Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018866.1 Corchorus olitorius cultivar O-4 contig18899, 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: 48703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:344 original size:21 final size:21
Alignment explanation
Indices: 315--495 Score: 145
Period size: 21 Copynumber: 8.8 Consensus size: 21
305 TCCTTGAACT
315 TCAGCCTCTTCCATGTCAAAA
1 TCAGCCTCTTCCATGTCAAAA
* *
336 TCAGTCTCTTCCATGTTAAAA
1 TCAGCCTCTTCCATGTCAAAA
* *
357 CCAACCTCTTCCATGTCAAAA
1 TCAGCCTCTTCCATGTCAAAA
* * *
378 TAATCCCCTTCCATGTCAAAA
1 TCAGCCTCTTCCATGTCAAAA
* ** * * *
399 CCAGCCTCCACAAAGTCCAAA
1 TCAGCCTCTTCCATGTCAAAA
* *
420 TAAG-C-C-TCCATGTTAAAA
1 TCAGCCTCTTCCATGTCAAAA
* *
438 TAAGCCTCTT-CAGCGTCAAAA
1 TCAGCCTCTTCCA-TGTCAAAA
* *
459 TCAGCATCTTCCATGTCGAAA
1 TCAGCCTCTTCCATGTCAAAA
*
480 TCATCCTCTTCCATGT
1 TCAGCCTCTTCCATGT
496 TAGAATTACA
Statistics
Matches: 121, Mismatches: 34, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
18 11 0.09
19 2 0.02
20 4 0.03
21 102 0.84
22 2 0.02
ACGTcount: A:0.31, C:0.32, G:0.09, T:0.28
Consensus pattern (21 bp):
TCAGCCTCTTCCATGTCAAAA
Found at i:4956 original size:21 final size:22
Alignment explanation
Indices: 4932--4976 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
4922 TAATTCTGAA
4932 TTGCTAAATACCG-CCCCCCTT
1 TTGCTAAATACCGCCCCCCCTT
**
4953 TTGCTACTTACCGCCCCCCCTT
1 TTGCTAAATACCGCCCCCCCTT
4975 TT
1 TT
4977 TACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.13, C:0.44, G:0.09, T:0.33
Consensus pattern (22 bp):
TTGCTAAATACCGCCCCCCCTT
Found at i:5110 original size:13 final size:13
Alignment explanation
Indices: 5092--5116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5082 CATGTCGGAT
5092 TTTGTAGATCTAA
1 TTTGTAGATCTAA
5105 TTTGTAGATCTA
1 TTTGTAGATCTA
5117 GAATTCTGTC
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:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTGTAGATCTAA
Found at i:7193 original size:7 final size:7
Alignment explanation
Indices: 7181--7256 Score: 59
Period size: 7 Copynumber: 10.7 Consensus size: 7
7171 TTGGCGCAAC
7181 AATTATT
1 AATTATT
7188 AATTATTT
1 AATTA-TT
*
7196 AATCATT
1 AATTATT
7203 AATTATT
1 AATTATT
7210 -ATTAATTT
1 AATT-A-TT
7218 AAATTATT
1 -AATTATT
*
7226 -TTTATT
1 AATTATT
7232 AATTA-T
1 AATTATT
*
7238 AATTAAT
1 AATTATT
*
7245 AATTAAT
1 AATTATT
7252 AATTA
1 AATTA
7257 AAAAGCAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
6 14 0.24
7 30 0.52
8 10 0.17
9 1 0.02
10 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (7 bp):
AATTATT
Found at i:7693 original size:10 final size:9
Alignment explanation
Indices: 7674--7715 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
7664 ACTCCAAAAA
7674 AATATAATT
1 AATATAATT
7683 AATATTAATT
1 AATA-TAATT
7693 AATATATATT
1 AATATA-ATT
7703 AATAATAA-T
1 AAT-ATAATT
7712 AATA
1 AATA
7716 ATTCCTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.03
9 10 0.33
10 16 0.53
11 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AATATAATT
Found at i:8155 original size:17 final size:16
Alignment explanation
Indices: 8135--8204 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 16
8125 TCAATTTTTG
8135 ATAACAAATAATTATAA
1 ATAA-AAATAATTATAA
8152 ATAAAAATATATCTCA-AA
1 ATAAAAATA-AT-T-ATAA
8170 A-AAAAATAATTATAA
1 ATAAAAATAATTATAA
*
8185 ATAAATAATAAATATAA
1 ATAAA-AATAATTATAA
8202 ATA
1 ATA
8205 GCGTTTCTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
14 1 0.02
15 4 0.09
16 10 0.22
17 26 0.57
18 4 0.09
19 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATAATTATAA
Found at i:20359 original size:61 final size:61
Alignment explanation
Indices: 20247--20390 Score: 200
Period size: 61 Copynumber: 2.4 Consensus size: 61
20237 ATTTTCGATG
* * * ** *
20247 TCAGGCCCTTATTTGAGCA-TTTTCGATAATGTTAGGCTCTTATTTGCCCAAATTAAAAGA
1 TCAGACCCTTATTTGAGCATTTTTCAATAACGTTACACCCTTATTTGCCCAAATTAAAAGA
* *
20307 TCGGACCCTTATTTGAGCATTTTTCAATAACGTTACACCCTTATTTGGCCAAATTAAAAGA
1 TCAGACCCTTATTTGAGCATTTTTCAATAACGTTACACCCTTATTTGCCCAAATTAAAAGA
*
20368 TCAGACCCTTATTTAAGCATTTT
1 TCAGACCCTTATTTGAGCATTTT
20391 GACAAATGTT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
60 17 0.23
61 56 0.77
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (61 bp):
TCAGACCCTTATTTGAGCATTTTTCAATAACGTTACACCCTTATTTGCCCAAATTAAAAGA
Found at i:24245 original size:3 final size:3
Alignment explanation
Indices: 24237--24265 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
24227 TTAAAAAGAA
24237 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
24266 ATAACATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:25015 original size:55 final size:55
Alignment explanation
Indices: 24949--25059 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
24939 TGTGTTTCCT
24949 TTTCACACAATAAATGTTATAATAAATCCTACCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCCTACCCCCTATCTCTACTTAATTATTC
*
25004 TTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCCTACCCCCTATCTCTACTTAATTATTC
25059 T
1 T
25060 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (55 bp):
TTTCACACAATAAATGTTATAATAAATCCTACCCCCTATCTCTACTTAATTATTC
Found at i:25182 original size:42 final size:42
Alignment explanation
Indices: 25123--25247 Score: 232
Period size: 42 Copynumber: 3.0 Consensus size: 42
25113 GCTAAGGATC
25123 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
25165 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
* *
25207 ATGATTTGAGTTGAGTATTTTTTAATTTACAGAGAATTTTC
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
25248 AAGACTTAGC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
Found at i:27201 original size:3 final size:3
Alignment explanation
Indices: 27193--27238 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
27183 GGTGAATGTT
27193 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
27239 AGCTTTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39727 original size:18 final size:17
Alignment explanation
Indices: 39697--39730 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39687 AAAGAGTATA
39697 TTTATTTTATTATGCAC
1 TTTATTTTATTATGCAC
*
39714 TTTACTTTTCTTATGCA
1 TTTA-TTTTATTATGCA
39731 AAGCAACAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTATTTTATTATGCAC
Found at i:42171 original size:12 final size:12
Alignment explanation
Indices: 42141--42171 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42131 AGAGATGCCA
42141 TTTTTTTCTTTT
1 TTTTTTTCTTTT
*
42153 TTCTTTTCTTTT
1 TTTTTTTCTTTT
42165 TTTTTTT
1 TTTTTTT
42172 TCGAGTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:42477 original size:10 final size:11
Alignment explanation
Indices: 42459--42488 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
42449 TGTCATCGTG
42459 AATTTTTTTAA
1 AATTTTTTTAA
42470 AATTTTTTTAA
1 AATTTTTTTAA
*
42481 TATTTTTT
1 AATTTTTT
42489 ATTTTCATTC
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
AATTTTTTTAA
Found at i:42533 original size:29 final size:30
Alignment explanation
Indices: 42471--42535 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
42461 TTTTTTTAAA
*
42471 ATTTTTTTAATATTTTTTATTTTCATTCCT
1 ATTTTTTAAATATTTTTTATTTTCATTCCT
42501 ATTTTTTAAATATTTTTTATTTTCATTCC-
1 ATTTTTTAAATATTTTTTATTTTCATTCCT
42530 ATTTTT
1 ATTTTT
42536 ATTTTTCTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 6 0.18
30 28 0.82
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (30 bp):
ATTTTTTAAATATTTTTTATTTTCATTCCT
Found at i:43288 original size:11 final size:11
Alignment explanation
Indices: 43264--43298 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
43254 TTGATAGCGT
43264 AACAAAAACAA
1 AACAAAAACAA
* *
43275 AACGAAAACGA
1 AACAAAAACAA
43286 AACAAAAACAA
1 AACAAAAACAA
43297 AA
1 AA
43299 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:44003 original size:39 final size:40
Alignment explanation
Indices: 43947--44027 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
43937 TTTAATTCCT
43947 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* * *
43987 ATGTAATA-CTATAATAACTGAAATACTTACATTGATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
44026 AT
1 AT
44028 TCTTAGGTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:44489 original size:202 final size:203
Alignment explanation
Indices: 44108--44517 Score: 663
Period size: 197 Copynumber: 2.0 Consensus size: 203
44098 TTCCTTAATA
*
44108 ATAAATAAATTGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
44173 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGGTATAGTTCTATATATAATAGTA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTCGGTATAGTTCTATATATAATAATA
44238 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATT-AATAACATT
131 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAAATAACATT
*
44302 CACCATTG
196 CACCATTC
44310 ATAAATAAATCGGATC-TTAATATC-TTTATAA-TTTGAAA-TTTG-TTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
44370 AATTTAATAATTCAACCACTAATGTTCAACTAATTTTTTTTCGGTATAGTT-TAATATATTAATA
66 AATTTAATAAATCAACCACTAATGTTCAACTAA-TTTTTTTCGGTATAGTTCT-ATATA-TAATA
*
44434 ATAATGTTGTTGTATCTTATTTCATCTACAACTTTGTTAGTAATCTTAGACTTAAAGAATTAAAT
128 ATAATG-TGTTGTATCTTA-TTCA-CTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAAAT
44499 AACATTCACCATTC
190 AACATTCACCATTC
44513 ATAAA
1 ATAAA
44518 GTTATTAAGC
Statistics
Matches: 195, Mismatches: 6, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
197 51 0.26
198 25 0.13
199 17 0.09
200 19 0.10
201 12 0.06
202 50 0.26
203 21 0.11
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTCGGTATAGTTCTATATATAATAATA
ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAAATAACATT
CACCATTC
Found at i:46468 original size:58 final size:57
Alignment explanation
Indices: 46368--46479 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 57
46358 AGCGTCATGC
* *
46368 CTCGGTCCTAAAACGTCTTTTTTAGGTATCTAATAAAAAACATGTCACTCGATAAGT
1 CTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGT
* * *
46425 CTCGGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 CTCGGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
46480 TTTGATTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 16 0.33
58 33 0.67
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (57 bp):
CTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGT
Found at i:48316 original size:25 final size:24
Alignment explanation
Indices: 48280--48326 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
48270 AATACTTACA
48280 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
48304 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
48327 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Done.