Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012413.1 Corchorus capsularis cultivar CVL-1 contig12434, 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: 60114
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:328 original size:37 final size:38
Alignment explanation
Indices: 280--357 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
270 TGTTGAAGAT
280 AAAGACAAAAAG-CAAAATTAAATA-CAACGATTGGAAAC
1 AAAGACAAAAAGACAAAATTAAATAGCAA-G-TTGGAAAC
* *
318 AAAGAC-AAAAGATAAAATTAAATAGGAAGTTGGAAAC
1 AAAGACAAAAAGACAAAATTAAATAGCAAGTTGGAAAC
355 AAA
1 AAA
358 AAGGCAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
37 16 0.44
38 18 0.50
39 2 0.06
ACGTcount: A:0.62, C:0.09, G:0.15, T:0.14
Consensus pattern (38 bp):
AAAGACAAAAAGACAAAATTAAATAGCAAGTTGGAAAC
Found at i:1226 original size:18 final size:23
Alignment explanation
Indices: 1179--1224 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1169 CCGATTTCAA
1179 ATATTTACTCTTAAAATACTATT
1 ATATTTACTCTTAAAATACTATT
*
1202 ATATTTACTCTTAAAATATTATT
1 ATATTTACTCTTAAAATACTATT
1225 TAGTAATGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTTACTCTTAAAATACTATT
Found at i:1306 original size:28 final size:30
Alignment explanation
Indices: 1266--1324 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1256 CTAAAAAAAT
* *
1266 ATATTTTT-TAAA-AAGGATACAATTGGAA
1 ATATTTTTAAAAATAAGGATACAATCGGAA
*
1294 ATATTTTTAAAAATAAGGGTACAATCGGAA
1 ATATTTTTAAAAATAAGGATACAATCGGAA
1324 A
1 A
1325 ACATAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.31
29 3 0.12
30 15 0.58
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.32
Consensus pattern (30 bp):
ATATTTTTAAAAATAAGGATACAATCGGAA
Found at i:5365 original size:129 final size:129
Alignment explanation
Indices: 5135--5392 Score: 462
Period size: 129 Copynumber: 2.0 Consensus size: 129
5125 AAACCAATGG
*
5135 TAACTCAATACTATTGAGTGCCTCAGATTGTTCCTTTATCTTCTCCTTATCCTGTTTCTCAGAGC
1 TAACTCAATACTATTGAGTGCCTCAGATTGTTCCTTTATCTTCTCCTTACCCTGTTTCTCAGAGC
*
5200 TTGTAGTCTGGAGGGTTTCTAAGAAGTCAGAACATCTCAAAAAGGCTAAACGATGAGATCTCCT
66 TTGTAGTCTGGAGGGTTGCTAAGAAGTCAGAACATCTCAAAAAGGCTAAACGATGAGATCTCCT
* **
5264 TAACTCAATACTATTGAGTGCCTCAGATTGTTCCTTTATCTTGTCCTTACCCTGTTTCTCAGTTC
1 TAACTCAATACTATTGAGTGCCTCAGATTGTTCCTTTATCTTCTCCTTACCCTGTTTCTCAGAGC
*
5329 TTGTAGTTTGGAGGGTTGCTAAGAAGTCAGAACATCTCAAAAAGGCTAAACGATGAGATCTCCT
66 TTGTAGTCTGGAGGGTTGCTAAGAAGTCAGAACATCTCAAAAAGGCTAAACGATGAGATCTCCT
5393 AGGTGGTAAG
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 123 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (129 bp):
TAACTCAATACTATTGAGTGCCTCAGATTGTTCCTTTATCTTCTCCTTACCCTGTTTCTCAGAGC
TTGTAGTCTGGAGGGTTGCTAAGAAGTCAGAACATCTCAAAAAGGCTAAACGATGAGATCTCCT
Found at i:9747 original size:1 final size:1
Alignment explanation
Indices: 9741--9767 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
9731 ACCCACAGAC
9741 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
9768 CACTGCATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18772 original size:74 final size:74
Alignment explanation
Indices: 18681--18837 Score: 244
Period size: 74 Copynumber: 2.1 Consensus size: 74
18671 TGGTCTTTTC
* * * *
18681 ACACTTTTCGGGTGACTAAAAAACCCCTCTATGAGTTTCCTC-TATTCCTTTTCCTTCTACCCTT
1 ACACTTTTTGGATGACTAAAAAACCCCTCTATGAGTTTCC-CACATTCCTTTTCCTTCTACCATT
18745 TTTCGTAATT
65 TTTCGTAATT
*
18755 ACACTTTTTGGATGACTAAAAAACCCCTTTATGAGTTTCCCACATTCCTTTTCCTTCTACCATTT
1 ACACTTTTTGGATGACTAAAAAACCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCATTT
18820 TTCGTAATT
66 TTCGTAATT
*
18829 ACACATTTT
1 ACACTTTTT
18838 CCTTCCTTAA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
73 1 0.01
74 75 0.99
ACGTcount: A:0.23, C:0.27, G:0.08, T:0.42
Consensus pattern (74 bp):
ACACTTTTTGGATGACTAAAAAACCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCATTT
TTCGTAATT
Found at i:20207 original size:88 final size:88
Alignment explanation
Indices: 20058--20228 Score: 229
Period size: 88 Copynumber: 1.9 Consensus size: 88
20048 TTTAGACCAA
* **
20058 ATTTGGTTATGTTTAAAGGTTTAGTCTCCAATTGAGCAAGTTTGGAAAGAATTAGACCCAATTTG
1 ATTTGGTTATGTTTAAAGGTTTAGTCTCAAATTGAGCAAGTTACGAAAGAATTAGACCCAATTTG
*
20123 GACATTAAGCCTGGAAAAATAGT
66 GACATTAAGCCTAGAAAAATAGT
* * * *
20146 ATTTGGTTCTTTTTAAAGGTTTAGAT-TCAAATTGAGGAAGTTACGAAA-AATTTAGGCCCAATT
1 ATTTGGTTATGTTTAAAGGTTTAG-TCTCAAATTGAGCAAGTTACGAAAGAA-TTAGACCCAATT
*
20209 TGGACATTAGGCCTAGAAAA
64 TGGACATTAAGCCTAGAAAA
20229 GTAGCACAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
87 2 0.03
88 69 0.96
89 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (88 bp):
ATTTGGTTATGTTTAAAGGTTTAGTCTCAAATTGAGCAAGTTACGAAAGAATTAGACCCAATTTG
GACATTAAGCCTAGAAAAATAGT
Found at i:32945 original size:22 final size:23
Alignment explanation
Indices: 32920--32969 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
32910 TCAAACCCAC
32920 ATAAAAAAG-ACACAAAATC-CAT
1 ATAAAAAAGTACA-AAAATCACAT
* *
32942 ATAAAATAGTACAAAACTCACAT
1 ATAAAAAAGTACAAAAATCACAT
32965 ATAAA
1 ATAAA
32970 TACGATTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.62, C:0.16, G:0.04, T:0.18
Consensus pattern (23 bp):
ATAAAAAAGTACAAAAATCACAT
Found at i:32947 original size:21 final size:23
Alignment explanation
Indices: 32917--32969 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
32907 TAATCAAACC
32917 CACATA-AAAA-AG-ACACAAAAT
1 CACATATAAAATAGTACA-AAAAT
*
32938 C-CATATAAAATAGTACAAAACT
1 CACATATAAAATAGTACAAAAAT
32960 CACATATAAA
1 CACATATAAA
32970 TACGATTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 7 0.26
23 11 0.41
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.17
Consensus pattern (23 bp):
CACATATAAAATAGTACAAAAAT
Found at i:33211 original size:5 final size:5
Alignment explanation
Indices: 33201--33228 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
33191 CAACTTTTAT
33201 ATATA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATA
33229 ATGATGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:34650 original size:15 final size:15
Alignment explanation
Indices: 34611--34651 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
34601 AATTATAAAA
34611 ACAAAATCAACAACC
1 ACAAAATCAACAACC
34626 -CAATAATCAA-AACC
1 ACAA-AATCAACAACC
34640 ACAAAACTCAAC
1 ACAAAA-TCAAC
34652 TTTATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.59, C:0.32, G:0.00, T:0.10
Consensus pattern (15 bp):
ACAAAATCAACAACC
Found at i:39442 original size:61 final size:61
Alignment explanation
Indices: 39347--39470 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
39337 AGTATTCCAA
39347 CAGATGTTATGTACGTTTATTTCTCATCAAAGTTCTGCTAGTTGTACTCTGAACTAATTTT
1 CAGATGTTATGTACGTTTATTTCTCATCAAAGTTCTGCTAGTTGTACTCTGAACTAATTTT
39408 CAGATGTTATGTACGTTTATTTCTCATCAAAGTTCTGCTAGTTGTACTCTGAACTAATTTT
1 CAGATGTTATGTACGTTTATTTCTCATCAAAGTTCTGCTAGTTGTACTCTGAACTAATTTT
39469 CA
1 CA
39471 ATTAATTATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (61 bp):
CAGATGTTATGTACGTTTATTTCTCATCAAAGTTCTGCTAGTTGTACTCTGAACTAATTTT
Found at i:49820 original size:56 final size:58
Alignment explanation
Indices: 49724--49832 Score: 186
Period size: 56 Copynumber: 1.9 Consensus size: 58
49714 GAACCGAAAA
49724 ATGTTAAAATTATTAATTATAATTAATAATTAATTACTACTCAAAACTCAATTGTATT
1 ATGTTAAAATTATTAATTATAATTAATAATTAATTACTACTCAAAACTCAATTGTATT
* *
49782 ATGTTAAAATTATTAA-T-TAGTTAATAATTAATTACTACTCAAAGCTCAATT
1 ATGTTAAAATTATTAATTATAATTAATAATTAATTACTACTCAAAACTCAATT
49833 ATTAATAGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
56 32 0.65
57 1 0.02
58 16 0.33
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (58 bp):
ATGTTAAAATTATTAATTATAATTAATAATTAATTACTACTCAAAACTCAATTGTATT
Found at i:50840 original size:23 final size:24
Alignment explanation
Indices: 50814--50860 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
50804 TAATGGATTG
*
50814 TTTG-CAACCCAATTCTAATTTTT
1 TTTGACAACCCAATTATAATTTTT
*
50837 TTTGAAGAACCCAATTATAATTTT
1 TTTG-ACAACCCAATTATAATTTT
50861 GAAACATCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
25 16 0.80
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (24 bp):
TTTGACAACCCAATTATAATTTTT
Found at i:57244 original size:16 final size:16
Alignment explanation
Indices: 57223--57257 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
57213 CGTTTGGTTG
*
57223 GTGGTGATCTTTGCAT
1 GTGGTGATCTTGGCAT
57239 GTGGTGATCTTGGCAT
1 GTGGTGATCTTGGCAT
57255 GTG
1 GTG
57258 ATCTCAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.37, T:0.40
Consensus pattern (16 bp):
GTGGTGATCTTGGCAT
Found at i:59587 original size:29 final size:31
Alignment explanation
Indices: 59553--59625 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 31
59543 ACTTGTAGCA
* *
59553 TTTGGATGTTTTGCTTCC-TTAACT-TCAAT
1 TTTGGATGTTTTGCTCCCATAAACTCTCAAT
*
59582 TTTGGATATTTTG-TCCCATAAACTCTCAAT
1 TTTGGATGTTTTGCTCCCATAAACTCTCAAT
*
59612 TTTGGACGTTTTGC
1 TTTGGATGTTTTGC
59626 CTCATCTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 3 0.08
29 17 0.47
30 16 0.44
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (31 bp):
TTTGGATGTTTTGCTCCCATAAACTCTCAAT
Done.