Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009483.1 Corchorus capsularis cultivar CVL-1 contig09504, 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: 24205
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1410 original size:22 final size:22
Alignment explanation
Indices: 1380--1421 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1370 CATGAGAAAC
* * *
1380 CAAGCCAAGGAAATGGGTGTTA
1 CAAGACAAGAAAAAGGGTGTTA
1402 CAAGACAAGAAAAAGGGTGT
1 CAAGACAAGAAAAAGGGTGT
1422 CTGAGTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.12, G:0.31, T:0.14
Consensus pattern (22 bp):
CAAGACAAGAAAAAGGGTGTTA
Found at i:1673 original size:13 final size:13
Alignment explanation
Indices: 1629--1691 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 13
1619 TTTTATGCAT
**
1629 TTAATATATTAAA
1 TTAATATAGAAAA
*
1642 TTAATAATGAGAATTA
1 TTAAT-AT-AGAA-AA
1658 TTAATATAGAAAA
1 TTAATATAGAAAA
1671 TTAATTTATAGAAAA
1 TTAA--TATAGAAAA
1686 TTAATA
1 TTAATA
1692 ATGAAAATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 12 0.29
14 6 0.15
15 17 0.41
16 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (13 bp):
TTAATATAGAAAA
Found at i:1683 original size:29 final size:28
Alignment explanation
Indices: 1629--1699 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 28
1619 TTTTATGCAT
** *
1629 TTAATATATTAAATTAATAATGAGAATTA
1 TTAATATAGAAAATTAATAATGAGAA-AA
*
1658 TTAATATAGAAAATTAATTTAT-AGAAAA
1 TTAATATAGAAAATTAA-TAATGAGAAAA
1686 TTAATA-ATGAAAAT
1 TTAATATA-GAAAAT
1700 ACTGTTTCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.03
28 13 0.36
29 19 0.53
30 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (28 bp):
TTAATATAGAAAATTAATAATGAGAAAA
Found at i:1699 original size:13 final size:14
Alignment explanation
Indices: 1639--1699 Score: 63
Period size: 15 Copynumber: 4.3 Consensus size: 14
1629 TTAATATATT
1639 AAATTAATAATGAGA
1 AAATTAATAAT-AGA
*
1654 ATTATTAAT-ATAGA
1 A-AATTAATAATAGA
*
1668 AAATTAATTTATAGA
1 AAATTAA-TAATAGA
1683 AAATTAATAAT-GA
1 AAATTAATAATAGA
1696 AAAT
1 AAAT
1700 ACTGTTTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.28
14 8 0.20
15 15 0.38
16 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.34
Consensus pattern (14 bp):
AAATTAATAATAGA
Found at i:2566 original size:3 final size:3
Alignment explanation
Indices: 2558--2587 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2548 TCCATTGCTA
*
2558 CTT CTT CTT GTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2588 GTTCCCCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:5538 original size:19 final size:19
Alignment explanation
Indices: 5514--5552 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5504 TCAATAACCA
5514 TTTTTAACATAAATCCAGG
1 TTTTTAACATAAATCCAGG
5533 TTTTTAACATAAATCCAGG
1 TTTTTAACATAAATCCAGG
5552 T
1 T
5553 ATGACAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TTTTTAACATAAATCCAGG
Found at i:6509 original size:11 final size:11
Alignment explanation
Indices: 6493--6528 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
6483 TGAATACGAT
6493 CCGAGAAAGAC
1 CCGAGAAAGAC
*
6504 CCGAGAAAGAT
1 CCGAGAAAGAC
*
6515 CCGAGAAAAAC
1 CCGAGAAAGAC
6526 CCG
1 CCG
6529 TTTGAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.44, C:0.28, G:0.25, T:0.03
Consensus pattern (11 bp):
CCGAGAAAGAC
Found at i:6665 original size:15 final size:15
Alignment explanation
Indices: 6631--6670 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
6621 GAAAAACTAG
* *
6631 AACCCGAAAAATGTAA
1 AACCCG-AACATGAAA
6647 AACCCGAACATGAAA
1 AACCCGAACATGAAA
6662 AACCCGAAC
1 AACCCGAAC
6671 TCAATGCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.53, C:0.28, G:0.12, T:0.07
Consensus pattern (15 bp):
AACCCGAACATGAAA
Found at i:6690 original size:2 final size:2
Alignment explanation
Indices: 6683--6721 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
6673 AATGCTAATC
*
6683 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
6722 AAAGTACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6792 original size:30 final size:30
Alignment explanation
Indices: 6751--6809 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
6741 CTTTATATTT
* *
6751 TCCATTTGTACCCTTTTTTTAAAACATATC
1 TCCAATTGTACCCTTTTTTTAAAAAATATC
6781 TCCAATTGTACCCTTTTTTTAAAAAATAT
1 TCCAATTGTACCCTTTTTTTAAAAAATAT
6810 ATTTCTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.46
Consensus pattern (30 bp):
TCCAATTGTACCCTTTTTTTAAAAAATATC
Found at i:7829 original size:22 final size:22
Alignment explanation
Indices: 7804--7907 Score: 88
Period size: 22 Copynumber: 4.7 Consensus size: 22
7794 ATCAAAGAGA
*
7804 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* * *
7826 TTAT-AAGAATTTTATAGCGTGT
1 TTATCAA-AATTTCATAGCGAGG
*
7848 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGCGAGG
* * *
7870 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGCGAGG
7892 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
7908 TGAATGTTAT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
21 5 0.08
22 53 0.83
23 6 0.09
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:8137 original size:22 final size:22
Alignment explanation
Indices: 8086--8159 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
8076 CAAAATATGA
*
8086 TTATCAGAATTTCATAGAGG-GG
1 TTATCAAAATTTCATA-AGGAGG
* * *
8108 TCAACAAAATTTTATAAGGAGG
1 TTATCAAAATTTCATAAGGAGG
*
8130 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAGGAGG
8152 TTATCAAA
1 TTATCAAA
8160 TTTTTCAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 3 0.07
22 40 0.93
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGAGG
Found at i:8297 original size:20 final size:20
Alignment explanation
Indices: 8272--8323 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
8262 TTATGGAGTA
*
8272 ATCAAAATTTTAGGGA-AGAT
1 ATCAAAATTTCAGGGAGA-AT
8292 ATCAAAATTTCAGGGAGAAT
1 ATCAAAATTTCAGGGAGAAT
8312 ATCAAAATTTCA
1 ATCAAAATTTCA
8324 TAGTTTAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTCAGGGAGAAT
Found at i:8405 original size:22 final size:22
Alignment explanation
Indices: 8272--8652 Score: 199
Period size: 22 Copynumber: 17.5 Consensus size: 22
8262 TTATGGAGTA
* *
8272 ATCAAAATTT--TAGGGAAGAT
1 ATCAAAATTTCATAGGGAGGTT
**
8292 ATCAAAATTTC--AGGGAGAAT
1 ATCAAAATTTCATAGGGAGGTT
**
8312 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
8334 TTC-AAATTTACATA-AGAGGGTT
1 ATCAAAATTT-CATAGGGA-GGTT
* * * *
8356 ATCCAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
**
8378 ATCAAAATTTCATAGGGAGAAT
1 ATCAAAATTTCATAGGGAGGTT
* **
8400 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
8422 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
8444 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
8466 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
8488 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ****
8510 TTTAAATTTTCATAATCTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
8532 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
8554 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
8577 ATAAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
**
8599 ATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
*
8622 -TCAAAATTTCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
8643 AACAAAATTT
1 ATCAAAATTT
8653 TATAAGAATG
Statistics
Matches: 265, Mismatches: 79, Indels: 32
0.70 0.21 0.09
Matches are distributed among these distances:
20 29 0.11
21 11 0.04
22 197 0.74
23 28 0.11
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:8939 original size:31 final size:30
Alignment explanation
Indices: 8904--8968 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
8894 AACTTTATGT
* * *
8904 TTTCCGATTGTGCCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCCTT-TTTTAAAAATATA
*
8935 TTTCCAATTGTATCCTTTTTTAAAAATATA
1 TTTCCAATTGTACCCTTTTTTAAAAATATA
8965 TTTC
1 TTTC
8969 TAAATTGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (30 bp):
TTTCCAATTGTACCCTTTTTTAAAAATATA
Found at i:9236 original size:22 final size:23
Alignment explanation
Indices: 9201--9416 Score: 116
Period size: 22 Copynumber: 9.7 Consensus size: 23
9191 TGGTAGAAGG
*
9201 TTATC-AAATCTCATAGAG-TGA
1 TTATCAAAATTTCATAGAGATGA
*
9222 TTATCGAAATTTCATAGAGATGGAA
1 TTATCAAAATTTCATAGAGAT-G-A
* *
9247 TTATCAAAATTT-ATTG-GAAGA
1 TTATCAAAATTTCATAGAGATGA
* *
9268 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGAGATGA
* * *
9290 TTATCAAAATTTCAAAGCGA-GG
1 TTATCAAAATTTCATAGAGATGA
* *
9312 TTATCAAAATTACATA-ATG-TAA
1 TTATCAAAATTTCATAGA-GATGA
* * *
9334 TTATCAGAATTTCATAGAG-GGG
1 TTATCAAAATTTCATAGAGATGA
* * * * *
9356 TCAACAAAATTTTATAAAGA-GG
1 TTATCAAAATTTCATAGAGATGA
*
9378 TTATCAAAATTTCA-AAATG-TGA
1 TTATCAAAATTTCATAGA-GATGA
9400 TTA-CAAAAATTTCATAG
1 TTATC-AAAATTTCATAG
9417 TGGTATTTCT
Statistics
Matches: 150, Mismatches: 30, Indels: 28
0.72 0.14 0.13
Matches are distributed among these distances:
21 23 0.15
22 104 0.69
23 7 0.05
24 4 0.03
25 12 0.08
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (23 bp):
TTATCAAAATTTCATAGAGATGA
Found at i:9364 original size:66 final size:66
Alignment explanation
Indices: 9267--9416 Score: 169
Period size: 66 Copynumber: 2.3 Consensus size: 66
9257 TTATTGGAAG
* ** * * * *
9267 ATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATG
1 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATG
9331 TA
65 TA
* * *
9333 ATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCAAAATGT
1 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGT
*
9398 G
66 A
9399 ATTA-CAAAAATTTCATAG
1 ATTATC-AAAATTTCATAG
9417 TGGTATTTCT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
65 1 0.01
66 67 0.96
67 2 0.03
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (66 bp):
ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGT
A
Found at i:9526 original size:20 final size:20
Alignment explanation
Indices: 9497--9548 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
9487 TTATGCTGTA
9497 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
* *
9517 ATCCAAATTTTAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
9537 ATCAAAATTTCA
1 ATCAAAATTTCA
9549 TAGTTTAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTCAGGGAGGAT
Found at i:9630 original size:22 final size:21
Alignment explanation
Indices: 9531--9974 Score: 129
Period size: 22 Copynumber: 20.3 Consensus size: 21
9521 AAATTTTAGG
*
9531 GAGGATATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTTCATA--T
* * * *
9554 TA-GTTTTCAAAATTTGATAA
1 GAGGTTATCAAAATTTCATAT
*
9574 GAGGTTTATCAAAATTTCATAGG
1 GAGG-TTATCAAAATTTCATA-T
* *
9597 GAGATTAACAAAATTTCATTAT
1 GAGGTTATCAAAATTTCA-TAT
**
9619 GAGGTTATCAAAAAATCATAT
1 GAGGTTATCAAAATTTCATAT
* *
9640 GGAGGTTATTAAAA-TT--TGT
1 -GAGGTTATCAAAATTTCATAT
* *
9659 -A-GTTATCAAGATTTCATAA
1 GAGGTTATCAAAATTTCATAT
* *
9678 GAAAGTTATCAAAA-TT-ATAGG
1 G-AGGTTATCAAAATTTCATA-T
* *
9699 GAGGTTTATATCAAAATTTTATAG
1 GAGG--T-TATCAAAATTTCATAT
* * *
9723 GAAGATTTATTAAAATTTCATAGC
1 G-AG-GTTATCAAAATTTCATA-T
* *
9747 GAGATTATCACAATTTCATAGT
1 GAGGTTATCAAAATTTCATA-T
* *
9769 GTGATTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATA-T
* * *
9791 GTGATTATTAACAA-TTCATAT
1 GAGGTTATCAA-AATTTCATAT
* * * * *
9812 GGAAGTTTTTAAATTTTCATAA
1 -GAGGTTATCAAAATTTCATAT
* * * *
9834 CATGCTTATCAATATATCATAT
1 GA-GGTTATCAAAATTTCATAT
* *
9856 GAAGGTTATCAACATCTCATAGT
1 G-AGGTTATCAAAATTTCATA-T
*
9879 GTTGGTTATCAAAATTTCAT-T
1 G-AGGTTATCAAAATTTCATAT
9900 G-GGAAATTATCAAAATTTCATATT
1 GAGG---TTATCAAAATTTCATA-T
* * * *
9924 GAAGTCT-TCAAAATTCCTTAGG
1 GAGGT-TATCAAAATTTCATA-T
* *
9946 GAGGTTAACAAAATTTCATAA
1 GAGGTTATCAAAATTTCATAT
9967 GAAGGTTA
1 G-AGGTTA
9975 AAAAAAAATT
Statistics
Matches: 316, Mismatches: 70, Indels: 71
0.69 0.15 0.16
Matches are distributed among these distances:
16 8 0.03
17 3 0.01
19 5 0.02
20 6 0.02
21 16 0.05
22 214 0.68
23 50 0.16
24 8 0.03
25 6 0.02
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (21 bp):
GAGGTTATCAAAATTTCATAT
Found at i:9737 original size:23 final size:25
Alignment explanation
Indices: 9684--9745 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 25
9674 ATAAGAAAGT
* *
9684 TATCAAAA--TTATAGGGAGGTTTA
1 TATCAAAATTTTATAGGAAGATTTA
9707 TATCAAAATTTTATAGGAAGATTTA
1 TATCAAAATTTTATAGGAAGATTTA
*
9732 T-T-AAAATTTCATAG
1 TATCAAAATTTTATAG
9746 CGAGATTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 19 0.56
24 1 0.03
25 14 0.41
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.39
Consensus pattern (25 bp):
TATCAAAATTTTATAGGAAGATTTA
Found at i:13727 original size:21 final size:21
Alignment explanation
Indices: 13701--13743 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
13691 TTTCGCCTTT
13701 GTGAATGAAAACAAAAGAAAG
1 GTGAATGAAAACAAAAGAAAG
13722 GTGAATGAAAACAAAAGAAAG
1 GTGAATGAAAACAAAAGAAAG
13743 G
1 G
13744 AGTCTTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.60, C:0.05, G:0.26, T:0.09
Consensus pattern (21 bp):
GTGAATGAAAACAAAAGAAAG
Found at i:15661 original size:13 final size:13
Alignment explanation
Indices: 15636--15672 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
15626 ATTCAAAGTC
15636 ATAAACCAAAATA
1 ATAAACCAAAATA
*
15649 ATAAACCAGAATA
1 ATAAACCAAAATA
*
15662 ATAAGCCAAAA
1 ATAAACCAAAA
15673 CAGCCGGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.65, C:0.16, G:0.05, T:0.14
Consensus pattern (13 bp):
ATAAACCAAAATA
Found at i:17683 original size:17 final size:18
Alignment explanation
Indices: 17655--17691 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
17645 CCTCCTCATA
17655 GTACCTAGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
17673 GTACC-AGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
17690 GT
1 GT
17692 GATAGGCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (18 bp):
GTACCTAGGTAGTATGAG
Found at i:18537 original size:22 final size:22
Alignment explanation
Indices: 18512--18558 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
18502 ATTTATTCAT
18512 TATTAATTAACCATTAATTAGA
1 TATTAATTAACCATTAATTAGA
* *
18534 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACCATTAATTAGA
18556 TAT
1 TAT
18559 AGTATAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (22 bp):
TATTAATTAACCATTAATTAGA
Found at i:18554 original size:11 final size:11
Alignment explanation
Indices: 18512--18554 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
18502 ATTTATTCAT
*
18512 TATTAATTAAC
1 TATTAATTAGC
* *
18523 CATTAATTAGA
1 TATTAATTAGC
18534 TATTAATTAGC
1 TATTAATTAGC
18545 TATTAATTAG
1 TATTAATTAG
18555 ATATAGTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:19631 original size:19 final size:20
Alignment explanation
Indices: 19604--19641 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
19594 TACTATTATT
19604 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
19624 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
19642 AAAGTCGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:19831 original size:22 final size:22
Alignment explanation
Indices: 19806--19990 Score: 162
Period size: 22 Copynumber: 8.3 Consensus size: 22
19796 TTGTCTCTAT
*
19806 ATGGTTATCAAAATTTCATAAG
1 ATGGTTATCAAAATTTCATAGG
* *
19828 ATGGTTATTATAATTTCATGAGG
1 ATGGTTATCAAAATTTCAT-AGG
*
19851 A-GGTTATCAAAATTCCATAGCG
1 ATGGTTATCAAAATTTCATAG-G
* *
19873 -TGGTTACCAAAATTTCGTATGG
1 ATGGTTATCAAAATTTCATA-GG
*
19895 A-AGTTATCAAAATTTCATAGTG
1 ATGGTTATCAAAATTTCATAG-G
*
19917 -TGGTTACCAAAATTTCATAGG
1 ATGGTTATCAAAATTTCATAGG
* *
19938 ATCAGGTTATTAAAATTTCTTAGG
1 AT--GGTTATCAAAATTTCATAGG
* **
19962 TTGGTTATTGAAATTTCATAGG
1 ATGGTTATCAAAATTTCATAGG
*
19984 GTGGTTA
1 ATGGTTA
19991 ATTATCAAAA
Statistics
Matches: 132, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
21 4 0.03
22 106 0.80
23 4 0.03
24 18 0.14
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
ATGGTTATCAAAATTTCATAGG
Found at i:20053 original size:22 final size:22
Alignment explanation
Indices: 20028--20154 Score: 87
Period size: 22 Copynumber: 5.8 Consensus size: 22
20018 ATCAAAGAGA
*
20028 TTATCAAAATGTCATAACGAGG
1 TTATCAAAATTTCATAACGAGG
** *
20050 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAACGAGG
* *
20072 TTAACAAAATTTCATTACGAGG
1 TTATCAAAATTTCATAACGAGG
* ***
20094 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAACGAGG
* ** **
20116 TTATCAAAATTTTATAGTGTTG
1 TTATCAAAATTTCATAACGAGG
20138 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
20155 AAGTCTCAAT
Statistics
Matches: 80, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
21 3 0.04
22 74 0.93
23 3 0.04
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAACGAGG
Found at i:20092 original size:44 final size:44
Alignment explanation
Indices: 20032--20127 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
20022 AAGAGATTAT
* * *
20032 CAAAATGTCATAACGAGGTTA-TAAGAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAACGAGGTTACTAA-AATTTCATAGGGAGGTTAA
* * * *
20076 CAAAATTTCATTACGAGGTTACTAATATTTCATGGGGAGGTTAT
1 CAAAATTTCATAACGAGGTTACTAAAATTTCATAGGGAGGTTAA
20120 CAAAATTT
1 CAAAATTT
20128 TATAGTGTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 41 0.93
45 3 0.07
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (44 bp):
CAAAATTTCATAACGAGGTTACTAAAATTTCATAGGGAGGTTAA
Found at i:20231 original size:22 final size:22
Alignment explanation
Indices: 20196--20324 Score: 108
Period size: 22 Copynumber: 5.8 Consensus size: 22
20186 TGATAGACGG
*
20196 TTATCAAATCTCATAGAG-TGA
1 TTATCAAATTTCATAGAGATGA
20217 TTATCGAAATTTCATAGAGATCGGA
1 TTATC-AAATTTCATAGAGAT--GA
*
20242 TTATCAAAATTT-ATAG-GAAGA
1 TTATC-AAATTTCATAGAGATGA
*
20263 TTATCAAATTTCATA-ATGTTG-
1 TTATCAAATTTCATAGA-GATGA
* *
20284 TTATCAAAATTACATA-ATATGA
1 TTATC-AAATTTCATAGAGATGA
20306 TTATCAGAATTTCATAGAG
1 TTATCA-AATTTCATAGAG
20325 GGGTCAATAA
Statistics
Matches: 87, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
20 6 0.07
21 23 0.26
22 37 0.43
23 4 0.05
24 4 0.05
25 13 0.15
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
TTATCAAATTTCATAGAGATGA
Done.