Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014019.1 Corchorus capsularis cultivar CVL-1 contig14040, 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: 32526
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:319 original size:21 final size:21
Alignment explanation
Indices: 294--334 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
284 TCCCTGGCAG
*
294 TGATTTCCAGAAATCAGGTGA
1 TGATTTCCAGAAATAAGGTGA
* *
315 TGATTTGCAGAGATAAGGTG
1 TGATTTCCAGAAATAAGGTG
335 TACAATCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (21 bp):
TGATTTCCAGAAATAAGGTGA
Found at i:3048 original size:31 final size:31
Alignment explanation
Indices: 3013--3078 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
3003 AACTTTATGT
* *
3013 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCATT-TTCTTTAAAACATA
3044 TTTCCAATTGTACCATTTTCTTTAAAACATA
1 TTTCCAATTGTACCATTTTCTTTAAAACATA
3075 TTTC
1 TTTC
3079 GAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCATTTTCTTTAAAACATA
Found at i:3622 original size:22 final size:22
Alignment explanation
Indices: 3594--3755 Score: 139
Period size: 22 Copynumber: 7.3 Consensus size: 22
3584 TGTCTCTATG
*
3594 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
3616 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
3639 -GGTTACCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* **
3660 TGGTTACCAAAATTTCATAATA
1 TGGTTATCAAAATTTCATAGGA
*
3682 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
3704 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
3728 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
3750 TGGTTA
1 TGGTTA
3756 ATTACCACAA
Statistics
Matches: 115, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
21 2 0.02
22 93 0.81
23 3 0.03
24 17 0.15
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:3845 original size:22 final size:22
Alignment explanation
Indices: 3791--3882 Score: 87
Period size: 22 Copynumber: 4.2 Consensus size: 22
3781 ATCAAAGAGA
* * *
3791 TTATTAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGGGAGG
3813 TTAT-AAGAATTTCATAGGGAGG
1 TTATCAA-AATTTCATAGGGAGG
* * *
3835 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGGGAGG
* * *
3857 TTATCAAAATTTTATATGAAGG
1 TTATCAAAATTTCATAGGGAGG
3879 TTAT
1 TTAT
3883 ACACTACAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
21 2 0.03
22 55 0.93
23 2 0.03
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:4130 original size:22 final size:22
Alignment explanation
Indices: 4061--4332 Score: 118
Period size: 22 Copynumber: 12.5 Consensus size: 22
4051 TAAAAGTCTC
* *
4061 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
4081 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
* *
4101 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
4123 AATTTCATAGAGATCGAATTATCAA
1 AATTTCATAGAG-T-G-ATTATCAA
**
4148 AATTT-ATAGAAAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
*
4169 AATTTCATAGTGTTG-TTA-CTAA
1 AATTTCATAGAG-TGATTATC-AA
* * * * *
4191 AATTTTAAAGCGAGTTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
4213 AATTACATA-ATGTGATTATCAG
1 AATTTCATAGA-GTGATTATCAA
* * * *
4235 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* * *
4257 AATCTT-ATAAAGAGGTTATCAA
1 AAT-TTCATAGAGTGATTATCAA
* * *
4279 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
4301 ATTTTCA-AAATGTGACTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
4323 AATTTCATAG
1 AATTTCATAG
4333 TGGTATTTTT
Statistics
Matches: 193, Mismatches: 39, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.01
20 18 0.09
21 29 0.15
22 119 0.62
23 7 0.04
24 6 0.03
25 12 0.06
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:4438 original size:20 final size:20
Alignment explanation
Indices: 4413--4463 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
4403 TCATGGAGTA
*
4413 ATCAAAATTTCAAGGATGAT
1 ATCAAAATTTCAAGGAGGAT
*
4433 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
4452 ATCAAAATTTCA
1 ATCAAAATTTCA
4464 TAGTTTAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:4692 original size:45 final size:44
Alignment explanation
Indices: 4413--4723 Score: 175
Period size: 44 Copynumber: 7.3 Consensus size: 44
4403 TCATGGAGTA
* * * *
4413 ATCAAAATTTCA-AG-GATGATATCAAAA-TTCA-GGGAGGA-T
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGAAGATT
** * * * * *
4452 ATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATAG-CGAGGTTATCAAAATTTCATAGGAAGATT
* * * *
4496 ATCAAAATTTCATAG-TATGTAGATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGCGAGGT-TATCAAAATTTCATAGGAAGATT
* * ** ** * *
4540 AACAAAAATTCATAATGAGGTTATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGAAGATT
* * *
4584 ATCAAAA-TT--T-G-TA-GTTATCAAGATTTCATAAGAA-AGTT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGAAGA-TT
* * * *
4622 ATCAAAATTTTATAGGGCGGTTTATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGCGAGG-TTATCAAAATTTCATAGGAAGA-TT
* *
4668 ATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAG-GAAGATT
4712 ATCAAAATTTCA
1 ATCAAAATTTCA
4724 GAGTGTGATT
Statistics
Matches: 210, Mismatches: 43, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
38 25 0.12
39 15 0.07
40 2 0.01
41 10 0.05
42 8 0.04
43 8 0.04
44 84 0.40
45 37 0.18
46 21 0.10
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.34
Consensus pattern (44 bp):
ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGAAGATT
Found at i:4728 original size:22 final size:22
Alignment explanation
Indices: 4451--4734 Score: 113
Period size: 22 Copynumber: 13.1 Consensus size: 22
4441 TCAGGGAGGA
*
4451 TATCAAAATTTCATAGT-TTAGT
1 TATCAAAATTTCATAGTGTGA-T
* * * *
4473 TTTCAAAATTTCACAAGAG-GGT
1 TATCAAAATTTCA-TAGTGTGAT
*
4495 TATCAAAATTTCATAGTATG-T
1 TATCAAAATTTCATAGTGTGAT
* * *
4516 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGTGTGAT
* * * * *
4539 TAACAAAAATTCATAATGAGGT
1 TATCAAAATTTCATAGTGTGAT
** * * *
4561 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
4583 TATCAAAA-TT--T-GT-AG-T
1 TATCAAAATTTCATAGTGTGAT
* * **
4599 TATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATAGTGTGA-T
* * * *
4621 TATCAAAATTTTATAGGGCGGTT
1 TATCAAAATTTCATAGTG-TGAT
* *
4644 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-TGA-T
* * *
4667 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
4689 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
4711 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
4733 TA
1 TA
4735 CTAACAATTC
Statistics
Matches: 201, Mismatches: 45, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
16 8 0.04
17 4 0.02
18 1 0.00
19 2 0.01
20 1 0.00
21 4 0.02
22 141 0.70
23 39 0.19
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:4745 original size:22 final size:23
Alignment explanation
Indices: 4666--4743 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 23
4656 ATAGGAAGAT
* * * *
4666 TTATCAA-AATTTCATAGCGAGG
1 TTATCAACAATTTCAGAGTGTGA
*
4688 TTATC-ACAATTTCATAGTGTGA
1 TTATCAACAATTTCAGAGTGTGA
4710 TTATCAA-AATTTCAGAGTGTGA
1 TTATCAACAATTTCAGAGTGTGA
4732 TTA-CTAACAATT
1 TTATC-AACAATT
4744 CATATGGAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.04
22 41 0.85
23 5 0.10
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (23 bp):
TTATCAACAATTTCAGAGTGTGA
Found at i:4790 original size:22 final size:22
Alignment explanation
Indices: 4765--4827 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
4755 TTTTAAATTT
*
4765 TCATAACGTGGTTATCAATATA
1 TCATAACGTGGTTATCAACATA
** * *
4787 TCATATGGAGGTTATCAACATC
1 TCATAACGTGGTTATCAACATA
**
4809 TCATAGTGTTGGTTATCAA
1 TCATAACG-TGGTTATCAA
4828 AATTTCATTA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 23 0.72
23 9 0.28
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (22 bp):
TCATAACGTGGTTATCAACATA
Found at i:4813 original size:44 final size:45
Alignment explanation
Indices: 4743--4827 Score: 102
Period size: 44 Copynumber: 1.9 Consensus size: 45
4733 TACTAACAAT
* * *
4743 TCATATGGAGGTTTTTAAATTTTCATAACG-TGGTTATCAATATA
1 TCATATGGAGGTTATCAAATTCTCATAACGTTGGTTATCAATATA
**
4787 TCATATGGAGGTTATCAACA-TCTCATAGTGTTGGTTATCAA
1 TCATATGGAGGTTATCAA-ATTCTCATAACGTTGGTTATCAA
4828 AATTTCATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 23 0.68
45 11 0.32
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40
Consensus pattern (45 bp):
TCATATGGAGGTTATCAAATTCTCATAACGTTGGTTATCAATATA
Found at i:4826 original size:23 final size:22
Alignment explanation
Indices: 4772--4827 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4762 TTTTCATAAC
*
4772 GTGGTTATCAATATATCATATG
1 GTGGTTATCAACATATCATATG
* *
4794 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAACATATCATA-TG
*
4817 TTGGTTATCAA
1 GTGGTTATCAA
4828 AATTTCATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAACATATCATATG
Found at i:7056 original size:21 final size:21
Alignment explanation
Indices: 7031--7071 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7021 TCCCTGGCAG
*
7031 TGATTTCCAGAAATCAGGTGA
1 TGATTTCCAGAAATAAGGTGA
* *
7052 TGATTTGCAGAGATAAGGTG
1 TGATTTCCAGAAATAAGGTG
7072 TACAATCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (21 bp):
TGATTTCCAGAAATAAGGTGA
Found at i:8191 original size:4 final size:4
Alignment explanation
Indices: 8184--8217 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
8174 GACCGACCTC
8184 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
8218 TTTTGAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:8254 original size:17 final size:16
Alignment explanation
Indices: 8232--8265 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
8222 GAGAATTTCG
8232 ACCCACCTAATTAATTA
1 ACCCACCTAATT-ATTA
*
8249 ACCCACCTGATTATTA
1 ACCCACCTAATTATTA
8265 A
1 A
8266 TTAATCAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.29
Consensus pattern (16 bp):
ACCCACCTAATTATTA
Found at i:9355 original size:56 final size:57
Alignment explanation
Indices: 9293--9433 Score: 202
Period size: 56 Copynumber: 2.5 Consensus size: 57
9283 TAAGACACCT
9293 CAAATTAAAAT-CTTAGAAAAAGATCAAACAACAATACAC-GCCGCGAAGCACGTG-CC
1 CAAATTAAAATCCTT-GAAAAAGATCAAACAACAATACACAG-CGCGAAGCACGTGTCC
* *
9349 CAAATTAAAATCCTT-AAAAAGATCAAACAACAGTACACAGCGCGAAGCGCGTGTCC
1 CAAATTAAAATCCTTGAAAAAGATCAAACAACAATACACAGCGCGAAGCACGTGTCC
*
9405 CAAATTAAAATCCTTG-CAAAGATCAAACA
1 CAAATTAAAATCCTTGAAAAAGATCAAACA
9434 GTACACGGCG
Statistics
Matches: 78, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
55 34 0.44
56 41 0.53
57 3 0.04
ACGTcount: A:0.46, C:0.24, G:0.13, T:0.16
Consensus pattern (57 bp):
CAAATTAAAATCCTTGAAAAAGATCAAACAACAATACACAGCGCGAAGCACGTGTCC
Found at i:10929 original size:21 final size:22
Alignment explanation
Indices: 10900--10945 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
10890 ATAGATTAAG
10900 CAGTAATTAAACAT-AGTCTGA
1 CAGTAATTAAACATAAGTCTGA
* *
10921 CAGTCATTAAACATAATTCTGA
1 CAGTAATTAAACATAAGTCTGA
10943 CAG
1 CAG
10946 CAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (22 bp):
CAGTAATTAAACATAAGTCTGA
Found at i:15230 original size:21 final size:22
Alignment explanation
Indices: 15186--15236 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
15176 CAAGCATGCA
15186 TAAACATAGATTAAGCAGTAAT
1 TAAACATAGATTAAGCAGTAAT
*
15208 TAAACATAG-TCTAA-CAGTCAT
1 TAAACATAGAT-TAAGCAGTAAT
15229 TAAACATA
1 TAAACATA
15237 ATTCTGACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (22 bp):
TAAACATAGATTAAGCAGTAAT
Found at i:18083 original size:12 final size:13
Alignment explanation
Indices: 18057--18096 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
18047 GGAAATGTGC
*
18057 GTTTAGTTAATTT
1 GTTTATTTAATTT
18070 GTTTATTT-ATTT
1 GTTTATTTAATTT
*
18082 GTTTGTTTAATTT
1 GTTTATTTAATTT
18095 GT
1 GT
18097 AGCTGGTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (13 bp):
GTTTATTTAATTT
Found at i:25926 original size:25 final size:25
Alignment explanation
Indices: 25898--25945 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
25888 TTGCCTAAAA
25898 GAAACACAAGAATTAGAAAGAAACC
1 GAAACACAAGAATTAGAAAGAAACC
25923 GAAACACAAGAATTAGAAAGAAA
1 GAAACACAAGAATTAGAAAGAAA
25946 TCTTCCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.62, C:0.12, G:0.17, T:0.08
Consensus pattern (25 bp):
GAAACACAAGAATTAGAAAGAAACC
Found at i:26594 original size:39 final size:39
Alignment explanation
Indices: 26535--26612 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
26525 GGTGAGTGAG
*
26535 TCGGAATTGAGAAGGCTACGAGGCAAG-GACATGACCGGT
1 TCGGAATTGAAAAGGCTACGAGGCAAGCGAC-TGACCGGT
*
26574 TCGGGATTGAAAAGGCTACGAGGCAAGCGACTGACCGGT
1 TCGGAATTGAAAAGGCTACGAGGCAAGCGACTGACCGGT
26613 CCGTGAGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 33 0.92
40 3 0.08
ACGTcount: A:0.29, C:0.19, G:0.36, T:0.15
Consensus pattern (39 bp):
TCGGAATTGAAAAGGCTACGAGGCAAGCGACTGACCGGT
Found at i:29850 original size:87 final size:86
Alignment explanation
Indices: 29721--29883 Score: 213
Period size: 87 Copynumber: 1.9 Consensus size: 86
29711 TGATAGGGTG
* * * *
29721 GAGAATAATTTGAATTCAATTAATTGTGATCTTCCTAATGGAGTTATGGGTGGTTATTG-TGCAA
1 GAGAATAATTTGAATTCAATT-ATTGTAATCTTCCTAATGGAGTTATAGGTAG-TAATGATGCAA
29785 AATCTTTGGAAAATATTATGGTA
64 AATCTTTGGAAAATATTATGGTA
* * *
29808 GAGAATAGTTTGAATTCAAATT-TTAGTAATCTTCCTAATGGAGTTTTAGTTAGTAATGATGCAA
1 GAGAATAATTTGAATTC-AATTATT-GTAATCTTCCTAATGGAGTTATAGGTAGTAATGATGCAA
29872 AATCTTTGGAAA
64 AATCTTTGGAAA
29884 CTGATTTGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
86 6 0.09
87 56 0.85
88 4 0.06
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (86 bp):
GAGAATAATTTGAATTCAATTATTGTAATCTTCCTAATGGAGTTATAGGTAGTAATGATGCAAAA
TCTTTGGAAAATATTATGGTA
Found at i:30689 original size:30 final size:29
Alignment explanation
Indices: 30655--30715 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
30645 AAAAATCTTT
30655 AAAGGCTAAAGCTGTATTTATTGCACCGTA
1 AAAGGCTAAA-CTGTATTTATTGCACCGTA
* ** * *
30685 AAAGGGTTCATTGTGTTTATTGCACCGTA
1 AAAGGCTAAACTGTATTTATTGCACCGTA
30714 AA
1 AA
30716 CGATGAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (29 bp):
AAAGGCTAAACTGTATTTATTGCACCGTA
Done.