT-TAAATATA-TTATAATTA
1 AATATATAAT-TTAATAAAATTCTTAATAATT-A-ATA-TTCTTATATGAATTTACTCA-AATCA
*
21705052 A
61 T
21705053 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
21705114 AATATAT
1 AATATAT
21705121 GATACTATAA
Statistics
Matches: 98, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
57 4 0.04
58 5 0.05
59 30 0.31
60 13 0.13
61 37 0.38
62 5 0.05
63 4 0.04
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:21705039 original size:120 final size:120
Alignment explanation
Indices: 21704901--21705189 Score: 483
Period size: 120 Copynumber: 2.4 Consensus size: 120
21704891 ATCATATTTA
21704901 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
21704966 TATTCTCATATGAATTTACTCAAATCATAATATATAATACTATAAAATATAAATT-
66 TATTCTCATATGAATTTACTCAAATCATAATATATAATACTATAAAAGA-AAATTG
*
21705021 AACATAGTTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* * *
21705086 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAATTTG
66 TATTCTCATATGAATTTACTCAAATCATAATATATAATACTATAAAAGAAAATTG
* * *
21705141 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAA
21705190 TTTAAAATAA
Statistics
Matches: 159, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
119 47 0.30
120 112 0.70
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTCATATGAATTTACTCAAATCATAATATATAATACTATAAAAGAAAATTG
Found at i:21705066 original size:14 final size:15
Alignment explanation
Indices: 21705028--21705068 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
21705018 ATTAACATAG
*
21705028 TTATTATTAAATATA
1 TTATAATTAAATATA
21705043 TTATAATTAAA-ATA
1 TTATAATTAAATATA
*
21705057 -TATAATTTAATA
1 TTATAATTAAATA
21705069 AAATTCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATAATTAAATATA
Found at i:21705119 original size:59 final size:59
Alignment explanation
Indices: 21704936--21705119 Score: 164
Period size: 59 Copynumber: 3.1 Consensus size: 59
21704926 TAATTAAAAT
*
21704936 ATATAATTTAATAAAATTCTTAATAATTAATATTCTCATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * * * *
21704995 ATAT-ATAATACTATAAAA-TATAAATTAACATAGTTATTATTAAAT-ATATTATAATTAAA--A
1 ATATAAT-TTA--ATAAAATTCTTAA-TAA-TTA-ATATTCTTATATGA-ATT-TACTCAAATCA
21705055 T-
58 TA
21705056 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
21705115 ATATA
1 ATATA
21705120 TGATACTATA
Statistics
Matches: 92, Mismatches: 19, Indels: 28
0.66 0.14 0.20
Matches are distributed among these distances:
56 6 0.07
57 12 0.13
58 7 0.08
59 20 0.22
60 8 0.09
61 15 0.16
62 7 0.08
63 11 0.12
64 6 0.07
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
Found at i:21707931 original size:19 final size:19
Alignment explanation
Indices: 21707907--21708019 Score: 154
Period size: 19 Copynumber: 5.8 Consensus size: 19
21707897 AATTTTTGAG
*
21707907 GATATGCAATCATAGATAT
1 GATATGCAATCTTAGATAT
**
21707926 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
21707945 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
21707966 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
21707985 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21708004 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
21708020 ATATATGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 65 0.79
21 17 0.21
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:21707952 original size:40 final size:40
Alignment explanation
Indices: 21707908--21708014 Score: 164
Period size: 40 Copynumber: 2.7 Consensus size: 40
21707898 ATTTTTGAGG
* *
21707908 ATATGCAATCATAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
**
21707948 ATATGCAATCTTAGATATGATATGCAATCTTAGAGATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
21707988 ATAT--AATCTTAGATATGATATGCAATC
1 ATATGCAATCTTAGATATGATATGCAATC
21708015 TTAGAATATA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 23 0.37
40 40 0.63
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
Found at i:21708398 original size:21 final size:21
Alignment explanation
Indices: 21708354--21708399 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
21708344 ATTAAGTTTT
* *
21708354 TTTATTTTTTTAATTTACCCA
1 TTTATTTTTTTAAATTACCAA
21708375 TTTATTTATTTTAAATT-CCAA
1 TTTATTT-TTTTAAATTACCAA
21708396 TTTA
1 TTTA
21708400 ATCCTTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTATTTTTTTAAATTACCAA
Found at i:21709449 original size:98 final size:98
Alignment explanation
Indices: 21709325--21709521 Score: 313
Period size: 98 Copynumber: 2.0 Consensus size: 98
21709315 GTAAAAATAA
* * * *
21709325 TAAATGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTAGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
21709390 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCCTGGATAAGTGGATGTTCTTTTAAAG
* * *
21709423 TAAAGGAAATATTCCGAGTTTAGGATTCTAGAGGAATCGTGTCCTAATGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTAGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
21709488 TTAAATCCTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCCTGGATAAGTGGATGTTCTTTTAAAG
21709521 T
1 T
21709522 TTTATTGTAC
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTAGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCCTGGATAAGTGGATGTTCTTTTAAAG
Found at i:21713618 original size:12 final size:12
Alignment explanation
Indices: 21713602--21713650 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
21713592 AAATATTTCA
*
21713602 AAAAAAAAAGAGG
1 AAAAAGAAA-AGG
21713615 AAAAAGAAAAGG
1 AAAAAGAAAAGG
*
21713627 AAAAAGGAAAAAAG
1 AAAAA-G-AAAAGG
21713641 AAAAAGAAAA
1 AAAAAGAAAA
21713651 AGTAAAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 12 0.38
13 10 0.31
14 10 0.31
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGG
Found at i:21713623 original size:6 final size:6
Alignment explanation
Indices: 21713614--21713658 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
21713604 AAAAAAAGAG
* *
21713614 GAAAAA GAAAAG GAAAAA GGAAAAAA GAAAAA GAAAAA GTAAAA G
1 GAAAAA GAAAAA GAAAAA -G-AAAAA GAAAAA GAAAAA GAAAAA G
21713659 GAGAAGCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 27 0.79
7 2 0.06
8 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:21713630 original size:20 final size:20
Alignment explanation
Indices: 21713601--21713657 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
21713591 AAAATATTTC
*
21713601 AAAAA-AAAAAGAGGAAAAAG
1 AAAAAGAAAAAG-GAAAAAAG
*
21713621 AAAAGGAAAAAGGAAAAAAG
1 AAAAAGAAAAAGGAAAAAAG
*
21713641 AAAAAGAAAAAGTAAAA
1 AAAAAGAAAAAGGAAAA
21713658 GGAGAAGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAAGGAAAAAAG
Found at i:21713633 original size:7 final size:7
Alignment explanation
Indices: 21713607--21713657 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
21713597 TTTCAAAAAA
21713607 AAAAGAGG
1 AAAA-AGG
21713615 AAAAA-G
1 AAAAAGG
21713621 -AAAAGG
1 AAAAAGG
21713627 AAAAAGG
1 AAAAAGG
*
21713634 AAAAAAG
1 AAAAAGG
21713641 AAAAA-G
1 AAAAAGG
*
21713647 AAAAAGT
1 AAAAAGG
21713654 AAAA
1 AAAA
21713658 GGAGAAGCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 4 0.11
6 8 0.21
7 22 0.58
8 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (7 bp):
AAAAAGG
Found at i:21715057 original size:44 final size:44
Alignment explanation
Indices: 21714877--21715235 Score: 168
Period size: 44 Copynumber: 8.2 Consensus size: 44
21714867 AAAATTGTAG
* * * *
21714877 ATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACGGTGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGA
** * * * *
21714921 ATCTTATCTTTCGAAG-A-TAGTGGGAAGCAGATTTAAGCCA-CCA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACAGCGA
* * * * * * * ** *
21714964 AGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG-TA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGA
*
21715008 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGA
* * * *
21715053 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCGA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACAGCGA
* * * *
21715097 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCA-CCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACAGCGA
* * * * * * **
21715140 AGCCTTGTCTCCCTGAGCAGTAGCGGAGAAGGTTGAA-A-ATTGTA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCG-A
*
21715184 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGA
21715229 ATCTTAT
1 ATCTTAT
21715236 ATTTCCAAGA
Statistics
Matches: 233, Mismatches: 62, Indels: 40
0.70 0.19 0.12
Matches are distributed among these distances:
42 9 0.04
43 14 0.06
44 190 0.82
45 14 0.06
46 6 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGA
Found at i:21715151 original size:132 final size:131
Alignment explanation
Indices: 21715015--21715525 Score: 525
Period size: 132 Copynumber: 3.9 Consensus size: 131
21715005 GTAGATCTTA
* * * *
21715015 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCG-A-ATCTTATCTTTCC-AAGATAGTGGG
1 TCTCCCTAAGCAGTAGCGGAGAAGATCGAA-A-AGTGTAGATCTTATC-TCCCTAAGATAGTGGG
*
21715077 AAGCAGATTTAAGCCACCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAG
63 -AGCAGATTGAAGCCACCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAG
21715142 CCTTG
127 CCTTG
* * * *
21715147 TCTCCCTGAGCAGTAGCGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT-GGA
1 TCTCCCTAAGCAGTAGCGGAGAAGATCGAAAAGTGTAGATCTTATCTCCCTAAG-A-TAGTGGGA
* ** *
21715211 GCAGATTGAAGACGGCGAATCTTATATTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCC
64 GCAGATTGAAGCCACCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCC
21715276 TTG
129 TTG
* * * * *
21715279 TCTCCCTGAGCAGCAGCGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAG-TAGTAGTGGA
1 TCTCCCTAAGCAGTAGCGGAGAAGATCGAAAAGTGTAGATCTTATCTCCCTAAGATAGT-G-GGA
* * ** *
21715343 GCATATCGAAGATGA-CAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
64 GCAGATTGAAG-CCACCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
21715407 CTTG
128 CTTG
* * * * * * * * *
21715411 TTTTCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT-GGA
1 TCTCCCTAAGCAGTAGCGGAGAAGATCGAAAAGTGTAGATCTTATCTCCCTAAG-A-TAGTGGGA
* ** * *
21715475 GCAGATCGAAGATGA-CAAATCATATCTTTCCAAGATAGTGGGAAGCAGATT
64 GCAGATTGAAG-CCACCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATT
21715526 AAAGTGGACA
Statistics
Matches: 340, Mismatches: 27, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
129 4 0.01
130 2 0.01
131 5 0.01
132 318 0.94
133 3 0.01
134 4 0.01
135 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (131 bp):
TCTCCCTAAGCAGTAGCGGAGAAGATCGAAAAGTGTAGATCTTATCTCCCTAAGATAGTGGGAGC
AGATTGAAGCCACCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTT
G
Found at i:21715171 original size:176 final size:176
Alignment explanation
Indices: 21714919--21715270 Score: 650
Period size: 176 Copynumber: 2.0 Consensus size: 176
21714909 CGAAGACGGT
*
21714919 GAATCTTATCTTTCGAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAG
1 GAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAG
*
21714984 CAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACA
66 CAGCGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACA
*
21715049 GCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
131 GCGAATCTTATATTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
21715095 GAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAG
1 GAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAG
* * *
21715160 TAGCGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACG
66 CAGCGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACA
21715225 GCGAATCTTATATTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
131 GCGAATCTTATATTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
21715271 AAGCCTTGTC
Statistics
Matches: 170, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
176 170 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (176 bp):
GAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAG
CAGCGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACA
GCGAATCTTATATTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
Found at i:21715595 original size:44 final size:44
Alignment explanation
Indices: 21715540--21716175 Score: 316
Period size: 44 Copynumber: 14.7 Consensus size: 44
21715530 TGGACAATCA
*
21715540 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCATAGATCT
* * ***
21715584 TATC-CCTCTGAAGTTGCAG-AGAGTAGA-TCGCATC-TAG-TCT
1 TATCTCC-CTGAAGTTGCAGTGGAGCAGATTAAAATCATAGATCT
* *
21715624 TATCTCCCTGAAGTTGC-GATGGA-CAAGACTAAGTAAGCA-AG-TCT
1 TATCTCCCTGAAGTTGCAG-TGGAGC-AGATTAA--AATCATAGATCT
* * * * * *
21715668 TATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGACAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCATAGATCT
* * * *
21715713 TATCTTCCTGAAGTTGCAGTGAAGCAGATT-AAATCCGACA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAT-C-ATAGATCT
* * * *
21715757 TATCTCCCTGAAGTTGCAGTGGAGCGGAATAAAATTACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCATAGATCT
* * * ***
21715801 TATCTCTCTGAAGTTACAG-AGAGCAGA-TCGCATC-TAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCATAGATCT
* * *
21715841 TATCTCCCTGAAGTTGCGGTGGA-CAAGACTAAGTATGCA-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGC-AGATTAA-AAT-CATAGATCT
* * *
21715885 TATCT-CCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCA-A-ATCT
1 TATCTCCCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CATAGATCT
* * *
21715929 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATCATAGATCT
* * *
21715973 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCATAGATCT
* * * * * *
21716017 TCTCTCTCTAAAGTTGCAG-AGAGCAGA-TCACATC-TAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCATAGATCT
* * * *
21716057 TATCTCCCTAAAGTTGCAGTGGAGTAGACTAAGGAAGCA-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCATAGATCT
* * *
21716101 TATC-CTCCTGAAGTTGCAGT-GAGGAAGACTGAAGATGGCA-AG-TCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CATAGATCT
*
21716146 TATCTCCCTGAAGTTGCAGTGGAGTAGATT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT
21716176 GAAGCACTAA
Statistics
Matches: 455, Mismatches: 87, Indels: 100
0.71 0.14 0.16
Matches are distributed among these distances:
39 1 0.00
40 57 0.13
41 25 0.05
42 18 0.04
43 58 0.13
44 204 0.45
45 86 0.19
46 6 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCATAGATCT
Found at i:21715986 original size:172 final size:174
Alignment explanation
Indices: 21715663--21715997 Score: 391
Period size: 172 Copynumber: 1.9 Consensus size: 174
21715653 TAAGTAAGCA
*
21715663 AGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGACAAATCTTATCTTCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTACAGTGAGACAGACTGAAGATGACAAATCTTATCTTCCTGAAGTT
* * * *
21715728 GCAGTGAAGCAGATTAAATCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAATAAAATT
66 ACAGTGAAGCAGATGAAATCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAATAAAATG
* *
21715793 ACAGATCTTATCTCTCTGAAGTTACAG-AGAGCAGATCGCATCT
131 ACAGATCCTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCT
* * *
21715836 AGTCTTAT-CTCCCTGAAGTTGCGGTG-GACAAGACT-AAGTATG-CAAGTCTTATC-TCCTGAA
1 AGTCTTATCCT-CCTGAAGTTACAGTGAGAC-AGACTGAAG-ATGACAAATCTTATCTTCCTGAA
* * * *
21715896 GTTACAGTGAGGCAGACTGAAGAT--GGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
63 GTTACAGTGAAGCAGA-TGAA-ATCCGAC-AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAAT
* * *
21715959 AAAGCTGATA-ATCCTATCTCCCTGAAGTTGCAGTAGAGC
125 AAA-ATGACAGATCCTATCTCCCTGAAGTTACAGTAGAGC
21715998 GGATTAAAAT
Statistics
Matches: 137, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
171 23 0.17
172 75 0.55
173 39 0.28
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (174 bp):
AGTCTTATCCTCCTGAAGTTACAGTGAGACAGACTGAAGATGACAAATCTTATCTTCCTGAAGTT
ACAGTGAAGCAGATGAAATCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAATAAAATG
ACAGATCCTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCT
Found at i:21716015 original size:216 final size:217
Alignment explanation
Indices: 21715518--21716180 Score: 1042
Period size: 217 Copynumber: 3.1 Consensus size: 217
21715508 GATAGTGGGA
* *
21715518 AGCAGATTAAAG-TGGACAATCATATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCATAGAT
1 AGCAGATTAAAGCT-GACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGAT
* * *
21715582 CTTATCCCTCTGAAGTTGCAGAGAGTAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGATGGA
65 CTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGA
*
21715647 CAAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGACAAATC
130 CAAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATC
* *
21715712 TTATCTTCCTGAAGTTGCAGTGA
195 TTATCTCCCTGAAGTTGCAGTGG
* * * *
21715735 AGCAGATTAAATCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAATAAAATTACAGATC
1 AGCAGATTAAAGCTGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
*
21715800 TTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGAC
66 TTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGAC
*
21715865 AAGACTAAGTATGCAAGTCTTAT-CTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
131 AAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
21715929 TATCTCCCTGAAGTTGCAGTGG
196 TATCTCCCTGAAGTTGCAGTGG
* *
21715951 AGCAGATTAAAGCTGATAATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATC
1 AGCAGATTAAAGCTGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
* * * * * *
21716016 TTCTCTCTCTAAAGTTGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAG
66 TTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGAC
* * * * *
21716081 TAGACTAAGGAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGAAGACTGAAGATGGCAAGTCT
131 AAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
21716146 TATCTCCCTGAAGTTGCAGTGG
196 TATCTCCCTGAAGTTGCAGTGG
* *
21716168 AGTAGATTGAAGC
1 AGCAGATTAAAGC
21716181 ACTAATTCCT
Statistics
Matches: 409, Mismatches: 35, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
216 197 0.48
217 212 0.52
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (217 bp):
AGCAGATTAAAGCTGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
TTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGAC
AAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
TATCTCCCTGAAGTTGCAGTGG
Found at i:21716407 original size:19 final size:19
Alignment explanation
Indices: 21716383--21716455 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
21716373 AATTTTTGAG
21716383 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
21716402 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
21716421 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21716440 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
21716456 ATATATGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:21716998 original size:12 final size:12
Alignment explanation
Indices: 21716965--21717043 Score: 52
Period size: 12 Copynumber: 6.5 Consensus size: 12
21716955 TTGCAATTCA
*
21716965 ATTTAGTTTTTT
1 ATTTATTTTTTT
* *
21716977 ATGT-TCTTTTT
1 ATTTATTTTTTT
21716988 ATTTATTTTTTT
1 ATTTATTTTTTT
* * ** *
21717000 AATTAATAGTGT
1 ATTTATTTTTTT
*
21717012 AATTATTATTTTT
1 ATTTATT-TTTTT
21717025 ATTCTATTTTTTT
1 ATT-TATTTTTTT
21717038 ATTTAT
1 ATTTAT
21717044 ATATATTCCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
11 8 0.16
12 25 0.51
13 12 0.24
14 4 0.08
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:21717888 original size:98 final size:98
Alignment explanation
Indices: 21717755--21717951 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
21717745 TTAAAAATAA
* *
21717755 TAAAGGAAATATTCCAAGTTTGAGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
21717820 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* * * *
21717853 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAATGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
21717918 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
21717951 T
1 T
21717952 TTTATTGTAC
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:21721109 original size:21 final size:20
Alignment explanation
Indices: 21721071--21721108 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21721061 TTACTAAGAC
**
21721071 TTTTTAAAAATTATAAAATA
1 TTTTTAAAAAAAATAAAATA
21721091 TTTTTAAAAAAAATAAAA
1 TTTTTAAAAAAAATAAAA
21721109 AAATTATAAA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTTTAAAAAAAATAAAATA
Found at i:21726573 original size:63 final size:62
Alignment explanation
Indices: 21726404--21726562 Score: 185
Period size: 63 Copynumber: 2.5 Consensus size: 62
21726394 TAACTTACTA
* * * ** *
21726404 TTTTTGGATTAAAGG-CACACAGGCGAAGGACACGAGCATGTGTCCAGGCTGGGTAACTTAT
1 TTTTTGGATTTAAGGTCACACAGGCCAGGGACACGAGCATGTGTCCAGGCCAGGTAACTCAT
* * * * * *
21726465 TGTTTGTATTTTATGGTCATACAGGCTAGGGACACGAGCATGTGTCCAGGCCATGTAACTCATT
1 TTTTTGGA-TTTAAGGTCACACAGGCCAGGGACACGAGCATGTGTCCAGGCCAGGTAACTCA-T
21726529 TTTTTGGATTTAAGGTCACACAGGCCAGGGACAC
1 TTTTTGGATTTAAGGTCACACAGGCCAGGGACAC
21726563 TGACGTGTGT
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
61 6 0.08
62 5 0.06
63 61 0.77
64 7 0.09
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (62 bp):
TTTTTGGATTTAAGGTCACACAGGCCAGGGACACGAGCATGTGTCCAGGCCAGGTAACTCAT
Found at i:21730838 original size:6 final size:6
Alignment explanation
Indices: 21730805--21730854 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
21730795 CAAAAATTGC
* **
21730805 ATCTGT ATCTG- ATATGT -TCTAC ATCTGT ATCTGT ATCTGT ATCTGT
1 ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT
21730851 -TCTG
1 ATCTG
21730855 CTCTTTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (6 bp):
ATCTGT
Found at i:21732417 original size:50 final size:50
Alignment explanation
Indices: 21732311--21732486 Score: 165
Period size: 50 Copynumber: 3.4 Consensus size: 50
21732301 GGGAATGAGA
* *
21732311 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGTATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG---CATCGA-G--ATGAGAGG
* *
21732367 TCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
** * * * * **
21732417 TCCCCCGTAAGACCATGTTTGGGACTTGGCATGGGCA-CGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
* *
21732466 TCCCATGTAAAACCATATCTG
1 TCCCATGTAAGACCATGTCTG
21732487 AGGTATGACA
Statistics
Matches: 101, Mismatches: 19, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
49 25 0.25
50 38 0.38
52 1 0.01
53 4 0.04
56 33 0.33
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
Found at i:21740739 original size:13 final size:13
Alignment explanation
Indices: 21740717--21740746 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21740707 TTTTTTCCTT
21740717 TTAATCTTCTTAG
1 TTAATCTTCTTAG
*
21740730 TTAATTTTCTTAG
1 TTAATCTTCTTAG
21740743 TTAA
1 TTAA
21740747 AATCTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATCTTCTTAG
Found at i:21742828 original size:28 final size:28
Alignment explanation
Indices: 21742788--21742842 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
21742778 CCATTGGTAG
21742788 AAGCACTTGAGCAGATGCAAAACTATGA
1 AAGCACTTGAGCAGATGCAAAACTATGA
21742816 AAGCACTTGAGCAGATGCAAAACTATG
1 AAGCACTTGAGCAGATGCAAAACTATG
21742843 TTAAATTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (28 bp):
AAGCACTTGAGCAGATGCAAAACTATGA
Found at i:21756250 original size:15 final size:15
Alignment explanation
Indices: 21756215--21756266 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
21756205 TTAAGAATTT
*
21756215 TATTAAATTAT-ATA
1 TATTTAATTATAATA
21756229 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
21756243 TATTTAATAATAAT-
1 TATTTAATTATAATA
21756257 TATGTTAATT
1 TAT-TTAATT
21756267 TATATTTTAC
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:21756292 original size:120 final size:120
Alignment explanation
Indices: 21756090--21756387 Score: 492
Period size: 120 Copynumber: 2.5 Consensus size: 120
21756080 AATTATTTTA
* * * *
21756090 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTTTCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTTTATTT
*
21756154 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
21756210 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTT-TATTT
* *
21756274 TACAGTATTATATATTATGATTTGAGTAAATTCATATGAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
21756330 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
21756388 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
119 5 0.03
120 155 0.93
121 4 0.02
122 3 0.02
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTTTATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:21756323 original size:66 final size:62
Alignment explanation
Indices: 21756128--21756326 Score: 166
Period size: 66 Copynumber: 3.2 Consensus size: 62
21756118 AAATATATTT
* *
21756128 AATATTAATTATTTCAAATTTTCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT--AATTTTATTTTA-AGTATTATATATTATGATTTGAGTAAATTCATAT-A
21756193 G
62 G
* * * **
21756194 AATATTAATTATTAAGAATTTTA--TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATATTT
1 AATATTAATTATT--TAATTTTATTTTAAGTATTATATATTATGATTTGAGTAAATTCATATAG
*
21756248 AATAATAATTATGTTAATTTATATTTTACAGTATTATATATTATGATTTGAGTAAATTCATATGA
1 AATATTAATTAT-TTAATTT-TATTTTA-AGTATTATATATTATGATTTGAGTAAATTCATAT-A
21756313 G
62 G
21756314 AATATTAATTATT
1 AATATTAATTATT
21756327 AAGAATTTTA
Statistics
Matches: 103, Mismatches: 14, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
53 5 0.05
54 13 0.13
55 5 0.05
56 4 0.04
57 3 0.03
58 1 0.01
59 11 0.11
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 4 0.04
65 5 0.05
66 30 0.29
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (62 bp):
AATATTAATTATTTAATTTTATTTTAAGTATTATATATTATGATTTGAGTAAATTCATATAG
Found at i:21756365 original size:16 final size:16
Alignment explanation
Indices: 21756344--21756385 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
21756334 TTATTAAATT
*
21756344 ATATATTTTAATTATA
1 ATATATTTTAATAATA
21756360 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
21756375 AT-TATGTTTAA
1 ATATAT-TTTAA
21756386 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:21756370 original size:15 final size:15
Alignment explanation
Indices: 21756335--21756376 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21756325 TTAAGAATTT
*
21756335 TATTAAATTAT-ATA
1 TATTTAATTATAATA
21756349 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
21756363 TATTTAATAATAAT
1 TATTTAATTATAAT
21756377 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:21756497 original size:157 final size:157
Alignment explanation
Indices: 21756319--21756635 Score: 598
Period size: 157 Copynumber: 2.0 Consensus size: 157
21756309 ATGAGAATAT
*
21756319 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
21756384 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
21756449 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
21756476 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
21756541 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
21756606 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
21756633 TAA
1 TAA
21756636 GGGTATTCTG
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:21756516 original size:18 final size:17
Alignment explanation
Indices: 21756488--21756522 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21756478 ATTATTAAGA
*
21756488 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
21756505 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
21756523 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:21756556 original size:75 final size:75
Alignment explanation
Indices: 21756320--21756558 Score: 191
Period size: 75 Copynumber: 3.1 Consensus size: 75
21756310 TGAGAATATT
*
21756320 AATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
21756385 AATATGATTA
66 AATATGATTA
* ** * * * * *
21756395 AATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATA-A--CAATAATAATT
1 AATTATTAAGAATT-TTATT-A-AA--TTA-TATATTTTAATTAA-AATATATTTAATAATAATT
**** * * *
21756457 -TACCAAAACAAAT-TTCTGCT
59 AT-GTTTAA-ATATGAT-T--A
21756477 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
21756542 AATATGATTA
66 AATATGATTA
21756552 AATTATT
1 AATTATT
21756559 TATTATTGAT
Statistics
Matches: 116, Mismatches: 31, Indels: 34
0.64 0.17 0.19
Matches are distributed among these distances:
75 22 0.19
76 16 0.14
77 8 0.07
78 16 0.14
79 16 0.14
80 8 0.07
81 15 0.13
82 15 0.13
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (75 bp):
AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTA
Found at i:21756713 original size:39 final size:40
Alignment explanation
Indices: 21756670--21756774 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
21756660 TTCCATTATG
21756670 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
21756709 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
21756754 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
21756775 ACACATCTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:21756768 original size:45 final size:44
Alignment explanation
Indices: 21756668--21756777 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
21756658 TTTTCCATTA
21756668 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
21756707 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
21756752 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
21756778 CATCTATTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:21756777 original size:16 final size:16
Alignment explanation
Indices: 21756756--21756825 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
21756746 TTGATTTGCT
*
21756756 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
* *
21756772 ATTACACATCTATTCC
1 ATTACACCTCTAATCC
21756788 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
* *
21756804 AATACACTTCTAATCC
1 ATTACACCTCTAATCC
*
21756820 AATACA
1 ATTACA
21756826 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.34, C:0.33, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:21756797 original size:32 final size:32
Alignment explanation
Indices: 21756756--21756825 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
21756746 TTGATTTGCT
* * *
21756756 ATTACACCTCTATTCCATTACACATCTATTCC
1 ATTACACCTCTAATCCAATACACATCTAATCC
*
21756788 ATTACACCTCTAATCCAATACACTTCTAATCC
1 ATTACACCTCTAATCCAATACACATCTAATCC
*
21756820 AATACA
1 ATTACA
21756826 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.33, G:0.00, T:0.33
Consensus pattern (32 bp):
ATTACACCTCTAATCCAATACACATCTAATCC
Found at i:21759242 original size:45 final size:46
Alignment explanation
Indices: 21759181--21759276 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 46
21759171 ACATATACAA
* * * *
21759181 GAGCTCGGAACCTATTCTTGTATTCTTAAGTTCATAACATA-GTAG
1 GAGCTCGGAACCTATTCATGTATTCTCAAGTCCACAACATATGTAG
* *
21759226 GAGCTCGGAACTTATTCATGTATTCTCGAGTCCACAACATATGTAG
1 GAGCTCGGAACCTATTCATGTATTCTCAAGTCCACAACATATGTAG
21759272 GAGCT
1 GAGCT
21759277 TAAAACCTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 35 0.80
46 9 0.20
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (46 bp):
GAGCTCGGAACCTATTCATGTATTCTCAAGTCCACAACATATGTAG
Found at i:21760168 original size:17 final size:18
Alignment explanation
Indices: 21760141--21760174 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
21760131 TTTGTTTTTA
21760141 TTTTTATTTATTTTAACC
1 TTTTTATTTATTTTAACC
21760159 TTTTTA-TTATTTTAAC
1 TTTTTATTTATTTTAAC
21760175 TTAGTTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTATTTATTTTAACC
Found at i:21760942 original size:17 final size:19
Alignment explanation
Indices: 21760905--21760946 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
21760895 TCAAAATGTA
21760905 AAAATAAATTTAAGAAAAT
1 AAAATAAATTTAAGAAAAT
*
21760924 AAAATAAA-TT-AGTAAAT
1 AAAATAAATTTAAGAAAAT
21760941 AAAATA
1 AAAATA
21760947 TTTTTAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
18 2 0.09
19 8 0.36
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAATAAATTTAAGAAAAT
Found at i:21761825 original size:13 final size:13
Alignment explanation
Indices: 21761783--21761838 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
21761773 TAGATTCTTC
21761783 CTAAATATTATCA
1 CTAAATATTATCA
*
21761796 C-AAA-ATAATC-
1 CTAAATATTATCA
21761806 CTAAATATTATCA
1 CTAAATATTATCA
*
21761819 TTAAATATTATCA
1 CTAAATATTATCA
21761832 CTAAATA
1 CTAAATA
21761839 ATTTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 1 0.03
11 8 0.22
12 8 0.22
13 19 0.53
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:21762779 original size:12 final size:12
Alignment explanation
Indices: 21762762--21762794 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21762752 TTAACCAAGC
21762762 TATTTATTT-AT
1 TATTTATTTAAT
21762773 ATATTTATTTAAT
1 -TATTTATTTAAT
21762786 TATTTATTT
1 TATTTATTT
21762795 CAATGAGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 18 0.90
13 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTTATTTAAT
Found at i:21769160 original size:27 final size:27
Alignment explanation
Indices: 21769122--21769575 Score: 318
Period size: 27 Copynumber: 16.8 Consensus size: 27
21769112 AGCCCAACAT
* *
21769122 ACCCCGAAGGGTAACATGACTAAAATA
1 ACCCCGAAGGGTAAAATGACTGAAATA
* *
21769149 ACCCCGAAGGGTAAAATAACCGAAATA
1 ACCCCGAAGGGTAAAATGACTGAAATA
* * *
21769176 CCCCCGAAGGTTAAAATGATTGAAATA
1 ACCCCGAAGGGTAAAATGACTGAAATA
* * * * *
21769203 CCCCCAAAAGGTAAAATAACTAAAAT-
1 ACCCCGAAGGGTAAAATGACTGAAATA
** **
21769229 ACCCTTAAAGGGTAAAATGACCAAAATA
1 ACCC-CGAAGGGTAAAATGACTGAAATA
* *
21769257 CCCCCGAATGGTAAAATGACTGAAATA
1 ACCCCGAAGGGTAAAATGACTGAAATA
* *
21769284 CCCCCGAAAGGTAAAATGA-TCGAAAT-
1 ACCCCGAAGGGTAAAATGACT-GAAATA
* *
21769310 ACCTTCTAAGGGTAAAATGACTGAAAT-
1 ACC-CCGAAGGGTAAAATGACTGAAATA
* * **
21769337 ACCTTCGAAGGGTAAAATAACCAAAATA
1 ACC-CCGAAGGGTAAAATGACTGAAATA
* *
21769365 CCCCCGAAGGGTAAAATGATTGAAATA
1 ACCCCGAAGGGTAAAATGACTGAAATA
* * * *
21769392 CCCCCGAAAGGTAAAATAACTAAAAT-
1 ACCCCGAAGGGTAAAATGACTGAAATA
* *
21769418 ACCCTCGAAAGATAAAATGA-TCGAAAT-
1 ACCC-CGAAGGGTAAAATGACT-GAAATA
21769445 ACCCCGAAAGGGTAAAATGA-TCGAAATA
1 ACCCCG-AAGGGTAAAATGACT-GAAATA
* * * * *
21769473 CCCCCAAAGGTTAAAACGATTGAAATA
1 ACCCCGAAGGGTAAAATGACTGAAATA
** *
21769500 ACCCTAAAGGGTAAAAT-AATCGAAAT-
1 ACCCCGAAGGGTAAAATGACT-GAAATA
* **
21769526 ACCCCTAAAGGGTAAAATGACCAAAAT-
1 ACCCC-GAAGGGTAAAATGACTGAAATA
*
21769553 ACCCCTATAGGGTAAAATGACTG
1 ACCCCGA-AGGGTAAAATGACTG
21769576 TTATACCCCT
Statistics
Matches: 345, Mismatches: 67, Indels: 30
0.78 0.15 0.07
Matches are distributed among these distances:
26 19 0.06
27 314 0.91
28 12 0.03
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.18
Consensus pattern (27 bp):
ACCCCGAAGGGTAAAATGACTGAAATA
Found at i:21769202 original size:54 final size:54
Alignment explanation
Indices: 21769123--21769573 Score: 356
Period size: 54 Copynumber: 8.4 Consensus size: 54
21769113 GCCCAACATA
* * * *
21769123 CCCCGAAGGGTAACATGACTAAAATAACCCCGAAGGGTAAAATAACCGAAATAC
1 CCCCGAAGGGTAAAATGACCAAAATAACCCCGAAGGGTAAAATGACTGAAATAC
* *** * * * * *
21769177 CCCCGAAGGTTAAAATGATTGAAATACCCCCAAAAGGTAAAATAACTAAAATAC
1 CCCCGAAGGGTAAAATGACCAAAATAACCCCGAAGGGTAAAATGACTGAAATAC
*** * *
21769231 CCTTAAAGGGTAAAATGACCAAAATACCCCCGAATGGTAAAATGACTGAAATAC
1 CCCCGAAGGGTAAAATGACCAAAATAACCCCGAAGGGTAAAATGACTGAAATAC
* * * * *
21769285 CCCCGAAAGGTAAAATGATCGAAAT-ACCTTCTAAGGGTAAAATGACTGAAATAC
1 CCCCGAAGGGTAAAATGACCAAAATAACC-CCGAAGGGTAAAATGACTGAAATAC
** * * *
21769339 CTTCGAAGGGTAAAATAACCAAAATACCCCCGAAGGGTAAAATGATTGAAATAC
1 CCCCGAAGGGTAAAATGACCAAAATAACCCCGAAGGGTAAAATGACTGAAATAC
* * * * *
21769393 CCCCGAAAGGTAAAATAACTAAAAT-ACCCTCGAAAGATAAAATGA-TCGAAATA-
1 CCCCGAAGGGTAAAATGACCAAAATAACCC-CGAAGGGTAAAATGACT-GAAATAC
* * * * * * * *
21769446 CCCCGAAAGGGTAAAATGATCGAAATACCCCCAAAGGTTAAAACGATTGAAATAA
1 CCCCG-AAGGGTAAAATGACCAAAATAACCCCGAAGGGTAAAATGACTGAAATAC
** * * * * **
21769501 CCCTAAAGGGTAAAATAATCGAAAT-ACCCCTAAAGGGTAAAATGACCAAAATA-
1 CCCCGAAGGGTAAAATGACCAAAATAACCCC-GAAGGGTAAAATGACTGAAATAC
*
21769554 CCCCTATAGGGTAAAATGAC
1 CCCCGA-AGGGTAAAATGAC
21769574 TGTTATACCC
Statistics
Matches: 317, Mismatches: 70, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
53 19 0.06
54 289 0.91
55 9 0.03
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.18
Consensus pattern (54 bp):
CCCCGAAGGGTAAAATGACCAAAATAACCCCGAAGGGTAAAATGACTGAAATAC
Found at i:21769272 original size:81 final size:80
Alignment explanation
Indices: 21769123--21769584 Score: 403
Period size: 81 Copynumber: 5.7 Consensus size: 80
21769113 GCCCAACATA
* * * * * * *
21769123 CCCCGAAGGGTAACATGACTAAAATAACCCC-GAAGGGTAAAATAACCGAAATACCCCCGAAGGT
1 CCCCAAAGGGTAAAATGA-TGAAAT-ACCCCTAAAGGGTAAAATGACTGAAATACCCCCGAAGGG
*
21769187 TAAAATGATTGAAATAC
64 TAAAATGATCGAAATAC
* * * * ** *
21769204 CCCCAAAAGGTAAAATAACTAAAATACCCTTAAAGGGTAAAATGACCAAAATACCCCCGAATGGT
1 CCCCAAAGGGTAAAATGA-TGAAATACCCCTAAAGGGTAAAATGACTGAAATACCCCCGAAGGGT
21769269 AAAATGA-CTGAAATAC
65 AAAATGATC-GAAATAC
* **
21769285 CCCCGAAA-GGTAAAATGATCGAAATACCTTCT-AAGGGTAAAATGACTGAAATACCTTCGAAGG
1 CCCC-AAAGGGTAAAATGAT-GAAATACC-CCTAAAGGGTAAAATGACTGAAATACCCCCGAAGG
* * *
21769348 GTAAAATAACCAAAATAC
63 GTAAAATGATCGAAATAC
* * * * * * *
21769366 CCCCGAAGGGTAAAATGATTGAAATACCCCCGAAA-GGTAAAATAACTAAAATACCCTCGAAAGA
1 CCCCAAAGGGTAAAATGA-TGAAATA-CCCCTAAAGGGTAAAATGACTGAAATACCCCCGAAGGG
21769430 TAAAATGATCGAAATAC
64 TAAAATGATCGAAATAC
* * * * * * **
21769447 CCCGAAAGGGTAAAATGATCGAAATACCCCCAAAGGTTAAAACGATTGAAATAACCCTAAAGGGT
1 CCCCAAAGGGTAAAATGAT-GAAATACCCCTAAAGGGTAAAATGACTGAAATACCCCCGAAGGGT
*
21769512 AAAATAATCGAAATAC
65 AAAATGATCGAAATAC
* ** * **
21769528 CCCTAAAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATGACTGTTATACCCC
1 CCCCAAAGGGTAAAATGA-TGAAATACCCCTAAAGGGTAAAATGACTGAAATACCCC
21769585 TAAGAGTCAA
Statistics
Matches: 309, Mismatches: 59, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
80 15 0.05
81 284 0.92
82 10 0.03
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (80 bp):
CCCCAAAGGGTAAAATGATGAAATACCCCTAAAGGGTAAAATGACTGAAATACCCCCGAAGGGTA
AAATGATCGAAATAC
Found at i:21769770 original size:26 final size:26
Alignment explanation
Indices: 21769741--21769795 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
21769731 TTTGCCACAT
*
21769741 ATACTTTTACTGGCAGCTTCGTTGCG
1 ATACTTTTACTGGCAGCTTCGGTGCG
*
21769767 ATACTTTTACTGGCAGCTTTGGTGCG
1 ATACTTTTACTGGCAGCTTCGGTGCG
21769793 ATA
1 ATA
21769796 TTGGTGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (26 bp):
ATACTTTTACTGGCAGCTTCGGTGCG
Found at i:21769933 original size:28 final size:28
Alignment explanation
Indices: 21769892--21769958 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
21769882 TTATATTATT
* **
21769892 ACACTGTTATTGTATTGGGCTAAGGACC
1 ACACTGTTACTGTATCAGGCTAAGGACC
* *
21769920 ACATTGTTACTGTATCAGGCTAAGGCCC
1 ACACTGTTACTGTATCAGGCTAAGGACC
21769948 ACACTG-TACTG
1 ACACTGTTACTG
21769959 ATACTAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 5 0.15
28 28 0.85
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (28 bp):
ACACTGTTACTGTATCAGGCTAAGGACC
Found at i:21774136 original size:50 final size:50
Alignment explanation
Indices: 21774075--21774233 Score: 158
Period size: 50 Copynumber: 3.1 Consensus size: 50
21774065 ACATGGCAGT
* * *
21774075 TCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACC
1 TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACC
* * * *
21774125 TCTCATCTCGGTGCTAACGCC-TCGTCCTAGACATGGTCTTACATGGGACC
1 TCTCATCTCGGTGCCAATGCCAT-GTCCCAGACATGGTCTTACAGGGGACC
* * *
21774175 TCTCATAACCTCAATGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
1 TCTCAT---CTC---GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACC
21774231 TCT
1 TCT
21774234 TTACCCAAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
49 1 0.01
50 47 0.53
53 3 0.03
56 37 0.42
57 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (50 bp):
TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACC
Found at i:21776055 original size:26 final size:26
Alignment explanation
Indices: 21776019--21776080 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
21776009 CTTGTAAGTG
* *
21776019 TTCTAAAACTGATACATGCTATGATA
1 TTCTGAAACTGATACATGCTATGAGA
* *
21776045 TTCTGAAACTGATATATGTTATGAGA
1 TTCTGAAACTGATACATGCTATGAGA
21776071 TTCTGAAACT
1 TTCTGAAACT
21776081 ACTGTAGGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGAGA
Found at i:21784774 original size:189 final size:187
Alignment explanation
Indices: 21784432--21784805 Score: 640
Period size: 189 Copynumber: 2.0 Consensus size: 187
21784422 CCGAAATGGA
*
21784432 AAAAAATGGGATCGACGAAAAACCAAAATTGCTTGCTGTCGAAAAATAAGAGAAATAAGAGAAAA
1 AAAAAATGGGATCGACGAAAAACCAAAATTGCTTGCCGTCGAAAAATAAGAGAAATAAGAGAAAA
*
21784497 TGATGCAAAAAATTATAGAGAAAAGAAATAAGGGTGTTATAATCTTGGAAATCAACAATCTGCAC
66 TGATGCAAAAAATTATAGAGAAAAGAAATAAGGGTGTTATAATCTTGGAAATCAACAATCTACAC
* *
21784562 TAAAATAGTTTTAGACAGCAGCAGTAGCCTAACTTTGAAAAATCATCTAAATTAGTGC
131 TAAAATAGTTTTAGACAGCAGCAGTAGCCTAAATTT-AAAAATCATCTAAAATAGTGC
* * *
21784620 AAAAAATGGGATTCGGCGAAAAGCCAAAATTTCTTGCCGTCGAAAAATAAGAGAAATAAGAGAAA
1 AAAAAATGGGA-TCGACGAAAAACCAAAATTGCTTGCCGTCGAAAAATAAGAGAAATAAGAGAAA
* *
21784685 ATGATGCAAAAAATTGTAGAGAAAGGAAATAAGGGTGTTATAATCTTGGAAATCAACAATCTACA
65 ATGATGCAAAAAATTATAGAGAAAAGAAATAAGGGTGTTATAATCTTGGAAATCAACAATCTACA
*
21784750 CTAAAATAGTTTTAGACAGCAGCAGTAGTCTAAATTTAAAAATCATCTAAAATAGT
130 CTAAAATAGTTTTAGACAGCAGCAGTAGCCTAAATTTAAAAATCATCTAAAATAGT
21784806 AGAAATTGAG
Statistics
Matches: 175, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
188 29 0.17
189 146 0.83
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (187 bp):
AAAAAATGGGATCGACGAAAAACCAAAATTGCTTGCCGTCGAAAAATAAGAGAAATAAGAGAAAA
TGATGCAAAAAATTATAGAGAAAAGAAATAAGGGTGTTATAATCTTGGAAATCAACAATCTACAC
TAAAATAGTTTTAGACAGCAGCAGTAGCCTAAATTTAAAAATCATCTAAAATAGTGC
Found at i:21790923 original size:29 final size:30
Alignment explanation
Indices: 21790869--21790927 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
21790859 AAGTTGAATC
*
21790869 AAATCAAAATTTAATGTATACAATTGCACA
1 AAATCAAAATTTAATATATACAATTGCACA
21790899 AAATCAAAATTT-ATATATA-ATATTGCACA
1 AAATCAAAATTTAATATATACA-ATTGCACA
21790928 TTAGACTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 14 0.52
30 12 0.44
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTAATATATACAATTGCACA
Found at i:21798640 original size:13 final size:13
Alignment explanation
Indices: 21798622--21798649 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21798612 AAAGTGTTAG
21798622 TTTAATGTAAAAT
1 TTTAATGTAAAAT
21798635 TTTAATGTAAAAT
1 TTTAATGTAAAAT
21798648 TT
1 TT
21798650 GACTTGATCT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTAATGTAAAAT
Found at i:21803357 original size:25 final size:25
Alignment explanation
Indices: 21803340--21803399 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
21803330 CAGCTCGAGA
*
21803340 GAGCTTACTGATATTCAGTTCGCAT
1 GAGCTTACTGATATTCAGCTCGCAT
* *
21803365 GAGCTTA-TCGATATTCAACTCGTAT
1 GAGCTTACT-GATATTCAGCTCGCAT
21803390 GAGCTTACTG
1 GAGCTTACTG
21803400 TTTACAGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 28 0.93
26 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (25 bp):
GAGCTTACTGATATTCAGCTCGCAT
Found at i:21805752 original size:43 final size:42
Alignment explanation
Indices: 21805704--21805842 Score: 183
Period size: 43 Copynumber: 3.3 Consensus size: 42
21805694 TGTGATTTCG
21805704 TGTAAGACCATGTCTAGGACATTGGCATCAATATGAGATTACA
1 TGTAAGACCATGTCTAGGACATTGGCATC-ATATGAGATTACA
*
21805747 TGTAAGACCATGTCTAGGACATTGGCATCATAT-ATGATTTCA
1 TGTAAGACCATGTCTAGGACATTGGCATCATATGA-GATTACA
* * * *
21805789 TATAAGA-CACTGTCTAGGACAGTGGCATCGATATGTGATAACA
1 TGTAAGACCA-TGTCTAGGACATTGGCATC-ATATGAGATTACA
21805832 TGTAAGACCAT
1 TGTAAGACCAT
21805843 ATCTTGGATA
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
41 3 0.04
42 34 0.40
43 45 0.54
44 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATGTCTAGGACATTGGCATCATATGAGATTACA
Found at i:21813324 original size:43 final size:43
Alignment explanation
Indices: 21813276--21813422 Score: 167
Period size: 43 Copynumber: 3.4 Consensus size: 43
21813266 TGTGATTTCG
21813276 TGTAAGACCATGTCTAGGACATTGGCATCGATATGAGATTAAA
1 TGTAAGACCATGTCTAGGACATTGGCATCGATATGAGATTAAA
* **
21813319 TGTAAGACCGTGTCTAGGACATTGGCATCG-TAT-ATGATTTCA
1 TGTAAGACCATGTCTAGGACATTGGCATCGATATGA-GATTAAA
* * * *
21813361 TATAAGA-CACTGTCTGGGACAGTGGCATCGATATGTGA-TAACA
1 TGTAAGACCA-TGTCTAGGACATTGGCATCGATATGAGATTAA-A
*
21813404 TGTAAGACCATATCTAGGA
1 TGTAAGACCATGTCTAGGA
21813423 TATGGCTTTG
Statistics
Matches: 85, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
41 2 0.02
42 33 0.39
43 48 0.56
44 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACATTGGCATCGATATGAGATTAAA
Found at i:21819232 original size:29 final size:28
Alignment explanation
Indices: 21819184--21819258 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 28
21819174 AAGAATAAGA
* *
21819184 AATTTCATTAGGTTACTTTAGGTTAATT
1 AATTTCATTAGATTAATTTAGGTTAATT
21819212 AATTTCCATTAGATTAATTTAGGTTAATT
1 AATTT-CATTAGATTAATTTAGGTTAATT
* *
21819241 AATTTAATTAGTTTAATT
1 AATTTCATTAGATTAATT
21819259 AATATTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 16 0.38
29 26 0.62
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (28 bp):
AATTTCATTAGATTAATTTAGGTTAATT
Found at i:21819243 original size:14 final size:14
Alignment explanation
Indices: 21819200--21819246 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
21819190 ATTAGGTTAC
21819200 TTTAGGTTAATTAA
1 TTTAGGTTAATTAA
***
21819214 TTTCCATTAGATTAA
1 TTTAGGTTA-ATTAA
21819229 TTTAGGTTAATTAA
1 TTTAGGTTAATTAA
21819243 TTTA
1 TTTA
21819247 ATTAGTTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (14 bp):
TTTAGGTTAATTAA
Found at i:21819256 original size:18 final size:19
Alignment explanation
Indices: 21819225--21819261 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
21819215 TTCCATTAGA
21819225 TTAATTTAGGTTAATTAAT
1 TTAATTTAGGTTAATTAAT
*
21819244 TTAA-TTAGTTTAATTAAT
1 TTAATTTAGGTTAATTAAT
21819262 ATTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTAATTTAGGTTAATTAAT
Found at i:21821307 original size:53 final size:53
Alignment explanation
Indices: 21821225--21821326 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
21821215 AATAGTAGAC
* * * *
21821225 TGATGGTGGTCTGACGATGATGAACGATGGCAAGGGTTGGTAGTGGAGGTTGA
1 TGATGGTGGTCTAACGATGATGAACGATGGCAAAGGTCGGTAGTAGAGGTTGA
*
21821278 TGATGGTGGTCTAAC-AGTGATGAATGATGGCAAAGGTCGGTAGTAGAGG
1 TGATGGTGGTCTAACGA-TGATGAACGATGGCAAAGGTCGGTAGTAGAGG
21821327 CTGAAAAAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 1 0.02
53 42 0.98
ACGTcount: A:0.25, C:0.08, G:0.41, T:0.25
Consensus pattern (53 bp):
TGATGGTGGTCTAACGATGATGAACGATGGCAAAGGTCGGTAGTAGAGGTTGA
Found at i:21821339 original size:53 final size:53
Alignment explanation
Indices: 21821229--21821341 Score: 129
Period size: 53 Copynumber: 2.1 Consensus size: 53
21821219 GTAGACTGAT
* * * * * ** *
21821229 GGTGGTCTGACGATGATGAACGATGGCAAGGGTTGGTAGTGGAGGTTGATGAT
1 GGTGGTCTAACGATGATGAACGATGGCAAAGGTCGGTAGTAGAGGCTGAAAAA
*
21821282 GGTGGTCTAAC-AGTGATGAATGATGGCAAAGGTCGGTAGTAGAGGCTGAAAAA
1 GGTGGTCTAACGA-TGATGAACGATGGCAAAGGTCGGTAGTAGAGGCTGAAAAA
21821335 GGTGGTC
1 GGTGGTC
21821342 GGTGAGGTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 1 0.02
53 49 0.98
ACGTcount: A:0.27, C:0.09, G:0.41, T:0.24
Consensus pattern (53 bp):
GGTGGTCTAACGATGATGAACGATGGCAAAGGTCGGTAGTAGAGGCTGAAAAA
Found at i:21831937 original size:25 final size:25
Alignment explanation
Indices: 21831909--21832004 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
21831899 CGAACTGTGA
* *
21831909 ATCGGTATGCTCACTCGAGCTATAG
1 ATCGGTATGCTCTCACGAGCTATAG
* * *
21831934 ATCGGTATGCTCTCACAAGCGATAA
1 ATCGGTATGCTCTCACGAGCTATAG
** * *
21831959 ATCAATATACTCTCACGAGCTGTAG
1 ATCGGTATGCTCTCACGAGCTATAG
*
21831984 ATCGGTATGCTCTCACAAGCT
1 ATCGGTATGCTCTCACGAGCT
21832005 GTGGGTCAGA
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (25 bp):
ATCGGTATGCTCTCACGAGCTATAG
Found at i:21852318 original size:30 final size:30
Alignment explanation
Indices: 21852282--21852371 Score: 139
Period size: 30 Copynumber: 3.0 Consensus size: 30
21852272 TATTAGTATA
*
21852282 GTGTGGGCCTTAGCCCATTACAGTAACAGT
1 GTGTGGGCCTTAGCCCAATACAGTAACAGT
21852312 GTGTGGGCCTTAGCCCAATACAGTAACAGT
1 GTGTGGGCCTTAGCCCAATACAGTAACAGT
*
21852342 G-G-GGGCCTTAGCCCAATACAATAATCAGT
1 GTGTGGGCCTTAGCCCAATACAGTAA-CAGT
21852371 G
1 G
21852372 CAATGTAGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
28 21 0.37
29 6 0.11
30 30 0.53
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (30 bp):
GTGTGGGCCTTAGCCCAATACAGTAACAGT
Found at i:21852717 original size:27 final size:26
Alignment explanation
Indices: 21852687--21852844 Score: 158
Period size: 27 Copynumber: 5.9 Consensus size: 26
21852677 TTTCAACTCC
**
21852687 TAGGGGTATAACAGTCATTTTACCCT
1 TAGGGGTATTTCAGTCATTTTACCCT
*
21852713 ATAGGGGTATTTTAGTCATTTTACCCT
1 -TAGGGGTATTTCAGTCATTTTACCCT
*
21852740 TAGGGGTATTTCGGTCATTTTA-CCT
1 TAGGGGTATTTCAGTCATTTTACCCT
* **
21852765 ATCAAGGGTATTTTGGTCATTTTACCCT
1 -T-AGGGGTATTTCAGTCATTTTACCCT
* *
21852793 TCGAGGGTATTTCAATCATTTTACCCT
1 TAG-GGGTATTTCAGTCATTTTACCCT
*
21852820 TCAAGGGTATTTC-GATCATTTTACC
1 T-AGGGGTATTTCAG-TCATTTTACC
21852845 TCATTTTACC
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
25 3 0.03
26 21 0.19
27 83 0.75
28 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (26 bp):
TAGGGGTATTTCAGTCATTTTACCCT
Found at i:21852745 original size:53 final size:54
Alignment explanation
Indices: 21852687--21852844 Score: 198
Period size: 53 Copynumber: 3.0 Consensus size: 54
21852677 TTTCAACTCC
** *
21852687 TAGGGGTATAACAGTCATTTTACCCTAT-AGGGGTATTTTAGTCATTTTACCCT
1 TAGGGGTATTTCAGTCATTTTACCCTATCAAGGGTATTTTAGTCATTTTACCCT
* *
21852740 TAGGGGTATTTCGGTCATTTTA-CCTATCAAGGGTATTTTGGTCATTTTACCCT
1 TAGGGGTATTTCAGTCATTTTACCCTATCAAGGGTATTTTAGTCATTTTACCCT
* * *
21852793 TCGAGGGTATTTCAATCATTTTACCCT-TCAAGGGTA-TTTCGATCATTTTACC
1 TAG-GGGTATTTCAGTCATTTTACCCTATCAAGGGTATTTTAG-TCATTTTACC
21852845 TCATTTTACC
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
52 5 0.05
53 48 0.52
54 36 0.39
55 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (54 bp):
TAGGGGTATTTCAGTCATTTTACCCTATCAAGGGTATTTTAGTCATTTTACCCT
Found at i:21852849 original size:37 final size:37
Alignment explanation
Indices: 21852808--21852881 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
21852798 GGTATTTCAA
*
21852808 TCATTTTACCCTTCAAGGGTATTTCGATCATTTTACC
1 TCATTTTACCCTTCAAAGGTATTTCGATCATTTTACC
* *
21852845 TCATTTTACCCTTCAAAGGTATTTTGGTCATTTTACC
1 TCATTTTACCCTTCAAAGGTATTTCGATCATTTTACC
21852882 CTTCAAGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.45
Consensus pattern (37 bp):
TCATTTTACCCTTCAAAGGTATTTCGATCATTTTACC
Found at i:21852876 original size:27 final size:27
Alignment explanation
Indices: 21852845--21852905 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
21852835 TCATTTTACC
21852845 TCATTTTACCCTTCAAAGGTATTTTGG
1 TCATTTTACCCTTCAAAGGTATTTTGG
*
21852872 TCATTTTACCCTTCAAGGGTATTTTGG
1 TCATTTTACCCTTCAAAGGTATTTTGG
21852899 TCATTTT
1 TCATTTT
21852906 CCCATGAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (27 bp):
TCATTTTACCCTTCAAAGGTATTTTGG
Found at i:21852882 original size:64 final size:64
Alignment explanation
Indices: 21852781--21852905 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 64
21852771 GGTATTTTGG
* *
21852781 TCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCCTTCAAGGGTATTTCGATCATTTTACC
1 TCATTTTACCCTTCAAAGGTATTTCAATCATTTTACCCTTCAAGGGTATTTCGATCATTTTACC
*** * *
21852845 TCATTTTACCCTTCAAAGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTTGGTCATTTT
1 TCATTTTACCCTTCAAAGGTATTTCAATCATTTTACCCTTCAAGGGTATTTCGATCATTTT
21852906 CCCATGAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (64 bp):
TCATTTTACCCTTCAAAGGTATTTCAATCATTTTACCCTTCAAGGGTATTTCGATCATTTTACC
Found at i:21859210 original size:20 final size:21
Alignment explanation
Indices: 21859172--21859211 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21859162 TAACCTTCAA
*
21859172 AAAAATTCAAGATTGTTTTCC
1 AAAAATTCAAGATTATTTTCC
*
21859193 AAAAATTCTAGA-TATTTTC
1 AAAAATTCAAGATTATTTTC
21859212 AAACCCATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAAATTCAAGATTATTTTCC
Found at i:21863359 original size:21 final size:21
Alignment explanation
Indices: 21863314--21863359 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
21863304 TTTTGCTATT
* *
21863314 GTTG-ATTATAATTCCCTTGT
1 GTTGAATTATAATTACCTTGA
*
21863334 CTTGAATTATAATTACCTTGA
1 GTTGAATTATAATTACCTTGA
21863355 GTTGA
1 GTTGA
21863360 TATATTCCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (21 bp):
GTTGAATTATAATTACCTTGA
Found at i:21871740 original size:13 final size:12
Alignment explanation
Indices: 21871721--21871750 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
21871711 TAACAATAGT
21871721 AAAAGAAAAGAA
1 AAAAGAAAAGAA
21871733 AGAAAGAAAAGAA
1 A-AAAGAAAAGAA
21871746 AAAAG
1 AAAAG
21871751 GAGAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:21883084 original size:28 final size:28
Alignment explanation
Indices: 21883052--21883106 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
21883042 AGAGATCGCC
21883052 TAGAGAAATCTGAGAAAGAGAAAGCTCT
1 TAGAGAAATCTGAGAAAGAGAAAGCTCT
*
21883080 TAGAGAAATTTGAGAAAGAGAAAGCTC
1 TAGAGAAATCTGAGAAAGAGAAAGCTC
21883107 AAACCACGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.25, T:0.18
Consensus pattern (28 bp):
TAGAGAAATCTGAGAAAGAGAAAGCTCT
Found at i:21887876 original size:25 final size:25
Alignment explanation
Indices: 21887818--21887877 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
21887808 GTCATTAGGG
* * *
21887818 TTACCAAT-TTCAGCTCTTCTGAGC
1 TTACCATTATTCAGCTCATATGAGC
* *
21887842 TTATCGTTATTCAGCTCATATGAGC
1 TTACCATTATTCAGCTCATATGAGC
21887867 TTACCATTATT
1 TTACCATTATT
21887878 TACCTCGAAG
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (25 bp):
TTACCATTATTCAGCTCATATGAGC
Found at i:21901582 original size:27 final size:27
Alignment explanation
Indices: 21901552--21901729 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
21901542 TTATTGAGCC
* *
21901552 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
21901579 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
21901606 CGCACACTTAGTGCCACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
21901634 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
21901661 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
21901688 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
21901715 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
21901730 GTACAATTTA
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 101 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:21901691 original size:82 final size:81
Alignment explanation
Indices: 21901573--21901728 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
21901563 TGCTATATAA
* * * *
21901573 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCCACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTGAGTGCAACATAGTCA-AATCGCA
21901638 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
21901655 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCA
*
21901719 CCCTTAGTGC
65 CACTTAGTGC
21901729 TGTACAATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 16 0.25
82 48 0.75
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:21905532 original size:41 final size:41
Alignment explanation
Indices: 21905487--21905618 Score: 131
Period size: 41 Copynumber: 3.2 Consensus size: 41
21905477 GAGTGTAAAT
* * *
21905487 AGGGGCATGTGTATGCAATTCAAGGGTATC-ATAGTACAAAC
1 AGGGGCACGTATATGCAATTCAAGGGTACCGA-AGTACAAAC
* * * *
21905528 AGGGGCACGTATGTGCAATTTAGGGGTACCGAAGTACAAAT
1 AGGGGCACGTATATGCAATTCAAGGGTACCGAAGTACAAAC
* * * * * *
21905569 AGGGGCACTTATGTACAATTTAGGGGTACCGAAGCACAAAC
1 AGGGGCACGTATATGCAATTCAAGGGTACCGAAGTACAAAC
21905610 AGGGGCACG
1 AGGGGCACG
21905619 AATGTGCACT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 77 0.99
42 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (41 bp):
AGGGGCACGTATATGCAATTCAAGGGTACCGAAGTACAAAC
Found at i:21905552 original size:21 final size:21
Alignment explanation
Indices: 21905528--21905594 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
21905518 TAGTACAAAC
*
21905528 AGGGGCACGTATGTGCAATTT
1 AGGGGCACGTATGTACAATTT
* * *
21905549 AGGGGTACCG-AAGTACAA-AT
1 AGGGGCA-CGTATGTACAATTT
*
21905569 AGGGGCACTTATGTACAATTT
1 AGGGGCACGTATGTACAATTT
21905590 AGGGG
1 AGGGG
21905595 TACCGAAGCA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
19 1 0.03
20 14 0.40
21 18 0.51
22 2 0.06
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (21 bp):
AGGGGCACGTATGTACAATTT
Found at i:21905573 original size:20 final size:20
Alignment explanation
Indices: 21905548--21905614 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
21905538 ATGTGCAATT
21905548 TAGGGGTACCGAAGTACAAA
1 TAGGGGTACCGAAGTACAAA
* ** * *
21905568 TAGGGGCACTTATGTACAATT
1 TAGGGGTACCGAAGTACAA-A
*
21905589 TAGGGGTACCGAAGCACAAA
1 TAGGGGTACCGAAGTACAAA
*
21905609 CAGGGG
1 TAGGGG
21905615 CACGAATGTG
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.18
Consensus pattern (20 bp):
TAGGGGTACCGAAGTACAAA
Found at i:21905607 original size:21 final size:21
Alignment explanation
Indices: 21905543--21905607 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
21905533 CACGTATGTG
21905543 CAATTTAGGGGTACCGAAGTA
1 CAATTTAGGGGTACCGAAGTA
* * ** *
21905564 CAA-ATAGGGGCACTTATGTA
1 CAATTTAGGGGTACCGAAGTA
*
21905584 CAATTTAGGGGTACCGAAGCA
1 CAATTTAGGGGTACCGAAGTA
21905605 CAA
1 CAA
21905608 ACAGGGGCAC
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (21 bp):
CAATTTAGGGGTACCGAAGTA
Found at i:21907612 original size:27 final size:27
Alignment explanation
Indices: 21907582--21907654 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
21907572 AGTCGGCCAC
21907582 AAAGGCTTCCATTTTATGGATCACCAA
1 AAAGGCTTCCATTTTATGGATCACCAA
* *
21907609 AAAGGCTTCCATTTCT-TAGATCACCAC
1 AAAGGCTTCCATTT-TATGGATCACCAA
*
21907636 AAAGGTTTCCATTTTATGG
1 AAAGGCTTCCATTTTATGG
21907655 GGTGTTCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 38 0.95
28 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (27 bp):
AAAGGCTTCCATTTTATGGATCACCAA
Found at i:21914250 original size:18 final size:19
Alignment explanation
Indices: 21914229--21914264 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21914219 TCAAGTCTAG
21914229 TTAGATTT-TAATTTTAAA
1 TTAGATTTATAATTTTAAA
*
21914247 TTAGATTTATATTTTTAA
1 TTAGATTTATAATTTTAA
21914265 TTCAATTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TTAGATTTATAATTTTAAA
Found at i:21914301 original size:98 final size:98
Alignment explanation
Indices: 21914113--21914339 Score: 287
Period size: 98 Copynumber: 2.3 Consensus size: 98
21914103 GTCCTAGCCA
* * *
21914113 TTAGA-TTTTAAGTTTAGCTAGATTTTAAGGTTAAATTGGATTTTAGATTTTAAATCCAATTAGA
1 TTAGATTTTTAAGTCTAGTTAGATTTTAAGGTTAAATTAGATTTTAGATTTTAAATCCAATTAGA
* *
21914177 TTGTAAGTTTAAATTTTAGGATTAAATTAGATT
66 TTATAAGTTTAAATTCTAGGATTAAATTAGATT
** * * *
21914210 TTAGATTTTTCAAGTCTAGTTAGATTTTAATTTTAAATTAGA-TTTATATTTTTAATTCAATTAG
1 TTAGATTTTT-AAGTCTAGTTAGATTTTAAGGTTAAATTAGATTTTAGATTTTAAATCCAATTAG
* *
21914274 GTTATAAGTTTAAATTCTAGGTTTAAATTAGATT
65 ATTATAAGTTTAAATTCTAGGATTAAATTAGATT
* *
21914308 TTATATTTTTTTAAGTGTAGTTAGATTTTAAG
1 TTAGA--TTTTTAAGTCTAGTTAGATTTTAAG
21914340 TTAGAAATCT
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
97 5 0.05
98 57 0.51
99 44 0.40
100 5 0.05
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (98 bp):
TTAGATTTTTAAGTCTAGTTAGATTTTAAGGTTAAATTAGATTTTAGATTTTAAATCCAATTAGA
TTATAAGTTTAAATTCTAGGATTAAATTAGATT
Found at i:21914551 original size:18 final size:17
Alignment explanation
Indices: 21914510--21914548 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
21914500 ATTTTTCAAA
*
21914510 ATTTTAAGTTTAATTAG
1 ATTTTAAGCTTAATTAG
21914527 ATTTTAAGCTTAACTT-G
1 ATTTTAAGCTTAA-TTAG
21914544 ATTTT
1 ATTTT
21914549 TAATAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (17 bp):
ATTTTAAGCTTAATTAG
Found at i:21921056 original size:9 final size:9
Alignment explanation
Indices: 21921039--21921102 Score: 101
Period size: 9 Copynumber: 7.1 Consensus size: 9
21921029 TGAGTTTTCG
21921039 AATTCGAAT
1 AATTCGAAT
*
21921048 AACTCGAAT
1 AATTCGAAT
21921057 AATTCGAAT
1 AATTCGAAT
21921066 AATTCGAAT
1 AATTCGAAT
*
21921075 AACTCGAAT
1 AATTCGAAT
21921084 AATTCGAAT
1 AATTCGAAT
*
21921093 AATTTGAAT
1 AATTCGAAT
21921102 A
1 A
21921103 TCAAACTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:21921072 original size:27 final size:27
Alignment explanation
Indices: 21921039--21921102 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
21921029 TGAGTTTTCG
21921039 AATTCGAATAACTCGAATAATTCGAAT
1 AATTCGAATAACTCGAATAATTCGAAT
21921066 AATTCGAATAACTCGAATAATTCGAAT
1 AATTCGAATAACTCGAATAATTCGAAT
*
21921093 AATTTGAATA
1 AATTCGAATA
21921103 TCAAACTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (27 bp):
AATTCGAATAACTCGAATAATTCGAAT
Found at i:21921348 original size:30 final size:31
Alignment explanation
Indices: 21921314--21921373 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
21921304 AAACCTTTTA
*
21921314 TTTTCCCCCAAAATTTTTACTCCC-TCCCAG
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAG
* *
21921344 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
21921374 TCCCAACTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.02, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAG
Found at i:21922499 original size:20 final size:19
Alignment explanation
Indices: 21922418--21922501 Score: 60
Period size: 20 Copynumber: 4.3 Consensus size: 19
21922408 AAATTAAGAT
* *
21922418 AAAATGATTTTAACGAAGGC
1 AAAATGATTTAAAC-AAGTC
* * *
21922438 AAAATGATTTCAACCAATTT
1 AAAATGATTT-AAACAAGTC
* * * *
21922458 AAAATCATTTTAAGATGTC
1 AAAATGATTTAAACAAGTC
21922477 AAAATGATTTCAAACAAGTC
1 AAAATGATTT-AAACAAGTC
21922497 AAAAT
1 AAAAT
21922502 TGCTCTAGGC
Statistics
Matches: 46, Mismatches: 16, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
19 12 0.26
20 32 0.70
21 2 0.04
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.30
Consensus pattern (19 bp):
AAAATGATTTAAACAAGTC
Found at i:21922501 original size:39 final size:40
Alignment explanation
Indices: 21922418--21922501 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 40
21922408 AAATTAAGAT
* * * *
21922418 AAAATGATTTTAACGAAGGCAAAATGATTTCAACCAATTT
1 AAAATCATTTTAACGAAGGCAAAATGATTTCAAACAAGTC
* *
21922458 AAAATCATTTTAA-GATGTCAAAATGATTTCAAACAAGTC
1 AAAATCATTTTAACGAAGGCAAAATGATTTCAAACAAGTC
21922497 AAAAT
1 AAAAT
21922502 TGCTCTAGGC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
39 26 0.68
40 12 0.32
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.30
Consensus pattern (40 bp):
AAAATCATTTTAACGAAGGCAAAATGATTTCAAACAAGTC
Found at i:21930616 original size:20 final size:20
Alignment explanation
Indices: 21930591--21930643 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
21930581 GGTAATTTGG
**
21930591 TATCGATACCACTTTAAAAA
1 TATCGATACCACTGGAAAAA
21930611 TATCGATACTCA-TGGAAAAA
1 TATCGATAC-CACTGGAAAAA
*
21930631 TATCAATACCACT
1 TATCGATACCACT
21930644 AGGTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (20 bp):
TATCGATACCACTGGAAAAA
Found at i:21932712 original size:20 final size:20
Alignment explanation
Indices: 21932683--21932736 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21932673 AAATCAAGAT
*
21932683 AAAATTATTTTAACCAAGTC
1 AAAATCATTTTAACCAAGTC
* * * *
21932703 ATAATGATTTCAACCAAGTT
1 AAAATCATTTTAACCAAGTC
21932723 AAAATCATTTTAAC
1 AAAATCATTTTAAC
21932737 ACATCAAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAATCATTTTAACCAAGTC
Found at i:21932761 original size:40 final size:40
Alignment explanation
Indices: 21932677--21932761 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
21932667 ATTTTAAAAT
* * * *
21932677 CAAGATAAAATTATTTTAACCAAGTCATAATGATTTCAAC
1 CAAGTTAAAATCATTTTAACCAAGTCAAAATGATTTCAAA
21932717 CAAGTTAAAATCATTTTAA-CACA-TCAAAATGATTTCCAAA
1 CAAGTTAAAATCATTTTAACCA-AGTCAAAATGATTT-CAAA
21932757 CAAGT
1 CAAGT
21932762 CAGAATTACT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 13 0.33
40 26 0.67
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (40 bp):
CAAGTTAAAATCATTTTAACCAAGTCAAAATGATTTCAAA
Found at i:21944410 original size:20 final size:20
Alignment explanation
Indices: 21944385--21944437 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
21944375 GGTAATTTGG
**
21944385 TATCGATACCACTTTAAAAA
1 TATCGATACCACTGGAAAAA
21944405 TATCGATACTCA-TGGAAAAA
1 TATCGATAC-CACTGGAAAAA
*
21944425 TATCAATACCACT
1 TATCGATACCACT
21944438 AGGTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (20 bp):
TATCGATACCACTGGAAAAA
Found at i:21946505 original size:20 final size:20
Alignment explanation
Indices: 21946476--21946529 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21946466 AAATCAAGAT
*
21946476 AAAATTATTTTAACCAAGTC
1 AAAATCATTTTAACCAAGTC
* * * *
21946496 ATAATGATTTCAACCAAGTT
1 AAAATCATTTTAACCAAGTC
21946516 AAAATCATTTTAAC
1 AAAATCATTTTAAC
21946530 ACATCAAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAATCATTTTAACCAAGTC
Found at i:21946554 original size:40 final size:40
Alignment explanation
Indices: 21946470--21946554 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
21946460 ATTTTAAAAT
* * * *
21946470 CAAGATAAAATTATTTTAACCAAGTCATAATGATTTCAAC
1 CAAGTTAAAATCATTTTAACCAAGTCAAAATGATTTCAAA
21946510 CAAGTTAAAATCATTTTAA-CACA-TCAAAATGATTTCCAAA
1 CAAGTTAAAATCATTTTAACCA-AGTCAAAATGATTT-CAAA
21946550 CAAGT
1 CAAGT
21946555 CAGAATTACT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 13 0.33
40 26 0.67
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (40 bp):
CAAGTTAAAATCATTTTAACCAAGTCAAAATGATTTCAAA
Found at i:21960195 original size:20 final size:20
Alignment explanation
Indices: 21960166--21960219 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
21960156 AAATCAAGAT
*
21960166 AAAATTATTTTAACCAAGTC
1 AAAATCATTTTAACCAAGTC
* * ** *
21960186 ATAATGATTTCGACCAAGTT
1 AAAATCATTTTAACCAAGTC
21960206 AAAATCATTTTAAC
1 AAAATCATTTTAAC
21960220 ACATCAAAAT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (20 bp):
AAAATCATTTTAACCAAGTC
Found at i:21960244 original size:40 final size:40
Alignment explanation
Indices: 21960160--21960244 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
21960150 ATTTTAAAAT
* * * * *
21960160 CAAGATAAAATTATTTTAACCAAGTCATAATGATTTCGAC
1 CAAGTTAAAATCATTTTAACCAAGTCAAAATGATTTCAAA
21960200 CAAGTTAAAATCATTTTAA-CACA-TCAAAATGATTTCCAAA
1 CAAGTTAAAATCATTTTAACCA-AGTCAAAATGATTT-CAAA
21960240 CAAGT
1 CAAGT
21960245 CAGAATTACT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 13 0.34
40 25 0.66
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (40 bp):
CAAGTTAAAATCATTTTAACCAAGTCAAAATGATTTCAAA
Found at i:21971844 original size:20 final size:20
Alignment explanation
Indices: 21971819--21971871 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
21971809 GGTAATTTGG
**
21971819 TATCGATACCACTTTAAAAA
1 TATCGATACCACTGGAAAAA
21971839 TATCGATACTCA-TGGAAAAA
1 TATCGATAC-CACTGGAAAAA
*
21971859 TATCAATACCACT
1 TATCGATACCACT
21971872 AGGTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (20 bp):
TATCGATACCACTGGAAAAA
Done.