Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015639.1 Corchorus capsularis cultivar CVL-1 contig15660, 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: 18576
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:2366 original size:24 final size:23
Alignment explanation
Indices: 2322--2368 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2312 TTTCTAAAGA
*
2322 ATTTGGGAATGGTGCATATGATT
1 ATTTGGGAATGGTGCAAATGATT
* *
2345 ATTTGGGGATGGTGAGAAATGATT
1 ATTTGGGAATGGTG-CAAATGATT
2369 TGGGTATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.28, C:0.02, G:0.34, T:0.36
Consensus pattern (23 bp):
ATTTGGGAATGGTGCAAATGATT
Found at i:2983 original size:220 final size:219
Alignment explanation
Indices: 2406--3136 Score: 1064
Period size: 222 Copynumber: 3.3 Consensus size: 219
2396 TACTGAATTT
* * *
2406 CACAATTTTGACTTTAAAAAGTGCTTTAAACCATATTTTTCATTCTAATTAATTGAATAAACCAC
1 CACAAATTTGACTTTAAAAAGTGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCAC
* * *
2471 GTTTATATGATTTTAGCGCCGTCTCATAATTAAACAAAATGCAAAATTCAGTATTCCCAAAATGA
66 GTCTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATGA
*
2536 TATAGTTTATACCCAAATCATTTTTCATCATCCCCAATTAATCTTATGCACCATCCCCAAATTCT
131 TATACTTTATACCCAAATCATTTTTCATCATCCCCAATTAATCTTATGCACCAT-CCCAAATTCT
* *
2601 TTAGAGATTGACATTTTTTTCGTATA
195 TTAGAGATTGACA-TTTTCTCATATA
* **
2627 CACAAATTTGACTTTAAAAAGTATTTTAATCCATATTTTAGGGA-TCTAATTAATTGAATAAACC
1 CACAAATTTGACTTTAAAAAGTGTTTTAATCCATATTTT--TCATTCTAATTAATTGAATAAACC
* * *
2691 ACGTATATATGATTTTAGCGTCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCAAAAAT
64 ACGTCTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAAT
2756 GATATACTTTATACCCAAATCATTTTTCATCATCCCCAATTAATCTTATGCACCATCCCGAAATT
129 GATATACTTTATACCCAAATCATTTTTCATCATCCCCAATTAATCTTATGCACCATCCC-AAATT
2821 CTTTAGAGATTGACATTTTCTCATATA
193 CTTTAGAGATTGACATTTTCTCATATA
*
2848 CACAAATTGGACTTTAAAAAGTGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCAC
1 CACAAATTTGACTTTAAAAAGTGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCAC
* *** *
2913 GTCTATATGATTTTAGCACCATCTCATAATTAAACAAAATATGAAATTCAGTATCCCCAAACTGA
66 GTCTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATGA
* * * *
2978 TATACTTTATACCCAAATCATTTCTCACCATCCCCAAATAATCATATGCACCATTCCCAAATTC-
131 TATACTTTATACCCAAATCATTTTTCATCATCCCCAATTAATCTTATGCACCA-TCCCAAATTCT
*
3042 ------ATTGATATTTTCTCATATA
195 TTAGAGATTGACATTTTCTCATATA
* * ****
3061 CACAAATTTGACTTTAAAAAATGTTTTAATACATATTTTAGGGTCTAATTAATTGAATAAACCAC
1 CACAAATTTGACTTTAAAAAGTGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCAC
3126 GTCTATATGAT
66 GTCTATATGAT
3137 GGTGGAAAAT
Statistics
Matches: 467, Mismatches: 38, Indels: 18
0.89 0.07 0.03
Matches are distributed among these distances:
213 87 0.19
219 1 0.00
220 134 0.29
221 89 0.19
222 155 0.33
223 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (219 bp):
CACAAATTTGACTTTAAAAAGTGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCAC
GTCTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATGA
TATACTTTATACCCAAATCATTTTTCATCATCCCCAATTAATCTTATGCACCATCCCAAATTCTT
TAGAGATTGACATTTTCTCATATA
Found at i:3176 original size:31 final size:30
Alignment explanation
Indices: 3140--3229 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 30
3130 ATATGATGGT
3140 GGAAAATAAATTTAAGAAAAAATTAAGAAAA
1 GGAAAATAAA-TTAAGAAAAAATTAAGAAAA
3171 GGAAAA-AGAA--AAGAAAAAATTAAGAAAA
1 GGAAAATA-AATTAAGAAAAAATTAAGAAAA
*
3199 --AAAGGTGAAATTAAGAAAAAATTTAAGAAAA
1 GGAAA-AT-AAATTAAGAAAAAA-TTAAGAAAA
3230 AATATACAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
26 3 0.06
28 20 0.39
29 1 0.02
30 10 0.20
31 17 0.33
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (30 bp):
GGAAAATAAATTAAGAAAAAATTAAGAAAA
Found at i:3195 original size:11 final size:11
Alignment explanation
Indices: 3181--3268 Score: 56
Period size: 11 Copynumber: 7.5 Consensus size: 11
3171 GGAAAAAGAA
3181 AAGAAAAAATT
1 AAGAAAAAATT
3192 AAG-AAAAA--
1 AAGAAAAAATT
***
3200 AAGGTGAAATT
1 AAGAAAAAATT
3211 AAGAAAAAATTT
1 AAGAAAAAA-TT
3223 AAGAAAAAATAT
1 AAGAAAAAAT-T
3235 ACAACGTATAAAAACTT
1 --AA-G-A-AAAAA-TT
3252 AAGAAAAAATT
1 AAGAAAAAATT
3263 AAGAAA
1 AAGAAA
3269 TTGGGGAAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
8 3 0.05
9 3 0.05
10 5 0.08
11 18 0.30
12 17 0.28
13 1 0.02
14 3 0.05
15 3 0.05
16 1 0.02
17 6 0.10
18 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.11, T:0.18
Consensus pattern (11 bp):
AAGAAAAAATT
Found at i:3201 original size:19 final size:19
Alignment explanation
Indices: 3179--3219 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3169 AAGGAAAAAG
3179 AAAAGAAAAAATTAAGAAA
1 AAAAGAAAAAATTAAGAAA
***
3198 AAAAGGTGAAATTAAGAAA
1 AAAAGAAAAAATTAAGAAA
3217 AAA
1 AAA
3220 TTTAAGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAAGAAAAAATTAAGAAA
Found at i:3357 original size:45 final size:45
Alignment explanation
Indices: 3298--3401 Score: 174
Period size: 45 Copynumber: 2.3 Consensus size: 45
3288 AAAAAAATTT
*
3298 AAGAAAAGAAATTGATAAATGCAGAAAACGGAGAAGAAAAGGAAG
1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
*
3343 AAGAAGAA-AAATTGATAAAAGCAGAAAATGGAGAAGAAAAGGAAG
1 AAGAA-AAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
3388 AAGAAAAGAAATTG
1 AAGAAAAGAAATTG
3402 GGGAAAATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
44 2 0.04
45 51 0.93
46 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.26, T:0.10
Consensus pattern (45 bp):
AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
Found at i:4115 original size:2 final size:2
Alignment explanation
Indices: 4110--4142 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4100 ATATATTGGT
4110 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4143 TAGAGATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4370 original size:2 final size:2
Alignment explanation
Indices: 4363--4390 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4353 GCATATTGCT
4363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4391 ATTCTACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4802 original size:25 final size:22
Alignment explanation
Indices: 4772--4826 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 22
4762 TTCTTTTTCC
4772 TGTTTTTCTGAAGTTAGCTAGTAAT
1 TGTTTTTCTGAAG-TA-CTA-TAAT
*
4797 TGTTTTTCTGGAGTACTATAAT
1 TGTTTTTCTGAAGTACTATAAT
4819 TGATTTTT
1 TG-TTTTT
4827 TTTTTCTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 6 0.21
23 8 0.29
24 2 0.07
25 12 0.43
ACGTcount: A:0.22, C:0.07, G:0.18, T:0.53
Consensus pattern (22 bp):
TGTTTTTCTGAAGTACTATAAT
Found at i:4825 original size:22 final size:25
Alignment explanation
Indices: 4775--4825 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 25
4765 TTTTTCCTGT
*
4775 TTTTCTGAAGTTAGCTAGTAATTGT
1 TTTTCTGAAGTTAGCTAGTAATTGA
*
4800 TTTTCTGGAG-TA-CTA-TAATTGA
1 TTTTCTGAAGTTAGCTAGTAATTGA
4822 TTTT
1 TTTT
4826 TTTTTTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.42
23 3 0.12
24 2 0.08
25 9 0.38
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.51
Consensus pattern (25 bp):
TTTTCTGAAGTTAGCTAGTAATTGA
Found at i:16428 original size:15 final size:15
Alignment explanation
Indices: 16373--16428 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
16363 AATTAGGTTG
*
16373 AATTTGGGTCAGATT
1 AATTCGGGTCAGATT
*
16388 AATTCGGATTC-GACTT
1 AATTCGG-GTCAGA-TT
*
16404 GAATTTGGGTCAGATT
1 -AATTCGGGTCAGATT
16420 AATTCGGGT
1 AATTCGGGT
16429 TTGGGTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
15 16 0.50
16 8 0.25
17 8 0.25
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.38
Consensus pattern (15 bp):
AATTCGGGTCAGATT
Found at i:16601 original size:16 final size:16
Alignment explanation
Indices: 16580--16641 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
16570 AATTTTCGGA
16580 TTCGGGTTCAGGTTTT
1 TTCGGGTTCAGGTTTT
*
16596 TTCGGGTT-TGAGTTTT
1 TTCGGGTTCAG-GTTTT
* **
16612 TTCGGATTTGGGTTTT
1 TTCGGGTTCAGGTTTT
*
16628 TTCGAGTTCAGGTT
1 TTCGGGTTCAGGTT
16642 CAGATGGATT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 1 0.03
16 35 0.95
17 1 0.03
ACGTcount: A:0.08, C:0.10, G:0.31, T:0.52
Consensus pattern (16 bp):
TTCGGGTTCAGGTTTT
Found at i:16730 original size:15 final size:15
Alignment explanation
Indices: 16702--16733 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
16692 ATTCGGATTT
16702 TCGGGCGGGTTTTTC
1 TCGGGCGGGTTTTTC
16717 TCGGGTCGGGTTTTTC
1 TCGGG-CGGGTTTTTC
16733 T
1 T
16734 TATGGATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.44
Consensus pattern (15 bp):
TCGGGCGGGTTTTTC
Done.