Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010867.1 Corchorus olitorius cultivar O-4 contig10899, 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: 33305
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Found at i:423 original size:2 final size:2
Alignment explanation
Indices: 416--440 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
406 GAATTATTAC
416 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
441 ATAATGAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1073 original size:2 final size:2
Alignment explanation
Indices: 1068--1098 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1058 TTGCAAATGG
1068 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1099 ATTAGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1088 original size:13 final size:13
Alignment explanation
Indices: 1070--1095 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1060 GCAAATGGTA
1070 TATATATATATAT
1 TATATATATATAT
1083 TATATATATATAT
1 TATATATATATAT
1096 ATAATTAGAT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:1088 original size:15 final size:15
Alignment explanation
Indices: 1068--1097 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1058 TTGCAAATGG
1068 TATATATATATATAT
1 TATATATATATATAT
1083 TATATATATATATAT
1 TATATATATATATAT
1098 AATTAGATTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:9461 original size:438 final size:437
Alignment explanation
Indices: 8645--10001 Score: 1683
Period size: 438 Copynumber: 3.1 Consensus size: 437
8635 CCCATTTTCA
* * * *
8645 ATAAACAAATCA-TTTTTTTGTTGGTTTATTTATCAAATGATAC-CTATACTTTTATGCTTTATG
1 ATAAACAAAT-ATTTTTTTTGTTCGATTATTTATCAAATGATACTC-ATACTTTTATACCTTATG
* * * * * * * * *
8708 CTATTTAGTCCCTCATAATTTCTGGGTTGGACAATTGAACGTTTCGACTTTAATTCTTT-TATTT
64 CTATTTAATCCTTTATAA-TTATGGGTTGGACGATTTAACGTTTTGGCTTTTATT-TTTGTA-TT
* * * *
8772 TTTGTTTTACTTGTCAAATCAAGGTGATTCAAGTGTCTATTAAAAGATGATTTCATGATCTACAA
126 TTTGTTTTATTTGTCCAATTAAGGTGATTCAAGTGTCTATTAAAAGGTGATTTCATGATCTACAA
* * * * * *
8837 CTTCCATGAAGGACTCAAAAGTCAATTTTAATGTTTTGATCCTCAAAAATGCTTCTGAAATTTTG
191 CTTTCATG-AGGACTTAAAAGTCAATTTTAATGTTTTAATTCTAAAAAATGCTTCTGAAATCTTG
* * * * * * *
8902 TGGTCTCGATTGCCAGTCTATCTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAGGTTGC
255 TGGTTTCAATTGCCGGTCTATCTAATGTTGTATAATTTTTGGTCCACTTGTCCGATTGAAGTTGT
* *
8967 TCAAGTGTCGGTTAAAAGGGTATTGTGTGATCTACGACTTTCGTTAAGGGCCTGAAAGCTGAATT
320 TCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCATTAAGGGCCTGAAAGCTGAATT
* *
9032 TGATTAATGAGTTTCGTGGAGGGTTCAAGAGGGAATTTTT-TGTTTGGTCTCC
385 TGATTAATGAGTTTCATGAAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCC
*
9084 ATAAACAAATATTTTTTTTGTTCGATTATTTATCAAATGATTCTCATACTTTTATACCTTATGCT
1 ATAAACAAATATTTTTTTTGTTCGATTATTTATCAAATGATACTCATACTTTTATACCTTATGCT
* *
9149 ATTTAATCCTTTACAATTATGGGTTGGACGATTTAACATTTTGGCTTTTATTTTTGTACTTTTTG
66 ATTTAATCCTTTATAATTATGGGTTGGACGATTTAACGTTTTGGCTTTTATTTTTGTA-TTTTTG
* * * *
9214 TTCTATTTGCCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTGATTTCATGATCTAAAACTTT
130 TTTTATTTGTCCAATTAAGGTGATTCAAGTGTCTATTAAAAGGTGATTTCATGATCTACAACTTT
* * * *
9279 CATTATGGACTTAGAAGCCAATTTTAATGTTTTAATTCTAAAAAATGCTTCCGAAATCTTGTGGT
195 CATGA-GGACTTAAAAGTCAATTTTAATGTTTTAATTCTAAAAAATGCTTCTGAAATCTTGTGGT
* * *
9344 TTCAATTGACGGTCTATCTAATGTTGTATAATTTTTGGTCTACTTGTCTGATTGAAGTTGTTCAA
259 TTCAATTGCCGGTCTATCTAATGTTGTATAATTTTTGGTCCACTTGTCCGATTGAAGTTGTTCAA
* *
9409 GTGTCGGTTAAAAGGTTATTTTGTGATCTACGACTTTCATTAAGGGCCTGAAAGTTGAATTTGAT
324 GTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCATTAAGGGCCTGAAAGCTGAATTTGAT
* *
9474 TCATAAGTTTCATGAAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCC
389 TAATGAGTTTCATGAAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCC
* * * *
9523 ATAAACAAATATTTTTTTTG-CCAGATTATTTATCAAATGATCCTCATACTTTT-TATGCTTCAC
1 ATAAACAAATATTTTTTTTGTTC-GATTATTTATCAAATGATACTCATACTTTTATA-CCTT-AT
* * *
9586 GCTATTTTATCCTTTATAA-TATGGGTTGGACGATTTATTAACGCTTTGGCTTATATTTTTGTAT
63 GCTATTTAATCCTTTATAATTATGGGTTGGACGA--T-TTAACGTTTTGGCTTTTATTTTTGTAT
* * *
9650 TTTCTGTTTTATTTGTCCAATTAAGGTGATTCAAGTGTCTATGAAGAGGTGATTTCATTATCTAC
125 TTT-TGTTTTATTTGTCCAATTAAGGTGATTCAAGTGTCTATTAAAAGGTGATTTCATGATCTAC
* * * * *
9715 AACTTTCATGAAGAATTCAAAAGTCAATTTTAATGTTTTATTTCTAAAAAA-GTTTCTTAAATCT
189 AACTTTCATGAGGACTT-AAAAGTCAATTTTAATGTTTTAATTCTAAAAAATGCTTCTGAAATCT
* * * *
9779 TGTGGTTTCAATTGCCGGTGTATTTCA-GTTGTATAATTTTTGATCCACTTGTCCGATTGAAGTT
253 TGTGGTTTCAATTGCCGGTCTATCTAATGTTGTATAATTTTTGGTCCACTTGTCCGATTGAAGTT
* ** * * ** * *
9843 GTTCAAGTGACGGTTAAAAGGTTATTGCATGATCTATGACTTTCA-TGAGAACCTGAGAGCTAAA
318 GTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCATTAAGGGCCTGAAAGCTGAA
* * * * *
9907 TTTGATTAACGAGTTTCATGAAGGGCTCGAGAGGAAATTTTTATGTTTCGTCTCC
383 TTTGATTAATGAGTTTCATGAAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCC
* * * *
9962 ATCAACAAACATTTTCTTAT-TTGGATTATTTATCAAATGA
1 ATAAACAAATATTTT-TTTTGTTCGATTATTTATCAAATGA
10002 CCCTCATAGT
Statistics
Matches: 795, Mismatches: 108, Indels: 30
0.85 0.12 0.03
Matches are distributed among these distances:
437 4 0.01
438 299 0.38
439 237 0.30
440 96 0.12
441 42 0.05
442 117 0.15
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.42
Consensus pattern (437 bp):
ATAAACAAATATTTTTTTTGTTCGATTATTTATCAAATGATACTCATACTTTTATACCTTATGCT
ATTTAATCCTTTATAATTATGGGTTGGACGATTTAACGTTTTGGCTTTTATTTTTGTATTTTTGT
TTTATTTGTCCAATTAAGGTGATTCAAGTGTCTATTAAAAGGTGATTTCATGATCTACAACTTTC
ATGAGGACTTAAAAGTCAATTTTAATGTTTTAATTCTAAAAAATGCTTCTGAAATCTTGTGGTTT
CAATTGCCGGTCTATCTAATGTTGTATAATTTTTGGTCCACTTGTCCGATTGAAGTTGTTCAAGT
GTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCATTAAGGGCCTGAAAGCTGAATTTGATTA
ATGAGTTTCATGAAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCC
Found at i:10134 original size:14 final size:14
Alignment explanation
Indices: 10111--10159 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
10101 AGAAATTCTA
*
10111 ATTTTCTTAATTTC
1 ATTTTTTTAATTTC
*
10125 ATTTTTTTAATTCTA
1 ATTTTTTTAATT-TC
10140 ATTTTTTTTAATTTC
1 A-TTTTTTTAATTTC
10155 ATTTT
1 ATTTT
10160 GATTCTTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 15 0.50
15 4 0.13
16 11 0.37
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTTTTAATTTC
Found at i:10145 original size:16 final size:15
Alignment explanation
Indices: 10104--10152 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
10094 GTCCTTTAGA
*
10104 AATTCTAATTTTCTT
1 AATTCTAATTTTTTT
*
10119 AATT-TCATTTTTTT
1 AATTCTAATTTTTTT
10133 AATTCTAATTTTTTTT
1 AATTCTAA-TTTTTTT
10149 AATT
1 AATT
10153 TCATTTTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 12 0.41
15 6 0.21
16 11 0.38
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTCTAATTTTTTT
Found at i:10257 original size:39 final size:39
Alignment explanation
Indices: 10188--10262 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
10178 TATCTTGATT
* *
10188 ATTATTTTGTTAATCATGTGATTTTTATTATGAATTTTG
1 ATTATTTTGTTAATCATGTGATTTTAATTATAAATTTTG
10227 ATTATTTTGTTAATCATGT-ATTTCTAATTATAAATT
1 ATTATTTTGTTAATCATGTGATTT-TAATTATAAATT
10263 ATTGGAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 4 0.12
39 29 0.88
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.57
Consensus pattern (39 bp):
ATTATTTTGTTAATCATGTGATTTTAATTATAAATTTTG
Found at i:10276 original size:20 final size:20
Alignment explanation
Indices: 10251--10292 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
10241 CATGTATTTC
*
10251 TAATTATAAATTATTGGAAT
1 TAATTATAAATTATTAGAAT
*
10271 TAATTATGAATTATTAGAAT
1 TAATTATAAATTATTAGAAT
10291 TA
1 TA
10293 TTAATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (20 bp):
TAATTATAAATTATTAGAAT
Found at i:10500 original size:60 final size:60
Alignment explanation
Indices: 10436--10555 Score: 179
Period size: 60 Copynumber: 2.0 Consensus size: 60
10426 TGATCAATCT
* * **
10436 ATTTTAATTTTAGATATTTTGTCATTTTATTATTGTTGGGGTTTA-GGATTATATTTTGTA
1 ATTTTAATTCTAGATATTTTGTCATTTTATTAGTGTCAGGGTTTACGG-TTATATTTTGTA
*
10496 ATTTTAATTCTAGATATTTTGTTATTTTATTAGTGTCAGGGTTTACGGTTATATTTTGTA
1 ATTTTAATTCTAGATATTTTGTCATTTTATTAGTGTCAGGGTTTACGGTTATATTTTGTA
10556 TGTATGTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 52 0.96
61 2 0.04
ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57
Consensus pattern (60 bp):
ATTTTAATTCTAGATATTTTGTCATTTTATTAGTGTCAGGGTTTACGGTTATATTTTGTA
Found at i:10887 original size:47 final size:47
Alignment explanation
Indices: 10818--10907 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 47
10808 TTGATTAATC
*
10818 ATTTAATCATGAAATATTGGTATTATTTATTAATCAAGGTTATCTGA
1 ATTTAATCATGAAATATTGGTATTATTAATTAATCAAGGTTATCTGA
10865 ATTTAATCATGAAATATTGGTATTATTAATTAATCAAGGTTAT
1 ATTTAATCATGAAATATTGGTATTATTAATTAATCAAGGTTAT
10908 TTTATTGGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (47 bp):
ATTTAATCATGAAATATTGGTATTATTAATTAATCAAGGTTATCTGA
Found at i:10933 original size:14 final size:14
Alignment explanation
Indices: 10897--10938 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
10887 TTATTAATTA
*
10897 ATCAAGGTTATTTT
1 ATCAAGGTTATTTG
*
10911 AT--TGGTTATTTG
1 ATCAAGGTTATTTG
10923 ATCAAGGTTATTTG
1 ATCAAGGTTATTTG
10937 AT
1 AT
10939 AATGTTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (14 bp):
ATCAAGGTTATTTG
Found at i:11018 original size:28 final size:28
Alignment explanation
Indices: 10986--11042 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
10976 TTTGGGTTCT
10986 TACTAATTGTTTTATTAATCATAATTAA
1 TACTAATTGTTTTATTAATCATAATTAA
11014 TACTAATTGTTTTATTAATCATAATTAA
1 TACTAATTGTTTTATTAATCATAATTAA
11042 T
1 T
11043 GAATATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.51
Consensus pattern (28 bp):
TACTAATTGTTTTATTAATCATAATTAA
Found at i:11252 original size:12 final size:12
Alignment explanation
Indices: 11235--11261 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11225 TAGAAGCCCT
11235 CTTGGTCTTTAG
1 CTTGGTCTTTAG
11247 CTTGGTCTTTAG
1 CTTGGTCTTTAG
11259 CTT
1 CTT
11262 AGTTCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.19, G:0.22, T:0.52
Consensus pattern (12 bp):
CTTGGTCTTTAG
Found at i:12167 original size:1 final size:1
Alignment explanation
Indices: 12161--12188 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
12151 TCCGAATTGT
12161 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
12189 CTTCATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16130 original size:24 final size:24
Alignment explanation
Indices: 16101--16181 Score: 117
Period size: 24 Copynumber: 3.4 Consensus size: 24
16091 AAGCCCAGCT
* * *
16101 ATGCATTGGGGTTGTCATCCCATC
1 ATGCATTGGAGTTCTCATGCCATC
*
16125 ATGCATTGGCGTTCTCATGCCATC
1 ATGCATTGGAGTTCTCATGCCATC
16149 ATGCATTGGAGTTCTCATGCCATC
1 ATGCATTGGAGTTCTCATGCCATC
*
16173 AAGCATTGG
1 ATGCATTGG
16182 TGTGGCTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (24 bp):
ATGCATTGGAGTTCTCATGCCATC
Found at i:18188 original size:13 final size:13
Alignment explanation
Indices: 18146--18190 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
18136 TAATGCATCC
*
18146 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
18160 AAAACCATTT-AT
1 AAAACAATTTAAT
18172 AAAACAATTTAAT
1 AAAACAATTTAAT
18185 AAAACA
1 AAAACA
18191 GTAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:18631 original size:27 final size:28
Alignment explanation
Indices: 18600--18664 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
18590 TTCGGCATTT
* *
18600 AAGGGCAAAATTATAA-TTTAGTCAACC
1 AAGGGCAAAATGATAATTTTAGCCAACC
* * *
18627 AAGGGTAAAATGGTAATTTTAGCCGACC
1 AAGGGCAAAATGATAATTTTAGCCAACC
18655 AAGGGCAAAA
1 AAGGGCAAAA
18665 CAGTAATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (28 bp):
AAGGGCAAAATGATAATTTTAGCCAACC
Found at i:22117 original size:21 final size:21
Alignment explanation
Indices: 22091--22133 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
22081 GAAACGTTGG
22091 AGACTTAATTAACCAAATTAA
1 AGACTTAATTAACCAAATTAA
22112 AGACTTAATTAACCAAATTAA
1 AGACTTAATTAACCAAATTAA
22133 A
1 A
22134 AGGTTAGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (21 bp):
AGACTTAATTAACCAAATTAA
Found at i:22602 original size:11 final size:11
Alignment explanation
Indices: 22568--22606 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
22558 TATATATATT
22568 ATATAATAATA
1 ATATAATAATA
*
22579 ATAGAATTAATA
1 ATATAA-TAATA
22591 ATATAATAATA
1 ATATAATAATA
22602 ATATA
1 ATATA
22607 GTATATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
ATATAATAATA
Found at i:22889 original size:61 final size:60
Alignment explanation
Indices: 22774--22892 Score: 204
Period size: 61 Copynumber: 2.0 Consensus size: 60
22764 TTTAAGTAAG
*
22774 ATTTTATATGTTAGTAATTAAGTTAAATGGAAGAGAACATTGTTAGAATTCTAATGTCAA
1 ATTTTATATGTTAGTAATTAAGTTAAATGGAAGAAAACATTGTTAGAATTCTAATGTCAA
22834 ATTTTATATGTAATAGTAATTAAGTTAAATGG-AGAAAACATTGTTAGAATTCTAATGTC
1 ATTTTATATGT--TAGTAATTAAGTTAAATGGAAGAAAACATTGTTAGAATTCTAATGTC
22893 TATCAAATAA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
60 11 0.20
61 26 0.46
62 19 0.34
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (60 bp):
ATTTTATATGTTAGTAATTAAGTTAAATGGAAGAAAACATTGTTAGAATTCTAATGTCAA
Found at i:23552 original size:5 final size:5
Alignment explanation
Indices: 23538--23598 Score: 64
Period size: 4 Copynumber: 13.4 Consensus size: 5
23528 CCTCAATACT
23538 AAAA- AAAAC AAAAC AAAAC AAAAC AAAAC -AAAC -AAAC -AAAC -AAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
23583 -AAAC -AAAC AACAAC AA
1 AAAAC AAAAC AA-AAC AA
23599 CAACTAAGAC
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
4 28 0.52
5 21 0.39
6 5 0.09
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:23633 original size:30 final size:30
Alignment explanation
Indices: 23599--23658 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
23589 ACAACAACAA
23599 CAACTAAGACCTCAAGGACCAAAAATATGT
1 CAACTAAGACCTCAAGGACCAAAAATATGT
23629 CAACTAAGACCTCAAGGACCAAAAATATGT
1 CAACTAAGACCTCAAGGACCAAAAATATGT
23659 GTTACTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.23, G:0.13, T:0.17
Consensus pattern (30 bp):
CAACTAAGACCTCAAGGACCAAAAATATGT
Found at i:24801 original size:7 final size:7
Alignment explanation
Indices: 24789--24814 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
24779 AGTGGTCATA
24789 TTTGAGC
1 TTTGAGC
24796 TTTGAGC
1 TTTGAGC
24803 TTTGAGC
1 TTTGAGC
24810 TTTGA
1 TTTGA
24815 AGAGTGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.27, T:0.46
Consensus pattern (7 bp):
TTTGAGC
Done.