Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015695.1 Corchorus capsularis cultivar CVL-1 contig15716, 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: 32529
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:199 original size:38 final size:38
Alignment explanation
Indices: 157--229 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
147 ACATAATGTG
*
157 ATTATCAAAAAATCATAGGGAGGTTATCAAAATTTGTA
1 ATTATCAAAAAATCATAAGGAGGTTATCAAAATTTGTA
* **
195 ATTATCAAGATTTCATAAGGAGGTTATCAAAATTT
1 ATTATCAAAAAATCATAAGGAGGTTATCAAAATTT
230 TATAGGGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (38 bp):
ATTATCAAAAAATCATAAGGAGGTTATCAAAATTTGTA
Found at i:212 original size:60 final size:61
Alignment explanation
Indices: 136--252 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 61
126 CAAAGCGAGG
* *
136 TTATCAAAATTACATAATGTGATTATCAAAAAATCATAGGGAG-GTTATCAAAATTTGTAA
1 TTATCAAAATTACATAAGGAGATTATCAAAAAATCATAGGGAGAGTTATCAAAATTTGTAA
* * * ** * *
196 TTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGATTTATCAAAATTT
1 TTATCAAAATTACATAAGGAGATTATCAAAAAATCATAGGGAGAGTTATCAAAATTT
253 TATAGGAAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
60 35 0.74
61 12 0.26
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.36
Consensus pattern (61 bp):
TTATCAAAATTACATAAGGAGATTATCAAAAAATCATAGGGAGAGTTATCAAAATTTGTAA
Found at i:248 original size:23 final size:22
Alignment explanation
Indices: 117--645 Score: 154
Period size: 22 Copynumber: 24.3 Consensus size: 22
107 TGGTCCAATT
* *
117 TCAAAATTTCAAAGCGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* ** * *
139 TCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
**
161 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
*
183 TCAAAATTT-GTA---A--TTA
1 TCAAAATTTCATAGGGAGGTTA
* *
199 TCAAGATTTCATAAGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* *
221 TCAAAATTTTATAGGGAGATTTA
1 TCAAAATTTCATAGGGAG-GTTA
* *
244 TCAAAATTTTATAGGAAGGTTTA
1 TCAAAATTTCATAGGGAGG-TTA
* *
267 TCAAAATGTCATAGCGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * * *
289 TCAAAAATTCATAGTGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
* * * *
311 TCAAAATTTCAGAGTGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
* * * *
333 CTGACAATATTCATATGGAGGTTT
1 -TCAAAAT-TTCATAGGGAGGTTA
* * ** * *
357 TTAAATTTTCATAACGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
* * * * * *
379 TTAATATATCACATGGAGATTA
1 TCAAAATTTCATAGGGAGGTTA
* ** *
401 TCAACATCTT-ATAGTGTTGATTA
1 TCAAAAT-TTCATAG-GGAGGTTA
* *
424 TCAAAATTTCATAGTGAGATCT-
1 TCAAAATTTCATAGGGAGGT-TA
* *
446 TCAAAATTCCTTAGGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
468 ACAAAATTTCATAAGAAGGTTAAA
1 TCAAAATTTCATAGGGAGGTT--A
*** *
492 T-AAAATTT-ATAAAAAGGTTC
1 TCAAAATTTCATAGGGAGGTTA
* * * *
512 TCGAAATTCCATA-GTATCGTTA
1 TCAAAATTTCATAGGGA-GGTTA
** * *
534 TTGAAATTTCAAAGGAAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
556 TCAAAATTTCATAAGGACGTCA
1 TCAAAATTTCATAGGGAGGTTA
* * *
578 T-AAAA---AATAGTGTA-ATTA
1 TCAAAATTTCATAG-GGAGGTTA
* * *
596 TCATAATTTCATAGGAATGTTA
1 TCAAAATTTCATAGGGAGGTTA
* *
618 TCAAAATTTCATAAGGACGTTA
1 TCAAAATTTCATAGGGAGGTTA
*
640 TAAAAA
1 TCAAAA
646 ATAGTGTAAT
Statistics
Matches: 367, Mismatches: 113, Indels: 54
0.69 0.21 0.10
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 7 0.02
19 5 0.01
20 2 0.01
21 15 0.04
22 241 0.66
23 74 0.20
24 10 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TCAAAATTTCATAGGGAGGTTA
Found at i:612 original size:62 final size:62
Alignment explanation
Indices: 538--689 Score: 259
Period size: 62 Copynumber: 2.5 Consensus size: 62
528 TCGTTATTGA
*
538 AATTTCAAAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* *
600 AATTTCATAGGAATGTTATCAAAATTTCATAAGGACGTTATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* *
662 AATTTAATAGGAAGGTTATCATAATTTC
1 AATTTCATAGGAAGGTTATCAAAATTTC
690 GTATGAATAT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 84 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
Found at i:902 original size:22 final size:22
Alignment explanation
Indices: 859--902 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
849 TATTCATACG
**
859 AAATTATGATAATCTCTTTATT
1 AAATTATGATAATCTCACTATT
881 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
903 TTTTGTGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:1175 original size:22 final size:22
Alignment explanation
Indices: 1137--1196 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
1127 AAAACCTCCA
*
1137 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* *
1159 TTTGAAATTTTGATAATCACAC
1 TATGAAATTGTGATAATCACAC
1181 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
1197 CCTATAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:1206 original size:18 final size:18
Alignment explanation
Indices: 1180--1214 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1170 GATAATCACA
*
1180 CTATGAAATTGTGATAAC
1 CTATAAAATTGTGATAAC
*
1198 CTATAAAATTTTGATAA
1 CTATAAAATTGTGATAA
1215 ACCTCCCTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (18 bp):
CTATAAAATTGTGATAAC
Found at i:1307 original size:60 final size:63
Alignment explanation
Indices: 1163--1312 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 63
1153 TCACACTTTG
* *
1163 AAATTTTGATAA-TCACACTATGAAATTGTGATAACCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAACTCTC-TTATGAAATTGTGATAACCTATAAAATTTTGATAAACCTCCCTATA
* * * *
1226 AAATTTTGATAACTTTCTTATGAAATCT-TGATAA-CTA-CAAATTTTGAT-AATCTCCCTATG
1 AAATTTTGATAACTCTCTTATGAAAT-TGTGATAACCTATAAAATTTTGATAAACCTCCCTATA
** *
1286 ATTTTTTGATAGC-CTCATTATGAAATT
1 AAATTTTGATAACTCTC-TTATGAAATT
1313 TTGTTAATCT
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
59 3 0.04
60 29 0.39
61 10 0.14
62 3 0.04
63 26 0.35
64 3 0.04
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (63 bp):
AAATTTTGATAACTCTCTTATGAAATTGTGATAACCTATAAAATTTTGATAAACCTCCCTATA
Found at i:1314 original size:22 final size:22
Alignment explanation
Indices: 1161--1432 Score: 135
Period size: 22 Copynumber: 12.8 Consensus size: 22
1151 AATCACACTT
* * *
1161 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCATTA
*
1183 TGAAATTGTGATAACCT-A-TA
1 TGAAATTTTGATAACCTCATTA
**
1203 --AAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTCATTA
* *
1224 TAAAATTTTGATAACTTTC-TTA
1 TGAAATTTTGATAAC-CTCATTA
*
1246 TGAAATCTTGATAA---C--TA
1 TGAAATTTTGATAACCTCATTA
* * **
1263 -CAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAACCTCATTA
** *
1284 TGATTTTTTGATAGCCTCATTA
1 TGAAATTTTGATAACCTCATTA
* * *
1306 TGAAATTTTGTTAATCT-ACCTA
1 TGAAATTTTGATAACCTCA-TTA
* * * *
1328 TGAAAATTTGATCTACAT-ACTA
1 TGAAATTTTGAT-AACCTCATTA
*
1350 TGAAATTTTGATAACCCTC-TTG
1 TGAAATTTTGATAA-CCTCATTA
* *
1372 TGAAATTTTGA-AAACTAATTA
1 TGAAATTTTGATAACCTCATTA
1393 TGAAATTTTGATAACCTTCA-TA
1 TGAAATTTTGATAACC-TCATTA
*
1415 TGAAATTTTGATATCCTC
1 TGAAATTTTGATAACCTC
1433 CCTGAATTTT
Statistics
Matches: 191, Mismatches: 40, Indels: 39
0.71 0.15 0.14
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
18 10 0.05
19 6 0.03
20 4 0.02
21 24 0.13
22 117 0.61
23 17 0.09
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCATTA
Found at i:1471 original size:19 final size:20
Alignment explanation
Indices: 1415--1465 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
1405 AACCTTCATA
1415 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
1435 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
1454 TGAAATTTTGAT
1 TGAAATTTTGAT
1466 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:1623 original size:22 final size:22
Alignment explanation
Indices: 1573--1624 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1563 TCACATTTTG
*
1573 AAAA-TTTAATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
*
1594 GAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
1616 AAAATTTTG
1 AAAATTTTG
1625 TTGATCCCTC
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:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:1668 original size:22 final size:21
Alignment explanation
Indices: 1635--1693 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
1625 TTGATCCCTC
*
1635 TGAAATTCTGATAA-TCACATT
1 TGAAATTTTGATAACTCAC-TT
*
1656 ATGTAATTTTGATAACCTCACTT
1 -TGAAATTTTGATAA-CTCACTT
1679 TGAAATTTTGATAAC
1 TGAAATTTTGATAAC
1694 AACACTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.03
22 25 0.78
23 2 0.06
24 4 0.12
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (21 bp):
TGAAATTTTGATAACTCACTT
Found at i:1699 original size:22 final size:21
Alignment explanation
Indices: 1635--1714 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 21
1625 TTGATCCCTC
*
1635 TGAAATTCTGATAATCACA-TT
1 TGAAATTTTGATAA-CACACTT
* *
1656 ATGTAATTTTGATAACCTCACTT
1 -TGAAATTTTGATAA-CACACTT
*
1679 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAAC-ACACTT
1701 T-AATATTTTGATAA
1 TGAA-ATTTTGATAA
1715 TCCGATCTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
21 3 0.06
22 43 0.90
23 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (21 bp):
TGAAATTTTGATAACACACTT
Found at i:1865 original size:22 final size:22
Alignment explanation
Indices: 1815--1865 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1805 TAACATTCAT
*
1815 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
1837 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
1859 ATGAAAT
1 ATGAAAT
1866 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:1929 original size:22 final size:22
Alignment explanation
Indices: 1870--1929 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
1860 TGAAATATTT
1870 AATGAAATTTTG-TGAACCACAC
1 AATGAAATTTTGAT-AACCACAC
*
1892 AATGAAATTCTT-ATAACCTCAC
1 AATGAAATT-TTGATAACCACAC
**
1914 TTTGAAATTTTGATAA
1 AATGAAATTTTGATAA
1930 TCTCTTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.06
22 27 0.84
23 3 0.09
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (22 bp):
AATGAAATTTTGATAACCACAC
Found at i:2104 original size:22 final size:22
Alignment explanation
Indices: 1972--2104 Score: 108
Period size: 22 Copynumber: 6.0 Consensus size: 22
1962 AATTAATCAC
** * *
1972 CCTATGAAATTTCAATATCCAA
1 CCTATGAAATTTTGATAACCAT
* * *
1994 CCTAAGAGATTTTAATAACCTGAT
1 CCTATGAAATTTTGATAACC--AT
*
2018 CCTATGAAATTTTGGTAACCA-
1 CCTATGAAATTTTGATAACCAT
2039 CACTATGAAATTTTGATAACC-T
1 C-CTATGAAATTTTGATAACCAT
* * *
2061 CTTCATGAAATTATAATAACCAT
1 CCT-ATGAAATTTTGATAACCAT
*
2084 CTTATGAAATTTTGATAACCA
1 CCTATGAAATTTTGATAACCA
2105 CATAGAGACA
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
21 2 0.02
22 67 0.74
23 4 0.04
24 17 0.19
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCAT
Found at i:2302 original size:19 final size:20
Alignment explanation
Indices: 2271--2308 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2261 ATTTGACATT
2271 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
2290 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
2309 AATTATAGTA
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:2477 original size:37 final size:36
Alignment explanation
Indices: 2432--2506 Score: 107
Period size: 38 Copynumber: 2.1 Consensus size: 36
2422 TTTAAGACCG
2432 AAGAAAAA-GCAAAATTAAATACAACGATTGGAAACA
1 AAGAAAAAGGCAAAATTAAATACAACG-TTGGAAACA
**
2468 AAGATAAAAGGCAAAATTAAATAGGACGTTGGAAACA
1 AAGA-AAAAGGCAAAATTAAATACAACGTTGGAAACA
2505 AA
1 AA
2507 AAGTCAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 4 0.11
37 15 0.43
38 16 0.46
ACGTcount: A:0.59, C:0.09, G:0.17, T:0.15
Consensus pattern (36 bp):
AAGAAAAAGGCAAAATTAAATACAACGTTGGAAACA
Found at i:3005 original size:22 final size:22
Alignment explanation
Indices: 2923--3007 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
2913 AATCTGATCC
* *
2923 TATGAAATTTTGGTAACCA-CAC
1 TATGAAATTTTGATAACCATC-T
* *
2945 TATGGAATTTTGATAAAC-TCT
1 TATGAAATTTTGATAACCATCT
* *
2966 TCATGAAATTATAATAACCATCT
1 T-ATGAAATTTTGATAACCATCT
2989 TATGAAATTTTGATAACCA
1 TATGAAATTTTGATAACCA
3008 CATAGAGACA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.02
22 45 0.90
23 4 0.08
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATCT
Found at i:3205 original size:19 final size:20
Alignment explanation
Indices: 3174--3211 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3164 ATTTGACATT
3174 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
3193 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
3212 AATAAAAGTA
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:3924 original size:20 final size:18
Alignment explanation
Indices: 3899--3943 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3889 AGATATGTTT
3899 TACTAATAAATATTAATATA
1 TACTAATAAATA--AATATA
*
3919 TACTAATAAATAAATATT
1 TACTAATAAATAAATATA
3937 TACTAAT
1 TACTAAT
3944 TTACTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.50
20 12 0.50
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:3940 original size:18 final size:19
Alignment explanation
Indices: 3897--3943 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
3887 TCAGATATGT
3897 TTTACTAATAAATATTAATA
1 TTTACTAATAAATA-TAATA
*
3917 TATACTAATAAATA-AATA
1 TTTACTAATAAATATAATA
3935 TTTACTAAT
1 TTTACTAAT
3944 TTACTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.48
20 13 0.52
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTACTAATAAATATAATA
Found at i:5956 original size:25 final size:25
Alignment explanation
Indices: 5918--5969 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
5908 ATGCAATCTC
5918 TCATAGAAAGACACCTTTTCATGTT
1 TCATAGAAAGACACCTTTTCATGTT
* *
5943 TCATGGAAATACACCTTTTCATGTT
1 TCATAGAAAGACACCTTTTCATGTT
5968 TC
1 TC
5970 TACAGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (25 bp):
TCATAGAAAGACACCTTTTCATGTT
Found at i:22616 original size:45 final size:45
Alignment explanation
Indices: 22566--22652 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
22556 GATTACTTCT
22566 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
* *
22611 CCAGCTTATCATTAATTCGGGGTAGGGATCTTTTAGTAATTC
1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTC
22653 TACTACTCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
Found at i:23596 original size:91 final size:89
Alignment explanation
Indices: 23423--23598 Score: 255
Period size: 91 Copynumber: 1.9 Consensus size: 89
23413 GGTAAGTTTA
* *
23423 ATGAGCTTCATTTATGGCTGAAGCTCAAACATTCCTCTACTTAGCGCTATTGTAAATATTTTTGT
1 ATGAGCTTCATTTATGGCTGAAGCTCAAACATTCCCCTACTTA-CGCTATTGTAAATATTTTTGG
* *
23488 CTGTAGAATTCTAACCATGCCTTAG
65 CTCTACAATTCTAACCATGCCTTAG
23513 ATGAGCTTCATTTATGGCTGAAGCTCTCAAACATTCCCCCTACTTA-GCTATTGTAAATATTTTT
1 ATGAGCTTCATTTATGGCTGAAG--CTCAAACATT-CCCCTACTTACGCTATTGTAAATATTTTT
* *
23577 GGGTCTACAATTCTGACCATGC
63 GGCTCTACAATTCTAACCATGC
23599 ATTATAGTCA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
90 23 0.30
91 35 0.45
92 10 0.13
93 9 0.12
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (89 bp):
ATGAGCTTCATTTATGGCTGAAGCTCAAACATTCCCCTACTTACGCTATTGTAAATATTTTTGGC
TCTACAATTCTAACCATGCCTTAG
Found at i:25679 original size:25 final size:25
Alignment explanation
Indices: 25644--25694 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
25634 TTTGATTCAC
25644 TCTAAAATTTGCTTCAATTTTGGGT
1 TCTAAAATTTGCTTCAATTTTGGGT
* * *
25669 TCTAAATTTTGTTTCAATTTTTGGT
1 TCTAAAATTTGCTTCAATTTTGGGT
25694 T
1 T
25695 AAACAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.55
Consensus pattern (25 bp):
TCTAAAATTTGCTTCAATTTTGGGT
Found at i:27305 original size:13 final size:13
Alignment explanation
Indices: 27289--27313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27279 AATTTTCGAT
27289 CAAAAGGGAGGCA
1 CAAAAGGGAGGCA
27302 CAAAAGGGAGGC
1 CAAAAGGGAGGC
27314 GGAATTTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.40, T:0.00
Consensus pattern (13 bp):
CAAAAGGGAGGCA
Found at i:28214 original size:31 final size:29
Alignment explanation
Indices: 28188--28261 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
28178 CTTTGTGTTG
28188 AAAGATTAAATCTTTGGAGTAATTTGTGAAT
1 AAAGATTAAAT-TTT-GAGTAATTTGTGAAT
* *
28219 AAAGATTGAATTTTTAGTAATTTGTGAAT
1 AAAGATTAAATTTTGAGTAATTTGTGAAT
* *
28248 AAGGATTGAATTTT
1 AAAGATTAAATTTT
28262 TTTTTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 27 0.68
30 3 0.08
31 10 0.25
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (29 bp):
AAAGATTAAATTTTGAGTAATTTGTGAAT
Found at i:28246 original size:29 final size:29
Alignment explanation
Indices: 28205--28262 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
28195 AAATCTTTGG
28205 AGTAATTTGTGAATAAAGATTGAATTTTT
1 AGTAATTTGTGAATAAAGATTGAATTTTT
*
28234 AGTAATTTGTGAATAAGGATTGAATTTTT
1 AGTAATTTGTGAATAAAGATTGAATTTTT
28263 TTTTATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (29 bp):
AGTAATTTGTGAATAAAGATTGAATTTTT
Found at i:28930 original size:35 final size:35
Alignment explanation
Indices: 28840--29140 Score: 307
Period size: 35 Copynumber: 9.1 Consensus size: 35
28830 AAAAGGTGAA
* *
28840 TAAGTAATTCAGTAATCAACTTAATTCAGGGTAAT
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAAT
* *
28875 TAAGTTAGT--G-AA-TAATTTAATTCAGGGTAAT
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAAT
28906 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAAT
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAAT
**
28941 TAAGTAAGTC-G---GCAACTTAATTCAGGGTAAT
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAAT
* *
28972 TAAGTAAGT-A-AAAGGTAACTTAATTCAGGGTAAT
1 TAAGTAAGTCAGTAA-TTAACTTAATTCAGGGTAAT
* *
29006 TAAGTTAGT--G-AA-TAATTTAATTCAGGGTAA-
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAAT
*
29036 T---TAAGTCAGTAATTAGCTTAATTCAGGGTAAT
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAAT
* * *
29068 TAAGTAAGTCAGTTAGTAATTTAATTCAGGGTAAT
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAAT
* *
29103 TAAGT-AGTTTAGTAATCAACTTAATTCAGGGTAAT
1 TAAGTAAG-TCAGTAATTAACTTAATTCAGGGTAAT
29138 TAA
1 TAA
29141 ATCAGTAGGC
Statistics
Matches: 224, Mismatches: 23, Indels: 38
0.79 0.08 0.13
Matches are distributed among these distances:
27 4 0.02
29 1 0.00
30 3 0.01
31 85 0.38
32 3 0.01
33 4 0.02
34 32 0.14
35 92 0.41
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.35
Consensus pattern (35 bp):
TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAAT
Found at i:29146 original size:66 final size:66
Alignment explanation
Indices: 28840--29334 Score: 486
Period size: 66 Copynumber: 7.6 Consensus size: 66
28830 AAAAGGTGAA
* * * * *
28840 TAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGTTAGTGAATAATTTAATTCAGGGTAA
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAATTAAGTCAGTTAGTAATTTAATTCAGGGTAA
28905 T
66 T
* ** * *
28906 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAATTAAGTAAGTCGGCAACTTAATTCAGGGTAA
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAATTAAGTCAGTTAGTAATTTAATTCAGGGTAA
28971 T
66 T
* * * * *
28972 TAAGTAAGT-A-AAAGGTAACTTAATTCAGGGTAATTAAGTTAGTGAATAATTTAATTCAGGGTA
1 TAAGTAAGTCAGTAA-TTAACTTAATTCAGGGTAATTAAGTCAGTTAGTAATTTAATTCAGGGTA
29035 A-
65 AT
*
29036 T---TAAGTCAGTAATTAGCTTAATTCAGGGTAATTAAGTAAGTCAGTTAGTAATTTAATTCAGG
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAA-T---TAAGTCAGTTAGTAATTTAATTCAGG
29098 GTAAT
62 GTAAT
* * * ** *
29103 TAAGT-AGTTTAGTAATCAACTTAATTCAGGGTAATTAAATCAG-TAG----GCAA--C---TTA
1 TAAGTAAG-TCAGTAATTAACTTAATTCAGGGTAATTAAGTCAGTTAGTAATTTAATTCAGGGTA
29157 AT
65 AT
* * *
29159 TAAGTCAGTCAGTAATTAACTTAATTCAGGATAATTAAGTAAGTTAGTTAGTAATTTAATTCAGG
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAA-T---TAAGTCAGTTAGTAATTTAATTCAGG
29224 GTAAT
62 GTAAT
* * * * *
29229 TAAGTAATTTAGTAATCAACTTAATTCAGGGTAATTATGTCAG-TAGGTAACTTAATTCAGGGTA
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAATTAAGTCAGTTA-GTAATTTAATTCAGGGTA
29293 AT
65 AT
*
29295 TAAGTCAGTCAGTAATTAACTTAATTCAGGGTAATTAAGT
1 TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAATTAAGT
29335 AATTCAGTTA
Statistics
Matches: 351, Mismatches: 50, Indels: 56
0.77 0.11 0.12
Matches are distributed among these distances:
56 32 0.09
57 3 0.01
59 1 0.00
60 6 0.02
61 10 0.03
62 18 0.05
63 3 0.01
64 3 0.01
65 51 0.15
66 161 0.46
67 2 0.01
69 4 0.01
70 57 0.16
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (66 bp):
TAAGTAAGTCAGTAATTAACTTAATTCAGGGTAATTAAGTCAGTTAGTAATTTAATTCAGGGTAA
T
Found at i:29157 original size:31 final size:31
Alignment explanation
Indices: 28857--29334 Score: 335
Period size: 31 Copynumber: 14.7 Consensus size: 31
28847 TTCAGTAATC
* *
28857 AACTTAATTCAGGGTAATTAAGTTAGT-GAAT
1 AACTTAATTCAGGGTAATTAAGTCAGTAG-GT
* **
28888 AATTTAATTCAGGGTAATTAAGTAAGTCAGTAATT
1 AACTTAATTCAGGGTAA-T---TAAGTCAGTAGGT
* * *
28923 AACTTAATTCAGGGTAATTAAGTAAGTCGGC
1 AACTTAATTCAGGGTAATTAAGTCAGTAGGT
*
28954 AACTTAATTCAGGGTAATTAAGTAAGTAAAAGGT
1 AACTTAATTCAGGGTAATTAAGTCAGT---AGGT
* *
28988 AACTTAATTCAGGGTAATTAAGTTAGT-GAAT
1 AACTTAATTCAGGGTAATTAAGTCAGTAG-GT
* **
29019 AATTTAATTCAGGGTAATTAAGTCAGTAATT
1 AACTTAATTCAGGGTAATTAAGTCAGTAGGT
* *
29050 AGCTTAATTCAGGGTAATTAAGTAAGTCAGTTAGT
1 AACTTAATTCAGGGTAATTAAGTCAGT-AG---GT
* *
29085 AATTTAATTCAGGGTAATTAAGT-AGTTTAGTAAT
1 AACTTAATTCAGGGTAATTAAGTCAG--TAG--GT
* *
29119 CAACTTAATTCAGGGTAATTAAATCAGTAGGC
1 -AACTTAATTCAGGGTAATTAAGTCAGTAGGT
* * **
29151 AACTTAA-T-----TAAGTCAGTCAGTAATT
1 AACTTAATTCAGGGTAATTAAGTCAGTAGGT
* *
29176 AACTTAATTCAGGATAATTAAGTAAGTTAGTTAGT
1 AACTTAATTCAGGGTAATTAAGTCAG-TAG---GT
* * * *
29211 AATTTAATTCAGGGTAATTAAGTAATTTAGTAAT
1 AACTTAATTCAGGGTAATTAAGTCA-GTAG--GT
*
29245 CAACTTAATTCAGGGTAATTATGTCAGTAGGT
1 -AACTTAATTCAGGGTAATTAAGTCAGTAGGT
*
29277 AACTTAATTCAGGGTAATTAAGTCAGTCAGTAATT
1 AACTTAATTCAGGGTAATTAAGTCAGT-AG---GT
29312 AACTTAATTCAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
29335 AATTCAGTTA
Statistics
Matches: 361, Mismatches: 52, Indels: 64
0.76 0.11 0.13
Matches are distributed among these distances:
25 18 0.05
26 1 0.00
30 2 0.01
31 144 0.40
32 7 0.02
34 43 0.12
35 143 0.40
36 3 0.01
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (31 bp):
AACTTAATTCAGGGTAATTAAGTCAGTAGGT
Found at i:29197 original size:35 final size:35
Alignment explanation
Indices: 29155--29353 Score: 235
Period size: 35 Copynumber: 5.8 Consensus size: 35
29145 GTAGGCAACT
* *
29155 TAATTAAGTCAGTCAGTAATTAACTTAATTCAGGA
1 TAATTAAGTAAGTCAGTAATTAACTTAATTCAGGG
* * * *
29190 TAATTAAGTAAGTTAGTTAGTAATTTAATTCAGGG
1 TAATTAAGTAAGTCAGTAATTAACTTAATTCAGGG
* * *
29225 TAATTAAGTAATTTAGTAATCAACTTAATTCAGGG
1 TAATTAAGTAAGTCAGTAATTAACTTAATTCAGGG
**
29260 TAATT-A-T--GTCAGTAGGTAACTTAATTCAGGG
1 TAATTAAGTAAGTCAGTAATTAACTTAATTCAGGG
*
29291 TAATTAAGTCAGTCAGTAATTAACTTAATTCAGGG
1 TAATTAAGTAAGTCAGTAATTAACTTAATTCAGGG
* * *
29326 TAATTAAGTAATTCAGTTATTAATTTAA
1 TAATTAAGTAAGTCAGTAATTAACTTAA
29354 CGAGAGGGGT
Statistics
Matches: 138, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
31 24 0.17
32 1 0.01
33 2 0.01
34 1 0.01
35 110 0.80
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (35 bp):
TAATTAAGTAAGTCAGTAATTAACTTAATTCAGGG
Found at i:29302 original size:14 final size:14
Alignment explanation
Indices: 29249--29302 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
29239 AGTAATCAAC
*
29249 TTAATTCAGGGTAA
1 TTAAGTCAGGGTAA
*
29263 TTATGTCAGTAGGTAA
1 TTAAGTCAG--GGTAA
*
29279 CTTAATTCAGGGTAA
1 -TTAAGTCAGGGTAA
29294 TTAAGTCAG
1 TTAAGTCAG
29303 TCAGTAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 15 0.47
15 5 0.16
16 5 0.16
17 7 0.22
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (14 bp):
TTAAGTCAGGGTAA
Done.