Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016294.1 Corchorus capsularis cultivar CVL-1 contig16315, 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: 22791
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:497 original size:24 final size:25
Alignment explanation
Indices: 449--497 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
439 GCGCCAATTG
*
449 GCGCCAAAATTGTGCGACCATATTT
1 GCGCCAAAATTGTGCGACCACATTT
* *
474 GCGCC-AAATTTTGCGACCGCATTT
1 GCGCCAAAATTGTGCGACCACATTT
498 CCGTACGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (25 bp):
GCGCCAAAATTGTGCGACCACATTT
Found at i:803 original size:24 final size:24
Alignment explanation
Indices: 758--805 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
748 AAGTGTGAAG
* **
758 ATTTTTTTTTCTTTTTGTTTTTTA
1 ATTTTTCTTTCTTTTTAATTTTTA
782 ATTTTTCTTTCTTTTTAATTTTTA
1 ATTTTTCTTTCTTTTTAATTTTTA
806 CTCCTTTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.79
Consensus pattern (24 bp):
ATTTTTCTTTCTTTTTAATTTTTA
Found at i:1337 original size:86 final size:83
Alignment explanation
Indices: 1185--1352 Score: 214
Period size: 86 Copynumber: 2.0 Consensus size: 83
1175 GCTCAATTGA
*
1185 AGCATTCAAAGGGCTTTCTTGCCTATCCAAACAATATATAAATGGGCTCATAGCTCAGCCTTAAT
1 AGCATTCAAAGGGCTTTCTTGCCCATCCAAACAATATATAAATGGGCTCATAGCTCAGCCTTAAT
1250 GGGAATTGGGCCATTTGG
66 GGGAATTGGGCCATTTGG
* * * *
1268 AGCATTCAAAGGGCATGTTTCTTGCCCATCTAAAGAATATATAAATGGGC-CAATGGCTGA-CCT
1 AGCATTCAAAGGGC---TTTCTTGCCCATCCAAACAATATATAAATGGGCTC-ATAGCTCAGCCT
* *
1331 TCAATGGGCATTTGGCCATTTG
62 T-AATGGGAATTGGGCCATTTG
1353 CATCGAGCAA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
83 14 0.19
85 5 0.07
86 54 0.74
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (83 bp):
AGCATTCAAAGGGCTTTCTTGCCCATCCAAACAATATATAAATGGGCTCATAGCTCAGCCTTAAT
GGGAATTGGGCCATTTGG
Found at i:1924 original size:32 final size:32
Alignment explanation
Indices: 1880--1949 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
1870 TCACCATTGG
*
1880 CAGGTCGCCCTCCTGGTGCGGCTTCGCCACGA
1 CAGGCCGCCCTCCTGGTGCGGCTTCGCCACGA
*
1912 CAGGCCGCCCTCCTGGTGCGGCTTCGCCACGG
1 CAGGCCGCCCTCCTGGTGCGGCTTCGCCACGA
1944 CAGGCC
1 CAGGCC
1950 CCCCGGTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.09, C:0.43, G:0.33, T:0.16
Consensus pattern (32 bp):
CAGGCCGCCCTCCTGGTGCGGCTTCGCCACGA
Found at i:2068 original size:33 final size:33
Alignment explanation
Indices: 2020--2162 Score: 166
Period size: 33 Copynumber: 4.3 Consensus size: 33
2010 TCTAGCCGCT
*
2020 CTAGTGGGGCA-GCTCCGTCATGGCT-GAGCCGTC
1 CTAGTGGGG-AGGCTCCGCCATGG-TAGAGCCGTC
* * * *
2053 CTAGCGAGGAGGCTCCGCAATAGCT-GAGCCGTC
1 CTAGTGGGGAGGCTCCGCCAT-GGTAGAGCCGTC
*
2086 CTAGTGGGGAGGCTCTGCCATGGTAGAGCCGTC
1 CTAGTGGGGAGGCTCCGCCATGGTAGAGCCGTC
*
2119 CTAGTGGGGAGGCTCCGCCATGGTGGAGCCGTC
1 CTAGTGGGGAGGCTCCGCCATGGTAGAGCCGTC
*
2152 TTAGTGGGGAG
1 CTAGTGGGGAG
2163 ACTAGTGTAA
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
32 3 0.03
33 90 0.96
34 1 0.01
ACGTcount: A:0.15, C:0.26, G:0.39, T:0.20
Consensus pattern (33 bp):
CTAGTGGGGAGGCTCCGCCATGGTAGAGCCGTC
Found at i:3256 original size:22 final size:21
Alignment explanation
Indices: 3231--3281 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
3221 AATTTTGTCC
3231 ATTTTAT-ATAAATAAATAGTAT
1 ATTTTATGATAAAT--ATAGTAT
*
3253 ATTTATTTGATAAATATAGTAT
1 ATTT-TATGATAAATATAGTAT
3275 ATTTTAT
1 ATTTTAT
3282 TTGATTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 2 0.08
22 15 0.60
23 2 0.08
24 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (21 bp):
ATTTTATGATAAATATAGTAT
Found at i:5266 original size:108 final size:108
Alignment explanation
Indices: 5077--5368 Score: 428
Period size: 108 Copynumber: 2.6 Consensus size: 108
5067 TAAATTAAAA
* *
5077 TGGTAAAATAAA-AAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAG
1 TGGTAAAATAAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAG
5140 AATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAA-TTTTT
64 AATAAAATTGTATATTAG-AAAAATTTTAATATATCCAAATTTTTT
5185 TGGTAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAA
1 TGGTAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAA
*
5250 TAAAATTGTATATTAGAAAAATTTTAGTATATCCAAATTTTTT
66 TAAAATTGTATATTAGAAAAATTTTAATATATCCAAATTTTTT
* * *
5293 TGGTAAAAATAAAGTAATTATAAGGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGT-AAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
5358 GTAGAATAAAA
60 GTAGAATAAAA
5369 CTATAATAGT
Statistics
Matches: 169, Mismatches: 6, Indels: 12
0.90 0.03 0.06
Matches are distributed among these distances:
107 20 0.12
108 78 0.46
109 40 0.24
110 2 0.01
111 1 0.01
114 28 0.17
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.38
Consensus pattern (108 bp):
TGGTAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAA
TAAAATTGTATATTAGAAAAATTTTAATATATCCAAATTTTTT
Found at i:8952 original size:2 final size:2
Alignment explanation
Indices: 8945--8985 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
8935 TTATAGTTAG
* *
8945 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA GA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8986 GGTTTTGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9171 original size:175 final size:175
Alignment explanation
Indices: 8967--9317 Score: 666
Period size: 175 Copynumber: 2.0 Consensus size: 175
8957 TATATATATA
*
8967 TATATATATATAGATATATGGTTTTGATAGAAGAATATATAATCTATCCTTTCTTCTAGTTCCTT
1 TATATACATATAGATATATGGTTTTGATAGAAGAATATATAATCTATCCTTTCTTCTAGTTCCTT
9032 ATATTTTAAGCTGTTTGTTCTATGTAAGAACTTTAAAAGTTGGTTATAAGATTTCGTTCGTATTG
66 ATATTTTAAGCTGTTTGTTCTATGTAAGAACTTTAAAAGTTGGTTATAAGATTTCGTTCGTATTG
* *
9097 CAAAAGGAAAATTCTAAACAACCAGAAAAATTGACTAGAATTTTG
131 CAAAAGGAAAATTCTAAACAACCAGAAAAATTGACCAGAACTTTG
*
9142 TATATACATATATATATATGGTTTTGATAGAAGAATATATAATCTATCCTTTCTTCTAGTTCCTT
1 TATATACATATAGATATATGGTTTTGATAGAAGAATATATAATCTATCCTTTCTTCTAGTTCCTT
9207 ATATTTTAAGCTGTTTGTTCTATGTAAGAACTTTAAAAGTTGGTTATAAGATTTCGTTCGTATTG
66 ATATTTTAAGCTGTTTGTTCTATGTAAGAACTTTAAAAGTTGGTTATAAGATTTCGTTCGTATTG
9272 CAAAAGGAAAATTCTAAACAACCAGAAAAATTGACCAGAACTTTG
131 CAAAAGGAAAATTCTAAACAACCAGAAAAATTGACCAGAACTTTG
9317 T
1 T
9318 CCCACATGAT
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
175 172 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (175 bp):
TATATACATATAGATATATGGTTTTGATAGAAGAATATATAATCTATCCTTTCTTCTAGTTCCTT
ATATTTTAAGCTGTTTGTTCTATGTAAGAACTTTAAAAGTTGGTTATAAGATTTCGTTCGTATTG
CAAAAGGAAAATTCTAAACAACCAGAAAAATTGACCAGAACTTTG
Found at i:11899 original size:25 final size:25
Alignment explanation
Indices: 11865--11948 Score: 127
Period size: 25 Copynumber: 3.4 Consensus size: 25
11855 TTCAAACCCT
*
11865 AAACTTCATTCCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACTTCTTC
*
11890 AAACTTCATTTCTAACAACTTCTCC
1 AAACTTCATTTCTAACAACTTCTTC
*
11915 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACTTCTTC
11939 AAAC-TCATTT
1 AAACTTCATTT
11949 TCCTTCATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 6 0.11
24 8 0.15
25 41 0.75
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.37
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACTTCTTC
Found at i:12139 original size:32 final size:32
Alignment explanation
Indices: 12101--12214 Score: 165
Period size: 32 Copynumber: 3.6 Consensus size: 32
12091 ATGAGGAAGT
* *
12101 CGCCCAAAATGGGTGGCTTGGCCATGGCAGGC
1 CGCCCAAAATGGGCGGCTTGGTCATGGCAGGC
* *
12133 CGCCCAAAATGGGCAGCTTGGTCATGGCAAGC
1 CGCCCAAAATGGGCGGCTTGGTCATGGCAGGC
**
12165 CGCCCAAAATGGGCGGCTTGGTCATCACAGGC
1 CGCCCAAAATGGGCGGCTTGGTCATGGCAGGC
*
12197 CGCCCAAAATGGCCGGCT
1 CGCCCAAAATGGGCGGCT
12215 GCCCATTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.22, C:0.31, G:0.32, T:0.15
Consensus pattern (32 bp):
CGCCCAAAATGGGCGGCTTGGTCATGGCAGGC
Found at i:12343 original size:14 final size:15
Alignment explanation
Indices: 12326--12367 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
12316 AAATTTAGTT
12326 TGTTT-ATTAGTTTA
1 TGTTTAATTAGTTTA
*
12340 TGTTTAATTATTTTA
1 TGTTTAATTAGTTTA
**
12355 TAATTAATTAGTT
1 TGTTTAATTAGTT
12368 CATTATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (15 bp):
TGTTTAATTAGTTTA
Found at i:12582 original size:15 final size:14
Alignment explanation
Indices: 12549--12585 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
12539 AGTTTATTAA
12549 AATTAGT-TTGTTT
1 AATTAGTATTGTTT
12562 -ATTAGTATATGTTT
1 AATTAGTAT-TGTTT
12576 AATTAGTATT
1 AATTAGTATT
12586 TAATTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 1 0.05
14 6 0.29
15 8 0.38
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (14 bp):
AATTAGTATTGTTT
Found at i:12906 original size:24 final size:27
Alignment explanation
Indices: 12873--12968 Score: 99
Period size: 30 Copynumber: 3.4 Consensus size: 27
12863 CTCCGCCCGT
*
12873 AGGGACAGAGAGG-AGCA-TTTG-CAG
1 AGGGAGAGAGAGGCAGCACTTTGCCAG
*
12897 AGGGAGAGAGAGGCAGCAGTTGCTGCTCAG
1 AGGGAGAGAGAGGCAGCACTT--TGC-CAG
12927 AGGGAGAGAGAGGCAGCAACTATTGCTCAG
1 AGGGAGAGAGAGGCAGC-ACT-TTGC-CAG
12957 AGGGAGAGAGAG
1 AGGGAGAGAGAG
12969 CTTGCTGCTG
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
24 12 0.19
25 4 0.06
26 2 0.03
28 2 0.03
30 39 0.63
31 2 0.03
32 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.43, T:0.11
Consensus pattern (27 bp):
AGGGAGAGAGAGGCAGCACTTTGCCAG
Found at i:12963 original size:28 final size:30
Alignment explanation
Indices: 12894--12968 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
12884 GGAGCATTTG
** *
12894 CAGAGGGAGAGAGAGGCAGCAGTTGCTGCT
1 CAGAGGGAGAGAGAGGCAGCAACTACTGCT
*
12924 CAGAGGGAGAGAGAGGCAGCAACTATTGCT
1 CAGAGGGAGAGAGAGGCAGCAACTACTGCT
12954 CAGAGGGAGAGAGAG
1 CAGAGGGAGAGAGAG
12969 CTTGCTGCTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.43, T:0.11
Consensus pattern (30 bp):
CAGAGGGAGAGAGAGGCAGCAACTACTGCT
Found at i:16114 original size:15 final size:15
Alignment explanation
Indices: 16096--16141 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
16086 TCATTAATTT
16096 ATTAATCATAAACTA
1 ATTAATCATAAACTA
16111 ATTAA--AT--ACTA
1 ATTAATCATAAACTA
16122 ATTAATCATAAACTA
1 ATTAATCATAAACTA
16137 ATTAA
1 ATTAA
16142 ATACTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 9 0.33
13 4 0.15
15 14 0.52
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAATCATAAACTA
Found at i:16121 original size:11 final size:11
Alignment explanation
Indices: 16107--16153 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 11
16097 TTAATCATAA
16107 ACTAATTAAAT
1 ACTAATTAAAT
16118 ACTAATTAATCAT
1 ACTAATTAA--AT
16131 AAACTAATTAAAT
1 --ACTAATTAAAT
16144 ACTAATTAAA
1 ACTAATTAAA
16154 CAAAAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 19 0.59
13 4 0.12
15 9 0.28
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:16126 original size:26 final size:26
Alignment explanation
Indices: 16096--16164 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
16086 TCATTAATTT
16096 ATTAATCATAAACTAATTAAATACTA
1 ATTAATCATAAACTAATTAAATACTA
16122 ATTAATCATAAACTAATTAAATACTA
1 ATTAATCATAAACTAATTAAATACTA
* *
16148 ATTAAACAAAAACTAAT
1 ATTAATCATAAACTAAT
16165 AAGCTAAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.32
Consensus pattern (26 bp):
ATTAATCATAAACTAATTAAATACTA
Found at i:16706 original size:50 final size:50
Alignment explanation
Indices: 16627--16760 Score: 241
Period size: 50 Copynumber: 2.7 Consensus size: 50
16617 AGGCTGGAAA
*
16627 TTGATTGACTTGAGACGATGCGGCGACTCGTAAAGCCGAATAGACTGAAT
1 TTGATTGACTTGAGACGATGCGGCAACTCGTAAAGCCGAATAGACTGAAT
16677 TTGATTGACTTGAGACGATGCGGCAACTCGTAAAGCCGAATAGACTGAAT
1 TTGATTGACTTGAGACGATGCGGCAACTCGTAAAGCCGAATAGACTGAAT
* *
16727 TTGGTTGACTTGAGACAATGCGGCAACTCGTAAA
1 TTGATTGACTTGAGACGATGCGGCAACTCGTAAA
16761 TCCATATAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 81 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (50 bp):
TTGATTGACTTGAGACGATGCGGCAACTCGTAAAGCCGAATAGACTGAAT
Found at i:18292 original size:2 final size:2
Alignment explanation
Indices: 18255--18279 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18245 GTTGCTGCTT
18255 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 T
18280 GGCCAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19651 original size:14 final size:14
Alignment explanation
Indices: 19632--19671 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
19622 TGGCCTCCAA
**
19632 ATATATATATTGAT
1 ATATATATATACAT
*
19646 ATATATACATACAT
1 ATATATATATACAT
19660 ATATATATATAC
1 ATATATATATAC
19672 TAGTTTTAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (14 bp):
ATATATATATACAT
Found at i:20151 original size:45 final size:45
Alignment explanation
Indices: 20056--20162 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 45
20046 GATAATCACA
* * * * *
20056 CTATGAAATTGTGATAAACTCGCTGTGAAATTTAGATAAATCTTC
1 CTATAAAATTTTGATAAACTCCCTATAAAATTTAGATAAATCTTC
* *
20101 CTATAAAATTTTGATAAATCTCCCTATAAAATTTTGAT-AATTTTC
1 CTATAAAATTTTGATAAA-CTCCCTATAAAATTTAGATAAATCTTC
* *
20146 TTATAAAATCTTGATAA
1 CTATAAAATTTTGATAA
20163 CTACAAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 37 0.71
46 15 0.29
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (45 bp):
CTATAAAATTTTGATAAACTCCCTATAAAATTTAGATAAATCTTC
Found at i:20153 original size:22 final size:23
Alignment explanation
Indices: 20083--20162 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
20073 ACTCGCTGTG
*
20083 AAATTTAGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
*
20106 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
* *
20129 AAATTTTGAT-AATTTTCTTATA
1 AAATTTTGATAAATCTTCCTATA
*
20151 AAATCTTGATAA
1 AAATTTTGATAA
20163 CTACAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
22 18 0.36
23 32 0.64
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.42
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:20217 original size:22 final size:22
Alignment explanation
Indices: 19924--20253 Score: 105
Period size: 22 Copynumber: 15.1 Consensus size: 22
19914 AAGATCTCAA
*
19924 TATGAAATTTTGATAACCAACAC-
1 TATGAAATTTTGATAACC-TC-CT
* *
19947 TAT-AAGATGTTGATAACCTCCA
1 TATGAA-ATTTTGATAACCTCCT
* * * *
19969 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCT
* * * *
19991 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCT
* *
20013 TATG-AATTGTT-AGTAATCACAC-
1 TATGAAATT-TTGA-TAACCTC-CT
* * *
20035 TCTGAAATTTTGATAATCACAC-
1 TATGAAATTTTGATAACCTC-CT
* *
20057 TATGAAATTGTGATAAACTCGC-
1 TATGAAATTTTGATAACCTC-CT
* * *
20079 TGTGAAATTTAGATAAATCTTCC-
1 TATGAAATTTTGAT-AA-CCTCCT
* * *
20102 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTCCT
* ** *
20125 TATAAAATTTTGATAATTTTCT
1 TATGAAATTTTGATAACCTCCT
* *
20147 TATAAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTCCT
*
20164 TA-CAAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCTCCT
** * *
20185 TATGATTTTTTAATAACCTCAT
1 TATGAAATTTTGATAACCTCCT
* * *
20207 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCT
20229 TATGAAATTTTGATAAACCT-CT
1 TATGAAATTTTGAT-AACCTCCT
20251 TAT
1 TAT
20254 TTTTTTTGGC
Statistics
Matches: 233, Mismatches: 56, Indels: 37
0.71 0.17 0.11
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 1 0.00
20 1 0.00
21 7 0.03
22 153 0.66
23 56 0.24
24 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCT
Found at i:20687 original size:21 final size:23
Alignment explanation
Indices: 20433--20687 Score: 100
Period size: 22 Copynumber: 11.6 Consensus size: 23
20423 AGAAATACTA
20433 CTATGAAATTTTTG-TAATCACATT
1 CTATGAAA-TTTTGATAATCAC-TT
* * *
20457 -T-TGAAAATTTGATAACCTCTT
1 CTATGAAATTTTGATAATCACTT
* * *
20478 -TATAAAATTTTGATAACCTCTT
1 CTATGAAATTTTGATAATCACTT
* * * *
20500 -TAT-AAGATTTTGTTGA-CCCCT
1 CTATGAA-ATTTTGATAATCACTT
** *
20521 CTATGAAATTCCGATAATCACAT
1 CTATGAAATTTTGATAATCACTT
* *
20544 -TATGTAATTTTGATAA-C-CTCG
1 CTATGAAATTTTGATAATCACT-T
* * *
20565 CTTTGCAATTTTGATAA-CAAC-A
1 CTATGAAATTTTGATAATC-ACTT
20587 CTATGAAATTTTGATAAT--CTT
1 CTATGAAATTTTGATAATCACTT
20608 CCTAT-AAATTTTGATAATCTGA-TCT
1 -CTATGAAATTTTGATAATC--ACT-T
*
20633 CTATGAAATTTCGATAATCAC-T
1 CTATGAAATTTTGATAATCACTT
*
20655 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCACTT
*
20675 CTATCAAATTTTG
1 CTATGAAATTTTG
20688 GTACTCCTTA
Statistics
Matches: 178, Mismatches: 31, Indels: 47
0.70 0.12 0.18
Matches are distributed among these distances:
19 1 0.01
20 10 0.06
21 37 0.21
22 103 0.58
23 7 0.04
24 6 0.03
25 14 0.08
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.42
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCACTT
Found at i:20739 original size:22 final size:22
Alignment explanation
Indices: 20544--20764 Score: 84
Period size: 22 Copynumber: 9.9 Consensus size: 22
20534 ATAATCACAT
* *
20544 TATGTAATTTTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-A
* * **
20566 TTTGCAATTTTGATAA-CAACA
1 TATGAAATTTTGATAACCTTCA
* *
20587 CTATGAAATTTTGATAATCTTCC
1 -TATGAAATTTTGATAACCTTCA
* *
20610 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAACCT--TC-A
*
20634 TATGAAATTTCGATAATCAC-TC-
1 TATGAAATTTTGATAA-C-CTTCA
*
20656 TATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAACCTTCA
* * *
20676 TATCAAATTTTGGTACTCCTT-A
1 TATGAAATTTTGATA-ACCTTCA
*
20698 TGAAATTGAGACTTTT-ATAACCTTCA
1 T---A-TGA-AATTTTGATAACCTTCA
*
20724 TATGAAATTTTGATAACC-ACA
1 TATGAAATTTTGATAACCTTCA
*
20745 CTATAAAATTTTGATAACCT
1 -TATGAAATTTTGATAACCT
20765 CCCCATGAAA
Statistics
Matches: 153, Mismatches: 24, Indels: 43
0.70 0.11 0.20
Matches are distributed among these distances:
19 1 0.01
20 8 0.05
21 36 0.24
22 69 0.45
23 5 0.03
24 6 0.04
25 16 0.10
26 6 0.04
27 6 0.04
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:20775 original size:22 final size:22
Alignment explanation
Indices: 20725--20801 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
20715 TAACCTTCAT
* * *
20725 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCTCCCA
* *
20747 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCTCCCA
* *
20769 ATGAAATATT-AGTAACCTCCTA
1 ATGAAATTTTGA-TAACCTCCCA
20791 ATGAAATTTTG
1 ATGAAATTTTG
20802 TTAATCACAC
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 1 0.02
22 43 0.98
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCCA
Found at i:20969 original size:22 final size:22
Alignment explanation
Indices: 20885--21072 Score: 116
Period size: 22 Copynumber: 8.4 Consensus size: 22
20875 TTGTGAAAAT
* **
20885 TAACCACCCTATGAAATTTCAA
1 TAACCACACTATGAAATTTTGA
* *
20907 TAACCA-ACCTAAGAAATTTTAA
1 TAACCACA-CTATGAAATTTTGA
* *
20929 TAACCTGATC-CTATATGAAAATTTGG
1 TAACC--A-CAC--TATGAAATTTTGA
20955 TAACCACACTATGAAATTTTGA
1 TAACCACACTATGAAATTTTGA
** *
20977 TAACTTCTA-TATGAAATTTTGG
1 TAACCAC-ACTATGAAATTTTGA
* *
20999 TAACAACACTATGGAATTTTGA
1 TAACCACACTATGAAATTTTGA
* * *
21021 TAACCTC-CTCATGAAATTATAA
1 TAACCACACT-ATGAAATTTTGA
*
21043 TAACCATC-TTATGAAATTTTGA
1 TAACCA-CACTATGAAATTTTGA
21065 TAACCACA
1 TAACCACA
21073 TAGAGACAAG
Statistics
Matches: 128, Mismatches: 25, Indels: 26
0.72 0.14 0.15
Matches are distributed among these distances:
21 4 0.03
22 102 0.80
23 4 0.03
24 4 0.03
26 14 0.11
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:21002 original size:44 final size:44
Alignment explanation
Indices: 20937--21068 Score: 151
Period size: 44 Copynumber: 3.0 Consensus size: 44
20927 AATAACCTGA
*
20937 TCCTATATGAAAATTTGGTAACCACACTATGAAATTTTGATAAC
1 TCCTATATGAAATTTTGGTAACCACACTATGAAATTTTGATAAC
* * *
20981 TTCTATATGAAATTTTGGTAACAACACTATGGAATTTTGATAACC
1 TCCTATATGAAATTTTGGTAACCACACTATGAAATTTTGATAA-C
* * ** *
21026 TCCT-CATGAAATTATAATAACCATC-TTATGAAATTTTGATAAC
1 TCCTATATGAAATTTTGGTAACCA-CACTATGAAATTTTGATAAC
21069 CACATAGAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
43 1 0.01
44 68 0.92
45 5 0.07
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (44 bp):
TCCTATATGAAATTTTGGTAACCACACTATGAAATTTTGATAAC
Found at i:21275 original size:19 final size:20
Alignment explanation
Indices: 21244--21281 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
21234 TATTGAAATT
21244 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
21263 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
21282 ACTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:21489 original size:31 final size:32
Alignment explanation
Indices: 21444--21511 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
21434 TTTAGTAATG
* *
21444 ACAATTTAGAAATATGTTTTAAAAAAAATGGT
1 ACAATTGAGAAATATGTTTTAAAAAAAAGGGT
*
21476 ACAATTGA-AAATATGTTTTAAAAATAAGGGT
1 ACAATTGAGAAATATGTTTTAAAAAAAAGGGT
21507 ACAAT
1 ACAAT
21512 CAGAAAACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.32
Consensus pattern (32 bp):
ACAATTGAGAAATATGTTTTAAAAAAAAGGGT
Done.