Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018490.1 Corchorus olitorius cultivar O-4 contig18523, 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: 41435
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:650 original size:28 final size:28
Alignment explanation
Indices: 619--693 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
609 TTAAGATATC
** *
619 AAAATTACTGTTTTGCCCTTGGTTAGCT
1 AAAATTACAATTTTGCCCTTGGTTAACT
* * *
647 AAAATTACCATTTTACCCCTGGTTAACT
1 AAAATTACAATTTTGCCCTTGGTTAACT
675 -AAATTACAATTTTGCCCTT
1 AAAATTACAATTTTGCCCTT
694 AAATGCCGGA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 16 0.41
28 23 0.59
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (28 bp):
AAAATTACAATTTTGCCCTTGGTTAACT
Found at i:2150 original size:3 final size:3
Alignment explanation
Indices: 2142--2230 Score: 178
Period size: 3 Copynumber: 29.7 Consensus size: 3
2132 GGGCGTGATA
2142 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2190 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2231 ATTTACCGAA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:14069 original size:21 final size:21
Alignment explanation
Indices: 14044--14323 Score: 190
Period size: 21 Copynumber: 13.6 Consensus size: 21
14034 AATTCCAAGA
14044 AGTAAAGAGTAATCAGAAAAG
1 AGTAAAGAGTAATCAGAAAAG
* * * *
14065 AGT-AATAGTAGTAAGTAAAG
1 AGTAAAGAGTAATCAGAAAAG
*
14085 AGTAAAGAATAATCAGTAAAAG
1 AGTAAAGAGTAATCAG-AAAAG
* *
14107 AGT-AATAGTAATCAGTAAAG
1 AGTAAAGAGTAATCAGAAAAG
*
14127 AAG-AAAGAGTAATCAAGAAATG
1 -AGTAAAGAGTAATC-AGAAAAG
14149 -GTAAAGAGTAATCAGAAAAGG
1 AGTAAAGAGTAATCAGAAAA-G
* * * * *
14170 GGT-AATAGTAGTAAGTAAAG
1 AGTAAAGAGTAATCAGAAAAG
14190 AGTAAAGAGTAATC-GAGAAAG
1 AGTAAAGAGTAATCAGA-AAAG
* * *
14211 AGT-AATAGCAATCAGTAAAG
1 AGTAAAGAGTAATCAGAAAAG
* *
14231 AGCAAAGAGT-A--A-AAATG
1 AGTAAAGAGTAATCAGAAAAG
*
14248 -GT-AATAGTAATCAGTAAAAG
1 AGTAAAGAGTAATCAG-AAAAG
*
14268 AGTAAATAGTAATCAGTAAAAG
1 AGTAAAGAGTAATCAG-AAAAG
* **
14290 AGTAAAGAGTAATCAGTAATC
1 AGTAAAGAGTAATCAGAAAAG
14311 AGTAAAAGAGTAA
1 AGT-AAAGAGTAA
14324 ATAACAATCA
Statistics
Matches: 199, Mismatches: 40, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
15 5 0.03
16 2 0.01
17 3 0.02
18 2 0.01
20 49 0.25
21 82 0.41
22 56 0.28
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.19
Consensus pattern (21 bp):
AGTAAAGAGTAATCAGAAAAG
Found at i:14193 original size:7 final size:7
Alignment explanation
Indices: 14183--14428 Score: 85
Period size: 7 Copynumber: 34.9 Consensus size: 7
14173 AATAGTAGTA
14183 AGTAAAG
1 AGTAAAG
14190 AGTAAAG
1 AGTAAAG
*
14197 AGTAATCG
1 AGTAA-AG
14205 AG-AAAG
1 AGTAAAG
*
14211 AGT-AAT
1 AGTAAAG
* **
14217 AGCAATC
1 AGTAAAG
14224 AGTAAAG
1 AGTAAAG
*
14231 AGCAAAG
1 AGTAAAG
*
14238 AGTAAAA
1 AGTAAAG
*
14245 ATGGT-AAT
1 A--GTAAAG
**
14253 AGTAATC
1 AGTAAAG
14260 AGTAAAAG
1 AGT-AAAG
*
14268 AGTAAAT
1 AGTAAAG
**
14275 AGTAATC
1 AGTAAAG
14282 AGTAAAAG
1 AGT-AAAG
14290 AGTAAAG
1 AGTAAAG
**
14297 AGTAATC
1 AGTAAAG
**
14304 AGTAATC
1 AGTAAAG
14311 AGTAAAAG
1 AGT-AAAG
*
14319 AGTAAAT
1 AGTAAAG
** **
14326 AACAATC
1 AGTAAAG
*
14333 AATAAAAG
1 AGT-AAAG
14341 AGTAATAG
1 AGTAA-AG
14349 TAGT--A-
1 -AGTAAAG
14354 AGTAAAG
1 AGTAAAG
14361 AGTAAAG
1 AGTAAAG
* *
14368 AATAATCG
1 AGTAA-AG
14376 AG-AAAG
1 AGTAAAG
*
14382 AGT-AAT
1 AGTAAAG
**
14388 AGTAATC
1 AGTAAAG
14395 AGTAAAG
1 AGTAAAG
14402 AGTAAAG
1 AGTAAAG
14409 AGTAAAG
1 AGTAAAG
*
14416 AATAAAG
1 AGTAAAG
14423 AGTAAA
1 AGTAAA
14429 AGGGTAATAA
Statistics
Matches: 175, Mismatches: 46, Indels: 36
0.68 0.18 0.14
Matches are distributed among these distances:
4 3 0.02
6 19 0.11
7 119 0.68
8 29 0.17
9 5 0.03
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.19
Consensus pattern (7 bp):
AGTAAAG
Found at i:14263 original size:22 final size:23
Alignment explanation
Indices: 14238--14428 Score: 108
Period size: 21 Copynumber: 8.7 Consensus size: 23
14228 AAGAGCAAAG
14238 AGTAAAAATG-GT-AATAGTAATC
1 AGTAAAAA-GAGTAAATAGTAATC
14260 AGT-AAAAGAGTAAATAGTAATC
1 AGTAAAAAGAGTAAATAGTAATC
*
14282 AGT-AAAAGAGTAAAGAGTAATC
1 AGTAAAAAGAGTAAATAGTAATC
**
14304 AGTAATCAGTAAAAGAGTAAATAACAATC
1 AG---T-A--AAAAGAGTAAATAGTAATC
* * *
14333 AAT-AAAAGAGT-AATAGTAGTA
1 AGTAAAAAGAGTAAATAGTAATC
* *
14354 AGT--AAAGAGTAAAGAATAATC
1 AGTAAAAAGAGTAAATAGTAATC
*
14375 -G-AGAAAGAGT-AATAGTAATC
1 AGTAAAAAGAGTAAATAGTAATC
*
14395 AGT--AAAGAGTAAAGAGTAA--
1 AGTAAAAAGAGTAAATAGTAATC
14414 AG-AATAAAGAGTAAA
1 AGTAA-AAAGAGTAAA
14429 AGGGTAATAA
Statistics
Matches: 134, Mismatches: 17, Indels: 37
0.71 0.09 0.20
Matches are distributed among these distances:
19 2 0.01
20 24 0.18
21 45 0.34
22 44 0.33
25 1 0.01
26 1 0.01
29 17 0.13
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.20
Consensus pattern (23 bp):
AGTAAAAAGAGTAAATAGTAATC
Found at i:14285 original size:29 final size:28
Alignment explanation
Indices: 14234--14326 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 28
14224 AGTAAAGAGC
*
14234 AAAGAGTAAAAATGGTAATAGTAATCAGTA
1 AAAGAGT--AAATAGTAATAGTAATCAGTA
14264 AAAGAG----TA--AATAGTAATCAGTA
1 AAAGAGTAAATAGTAATAGTAATCAGTA
*
14286 AAAGAGTAAAGAGTAATCAGTAATCAGTA
1 AAAGAGTAAATAGTAAT-AGTAATCAGTA
14315 AAAGAGTAAATA
1 AAAGAGTAAATA
14327 ACAATCAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
22 20 0.38
24 1 0.02
26 1 0.02
28 3 0.06
29 22 0.42
30 6 0.11
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.22
Consensus pattern (28 bp):
AAAGAGTAAATAGTAATAGTAATCAGTA
Found at i:14308 original size:51 final size:50
Alignment explanation
Indices: 14234--14354 Score: 161
Period size: 51 Copynumber: 2.3 Consensus size: 50
14224 AGTAAAGAGC
* ** *
14234 AAAGAGTAAAAATGGTAATAGTAATCAGTAAAAGAGTAAATAGTAATCAGTA
1 AAAGAGTAAAGA--GTAATAGTAATCAGTAAAAGAGTAAATAACAATCAATA
14286 AAAGAGTAAAGAGTAATCAGTAATCAGTAAAAGAGTAAATAACAATCAATA
1 AAAGAGTAAAGAGTAAT-AGTAATCAGTAAAAGAGTAAATAACAATCAATA
14337 AAAGAGTAATAGTAGTAA
1 AAAGAGTAA-AG-AGTAA
14355 GTAAAGAGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
50 5 0.08
51 39 0.63
52 13 0.21
53 5 0.08
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.21
Consensus pattern (50 bp):
AAAGAGTAAAGAGTAATAGTAATCAGTAAAAGAGTAAATAACAATCAATA
Found at i:14332 original size:29 final size:29
Alignment explanation
Indices: 14275--14333 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
14265 AAGAGTAAAT
**
14275 AGTAATCAGTAAAAGAGTAAAGAGTAATC
1 AGTAATCAGTAAAAGAGTAAAGAACAATC
*
14304 AGTAATCAGTAAAAGAGTAAATAACAATC
1 AGTAATCAGTAAAAGAGTAAAGAACAATC
14333 A
1 A
14334 ATAAAAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.20
Consensus pattern (29 bp):
AGTAATCAGTAAAAGAGTAAAGAACAATC
Found at i:14357 original size:171 final size:161
Alignment explanation
Indices: 14094--14414 Score: 448
Period size: 171 Copynumber: 1.9 Consensus size: 161
14084 GAGTAAAGAA
*
14094 TAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAAGAAAGAGTAATCAAGAAATGGTAAAGAGTA
1 TAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAAGAAAGAGTAATCAAGAAATAGTAAAGAGTA
* * * *
14159 ATCAGAAAAGGGGTAATAGTAGTAAGTAAAGAGTAAAGAGTAATCGAGAAAGAGTAATAGCAATC
66 ATCAAAAAAAGAGTAATAGTAGTAAGTAAAGAGTAAAGAATAATCGAGAAAGAGTAATAGCAATC
14224 AGTAAAGAGCAAAGAGTAAAAATGGTAATAG
131 AGTAAAGAGCAAAGAGTAAAAATGGTAATAG
*
14255 TAATCAGTAAAAGAGTAAATAGTAATCAGTAAA-AGAGTAAAGAGTAATC-AGTAATCAGTAAAA
1 TAATCAGTAAAAGAGT-AATAGTAATCAGTAAAGA-AG-AAAGAGTAATCAAGAAAT-AGT-AAA
14318 GAGTAAATAACAATCAATAAAAGAGTAATAGTAGTAAGTAAAGAGTAAAGAATAATCGAGAAAGA
61 GAGT-AAT--C-A--AA-AAAAGAGTAATAGTAGTAAGTAAAGAGTAAAGAATAATCGAGAAAGA
* *
14383 GTAATAGTAATCAGTAAAGAGTAAAGAGTAAA
119 GTAATAGCAATCAGTAAAGAGCAAAGAGTAAA
14415 GAATAAAGAG
Statistics
Matches: 140, Mismatches: 8, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
161 17 0.12
162 23 0.16
163 13 0.09
164 7 0.05
165 3 0.02
167 1 0.01
168 1 0.01
170 1 0.01
171 74 0.53
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.20
Consensus pattern (161 bp):
TAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAAGAAAGAGTAATCAAGAAATAGTAAAGAGTA
ATCAAAAAAAGAGTAATAGTAGTAAGTAAAGAGTAAAGAATAATCGAGAAAGAGTAATAGCAATC
AGTAAAGAGCAAAGAGTAAAAATGGTAATAG
Found at i:14463 original size:49 final size:48
Alignment explanation
Indices: 14354--14455 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 48
14344 AATAGTAGTA
* * *
14354 AGTAAAGAGTAAAGAATAATCGAGAAAGAGTAATAGTAATCAGTAAAG
1 AGTAAACAGTAAAGAATAATAGAGAAAGAGTAATAATAATCAGTAAAG
* * *
14402 AGTAAAGAGTAAAGAATAA-AGAGTAAAAGGGTAATAATAGTCAGTAAAG
1 AGTAAACAGTAAAGAATAATAGAG--AAAGAGTAATAATAATCAGTAAAG
14451 AGTAA
1 AGTAA
14456 TCTGTAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
47 3 0.06
48 19 0.40
49 26 0.54
ACGTcount: A:0.55, C:0.03, G:0.24, T:0.19
Consensus pattern (48 bp):
AGTAAACAGTAAAGAATAATAGAGAAAGAGTAATAATAATCAGTAAAG
Found at i:14514 original size:18 final size:18
Alignment explanation
Indices: 14493--14531 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
14483 ATTAAAATTC
14493 AAAGAGTAAAA-GAGGTAA
1 AAAGAGTAAAAGGA-GTAA
*
14511 AAAGATTAAAAGGAGTAA
1 AAAGAGTAAAAGGAGTAA
14529 AAA
1 AAA
14532 TGGTATTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.13
Consensus pattern (18 bp):
AAAGAGTAAAAGGAGTAA
Found at i:14562 original size:35 final size:35
Alignment explanation
Indices: 14518--14624 Score: 180
Period size: 35 Copynumber: 3.1 Consensus size: 35
14508 TAAAAAGATT
*
14518 AAAAGGAGTAAAAATGGTATTCAGTAATTAAAGTA
1 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTA
14553 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTA
1 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTA
* *
14588 AAAAA-ACTAAAAATGGTATTCAGTAATTTAAGTA
1 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTA
14622 AAA
1 AAA
14625 CAGGGCAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
34 30 0.43
35 39 0.57
ACGTcount: A:0.54, C:0.04, G:0.16, T:0.26
Consensus pattern (35 bp):
AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTA
Found at i:21531 original size:11 final size:12
Alignment explanation
Indices: 21502--21534 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21492 TTTATTTCCC
21502 CAATTTTTGAAA
1 CAATTTTTGAAA
21514 CAATTTTTGAAA
1 CAATTTTTGAAA
*
21526 -ATTTTTTGA
1 CAATTTTTGA
21535 GAAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (12 bp):
CAATTTTTGAAA
Found at i:21874 original size:17 final size:17
Alignment explanation
Indices: 21854--21887 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21844 GGGTAATTAC
*
21854 AAAAAAATTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
21871 AAAAAAAGTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
21888 GATAAGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (17 bp):
AAAAAAAGTGTTTTCAT
Found at i:24056 original size:22 final size:22
Alignment explanation
Indices: 24006--24058 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
23996 TGCTTTCTTA
*
24006 TTAATTGTTTTCTTTAATTTTG
1 TTAATTGTTTTCTTTAATATTG
*
24028 TTGATTGTTTTC-TTAGATGATT-
1 TTAATTGTTTTCTTTA-AT-ATTG
24050 TTAATTGTT
1 TTAATTGTT
24059 GGTTTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 21 0.81
23 2 0.08
ACGTcount: A:0.19, C:0.04, G:0.13, T:0.64
Consensus pattern (22 bp):
TTAATTGTTTTCTTTAATATTG
Found at i:26843 original size:50 final size:53
Alignment explanation
Indices: 26789--26906 Score: 165
Period size: 52 Copynumber: 2.3 Consensus size: 53
26779 TTTGCGTCAA
* *
26789 GTAACGTATC-TTTTTGTGGGACCCATAT-A-AAGTTCTAGATTTCACTTTGG
1 GTAACGTATCATTTTTGTGGGACCCACATAAGAAGTTCTAGATTTCACTTTGC
* *
26839 GTAACGTA-CATTTTTATGGGACCCACATAAGAAGTTCTAGATTTCACTTTTC
1 GTAACGTATCATTTTTGTGGGACCCACATAAGAAGTTCTAGATTTCACTTTGC
26891 GTAACGT-TCATTTTTG
1 GTAACGTATCATTTTTG
26907 AAAATATATA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
49 1 0.02
50 24 0.41
51 1 0.02
52 33 0.56
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (53 bp):
GTAACGTATCATTTTTGTGGGACCCACATAAGAAGTTCTAGATTTCACTTTGC
Found at i:31318 original size:13 final size:13
Alignment explanation
Indices: 31276--31320 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
31266 TCATGCACCA
*
31276 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
31290 AAAACCATTT-AT
1 AAAACAATTTAAT
31302 AAAACAATTTAAT
1 AAAACAATTTAAT
31315 AAAACA
1 AAAACA
31321 GTAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:35177 original size:2 final size:2
Alignment explanation
Indices: 35170--35194 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35160 TCTCAATTAA
35170 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
35195 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40406 original size:26 final size:26
Alignment explanation
Indices: 40354--40406 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
40344 AGCATTTGAT
* *
40354 TCAGATTTCCTTTGATATTAGTATAA
1 TCAGATCTCCTTTGATATGAGTATAA
40380 TCAGATCTCCTTTGAT-TGAGTACTAA
1 TCAGATCTCCTTTGATATGAGTA-TAA
40406 T
1 T
40407 TTATGATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (26 bp):
TCAGATCTCCTTTGATATGAGTATAA
Done.