Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015860.1 Corchorus capsularis cultivar CVL-1 contig15881, 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: 59642
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2254 original size:57 final size:58
Alignment explanation
Indices: 2185--2293 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 58
2175 TTTGTTAACA
* * * **
2185 ACTGATTCTCTTT-TTTGTTTTTTAATTGACTCCATTACCCTGAATTAAGCCTTTATT
1 ACTGATTCTCTTTCTTTGATTCTTAACTGACTAAATTACCCTGAATTAAGCCTTTATT
*
2242 ACTGATTGTCTTTCTTTGATTCTTAACTGACTAAATTACCCTGAATTAAGCC
1 ACTGATTCTCTTTCTTTGATTCTTAACTGACTAAATTACCCTGAATTAAGCC
2294 ACTTTATTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 12 0.27
58 33 0.73
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (58 bp):
ACTGATTCTCTTTCTTTGATTCTTAACTGACTAAATTACCCTGAATTAAGCCTTTATT
Found at i:2373 original size:35 final size:34
Alignment explanation
Indices: 2327--2724 Score: 413
Period size: 35 Copynumber: 11.6 Consensus size: 34
2317 TTCTTACTAA
* *
2327 ACTTAATTTCCCTGAATTAAGTTACTTATTGAACT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGAACT
* *
2362 ACTTAACTT-CCCTAAATTAAGTTGATTA-TTAACT
1 ACTTAA-TTACCCTGAATTAAGTT-ATTACTGAACT
*
2396 CACTTAATTACCCTGAATTAAGTTGATTCCTG-ACT
1 -ACTTAATTACCCTGAATTAAGTT-ATTACTGAACT
*
2431 CACTTAATTACCCTGAATTAAGTTAATTACTGAATT
1 -ACTTAATTACCCTGAATTAAGTT-ATTACTGAACT
*
2467 ACTTAATTACCCTGAATTAAGTTGATTCCTG-ACT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGAACT
*
2501 CACTTAATTACCCTGAATTAAGTGGATTACTG-ACTT
1 -ACTTAATTACCCTGAATTAAGT-TATTACTGAAC-T
**
2537 ACTTAATTACCCTGAATTAAGTTGATTACTGAGTT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGAACT
* * *
2572 ACTTAATTAACCTGAATTAAGTTACTAACTGACCT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGAACT
* *
2607 GCTTAATTACCCTGAATT-AG--AGT--TGAACT
1 ACTTAATTACCCTGAATTAAGTTATTACTGAACT
* *
2636 ACTTAATTACCCTGAATTAAGTTACTAGCTGAATT
1 ACTTAATTACCCTGAATTAAGTTATTA-CTGAACT
*
2671 ACTTAATTACCCTGAATTAAGTTAATTATTG-ACT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGAACT
2705 CACTTAATTACCCTGAATTA
1 -ACTTAATTACCCTGAATTA
2725 GGGTTACTTA
Statistics
Matches: 312, Mismatches: 31, Indels: 40
0.81 0.08 0.10
Matches are distributed among these distances:
29 22 0.07
30 2 0.01
32 3 0.01
34 14 0.04
35 261 0.84
36 10 0.03
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (34 bp):
ACTTAATTACCCTGAATTAAGTTATTACTGAACT
Found at i:2448 original size:105 final size:103
Alignment explanation
Indices: 2327--2724 Score: 501
Period size: 105 Copynumber: 3.9 Consensus size: 103
2317 TTCTTACTAA
* * * * *
2327 ACTTAATTTCCCTGAATTAAGTTACTTATTGAACTACTTAACTT-CCCTAAATTAAGTTGATTAT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGAATTACTTAA-TTACCCTGAATTAAGTTGATTAC
*
2391 TAACTCACTTAATTACCCTGAATTAAGTTGATTCCTGACT
65 TGACTCACTTAATTACCCTGAATTAAGTTGATT-CTGACT
* *
2431 CACTTAATTACCCTGAATTAAGTTAATTACTGAATTACTTAATTACCCTGAATTAAGTTGATTCC
1 -ACTTAATTACCCTGAATTAAGTTACTTACTGAATTACTTAATTACCCTGAATTAAGTTGATTAC
*
2496 TGACTCACTTAATTACCCTGAATTAAGTGGATTACTGACTT
65 TGACTCACTTAATTACCCTGAATTAAGTTGATT-CTGAC-T
* * *
2537 ACTTAATTACCCTGAATTAAGTTGA-TTACTGAGTTACTTAATTAACCTGAATTAAGTT-ACTAA
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGAATTACTTAATTACCCTGAATTAAGTTGA-TTA
*
2600 CTGAC-CTGCTTAATTACCCTGAATTAGAGTTGA-----ACT
64 CTGACTC-ACTTAATTACCCTGAATTA-AGTTGATTCTGACT
* *
2636 ACTTAATTACCCTGAATTAAGTTAC-TAGCTGAATTACTTAATTACCCTGAATTAAGTTAATTAT
1 ACTTAATTACCCTGAATTAAGTTACTTA-CTGAATTACTTAATTACCCTGAATTAAGTTGATTAC
2700 TGACTCACTTAATTACCCTGAATTA
65 TGACTCACTTAATTACCCTGAATTA
2725 GGGTTACTTA
Statistics
Matches: 262, Mismatches: 21, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
98 3 0.01
99 76 0.29
100 4 0.02
104 4 0.02
105 168 0.64
106 7 0.03
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (103 bp):
ACTTAATTACCCTGAATTAAGTTACTTACTGAATTACTTAATTACCCTGAATTAAGTTGATTACT
GACTCACTTAATTACCCTGAATTAAGTTGATTCTGACT
Found at i:4946 original size:2 final size:2
Alignment explanation
Indices: 4939--4968 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4929 CTTGACTTGA
4939 AT 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
4969 GTACCCAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14633 original size:13 final size:13
Alignment explanation
Indices: 14615--14640 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14605 CAATCAAGAA
14615 AATTAAAGAAAAC
1 AATTAAAGAAAAC
14628 AATTAAAGAAAAC
1 AATTAAAGAAAAC
14641 CCTCCAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AATTAAAGAAAAC
Found at i:15914 original size:19 final size:18
Alignment explanation
Indices: 15881--15917 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
15871 TTGAAATAGT
15881 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
15899 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
15918 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:22134 original size:2 final size:2
Alignment explanation
Indices: 22125--22154 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22115 CTGCTTCTGT
22125 TG TG -G TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
22155 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:25232 original size:24 final size:25
Alignment explanation
Indices: 25195--25243 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
25185 AAAGTGAGGT
25195 AATTAAAAAGCATATCATTCTCTAA
1 AATTAAAAAGCATATCATTCTCTAA
25220 AATTAAAAA-CATATCATTCTCTAA
1 AATTAAAAAGCATATCATTCTCTAA
25244 GCTTATTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (25 bp):
AATTAAAAAGCATATCATTCTCTAA
Found at i:33367 original size:75 final size:74
Alignment explanation
Indices: 33113--33359 Score: 206
Period size: 75 Copynumber: 3.3 Consensus size: 74
33103 AGGTTGCTAA
* * * * * * * *
33113 TTCGAATTCAAATAATGAGTTTTCTGATGGTGTTAGGCAAAATCTTGAAGATGATTCACCTGATC
1 TTCGAATTCAAATACTGAG-CTTCTAATGATGATAGGCAACATCTTGAAGATGATTCACTTAATC
*
33178 AGTTTCCTGT
65 AGGTTCCTGT
* * * * ** * * * *
33188 TTTGAATTCAAATACTAAGTTTTCTGATGATGATTTGCAACATCTTGAAGCTGATTCGCTTTAGC
1 TTCGAATTCAAATACTGAG-CTTCTAATGATGATAGGCAACATCTTGAAGATGATTCACTTAATC
* *
33253 AGGTTTCTGA
65 AGGTTCCTGT
** * * *
33263 TTCGAATTCAAATTTTGAGCATCATAATGATGATAGGCAACATCTTGAAGTTGATTCTCTTAATC
1 TTCGAATTCAAATACTGAGCTTC-TAATGATGATAGGCAACATCTTGAAGATGATTCACTTAATC
* *
33328 AGGATGCTGT
65 AGGTTCCTGT
*
33338 TTCGAATTCTAATACTGAGCTT
1 TTCGAATTCAAATACTGAGCTT
33360 ACCAATGAAG
Statistics
Matches: 135, Mismatches: 36, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
74 2 0.01
75 133 0.99
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (74 bp):
TTCGAATTCAAATACTGAGCTTCTAATGATGATAGGCAACATCTTGAAGATGATTCACTTAATCA
GGTTCCTGT
Found at i:34934 original size:30 final size:30
Alignment explanation
Indices: 34898--34983 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 30
34888 AGGGGCGGCC
**
34898 TGCCGTGGCAAAGCCGCCCCATGGGTGGTT
1 TGCCGTGGCAAAGCCGCCCCATGGGCAGTT
* **
34928 TGCCGTGGCGAAGCCGCCTTATGGGCAGTT
1 TGCCGTGGCAAAGCCGCCCCATGGGCAGTT
34958 TGCCGTGGCAAAGCCGCCCCAGTGGG
1 TGCCGTGGCAAAGCCGCCCCA-TGGG
34984 ACGGTCTGCC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 43 0.91
31 4 0.09
ACGTcount: A:0.14, C:0.30, G:0.37, T:0.19
Consensus pattern (30 bp):
TGCCGTGGCAAAGCCGCCCCATGGGCAGTT
Found at i:35582 original size:32 final size:32
Alignment explanation
Indices: 35521--35583 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
35511 AGTTTTGTAA
*
35521 AACTTTTAAAATGTCTATTATACTTTTATTTT
1 AACTTTTAAAATGTCTATTATACTCTTATTTT
35553 AACTTTTAAAATGTCTATTATA-TCCTTATTT
1 AACTTTTAAAATGTCTATTATACT-CTTATTT
35584 GTCTAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.54
Consensus pattern (32 bp):
AACTTTTAAAATGTCTATTATACTCTTATTTT
Found at i:36028 original size:5 final size:5
Alignment explanation
Indices: 36018--36042 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
36008 TCATACCAAT
36018 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
36043 ATAGTAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:44639 original size:30 final size:32
Alignment explanation
Indices: 44585--44650 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
44575 AACTTTATGT
*
44585 TTTCCGATTGTACCCTTATTTTT-AAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
44616 TTTCCAATTGTACCCTT-TTTTTAAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
44647 TTTC
1 TTTC
44651 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.47
Consensus pattern (32 bp):
TTTCCAATTGTACCCTTATTTTTAAAAACATA
Found at i:44788 original size:22 final size:21
Alignment explanation
Indices: 44750--44826 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 21
44740 TGGTTATTAT
* * *
44750 AATTCCATGAGGAGGTTATCGA
1 AATTCCAT-AGGTGGTTACCAA
44772 AATTCCATAGTGTGGTTACCAA
1 AATTCCATAG-GTGGTTACCAA
*
44794 AATTTCATAGAGTGGTTACCAA
1 AATTCCATAG-GTGGTTACCAA
*
44816 AATTTCATAGG
1 AATTCCATAGG
44827 ATCAGGTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
21 3 0.06
22 46 0.94
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (21 bp):
AATTCCATAGGTGGTTACCAA
Found at i:44877 original size:22 final size:22
Alignment explanation
Indices: 44763--44879 Score: 90
Period size: 22 Copynumber: 5.2 Consensus size: 22
44753 TCCATGAGGA
* * *
44763 GGTTATCGAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAGGGT
* *
44785 GGTTACCAAAATTTCATAGAGT
1 GGTTATCAAAATTTCATAGGGT
* *
44807 GGTTACCAAAATTTCATAGGAT
1 GGTTATCAAAATTTCATAGGGT
* * ** *
44829 CAGGTTATTAAAATTTCTTCTGTT
1 --GGTTATCAAAATTTCATAGGGT
**
44853 GGTTATTGAAATTTCATAGGGT
1 GGTTATCAAAATTTCATAGGGT
44875 GGTTA
1 GGTTA
44880 ATTATCACAA
Statistics
Matches: 76, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
22 60 0.79
24 16 0.21
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGGT
Found at i:44968 original size:22 final size:22
Alignment explanation
Indices: 44918--45048 Score: 72
Period size: 22 Copynumber: 6.0 Consensus size: 22
44908 AAAAAGATTT
* *
44918 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* *
44941 C-GAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
* *
44962 CAAAATTCCATTAG-AAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * * *
44983 CTAATACTTCATCGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * *
45006 CAAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
45028 CAAAATTTCATA-TGAAGGTTA
1 CAAAATTTCATAGTG-AGGTTA
45049 TAAAAGTCTC
Statistics
Matches: 80, Mismatches: 22, Indels: 13
0.70 0.19 0.11
Matches are distributed among these distances:
21 8 0.10
22 67 0.84
23 5 0.06
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:45049 original size:22 final size:22
Alignment explanation
Indices: 44999--45305 Score: 104
Period size: 22 Copynumber: 13.8 Consensus size: 22
44989 CTTCATCGGG
*
44999 AGGTTATCAAAATTTTATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
*
45021 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
*
45043 AGGTTAT-AAAAGTCTCAATTTCAT-A
1 AGGTTATCAAAA-TTTC-A--T-ATGA
* * *
45068 AGGAGTACCAAAATTTGATA-GA
1 AGG-TTATCAAAATTTCATATGA
*
45090 AGGTTATC-AAATCTCATA-G-
1 AGGTTATCAAAATTTCATATGA
* *
45109 AGTGATTATCGAAATTTCATAAAGA
1 AG-G-TTATCAAAATTTCAT-ATGA
*
45134 TATGATTATCAAAATTT-ATATGA
1 -A-GGTTATCAAAATTTCATATGA
*
45157 AGATTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** * *
45179 TTGTTATCAAAATTTCA-AAGCG
1 AGGTTATCAAAATTTCATATG-A
*
45201 AGGTTATCAAAATTGCATAATG-
1 AGGTTATCAAAATTTCAT-ATGA
* * *
45223 TGATTATCAAAGTTTCATA-GA
1 AGGTTATCAAAATTTCATATGA
* * * *
45244 GGGGTCAACAAAATTT--TATAA
1 -AGGTTATCAAAATTTCATATGA
* *
45265 AGATGTTATCAAAATTTTATA-AA
1 AG--GTTATCAAAATTTCATATGA
*
45288 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
45306 AAATCTGATT
Statistics
Matches: 215, Mismatches: 39, Indels: 62
0.68 0.12 0.20
Matches are distributed among these distances:
19 2 0.01
20 15 0.07
21 31 0.14
22 119 0.55
23 10 0.05
24 9 0.04
25 17 0.08
26 7 0.03
27 5 0.02
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:45156 original size:18 final size:19
Alignment explanation
Indices: 45133--45171 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
45123 TTTCATAAAG
45133 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
45151 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
45172 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:45230 original size:44 final size:44
Alignment explanation
Indices: 45092--45330 Score: 150
Period size: 44 Copynumber: 5.4 Consensus size: 44
45082 TTGATAGAAG
* * * * * *
45092 GTTATC-AAATCTCATAGAGTGATTATCGAAATTTCATAAAGATAT
1 GTTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG--AT
* * * *
45137 GATTATCAAAATTT-ATATGA-AGATTATCAAAATTTCATAGTGTT
1 G-TTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGAT
* *
45181 GTTATCAAAATTTCAAAGCGAGGTTATCAAAATTGCATAATG-T
1 GTTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAT
* * * * * * *
45224 GATTATCAAAGTTTCATAGAGGGGTCAACAAAATTTTATAAAGAT
1 G-TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAT
* * * *
45269 GTTATCAAAATTTTATAA-AGAGGTTATCAAATTTTCAAAAT-CT
1 GTTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGAT
45312 GATTA-CAATAATTTCAAAG
1 G-TTATCAA-AATTTCAAAG
45331 TGGTATTTTT
Statistics
Matches: 149, Mismatches: 34, Indels: 23
0.72 0.17 0.11
Matches are distributed among these distances:
43 23 0.15
44 91 0.61
45 4 0.03
46 24 0.16
47 7 0.05
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (44 bp):
GTTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAT
Found at i:45305 original size:66 final size:65
Alignment explanation
Indices: 45059--45302 Score: 194
Period size: 66 Copynumber: 3.7 Consensus size: 65
45049 TAAAAGTCTC
* * * * * * *
45059 AATTTCATAAGGA-G-TACCAAAATTTGATAGA-AGGTTATCAAATCTCATAGAGTGATTATCGA
1 AATTTCATAAAGATGTTATCAAAATTTTATAAAGAGGTTATCAAATTTCATAGAGTGGTTATCAA
* * *
45121 AATTTCATAAAGATATGATTATCAAAATTTATATGAAGA--TTATCAAAATTTCATAGTGTTGTT
1 AATTTCATAAAG--ATG-TTATCAAAATTT-TATAAAGAGGTTATC-AAATTTCATAGAGTGGTT
45184 ATCAA
61 ATCAA
* * ** * * * * * *
45189 AATTTCA-AAGCGAGGTTATCAAAATTGCATAATGTGATTATCAAAGTTTCATAGAGGGGTCAAC
1 AATTTCATAA-AGATGTTATCAAAATTTTATAAAGAGGTTATCAAA-TTTCATAGAGTGGTTATC
45253 AA
64 AA
*
45255 AATTTTATAAAGATGTTATCAAAATTTTATAAAGAGGTTATCAAATTT
1 AATTTCATAAAGATGTTATCAAAATTTTATAAAGAGGTTATCAAATTT
45303 TCAAAATCTG
Statistics
Matches: 139, Mismatches: 30, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
62 11 0.08
64 5 0.04
65 18 0.13
66 56 0.40
67 19 0.14
68 29 0.21
69 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (65 bp):
AATTTCATAAAGATGTTATCAAAATTTTATAAAGAGGTTATCAAATTTCATAGAGTGGTTATCAA
Found at i:45371 original size:22 final size:21
Alignment explanation
Indices: 45345--45988 Score: 185
Period size: 22 Copynumber: 29.9 Consensus size: 21
45335 ATTTTTAGGG
45345 AGGTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
* * *
45366 ATGGTTA-CCAAA-TT-A-GGA
1 A-GGTTATCAAAATTTCATAGT
* *
45384 AGGTTATTAAAATTTTAT-GAT
1 AGGTTATCAAAATTTCATAG-T
* * * *
45405 GGAGTAATCAAAATTTCA-GGG
1 AG-GTTATCAAAATTTCATAGT
* *
45426 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GT
*
45448 AGGTTATCAAATTTTCATAGTT
1 AGGTTATCAAAATTTCATAG-T
* *
45470 TGGTTTTCAAAATTTCATAAG-
1 AGGTTATCAAAATTTCAT-AGT
45491 AGGGTTATCAAAATTTCATAGT
1 A-GGTTATCAAAATTTCATAGT
* * *
45513 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATA-GT
* * *
45536 AGATTAACAAAATTTCATAAT
1 AGGTTATCAAAATTTCATAGT
** *
45557 GAGGTTATCAAAAAATCATAGGG
1 -AGGTTATCAAAATTTCATA-GT
*
45580 AGCTTATCAAAA-TT--T-GT
1 AGGTTATCAAAATTTCATAGT
* * *
45597 A-GTTATTAAGATTTCATAAGA
1 AGGTTATCAAAATTTCAT-AGT
* * *
45618 AAGTTATCAAAATTTTATAGG
1 AGGTTATCAAAATTTCATAGT
* * *
45639 AGGTTTATTAAAATTTTATAGAA
1 AGG-TTATCAAAATTTCATAG-T
* * *
45662 AGATTTATCAAAATTTGATAGCG
1 AG-GTTATCAAAATTTCATAG-T
*
45685 AGGTTATCACAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
* *
45706 -GTGATTATCAAAATTTTAAAGT
1 AG-G-TTATCAAAATTTCATAGT
*
45728 -GTGATTA-CTAACAA-TTCATATGG
1 AG-G-TTATC-AA-AATTTCATA-GT
* * * *
45751 AGGTTTTTAAATTTTTATAAAGT
1 AGGTTATCAAAATTTCAT--AGT
* * *
45774 -GGTTATCAATATATCATATGG
1 AGGTTATCAAAATTTCATA-GT
* * *
45795 AGGTTATTAACATTTTATAGTGT
1 AGGTTATCAAAATTTCATA--GT
* * *
45818 TGGTTATCAAAATTTCATTGGG
1 AGGTTATCAAAATTTCA-TAGT
* *
45840 AAGTTATCAAAATTTCATATT
1 AGGTTATCAAAATTTCATAGT
* * *
45861 GAGGTCT-TCAAAATTCCTTAGGG
1 -AGGT-TATCAAAATTTCATA-GT
* * *
45884 AGGTTAACAAAATTTCACAAGA
1 AGGTTATCAAAATTTCA-TAGT
* * **
45906 AAGTT-TAAAAAATTT-ATAAA
1 AGGTTAT-CAAAATTTCATAGT
* ** *
45926 AGGATTCTTGAAATTCCATAGT
1 AGG-TTATCAAAATTTCATAGT
* *
45948 ACCGTTATCAAAATTTCATAGG
1 A-GGTTATCAAAATTTCATAGT
45970 AGGTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
45989 ATGGGATCAT
Statistics
Matches: 448, Mismatches: 124, Indels: 102
0.66 0.18 0.15
Matches are distributed among these distances:
16 7 0.02
17 9 0.02
18 5 0.01
19 5 0.01
20 23 0.05
21 50 0.11
22 299 0.67
23 47 0.10
24 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGT
Found at i:45567 original size:44 final size:44
Alignment explanation
Indices: 45384--45900 Score: 251
Period size: 44 Copynumber: 11.9 Consensus size: 44
45374 CAAATTAGGA
* * * * *
45384 AGGTTATTAAAATTTTATGATGGAG-TAATCAAAATTTC--AGGG
1 AGGTTATCAAAATTTCAT-AGGGAGATTATCAAAATTTCATAGTG
* * * * * *
45426 AGGATATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTT
1 AGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG
* *
45470 TGGTTTTCAAAATTTCATAAGAGG-G-TTATCAAAATTTCATAGT-
1 AGGTTATCAAAATTTCAT-AG-GGAGATTATCAAAATTTCATAGTG
* * * *
45513 ATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATG
1 AGGT-TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG
** *
45558 AGGTTATCAAAAAATCATAGGGAGCTTATCAAAA-TT--T-GT-
1 AGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG
* * * * *
45597 A-GTTATTAAGATTTCATA-AGAAAGTTATCAAAATTTTATAG-G
1 AGGTTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTG
* * ** * *
45639 AGGTTTATTAAAATTTTATAGAAAGATTTATCAAAATTTGATAGCG
1 AGG-TTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTG
* * * * *
45685 AGGTTATCACAATTTCATAGTGTGATTATCAAAATTTTAAAGTG
1 AGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG
* * * * * * * * **
45729 TGATTA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTTATAAAG
1 AGGTTATC-AA-AATTTCATAGGGAGATTATCAAAATTTCATAGTG
* * * * * * * *
45773 TGGTTATCAATATATCATATGGAGGTTATTAACATTTTATAGTG
1 AGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG
* * *
45817 TTGGTTATCAAAATTTCATTGGGA-AGTTATCAAAATTTCATATTG
1 -AGGTTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTG
* * * *
45862 AGGTCT-TCAAAATTCCTTAGGGAGGTTAACAAAATTTCA
1 AGGT-TATCAAAATTTCATAGGGAGATTATCAAAATTTCA
45901 CAAGAAAGTT
Statistics
Matches: 363, Mismatches: 85, Indels: 52
0.73 0.17 0.10
Matches are distributed among these distances:
37 2 0.01
38 22 0.06
39 3 0.01
40 1 0.00
41 7 0.02
42 30 0.08
43 10 0.03
44 205 0.56
45 78 0.21
46 5 0.01
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG
Found at i:45652 original size:126 final size:127
Alignment explanation
Indices: 45481--45721 Score: 286
Period size: 126 Copynumber: 1.9 Consensus size: 127
45471 GGTTTTCAAA
** * * **
45481 ATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGA-TTAACA
1 ATTTCATAAGAAAGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGAAAGATTTAACA
* *
45545 AAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGCTTATCAAAATTTGTAGTTATTAAG
66 AAATTTCATAACGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTTGTAGTTATTAAG
* ** * * *
45607 ATTTCATAAGAAAGTTATCAAAATTTTATAGGAGGTTTATTAAAATTTTATAGAAAGATTTATCA
1 ATTTCATAAGAAAGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGAAAGATTTAACA
* * * ** * *
45672 AAATTTGATAGCGAGGTTATCACAATTTCATAGTGTGATTATCAAAATTT
66 AAATTTCATAACGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTT
45722 TAAAGTGTGA
Statistics
Matches: 93, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
126 47 0.51
127 46 0.49
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (127 bp):
ATTTCATAAGAAAGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGAAAGATTTAACA
AAATTTCATAACGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTTGTAGTTATTAAG
Found at i:45672 original size:45 final size:44
Alignment explanation
Indices: 45598--45723 Score: 139
Period size: 45 Copynumber: 2.8 Consensus size: 44
45588 AAAATTTGTA
*
45598 GTTATTAAGATTTCATAAGAAAG-TTATCAAAATTTTATAG-GAG
1 GTTATTAAAATTTCAT-AGAAAGATTATCAAAATTTTATAGCGAG
* *
45641 GTTTATTAAAATTTTATAGAAAGATTTATCAAAATTTGATAGCGAG
1 G-TTATTAAAATTTCATAGAAAGA-TTATCAAAATTTTATAGCGAG
* * ***
45687 GTTATCACAATTTCATAGTGTGATTATCAAAATTTTA
1 GTTATTAAAATTTCATAGAAAGATTATCAAAATTTTA
45724 AAGTGTGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
43 7 0.10
44 26 0.38
45 32 0.46
46 4 0.06
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (44 bp):
GTTATTAAAATTTCATAGAAAGATTATCAAAATTTTATAGCGAG
Found at i:45674 original size:23 final size:22
Alignment explanation
Indices: 45621--45682 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
45611 CATAAGAAAG
* *
45621 TTATCAAAATTTTATAGGAGGT
1 TTATCAAAATTTTATAGAAGAT
*
45643 TTATTAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAG-AAGAT
*
45666 TTATCAAAATTTGATAG
1 TTATCAAAATTTTATAG
45683 CGAGGTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTTATAGAAGAT
Found at i:46116 original size:2 final size:2
Alignment explanation
Indices: 46109--46137 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46099 CTAAAACTAG
46109 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 T
46138 CTTGAACCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46191 original size:15 final size:15
Alignment explanation
Indices: 46164--46201 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
46154 GTTCTATTAT
46164 TTATTTTTCAATTTCA
1 TTATTTTTCAATTT-A
46180 TTATTTTT-AATTTA
1 TTATTTTTCAATTTA
46194 TATATTTT
1 T-TATTTT
46202 CCTTTATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 8 0.38
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTTTCAATTTA
Found at i:47776 original size:179 final size:179
Alignment explanation
Indices: 47476--47830 Score: 665
Period size: 179 Copynumber: 2.0 Consensus size: 179
47466 TCTTTTAACG
* *
47476 ATCTATTGACTGTTGATGGAATCCCGTGCTCAACATTAAAGGAAGTTGCAATGAAAAGGGGATTA
1 ATCTATTGACTGTTGATGGAATCCCGTGCTCAACATTAAAGGAAGCTACAATGAAAAGGGGATTA
*
47541 CTGGAATCTGATCAGAGCATATCAGAATGCATGATGGAAGTTGTTGCGTGTCAAATGCCCAAAGA
66 CTGGAATCTGATCAGAGCATATCAGAATGCATGATGCAAGTTGTTGCGTGTCAAATGCCCAAAGA
*
47606 ACTGAGACATCTCTTTGCAACTTTATTAGTCAATTGTCAACCAACAGAA
131 ACTGAGACATCTCTTTGCAACTTTATTAGTAAATTGTCAACCAACAGAA
47655 ATCTATTGACTGTTGATGGAATCCCGTGCTCAACATTAAAGGAAGCTACAATGAAAAGGGGATTA
1 ATCTATTGACTGTTGATGGAATCCCGTGCTCAACATTAAAGGAAGCTACAATGAAAAGGGGATTA
*
47720 CTGGAATCTGATCAGAGCATATCAGAATGCATGATGCAAGTTGTTGCGTGTCAAATGCCCAACGA
66 CTGGAATCTGATCAGAGCATATCAGAATGCATGATGCAAGTTGTTGCGTGTCAAATGCCCAAAGA
47785 ACTGAGACATCTCTTTGCAACTTTATTAGTAAATTGTCAACCAACA
131 ACTGAGACATCTCTTTGCAACTTTATTAGTAAATTGTCAACCAACA
47831 AATGTGAGGA
Statistics
Matches: 171, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
179 171 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (179 bp):
ATCTATTGACTGTTGATGGAATCCCGTGCTCAACATTAAAGGAAGCTACAATGAAAAGGGGATTA
CTGGAATCTGATCAGAGCATATCAGAATGCATGATGCAAGTTGTTGCGTGTCAAATGCCCAAAGA
ACTGAGACATCTCTTTGCAACTTTATTAGTAAATTGTCAACCAACAGAA
Found at i:49030 original size:45 final size:45
Alignment explanation
Indices: 48961--49051 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
48951 GTCTGCTTAC
* *
48961 AACCATTTACATATCATAGAAAGTTTTAGCCAAGTTGAAATGGCA
1 AACCATTCACATATCAGAGAAAGTTTTAGCCAAGTTGAAATGGCA
49006 AACCATTCACATATCAGATG-AAGTTTTAGCCAAGTTGAAATGGCA
1 AACCATTCACATATCAGA-GAAAGTTTTAGCCAAGTTGAAATGGCA
49051 A
1 A
49052 CCTGTCTCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (45 bp):
AACCATTCACATATCAGAGAAAGTTTTAGCCAAGTTGAAATGGCA
Found at i:51786 original size:30 final size:30
Alignment explanation
Indices: 51746--51803 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
51736 TAACAGCCAG
*
51746 CTGTAAATCCTGCAGCACTGGAGCATCTGT
1 CTGTAAATCCTGCAGCACTGGAACATCTGT
* * *
51776 CTGTACATCCTGCGGCAGTGGAACATCT
1 CTGTAAATCCTGCAGCACTGGAACATCT
51804 ACCTATACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (30 bp):
CTGTAAATCCTGCAGCACTGGAACATCTGT
Found at i:51813 original size:30 final size:30
Alignment explanation
Indices: 51752--51816 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
51742 CCAGCTGTAA
* ** *
51752 ATCCTGCAGCACTGGAGCATCTGTCTGTAC
1 ATCCTGCAGCACTGGAACATCTACCTATAC
* *
51782 ATCCTGCGGCAGTGGAACATCTACCTATAC
1 ATCCTGCAGCACTGGAACATCTACCTATAC
51812 ATCCT
1 ATCCT
51817 ACGGTGGAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (30 bp):
ATCCTGCAGCACTGGAACATCTACCTATAC
Found at i:54387 original size:34 final size:28
Alignment explanation
Indices: 54313--54374 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
54303 ATCTTTCTCA
*
54313 TGGTCACTTTACAAAACAAAGGATAAGT
1 TGGTCAATTTACAAAACAAAGGATAAGT
54341 TGGTCAATTTACAAAACAAAGGATAAGT
1 TGGTCAATTTACAAAACAAAGGATAAGT
54369 TGGTCA
1 TGGTCA
54375 CTTATCCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (28 bp):
TGGTCAATTTACAAAACAAAGGATAAGT
Found at i:57114 original size:18 final size:18
Alignment explanation
Indices: 57091--57129 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
57081 ACACCCTATG
*
57091 AAATTCCAAAAAATTTTC
1 AAATTCCAAAAAATCTTC
57109 AAATTCCAAAAAATCTTC
1 AAATTCCAAAAAATCTTC
57127 AAA
1 AAA
57130 AAACATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATTCCAAAAAATCTTC
Found at i:58161 original size:2 final size:2
Alignment explanation
Indices: 58156--58186 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
58146 AAAGAATTAC
*
58156 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58187 CACACCTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Done.