Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006833.1 Corchorus capsularis cultivar CVL-1 contig06854, 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: 78336
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3318 original size:36 final size:35
Alignment explanation
Indices: 3278--3385 Score: 102
Period size: 36 Copynumber: 3.1 Consensus size: 35
3268 GAGAAAGGAG
*
3278 TAATTCAGTGTAATTAAGTGAGGTCAATAAAAG-GCT
1 TAATTCAG-GTAATTAAGTGA-GTCAATAAAAGAACT
3314 TAATTCAGGGTAATTAAGT-AG--AAT-AAAGAACT
1 TAATTCA-GGTAATTAAGTGAGTCAATAAAAGAACT
* *
3346 TAATTCAAGGTAATTAAGTGAAATCAAT-AAAGAATT
1 TAATTC-AGGTAATTAAGTG-AGTCAATAAAAGAACT
3382 TAAT
1 TAAT
3386 CTAAAAAAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
31 4 0.06
32 22 0.35
33 1 0.02
34 2 0.03
35 1 0.02
36 31 0.50
37 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (35 bp):
TAATTCAGGTAATTAAGTGAGTCAATAAAAGAACT
Found at i:3772 original size:19 final size:20
Alignment explanation
Indices: 3745--3789 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3735 CATAGACTCG
*
3745 GGTTAAGCA-GACCTTATTA
1 GGTTAAGCATGACCTAATTA
* *
3764 GGTTTAGCATTACCTAATTA
1 GGTTAAGCATGACCTAATTA
3784 GGTTAA
1 GGTTAA
3790 TATTAGACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (20 bp):
GGTTAAGCATGACCTAATTA
Found at i:10666 original size:20 final size:22
Alignment explanation
Indices: 10630--10673 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
10620 ATTAAAATGA
10630 AAAAGAAGAAGAAAACGAAAAC
1 AAAAGAAGAAGAAAACGAAAAC
*
10652 AAAAG-AGAA-AAAACGAACAC
1 AAAAGAAGAAGAAAACGAAAAC
10672 AA
1 AA
10674 CACAAGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 4 0.19
22 5 0.24
ACGTcount: A:0.73, C:0.11, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAAGAAGAAGAAAACGAAAAC
Found at i:11877 original size:2 final size:2
Alignment explanation
Indices: 11865--11897 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
11855 GACCACAGAA
11865 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11898 CCCTAGCTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12674 original size:21 final size:21
Alignment explanation
Indices: 12648--12687 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
12638 GGCCAGCAAT
12648 TAAACAAACACAAAATCAAAA
1 TAAACAAACACAAAATCAAAA
12669 TAAACAAACACAAAATCAA
1 TAAACAAACACAAAATCAA
12688 CAGATCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.20, G:0.00, T:0.10
Consensus pattern (21 bp):
TAAACAAACACAAAATCAAAA
Found at i:13845 original size:15 final size:16
Alignment explanation
Indices: 13825--13854 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13815 AAGGAGGAGG
13825 AGGAAAA-AAAAGAAA
1 AGGAAAAGAAAAGAAA
13840 AGGAAAAGAAAAGAA
1 AGGAAAAGAAAAGAA
13855 GAAAAGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGGAAAAGAAAAGAAA
Found at i:13851 original size:19 final size:19
Alignment explanation
Indices: 13829--13894 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
13819 AGGAGGAGGA
13829 AAAAAAAGAAAAGGAAAAG
1 AAAAAAAGAAAAGGAAAAG
* **
13848 AAAAGAAGAAAA-GAGAGGG
1 AAAAAAAGAAAAGGA-AAAG
*
13867 AAAAAAAGAAAAATGAAAAAG
1 AAAAAAAG-AAAA-GGAAAAG
13888 AAAAAAA
1 AAAAAAA
13895 AAGCCACGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.06
19 20 0.56
20 4 0.11
21 9 0.25
22 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (19 bp):
AAAAAAAGAAAAGGAAAAG
Found at i:16538 original size:1 final size:1
Alignment explanation
Indices: 16532--16566 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
16522 TGAAATAGAT
16532 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16567 GCTACTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17211 original size:38 final size:38
Alignment explanation
Indices: 17148--17244 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 38
17138 AATTTGCCTT
*
17148 TTTGTTTCCAACGTCCTATTTAATTTGG-TCTTTTATC
1 TTTGTTTCCAAAGTCCTATTTAATTTGGTTCTTTTATC
* * *
17185 TTTGTTTCCAATAGTTCTATTTAATTTGGTTTTTTTGTC
1 TTTGTTTCCAA-AGTCCTATTTAATTTGGTTCTTTTATC
* * *
17224 TTTGTTTTCAACGTCTTATTT
1 TTTGTTTCCAAAGTCCTATTT
17245 GGGTTTAGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 11 0.22
38 22 0.44
39 17 0.34
ACGTcount: A:0.15, C:0.14, G:0.11, T:0.59
Consensus pattern (38 bp):
TTTGTTTCCAAAGTCCTATTTAATTTGGTTCTTTTATC
Found at i:17618 original size:22 final size:22
Alignment explanation
Indices: 17590--17717 Score: 100
Period size: 22 Copynumber: 5.7 Consensus size: 22
17580 TGTCTATATG
17590 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
17612 TGGTTATTATAATTTCATGAGA
1 TGGTTATCAAAATTTCATAAGA
* *
17634 AGGTTATCAAAATTCCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
* *
17654 TGTAGTTACCAAAATTTCATATGGA
1 TG--GTTATCAAAATTTCATA-AGA
* *
17679 -AGTTATCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
*
17700 TCAGGTTATTAAAATTTC
1 T--GGTTATCAAAATTTC
17718 TTAGGTTGGT
Statistics
Matches: 83, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
20 1 0.01
21 5 0.06
22 63 0.76
24 14 0.17
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:17731 original size:22 final size:22
Alignment explanation
Indices: 17680--17751 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
17670 TCATATGGAA
* * *
17680 GTTATCAAAATTTCATAGGATCAG
1 GTTATTAAAATTTCTTAGG-T-TG
17704 GTTATTAAAATTTCTTAGGTTG
1 GTTATTAAAATTTCTTAGGTTG
*
17726 GTTATTGAAATTT-TATAGGTTG
1 GTTATTAAAATTTCT-TAGGTTG
17748 GTTA
1 GTTA
17752 ATTATCACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.02
22 24 0.56
23 1 0.02
24 17 0.40
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (22 bp):
GTTATTAAAATTTCTTAGGTTG
Found at i:17921 original size:22 final size:21
Alignment explanation
Indices: 17787--17925 Score: 81
Period size: 22 Copynumber: 6.4 Consensus size: 21
17777 ATCAAATTGA
* * *
17787 TTATCAAAATGTCATAGCGAGA
1 TTATCAAAATTTCATA-TGAGG
17809 TTAT-AAGAATTTCATA-GTATGG
1 TTATCAA-AATTTCATATG-A-GG
*
17831 TTAACAAAATTTCATTATGAGG
1 TTATCAAAATTTCA-TATGAGG
* **
17853 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-ATGAGG
* *
17875 TTATC-AAATTTTATAGTGTGG
1 TTATCAAAATTTCATA-TGAGG
17896 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATG-AGG
17918 TTAT-AAAA
1 TTATCAAAA
17926 GTCTCAATTT
Statistics
Matches: 92, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
20 1 0.01
21 26 0.28
22 58 0.63
23 6 0.07
24 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATATGAGG
Found at i:18012 original size:25 final size:23
Alignment explanation
Indices: 17984--18029 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
17974 CTTATACAGT
*
17984 GATTATCGAAATTTCATAGAGATCA
1 GATTATCAAAATTT-ATA-AGATCA
18009 GATTATCAAAATTTATAAGAT
1 GATTATCAAAATTTATAAGAT
18030 TATCAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
25 13 0.65
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (23 bp):
GATTATCAAAATTTATAAGATCA
Found at i:18054 original size:22 final size:22
Alignment explanation
Indices: 17982--18111 Score: 88
Period size: 22 Copynumber: 6.0 Consensus size: 22
17972 ATCTTATACA
* *
17982 GTGATTATCGAAATTTCATAGA
1 GTGATTATCAAAATTTCATAGT
18004 GATCAGATTATCAAAATTT-ATA--
1 G-T--GATTATCAAAATTTCATAGT
*
18026 -AGATTATCAAAATTTCATAGT
1 GTGATTATCAAAATTTCATAGT
* * * *
18047 GTTATTATCAAAATTCCAAAGC
1 GTGATTATCAAAATTTCATAGT
* * * *
18069 GAGGTTATCAAAATTACATAAT
1 GTGATTATCAAAATTTCATAGT
* *
18091 GTGATTATTAGAATTTCATAG
1 GTGATTATCAAAATTTCATAG
18112 AGGGGTCAAA
Statistics
Matches: 81, Mismatches: 20, Indels: 14
0.70 0.17 0.12
Matches are distributed among these distances:
18 14 0.17
19 3 0.04
22 47 0.58
23 1 0.01
24 3 0.04
25 13 0.16
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
GTGATTATCAAAATTTCATAGT
Found at i:18324 original size:22 final size:22
Alignment explanation
Indices: 18299--18547 Score: 117
Period size: 22 Copynumber: 11.5 Consensus size: 22
18289 AGTTTAGTTT
18299 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
18321 TCAAAATTTCAT-AGTA-TGTAGA
1 TCAAAATTTCATAAG-AGGGT-TA
*
18343 TCAAAATTTCAT-AGGGAGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
* * *
18365 ACAAAATTTCATAATAAGGTTA
1 TCAAAATTTCATAAGAGGGTTA
** *
18387 TCAAAAAATCAT-AGGGAGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
*
18409 TCAAAATTT-GT---A--GTTA
1 TCAAAATTTCATAAGAGGGTTA
* **
18425 TCAATATTTCATAAGAAAGTTA
1 TCAAAATTTCATAAGAGGGTTA
* * * *
18447 TCAAAATTTTATAGGGAAGTTTA
1 TCAAAATTTCATA-AGAGGGTTA
* * **
18470 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAAG-AGGGTTA
18493 TCAAAATTTCATAACGA-GGTTA
1 TCAAAATTTCATAA-GAGGGTTA
* * * *
18515 TCACAATTTTAT-AGTGTGATTA
1 TCAAAATTTCATAAGAG-GGTTA
18537 TCAAAATTTCA
1 TCAAAATTTCA
18548 GAGTTGATTA
Statistics
Matches: 172, Mismatches: 38, Indels: 34
0.70 0.16 0.14
Matches are distributed among these distances:
16 12 0.07
17 1 0.01
20 2 0.01
21 7 0.04
22 109 0.63
23 40 0.23
24 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:18329 original size:44 final size:44
Alignment explanation
Indices: 18275--18505 Score: 142
Period size: 44 Copynumber: 5.3 Consensus size: 44
18265 TCAAGGAGGA
* *
18275 TATCACAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAGTTTAGTTATCAAAATTTCATAAGAGGGT
*
18319 TATCAAAATTTCATAGTATGTAG--ATCAAAATTTCAT-AGGGAGGT
1 TATCAAAATTTCATAGT-T-TAGTTATCAAAATTTCATAAGAG-GGT
* * * ** *
18363 TAACAAAATTTCATA-ATAAGGTTATCAAAAAATCAT-AGGGAGGT
1 TATCAAAATTTCATAGTTTA-GTTATCAAAATTTCATAAGAG-GGT
* **
18407 TATCAAAA-TT--T-G--TAGTTATCAATATTTCATAAGAAAGT
1 TATCAAAATTTCATAGTTTAGTTATCAAAATTTCATAAGAGGGT
* *** * * **
18445 TATCAAAATTTTATAGGGAAGTTTATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGTTTAG-TTATCAAAATTTCATAAG-AGGGT
18491 TATCAAAATTTCATA
1 TATCAAAATTTCATA
18506 ACGAGGTTAT
Statistics
Matches: 148, Mismatches: 23, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
38 23 0.16
39 5 0.03
41 3 0.02
42 3 0.02
43 5 0.03
44 73 0.49
45 16 0.11
46 20 0.14
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAGTTTAGTTATCAAAATTTCATAAGAGGGT
Found at i:18463 original size:60 final size:61
Alignment explanation
Indices: 18361--18478 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 61
18351 TCATAGGGAG
* *
18361 GTTAACAAAATTTCATAATAAGGTTATCAAAAAATCATAGGG-AGGTTATCAAAATTTGTA
1 GTTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAAGGTTATCAAAATTTGTA
* * ** * *
18421 GTTATCAATATTTCATAAGAAAGTTATCAAAATTTTATAGGGAAGTTTATCAAAATTT
1 GTTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAAGGTTATCAAAATTT
18479 TATAGGAAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 35 0.71
61 14 0.29
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.36
Consensus pattern (61 bp):
GTTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAAGGTTATCAAAATTTGTA
Found at i:18516 original size:45 final size:45
Alignment explanation
Indices: 18421--18547 Score: 125
Period size: 45 Copynumber: 2.8 Consensus size: 45
18411 AAAATTTGTA
* * * * **
18421 GTTATCAATATTTCATAAGAA-AGTTATCAAAATTTTATAGGGAAG
1 GTTATCAAAATTTTATAGGAAGA-TTATCAAAATTTCATAACGAAG
*
18466 TTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAACG-AG
1 GTTATCAAAATTTTATAGGAAGA-TTATCAAAATTTCATAACGAAG
* *
18511 GTTATCACAATTTTATAGTG-TGATTATCAAAATTTCA
1 GTTATCAAAATTTTATAG-GAAGATTATCAAAATTTCA
18548 GAGTTGATTA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
44 14 0.20
45 37 0.54
46 18 0.26
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (45 bp):
GTTATCAAAATTTTATAGGAAGATTATCAAAATTTCATAACGAAG
Found at i:18557 original size:21 final size:22
Alignment explanation
Indices: 18512--18557 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
18502 CATAACGAGG
* * *
18512 TTATCACAATTTTATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
18534 TTATCAAAATTTCAGAGT-TGA
1 TTATCAAAATTTCAGAGTGTGA
18555 TTA
1 TTA
18558 CTAACAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:30552 original size:2 final size:2
Alignment explanation
Indices: 30545--30590 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
30535 ACTAACCATC
30545 TA TA TA TA TA TA TA TA TA TA T- TA T- TA TA TA TA TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
30586 TA TA T
1 TA TA T
30591 TATTTTTGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30575 original size:22 final size:22
Alignment explanation
Indices: 30547--30593 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
30537 TAACCATCTA
30547 TATATATATATATA-TATATTAT
1 TATATATATATATACTATA-TAT
30569 TATATATATATATACTATATAT
1 TATATATATATATACTATATAT
30591 TAT
1 TAT
30594 TTTTGTCCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATATATATATATACTATATAT
Found at i:30747 original size:11 final size:11
Alignment explanation
Indices: 30731--30773 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
30721 TATACTATAT
30731 CTAATTAATAG
1 CTAATTAATAG
*
30742 CTAATTAATAT
1 CTAATTAATAG
30753 CTAATTAATAG
1 CTAATTAATAG
*
30764 TTAATTAATA
1 CTAATTAATA
30774 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:30752 original size:22 final size:22
Alignment explanation
Indices: 30727--30773 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
30717 CCATTATACT
30727 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
30749 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
30771 ATA
1 ATA
30774 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:32636 original size:24 final size:27
Alignment explanation
Indices: 32608--32663 Score: 82
Period size: 24 Copynumber: 2.2 Consensus size: 27
32598 AAAAAAACTG
*
32608 TACTTTTATGTTTTA-TCTTAAA-AAA
1 TACTTTTATGTTTAACTCTTAAATAAA
32633 -ACTTTTATGTTTAACTCTTAAATAAA
1 TACTTTTATGTTTAACTCTTAAATAAA
32659 TACTT
1 TACTT
32664 ATAACTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 13 0.48
25 7 0.26
26 3 0.11
27 4 0.15
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.50
Consensus pattern (27 bp):
TACTTTTATGTTTAACTCTTAAATAAA
Found at i:33040 original size:22 final size:22
Alignment explanation
Indices: 33015--33056 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
33005 GGAATCAAGA
* *
33015 CAAAATTTCAAGTGATTAAAGC
1 CAAAATTACAAGTCATTAAAGC
33037 CAAAATTACAAGTCATTAAA
1 CAAAATTACAAGTCATTAAA
33057 TACAATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (22 bp):
CAAAATTACAAGTCATTAAAGC
Found at i:33486 original size:26 final size:27
Alignment explanation
Indices: 33428--33487 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
33418 TCGGTCAACT
*
33428 TTATAAATGGAATTATTATTAAATTATA
1 TTATAAATGGAATTA-TAGTAAATTATA
* *
33456 ATATAAATGGAATTA-AGTATATTATA
1 TTATAAATGGAATTATAGTAAATTATA
33482 TTATAA
1 TTATAA
33488 CATATGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 14 0.50
28 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.43
Consensus pattern (27 bp):
TTATAAATGGAATTATAGTAAATTATA
Found at i:36232 original size:48 final size:48
Alignment explanation
Indices: 36161--36340 Score: 342
Period size: 48 Copynumber: 3.8 Consensus size: 48
36151 CCTCGACTCG
36161 TTCATCGTCAACTTCTTCAAGGTTTCACGGCGGCGATGGCCCAAGAAA
1 TTCATCGTCAACTTCTTCAAGGTTTCACGGCGGCGATGGCCCAAGAAA
36209 TTCATCGTCAACTTCTTCAAGGTTTCACGGCGGCGATGGCCCAAGAAA
1 TTCATCGTCAACTTCTTCAAGGTTTCACGGCGGCGATGGCCCAAGAAA
36257 TTCATCGTCAACTTCTTCAAGGTTTCACGGCGGCGATGGCCCAAGAAA
1 TTCATCGTCAACTTCTTCAAGGTTTCACGGCGGCGATGGCCCAAGAAA
* *
36305 TTCATCGTCAACTTCTTTAAGGTTTCTCGGCGGCGA
1 TTCATCGTCAACTTCTTCAAGGTTTCACGGCGGCGA
36341 CGGCTCTGGT
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 130 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (48 bp):
TTCATCGTCAACTTCTTCAAGGTTTCACGGCGGCGATGGCCCAAGAAA
Found at i:36369 original size:21 final size:21
Alignment explanation
Indices: 36345--36387 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
36335 CGGCGACGGC
*
36345 TCTGGTCATGGCGCAAGCAAT
1 TCTGGTCATGGCGCAAGAAAT
*
36366 TCTGGTGATGGCGCAAGAAAT
1 TCTGGTCATGGCGCAAGAAAT
36387 T
1 T
36388 TTGGACGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (21 bp):
TCTGGTCATGGCGCAAGAAAT
Found at i:37076 original size:16 final size:16
Alignment explanation
Indices: 37055--37086 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
37045 TCTCGTAAGT
37055 GAACAAGTGAACTTAG
1 GAACAAGTGAACTTAG
37071 GAACAAGTGAACTTAG
1 GAACAAGTGAACTTAG
37087 TTTCCTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (16 bp):
GAACAAGTGAACTTAG
Found at i:37165 original size:34 final size:34
Alignment explanation
Indices: 37096--37167 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
37086 GTTTCCTAGA
*
37096 TTTTGTTGCCACCTCTGGTGTGGTTGTGGTTTTG
1 TTTTGTTGCCACCTCTGGTGTGGTTGTGATTTTG
*
37130 TTTTGTTGCCACCTCTGGTGTGGTT-TTATTGTTG
1 TTTTGTTGCCACCTCTGGTGTGGTTGTGATT-TTG
37164 TTTT
1 TTTT
37168 CTTCATCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 3 0.09
34 32 0.91
ACGTcount: A:0.04, C:0.14, G:0.28, T:0.54
Consensus pattern (34 bp):
TTTTGTTGCCACCTCTGGTGTGGTTGTGATTTTG
Found at i:37279 original size:25 final size:25
Alignment explanation
Indices: 37245--37295 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
37235 TTCCTTTGTA
37245 TTTTACATTACCAAATACCAAGCAG
1 TTTTACATTACCAAATACCAAGCAG
37270 TTTTACATTACCAAATACCAAGCAG
1 TTTTACATTACCAAATACCAAGCAG
37295 T
1 T
37296 GCTTTACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (25 bp):
TTTTACATTACCAAATACCAAGCAG
Found at i:37665 original size:32 final size:32
Alignment explanation
Indices: 37624--37688 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
37614 CAGTCCCTTT
37624 CCCTCTTGAGTTCTCAATTTCTATCTGATAGG
1 CCCTCTTGAGTTCTCAATTTCTATCTGATAGG
37656 CCCTCTTGAGTTCTCAATTTCTATCTGATAGG
1 CCCTCTTGAGTTCTCAATTTCTATCTGATAGG
37688 C
1 C
37689 ACAACTTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.40
Consensus pattern (32 bp):
CCCTCTTGAGTTCTCAATTTCTATCTGATAGG
Found at i:38061 original size:31 final size:31
Alignment explanation
Indices: 38026--38167 Score: 149
Period size: 31 Copynumber: 4.9 Consensus size: 31
38016 GGCATGCCAC
* *
38026 GTGTCACTTTTTGATACACGTGGTGTGACAT
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
*
38057 GTGTCACATTTTGGTACACGTGGCGTGACAT
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
*
38088 GTGTCACTTTTTGGTACATGTGGC---AC--
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
* * *
38114 --G--ACTTTTTGGTACATGTGGCGTGCCAC
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
*
38141 ATGTCACTTTTTGGTACACGTGGCGTG
1 GTGTCACTTTTTGGTACACGTGGCGTG
38168 CCACGTCGGA
Statistics
Matches: 95, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
22 19 0.20
24 1 0.01
25 1 0.01
28 2 0.02
29 1 0.01
31 71 0.75
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (31 bp):
GTGTCACTTTTTGGTACACGTGGCGTGACAT
Found at i:38482 original size:15 final size:15
Alignment explanation
Indices: 38462--38491 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38452 TACCAACCAA
38462 GCTTTGATTTGGTGT
1 GCTTTGATTTGGTGT
38477 GCTTTGATTTGGTGT
1 GCTTTGATTTGGTGT
38492 TGGGGGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.33, T:0.53
Consensus pattern (15 bp):
GCTTTGATTTGGTGT
Found at i:38499 original size:24 final size:25
Alignment explanation
Indices: 38472--38522 Score: 86
Period size: 24 Copynumber: 2.0 Consensus size: 25
38462 GCTTTGATTT
38472 GGTGTGCTTTGATTT-GGTGTTGGG
1 GGTGTGCTTTGATTTGGGTGTTGGG
38496 GGTGTGCTTTGATTTGGGGTGTTGGG
1 GGTGTGCTTTGATTT-GGGTGTTGGG
38522 G
1 G
38523 TGACAGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 15 0.60
26 10 0.40
ACGTcount: A:0.04, C:0.04, G:0.49, T:0.43
Consensus pattern (25 bp):
GGTGTGCTTTGATTTGGGTGTTGGG
Found at i:38591 original size:12 final size:12
Alignment explanation
Indices: 38574--38598 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38564 AACAAGCTTT
38574 ACAATTAGGGAA
1 ACAATTAGGGAA
38586 ACAATTAGGGAA
1 ACAATTAGGGAA
38598 A
1 A
38599 AATATACTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (12 bp):
ACAATTAGGGAA
Found at i:55184 original size:40 final size:39
Alignment explanation
Indices: 55138--55224 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 39
55128 TGCCTGGCGT
** *
55138 GGCCCAGGCGTGCCAGGCC-ATGCACGTTGGGCCAGCGCGC
1 GGCCCAGGCGCACCAGGCCAACGCAC-TT-GGCCAGCGCGC
55178 GGCCCAGGCGCACCAGGCCAGACGCACTTGGCCAGCGCGC
1 GGCCCAGGCGCACCAGGCCA-ACGCACTTGGCCAGCGCGC
55218 GGCCCAG
1 GGCCCAG
55225 CAAGCTTGGC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 35 0.83
41 2 0.05
42 5 0.12
ACGTcount: A:0.15, C:0.40, G:0.38, T:0.07
Consensus pattern (39 bp):
GGCCCAGGCGCACCAGGCCAACGCACTTGGCCAGCGCGC
Found at i:60591 original size:21 final size:21
Alignment explanation
Indices: 60546--60617 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
60536 AAGTGGGTAA
*
60546 TTTTATTTATTT-TTT-TCTT
1 TTTTATTTATTTATTTATATT
60565 GCTTTTATTTATTTATTTATATT
1 --TTTTATTTATTTATTTATATT
*
60588 TTTTATTT-TTATAATTTATTTCT
1 TTTTATTTATT-T-ATTTATAT-T
60611 TTTTATT
1 TTTTATT
60618 ACCATTGTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 2 0.05
21 21 0.48
22 10 0.23
23 11 0.25
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (21 bp):
TTTTATTTATTTATTTATATT
Found at i:60600 original size:15 final size:17
Alignment explanation
Indices: 60568--60616 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
60558 TTTTCTTGCT
60568 TTTATTTATTTATT-TATA
1 TTTATTTATTT-TTATA-A
60586 TTT-TTTATTTTTATAA
1 TTTATTTATTTTTATAA
*
60602 TTTATTTCTTTTTAT
1 TTTATTTATTTTTAT
60617 TACCATTGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.21
17 19 0.68
18 3 0.11
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTATTTTTATAA
Found at i:60776 original size:27 final size:27
Alignment explanation
Indices: 60743--60813 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
60733 AAAGTCAGAC
*
60743 TCTCATTCCAAGTTAGTCAAGACAG-T
1 TCTCATTCAAAGTTAGTCAAGACAGTT
* *
60769 TCTCCATTCAAAGCTAGTCAGGACAGTT
1 TCT-CATTCAAAGTTAGTCAAGACAGTT
60797 TCTCATTCAAAGTTAGT
1 TCTCATTCAAAGTTAGT
60814 TCCCTAGGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 3 0.08
27 32 0.82
28 4 0.10
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (27 bp):
TCTCATTCAAAGTTAGTCAAGACAGTT
Found at i:65262 original size:27 final size:27
Alignment explanation
Indices: 65232--65299 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
65222 GTCAGACTCT
*
65232 CATTCCAAGTTAGTCA-AGACAG-TTCTC
1 CATTCAAAGTTAGTCAGA-ACAGTTTC-C
*
65259 CATTCAAAGCTAGTCAGAACAGTTTCC
1 CATTCAAAGTTAGTCAGAACAGTTTCC
65286 CATTCAAAGTTAGT
1 CATTCAAAGTTAGT
65300 TCCCTAGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 32 0.89
28 4 0.11
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (27 bp):
CATTCAAAGTTAGTCAGAACAGTTTCC
Found at i:66709 original size:6 final size:6
Alignment explanation
Indices: 66670--66707 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
66660 ACTAAGCAAA
*
66670 CTAAAT -TAAAT CTAAAT CTAAAT CTAAAT CTATAT CTA
1 CTAAAT CTAAAT CTAAAT CTAAAT CTAAAT CTAAAT CTA
66708 TAGCAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (6 bp):
CTAAAT
Found at i:70340 original size:15 final size:16
Alignment explanation
Indices: 70309--70341 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
70299 AAAAAAGATG
70309 AAAGAAAAATTTAAAAA
1 AAAGAAAAA-TTAAAAA
70326 AAAGAAAAA-TAAAAA
1 AAAGAAAAATTAAAAA
70341 A
1 A
70342 GGGTGAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAGAAAAATTAAAAA
Found at i:70888 original size:54 final size:55
Alignment explanation
Indices: 70783--70896 Score: 212
Period size: 54 Copynumber: 2.1 Consensus size: 55
70773 AAAGCCATAG
70783 TCAATGGAATCATGTTTGAACATTTTTTTAAAAATGGGAAGCTGATCCAGAACCA
1 TCAATGGAATCATGTTTGAACATTTTTTTAAAAATGGGAAGCTGATCCAGAACCA
*
70838 TCAATGGAATCATGTTTGAACATTTTTTT-AAGATGGGAAGCTGATCCAGAACCA
1 TCAATGGAATCATGTTTGAACATTTTTTTAAAAATGGGAAGCTGATCCAGAACCA
70892 TCAAT
1 TCAAT
70897 CGAGTTGGGA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
54 29 0.50
55 29 0.50
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (55 bp):
TCAATGGAATCATGTTTGAACATTTTTTTAAAAATGGGAAGCTGATCCAGAACCA
Found at i:71718 original size:37 final size:37
Alignment explanation
Indices: 71666--72208 Score: 433
Period size: 37 Copynumber: 14.8 Consensus size: 37
71656 TTCTTTTTGA
* * * **
71666 CAAATCCTTATTTAAGGTCTCTGTTTAGGTGTCACAT
1 CAAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
*
71703 CAAAAT-CTTATTTAAGATCCCTGTTTATGTTTCTTAT
1 C-AAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * * * *
71740 CAAATCCTTATTTAAGGTCCCTATCTAGGTGTCTCAT
1 CAAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * *
71777 CAGAAT-CATGTTCAAGAT-CC--TTTAGGTTTCTTAT
1 CA-AATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * * *
71811 CAAATCCTTATTTAAGGTCCTTGTTTAGGTGTCTCAT
1 CAAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * * * *
71848 CAAAAT-CATGTTCAAGATCCCTGTTTAGGTTTTTTGT
1 C-AAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * * * *
71885 CAAATCCTTATTTAAGGTCTCTTTTTAGGTGTCTCAT
1 CAAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * * * *
71922 CAAAAT-CATGTTCAAGATCCATGTCTAGGTTTCTTAT
1 C-AAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * *
71959 CAAATCCTTATTTAAGGTCCCTATTTAAGTTTCTT-T
1 CAAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * * * *
71995 CAAATCCTTATTTAAAATCCCTATTTAGATGTCTCAT
1 CAAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * * *
72032 CAAAAT-CTTGTTCAAAATCCCGGTTTAGGTTTCTTAT
1 C-AAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * *
72069 CAAATTCTTGTTT-AGATTCCTGTTTAGGTTTCTTAT
1 CAAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * *
72105 CAAATCCTTATTTAAGATCCCTATTTAGGTGTCTCAT
1 CAAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * * *
72142 CAAAAT-CTTGTTCAAGATCCCTGTTTAGCTTTCTGAT
1 C-AAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
* * *
72179 CAAATCCTTATTTAAGGTTCCTATTTAGGT
1 CAAATCCTTATTTAAGATCCCTGTTTAGGT
72209 GTCTCTTTAA
Statistics
Matches: 391, Mismatches: 98, Indels: 34
0.75 0.19 0.07
Matches are distributed among these distances:
33 3 0.01
34 21 0.05
35 1 0.00
36 83 0.21
37 260 0.66
38 23 0.06
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (37 bp):
CAAATCCTTATTTAAGATCCCTGTTTAGGTTTCTTAT
Found at i:71794 original size:74 final size:74
Alignment explanation
Indices: 71666--72232 Score: 646
Period size: 74 Copynumber: 7.7 Consensus size: 74
71656 TTCTTTTTGA
* * * * * *
71666 CAAATCCTTATTTAAGGTCTCTGTTTAGGTGTCACATCAAAATCTTATTTAAGATCCCTGTTTAT
1 CAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
71731 GTTTCTTAT
66 GTTTCTTAT
* * *
71740 CAAATCCTTATTTAAGGTCCCTATCTAGGTGTCTCATCAGAATCATGTTCAAGAT-CC--TTTAG
1 CAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
71802 GTTTCTTAT
66 GTTTCTTAT
* * *
71811 CAAATCCTTATTTAAGGTCCTTGTTTAGGTGTCTCATCAAAATCATGTTCAAGATCCCTGTTTAG
1 CAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
* *
71876 GTTTTTTGT
66 GTTTCTTAT
* * * * *
71885 CAAATCCTTATTTAAGGTCTCTTTTTAGGTGTCTCATCAAAATCATGTTCAAGATCCATGTCTAG
1 CAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
71950 GTTTCTTAT
66 GTTTCTTAT
* * * * * * *
71959 CAAATCCTTATTTAAGGTCCCTATTTAAGTTTCT-TTC-AAATCCTTATTTAAAATCCCTATTTA
1 CAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAAT-CTTGTTCAAGATCCCTGTTTA
* * *
72022 GATGTCTCAT
65 GGTTTCTTAT
* * ** ** * * * * *
72032 CAAAAT-CTTGTTCAAAATCCCGGTTTAGGTTTCTTATCAAATTCTTGTT-TAGATTCCTGTTTA
1 C-AAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTA
72095 GGTTTCTTAT
65 GGTTTCTTAT
*
72105 CAAATCCTTATTTAAGATCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
1 CAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
* *
72170 CTTTCTGAT
66 GTTTCTTAT
* **
72179 CAAATCCTTATTTAAGGTTCCTATTTAGGTGTCTC-TTTAAATCTTGTTCAAGAT
1 CAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGAT
72233 GGTTTCTTAT
Statistics
Matches: 414, Mismatches: 70, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
71 64 0.15
72 10 0.02
73 117 0.28
74 220 0.53
75 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (74 bp):
CAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
GTTTCTTAT
Found at i:72028 original size:110 final size:111
Alignment explanation
Indices: 71666--72208 Score: 580
Period size: 110 Copynumber: 4.9 Consensus size: 111
71656 TTCTTTTTGA
* * * * * * *
71666 CAAATCCTTATTTAAGGTCTCTGTTTAGGTGTCACATCAAAATCTTATTTAAGATCCCTGTTTAT
1 CAAATCCTTATTTAAGATCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
* * *
71731 GTTTCTTATCAAATCCTTATTTAAGGTCCCTATCTAGGTGTCTCAT
66 GTTTCTTATCAAATCCTTATTTAAGGTCCCTATTTAGGTTTCTTAT
* * * * * * * * *
71777 CAGAAT-CATGTTCAAGAT-CC--TTTAGGTTTCTTATC-AAATCCTTATTTAAGGTCCTTGTTT
1 CA-AATCCTTATTTAAGATCCCTATTTAGGTGTCTCATCAAAAT-CTTGTTCAAGATCCCTGTTT
* * * * * * * * *
71837 AGGTGTCTCATCAAAAT-CATGTTCAAGATCCCTGTTTAGGTTTTTTGT
64 AGGTTTCTTATC-AAATCCTTATTTAAGGTCCCTATTTAGGTTTCTTAT
* * * * * *
71885 CAAATCCTTATTTAAGGTCTCTTTTTAGGTGTCTCATCAAAATCATGTTCAAGATCCATGTCTAG
1 CAAATCCTTATTTAAGATCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
*
71950 GTTTCTTATCAAATCCTTATTTAAGGTCCCTATTTAAGTTTCTT-T
66 GTTTCTTATCAAATCCTTATTTAAGGTCCCTATTTAGGTTTCTTAT
* * * *
71995 CAAATCCTTATTTAAAATCCCTATTTAGATGTCTCATCAAAATCTTGTTCAAAATCCCGGTTTAG
1 CAAATCCTTATTTAAGATCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
* * * * *
72060 GTTTCTTATCAAATTCTTGTTT-AGATTCCTGTTTAGGTTTCTTAT
66 GTTTCTTATCAAATCCTTATTTAAGGTCCCTATTTAGGTTTCTTAT
72105 CAAATCCTTATTTAAGATCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
1 CAAATCCTTATTTAAGATCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
* * *
72170 CTTTCTGATCAAATCCTTATTTAAGGTTCCTATTTAGGT
66 GTTTCTTATCAAATCCTTATTTAAGGTCCCTATTTAGGT
72209 GTCTCTTTAA
Statistics
Matches: 350, Mismatches: 71, Indels: 22
0.79 0.16 0.05
Matches are distributed among these distances:
107 7 0.02
108 70 0.20
109 22 0.06
110 161 0.46
111 83 0.24
112 7 0.02
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (111 bp):
CAAATCCTTATTTAAGATCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAG
GTTTCTTATCAAATCCTTATTTAAGGTCCCTATTTAGGTTTCTTAT
Found at i:72095 original size:73 final size:73
Alignment explanation
Indices: 71957--72190 Score: 202
Period size: 73 Copynumber: 3.2 Consensus size: 73
71947 TAGGTTTCTT
* ** * * * * * *
71957 ATCAAATCCTTATTTAAGGTCCCTATTTAAGTTTCTT-TCAAATCCTTATTTAAAATCCCTATTT
1 ATCAAATCCTTATTCAAAATCCCGATTTAGGTTTCTTATCAAATTCTTGTTT-AGATCCCTGTTT
72021 AGATGTCTC
65 AGATGTCTC
* * *
72030 ATCAAAAT-CTTGTTCAAAATCCCGGTTTAGGTTTCTTATCAAATTCTTGTTTAGATTCCTGTTT
1 ATC-AAATCCTTATTCAAAATCCCGATTTAGGTTTCTTATCAAATTCTTGTTTAGATCCCTGTTT
* * *
72094 AGGTTTCTT
65 AGATGTCTC
* * * * * * *
72103 ATCAAATCCTTATTTAAGATCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAGATCCCTGTTT
1 ATCAAATCCTTATTCAAAATCCCGATTTAGGTTTCTTATCAAATTCTTGTT-TAGATCCCTGTTT
* * *
72168 AGCTTTCTG
65 AGATGTCTC
72177 ATCAAATCCTTATT
1 ATCAAATCCTTATT
72191 TAAGGTTCCT
Statistics
Matches: 130, Mismatches: 27, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
72 4 0.03
73 78 0.60
74 48 0.37
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (73 bp):
ATCAAATCCTTATTCAAAATCCCGATTTAGGTTTCTTATCAAATTCTTGTTTAGATCCCTGTTTA
GATGTCTC
Found at i:72529 original size:31 final size:31
Alignment explanation
Indices: 72493--72579 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
72483 TATCCCCTAG
* *
72493 TTGAGATAGACT-TTTATATTTCATTCCTCGA
1 TTGAGA-AGACTCTTTACATTTCATTCCTCAA
* *
72524 TTGAGAAGATTCTTTGCATTTCATTCCTCAA
1 TTGAGAAGACTCTTTACATTTCATTCCTCAA
* *
72555 TTGAGAAGATTCTTTGCATTTCATT
1 TTGAGAAGACTCTTTACATTTCATT
72580 ATTCAAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 4 0.08
31 47 0.92
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (31 bp):
TTGAGAAGACTCTTTACATTTCATTCCTCAA
Found at i:72621 original size:28 final size:28
Alignment explanation
Indices: 72589--72647 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
72579 TATTCAAAAA
* *
72589 TCAAAATTCAAAATC-AGCATTTCATGGT
1 TCAAAATTCAAAACCTA-CATTTCATGCT
72617 TCAAAATTCAAAACCTACATTTCATGCT
1 TCAAAATTCAAAACCTACATTTCATGCT
72645 TCA
1 TCA
72648 TTCTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (28 bp):
TCAAAATTCAAAACCTACATTTCATGCT
Found at i:72663 original size:42 final size:43
Alignment explanation
Indices: 72617--72714 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
72607 ATTTCATGGT
72617 TCAAAATTCAAAACCTACATTTCATGC-TT-CATTCTTCAAAAA
1 TCAAAATTCAAAACCTACATTTCA-GCATTCCATTCTTCAAAAA
* * * * *
72659 TCAAAATCCAAAACTTGCATTTTAGCATTCCATTCTTCGAAAA
1 TCAAAATTCAAAACCTACATTTCAGCATTCCATTCTTCAAAAA
*
72702 TCAAAGTTCAAAA
1 TCAAAATTCAAAA
72715 TTTGCATTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 2 0.04
42 22 0.47
43 23 0.49
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (43 bp):
TCAAAATTCAAAACCTACATTTCAGCATTCCATTCTTCAAAAA
Found at i:72740 original size:33 final size:34
Alignment explanation
Indices: 72702--72766 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
72692 TCTTCGAAAA
* *
72702 TCAAAGTTCAAAATTTGCATTTCAT-TTCAAATT
1 TCAAAGTTCAAAATCTGCATCTCATGTTCAAATT
72735 TCAAAGTTCAAAATCTGCATCTCATGTTCAAA
1 TCAAAGTTCAAAATCTGCATCTCATGTTCAAA
72767 ACAAAAATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 23 0.79
34 6 0.21
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (34 bp):
TCAAAGTTCAAAATCTGCATCTCATGTTCAAATT
Found at i:76324 original size:12 final size:12
Alignment explanation
Indices: 76296--76334 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
76286 TTAATTATTG
*
76296 TTTGCTTTATTAA
1 TTTGCTTTA-TAT
76309 TTTGCTTTATAT
1 TTTGCTTTATAT
*
76321 TTTGCTTTAGAT
1 TTTGCTTTATAT
76333 TT
1 TT
76335 AAGATTTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.64
Consensus pattern (12 bp):
TTTGCTTTATAT
Done.