Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008294.1 Hibiscus syriacus cultivar Beakdansim tig00110959_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 362436
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:253383 original size:21 final size:21
Alignment explanation
Indices: 253354--253395 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
253344 TTACTGCTAT
*
253354 GGTATCGATACCATGCTACAG
1 GGTACCGATACCATGCTACAG
*
253375 GGTACCGATACCCTGCTACAG
1 GGTACCGATACCATGCTACAG
253396 TACTTCCGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (21 bp):
GGTACCGATACCATGCTACAG
Found at i:253941 original size:22 final size:22
Alignment explanation
Indices: 253916--253976 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
253906 GGCATGTGAA
253916 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
* *
253938 ATTTGTTCCGAATGACCTCTGT
1 ATTTGTCCCGAATGACCTATGT
** *
253960 ATACGTCCCGAAGGACC
1 ATTTGTCCCGAATGACC
253977 GCATAGACCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (22 bp):
ATTTGTCCCGAATGACCTATGT
Found at i:255746 original size:26 final size:28
Alignment explanation
Indices: 255694--255787 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 28
255684 TTACTAATAA
*
255694 TGATTTAATAATTATTATTAATCTAATTATT
1 TGATTT-ATAATGATTATTAA--TAATTATT
* *
255725 TGATATT-TAATGA-T-TTAATAATAATA
1 TGAT-TTATAATGATTATTAATAATTATT
255751 TGATTTAGTAATGATTATTAATAATTATT
1 TGATTTA-TAATGATTATTAATAATTATT
255780 T-A-TTATAA
1 TGATTTATAA
255788 ATATTTAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
25 2 0.04
26 13 0.25
27 9 0.17
28 6 0.11
29 12 0.23
30 5 0.09
31 4 0.08
32 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (28 bp):
TGATTTATAATGATTATTAATAATTATT
Found at i:255994 original size:17 final size:17
Alignment explanation
Indices: 255972--256031 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 17
255962 CTAATATAAA
255972 TTAAACAAAATATTTTT
1 TTAAACAAAATATTTTT
* *
255989 TTAAACAACATAAATATTT
1 TTAAACAA-A-ATATTTTT
*
256008 TTAAACATAATATTTTTT
1 TTAAACAAAATA-TTTTT
256026 TTAAAC
1 TTAAAC
256032 GGGAATAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 10 0.29
18 12 0.34
19 13 0.37
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAACAAAATATTTTT
Found at i:256021 original size:15 final size:16
Alignment explanation
Indices: 255995--256024 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
255985 TTTTTTAAAC
255995 AACATAAATATTTTTA
1 AACATAAATATTTTTA
256011 AACAT-AATATTTTT
1 AACATAAATATTTTT
256025 TTTAAACGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
AACATAAATATTTTTA
Found at i:256500 original size:44 final size:50
Alignment explanation
Indices: 256442--256549 Score: 138
Period size: 50 Copynumber: 2.3 Consensus size: 50
256432 GTTTAAACAC
*
256442 ACTAACAAATTAATTAAATAA-TTTTT-T-T-ACAT-ATA-ATAACTTAA
1 ACTAACAAACTAATTAAATAATTTTTTATATAACATAATATATAACTTAA
* * *
256486 ACTAATAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAAATAATTTTTTATATAACATAATATATAACTTAA
256536 ACTAACAAACTAAT
1 ACTAACAAACTAAT
256550 AATTTATACT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
44 18 0.34
45 5 0.09
46 1 0.02
47 1 0.02
48 3 0.06
49 3 0.06
50 22 0.42
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (50 bp):
ACTAACAAACTAATTAAATAATTTTTTATATAACATAATATATAACTTAA
Found at i:256560 original size:21 final size:21
Alignment explanation
Indices: 256527--256575 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
256517 AATATAATAT
256527 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
256548 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
256569 ATTAACT
1 A-TAACT
256576 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:256729 original size:19 final size:19
Alignment explanation
Indices: 256705--256750 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
256695 CTTCCTTTCC
256705 TTTCTTTCGAAAAAATTTA
1 TTTCTTTCGAAAAAATTTA
* *
256724 TTTCTTTCGACAAAATTTC
1 TTTCTTTCGAAAAAATTTA
256743 TTTCTTTC
1 TTTCTTTC
256751 TTATGCTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTCTTTCGAAAAAATTTA
Found at i:256829 original size:25 final size:24
Alignment explanation
Indices: 256795--256856 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 24
256785 TATAACTCAC
256795 TTTGAGCGTTGAAGGCTACAATAAA
1 TTTGAGCGTTGAAGGCTACAAT-AA
** *
256820 TTTGAGCGTTGAAGGCTGTAATTA
1 TTTGAGCGTTGAAGGCTACAATAA
256844 TTTGAGCGTTGAA
1 TTTGAGCGTTGAA
256857 CGCTGTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 14 0.41
25 20 0.59
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (24 bp):
TTTGAGCGTTGAAGGCTACAATAA
Found at i:256851 original size:24 final size:25
Alignment explanation
Indices: 256795--256867 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 25
256785 TATAACTCAC
**
256795 TTTGAGCGTTGAAGGCTACAATAAA
1 TTTGAGCGTTGAAGGCTGTAATAAA
*
256820 TTTGAGCGTTGAAGGCTGTAAT-TA
1 TTTGAGCGTTGAAGGCTGTAATAAA
*
256844 TTTGAGCGTTGAACGCTGTAATAA
1 TTTGAGCGTTGAAGGCTGTAATAA
256868 TGCAGCAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 22 0.52
25 20 0.48
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (25 bp):
TTTGAGCGTTGAAGGCTGTAATAAA
Found at i:257072 original size:28 final size:28
Alignment explanation
Indices: 257052--257121 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
257042 TCGCCATGAT
*
257052 TGCATGGCGACCTATAGGTCGCTGGGTG
1 TGCATGGCGACCTATAGGTCGCTGGATG
* **
257080 TGCATGGCGACCTATAGGTCGATGGGCG
1 TGCATGGCGACCTATAGGTCGCTGGATG
*
257108 TGCATGGAGACCTA
1 TGCATGGCGACCTA
257122 CCCCATCTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.23
Consensus pattern (28 bp):
TGCATGGCGACCTATAGGTCGCTGGATG
Found at i:259532 original size:36 final size:36
Alignment explanation
Indices: 259492--259584 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
259482 GTTGTTAAAC
* *
259492 TTGATCTGCAGTAGTTACAACTGTATGTTGCTGCAT
1 TTGATCTGCAGCAGTTTCAACTGTATGTTGCTGCAT
* *
259528 TTGATCTGCAGCAGTTTCAACTGTGTGTTGTTGCAT
1 TTGATCTGCAGCAGTTTCAACTGTATGTTGCTGCAT
*
259564 TTGATTTGCAGCAGTTTCAAC
1 TTGATCTGCAGCAGTTTCAAC
259585 CTCCTCCTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (36 bp):
TTGATCTGCAGCAGTTTCAACTGTATGTTGCTGCAT
Found at i:268067 original size:14 final size:16
Alignment explanation
Indices: 268032--268065 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
268022 GTTTAGGATA
268032 ATATTTTAAACATTAT
1 ATATTTTAAACATTAT
268048 ATATTTTAAACATTAT
1 ATATTTTAAACATTAT
268064 AT
1 AT
268066 TTATCTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTTTAAACATTAT
Found at i:268136 original size:32 final size:32
Alignment explanation
Indices: 268093--268154 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
268083 TTTAAATAAG
268093 TTTTAGTATTTTA-ATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTATATT-AGTTTTAGG-TATTAT
*
268126 TTTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTTAGTATTTTATATTAGTTTTAGGTATT
268155 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTAGTATTTTATATTAGTTTTAGGTATTAT
Found at i:268187 original size:19 final size:19
Alignment explanation
Indices: 268159--268197 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
268149 GGTATTTTAG
* *
268159 TTTAAATAGGTTTTAGTAT
1 TTTAAATAGGATTTAATAT
*
268178 TTTAATTAGGATTTAATAT
1 TTTAAATAGGATTTAATAT
268197 T
1 T
268198 ATATCATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (19 bp):
TTTAAATAGGATTTAATAT
Found at i:268220 original size:62 final size:63
Alignment explanation
Indices: 268130--268255 Score: 195
Period size: 62 Copynumber: 2.0 Consensus size: 63
268120 TATTATTTTT
*
268130 ATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTA
1 ATATTATATATTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTATTTTAATTAGGATTTA
*
268193 ATATTATATCATTT-TTTT-GGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 ATATTATAT-ATTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTA
268255 A
1 A
268256 GATGTTTTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
61 5 0.08
62 38 0.64
63 12 0.20
64 4 0.07
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.56
Consensus pattern (63 bp):
ATATTATATATTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTA
Found at i:268861 original size:19 final size:18
Alignment explanation
Indices: 268832--268880 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
268822 AATCTCTTTA
268832 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* * *
268851 TTTCTTTTATTTGATTCTT
1 ATT-TTTTATTTAATTATT
268870 ATTTTTTATTT
1 ATTTTTTATTT
268881 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 8 0.32
19 16 0.64
20 1 0.04
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:268974 original size:20 final size:21
Alignment explanation
Indices: 268936--268976 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
268926 ACTATTAATA
268936 TTTATTCTTATATTATTTTTT
1 TTTATTCTTATATTATTTTTT
268957 TTTATT-TTA-ATATATTTTTT
1 TTTATTCTTATAT-TATTTTTT
268977 CAATTTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 11 0.58
21 6 0.32
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTATTCTTATATTATTTTTT
Found at i:269938 original size:19 final size:19
Alignment explanation
Indices: 269914--269955 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
269904 TATTCTATAC
*
269914 AAGTTTAATCGTTATTTTT
1 AAGTTTAAACGTTATTTTT
269933 AAGTTTAAACGTTATTTTT
1 AAGTTTAAACGTTATTTTT
269952 AAGT
1 AAGT
269956 ATTTGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (19 bp):
AAGTTTAAACGTTATTTTT
Found at i:270660 original size:2 final size:2
Alignment explanation
Indices: 270653--270703 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
270643 TTGGGCAGGG
* * * *
270653 TA TA TA TA TT TA AA T- TA AA TA TA AA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
270693 TA TA TA TA TA T
1 TA TA TA TA TA T
270704 TTAATTTAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:270750 original size:6 final size:7
Alignment explanation
Indices: 270655--270751 Score: 50
Period size: 6 Copynumber: 14.4 Consensus size: 7
270645 GGGCAGGGTA
270655 TATATAT
1 TATATAT
*
270662 T-TAAAT
1 TATATAT
*
270668 TAAATA-
1 TATATAT
*
270674 TAAATAT
1 TATATAT
270681 TATATAT
1 TATATAT
270688 ATATATAT
1 -TATATAT
270696 ATATATAT
1 -TATATAT
270704 T-TA-AT
1 TATATAT
270709 T-TA-AT
1 TATATAT
*
270714 T-TAAATT
1 TATATA-T
270721 TATTAATAT
1 TA-T-ATAT
270730 TATATA-
1 TATATAT
270736 TATATAT
1 TATATAT
270743 TATA-AT
1 TATATAT
270749 TAT
1 TAT
270752 TTTTAATATT
Statistics
Matches: 76, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
5 10 0.13
6 25 0.33
7 19 0.25
8 16 0.21
9 4 0.05
10 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:270845 original size:30 final size:31
Alignment explanation
Indices: 270809--270872 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
270799 GATTACTAAA
270809 CCCGTCCCCATTTAACATAAAC-AGTTTTTC
1 CCCGTCCCCATTTAACATAAACGAGTTTTTC
* * *
270839 CCCGTCCCCGTTTAGCATAAACGATTTTTTC
1 CCCGTCCCCATTTAACATAAACGAGTTTTTC
270870 CCC
1 CCC
270873 CCTGGATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.22, C:0.36, G:0.09, T:0.33
Consensus pattern (31 bp):
CCCGTCCCCATTTAACATAAACGAGTTTTTC
Found at i:274921 original size:21 final size:21
Alignment explanation
Indices: 274895--274939 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
274885 GATTTCTGGG
* *
274895 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
274916 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
274937 CAA
1 CAA
274940 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:275546 original size:23 final size:24
Alignment explanation
Indices: 275503--275549 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
275493 ATATGGCATG
*
275503 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
275527 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
275550 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:275760 original size:31 final size:31
Alignment explanation
Indices: 275722--275877 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
275712 AGGGTCGAGG
275722 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
275753 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
275784 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
275815 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
275846 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
275877 G
1 G
275878 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:278892 original size:21 final size:21
Alignment explanation
Indices: 278866--278910 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
278856 GATTTCTGGG
* *
278866 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
278887 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
278908 CAA
1 CAA
278911 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:279519 original size:23 final size:24
Alignment explanation
Indices: 279476--279522 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
279466 ATATGGCATG
*
279476 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
279500 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
279523 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:279740 original size:31 final size:31
Alignment explanation
Indices: 279702--279826 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
279692 AGGGTCGAGG
279702 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
279733 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
279764 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
279795 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
279826 G
1 G
279827 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:285944 original size:6 final size:6
Alignment explanation
Indices: 285929--285980 Score: 63
Period size: 6 Copynumber: 8.5 Consensus size: 6
285919 CACCAAACGT
285929 AAAA-A AAAATA AAAATAA AAAATAAA AAAATA AAAATA AAAATA AAAA-A
1 AAAATA AAAATA AAAAT-A AAAAT--A AAAATA AAAATA AAAATA AAAATA
285978 AAA
1 AAA
285981 CCCAACAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
5 8 0.18
6 23 0.52
7 6 0.14
8 7 0.16
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:285957 original size:21 final size:20
Alignment explanation
Indices: 285931--285978 Score: 87
Period size: 21 Copynumber: 2.4 Consensus size: 20
285921 CCAAACGTAA
285931 AAAAAAATAAAAATAAAAAAT
1 AAAAAAATAAAAAT-AAAAAT
285952 AAAAAAATAAAAATAAAAAT
1 AAAAAAATAAAAATAAAAAT
285972 AAAAAAA
1 AAAAAAA
285979 AACCCAACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAAAAATAAAAATAAAAAT
Found at i:285993 original size:1 final size:1
Alignment explanation
Indices: 285929--285980 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
285919 CACCAAACGT
* * * * * *
285929 AAAAAAAAATAAAAATAAAAAATAAAAAAATAAAAATAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
285981 CCCAACAGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (1 bp):
A
Found at i:289478 original size:29 final size:30
Alignment explanation
Indices: 289436--289498 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
289426 GACAGCATAA
289436 TGAAACTATTTTAATACAATATT-AAATAT
1 TGAAACTATTTTAATACAATATTAAAATAT
* *
289465 TGAAACTATTTTAATATAATCTTAAAATAT
1 TGAAACTATTTTAATACAATATTAAAATAT
289495 TGAA
1 TGAA
289499 GGAATTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (30 bp):
TGAAACTATTTTAATACAATATTAAAATAT
Found at i:289997 original size:26 final size:24
Alignment explanation
Indices: 289955--290008 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 24
289945 GAAATGAGTA
289955 TTAAGAAAGTAAATTTATAAAATT
1 TTAAGAAAGTAAATTTATAAAATT
289979 TTAAGAAATGTTAAATTTATAAAATT
1 TTAAGAAA-G-TAAATTTATAAAATT
290005 TTAA
1 TTAA
290009 AGATAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 8 0.29
25 1 0.04
26 19 0.68
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (24 bp):
TTAAGAAAGTAAATTTATAAAATT
Found at i:291732 original size:34 final size:32
Alignment explanation
Indices: 291676--291758 Score: 80
Period size: 34 Copynumber: 2.5 Consensus size: 32
291666 ACTCTTTTCT
291676 TAATATTA-AAAAATAAATAAAT-ATTAATAAAA
1 TAAT-TTATAAAAATAAATAAATAATTAAT-AAA
* * *
291708 TATTTCTATAAAAATAATTAAAATAAATTAATATA
1 TAATT-TATAAAAATAAAT-AAAT-AATTAATAAA
291743 TAATTTATAAAAATAA
1 TAATTTATAAAAATAA
291759 GGTATTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
31 1 0.02
32 5 0.12
33 9 0.21
34 15 0.36
35 6 0.14
36 6 0.14
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (32 bp):
TAATTTATAAAAATAAATAAATAATTAATAAA
Found at i:291785 original size:143 final size:141
Alignment explanation
Indices: 291595--291851 Score: 356
Period size: 143 Copynumber: 1.8 Consensus size: 141
291585 ATATATATAT
* ** *
291595 ATATATATATTTTATAAATAAGATATATTTACTTAGAAATATCAGAAATTAACTCTAGGTGCTTT
1 ATATATATATTTTAAAAATAAGATATATTTACTTAGAAATATCAGAAAAGAACTCTAGGTACTTT
* * *
291660 AAGACAACTCTTTTCTTAATATTAAAAAATAAATAAATATTAATAAAATATTTCTATAAAAATAA
66 AAGACAAC-CATTTCTTAATATAAAAAAATAAAAAAATA-TAATAAAATATTTCTATAAAAATAA
291725 TTAAAATAAATTA
129 TTAAAATAAATTA
* * *
291738 ATATATA-ATTTATAAAAATAAGGTATTTATTATTTAG-AATATCAGAAAAGAACTCTAGGTACT
1 ATATATATATTT-TAAAAATAAGATATAT-TTACTTAGAAATATCAGAAAAGAACTCTAGGTACT
* *
291801 TTAAGACAGCCATTTCTTAATATAAAAAAATAAAAAAATATATTAAAATAT
64 TTAAGACAACCATTTCTTAATATAAAAAAATAAAAAAATATAATAAAATAT
291852 ATATATATAT
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
141 10 0.10
142 31 0.31
143 52 0.52
144 7 0.07
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (141 bp):
ATATATATATTTTAAAAATAAGATATATTTACTTAGAAATATCAGAAAAGAACTCTAGGTACTTT
AAGACAACCATTTCTTAATATAAAAAAATAAAAAAATATAATAAAATATTTCTATAAAAATAATT
AAAATAAATTA
Found at i:291853 original size:2 final size:2
Alignment explanation
Indices: 291848--291892 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
291838 ATATATTAAA
291848 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
291889 AT AT
1 AT AT
291893 TTAAAGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:291941 original size:21 final size:22
Alignment explanation
Indices: 291917--291964 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
291907 TAAACATATC
291917 AAAAGTATAATAA-AA-CAAAAT
1 AAAAGTATAATAATAATC-AAAT
*
291938 AAAATTATAATAATAATCAAAT
1 AAAAGTATAATAATAATCAAAT
291960 AAAAG
1 AAAAG
291965 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.52
22 10 0.43
23 1 0.04
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (22 bp):
AAAAGTATAATAATAATCAAAT
Found at i:293429 original size:47 final size:46
Alignment explanation
Indices: 293340--293433 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 46
293330 AACGGAAATG
293340 TTGAAAACATCATGCACTGAAGGTCTTATGGATGACCTGAAGGCTTT
1 TTGAAAACATCATGCACTGAAGGTCTTATGGATGACCTGAAGG-TTT
*
293387 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGA-CTCGAAGGTTT
1 TTGAAAACATCATGCACTGAAGGTCTTATGGATGACCT-GAAGGTTT
293433 T
1 T
293434 AAATATCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
46 6 0.13
47 39 0.87
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (46 bp):
TTGAAAACATCATGCACTGAAGGTCTTATGGATGACCTGAAGGTTT
Found at i:293519 original size:46 final size:46
Alignment explanation
Indices: 293449--293600 Score: 243
Period size: 46 Copynumber: 3.3 Consensus size: 46
293439 TCAAAAAGCT
* *
293449 CCCGAAGGTTTTTTTGGA-AACATCATGCACTGTAGGTCTTACAGATGA
1 CCCGAAGG--TTTTT-GATAACATCATGCACTGAAGGGCTTACAGATGA
*
293497 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGGATTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGGCTTACAGATGA
293543 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGGCTTACAGATGA
293589 CCCGAAGGTTTT
1 CCCGAAGGTTTT
293601 GAAAATATCA
Statistics
Matches: 99, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
45 2 0.02
46 89 0.90
48 8 0.08
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (46 bp):
CCCGAAGGTTTTTGATAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:293693 original size:45 final size:45
Alignment explanation
Indices: 293629--293732 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
293619 CCAAAGGCTT
* * * * **
293629 TTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTAACAGATGACCCGAAGG
*
293674 TTTTGAAAGCATCATGCACTGAAGGGCTAACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTAACAGATGACCCGAAGG
*
293719 TTTTGAAAATATCA
1 TTTTGAAAACATCA
293733 AAAAGCTCCC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTAACAGATGACCCGAAGG
Found at i:293722 original size:122 final size:122
Alignment explanation
Indices: 293505--293854 Score: 576
Period size: 122 Copynumber: 2.9 Consensus size: 122
293495 GACCCGAAGG
* * * ** **
293505 TTTTTGATAACATCATGCACTGAAGGGATTACAGATGACCCGAAGGTTTTTGATAA-CATCATGC
1 TTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGG-TTTTGA-AAGCATCATGC
293569 ACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCAAAGGCT
64 ACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCAAAGGCT
293628 TTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCAC
1 TTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCAC
* *
293693 TGAAGGGCTAACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCT
66 TGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCAAAGGCT
*
293750 TTTTTGACAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCAC
1 TTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCAC
*
293815 TGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
66 TGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCA
293855 TGCACTGAAG
Statistics
Matches: 214, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
121 2 0.01
122 173 0.81
123 39 0.18
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (122 bp):
TTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCAC
TGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCAAAGGCT
Found at i:293856 original size:167 final size:167
Alignment explanation
Indices: 293629--293998 Score: 641
Period size: 167 Copynumber: 2.2 Consensus size: 167
293619 CCAAAGGCTT
* * * * * *
293629 TTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACT
1 TTTTGAAAGCATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACT
* *
293694 GAAGGGCTAACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTTGACA
66 GAAGGGCTAACAGATGACCAGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTTGAAA
293759 ACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGG
131 ACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGG
*
293796 TTTTGAAAGCATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAGCATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACT
*
293861 GAAGGGCTTACAGATGACCAGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTTGAAA
66 GAAGGGCTAACAGATGACCAGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTTGAAA
*
293926 ACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGG
131 ACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGG
293963 TTTTGAAAGCATCATGCACTGAAGGGCTTATAGATG
1 TTTTGAAAGCATCATGCACTGAAGGGCTTATAGATG
293999 TGGGAAATAG
Statistics
Matches: 191, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
167 191 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (167 bp):
TTTTGAAAGCATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACT
GAAGGGCTAACAGATGACCAGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTTGAAA
ACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGG
Found at i:293894 original size:45 final size:45
Alignment explanation
Indices: 293751--293899 Score: 217
Period size: 45 Copynumber: 3.3 Consensus size: 45
293741 CCGAAGGCTT
* * * * **
293751 TTTTGACAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
293796 TTTTGAAAGCATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
293841 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
293886 TTTTGAAAATATCA
1 TTTTGAAAACATCA
293900 AAAAGCTCCC
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 94 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:293917 original size:289 final size:289
Alignment explanation
Indices: 293340--293990 Score: 1040
Period size: 289 Copynumber: 2.2 Consensus size: 289
293330 AACGGAAATG
* * * *
293340 TTGAAAACATCATGCACTGAAGGTCTTATGGATGACCTGAAGGCTTTTTGAAAACATCCTGCACT
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGG--TTTTGAAAGCATCATGCACT
* * ** * *
293405 GAAGGTCTTATGGATGACTCGAAGGTTTTAAATATCAAAAAGCTCCCGAAGGTTTTTTTGGAAAC
64 GAAGGGCTAACAGATGACCCGAAGGTTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTTGGAAAC
*
293470 ATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGGATT
129 ATCATGCACTGCAGGTCTTACAGATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGGATT
* *
293535 ACAGATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
194 ACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGGTTT
293600 TGAAAATATCAAAAAGCTCCCAAAGGCTTTT
259 TGAAAATATCAAAAAGCTCCCAAAGGCTTTT
*
293631 TTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGA
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGA
293696 AGGGCTAACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTT-GACAA
66 AGGGCTAACAGATGACCCGAAGGTTTT--AAATATCAAAAAGCTCCCGAAGGCTTTTTTGGA-AA
* ** *
293760 CATCCTGCACTGCAGGTCTTATGGATGACCCGAAGG-TTTTGA-AAGCATCATGCACTGAAGGGC
128 CATCATGCACTGCAGGTCTTACAGATGACCCGAAGGTTTTTGATAA-CATCATGCACTGAAGGGA
293823 TTACAGATGACCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGGT
192 TTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGGT
*
293887 TTTGAAAATATCAAAAAGCTCCCGAAGGCTTTT
257 TTTGAAAATATCAAAAAGCTCCCAAAGGCTTTT
*
293920 TTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGA
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGA
293985 AGGGCT
66 AGGGCT
293991 TATAGATGTG
Statistics
Matches: 336, Mismatches: 20, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
289 190 0.57
290 43 0.13
291 103 0.31
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (289 bp):
TTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGA
AGGGCTAACAGATGACCCGAAGGTTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACAT
CATGCACTGCAGGTCTTACAGATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGGATTAC
AGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGGTTTTG
AAAATATCAAAAAGCTCCCAAAGGCTTTT
Found at i:299036 original size:16 final size:17
Alignment explanation
Indices: 299015--299047 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
299005 CTTGGTTCAA
299015 TTTTTTCC-TTTTTTTC
1 TTTTTTCCATTTTTTTC
299031 TTTTTTCCATTTTTTTC
1 TTTTTTCCATTTTTTTC
299048 AAGTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCCATTTTTTTC
Found at i:301802 original size:16 final size:16
Alignment explanation
Indices: 301781--301811 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
301771 AATAATGTAA
*
301781 TATAAATGCGAAAATG
1 TATAAATGCAAAAATG
301797 TATAAATGCAAAAAT
1 TATAAATGCAAAAAT
301812 AAGAATGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (16 bp):
TATAAATGCAAAAATG
Found at i:304815 original size:18 final size:20
Alignment explanation
Indices: 304775--304814 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
304765 AGAAAATATA
* *
304775 TTATATATATATATTTTATT
1 TTATAAATAGATATTTTATT
304795 TTATAAATAGATA-TTTATT
1 TTATAAATAGATATTTTATT
304814 T
1 T
304815 ACTTAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TTATAAATAGATATTTTATT
Found at i:305136 original size:27 final size:27
Alignment explanation
Indices: 305083--305147 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
305073 AAAACATATC
305083 AAAAGTAATAATAAAACAAAATAAAATT
1 AAAA-TAATAATAAAACAAAATAAAATT
* * *
305111 ATAATAATAATCAAAATAAAA-GAAATT
1 AAAATAATAAT-AAAACAAAATAAAATT
*
305138 AAAATTATAA
1 AAAATAATAA
305148 AAATTAACTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (27 bp):
AAAATAATAATAAAACAAAATAAAATT
Found at i:308340 original size:29 final size:29
Alignment explanation
Indices: 308298--308356 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
308288 ATCTTCACCT
308298 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
308327 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
308356 A
1 A
308357 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:312298 original size:16 final size:16
Alignment explanation
Indices: 312277--312309 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
312267 TAATAAATAA
312277 ACAAACATAAACGAAC
1 ACAAACATAAACGAAC
312293 ACAAACATAAACGAAC
1 ACAAACATAAACGAAC
312309 A
1 A
312310 ATTTTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.24, G:0.06, T:0.06
Consensus pattern (16 bp):
ACAAACATAAACGAAC
Found at i:312689 original size:126 final size:129
Alignment explanation
Indices: 312442--312693 Score: 440
Period size: 126 Copynumber: 2.0 Consensus size: 129
312432 AAGCGAATGT
312442 AAAAAAAGTAAACAACAAGAATAACAATACATTAATATAACCTGCAACTTTAGAGCTAATTTGTT
1 AAAAAAAGTAAACAACAAGAATAACAATACATTAATATAACCTGCAACTTTAGAGCTAATTTGTT
312507 CGAATACGACAAAAACATACATAAATCATAAATAAGCTATATGAACATAATAAAATCTTAATGGA
66 CGAATACGAC-AAAACATACATAAATCATAAATAAGCTATATGAACATAATAAAATCTTAATGGA
* *
312572 AAAAAAAGTAAACAACAAGAATAACAATTCATT-A-ATAACCTGCAAACTTTAGAGTTAATTTGT
1 AAAAAAAGTAAACAACAAGAATAACAATACATTAATATAACCTGC-AACTTTAGAGCTAATTTGT
312635 TCGAATACGAC-AAA-ATACATAAATCATAAATAAGCTATATGAACATAATAAAATCTTAA
65 TCGAATACGACAAAACATACATAAATCATAAATAAGCTATATGAACATAATAAAATCTTAA
312694 AGTTAATTTG
Statistics
Matches: 119, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
126 45 0.38
127 3 0.03
128 9 0.08
129 30 0.25
130 32 0.27
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.25
Consensus pattern (129 bp):
AAAAAAAGTAAACAACAAGAATAACAATACATTAATATAACCTGCAACTTTAGAGCTAATTTGTT
CGAATACGACAAAACATACATAAATCATAAATAAGCTATATGAACATAATAAAATCTTAATGGA
Found at i:313203 original size:16 final size:17
Alignment explanation
Indices: 313182--313213 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
313172 TTGGCTCGGC
313182 CTGGCCTG-TTAAAAGT
1 CTGGCCTGTTTAAAAGT
313198 CTGGCCTGTTTAAAAG
1 CTGGCCTGTTTAAAAG
313214 CCTGTTTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (17 bp):
CTGGCCTGTTTAAAAGT
Found at i:332458 original size:5 final size:5
Alignment explanation
Indices: 332448--332500 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
332438 AACGGTCAAC
* *
332448 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
332497 GGTC
1 GGTC
332501 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:332463 original size:17 final size:17
Alignment explanation
Indices: 332441--332501 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
332431 AACGGTCAAC
332441 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
332458 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
332480 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
332497 GGTCA
1 GGTCA
332502 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:332468 original size:7 final size:7
Alignment explanation
Indices: 332414--332451 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
332404 GTCAAAGAAA
*
332414 GTCAATG
1 GTCAACG
332421 GTCAACG
1 GTCAACG
332428 GTCAACG
1 GTCAACG
332435 GTCAACG
1 GTCAACG
332442 GTCAACG
1 GTCAACG
332449 GTC
1 GTC
332452 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:332476 original size:22 final size:22
Alignment explanation
Indices: 332434--332500 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
332424 AACGGTCAAC
*
332434 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
332458 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
332480 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
332501 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:332515 original size:9 final size:9
Alignment explanation
Indices: 332497--332595 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
332487 GGTCGGGTCG
*
332497 GGTCAGACC
1 GGTCAAACC
332506 GGTCAAACC
1 GGTCAAACC
* *
332515 GATTCAGACC
1 G-GTCAAACC
332525 GGTCAAACC
1 GGTCAAACC
*
332534 GGTTCGAACC
1 GG-TCAAACC
*
332544 GGTTGAAACC
1 GG-TCAAACC
332554 GGTCAAACC
1 GGTCAAACC
332563 GGTCAGAACC
1 GGTCA-AACC
*
332573 GGTTGAAAACC
1 GG-T-CAAACC
*
332584 GGTTAAACC
1 GGTCAAACC
332593 GGT
1 GGT
332596 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:332554 original size:29 final size:31
Alignment explanation
Indices: 332522--332596 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
332512 ACCGATTCAG
332522 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
332551 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
332581 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
332597 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:332574 original size:19 final size:19
Alignment explanation
Indices: 332497--332595 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
332487 GGTCGGGTCG
332497 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
332515 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
332534 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
332554 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
332573 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
332593 GGT
1 GGT
332596 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.06
19 39 0.58
20 16 0.24
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:339763 original size:7 final size:7
Alignment explanation
Indices: 339747--339784 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
339737 GTCAAAGAAA
*
339747 GTCAATG
1 GTCAACG
339754 GTCAACG
1 GTCAACG
339761 GTCAACG
1 GTCAACG
339768 GTCAACG
1 GTCAACG
339775 GTCAACG
1 GTCAACG
339782 GTC
1 GTC
339785 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:339791 original size:5 final size:5
Alignment explanation
Indices: 339781--339838 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
339771 AACGGTCAAC
* *
339781 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
339830 GGTCG GGTC
1 GGTCG GGTC
339839 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:339802 original size:22 final size:22
Alignment explanation
Indices: 339774--339838 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
339764 AACGGTCAAC
339774 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
339796 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
339818 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
339839 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:339853 original size:9 final size:9
Alignment explanation
Indices: 339835--339933 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
339825 GGTCGGGTCG
*
339835 GGTCAGACC
1 GGTCAAACC
339844 GGTCAAACC
1 GGTCAAACC
* *
339853 GATTCAGACC
1 G-GTCAAACC
339863 GGTCAAACC
1 GGTCAAACC
*
339872 GGTTCGAACC
1 GG-TCAAACC
*
339882 GGTTGAAACC
1 GG-TCAAACC
339892 GGTCAAACC
1 GGTCAAACC
339901 GGTCAGAACC
1 GGTCA-AACC
*
339911 GGTTGAAAACC
1 GG-T-CAAACC
*
339922 GGTTAAACC
1 GGTCAAACC
339931 GGT
1 GGT
339934 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:339892 original size:29 final size:31
Alignment explanation
Indices: 339860--339934 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
339850 ACCGATTCAG
339860 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
339889 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
339919 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
339935 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:339912 original size:19 final size:19
Alignment explanation
Indices: 339835--339933 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
339825 GGTCGGGTCG
339835 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
339853 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
339872 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
339892 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
339911 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
339931 GGT
1 GGT
339934 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.06
19 39 0.58
20 16 0.24
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:341861 original size:14 final size:14
Alignment explanation
Indices: 341838--341880 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
341828 CTGTTCGAAC
*
341838 ATAAATGAACATAA
1 ATAAACGAACATAA
341852 ATAAACGAACATAA
1 ATAAACGAACATAA
*
341866 ATGAACGAACATAA
1 ATAAACGAACATAA
341880 A
1 A
341881 CGAACGTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.63, C:0.12, G:0.09, T:0.16
Consensus pattern (14 bp):
ATAAACGAACATAA
Found at i:341885 original size:14 final size:14
Alignment explanation
Indices: 341844--341901 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
341834 GAACATAAAT
**
341844 GAACATAAATAAAC
1 GAACATAAACGAAC
*
341858 GAACATAAATGAAC
1 GAACATAAACGAAC
341872 GAACATAAACGAAC
1 GAACATAAACGAAC
*
341886 GTAA-ATGAACGAAC
1 G-AACATAAACGAAC
341900 GA
1 GA
341902 GCCCTTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
13 1 0.03
14 37 0.93
15 2 0.05
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.12
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:341899 original size:24 final size:24
Alignment explanation
Indices: 341833--341899 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
341823 GCTCTCTGTT
*
341833 CGAACATAAATGAAC-ATAAATAAA
1 CGAACATAAATGAACGA-ACATAAA
341857 CGAACATAAATGAACGAACATAAA
1 CGAACATAAATGAACGAACATAAA
*
341881 CGAACGTAAATGAACGAAC
1 CGAACATAAATGAACGAAC
341900 GAGCCCTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
24 39 0.98
25 1 0.03
ACGTcount: A:0.57, C:0.16, G:0.13, T:0.13
Consensus pattern (24 bp):
CGAACATAAATGAACGAACATAAA
Found at i:341978 original size:43 final size:40
Alignment explanation
Indices: 341907--341986 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
341897 AACGAGCCCT
* * *
341907 TTGTTCGTGTTCGTTCATTTAATTAAACGAACGTAAAATC
1 TTGTTCATGTTCATTCATTTAATTAAACGAACATAAAATC
341947 TTGTTCATGTTCATTCATTTAATAAATAAACGAACATAAA
1 TTGTTCATGTTCATTCATTTAAT---TAAACGAACATAAA
341987 CTAACTTTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 21 0.62
43 13 0.38
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (40 bp):
TTGTTCATGTTCATTCATTTAATTAAACGAACATAAAATC
Found at i:344963 original size:22 final size:22
Alignment explanation
Indices: 344935--345016 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
344925 ATCAGCGCCT
** *
344935 GTGCAGCCCGCTTCCAACATTC
1 GTGCAGCCTACTTCCAGCATTC
*
344957 GTGCAGCCTACTTCTAGCATTC
1 GTGCAGCCTACTTCCAGCATTC
*
344979 GTGCAACCTACTTCCAGCATTC
1 GTGCAGCCTACTTCCAGCATTC
* *
345001 GTGCAACCTTCTTCCA
1 GTGCAGCCTACTTCCA
345017 CCATCCGTAG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.20, C:0.37, G:0.16, T:0.28
Consensus pattern (22 bp):
GTGCAGCCTACTTCCAGCATTC
Found at i:345291 original size:29 final size:28
Alignment explanation
Indices: 345257--345323 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
345247 GATATTTTAT
*
345257 TTTATAAAAAGTTT-TACACTTTATTATAA
1 TTTATAAAAAGTTTGTA-A-TTCATTATAA
*
345286 TTTATAAACAATTTTGTAATTCATTATAA
1 TTTATAAA-AAGTTTGTAATTCATTATAA
345315 TTTATAAAA
1 TTTATAAAA
345324 CCTTTTGTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 25 0.74
30 6 0.18
31 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (28 bp):
TTTATAAAAAGTTTGTAATTCATTATAA
Found at i:346218 original size:14 final size:15
Alignment explanation
Indices: 346188--346220 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
346178 TCAGTTAAAT
*
346188 AAAATTAAAGAATAA
1 AAAATTAAAGAAGAA
346203 AAAATTAAA-AAGAA
1 AAAATTAAAGAAGAA
346217 AAAA
1 AAAA
346221 ATAAGAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (15 bp):
AAAATTAAAGAAGAA
Found at i:346469 original size:26 final size:26
Alignment explanation
Indices: 346440--346490 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
346430 ATATCTCTGA
346440 TTTTTTAAAATTTAATAATAAAATTG
1 TTTTTTAAAATTTAATAATAAAATTG
346466 TTTTTTAAAATTTAATAATAAAATT
1 TTTTTTAAAATTTAATAATAAAATT
346491 AATATAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTTTTAAAATTTAATAATAAAATTG
Found at i:346494 original size:12 final size:13
Alignment explanation
Indices: 346445--346494 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
346435 TCTGATTTTT
346445 TAAAATTTAATAA
1 TAAAATTTAATAA
* **
346458 TAAAATTGT-TTTT
1 TAAAATT-TAATAA
346471 TAAAATTTAATAA
1 TAAAATTTAATAA
346484 TAAAA-TTAATA
1 TAAAATTTAATA
346495 TAACCATGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
12 7 0.24
13 21 0.72
14 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
TAAAATTTAATAA
Found at i:356228 original size:18 final size:19
Alignment explanation
Indices: 356195--356232 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
356185 AAATATGTTG
356195 AATGGAATCAACGAATAGA
1 AATGGAATCAACGAATAGA
356214 AATGGAATC-ACGAATAGA
1 AATGGAATCAACGAATAGA
356232 A
1 A
356233 GGGGGGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (19 bp):
AATGGAATCAACGAATAGA
Found at i:356993 original size:2 final size:2
Alignment explanation
Indices: 356986--357030 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
356976 GGAAAAGATC
356986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
357028 TA T
1 TA T
357031 GATTTCAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.