Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007966.1 Corchorus capsularis cultivar CVL-1 contig07987, 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: 34631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2658 original size:18 final size:19
Alignment explanation
Indices: 2635--2672 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2625 GAAATAGGAT
2635 TTCAAATCCAACAGA-AGA
1 TTCAAATCCAACAGATAGA
*
2653 TTCAAATTCAACAGATAGA
1 TTCAAATCCAACAGATAGA
2672 T
1 T
2673 AGGATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCAAATCCAACAGATAGA
Found at i:3147 original size:32 final size:32
Alignment explanation
Indices: 3107--3169 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
3097 TGGGGCATTT
* *
3107 TTTTATCTCACTTATGGTTTATATATCATGTA
1 TTTTATCTCACTTAGGGTTTAGATATCATGTA
*
3139 TTTTATCTCACTTAGGGTTTAGATTTCATGT
1 TTTTATCTCACTTAGGGTTTAGATATCATGT
3170 CATGTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.52
Consensus pattern (32 bp):
TTTTATCTCACTTAGGGTTTAGATATCATGTA
Found at i:3348 original size:32 final size:32
Alignment explanation
Indices: 3302--3363 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
3292 GGGGCATTTC
*
3302 TTTATCTCACTTAGGGTTTATATATCATGTAT
1 TTTATCTCACTTAGGGTTTAGATATCATGTAT
* *
3334 TTTATCTCATTTAGGGTTTAGATTTCATGT
1 TTTATCTCACTTAGGGTTTAGATATCATGT
3364 CATGTCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.52
Consensus pattern (32 bp):
TTTATCTCACTTAGGGTTTAGATATCATGTAT
Found at i:3350 original size:194 final size:194
Alignment explanation
Indices: 3014--3396 Score: 687
Period size: 194 Copynumber: 2.0 Consensus size: 194
3004 TGTCACAACT
*
3014 TTTGAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAGACTATTTCACT
1 TTTGAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAGACTATCTCACT
* * *
3079 TAGGGTTTAATATTGTTTTGGGGCATTTTTTTATCTCACTTATGGTTTATATATCATGTATTTTA
66 TAGGGTTTAATATAGTTTTGGGGCATTTCTTTATCTCACTTAGGGTTTATATATCATGTATTTTA
3144 TCTCACTTAGGGTTTAGATTTCATGTCATGTCA-TTTTTTTGTCTCTCATAGTCTTTTTTCTTTA
131 TCTCACTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTTGTCTCTCATAG-CTTTTTTCTTTA
* *
3208 TTTGAAATTTTGACTCTTCCACCACTTTTTATGACATAGAATGTTGAAATTTAGACTATCTCACT
1 TTTGAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAGACTATCTCACT
3273 TAGGGTTTAATATAGTTTTGGGGCATTTCTTTATCTCACTTAGGGTTTATATATCATGTATTTTA
66 TAGGGTTTAATATAGTTTTGGGGCATTTCTTTATCTCACTTAGGGTTTATATATCATGTATTTTA
*
3338 TCTCATTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTTGTCTCTCATAGCTTTTTT
131 TCTCACTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTTGTCTCTCATAGCTTTTTT
3397 TTCTTAAAAA
Statistics
Matches: 181, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
194 163 0.90
195 18 0.10
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.50
Consensus pattern (194 bp):
TTTGAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAGACTATCTCACT
TAGGGTTTAATATAGTTTTGGGGCATTTCTTTATCTCACTTAGGGTTTATATATCATGTATTTTA
TCTCACTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTTGTCTCTCATAGCTTTTTTCTTTA
Found at i:4564 original size:19 final size:19
Alignment explanation
Indices: 4535--4572 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
4525 TTGAGAAAAT
4535 TTTGAAACATTTAGTCCTTA
1 TTTGAAACATTTAG-CCTTA
4555 TTTG-AACATTTAGCCTTA
1 TTTGAAACATTTAGCCTTA
4573 GCAATAGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGAAACATTTAGCCTTA
Found at i:9333 original size:22 final size:22
Alignment explanation
Indices: 9308--9477 Score: 78
Period size: 22 Copynumber: 7.7 Consensus size: 22
9298 AGGATCCCAT
9308 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAATCTTCC
* ** *
9330 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAATCTTCC
* * * **
9352 TATGGAATTTCGAGAATCTTTT
1 TATGAAATTTTGATAATCTTCC
** * *
9374 TAT-AAATTTTTTTAAACCTTCT
1 TATGAAATTTTGAT-AATCTTCC
* * * *
9396 TATGAAATTCTGTTAACCTCCC
1 TATGAAATTTTGATAATCTTCC
* * * *
9418 TAAGGAATTTTGA-AGA-CCTCAA
1 TATGAAATTTTGATA-ATCTTC-C
9440 TATGAAATTTTGATAA-CTTCTC
1 TATGAAATTTTGATAATCTTC-C
*
9462 AATGAAATTTTGATAA
1 TATGAAATTTTGATAA
9478 CCAACTGTTG
Statistics
Matches: 107, Mismatches: 36, Indels: 10
0.70 0.24 0.07
Matches are distributed among these distances:
21 8 0.07
22 90 0.84
23 9 0.08
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTCC
Found at i:11729 original size:22 final size:22
Alignment explanation
Indices: 11704--11752 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11694 GAATTGTTAG
* * **
11704 TAATCATACTCTGAAATTTCGA
1 TAATCACACTATGAAATTGAGA
11726 TAATCACACTATGAAATTGAGA
1 TAATCACACTATGAAATTGAGA
11748 TAATC
1 TAATC
11753 TCGTTATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (22 bp):
TAATCACACTATGAAATTGAGA
Found at i:11771 original size:22 final size:21
Alignment explanation
Indices: 11715--12048 Score: 177
Period size: 22 Copynumber: 15.6 Consensus size: 21
11705 AATCATACTC
* *
11715 TGAAATTTCGATAATCACACTA
1 TGAAATTTTGATAATCTC-CTA
** *
11737 TGAAATTGAGATAATCTCGTTA
1 TGAAATTTTGATAATCTC-CTA
11759 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGAT-AATC-TCCTA
* *
11782 TAAAATTTTGATAAACCTGCCTA
1 TGAAATTTTGAT-AATCT-CCTA
* * *
11805 TAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAA-TCTCCTA
* *
11827 TAAAATCTTGATAA----CTA
1 TGAAATTTTGATAATCTCCTA
* *
11844 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAATCT-CCTA
** * *
11865 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAATCTC-CTA
*
11887 TGAAATTTTGTTAATCTCGCTA
1 TGAAATTTTGATAATCTC-CTA
* *
11909 TGAAATTTTGAT-CTACATACTA
1 TGAAATTTTGATAAT-C-TCCTA
*
11931 TGAAATTTTGATAATCCTCTTA
1 TGAAATTTTGATAAT-CTCCTA
* *
11953 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAATCT--CCTA
* *
11975 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAATC-TCCTA
*
11997 TGAAATTTTGAT-ATCCTCC-G
1 TGAAATTTTGATAAT-CTCCTA
*
12017 TGAAATTTTGAT-ATC-CTCTC
1 TGAAATTTTGATAATCTC-CTA
12037 TGAAATTTTGAT
1 TGAAATTTTGAT
12049 TATTCCATAA
Statistics
Matches: 247, Mismatches: 44, Indels: 44
0.74 0.13 0.13
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
19 2 0.01
20 28 0.11
21 10 0.04
22 146 0.59
23 44 0.18
24 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (21 bp):
TGAAATTTTGATAATCTCCTA
Found at i:11787 original size:23 final size:23
Alignment explanation
Indices: 11761--11840 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
11751 TCTCGTTATG
11761 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
* *
11784 AAATTTTGATAAACCTGCCTATA
1 AAATTTTGATAAATCTTCCTATA
* *
11807 AAATTTTGATAACT-TTCTTATA
1 AAATTTTGATAAATCTTCCTATA
*
11829 AAATCTTGATAA
1 AAATTTTGATAA
11841 CTACAAATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 17 0.34
23 33 0.66
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:12022 original size:20 final size:20
Alignment explanation
Indices: 11975--12048 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
11965 AACTAAACTA
* *
11975 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATATCC-TC-TC
11997 TGAAATTTTGATATCCTC-C
1 TGAAATTTTGATATCCTCTC
12016 GTGAAATTTTGATATCCTCTC
1 -TGAAATTTTGATATCCTCTC
12037 TGAAATTTTGAT
1 TGAAATTTTGAT
12049 TATTCCATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
20 30 0.62
21 3 0.06
22 15 0.31
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCTC
Found at i:12206 original size:22 final size:22
Alignment explanation
Indices: 12156--12207 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
12146 TCACATTTTG
*
12156 AAAA-TTTGATAACCTTTTTAT
1 AAAATTTTGATAACCTCTTTAT
*
12177 GAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
12199 AAAATTTTG
1 AAAATTTTG
12208 TTGACCCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:12225 original size:22 final size:22
Alignment explanation
Indices: 12154--12233 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
12144 AATCACATTT
* ** *
12154 TGAAAATTTGATAACCTTTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
12176 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
12198 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
*
12220 TGAAATTCTGATAA
1 TGAAATTTTGATAA
12234 TCACATTACA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:12855 original size:22 final size:22
Alignment explanation
Indices: 12830--12931 Score: 77
Period size: 22 Copynumber: 4.6 Consensus size: 22
12820 ACCTCGCTTA
12830 GAAATTTTGATAA-CAACACTAT
1 GAAATTTTGATAATCAAC-CTAT
* **
12852 GAAATTTGGATAATCTTCCTAT
1 GAAATTTTGATAATCAACCTAT
*
12874 -AAATTTTGATAATCTGATCTCTAT
1 GAAATTTTGATAATC--AAC-CTAT
*
12898 GAAATTTCGATAATC-ACTCTAT
1 GAAATTTTGATAATCAAC-CTAT
*
12920 GAGA-TTTGATAA
1 GAAATTTTGATAA
12932 CCTTCTATCA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
21 20 0.30
22 25 0.38
23 4 0.06
24 4 0.06
25 13 0.20
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (22 bp):
GAAATTTTGATAATCAACCTAT
Found at i:12877 original size:21 final size:24
Alignment explanation
Indices: 12848--12931 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 24
12838 GATAACAACA
*
12848 CTATGAAATTTGGATAATCT-TC-
1 CTATGAAATTTCGATAATCTATCT
*
12870 CTAT-AAATTTTGATAATCTGATCT
1 CTATGAAATTTCGATAATCT-ATCT
12894 CTATGAAATTTCGATAATC-A-CT
1 CTATGAAATTTCGATAATCTATCT
*
12916 CTATGAGATTT-GATAA
1 CTATGAAATTTCGATAA
12932 CCTTCTATCA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
21 19 0.35
22 16 0.29
23 3 0.05
24 4 0.07
25 13 0.24
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (24 bp):
CTATGAAATTTCGATAATCTATCT
Found at i:13000 original size:22 final size:22
Alignment explanation
Indices: 12971--13088 Score: 95
Period size: 22 Copynumber: 5.4 Consensus size: 22
12961 AAATTGAGAC
*
12971 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTCCTATGAAA
*
12992 TTTTGATAACCTTCCCATGAAA
1 TTTTGATAACCTTCCTATGAAA
*
13014 TATT-AGTAACC-TCCTAATGAAA
1 TTTTGA-TAACCTTCCT-ATGAAA
* *
13036 TTTTGTTAA-CTACACTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
*
13058 TTCTT-ATAACC-TCGCTATGACA
1 TT-TTGATAACCTTC-CTATGAAA
13080 TTTTGATAA
1 TTTTGATAA
13089 TCTCTTTGAT
Statistics
Matches: 77, Mismatches: 11, Indels: 17
0.73 0.10 0.16
Matches are distributed among these distances:
21 11 0.14
22 61 0.79
23 5 0.06
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:13034 original size:44 final size:44
Alignment explanation
Indices: 12985--13088 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
12975 ATAACCTTCA
*
12985 TATGAAATTTTGATAACCTTC-CCATGAAA-TATTAGTAACCTC-C
1 TATGAAATTTTGATAA-CTACACCATGAAATTATTA-TAACCTCGC
* * *
13028 TAATGAAATTTTGTTAACTACACTATGAAATTCTTATAACCTCGC
1 T-ATGAAATTTTGATAACTACACCATGAAATTATTATAACCTCGC
*
13073 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
13089 TCTCTTTGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
43 4 0.08
44 41 0.80
45 6 0.12
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACACCATGAAATTATTATAACCTCGC
Found at i:13206 original size:22 final size:21
Alignment explanation
Indices: 13124--13286 Score: 137
Period size: 22 Copynumber: 7.3 Consensus size: 21
13114 TTGTGATAAT
**
13124 TAACCACCCTATGAAATTTCAA
1 TAACCA-CCTATGAAATTTTGA
* * *
13146 TAACCAACATAAGAAATTTTAA
1 TAACC-ACCTATGAAATTTTGA
*
13168 TAACCTGGTCCTATGAAATTTTGA
1 TAACC---ACCTATGAAATTTTGA
*
13192 TAACCACGCTATGAAATTTTGG
1 TAACCAC-CTATGAAATTTTGA
*
13214 TAACCACACTATGGAATTTTGA
1 TAACCAC-CTATGAAATTTTGA
* * *
13236 TAACCTCCTCATGAAATTATAA
1 TAACCACCT-ATGAAATTTTGA
*
13258 TAACCATCTTATGAAATTTTGA
1 TAACCA-CCTATGAAATTTTGA
13280 TAACCAC
1 TAACCAC
13287 ATAGAGACAA
Statistics
Matches: 114, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
21 4 0.04
22 90 0.79
23 3 0.03
24 17 0.15
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (21 bp):
TAACCACCTATGAAATTTTGA
Found at i:13232 original size:68 final size:66
Alignment explanation
Indices: 13119--13287 Score: 173
Period size: 68 Copynumber: 2.5 Consensus size: 66
13109 TAAAATTGTG
**
13119 ATAATTAACCACCCTATGAAATTTCAATAACCA-ACATAAGAAATTTTAATAACCTGGTCCT-AT
1 ATAA-TAACCA-CCTATGAAATTTTGATAACCACACATAAGAAATTTTAATAACC---TCCTCAT
13182 GAAATT
61 GAAATT
* * * * * *
13188 TTGATAACCACGCTATGAAATTTTGGTAACCACAC-TATGGAATTTTGATAACCTCCTCATGAAA
1 ATAATAACCAC-CTATGAAATTTTGATAACCACACATAAGAAATTTTAATAACCTCCTCATGAAA
13252 TT
65 TT
*
13254 ATAATAACCATCTTATGAAATTTTGATAACCACA
1 ATAATAACCA-CCTATGAAATTTTGATAACCACA
13288 TAGAGACAAG
Statistics
Matches: 84, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
65 4 0.05
66 36 0.43
67 2 0.02
68 38 0.45
69 4 0.05
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (66 bp):
ATAATAACCACCTATGAAATTTTGATAACCACACATAAGAAATTTTAATAACCTCCTCATGAAAT
T
Found at i:14673 original size:38 final size:37
Alignment explanation
Indices: 14631--14754 Score: 178
Period size: 38 Copynumber: 3.3 Consensus size: 37
14621 AAATAGGACG
*
14631 TTGGAGACAAAGACAACAAGCAAAATTAAATACAACGA
1 TTGGAAACAAAGACAA-AAGCAAAATTAAATACAACGA
14669 TTGGAAACAAAGACAAAAAGCAAAATTAAATACAACGA
1 TTGGAAACAAAGAC-AAAAGCAAAATTAAATACAACGA
* **
14707 TTGGAAACAAAAACAAAAGGCAAAATTAAATAGGACG-
1 TTGGAAACAAAGACAAAA-GCAAAATTAAATACAACGA
14744 TTGGAAACAAA
1 TTGGAAACAAA
14755 AAGACAAATT
Statistics
Matches: 80, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
37 15 0.19
38 63 0.79
39 2 0.03
ACGTcount: A:0.57, C:0.13, G:0.16, T:0.14
Consensus pattern (37 bp):
TTGGAAACAAAGACAAAAGCAAAATTAAATACAACGA
Found at i:15453 original size:33 final size:33
Alignment explanation
Indices: 15414--15477 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
15404 CTAAAATTAA
*
15414 GTTATAAAATTGTGTAAAACAAATTTGTTTACG
1 GTTATAAAATTATGTAAAACAAATTTGTTTACG
15447 GTTATAAAATTATGTAAAACAAATTTGTTTA
1 GTTATAAAATTATGTAAAACAAATTTGTTTA
15478 TACTGTGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (33 bp):
GTTATAAAATTATGTAAAACAAATTTGTTTACG
Found at i:32305 original size:2 final size:2
Alignment explanation
Indices: 32289--32345 Score: 70
Period size: 2 Copynumber: 30.5 Consensus size: 2
32279 GTTTAACATC
32289 AT AT AT -T AT AT -T AT AT AT AT AT AT AT A- ACT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
32327 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
32346 ATTTGGGCTG
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
1 5 0.10
2 44 0.90
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32321 original size:24 final size:24
Alignment explanation
Indices: 32294--32339 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
32284 ACATCATATA
*
32294 TTATATTATATATATATATATAAC
1 TTATAATATATATATATATATAAC
32318 TTATAATATATATATATATATA
1 TTATAATATATATATATATATA
32340 TATATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATAATATATATATATATATAAC
Found at i:33260 original size:32 final size:33
Alignment explanation
Indices: 33189--33260 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
33179 AAAAATTGCA
**
33189 TATGCCGCCCCCTGGGGCGGCCATAAACCATGG
1 TATGCCGCCCCCTAAGGCGGCCATAAACCATGG
* *
33222 TATGCCGCCCCCTAAGGCGG-CATGAGCCATGG
1 TATGCCGCCCCCTAAGGCGGCCATAAACCATGG
*
33254 TTTGCCG
1 TATGCCG
33261 TCCCGGAGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 16 0.47
33 18 0.53
ACGTcount: A:0.17, C:0.35, G:0.31, T:0.18
Consensus pattern (33 bp):
TATGCCGCCCCCTAAGGCGGCCATAAACCATGG
Found at i:33789 original size:15 final size:16
Alignment explanation
Indices: 33769--33806 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
33759 CGTTCAAATG
33769 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
33784 TCGGGTCAATTATGGGT
1 TCGGGTCAATT-TGGGT
33801 T-GGGTC
1 TCGGGTC
33807 GTTTTTGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.11, C:0.13, G:0.39, T:0.37
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Done.