Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024326.1 Corchorus olitorius cultivar O-4 contig24359, 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: 6089
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:282 original size:154 final size:154
Alignment explanation
Indices: 1--340 Score: 635
Period size: 154 Copynumber: 2.2 Consensus size: 154
1 CCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGAAACCCTCGATGCCTTTCTT
1 CCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGAAACCCTCGATGCCTTTCTT
*
66 TCCATTGTTTATGGCCTAACTATAATCATTTTGCTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
66 TCCATTGTTTATGGCCTAACTAAAATCATTTTGCTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
131 ATTTGGAACACTTGTTATTTTGTG
131 ATTTGGAACACTTGTTATTTTGTG
* *
155 TCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGAAACCCTCTATGCCTTTCTT
1 CCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGAAACCCTCGATGCCTTTCTT
*
220 TCCATTGTTTATGGCCTAACTAAAATCATTTTGCTTAGATTAGTCCACTGTGAAGTTTTTAGCTC
66 TCCATTGTTTATGGCCTAACTAAAATCATTTTGCTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
285 ATTTGGAACACTTGTTATTTTGTG
131 ATTTGGAACACTTGTTATTTTGTG
*
309 CCTTTCGGGGCCCATTAGTTCCGTTTTGAATC
1 CCTTTCGGGGCCCATTAGTTCTGTTTTGAATC
341 AACCCAAATA
Statistics
Matches: 180, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 180 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (154 bp):
CCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGAAACCCTCGATGCCTTTCTT
TCCATTGTTTATGGCCTAACTAAAATCATTTTGCTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
ATTTGGAACACTTGTTATTTTGTG
Found at i:2563 original size:6 final size:6
Alignment explanation
Indices: 2548--2581 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2538 TGAAATGAAA
*
2548 AAAATC AAAATG AAAATG AAAAT- AAAATG AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT
2582 AAAGGCACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.18
Consensus pattern (6 bp):
AAAATG
Found at i:2576 original size:11 final size:11
Alignment explanation
Indices: 2540--2584 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
2530 AAAAATGATG
2540 AAATG-AAA-A
1 AAATGAAAATA
*
2549 AAATCAAAATGA
1 AAATGAAAAT-A
2561 AAATGAAAATA
1 AAATGAAAATA
2572 AAATGAAAATA
1 AAATGAAAATA
2583 AA
1 AA
2585 GGCACTTGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 4 0.13
10 3 0.10
11 14 0.45
12 10 0.32
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (11 bp):
AAATGAAAATA
Found at i:2576 original size:17 final size:18
Alignment explanation
Indices: 2548--2581 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2538 TGAAATGAAA
2548 AAAATCAAAATGAAAATG
1 AAAATCAAAATGAAAATG
2566 AAAAT-AAAATGAAAAT
1 AAAATCAAAATGAAAAT
2582 AAAGGCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.18
Consensus pattern (18 bp):
AAAATCAAAATGAAAATG
Found at i:2981 original size:16 final size:15
Alignment explanation
Indices: 2958--3010 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 15
2948 TTAAGAAATT
2958 AAAAAAAATCAATCAATC
1 AAAAAAAA--AATCAA-C
2976 AAAAAAAAAATCAAC
1 AAAAAAAAAATCAAC
2991 --AAAAAAAAT-AAC
1 AAAAAAAAAATCAAC
3003 AAAAAAAA
1 AAAAAAAA
3011 TCAAAATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.09
13 9 0.27
14 6 0.18
15 1 0.03
16 6 0.18
18 8 0.24
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAAAAAAATCAAC
Found at i:2989 original size:12 final size:12
Alignment explanation
Indices: 2972--3028 Score: 71
Period size: 12 Copynumber: 4.7 Consensus size: 12
2962 AAAATCAATC
2972 AATCAAAAAAAA
1 AATCAAAAAAAA
2984 AATCAACAAAAAA
1 AATCAA-AAAAAA
2997 AAT-AACAAAAAA
1 AATCAA-AAAAAA
**
3009 AATCAAAATCAA
1 AATCAAAAAAAA
3021 AATCAAAA
1 AATCAAAA
3029 TCAAACGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
12 30 0.73
13 11 0.27
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.11
Consensus pattern (12 bp):
AATCAAAAAAAA
Found at i:3018 original size:6 final size:6
Alignment explanation
Indices: 3007--3033 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2997 AATAACAAAA
3007 AAAATC AAAATC AAAATC AAAATC AAA
1 AAAATC AAAATC AAAATC AAAATC AAA
3034 CGAGAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:4364 original size:50 final size:50
Alignment explanation
Indices: 4305--4488 Score: 271
Period size: 50 Copynumber: 3.7 Consensus size: 50
4295 CGAATGTTTT
** * *
4305 GGCTTTTCCATTAGTCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
4355 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
4405 GGCTTTTCCACAAACCAAACTCGTTTCCATACGAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* **
4455 GGCTTTTCCATAAG-CACAGTTCGTTTCCATACGA
1 GGCTTTTCCACAAGCCA-AACTCGTTTCCATACGA
4489 TACATTACCA
Statistics
Matches: 123, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
49 2 0.02
50 121 0.98
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
Found at i:4554 original size:35 final size:35
Alignment explanation
Indices: 4508--4879 Score: 531
Period size: 35 Copynumber: 10.7 Consensus size: 35
4498 ATCTTCTTAA
* * *
4508 ATGACTTGGTGTAGCATCTTCAAAG-TTATATTCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGA-ATCCAG
* *
4543 ATGACTCGGTGTAGCATCTTCAAAG-TTATATTCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGA-ATCCAG
* *
4578 ATGACTCGATGTAGCATCTTCAAAGCTGAATCCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATCCAG
*
4613 ATGACTCGGTGTAGCATCTTCGAAA-TTGAATCCAG
1 ATGACTCGGTGTAGCATCTTC-AAAGATGAATCCAG
* *
4648 ATGACTCGGTGTAGCACCTTCGAAA-TTGAATCCAG
1 ATGACTCGGTGTAGCATCTTC-AAAGATGAATCCAG
*
4683 ATGACTCGGTGTAGCATCTTCAAAGATGAATTCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATCCAG
4718 ATGACTCGGTGTAGCATCTTCAAAGATGAATCCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATCCAG
*
4753 ATGACTCGGTGTAGCATCTTCAAAGATGAA-CTCGG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATC-CAG
4788 ATGACTCGGTGTAGCATCTTCAAAGATGAATCCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATCCAG
* *
4823 ATGA-TCGGTGTAGTATCTTCAAAGATGAATTCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATCCAG
4857 ATGACTCGGTGTAGCATCTTCAA
1 ATGACTCGGTGTAGCATCTTCAA
4880 TATGGACTCA
Statistics
Matches: 315, Mismatches: 16, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
34 36 0.11
35 273 0.87
36 6 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (35 bp):
ATGACTCGGTGTAGCATCTTCAAAGATGAATCCAG
Found at i:5235 original size:29 final size:28
Alignment explanation
Indices: 5169--5246 Score: 111
Period size: 29 Copynumber: 2.8 Consensus size: 28
5159 TCAAAAAACC
*
5169 CAGGGGCATTTTGGTCATTTTTCACATT
1 CAGGGGCATTTTGGTCATTTTGCACATT
* *
5197 CAGGGGCATTATGGTCATTTCTGCATATT
1 CAGGGGCATTTTGGTCATTT-TGCACATT
*
5226 CAGGGACATTTTGGTCATTTT
1 CAGGGGCATTTTGGTCATTTT
5247 AAGTTCATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 20 0.45
29 24 0.55
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (28 bp):
CAGGGGCATTTTGGTCATTTTGCACATT
Found at i:5696 original size:21 final size:21
Alignment explanation
Indices: 5670--5782 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
5660 TGCTAGAAGT
5670 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
5691 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
5712 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
5733 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
5754 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
5775 TCATTGGA
1 TCATTGGA
5783 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Done.