Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016628.1 Corchorus olitorius cultivar O-4 contig16661, 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: 48455
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:826 original size:22 final size:22
Alignment explanation
Indices: 801--917 Score: 73
Period size: 22 Copynumber: 5.3 Consensus size: 22
791 ACAATCAAAC
801 CAAAATTACATAGGAAGGTTAT
1 CAAAATTACATAGGAAGGTTAT
* *
823 CAAAATTTA-ATAGTG-TGGTTAC
1 CAAAA-TTACATAG-GAAGGTTAT
*
845 CAAAATTTCATATGG-AGGTTAT
1 CAAAATTACATA-GGAAGGTTAT
**
867 CAAAACTT-CATATTATA-GTTAT
1 CAAAA-TTACATAGGA-AGGTTAT
** **
889 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTACATAGGAAGGTTAT
911 CAAAATT
1 CAAAATT
918 TCTTAGACTC
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
21 5 0.07
22 63 0.83
23 8 0.11
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (22 bp):
CAAAATTACATAGGAAGGTTAT
Found at i:864 original size:44 final size:43
Alignment explanation
Indices: 799--918 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 43
789 TGACAATCAA
* * *
799 ACCAAAATTACATAGGAAGGTTATCAAAATTTAATAGTGTGGTT
1 ACCAAAATTTCATAGG-AGGTTATCAAAATTTAATAGTATAGTT
* * *
843 ACCAAAATTTCATATGGAGGTTATCAAAACTTCATATTATAGTT
1 ACCAAAATTTCATA-GGAGGTTATCAAAATTTAATAGTATAGTT
* * **
887 ATCAAAATTTTATAAAAAGGTTATCAAAATTT
1 ACCAAAATTTCAT-AGGAGGTTATCAAAATTT
919 CTTAGACTCC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 60 0.95
45 3 0.05
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (43 bp):
ACCAAAATTTCATAGGAGGTTATCAAAATTTAATAGTATAGTT
Found at i:1157 original size:22 final size:22
Alignment explanation
Indices: 1130--1212 Score: 62
Period size: 22 Copynumber: 3.8 Consensus size: 22
1120 AGCCTTAGGG
*
1130 AGGTTAACAAAATTTCATACGA
1 AGGTTAACAAAATTTCATAAGA
* * * *
1152 AGGTTATCAAACTTT-ATAGTGT
1 AGGTTAACAAAATTTCATA-AGA
*
1174 A-GTTATCAAAATTTCATAAGA
1 AGGTTAACAAAATTTCATAAGA
* * *
1195 ATGTTAATAAAATATCAT
1 AGGTTAACAAAATTTCAT
1213 TGGGAGGGAG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
21 17 0.35
22 31 0.65
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (22 bp):
AGGTTAACAAAATTTCATAAGA
Found at i:1437 original size:22 final size:22
Alignment explanation
Indices: 1361--1505 Score: 123
Period size: 22 Copynumber: 6.6 Consensus size: 22
1351 CATAAGGATG
* * * *
1361 TTATCTAAATTTCATGGTGTGT
1 TTATCAAAATTTCATAGTGAGA
* *
1383 TTATCAAAATTTTCATAGTGCGG
1 TTATCAAAA-TTTCATAGTGAGA
* * **
1406 TTA-C-CAATTTTATAGTTTGA
1 TTATCAAAATTTCATAGTGAGA
*
1426 TTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGTGAGA
* * *
1448 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGTGAGA
* *
1470 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGA
1492 TTATCAAAATTTCA
1 TTATCAAAATTTCA
1506 CAATGTGGTT
Statistics
Matches: 99, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
20 12 0.12
21 3 0.03
22 71 0.72
23 13 0.13
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGA
Found at i:1476 original size:44 final size:44
Alignment explanation
Indices: 1426--1571 Score: 161
Period size: 44 Copynumber: 3.3 Consensus size: 44
1416 TATAGTTTGA
* *
1426 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATGAGG
* * *
1470 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAATGTGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATGAGG
* * * *
1514 TTATCGAACTTTCATGGGGAGGTTAT-AGAAA-TTCTATAATGAGG
1 TTATCAAAATTTCATAGGGAGGTTATCA-AAATTTC-ACAATGAGG
* *
1558 TTATCGAATTTTCA
1 TTATCAAAATTTCA
1572 GTATGGTTAT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
43 4 0.05
44 83 0.95
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATGAGG
Found at i:1512 original size:22 final size:22
Alignment explanation
Indices: 1448--1527 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
1438 CATAGGGAGA
* *
1448 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCACAATGTGG
* *
1470 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCACAATGTGG
1492 TTATCAAAATTTCACAATGTGG
1 TTATCAAAATTTCACAATGTGG
* *
1514 TTATCGAACTTTCA
1 TTATCAAAATTTCA
1528 TGGGGAGGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCACAATGTGG
Found at i:2092 original size:170 final size:169
Alignment explanation
Indices: 1730--2093 Score: 405
Period size: 170 Copynumber: 2.1 Consensus size: 169
1720 TCTAAGAAAT
* *
1730 CTAAAACCTCAACTTCCCGA-TTTAGCACGTTTGTGCGTAGAACGTGGTTCTCGGGAAATTAAAC
1 CTAAAACCTCAACTTCACGATTTTAGCACGATTGTGCGTAGAACGTGGTTCTC-GGAAA-TAAAC
* *
1794 GCTCATTCCAAATACATTATTTGTGAAACCAACACTGAAATGTTGTGTTTCAGAGCGAGTAAGCT
64 GCTCATTCCAAATACATTATTTGTGAAACCAACACTCAAATGTCGTGTTTCAGAGCGAGTAAGCT
*
1859 CATTGGAAAGTGGGGTTGCCAGAAAAAACTTTCTTCAAAAC
129 CATTGGAAAGTGGGCTTGCCAGAAAAAACTTTCTTCAAAAC
* * * * * * * * *
1900 CTAAAACTTGAAATTTACGATTTTA-CACGATTGTGCGTAGAACGTTGTTCT-TGAGA-AAATGT
1 CTAAAACCTCAACTTCACGATTTTAGCACGATTGTGCGTAGAACGTGGTTCTCGGAAATAAACGC
* * * * ** * * **
1962 TCATTCCGAATGCGTTATTTGTGTAACCAATGCTCAGATGTCGTGTTTCGGAGTTAGTAGAGCTC
66 TCATTCCAAATACATTATTTGTGAAACCAACACTCAAATGTCGTGTTTCAGAGCGAGTA-AGCTC
*
2027 ATTGGAAAGT-GGCTTGCCAGCCAAACAAAGCTTTCTTCAAAGC
130 ATTGGAAAGTGGGCTTGCCAG--AAA-AAA-CTTTCTTCAAAAC
2070 CTAAAACCTCAACTTCACGATTTT
1 CTAAAACCTCAACTTCACGATTTT
2094 CTGCAATTTG
Statistics
Matches: 159, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
166 60 0.38
167 15 0.09
168 6 0.04
169 3 0.02
170 71 0.45
171 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (169 bp):
CTAAAACCTCAACTTCACGATTTTAGCACGATTGTGCGTAGAACGTGGTTCTCGGAAATAAACGC
TCATTCCAAATACATTATTTGTGAAACCAACACTCAAATGTCGTGTTTCAGAGCGAGTAAGCTCA
TTGGAAAGTGGGCTTGCCAGAAAAAACTTTCTTCAAAAC
Found at i:4197 original size:22 final size:22
Alignment explanation
Indices: 4149--4197 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
4139 TTGCCCTTCT
*
4149 TCTCT-CTCCCCCCACTAACTC
1 TCTCTCCTCCCCCCACTAACTA
* * *
4170 TTTCTCCTCCTCCCACTCACTA
1 TCTCTCCTCCCCCCACTAACTA
4192 TCTCTC
1 TCTCTC
4198 TTCATAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.35
Consensus pattern (22 bp):
TCTCTCCTCCCCCCACTAACTA
Found at i:18517 original size:11 final size:11
Alignment explanation
Indices: 18498--18527 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
18488 TTTTCACCTT
*
18498 GTTCATCACTC
1 GTTCTTCACTC
18509 GTTCTTCACTC
1 GTTCTTCACTC
18520 GTTCTTCA
1 GTTCTTCA
18528 TATTTTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.33, G:0.10, T:0.43
Consensus pattern (11 bp):
GTTCTTCACTC
Found at i:18631 original size:51 final size:50
Alignment explanation
Indices: 18530--18631 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
18520 GTTCTTCATA
* **
18530 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
*
18580 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT
18631 T
1 T
18632 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 9 0.20
51 34 0.77
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:19009 original size:21 final size:21
Alignment explanation
Indices: 18972--19047 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
18962 TCTCACAGGG
18972 AGGTTATCAAAAATCAT-TGGA
1 AGGTTATCAAAAATCATAT-GA
*
18993 AGGTTA-CAAAATTTCATATGA
1 AGGTTATCAAAA-ATCATATGA
* * **
19014 AGGTTTATTAAAATTCCATATTT
1 AGG-TTATCAAAAAT-CATATGA
19037 AGGTTATCAAA
1 AGGTTATCAAA
19048 GTTTTATATG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
20 5 0.11
21 15 0.33
22 13 0.29
23 12 0.27
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (21 bp):
AGGTTATCAAAAATCATATGA
Found at i:19111 original size:22 final size:21
Alignment explanation
Indices: 18995--19143 Score: 95
Period size: 22 Copynumber: 6.8 Consensus size: 21
18985 TCATTGGAAG
* *
18995 GTTA-CAAAATTTCATATGAA
1 GTTATCAAAATTTCATAGGTA
* * **
19015 GGTTTATTAAAATTCCATATTTA
1 -G-TTATCAAAATTTCATAGGTA
* *
19038 GGTTATCAAAGTTTTATATGG-A
1 -GTTATCAAAATTTCATA-GGTA
*
19060 GTTTATCACAATTTCATAGGTA
1 G-TTATCAAAATTTCATAGGTA
* * *
19082 ATTATCAAATTTTCATAGCGTG
1 GTTATCAAAATTTCATAG-GTA
*
19104 GTTATCAAAATTTAATAGGGTA
1 GTTATCAAAATTTCATA-GGTA
19126 GTTAATCAAAATTTCATA
1 GTT-ATCAAAATTTCATA
19144 AAAATATTCA
Statistics
Matches: 98, Mismatches: 22, Indels: 14
0.73 0.16 0.10
Matches are distributed among these distances:
21 19 0.19
22 51 0.52
23 28 0.29
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.40
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGTA
Found at i:20710 original size:40 final size:40
Alignment explanation
Indices: 20655--20733 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
20645 AGGTTTTTTT
*
20655 ATTGAGTAATTATTTGATACATTGACCGTATAAATTTTGG
1 ATTGAGTAATTATTTGATACATTGACAGTATAAATTTTGG
20695 ATTGAGTAATTATTTGATACATTGACAGTATAAATTTTG
1 ATTGAGTAATTATTTGATACATTGACAGTATAAATTTTG
20734 AAAACTCCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.43
Consensus pattern (40 bp):
ATTGAGTAATTATTTGATACATTGACAGTATAAATTTTGG
Found at i:20718 original size:20 final size:20
Alignment explanation
Indices: 20655--20719 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
20645 AGGTTTTTTT
20655 ATTGAGTAATTATTTGATAC
1 ATTGAGTAATTATTTGATAC
* **
20675 ATTGACCGT-ATAAATTT--TGG
1 ATTGA--GTAAT-TATTTGATAC
20695 ATTGAGTAATTATTTGATAC
1 ATTGAGTAATTATTTGATAC
20715 ATTGA
1 ATTGA
20720 CAGTATAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
18 6 0.18
19 2 0.06
20 17 0.52
21 2 0.06
22 6 0.18
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (20 bp):
ATTGAGTAATTATTTGATAC
Found at i:20731 original size:22 final size:22
Alignment explanation
Indices: 20666--20731 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
20656 TTGAGTAATT
*
20666 ATTTGATACATTGACCGTATAA
1 ATTTGATACATTGACAGTATAA
** *
20688 ATTT--TGGATTG--AGTA-ATT
1 ATTTGATACATTGACAGTATA-A
20706 ATTTGATACATTGACAGTATAA
1 ATTTGATACATTGACAGTATAA
20728 ATTT
1 ATTT
20732 TGAAAACTCC
Statistics
Matches: 31, Mismatches: 7, Indels: 12
0.62 0.14 0.24
Matches are distributed among these distances:
17 1 0.03
18 7 0.23
20 10 0.32
22 12 0.39
23 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (22 bp):
ATTTGATACATTGACAGTATAA
Found at i:20823 original size:37 final size:37
Alignment explanation
Indices: 20782--20853 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
20772 TCCACTGACA
*
20782 GTATAAAGGATGGATTTGAGCATGAGGTTCCTCTGCT
1 GTATAAAAGATGGATTTGAGCATGAGGTTCCTCTGCT
20819 GTATAAAAGATGGATTTGAGCATGAGGTTCCTCTG
1 GTATAAAAGATGGATTTGAGCATGAGGTTCCTCTG
20854 TTGTTTACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (37 bp):
GTATAAAAGATGGATTTGAGCATGAGGTTCCTCTGCT
Found at i:21410 original size:22 final size:22
Alignment explanation
Indices: 21382--21426 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21372 ATACTAAGAA
21382 ACTTTCTAGGACAGGGACTAAG
1 ACTTTCTAGGACAGGGACTAAG
21404 ACTTTCTAGGACAGGGACTAAG
1 ACTTTCTAGGACAGGGACTAAG
21426 A
1 A
21427 GTCCAAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (22 bp):
ACTTTCTAGGACAGGGACTAAG
Found at i:21484 original size:57 final size:57
Alignment explanation
Indices: 21404--21535 Score: 219
Period size: 57 Copynumber: 2.3 Consensus size: 57
21394 AGGGACTAAG
* *
21404 ACTTTCTAGGACAGGGACTAAGAGTCCAAGATTCCTCCCTCCTACGAATACTAAGAA
1 ACTTTCTAGGACAGGGACTAAGAGTCAAAGATTCCTCCCTCCCACGAATACTAAGAA
* * *
21461 ACTTTCTGGGACTGGGACTAAGAGTCAAAGATTCCTCCCTCCCATGAATACTAAGAA
1 ACTTTCTAGGACAGGGACTAAGAGTCAAAGATTCCTCCCTCCCACGAATACTAAGAA
21518 ACTTTCTAGGACAGGGAC
1 ACTTTCTAGGACAGGGAC
21536 AAGGATGGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 68 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (57 bp):
ACTTTCTAGGACAGGGACTAAGAGTCAAAGATTCCTCCCTCCCACGAATACTAAGAA
Found at i:23827 original size:21 final size:18
Alignment explanation
Indices: 23778--23826 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
23768 CTGATTCTAT
23778 CTCTCTTCTTCTTGCGAA
1 CTCTCTTCTTCTTGCGAA
23796 CTCTCTTCTTCTTGCGAA
1 CTCTCTTCTTCTTGCGAA
23814 CTCGT-TTCTTCTT
1 CTC-TCTTCTTCTT
23827 CGTCGACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 29 0.97
19 1 0.03
ACGTcount: A:0.08, C:0.33, G:0.10, T:0.49
Consensus pattern (18 bp):
CTCTCTTCTTCTTGCGAA
Found at i:24207 original size:28 final size:28
Alignment explanation
Indices: 24167--24222 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
24157 GAGTTATTTT
24167 AGGTTTCCAAAGACTTTCATCCATAAAC
1 AGGTTTCCAAAGACTTTCATCCATAAAC
24195 AGGTTTCCAAAGACTTTCATCCATAAAC
1 AGGTTTCCAAAGACTTTCATCCATAAAC
24223 TTAACATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.29
Consensus pattern (28 bp):
AGGTTTCCAAAGACTTTCATCCATAAAC
Found at i:27790 original size:15 final size:15
Alignment explanation
Indices: 27770--27801 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27760 CATACCTGAA
*
27770 CAGATCTGAAAATGG
1 CAGATCCGAAAATGG
27785 CAGATCCGAAAATGG
1 CAGATCCGAAAATGG
27800 CA
1 CA
27802 AAAAATAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.16
Consensus pattern (15 bp):
CAGATCCGAAAATGG
Found at i:37163 original size:119 final size:119
Alignment explanation
Indices: 36947--37185 Score: 426
Period size: 119 Copynumber: 2.0 Consensus size: 119
36937 CTAAAAGACT
*
36947 TCTCTAGATGAAAGACGGATTATGTCCCAGTGAAGTATTAAAGAAATCCCCAATTGGAAAATTCT
1 TCTCCAGATGAAAGACGGATTATGTCCCAGTGAAGTATTAAAGAAATCCCCAATTGGAAAATTCT
*
37012 AATTTCTGACTATTGTTTCCATTCTTTTGTCAATGAATATTCACATCTATAAGG
66 AATTTCTAACTATTGTTTCCATTCTTTTGTCAATGAATATTCACATCTATAAGG
*
37066 TCTCCAGATGAAAGACGGATTATGTCCC-GATGAAGTATTAAAGAAATCCCCAGTTGGAAAATTC
1 TCTCCAGATGAAAGACGGATTATGTCCCAG-TGAAGTATTAAAGAAATCCCCAATTGGAAAATTC
*
37130 TAATTTTTAACTATTGTTTCCATTCTTTTGTCAATGAATATTCACATCTATAAGG
65 TAATTTCTAACTATTGTTTCCATTCTTTTGTCAATGAATATTCACATCTATAAGG
37185 T
1 T
37186 AGTGACAATG
Statistics
Matches: 115, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
118 1 0.01
119 114 0.99
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (119 bp):
TCTCCAGATGAAAGACGGATTATGTCCCAGTGAAGTATTAAAGAAATCCCCAATTGGAAAATTCT
AATTTCTAACTATTGTTTCCATTCTTTTGTCAATGAATATTCACATCTATAAGG
Found at i:37648 original size:38 final size:38
Alignment explanation
Indices: 37597--37675 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
37587 ATACTACATA
*
37597 TTATTTGAAACACCTAATGAAATTACTCAACGCCCCTT
1 TTATTCGAAACACCTAATGAAATTACTCAACGCCCCTT
*
37635 TTATTCGAAACACCTAATGAAATTACTCAATGCCCCTT
1 TTATTCGAAACACCTAATGAAATTACTCAACGCCCCTT
37673 TTA
1 TTA
37676 AGGATCGATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (38 bp):
TTATTCGAAACACCTAATGAAATTACTCAACGCCCCTT
Found at i:46181 original size:18 final size:19
Alignment explanation
Indices: 46153--46188 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
46143 GTAGTTTTTT
*
46153 GTAGTTTTTTTTTAAATGG
1 GTAGTTTTTTTTAAAATGG
46172 GTAG-TTTTTTTAAAATG
1 GTAGTTTTTTTTAAAATG
46189 ATATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (19 bp):
GTAGTTTTTTTTAAAATGG
Found at i:47442 original size:18 final size:18
Alignment explanation
Indices: 47408--47461 Score: 90
Period size: 18 Copynumber: 2.9 Consensus size: 18
47398 TGAAGACTTA
*
47408 TTGAAGACAATTTGAAGAT
1 TTGAAGACCA-TTGAAGAT
47427 TTGAAGACCATTGAAGAT
1 TTGAAGACCATTGAAGAT
47445 TTGAAGACCATTGAAGA
1 TTGAAGACCATTGAAGA
47462 ATAATTTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 25 0.74
19 9 0.26
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACCATTGAAGAT
Done.