Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017737.1 Corchorus olitorius cultivar O-4 contig17770, 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: 67458
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7769 original size:45 final size:45
Alignment explanation
Indices: 7720--7825 Score: 149
Period size: 45 Copynumber: 2.4 Consensus size: 45
7710 AGCTTCATCT
* *
7720 ATCATCTCTCTCTTCTCCATCATCTATTTCATCTAGATCTAGCTC
1 ATCATCTCTCTCTTCTACAGCATCTATTTCATCTAGATCTAGCTC
* * * *
7765 ATCATCTCTTTCTTCTACAGCATCTATTTCTTCTGGATCTTGCTC
1 ATCATCTCTCTCTTCTACAGCATCTATTTCATCTAGATCTAGCTC
*
7810 ATCATCTTTCTCTTCT
1 ATCATCTCTCTCTTCT
7826 GTCAAATCTG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.17, C:0.31, G:0.06, T:0.46
Consensus pattern (45 bp):
ATCATCTCTCTCTTCTACAGCATCTATTTCATCTAGATCTAGCTC
Found at i:8781 original size:40 final size:40
Alignment explanation
Indices: 8683--8996 Score: 251
Period size: 40 Copynumber: 7.8 Consensus size: 40
8673 AGAAATGTAG
* * * *
8683 ACAACACCTTCCAATTAGGAAGGGCAAACTGGTGAACTTAA
1 ACAACACCTTTCGATGAGGAAGGGCAAACTGGTAAACTT-A
*
8724 ACAACACCTTTCGATGAGGAAGGGCAAACTGGTAAACATA
1 ACAACACCTTTCGATGAGGAAGGGCAAACTGGTAAACTTA
* * * * **
8764 AAAACACATTTCGATGAGGAAAGACAAACCAGTAAACTTA
1 ACAACACCTTTCGATGAGGAAGGGCAAACTGGTAAACTTA
* * * *
8804 ACAACACCTTCCGATCAGGAATGGCAAACTCGG-AATAC-TG
1 ACAACACCTTTCGATGAGGAAGGGCAAACT-GGTAA-ACTTA
* * * * *
8844 ACAACACCTTCCGCTGAGGAATGGCAGACTAGTAAACTTA
1 ACAACACCTTTCGATGAGGAAGGGCAAACTGGTAAACTTA
* *
8884 ACAACA-CTTTCCGATGAGGAAGGGCAAACTGTTAAACTTTG
1 ACAACACCTTT-CGATGAGGAAGGGCAAACTGGTAAAC-TTA
* * * * * *
8925 ACAACAGCTTCCGCTGAGGAAGGGCAGATTAGG-AATAC-TG
1 ACAACACCTTTCGATGAGGAAGGGCAAACT-GGTAA-ACTTA
* * *
8965 ACAACACATTCCGATGAGGAGGGGCAAACTGG
1 ACAACACCTTTCGATGAGGAAGGGCAAACTGG
8997 GAAAAGTAGA
Statistics
Matches: 220, Mismatches: 44, Indels: 20
0.77 0.15 0.07
Matches are distributed among these distances:
39 8 0.04
40 143 0.65
41 63 0.29
42 6 0.03
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (40 bp):
ACAACACCTTTCGATGAGGAAGGGCAAACTGGTAAACTTA
Found at i:8890 original size:120 final size:121
Alignment explanation
Indices: 8683--8994 Score: 328
Period size: 121 Copynumber: 2.6 Consensus size: 121
8673 AGAAATGTAG
* * * * *
8683 ACAACACCTTCCAATTAGGAAGGGCAAACT-GGTGA-ACTTAAACAACACCTTTCGATGAGGAAG
1 ACAACACCTTCCGATCAGGAAGGGCAAACTAGG-AATAC-T-GACAACACCTTCCGATGAGGAAG
*
8746 GGCAAACTGGTAAACATAAAAACACATTT-CGATGAGGAAAGACAAACCAG-TAAAC-TTA
63 GGCAAACTAGTAAACATAAAAACAC-TTTCCGATGAGGAAAGACAAA-CAGTTAAACTTTA
* * * *
8804 ACAACACCTTCCGATCAGGAATGGCAAACTCGGAATACTGACAACACCTTCCGCTGAGGAATGGC
1 ACAACACCTTCCGATCAGGAAGGGCAAACTAGGAATACTGACAACACCTTCCGATGAGGAAGGGC
* * * * * * *
8869 AGACTAGTAAACTTAACAACACTTTCCGATGAGGAAGGGCAAACTGTTAAACTTTG
66 AAACTAGTAAACATAAAAACACTTTCCGATGAGGAAAGACAAACAGTTAAACTTTA
* * * * * * *
8925 ACAACAGCTTCCGCTGAGGAAGGGCAGATTAGGAATACTGACAACACATTCCGATGAGGAGGGGC
1 ACAACACCTTCCGATCAGGAAGGGCAAACTAGGAATACTGACAACACCTTCCGATGAGGAAGGGC
8990 AAACT
66 AAACT
8995 GGGAAAAGTA
Statistics
Matches: 158, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
119 5 0.03
120 60 0.38
121 89 0.56
122 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (121 bp):
ACAACACCTTCCGATCAGGAAGGGCAAACTAGGAATACTGACAACACCTTCCGATGAGGAAGGGC
AAACTAGTAAACATAAAAACACTTTCCGATGAGGAAAGACAAACAGTTAAACTTTA
Found at i:9009 original size:81 final size:80
Alignment explanation
Indices: 8664--9010 Score: 270
Period size: 81 Copynumber: 4.3 Consensus size: 80
8654 GATAAAGGCC
* ** ** * * *
8664 GGCAAACTGAGAAATGTAGACAACACCTTCCAATTAGGAAGGGCAAACT-GGTGAACTTAAACAA
1 GGCAAACTGGGAAAACT-GACAACACCTTCCGCTGAGGAAGGGCAGACTAGG-AAACTT-AACAA
* *
8728 CACCTTTCGATGAGGAAG
63 CACATTCCGATGAGGAAG
* * * * * * * * * * *
8746 GGCAAACT-GGTAAACATAAAAACACATTTCGATGAGGAAAGACAAACCAGTAAACTTAACAACA
1 GGCAAACTGGGAAAAC-TGACAACACCTTCCGCTGAGGAAGGGCAGACTAGGAAACTTAACAACA
* * *
8810 CCTTCCGATCAGGAAT
65 CATTCCGATGAGGAAG
* * * *
8826 GGCAAACTCGGAATACTGACAACACCTTCCGCTGAGGAATGGCAGACTAGTAAACTTAACAACAC
1 GGCAAACTGGGAAAACTGACAACACCTTCCGCTGAGGAAGGGCAGACTAGGAAACTTAACAACAC
*
8891 TTTCCGATGAGGAAG
66 ATTCCGATGAGGAAG
** * * *
8906 GGCAAACT-GTTAAACTTTGACAACAGCTTCCGCTGAGGAAGGGCAGATTAGGAATAC-TGACAA
1 GGCAAACTGGGAAAAC--TGACAACACCTTCCGCTGAGGAAGGGCAGACTAGGAA-ACTTAACAA
*
8969 CACATTCCGATGAGGAGG
63 CACATTCCGATGAGGAAG
*
8987 GGCAAACTGGGAAAAGTAGACAAC
1 GGCAAACTGGGAAAACT-GACAAC
9011 CGGGACCTTC
Statistics
Matches: 212, Mismatches: 45, Indels: 17
0.77 0.16 0.06
Matches are distributed among these distances:
79 4 0.02
80 89 0.42
81 103 0.49
82 16 0.08
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.18
Consensus pattern (80 bp):
GGCAAACTGGGAAAACTGACAACACCTTCCGCTGAGGAAGGGCAGACTAGGAAACTTAACAACAC
ATTCCGATGAGGAAG
Found at i:9068 original size:46 final size:46
Alignment explanation
Indices: 9013--9840 Score: 753
Period size: 46 Copynumber: 17.7 Consensus size: 46
9003 TAGACAACCG
* *
9013 GGACCTTCCAACCAGGAAGGGACATTTTTGGAATAAAAGAAAATGA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATCA
* *
9059 GGACCTTCCAACCAAGAAGGGGCATTTTTGGAAATAGAAGAAAA-CA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGG-AATAAAAGAAAATCA
* *
9105 TGGACCTTCCAACTA-GAAGGGGCGTTTTTGGAATAAAAGAAAA-CA
1 -GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATCA
*
9150 GGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATAGAAGAAAAT-A
1 -GGACCTTCCAACCAGGAAGGGGCATTTTTGG-AATAAAAGAAAATCA
* * * * *
9197 GGGATCATCCAACTAGGAA-GGGCATTTTTGGAACAAAAGAAAA-CGG
1 -GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATC-A
* *
9243 GGACCTTCCAACCAGGAAGGAGCATTTTTGGAATAAAAGAAAATTA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATCA
* * *
9289 GGACCTTCCAACCAGGAAGGGGCGTTTTTAGAA-AGAGATATTGAAAA-CTG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATA-A-A-A--GAAAATC-A
* * *
9339 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAGAAGAAAA-CA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATCA
* * * * * *
9384 GGAACCTTCCAATCGGGATGGGGCAATTTTGTAAATAGAAGAAAA-CA
1 GG-ACCTTCCAACCAGGAAGGGGCATTTTTG-GAATAAAAGAAAATCA
**
9431 GGGACCTTCCAACCAGGAAGGGGCATTTTTGGAA-AGAGATATTGAAAATTG
1 -GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATA-A-A-A--GAAAATCA
* * *
9482 GGACCTTCCGACTAGGAAGGGGCATTTTTGGAATAAACGAAAAT-A
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATCA
* *
9527 GGGACCTTCCAACTAGGAAGGGGCATTTTTGGTATAAAAGAAAA-CA
1 -GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATCA
* *
9573 GGGACCTTCCAACCAGGAAGGGGCATTTTTGGAACAAAA-AAAAACA
1 -GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATCA
* * ** * *
9619 GGGACCTTCCATCTAGGAAGGGGCATTTTTTAAACAAAAGAAAAT-G
1 -GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATCA
*
9665 GGACCTTCCAACCAGGAAGAGGCATTTTTGGAATAAAAGAAAA-CGA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATC-A
* * * *
9711 GGACCTTCCAACTAGGAAGGGGCATTTTTGGAA-AGAGATGTTGAAGA-CTG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATA-A-A---AGAAAATC-A
* * *
9761 GGACCCTCCGAA-CAGGAAGGGGCATCTTTGGGGAATAGAAGAAAA-CA
1 GGACCTTCC-AACCAGGAAGGGGCAT-TTT-TGGAATAAAAGAAAATCA
*
9808 GGGACCTTCCAACCAGGAA-GGGCATTTTAGGAA
1 -GGACCTTCCAACCAGGAAGGGGCATTTTTGGAA
9841 AGAGATAAGA
Statistics
Matches: 653, Mismatches: 86, Indels: 87
0.79 0.10 0.11
Matches are distributed among these distances:
45 101 0.15
46 312 0.48
47 105 0.16
48 24 0.04
49 2 0.00
50 96 0.15
51 8 0.01
52 4 0.01
53 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (46 bp):
GGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAGAAAATCA
Found at i:15592 original size:438 final size:437
Alignment explanation
Indices: 14880--15913 Score: 1179
Period size: 438 Copynumber: 2.3 Consensus size: 437
14870 CAATCGAAAT
* * * ** * *
14880 CACAAAATTTCAAAAGTATTTTTCAGAATTTAAACATGAAAATTAGCTTTTGAGTCTTTCATGAA
1 CACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATAAAAATTAGCTTTTGAGTCCTTCATG-A
* * * * * *
14945 AGAGTTGTAGATTATAAAATTACTTTTTAATAGACACTTGAATTACCTTAATTGGAGAAATAGAA
65 A-AGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATTAACTTAATCGGACAAATAGAA
* * *
15010 CAAAGAAAATAAAAAATGAAGCGTTAAATCGAGTAAGATAGAATTTGTAAAGAACTAAGTAGCAT
129 CAAAGAATA-AAAAAATAAATCGTTAAATCGAGTAAGATAGAATTTGTAAAGAACTAAGTAG---
* ** * *
15075 AAAATATATAAAATAGAAAAGTATGAGGGTCATTTGGTAACTAATTCAAATAAGAAATTATTTCT
190 -----ATATAAAATAGAAAAATATGAGGGTCATTTAATAAATAATTCAAATAAGAAAATATTTCT
* * *
15140 TAATGGATATCTTGAAACATAAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGCTCAAA-T
250 TAATGGAGATCTTGAAACAT-AAAAACTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATT
* * * * * * *
15204 TAACTTTTGGGTTATTCATGAAAGTCGTAGATCATATAGTAACCTTTTAACCGACACTT-GAATA
314 TAACTTTCGGGTCATTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAAATA
* * * * *
15268 ACTTTAATCGGACATGTGGATC-GAAAATTATATGGTATTAAATAGACCAACAATCGAAAC
379 ACTTCAATCGGACATGTGGA-CAAAAAATTATACGATATTAAATAGACCAACAAT-AAAAC
* * * * *
15328 GACCAAATTT-AGGAAGCATTTTTTTGAA-CTAAAACATAAAAATTTGCTTTTGAATCCTTCATG
1 CACAAAATTTCA-GAAGCATTTTTTAGAATC-AAAACATAAAAATTAGCTTTTGAGTCCTTCATG
* * *
15391 AAAGTTTTAGATCATGAAATCACCTTTTAATAGACACATGAATTAACTTAATCGGACAAATAGAA
64 AAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATTAACTTAATCGGACAAATAGAA
15456 CAAAGAATAAAAAAATAAATC-TTAAA-CGTTAGATGAAGATAGAATTTGTAAAGAACTAAGTAG
129 CAAAGAATAAAAAAATAAATCGTTAAATCG--AG-T-AAGATAGAATTTGTAAAGAACTAAGTAG
* * * *
15519 -TATAAAGTAGAAAAATATGAGGGTTATTTAATAAAT-ATTCCAAATAAGAAAATGTTTGTTAAT
190 ATATAAAATAGAAAAATATGAGGGTCATTTAATAAATAATT-CAAATAAGAAAATATTTCTTAAT
* * *
15582 GGAGATCTTGAAGCATAAAAACTCTCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAGCT
254 GGAGATCTTGAAACATAAAAACTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACT
* *
15647 TTCGGGTCCTTCAAGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAAATAACTTC
319 TTCGGGTCATTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAAATAACTTC
* * * **
15712 AATCGGATATGTGGACAAAAAATTATACGATATTACATTGACCGGCAATAAAAC
384 AATCGGACATGTGGACAAAAAATTATACGATATTAAATAGACCAACAATAAAAC
* * * * *
15766 CACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGTTTTTGAGTTCTCCATGAA
1 CACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAA
* * *
15831 AATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCATCTTAATCGGACAAATAGGAA-
66 AGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATTAACTTAATCGGACAAATA-GAAC
* * *
15895 AAAAAATACAAAAACAAAT
130 AAAGAATAAAAAAATAAAT
15914 GGGAACGCGT
Statistics
Matches: 497, Mismatches: 76, Indels: 36
0.82 0.12 0.06
Matches are distributed among these distances:
437 42 0.08
438 242 0.49
439 52 0.10
443 2 0.00
444 5 0.01
445 12 0.02
446 63 0.13
447 31 0.06
448 48 0.10
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (437 bp):
CACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAA
AGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATTAACTTAATCGGACAAATAGAACA
AAGAATAAAAAAATAAATCGTTAAATCGAGTAAGATAGAATTTGTAAAGAACTAAGTAGATATAA
AATAGAAAAATATGAGGGTCATTTAATAAATAATTCAAATAAGAAAATATTTCTTAATGGAGATC
TTGAAACATAAAAACTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAACTTTCGGGT
CATTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAAATAACTTCAATCGGA
CATGTGGACAAAAAATTATACGATATTAAATAGACCAACAATAAAAC
Found at i:18655 original size:28 final size:30
Alignment explanation
Indices: 18614--18685 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
18604 TTTGAAACGC
* * *
18614 AAGGGATTAATTTGT-TCAAAAA-AAATAT
1 AAGGGATTATTTTGTCCCAAAAAGAAACAT
18642 AAGGGATTATTTTGTCCCAAAAATGAAACAT
1 AAGGGATTATTTTGTCCCAAAAA-GAAACAT
*
18673 AAGGGATTTTTTT
1 AAGGGATTATTTT
18686 AGGTATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 14 0.38
29 6 0.16
31 17 0.46
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (30 bp):
AAGGGATTATTTTGTCCCAAAAAGAAACAT
Found at i:19079 original size:2 final size:2
Alignment explanation
Indices: 19072--19108 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19062 ATTGATCTAT
19072 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19109 GCATTGATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30110 original size:16 final size:16
Alignment explanation
Indices: 30085--30128 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
30075 TTATTACTTC
30085 TTTTCATTTTTCTGAT
1 TTTTCATTTTTCTGAT
30101 TTTTC-TTTTT-TGGAT
1 TTTTCATTTTTCT-GAT
*
30116 TTTTCCTTTTTCT
1 TTTTCATTTTTCT
30129 ATCTCTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 13 0.52
16 10 0.40
17 1 0.04
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTTCATTTTTCTGAT
Found at i:31462 original size:24 final size:24
Alignment explanation
Indices: 31419--31469 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
31409 CTTAGTCGAG
*
31419 CTTCTTCTTCTCCTTCGCTAGTTT
1 CTTCTTCTCCTCCTTCGCTAGTTT
*
31443 CTTCTTCCTCCTCCTT-GCTATTTT
1 CTTCTT-CTCCTCCTTCGCTAGTTT
31467 CTT
1 CTT
31470 GGAACCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.04, C:0.35, G:0.06, T:0.55
Consensus pattern (24 bp):
CTTCTTCTCCTCCTTCGCTAGTTT
Found at i:31931 original size:30 final size:30
Alignment explanation
Indices: 31892--32163 Score: 438
Period size: 30 Copynumber: 9.1 Consensus size: 30
31882 ATATGGACAT
* **
31892 GATTTAAATAAAGCAACGATTTTCAACCAG
1 GATTAAAATAAAGCAACGATCCTCAACCAG
* *
31922 GATTAAAATAAAGCAACAATCCTCAACCAA
1 GATTAAAATAAAGCAACGATCCTCAACCAG
**
31952 GATTAAAATAAAGCAACGATTTTCAACCAG
1 GATTAAAATAAAGCAACGATCCTCAACCAG
* *
31982 GATTAAAATAAAGCAACAATCCTCAACCAA
1 GATTAAAATAAAGCAACGATCCTCAACCAG
32012 GATTAAAATAAAGCAACGATCCTCAACCAG
1 GATTAAAATAAAGCAACGATCCTCAACCAG
*
32042 GATTAATATAAAGCAACGATCCTCAACCAG
1 GATTAAAATAAAGCAACGATCCTCAACCAG
32072 GATTAAAATAAAGCAACGATCCTCAACCAG
1 GATTAAAATAAAGCAACGATCCTCAACCAG
32102 GATTAAAATAAAGCAACGATCCTCAA-CAG
1 GATTAAAATAAAGCAACGATCCTCAACCAG
*
32131 GATTAAAATAAAGCAATGATCCTCAACCAG
1 GATTAAAATAAAGCAACGATCCTCAACCAG
32161 GAT
1 GAT
32164 CGAAATTAAC
Statistics
Matches: 223, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
29 28 0.13
30 195 0.87
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.19
Consensus pattern (30 bp):
GATTAAAATAAAGCAACGATCCTCAACCAG
Found at i:32505 original size:168 final size:169
Alignment explanation
Indices: 32209--32825 Score: 808
Period size: 168 Copynumber: 3.7 Consensus size: 169
32199 AAAAAATGAG
** * * * * * * *
32209 GTGCCCGGAGGTTTTTATCAATGCAAACTTTAAATTGAAACCTTAATC-AAGAATTTTAAACCTA
1 GTGCCCGGAGG-ACTTACCAATGCAAACCTTGAATTGAGACCTTGACCAAAG-ATTTTAAACTTA
* *
32273 AACATGAATCTTTGATG-AAAACTTGATAAAATGAAATGATACCCGGAGGCTTTACCAATTGCCC
64 AACATGAATCTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTACCAATTGCCC
* *
32337 GGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTT
129 GGAGGACTTATCAGAATTACTACCCGGAGGTTTCTGAATTT
32378 GTGCCCGGAGGACTTACCAATGCAAACCTTGAATTGAGACCTTAGA-CAAAGATTTTAAACTTAA
1 GTGCCCGGAGGACTTACCAATGCAAACCTTGAATTGAGACCTT-GACCAAAGATTTTAAACTTAA
* *
32442 ACATGAAT-TTTGATGAAAACCTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCG
65 ACATGAATCTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTACCAATTGCCCG
* *
32506 GAGGACTTATCAAAATTACTACCCGGAGGTTTCCGAATTT
130 GAGGACTTATCAGAATTACTACCCGGAGGTTTCTGAATTT
* * * * *
32546 GTGCCCGGAGGACTTACCAGTGCAAACTTTGAAATGAGACATTGAACAAAGATTTTAAACTTAAA
1 GTGCCCGGAGGACTTACCAATGCAAACCTTGAATTGAGACCTTGACCAAAGATTTTAAACTTAAA
* * *
32611 CATGAATCTTTGATGAAAAACGTGATGAAATGAAATGGTACTCGGAGG--TT-----TTGCCCGG
66 CATGAATCTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTACCAATTGCCCGG
*
32669 AGGACTTAACAGAATTACTACCCGGAGGTTTCTGAATTT
131 AGGACTTATCAGAATTACTACCCGGAGGTTTCTGAATTT
** * *
32708 GTGCCCGGAGGACTTACCAATGTTAA-CTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTAA
1 GTGCCCGGAGGACTTACCAATGCAAACCT-TGAATTGAGACCTTGACCAAAGATTTTAAACTTAA
* * * *
32772 ATATGGATTTTTAATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTA
65 ACATGAATCTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTA
32826 TCAAATGGAA
Statistics
Matches: 397, Mismatches: 42, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
161 1 0.00
162 139 0.35
164 2 0.01
167 11 0.03
168 192 0.48
169 52 0.13
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (169 bp):
GTGCCCGGAGGACTTACCAATGCAAACCTTGAATTGAGACCTTGACCAAAGATTTTAAACTTAAA
CATGAATCTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTACCAATTGCCCGG
AGGACTTATCAGAATTACTACCCGGAGGTTTCTGAATTT
Found at i:33014 original size:70 final size:70
Alignment explanation
Indices: 32870--33047 Score: 304
Period size: 70 Copynumber: 2.6 Consensus size: 70
32860 GAAGTAAGGC
* *
32870 TTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAG-CATATATGGCTTGGATGGAACCAAGGC
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCAAATATGGCTTGGATGGAACCAAGGC
32934 TTAAA
66 TTAAA
* *
32939 CTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCAAATGTGGCTTGGATGGAACCAAGGC
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCAAATATGGCTTGGATGGAACCAAGGC
33004 TTAAA
66 TTAAA
*
33009 TTGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCC
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
33048 TAAAGCATTC
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
69 35 0.34
70 67 0.66
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (70 bp):
TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCAAATATGGCTTGGATGGAACCAAGGC
TTAAA
Found at i:34672 original size:20 final size:19
Alignment explanation
Indices: 34649--34722 Score: 96
Period size: 19 Copynumber: 3.7 Consensus size: 19
34639 TTTATTTTGA
34649 TTTGATTATTTTTTTTATTT
1 TTTGATT-TTTTTTTTATTT
*
34669 TTTGATTATTTTTTTATTT
1 TTTGATTTTTTTTTTATTT
34688 TTTGATTTTTGATTTTTGA-TT
1 TTTGATTTTT--TTTTT-ATTT
34709 TTTGATTTTTTTTT
1 TTTGATTTTTTTTT
34723 GTTTTTGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
19 24 0.49
20 7 0.14
21 17 0.35
22 1 0.02
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTGATTTTTTTTTTATTT
Found at i:34696 original size:14 final size:15
Alignment explanation
Indices: 34678--34719 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
34668 TTTTGATTAT
*
34678 TTTTTTATTTTTTGA
1 TTTTTGATTTTTTGA
34693 TTTTTGA-TTTTTGA
1 TTTTTGATTTTTTGA
34707 TTTTTGATTTTTT
1 TTTTTGATTTTTT
34720 TTTGTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.79
Consensus pattern (15 bp):
TTTTTGATTTTTTGA
Found at i:34728 original size:7 final size:7
Alignment explanation
Indices: 34686--34718 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
34676 ATTTTTTTAT
34686 TTTTTGA
1 TTTTTGA
34693 TTTTTGA
1 TTTTTGA
34700 TTTTTGA
1 TTTTTGA
34707 TTTTTGA
1 TTTTTGA
34714 TTTTT
1 TTTTT
34719 TTTTGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTTGA
Found at i:35130 original size:11 final size:12
Alignment explanation
Indices: 35114--35158 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
35104 TGCCTTTATT
35114 TTCA-TTTTTCA
1 TTCATTTTTTCA
35125 TTCATTTTTTTC-
1 TTCA-TTTTTTCA
*
35137 TTTATTTTTTCA
1 TTCATTTTTTCA
35149 TTCATTTTTT
1 TTCATTTTTT
35159 ATGGGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 11 0.38
12 12 0.41
13 6 0.21
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (12 bp):
TTCATTTTTTCA
Found at i:35143 original size:12 final size:13
Alignment explanation
Indices: 35118--35158 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
35108 TTTATTTTCA
35118 TTTTTCATTCATT
1 TTTTTCATTCATT
*
35131 TTTTTC-TTTA-T
1 TTTTTCATTCATT
35142 TTTTTCATTCATT
1 TTTTTCATTCATT
35155 TTTT
1 TTTT
35159 ATGGGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 7 0.29
12 6 0.25
13 11 0.46
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCATTCATT
Found at i:39253 original size:16 final size:16
Alignment explanation
Indices: 39228--39271 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
39218 TTATTACTTC
39228 TTTTCATTTTTCTGAT
1 TTTTCATTTTTCTGAT
39244 TTTTC-TTTTT-TGGAT
1 TTTTCATTTTTCT-GAT
*
39259 TTTTCCTTTTTCT
1 TTTTCATTTTTCT
39272 ATCTCTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 13 0.52
16 10 0.40
17 1 0.04
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTTCATTTTTCTGAT
Found at i:39306 original size:13 final size:14
Alignment explanation
Indices: 39283--39311 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39273 TCTCTAAATT
39283 AATGCATGAATGCA
1 AATGCATGAATGCA
39297 AATG-ATGAATGCA
1 AATGCATGAATGCA
39310 AA
1 AA
39312 GTCCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (14 bp):
AATGCATGAATGCA
Found at i:40626 original size:24 final size:24
Alignment explanation
Indices: 40583--40633 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
40573 TTTAGTCGAG
40583 CTTCTTCTTCTCCTTCGCTAGTTT
1 CTTCTTCTTCTCCTTCGCTAGTTT
* *
40607 CTTCTTCCTTCTGCTT-GCTATTTT
1 CTTCTT-CTTCTCCTTCGCTAGTTT
40631 CTT
1 CTT
40634 GGAACCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.04, C:0.31, G:0.08, T:0.57
Consensus pattern (24 bp):
CTTCTTCTTCTCCTTCGCTAGTTT
Found at i:52861 original size:64 final size:64
Alignment explanation
Indices: 52773--53448 Score: 991
Period size: 64 Copynumber: 10.6 Consensus size: 64
52763 TGCTAGAAAG
* * *
52773 AATTTTCAGAAGTTGATCGAAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCCCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * * *
52837 AGTTTTTAGAAGTTGATCAGAAGACGGTCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * ** *
52901 AGTTTTCAGAAGTTGATCGAAAGACGGCCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
*
52965 AATTTTCAGAAGTTGATCGGAAGACGATCTTATCAAGAAGTACACCAGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* *
53029 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * * *
53093 AATTTTCAGTAGTTGATCGGAAGATGATCTTGTCAAGAAGTACGCCAG-AGATGGTTCCTCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * *
53156 AGTTTTCAGTAGATGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * *
53220 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAAAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
*
53284 AATTTTCAGAAGTTGATCGGAACACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * *
53348 AATTTTCAGAACTTGATTGGAAGACGATCTTGT-TAGAAAGTACACCAGAAGATAGTTTCTCGAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAG-AAGTACACCAGAAGATGGTTTCTC-AA
53412 A
64 A
** *
53413 AGGTTTCAGAAGTTGATCGG-A-ACGATCTTGTTAAGA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
53449 GATGCACCGA
Statistics
Matches: 556, Mismatches: 52, Indels: 9
0.90 0.08 0.01
Matches are distributed among these distances:
63 70 0.13
64 467 0.84
65 19 0.03
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
Found at i:53353 original size:319 final size:320
Alignment explanation
Indices: 52773--53448 Score: 1065
Period size: 319 Copynumber: 2.1 Consensus size: 320
52763 TGCTAGAAAG
*
52773 AATTTTCAGAAGTTGATCGAAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCCCAAGA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCCCAAGA
* * * * *
52838 GTTTTTAGAAGTTGATCAGAAGACGGTCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAG
66 GTTTTCAGAAGATGATCAGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAA
* *
52903 TTTTCAGAAGTTGATCGAAAGACGGCCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACAAT
131 TTTTCAGAAGTTGATCGAAAGACGACCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAACAAT
*
52968 TTTCAGAAGTTGATCGGAAGACGATCTTATCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATT
196 TTTCAGAAGTTGATCGGAACACGATCTTATCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATT
* *
53033 TTCAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTC-AA
261 TTCAGAACTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATAGTTTCTCGAA
* * *
53092 CAATTTTCAGTAGTTGATCGGAAGATGATCTTGTCAAGAAGTACGCCAG-AGATGG-TTCCTCAA
1 -AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCC-CAA
* *
53155 GAGTTTTCAGTAGATGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
64 GAGTTTTCAGAAGATGATCAGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * *
53220 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAAAAGTACACCAGAAGATGGTTTCTCAACA
129 AATTTTCAGAAGTTGATCGAAAGACGACCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAACA
*
53285 ATTTTCAGAAGTTGATCGGAACACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAA
194 ATTTTCAGAAGTTGATCGGAACACGATCTTATCAAGAAGTACACCAGAAGATGGTTTCTCAAAAA
* * *
53350 TTTTCAGAACTTGATTGGAAGACGATCTTGTTAGAAAGTACACCAGAAGATAGTTTCTCGAA
259 TTTTCAGAACTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATAGTTTCTCGAA
* *
53412 AAGGTTTCAGAAGTTGATCGG-A-ACGATCTTGTTAAGA
1 AA-TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
53449 GATGCACCGA
Statistics
Matches: 326, Mismatches: 27, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
318 17 0.05
319 247 0.76
320 62 0.19
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (320 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCCCAAGA
GTTTTCAGAAGATGATCAGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAA
TTTTCAGAAGTTGATCGAAAGACGACCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAACAAT
TTTCAGAAGTTGATCGGAACACGATCTTATCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATT
TTCAGAACTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATAGTTTCTCGAA
Found at i:63794 original size:31 final size:31
Alignment explanation
Indices: 63757--63815 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
63747 TCCAAACCCA
63757 GATATCGGCCCAGATCCACCGCACCTCCATC
1 GATATCGGCCCAGATCCACCGCACCTCCATC
63788 GATATCGGCCCAGATCCACCGCACCTCC
1 GATATCGGCCCAGATCCACCGCACCTCC
63816 GTCGTTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.22, C:0.46, G:0.17, T:0.15
Consensus pattern (31 bp):
GATATCGGCCCAGATCCACCGCACCTCCATC
Found at i:66956 original size:46 final size:46
Alignment explanation
Indices: 66906--67458 Score: 419
Period size: 46 Copynumber: 12.2 Consensus size: 46
66896 CTTTTATACA
* *
66906 AAAAATGCCCATTCCCGGTCGGAAGGTTCCAGTTTGCTTTCTTTCC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTCCAGTTTTCTTTCTTTCC
* * *
66952 AAAAAGGACCCTTCCCAGTCGGAAGG-TCACAGTTTTCTTTCTTTCC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTC-CAGTTTTCTTTCTTTCC
** * * * * *
66998 AAAAATGCCCCTTCTTGGTTGAAAGG-TCC-CTGTT-TTTATTTCC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTCCAGTTTTCTTTCTTTCC
* * * * * * *
67041 AAAAATGCCCTTTCCTGCTTGGAAGGTCCCCGTTTTC---ATTTCC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTCCAGTTTTCTTTCTTTCC
* * * * *
67084 AAAAATGCCCCTTCCTGGTTGGAA-GTCCCTA-TTTTCATTT-ATACC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTCC-AGTTTTC-TTTCTTTCC
67129 AAAAATGCCCCTTCCCGGTCGGAAGG-TCCTAGTTTTCTTTCTTTCC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTCC-AGTTTTCTTTCTTTCC
67175 AAAAA-GCCCCTTTCCCGGTCGGAAGG-TCACAGTTTTCTTTCTTTCC
1 AAAAATGCCCC-TTCCCGGTCGGAAGGTTC-CAGTTTTCTTTCTTTCC
* * * * * * *
67221 AAAAATACCCCTTCCTGGTTGGAAGCTCCCTGTTTTC---ATTTCC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTCCAGTTTTCTTTCTTTCC
* * * * * *
67264 AAAATTGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTC---ATTTCC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTCCAGTTTTCTTTCTTTCC
* * *
67307 AAAAATGCCCCTTCCCAGTCGGAAGG-TCACAGTTTTATCTCTTTCC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTC-CAGTTTTCTTTCTTTCC
* * *
67353 AAAAACGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCAATATCTCTTTCC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTCCAGTTTTC--T-T-TCTTTCC
* * * * *
67403 AAAAAGGTCCCTTCCCGGTCGGAAGG-ACACAGTTTTATCTCTTTCC
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTC-CAGTTTTCTTTCTTTCC
67449 AAAAATGCCC
1 AAAAATGCCC
Statistics
Matches: 416, Mismatches: 65, Indels: 52
0.78 0.12 0.10
Matches are distributed among these distances:
42 11 0.03
43 130 0.31
44 5 0.01
45 43 0.10
46 180 0.43
47 7 0.02
48 2 0.00
49 1 0.00
50 37 0.09
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.33
Consensus pattern (46 bp):
AAAAATGCCCCTTCCCGGTCGGAAGGTTCCAGTTTTCTTTCTTTCC
Found at i:67067 original size:43 final size:43
Alignment explanation
Indices: 66989--67390 Score: 398
Period size: 43 Copynumber: 9.1 Consensus size: 43
66979 CACAGTTTTC
* *
66989 TTTC-TTTCCAAAAATGCCCCTTCTTGGTTGAAAGGTCCCTGT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGT
* * * *
67031 TTTTATTTCCAAAAATGCCCTTTCCTGCTTGGAAGGTCCCCGT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGT
*
67074 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAA-GTCCCTAT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGT
* *
67116 TTTCATTTATACCAAAAATGCCCCTTCCCGGTCGGAAGGT-CCTAGT
1 TTTCA-TT-T-CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCT-GT
* * * * *
67162 TTTCTTTCTTTCCAAAAA-GCCCCTTTCCCGGTCGGAAGGTCACAGT
1 TTTC---ATTTCCAAAAATGCCCC-TTCCTGGTTGGAAGGTCCCTGT
* * *
67208 TTTCTTTCTTTCCAAAAATACCCCTTCCTGGTTGGAAGCTCCCTGT
1 TTTC---ATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGT
* *
67254 TTTCATTTCCAAAATTGCCCCTTCCTGGTTGGAAGGTCCCCGT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGT
** * * *
67297 TTTCATTTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCACAGTT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG-T
* * * *
67341 TTATCTCTTTCCAAAAACGCCCCTTCCTGGTCGGAAGGTCCCAGT
1 TT-TC-ATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGT
67386 TTTCA
1 TTTCA
67391 ATATCTCTTT
Statistics
Matches: 305, Mismatches: 40, Indels: 29
0.82 0.11 0.08
Matches are distributed among these distances:
42 14 0.05
43 136 0.45
44 6 0.02
45 37 0.12
46 104 0.34
47 6 0.02
48 2 0.01
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.34
Consensus pattern (43 bp):
TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGT
Found at i:67288 original size:223 final size:223
Alignment explanation
Indices: 66874--67454 Score: 803
Period size: 223 Copynumber: 2.6 Consensus size: 223
66864 GTTTTGGTTT
* * *
66874 CTGGTTGGAAGGTCCCTATTTTCTTTTATACAAAAAATGCCCATTCCCGGTCGGAAGGTTCCAGT
1 CTGGTTGGAAGGTCCCTATTTTCATTTATACCAAAAATGCCCCTTCCCGGTCGGAAGG-TCCAGT
* *
66939 TTGCTTTCTTTCCAAAAAGGACCCTTCCCAGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAAT
65 TTTCTTTCTTTCCAAAAAGGACCCTTCCCGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAAT
* * * * *
67004 GCCCCTTCTTGGTTGAAAGGTCCCTGTTTTTATTTCCAAAAATGCCCTTTCCTGCTTGGAAGGTC
130 ACCCCTTCCTGGTTGAAAGCTCCCTGTTTTCATTTCCAAAAATGCCCCTTCCTGCTTGGAAGGTC
67069 CCCGTTTTCATTTCCAAAAATGCCCCTTC
195 CCCGTTTTCATTTCCAAAAATGCCCCTTC
67098 CTGGTTGGAA-GTCCCTATTTTCATTTATACCAAAAATGCCCCTTCCCGGTCGGAAGGTCCTAGT
1 CTGGTTGGAAGGTCCCTATTTTCATTTATACCAAAAATGCCCCTTCCCGGTCGGAAGGTCC-AGT
*
67162 TTTCTTTCTTTCCAAAAA-GCCCCTTTCCCGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAA
65 TTTCTTTCTTTCCAAAAAGGACCC-TTCCCGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAA
* * *
67226 TACCCCTTCCTGGTTGGAAGCTCCCTGTTTTCATTTCCAAAATTGCCCCTTCCTGGTTGGAAGGT
129 TACCCCTTCCTGGTTGAAAGCTCCCTGTTTTCATTTCCAAAAATGCCCCTTCCTGCTTGGAAGGT
67291 CCCCGTTTTCATTTCCAAAAATGCCCCTTC
194 CCCCGTTTTCATTTCCAAAAATGCCCCTTC
** * * * * *
67321 CCAGTCGGAAGGTCAC-AGTTTT-ATCTCT-TTCCAAAAACGCCCCTTCCTGGTCGGAAGGTCCC
1 CTGGTTGGAAGGTCCCTA-TTTTCAT-T-TATACCAAAAATGCCCCTTCCCGGTCGGAAGGT-CC
* * * *
67383 AGTTTTCAATATCTCTTTCCAAAAAGGTCCCTTCCCGGTCGGAAGGACACAGTTTTATCTCTTTC
62 AGTTTTC--T-T-TCTTTCCAAAAAGGACCCTTCCCGGTCGGAAGGTCACAGTTTTCTTTCTTTC
67448 CAAAAAT
123 CAAAAAT
67455 GCCC
Statistics
Matches: 320, Mismatches: 25, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
222 7 0.02
223 200 0.62
224 54 0.17
225 3 0.01
226 1 0.00
227 1 0.00
228 50 0.16
229 4 0.01
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.34
Consensus pattern (223 bp):
CTGGTTGGAAGGTCCCTATTTTCATTTATACCAAAAATGCCCCTTCCCGGTCGGAAGGTCCAGTT
TTCTTTCTTTCCAAAAAGGACCCTTCCCGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAATA
CCCCTTCCTGGTTGAAAGCTCCCTGTTTTCATTTCCAAAAATGCCCCTTCCTGCTTGGAAGGTCC
CCGTTTTCATTTCCAAAAATGCCCCTTC
Done.