Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009911.1 Corchorus capsularis cultivar CVL-1 contig09932, 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: 38847
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:106 original size:37 final size:37
Alignment explanation
Indices: 60--135 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
50 GCAGAAACAG
*
60 AAAATAAAAA-TATATATTTTTTTAAAGGAAAAA-CGGA
1 AAAAGAAAAATTA-ATATTTTTTTAAA-GAAAAATCGGA
*
97 AAAAGAAAAATTAATTTTTTTTTAAAGAAAAATCGGA
1 AAAAGAAAAATTAATATTTTTTTAAAGAAAAATCGGA
134 AA
1 AA
136 CCCTAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 6 0.17
37 27 0.77
38 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.30
Consensus pattern (37 bp):
AAAAGAAAAATTAATATTTTTTTAAAGAAAAATCGGA
Found at i:8897 original size:15 final size:15
Alignment explanation
Indices: 8840--8898 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
8830 CACAACATGA
*
8840 TTGTTCGCACCATTG
1 TTGTTTGCACCATTG
* * * *
8855 TGGTTCGGACCATGG
1 TTGTTTGCACCATTG
8870 TTGTTTGCACCATTG
1 TTGTTTGCACCATTG
*
8885 TTGTTTGCGCCATT
1 TTGTTTGCACCATT
8899 CACCCTAGCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.41
Consensus pattern (15 bp):
TTGTTTGCACCATTG
Found at i:12707 original size:9 final size:9
Alignment explanation
Indices: 12693--12731 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
12683 GTTTTCAACA
*
12693 TAATTTACT
1 TAATTTAAT
*
12702 TAATTTATT
1 TAATTTAAT
12711 TAATTTAAT
1 TAATTTAAT
*
12720 TAATTAAAT
1 TAATTTAAT
12729 TAA
1 TAA
12732 AAGAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (9 bp):
TAATTTAAT
Found at i:13084 original size:21 final size:21
Alignment explanation
Indices: 13051--13146 Score: 67
Period size: 21 Copynumber: 4.5 Consensus size: 21
13041 TCAGGTTATT
13051 ATTTTGATAACCTTTGTATGAA
1 ATTTTG-TAACCTTTGTATGAA
*
13073 ATTTTGTAACC-TTGATACGAA
1 ATTTTGTAACCTTTG-TATGAA
*
13094 ATTTTG-ATACCTTTTTTATGAAA
1 ATTTTGTA-ACC-TTTGTATG-AA
*
13117 ATTTTG-AA--TTCTCTATGAA
1 ATTTTGTAACCTT-TGTATGAA
13136 ATTTTGATAAC
1 ATTTTG-TAAC
13147 TATACTATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
19 10 0.16
20 9 0.15
21 21 0.34
22 10 0.16
23 11 0.18
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.46
Consensus pattern (21 bp):
ATTTTGTAACCTTTGTATGAA
Found at i:13159 original size:22 final size:22
Alignment explanation
Indices: 13129--13185 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
13119 TTTGAATTCT
13129 CTATGAAATTTTGATAA-CTATA
1 CTATGAAATTTTGATAACCTA-A
* * *
13151 CTATAAAATTTTAATAACCTAC
1 CTATGAAATTTTGATAACCTAA
13173 CTATGAAATTTTG
1 CTATGAAATTTTG
13186 GTAATCACGC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTAA
Found at i:13487 original size:59 final size:60
Alignment explanation
Indices: 13421--13544 Score: 223
Period size: 59 Copynumber: 2.1 Consensus size: 60
13411 TCGATTTATC
*
13421 TGATGATCTCATTATTGTTTTATTTTTTTCTAC-ATATCTCTATATGAATCGTTATTACT
1 TGATGATCTCATTATTGTTTTATTTTTTTCTACAATATCTCTATATGAATCATTATTACT
13480 TGATGATCTCATTATTGTTTTATTTTTTTCTACATATATCTCTATATGAATCATTATTACT
1 TGATGATCTCATTATTGTTTTATTTTTTTCTACA-ATATCTCTATATGAATCATTATTACT
13541 TGAT
1 TGAT
13545 CCGTACGTAA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
59 33 0.53
61 29 0.47
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.54
Consensus pattern (60 bp):
TGATGATCTCATTATTGTTTTATTTTTTTCTACAATATCTCTATATGAATCATTATTACT
Found at i:17049 original size:44 final size:43
Alignment explanation
Indices: 16992--17103 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 43
16982 CCAAAATTAA
*
16992 ATAGAAAGATTATCAAAATATCATAGTGTGGTTACCAAAATTCCAT
1 ATAG-AAG-TTATCAAAAT-TCATAGTGTAGTTACCAAAATTCCAT
* *
17038 ATAGAAGTTATCAAAACTTCATAGTGTAGTTATCAAAATTTCAT
1 ATAGAAGTTATCAAAA-TTCATAGTGTAGTTACCAAAATTCCAT
* * *
17082 -CAGAGGTTACCAAAATTTCATA
1 ATAGAAGTTATCAAAA-TTCATA
17104 AAAAGTTTAC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
43 18 0.31
44 32 0.55
45 4 0.07
46 4 0.07
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (43 bp):
ATAGAAGTTATCAAAATTCATAGTGTAGTTACCAAAATTCCAT
Found at i:17118 original size:65 final size:66
Alignment explanation
Indices: 17021--17169 Score: 155
Period size: 65 Copynumber: 2.3 Consensus size: 66
17011 ATCATAGTGT
* * * *
17021 GGTTACCAAAATTCCATATAGAAGTTATCAAAACTTCATAGTG-TAGTT-ATCAAAATTTCATCA
1 GGTTACCAAAATTTCATATAAAAGTTACCAAAACTTCATAGGGAT-GTTAAT-AAAATTTCAT-A
17084 -G-A
63 TGAA
* *
17086 GGTTACCAAAATTTCATA-AAAAGTTTACCAAAATTTCTTAGGGATGTTAATAAAATTTCATATG
1 GGTTACCAAAATTTCATATAAAAG-TTACCAAAACTTCATAGGGATGTTAATAAAATTTCATATG
17150 AA
65 AA
* *
17152 AGTTAACAAAATTTCATA
1 GGTTACCAAAATTTCATA
17170 GGGAGGGAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
64 5 0.07
65 46 0.65
66 20 0.28
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (66 bp):
GGTTACCAAAATTTCATATAAAAGTTACCAAAACTTCATAGGGATGTTAATAAAATTTCATATGA
A
Found at i:17140 original size:22 final size:22
Alignment explanation
Indices: 17022--17173 Score: 94
Period size: 22 Copynumber: 7.0 Consensus size: 22
17012 TCATAGTGTG
* * **
17022 GTTACCAAAATTCCATATAGAA
1 GTTAACAAAATTTCATAGGGAA
* * * *
17044 GTTATCAAAACTTCATAGTGTA
1 GTTAACAAAATTTCATAGGGAA
* *
17066 GTTATCAAAATTTCATCA--GAG
1 GTTAACAAAATTTCAT-AGGGAA
* **
17087 GTTACCAAAATTTCATA-AAAA
1 GTTAACAAAATTTCATAGGGAA
* * *
17108 GTTTACCAAAATTTCTTAGGGAT
1 G-TTAACAAAATTTCATAGGGAA
* * *
17131 GTTAATAAAATTTCATATGAAA
1 GTTAACAAAATTTCATAGGGAA
17153 GTTAACAAAATTTCATAGGGA
1 GTTAACAAAATTTCATAGGGA
17174 GGGAGGTTAC
Statistics
Matches: 101, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.01
21 18 0.18
22 79 0.78
23 3 0.03
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
GTTAACAAAATTTCATAGGGAA
Found at i:17343 original size:19 final size:20
Alignment explanation
Indices: 17298--17355 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
17288 TTCTCATAGG
*
17298 GTGGTTATCGAAATTTTATGGT
1 GTGGTTATCAAAATTTTA--GT
17320 GTGGTTATCAAAATTTTA-T
1 GTGGTTATCAAAATTTTAGT
17339 GTGGTTATCAAAATTTT
1 GTGGTTATCAAAATTTT
17356 CATAGTACGG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 18 0.51
22 17 0.49
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.47
Consensus pattern (20 bp):
GTGGTTATCAAAATTTTAGT
Found at i:17467 original size:23 final size:22
Alignment explanation
Indices: 17410--17547 Score: 143
Period size: 22 Copynumber: 6.2 Consensus size: 22
17400 TATAGGCAGA
* * *
17410 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAATGTGG
* *
17432 TTATCGAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAATGTGG
* *
17454 TTACCAAAAATTTCACAATGTGG
1 TTATC-AAAATTTCATAATGTGG
* *
17477 TTATCAAATTTTCAT-ATGGAGG
1 TTATCAAAATTTCATAAT-GTGG
* *
17499 TTATCTAAATTTCATAATGAGG
1 TTATCAAAATTTCATAATGTGG
*
17521 TTATCAAAATTTCAAAATGTGG
1 TTATCAAAATTTCATAATGTGG
17543 TTATC
1 TTATC
17548 CATATTTCTA
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
21 2 0.02
22 74 0.77
23 20 0.21
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGTGG
Found at i:17470 original size:45 final size:42
Alignment explanation
Indices: 17414--17545 Score: 138
Period size: 45 Copynumber: 3.0 Consensus size: 42
17404 GGCAGATTAT
*
17414 CAAAATTTCACACTGAGGTTATCGAAATTTCATAGTGTGGTTAC
1 CAAAATTTCACAATGAGGTTATC-AAATTTCATA-TGTGGTTAC
* * *
17458 CAAAAATTTCACAATGTGGTTATCAAATTTTCATATGGAGGTTAT
1 C-AAAATTTCACAATGAGGTTATCAAA-TTTCATAT-GTGGTTAC
* * *
17503 CTAAATTTCATAATGAGGTTATCAAAATTTCAAAATGTGGTTA
1 CAAAATTTCACAATGAGGTTATC-AAATTTC-ATATGTGGTTA
17546 TCCATATTTC
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
44 34 0.46
45 40 0.54
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (42 bp):
CAAAATTTCACAATGAGGTTATCAAATTTCATATGTGGTTAC
Found at i:17481 original size:67 final size:66
Alignment explanation
Indices: 17410--17547 Score: 188
Period size: 67 Copynumber: 2.1 Consensus size: 66
17400 TATAGGCAGA
* * *
17410 TTATCAAAATTTCACACT-GAGGTTATCGAAATTTCATAGTGTGGTTACCAAAAATTTCACAATG
1 TTATCAAAATTTCACA-TGGAGGTTATCGAAATTTCATAATGAGGTTACC-AAAATTTCAAAATG
17474 TGG
64 TGG
* * * *
17477 TTATCAAATTTTCATATGGAGGTTATCTAAATTTCATAATGAGGTTATCAAAATTTCAAAATGTG
1 TTATCAAAATTTCACATGGAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTTCAAAATGTG
17542 G
66 G
17543 TTATC
1 TTATC
17548 CATATTTCTA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
66 22 0.35
67 41 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (66 bp):
TTATCAAAATTTCACATGGAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTTCAAAATGTG
G
Found at i:28949 original size:31 final size:31
Alignment explanation
Indices: 28907--28966 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
28897 CAACTAACCT
* *
28907 TAGACTTGTATGATTCAACTTTCAATCTCCG
1 TAGACTCGTATGATTAAACTTTCAATCTCCG
28938 TAGACTCGTATGATTAAACTTTCAATCTC
1 TAGACTCGTATGATTAAACTTTCAATCTC
28967 GATCTTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (31 bp):
TAGACTCGTATGATTAAACTTTCAATCTCCG
Found at i:29012 original size:36 final size:36
Alignment explanation
Indices: 28965--29037 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
28955 ACTTTCAATC
*
28965 TCGATCTTTTTGAGCTTCTTGATCATCACTTAAACT
1 TCGATCTTTTTGAACTTCTTGATCATCACTTAAACT
*
29001 TCGATCTTTTTGAACTTCTTGATCGTCACTTAAACT
1 TCGATCTTTTTGAACTTCTTGATCATCACTTAAACT
29037 T
1 T
29038 GTACGATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (36 bp):
TCGATCTTTTTGAACTTCTTGATCATCACTTAAACT
Found at i:29265 original size:27 final size:26
Alignment explanation
Indices: 29235--29318 Score: 92
Period size: 27 Copynumber: 3.4 Consensus size: 26
29225 AATAGCCTAT
29235 TTAAATACATAGGTAAATGTCCATGAA
1 TTAAATACATAGGTAAATGT-CATGAA
29262 TTAAATACA-AGG---A-G--ATGAA
1 TTAAATACATAGGTAAATGTCATGAA
*
29281 TTAAATACATAGATAAATGTGCATGAA
1 TTAAATACATAGGTAAATGT-CATGAA
29308 TTAAATACATA
1 TTAAATACATA
29319 TCTTAATTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
19 14 0.29
20 2 0.04
22 1 0.02
23 2 0.04
24 1 0.02
26 3 0.06
27 25 0.52
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (26 bp):
TTAAATACATAGGTAAATGTCATGAA
Found at i:29860 original size:4 final size:4
Alignment explanation
Indices: 29853--29888 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
29843 TAGCAAAAAA
*
29853 AAAG AAAG AAAG AAAG AAAG AAAAC AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAA
29889 CATGCATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.90
5 3 0.10
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:33667 original size:132 final size:132
Alignment explanation
Indices: 33442--33702 Score: 357
Period size: 132 Copynumber: 2.0 Consensus size: 132
33432 AGTTCATAGT
* ** *
33442 CTTTTCGCAACAACTTCTTTTAGTCGTTGTTTAATATATTTTACAAATTGATTTTCGAAGCGACC
1 CTTTTCGCAACAACTTCTTTTAGACGTTGCATAAAATATTTTACAAATTGATTTTCGAAGCGACC
* * * * *
33507 TTGAAAGTCCCTACAAAAAACATGATTACTTTTGAA-ACGACAGATTAAGTTGCTGCGAAATCTT
66 TTGAAAGTCACTACAAAAAACATAATTACTTTTGAAGAC-ACAAATGAAGTCGCTGCGAAATCTT
33571 AAA
130 AAA
* *
33574 CTTTTGGCAACGACTT-TTGTTAGACGTTGCATAAAATATTTTACAAATTGATTTTCGCAA-CGA
1 CTTTTCGCAACAACTTCTT-TTAGACGTTGCATAAAATATTTTACAAATTGATTTTCG-AAGCGA
* *
33637 CCTTGAAAGTCACTACAACAAACATAATTACTTTTGAAGTCACAAATGAAGTCGCTGCGAAATCT
64 CCTTGAAAGTCACTACAAAAAACATAATTACTTTTGAAGACACAAATGAAGTCGCTGCGAAATCT
33702 T
129 T
33703 TCATTGCTTA
Statistics
Matches: 113, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
131 2 0.02
132 108 0.96
133 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (132 bp):
CTTTTCGCAACAACTTCTTTTAGACGTTGCATAAAATATTTTACAAATTGATTTTCGAAGCGACC
TTGAAAGTCACTACAAAAAACATAATTACTTTTGAAGACACAAATGAAGTCGCTGCGAAATCTTA
AA
Found at i:34007 original size:132 final size:131
Alignment explanation
Indices: 33703--34060 Score: 376
Period size: 132 Copynumber: 2.8 Consensus size: 131
33693 GCGAAATCTT
* * * * * *
33703 TCATTGCTTAATATATTTTACTAATTGATTTTCGCAACGACCTTGAAAGTCGCT--------ATG
1 TCATTGCTTAATATATTTTACAAATTGATTTTCGCAGCAACCTTCAAAGTTGCTAAAAAAACATA
* * * * * * * *
33760 ATTACTTTTGAAACGACAGATTAAGTCGCTACAAAATATTACTCTTTTCGCAACGACTTTTGTTA
66 ATTACTTTTGAAACGACAAATTAAGTCGTTGCGAAATCTTACTCTATTCGCAACGACTTCTATTA
33825 G
131 G
* **
33826 TCATTTCTTAATATATTTTACAAATTGATTTTCGCAGTGACCTTCAAAGTTGCTACAAAAGAACA
1 TCATTGCTTAATATATTTTACAAATTGATTTTCGCAGCAACCTTCAAAGTTGCTA-AAAA-AACA
* *
33891 TAATTACTTTTGAAATGACAAATTAAGTCATTGCGAAATCTTA-TCTATTCGCAACGACTTCTAT
64 TAATTACTTTTGAAACGACAAATTAAGTCGTTGCGAAATCTTACTCTATTCGCAACGACTTCTAT
33955 TAG
129 TAG
* * * * *
33958 TCGTTGCTTAATGTATTTTTCAAATTGATTTTTGCAGCAACAC-TGAAAGTTGCTAAAAAAACAT
1 TCATTGCTTAATATATTTTACAAATTGATTTTCGCAGCAAC-CTTCAAAGTTGCTAAAAAAACAT
* * *
34022 CATTACTTTTGAGACGACAAATTAAGTCGTTGTGAAATC
65 AATTACTTTTGAAACGACAAATTAAGTCGTTGCGAAATC
34061 CTATTATGTT
Statistics
Matches: 194, Mismatches: 30, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
123 48 0.25
130 39 0.20
131 4 0.02
132 66 0.34
133 37 0.19
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (131 bp):
TCATTGCTTAATATATTTTACAAATTGATTTTCGCAGCAACCTTCAAAGTTGCTAAAAAAACATA
ATTACTTTTGAAACGACAAATTAAGTCGTTGCGAAATCTTACTCTATTCGCAACGACTTCTATTA
G
Found at i:34472 original size:152 final size:143
Alignment explanation
Indices: 34121--34547 Score: 408
Period size: 144 Copynumber: 2.9 Consensus size: 143
34111 AATCAACGAG
* * * * * ** *
34121 TGGCAAAGTTTTGGAGTAGATGTGGGCAAGTCTCAAACTTATTGTTAGGCAACTTCCACTAGGTT
1 TGGCCAAGTTTTGGTGTGGATCTAGGCAAGTCTCAAACTTATACTTAGGCAAATTCCACTAGGTT
* * * * * *
34186 AAATCCTTGACAAGTTGCATTCAAGACTTGGCCAAGTGTTTTCATGATTTTTTCCTACTCTATTC
66 AAGT-CTTGACAAGTTGTATTCAAGACCTGGCCAAATGTTTTCATAATTTTTTCCTACCCTATTC
*
34251 ATCCGAGTCAACTC
130 ATCCGAATCAACTC
*
34265 TGGCCAAGTTTTGGTGTGGATCTAGGCAAGTCTCGAAA-TTATACTTAGGCGAATTCCACTAGGT
1 TGGCCAAGTTTTGGTGTGGATCTAGGCAAGTCTC-AAACTTATACTTAGGCAAATTCCACTAGGT
* * * *
34329 TAGGTCTTGAACAAGTTGTATTCAGGACCTGGTCAAATGTTTTCCTAATTTTTTCCTACCCTATC
65 TAAGTCTTG-ACAAGTTGTATTCAAGACCTGGCCAAATGTTTTCATAATTTTTTCCTACCCTAT-
* * *
34394 CACCTCGTCCTACATGCATACTT
128 ----TCATCCGA-AT-CA-ACTC
* * * * *
34417 TGGCCAAGTTTTGTTGTGGATCTAGGGAAGTCTCAAACTTATACTTATGCAAATTCCACCAGATT
1 TGGCCAAGTTTTGGTGTGGATCTAGGCAAGTCTCAAACTTATACTTAGGCAAATTCCACTAGGTT
* * * ** *
34482 AAGTCTTTGGCAAGTTGTATTGAAGACATGGCCAAGA-GTTTTTTTGATTTTTTCCCTACCCTAT
66 AAGTC-TTGACAAGTTGTATTCAAGACCTGGCCAA-ATGTTTTCATAATTTTTT-CCTACCCTAT
34546 TC
128 TC
34548 GGCTGAATCA
Statistics
Matches: 231, Mismatches: 38, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
143 4 0.02
144 100 0.43
145 3 0.01
148 2 0.01
149 6 0.03
150 1 0.00
151 5 0.02
152 96 0.42
153 14 0.06
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (143 bp):
TGGCCAAGTTTTGGTGTGGATCTAGGCAAGTCTCAAACTTATACTTAGGCAAATTCCACTAGGTT
AAGTCTTGACAAGTTGTATTCAAGACCTGGCCAAATGTTTTCATAATTTTTTCCTACCCTATTCA
TCCGAATCAACTC
Found at i:35480 original size:167 final size:166
Alignment explanation
Indices: 35205--35688 Score: 668
Period size: 167 Copynumber: 2.9 Consensus size: 166
35195 AACATATGGA
* ** * *
35205 AATTACTAAAAGATCCCCACCCCGGATTAATGA-GGAGCTAGAGAACAAATTTTTTTCGTCTTTT
1 AATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAACTAATTTTTTTCGTCTTTT
* * * *
35269 CCAACTTGATAGATTACTTAAATGTCCTAACTTTTAATTCTTGAGGGGATTAAATAACTAGACTT
66 CCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAACTA-ACTT
*
35334 TTTTGTCATTTCTCAATTGACTTTAATAGAGTAGTGG
130 TTTTGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
* * * ** * *
35371 AATTACTAAAAGATCCCTACCAA-GACTTGCTTTTGGAGTTAGAGAACTTATTTTTTTCGTCTTT
1 AATTAATAAAAGATCCCCACCAAGGA-TTGATGATGGAGCTAGAGAACTAATTTTTTTCGTCTTT
* * *
35435 TCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAAGTAATTT
65 TCCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAACTAACTT
*
35500 TTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGG
130 TTTT-GTCATTTCTCAATTGACTTGAATAGAGTAGTGG
* * *
35538 AATTAATAAAAGATCCCCATCAAGGATTGATGAT-GAGCTAGAGAACTAATCTTTTTCGTCTTTA
1 AATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAACTAATTTTTTTCGTCTTTT
*
35602 CCTACTTGACAGATTACTTAAAATGTCCTATCTTTTGATTCTTGAGGAGATTAAATAACTAAACT
66 CCTACTTGACAGATTACTT-AAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAACT-AACT
*
35667 TTTTGGTCATTTCTCAATTGAC
129 TTTTTGTCATTTCTCAATTGAC
35689 AAATGACTCA
Statistics
Matches: 277, Mismatches: 35, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
165 2 0.01
166 74 0.27
167 192 0.69
168 9 0.03
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (166 bp):
AATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAACTAATTTTTTTCGTCTTTT
CCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAACTAACTTT
TTTGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
Found at i:36310 original size:13 final size:13
Alignment explanation
Indices: 36279--36309 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
36269 TGAATATTCA
36279 TTTTTTAATTTAT
1 TTTTTTAATTTAT
36292 TTTTTTAA-TTAT
1 TTTTTTAATTTAT
36304 TTTTTT
1 TTTTTT
36310 TGGAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTAATTTAT
Done.