Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019607.1 Corchorus olitorius cultivar O-4 contig19640, 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: 9938
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:1163 original size:40 final size:39
Alignment explanation
Indices: 981--1456 Score: 344
Period size: 39 Copynumber: 12.3 Consensus size: 39
971 ACTGGCAAAA
* * * * *
981 CAATGACCCTG-ATCAGGATTCTGAAGTTAACAGATAAAA
1 CAATGATCCTGAAT-AGGATTCTGAAATTGACTGATAAAG
* ** * * *
1020 CAATGATCCTAAATAGCCTTCTAAAATTGACGGATAAAA
1 CAATGATCCTGAATAGGATTCTGAAATTGACTGATAAAG
* * * * **
1059 CAATAATCCTGAATAGGATTCTAAAAATGACCGACGAAG
1 CAATGATCCTGAATAGGATTCTGAAATTGACTGATAAAG
* * * ** *
1098 AAATGATGCTAAATAAAATTTTGAAATTGATCTGATAAAG
1 CAATGATCCTGAATAGGATTCTGAAATTGA-CTGATAAAG
*
1138 CAATGATCCTGAATAGGATTCTGAAATTCACTCGATAAAG
1 CAATGATCCTGAATAGGATTCTGAAATTGACT-GATAAAG
* * * * *
1178 CAATGATCCTGAGTAGGATTTTGAAATTAATTTGATACAG
1 CAATGATCCTGAATAGGATTCTGAAATTGA-CTGATAAAG
* * * * *
1218 CAGTGATCCT-AAGTAGGATTGTGAAATCGATTAATAAAG
1 CAATGATCCTGAA-TAGGATTCTGAAATTGACTGATAAAG
* * *
1257 CAATGATCGTGAATAGGA-T-TAAAATTGACTGGTAAAG
1 CAATGATCCTGAATAGGATTCTGAAATTGACTGATAAAG
* ** *
1294 AAATGATCCTGAGCAGGATTCTGAAATTGACTAATAAAG
1 CAATGATCCTGAATAGGATTCTGAAATTGACTGATAAAG
* * *
1333 CAATGATCGTGAATAGGA-T-TAAAATTGAC-CAGTAAAG
1 CAATGATCCTGAATAGGATTCTGAAATTGACTGA-TAAAG
* ** * *
1370 AAATGATCCTGAGCAGGATTCTGAAATCGACTAATAAAG
1 CAATGATCCTGAATAGGATTCTGAAATTGACTGATAAAG
* * *
1409 CAATGATCATGAATAGGA-T-TAAAATTGACTGGT-AA-
1 CAATGATCCTGAATAGGATTCTGAAATTGACTGATAAAG
1444 CAAATGATCCTGA
1 C-AATGATCCTGA
1457 GCAGGATTAA
Statistics
Matches: 340, Mismatches: 84, Indels: 29
0.75 0.19 0.06
Matches are distributed among these distances:
35 1 0.00
36 13 0.04
37 65 0.19
38 5 0.01
39 158 0.46
40 97 0.29
41 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (39 bp):
CAATGATCCTGAATAGGATTCTGAAATTGACTGATAAAG
Found at i:1312 original size:37 final size:37
Alignment explanation
Indices: 1252--1468 Score: 202
Period size: 37 Copynumber: 5.8 Consensus size: 37
1242 AATCGATTAA
* * * *
1252 TAAAGCAATGATCGTGAATAGGATTAAAATTGACTGG
1 TAAAGAAATGATCCTGAACAGGATTAAAATTGACTAG
* * *
1289 TAAAGAAATGATCCTGAGCAGGATTCTGAAATTGACTAA
1 TAAAGAAATGATCCTGAACAGGA-T-TAAAATTGACTAG
* * * *
1328 TAAAGCAATGATCGTGAATAGGATTAAAATTGACCAG
1 TAAAGAAATGATCCTGAACAGGATTAAAATTGACTAG
* * * *
1365 TAAAGAAATGATCCTGAGCAGGATTCTGAAATCGACTAA
1 TAAAGAAATGATCCTGAACAGGA-T-TAAAATTGACTAG
* * * *
1404 TAAAGCAATGATCATGAATAGGATTAAAATTGACTGG
1 TAAAGAAATGATCCTGAACAGGATTAAAATTGACTAG
* *
1441 T-AACAAATGATCCTGAGCAGGATTAAAA
1 TAAAGAAATGATCCTGAACAGGATTAAAA
1469 CACATATTGA
Statistics
Matches: 141, Mismatches: 35, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
36 22 0.16
37 58 0.41
38 4 0.03
39 57 0.40
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (37 bp):
TAAAGAAATGATCCTGAACAGGATTAAAATTGACTAG
Found at i:1329 original size:76 final size:76
Alignment explanation
Indices: 1121--1464 Score: 413
Period size: 76 Copynumber: 4.5 Consensus size: 76
1111 TAAAATTTTG
* * ** *
1121 AAATTGATCTGATAAAGCAATGATCCTGAATAGGATTCTGAAATTC-ACTCGATAAAGCAATGAT
1 AAATTGA-CTGGTAAAGAAATGATCCTGAGCAGGATTCTGAAA-TCGACT-AATAAAGCAATGAT
* * *
1185 CCTGAGTAGGATTTTG
63 CGTGAATAGGA--TTA
* * * * * * * * * *
1201 AAATTAATTTGATACAGCAGTGATCCTAAGTAGGATTGTGAAATCGATTAATAAAGCAATGATCG
1 AAATTGA-CTGGTAAAGAAATGATCCTGAGCAGGATTCTGAAATCGACTAATAAAGCAATGATCG
1266 TGAATAGGATTA
65 TGAATAGGATTA
*
1278 AAATTGACTGGTAAAGAAATGATCCTGAGCAGGATTCTGAAATTGACTAATAAAGCAATGATCGT
1 AAATTGACTGGTAAAGAAATGATCCTGAGCAGGATTCTGAAATCGACTAATAAAGCAATGATCGT
1343 GAATAGGATTA
66 GAATAGGATTA
** *
1354 AAATTGACCAGTAAAGAAATGATCCTGAGCAGGATTCTGAAATCGACTAATAAAGCAATGATCAT
1 AAATTGACTGGTAAAGAAATGATCCTGAGCAGGATTCTGAAATCGACTAATAAAGCAATGATCGT
1419 GAATAGGATTA
66 GAATAGGATTA
*
1430 AAATTGACTGGT-AACAAATGATCCTGAGCAGGATT
1 AAATTGACTGGTAAAGAAATGATCCTGAGCAGGATT
1465 AAAACACATA
Statistics
Matches: 233, Mismatches: 30, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
75 22 0.09
76 141 0.61
77 8 0.03
79 24 0.10
80 38 0.16
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (76 bp):
AAATTGACTGGTAAAGAAATGATCCTGAGCAGGATTCTGAAATCGACTAATAAAGCAATGATCGT
GAATAGGATTA
Found at i:1695 original size:141 final size:141
Alignment explanation
Indices: 1512--2157 Score: 865
Period size: 142 Copynumber: 4.6 Consensus size: 141
1502 AAATATAGAA
* * * *
1512 TGCCCGGAGGACTTACAAATGCCAACTCGACCTTGAACAAGGTTTATTGAAATTTAAACGCAAAT
1 TGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTTTGAAATTTAAACGCAAAT
* * * *
1577 TTGATTAACAA-TATGATGAAATGAAATGACACCCGGAGGATTTATCAGAATTAATACCCGGAGG
66 TTGATTAAAAACT-TGATAAAATGAGATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGG
1641 TTTCTGAAACTG
130 TTTCTGAAACTG
** ****
1653 TGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTTT--TTTTTTTTTG--AAT
1 TGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTTTGAAATTTAAACGCAAAT
* * * * * *
1714 CTTAAAT-ACAATTTCGATTAACAATATGAGGTGATACCCGGAGGATTTATCAGAATTAATATCC
66 -TTGATTAAAAACTT-GA-T-A-AA-ATGAGATGATACCCGGAGGATTTATCAGAATTAATACCC
*
1778 GGAGGCTTCTGAAA-TGG
125 GGAGGTTTCTGAAACT-G
* * * *
1795 TGCCCGGAGGTCTTACAAATGCAAACTCAACCTTGAGCAGGGTGCTTTTGAAATTTAAACGCAAC
1 TGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGT-TTTTTGAAATTTAAACGCAAA
* *
1860 TTTGATTAAAAACTTGATAAAATGAGATGATACCCGGAGGATTTATCAGAATTGATACCCGGTGG
65 TTTGATTAAAAACTTGATAAAATGAGATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGG
*
1925 TTTTTGAAACTG
130 TTTCTGAAACTG
*
1937 TGCCCGGAGGTCTTACAAATGCAAACTTGACCTTGAGCAAGGTTTTTTGAAATTTAAACGCAAAT
1 TGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTTTGAAATTTAAACGCAAAT
2002 TTGATTAAAAACTTGATAAAATGAGATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGT
66 TTGATTAAAAACTTGATAAAATGAGATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGT
2067 TTCTGAAACTG
131 TTCTGAAACTG
* * *
2078 TGCCCGGAGGTCTTACAAATGCAAACTTGACCTTGAGCAAGGTTTTTTTGACATTTAAACGCAAC
1 TGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGG-TTTTTTGAAATTTAAACGCAAA
2143 TTTGATTAAAAACTT
65 TTTGATTAAAAACTT
2158 ACCAAAATGG
Statistics
Matches: 441, Mismatches: 48, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
137 8 0.02
138 7 0.02
139 5 0.01
141 182 0.41
142 213 0.48
143 7 0.02
144 1 0.00
145 5 0.01
146 6 0.01
147 7 0.02
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (141 bp):
TGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTTTGAAATTTAAACGCAAAT
TTGATTAAAAACTTGATAAAATGAGATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGT
TTCTGAAACTG
Found at i:3049 original size:16 final size:15
Alignment explanation
Indices: 3028--3058 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3018 GCCTTATTCC
3028 CTTTTTCTTTTCTTTT
1 CTTTTTCTTTT-TTTT
3044 CTTTTTCTTTTTTTT
1 CTTTTTCTTTTTTTT
3059 GGCACTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
CTTTTTCTTTTTTTT
Done.