Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008685.1 Corchorus capsularis cultivar CVL-1 contig08706, 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: 37032
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:1765 original size:16 final size:17
Alignment explanation
Indices: 1725--1769 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1715 AAAAACCAAT
*
1725 CAATTAGAATGCCTAAAC
1 CAATTAAAATGCCT-AAC
*
1743 AAATTAAAATGCCT-AC
1 CAATTAAAATGCCTAAC
1759 CAATTAAAATG
1 CAATTAAAATG
1770 GATGTGCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.50
18 12 0.50
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.24
Consensus pattern (17 bp):
CAATTAAAATGCCTAAC
Found at i:2892 original size:17 final size:19
Alignment explanation
Indices: 2858--2894 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
2848 TTTGCTTGTT
2858 TTTTCTTCTTTCTTTTTCA
1 TTTTCTTCTTTCTTTTTCA
2877 TTTTCTT-TTT-TTTTTCA
1 TTTTCTTCTTTCTTTTTCA
2894 T
1 T
2895 GTGCTTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCTTCTTTCTTTTTCA
Found at i:3717 original size:36 final size:36
Alignment explanation
Indices: 3653--3732 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
3643 CTTTTTATTC
*
3653 TCTTTTTGCGACCTCTTTTTTTTTTAGGCTCAGTTTTT
1 TCTTTTTGCGACCTC-TTTTTTTTTAGGCCCAG-TTTT
3691 TCTTTTTGCGACCTC-TTTTTTTTAGGCCCAGTTTT
1 TCTTTTTGCGACCTCTTTTTTTTTAGGCCCAGTTTT
3726 TCTTTTT
1 TCTTTTT
3733 CTTTGATGGG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 11 0.27
36 15 0.37
38 15 0.37
ACGTcount: A:0.07, C:0.20, G:0.12, T:0.60
Consensus pattern (36 bp):
TCTTTTTGCGACCTCTTTTTTTTTAGGCCCAGTTTT
Found at i:6480 original size:50 final size:50
Alignment explanation
Indices: 6404--7734 Score: 1263
Period size: 50 Copynumber: 26.8 Consensus size: 50
6394 AAATGTGAAG
* * * *
6404 AGAAAAC-TGGACCTTCCGACCGGGAAGGGGCATTTTGGGGAAGAAAGAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * * *
6453 AGAAAACTGGGACCTTCCAACCAGGAAGGGGTATTTTTGGAAACAAACAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * * * **
6503 AGAAAACAGGGACCTTTCGACCGGGAAGGAGCATTTTAGAAAACGAATGA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
*
6553 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * * *
6603 AGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
** **
6653 AGAAAACAGGGACCTTCTAACCAAG-AGAGGGCATTTTGGGAAACAAACAA
1 AGAAAACAGGGACCTTCCGACCGGGAAG-GGGCATTTTGGGAAACAAACAA
* * * * * *
6703 ATAAAACAGGGACATTCCAACCAGG-ATGGGCATTTTTGGAAACAAACAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * *
6752 AGAAAACAAGAACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
** * * *
6802 AGAAAACAGGGACCTTCTAACCAGGAAGGGGCATTTTTGGAAACAAACAG
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
** * * * *
6852 AGAAAGTAAGGACCTT-CGACCGGGAACGAGCATTTTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * **
6901 ATAAAACAGGGACCTTCC-AGTCATGAAGGGGCAGTTTT-GGAAACAAACAA
1 AGAAAACAGGGACCTTCCGA-CCGGGAAGGGGCA-TTTTGGGAAACAAACAA
* * * * **
6951 AGAAAGCAAGGACCTTCCGACCGGGAAAGGGCGTTTTGGGAAGTAAACAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
** * *
7001 AGAAAACAGTAACCTTCCGACCGGGAATGGGCATTTTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * ** ** * *
7051 AGAAAATAAGGACCTTCAAACCAAGAAGGGGCATTTTGGGAAAGAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * * *
7101 ATAAAACAGGGACCTTTTCAACCAGGAAGGGGCATTTTTGGAAACAAACAA
1 AGAAAACAGGGACC-TTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * * **
7152 AGAAAACAGGGACCTTTCGACCGGGAAGGGGCATTTTAGAAAACGAATGA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
*
7202 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * * *
7252 AGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAACAAACAG
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
** * * *
7302 AGAAAGTAAGGACCTTCCGACCGGGAACGGGCATTTTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * *
7352 ATAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAACAAACAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * * *
7402 AGAAAGCAAGGACCTTCCGACCGGGAAAGGGCGTTTTGGGAAGCAAACAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * *
7452 AGAAAACAGGGACCTTCTGACCGGGAATGGGCATTTTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
** ** * *
7502 AGAAAACAGGGACCTTCAAACCAAGAAGGGGCATTTTGGGAAGCAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * * * * *
7552 AGAAGACTA-TGACCTTCTGACTGGGAAGGGGC-TTTTTGG-AATAAATAA
1 AGAAAAC-AGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
** * * * * * **
7600 AGAAGATTA-TGACCTTCCGAACGGAAAGGGGC-TTTTTGG-AATAAGTAA
1 AGAA-AACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * * *
7648 AGACAACTA-TGACCTTCCGACCGTGAAGGGGC-TTTTTGGAATA-AGA-AA
1 AGAAAAC-AGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAA-ACAAACAA
** ** * *
7696 AGCCAATTGTGACCTTCCGACCGGGAAGGGGCTTTTTGG
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGG
7735 AATAAGAAAA
Statistics
Matches: 1061, Mismatches: 205, Indels: 32
0.82 0.16 0.02
Matches are distributed among these distances:
47 1 0.00
48 106 0.10
49 104 0.10
50 801 0.75
51 49 0.05
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (50 bp):
AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
Found at i:7568 original size:150 final size:150
Alignment explanation
Indices: 6404--7555 Score: 1396
Period size: 150 Copynumber: 7.7 Consensus size: 150
6394 AAATGTGAAG
* * * * *
6404 AGAAAAC-TGGACCTTCCGACCGGGAAGGGGCATTTTGGGGAAGAAAGAAAGAAAACTGGGACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCT
* * * * * *
6468 TCCAACCAGGAAGGGGTATTTTTGGAAACAAACAAAGAAAACAGGGACCTTTCGACC-GGGAAGG
66 TCCAACCAGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCAACCAGGAAAGG
* * * **
6532 AGCATTTTAGAAAACGAATGA
131 -GCATTTTGGGAAACAAACAA
*
6553 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAAGGACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCT
* * * *
6618 TCCAACCAGGAAGGGGCATTTTTGGAAACAAATAAAGAAAACAGGGACCTTCTAACCAAGAGAGG
66 TCCAACCAGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCAACCAGGAAAGG
6683 GCATTTTGGGAAACAAACAA
131 GCATTTTGGGAAACAAACAA
* * * * * * * * *
6703 ATAAAACAGGGACATTCCAACCAGG-ATGGGCATTTTTGGAAACAAACAAAGAAAACAAGAACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCT
* * * *
6767 TCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCTAACCAGGAAGGG
66 TCCAACCAGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCAACCAGGAAAGG
* *
6832 GCATTTTTGGAAACAAACAG
131 GCATTTTGGGAAACAAACAA
** * * * *
6852 AGAAAGTAAGGACCTT-CGACCGGGAACGAGCATTTTGGGAAACAAATAAATAAAACAGGGACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCT
** * * * * * *
6916 TCCAGTCATGAAGGGGCAGTTTT-GGAAACAAACAAAGAAAGCAAGGACCTTCCGACCGGGAAAG
66 TCCAACCAGGAAGGGGCA-TTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCAACCAGGAAAG
* **
6980 GGCGTTTTGGGAAGTAAACAA
130 GGCATTTTGGGAAACAAACAA
** * * *
7001 AGAAAACAGTAACCTTCCGACCGGGAATGGGCATTTTGGGAAACAAATAAAGAAAATAAGGACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCT
* * * * * *
7066 TCAAACCAAGAAGGGGCATTTTGGGAAAGAAATAAATAAAACAGGGACCTTTTCAACCAGGAAGG
66 TCCAACCAGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACC-TTCCAACCAGGAAAG
*
7131 GGCATTTTTGGAAACAAACAA
130 GGCATTTTGGGAAACAAACAA
* * * * *
7152 AGAAAACAGGGACCTTTCGACCGGGAAGGGGCATTTTAGAAAACGAATGAAGAAAACAGGGACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCT
* * * *
7217 TCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAAGGACCTTCCAACCAGGAAGGG
66 TCCAACCAGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCAACCAGGAAAGG
* *
7282 GCATTTTTGGAAACAAACAG
131 GCATTTTGGGAAACAAACAA
** * * *
7302 AGAAAGTAAGGACCTTCCGACCGGGAACGGGCATTTTGGGAAACAAATAAATAAAACAGGGACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCT
* * * * * *
7367 TCCAACCAGGAAGGGGCATTTTTGGAAACAAACAAAGAAAGCAAGGACCTTCCGACCGGGAAAGG
66 TCCAACCAGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCAACCAGGAAAGG
* *
7432 GCGTTTTGGGAAGCAAACAA
131 GCATTTTGGGAAACAAACAA
* *
7452 AGAAAACAGGGACCTTCTGACCGGGAATGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCT
* * *
7517 TCAAACCAAGAAGGGGCATTTTGGGAAGCAAATAAAGAA
66 TCCAACCAGGAAGGGGCATTTTGGGAAACAAATAAAGAA
7556 GACTATGACC
Statistics
Matches: 851, Mismatches: 145, Indels: 13
0.84 0.14 0.01
Matches are distributed among these distances:
148 6 0.01
149 240 0.28
150 476 0.56
151 129 0.15
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.16
Consensus pattern (150 bp):
AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCT
TCCAACCAGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCAACCAGGAAAGG
GCATTTTGGGAAACAAACAA
Found at i:7740 original size:48 final size:47
Alignment explanation
Indices: 7559--7745 Score: 250
Period size: 48 Copynumber: 3.9 Consensus size: 47
7549 TAAAGAAGAC
* * *
7559 TATGACCTTCTGACTGGGAAGGGGCTTTTTGGAATAA-ATAAAGAAGAT
1 TATGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGA-AAAGCA-AT
* * * *
7607 TATGACCTTCCGAACGGAAAGGGGCTTTTTGGAATAAGTAAAGACAAC
1 TATGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGAAAAG-CAAT
*
7655 TATGACCTTCCGACCGTGAAGGGGCTTTTTGGAATAAGAAAAGCCAAT
1 TATGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGAAAAG-CAAT
*
7703 TGTGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGAAAAG
1 TATGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGAAAAG
7746 TAAACAACAC
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
48 121 0.99
49 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (47 bp):
TATGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGAAAAGCAAT
Found at i:7823 original size:40 final size:40
Alignment explanation
Indices: 7748--7842 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
7738 AAGAAAAGTA
* * *
7748 AACAACACCTTCTGATGAGGAAGGGCAGACTGGGAAAACT
1 AACAACACCTTCCGATGAGAAAGGGCAAACTGGGAAAACT
*
7788 GAACAACACCTTCCGATG-GAAAGGGCAAACTGGGAAATCT
1 -AACAACACCTTCCGATGAGAAAGGGCAAACTGGGAAAACT
7828 AACCAACACCTTCCG
1 AA-CAACACCTTCCG
7843 GCGGGGAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.04
40 31 0.63
41 16 0.33
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (40 bp):
AACAACACCTTCCGATGAGAAAGGGCAAACTGGGAAAACT
Found at i:7873 original size:41 final size:40
Alignment explanation
Indices: 7750--7881 Score: 110
Period size: 40 Copynumber: 3.3 Consensus size: 40
7740 GAAAAGTAAA
* * * *
7750 CAACACCTTCTGATGAGG-AAGGGCAGACTGGGAAAACTGAA-
1 CAACACCTTCCGA-G-GGAAAGGGCAAACTAGGAAATCT-AAC
* *
7791 CAACACCTTCCGATGGAAAGGGCAAACTGGGAAATCTAAC
1 CAACACCTTCCGAGGGAAAGGGCAAACTAGGAAATCTAAC
* * *
7831 CAACACCTTCCGGCGGGGAAGGGCAAACTAGG-AATTTAAAC
1 CAACACCTTCC-GAGGGAAAGGGCAAACTAGGAAATCT-AAC
7872 C-ACACCTTCC
1 CAACACCTTCC
7882 AGTGAGGAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
39 4 0.05
40 42 0.54
41 32 0.41
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (40 bp):
CAACACCTTCCGAGGGAAAGGGCAAACTAGGAAATCTAAC
Found at i:7891 original size:40 final size:41
Alignment explanation
Indices: 7764--7898 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 41
7754 ACCTTCTGAT
* * *
7764 GAGGAAGGGCAGACTGGGAAAACTGAA-CAACACCTT-C--C
1 GAGGAAGGGCAAACTAGGAAATCT-AACCAACACCTTCCAGC
* *
7802 GATGGAAAGGGCAAACTGGGAAATCTAACCAACACCTTCCGGC
1 GA-GG-AAGGGCAAACTAGGAAATCTAACCAACACCTTCCAGC
* * *
7845 GGGGAAGGGCAAACTAGG-AATTTAAACC-ACACCTTCCAGT
1 GAGGAAGGGCAAACTAGGAAATCT-AACCAACACCTTCCAGC
*
7885 GAGGAAGAGCAAAC
1 GAGGAAGGGCAAAC
7899 AAGAATAGTA
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
38 2 0.02
39 4 0.05
40 53 0.65
41 18 0.22
42 2 0.02
43 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.13
Consensus pattern (41 bp):
GAGGAAGGGCAAACTAGGAAATCTAACCAACACCTTCCAGC
Found at i:8014 original size:46 final size:45
Alignment explanation
Indices: 7746--8306 Score: 203
Period size: 47 Copynumber: 12.8 Consensus size: 45
7736 ATAAGAAAAG
* * *
7746 TAAACAACACCTTCTGATGAGGAAGGGCAGACTGGG-A--A--AAC
1 TAAACAACACCTTCCGGTG-GGAAGGGCAAACTGGGAATTAGCAAC
* * * *
7787 TGAACAACACCTTCCGATGGAAAGGGCAAACTGGG-A--A--ATC
1 TAAACAACACCTTCCGGTGGGAAGGGCAAACTGGGAATTAGCAAC
* * *
7827 TAACCAACACCTTCCGGCGGGGAAGGGCAAACTAGGAATT------
1 TAAACAACACCTTCCGG-TGGGAAGGGCAAACTGGGAATTAGCAAC
* * * ** *
7867 TAAACCACACCTTCCAGTGAGGAAGAGCAAAC-AAGAATAGTAAACAAC
1 TAAACAACACCTTCCGGTG-GGAAGGGCAAACTGGGAAT--T-AGCAAC
*
7915 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTAGCAAC
1 TAAACAACACCTTCCGGT-GGGAAGGGCAAACTGGGAATTAGCAAC
* * * * * * *
7961 TAGACAACATCTTCTGGTGGGAAGGACAAATTGGGAATTTGATAAC
1 TAAACAACACCTTCCGGTGGGAAGGGCAAACTGGGAATTAG-CAAC
** *
8007 TAAACAACACCTTCCGAGTGGGAAGGGCAAACTACG-A--A--AAG
1 TAAACAACACCTTCCG-GTGGGAAGGGCAAACTGGGAATTAGCAAC
* * * *
8048 TAAACAGCACCTTCCGATGGGGAAGGGCAAACTGAGAATGAGACAAC
1 TAAACAACACCTTCCGGT-GGGAAGGGCAAACTGGGAATTAG-CAAC
* * *
8095 TGAGCAACACCTTCCGATTGGGAAGGGCAAA-----ACA--AG-AA-
1 TAAACAACACCTTCCG-GTGGGAAGGGCAAACTGGGA-ATTAGCAAC
* *
8133 TAAGGCAACACCTTCCGACG-GGGAAAGGCAAACTGGG-A--AG---C
1 TAA-ACAACACCTTCCG--GTGGGAAGGGCAAACTGGGAATTAGCAAC
* * *
8174 TAAACAACACCTTCCTGTGGGGAAGGGCAAACTTGGG-ATAAAGAAAC
1 TAAACAACACCTTCCGGT-GGGAAGGGCAAAC-TGGGAAT-TAGCAAC
* * ** **
8221 TAGACAACACCTTCCGATTGGGAAGGGTGAACT-GGAACAAGACAAAC
1 TAAACAACACCTTCCG-GTGGGAAGGGCAAACTGGGAATTAG-C-AAC
* **
8268 TATACAACACCTTCTAGTGGGGAAGGGCAAACTGGGAAT
1 TAAACAACACCTTCCGGT-GGGAAGGGCAAACTGGGAAT
8307 AAGCGGATTT
Statistics
Matches: 399, Mismatches: 71, Indels: 93
0.71 0.13 0.17
Matches are distributed among these distances:
38 3 0.01
39 32 0.08
40 81 0.20
41 75 0.19
42 6 0.02
43 1 0.00
44 3 0.01
45 25 0.06
46 39 0.10
47 97 0.24
48 32 0.08
49 5 0.01
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (45 bp):
TAAACAACACCTTCCGGTGGGAAGGGCAAACTGGGAATTAGCAAC
Found at i:8196 original size:126 final size:126
Alignment explanation
Indices: 7915--8247 Score: 315
Period size: 126 Copynumber: 2.6 Consensus size: 126
7905 AGTAAACAAC
* * * * * *
7915 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAT-TAGCAACTAGACAACATCTTCTG-G
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTTGGAATAAAGAAACTAGACAACACCTTCCGAT
* ** * *
7978 TGGGAAGGACAAATTGGGAATTTGATAACTAA-ACAACACCTTCCGAGTGGGAAGGGCAAACTAC
66 TGGGAAGGGCAAA---ACAA---G--AA-TAAGGCAACACCTTCCGAGTGGGAAAGGCAAACTA-
8042 GAAAAG
121 GAAAAG
* *
8048 TAAACAGCACCTTCCGATGGGGAAGGGCAAAC-TGAGAAT-GAGACAACT-GAGCAACACCTTCC
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTTG-GAATAAAGA-AACTAGA-CAACACCTTCC
**
8110 GATTGGGAAGGGCAAAACAAGAATAAGGCAACACCTTCCGACG-GGGAAAGGCAAACT-GGGAAG
63 GATTGGGAAGGGCAAAACAAGAATAAGGCAACACCTTCCGA-GTGGGAAAGGCAAACTAGAAAAG
*
8173 CTAAACAACACCTTCCTG-TGGGGAAGGGCAAACTTGGGATAAAGAAACTAGACAACACCTTCCG
1 -TAAACAACACCTTCC-GATGGGGAAGGGCAAACTTGGAATAAAGAAACTAGACAACACCTTCCG
8237 ATTGGGAAGGG
64 ATTGGGAAGGG
8248 TGAACTGGAA
Statistics
Matches: 172, Mismatches: 17, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
125 4 0.02
126 62 0.36
127 36 0.21
128 1 0.01
129 1 0.01
132 3 0.02
133 39 0.23
134 14 0.08
135 12 0.07
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16
Consensus pattern (126 bp):
TAAACAACACCTTCCGATGGGGAAGGGCAAACTTGGAATAAAGAAACTAGACAACACCTTCCGAT
TGGGAAGGGCAAAACAAGAATAAGGCAACACCTTCCGAGTGGGAAAGGCAAACTAGAAAAG
Found at i:8979 original size:50 final size:50
Alignment explanation
Indices: 8907--9049 Score: 128
Period size: 50 Copynumber: 2.8 Consensus size: 50
8897 ATCACCAATT
* * * *
8907 AATCAAAAATTTTC-TCTCTTAGCTTAAAGATTTCATTTTTAACTTAACTC
1 AATCAAAAA-TTTCATCTTTTAGCTCAAAGATTTCATTTTTAACATAAATC
** * * *
8957 AATCAAAAATTTCATCTTTTAGCATGGAA-ATTACATCTTTATCATAAATC
1 AATCAAAAATTTCATCTTTTAGC-TCAAAGATTTCATTTTTAACATAAATC
* * *
9007 AATCAAAAATTTCATTTTTTTTAACTCAAAGATTTAATTTTTA
1 AATCAAAAATTTCA--TCTTTTAGCTCAAAGATTTCATTTTTA
9050 TTTACAAATT
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
49 4 0.05
50 47 0.64
51 6 0.08
52 16 0.22
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (50 bp):
AATCAAAAATTTCATCTTTTAGCTCAAAGATTTCATTTTTAACATAAATC
Found at i:9035 original size:23 final size:24
Alignment explanation
Indices: 9009--9053 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
8999 CATAAATCAA
*
9009 TCAAAAATTTCATTTTT-TTTAAC
1 TCAAAAATTTAATTTTTATTTAAC
*
9032 TCAAAGATTTAATTTTTATTTA
1 TCAAAAATTTAATTTTTATTTA
9054 CAAATTAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (24 bp):
TCAAAAATTTAATTTTTATTTAAC
Found at i:10992 original size:13 final size:13
Alignment explanation
Indices: 10974--10999 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10964 GATGTGCTAT
10974 ACAAAATGCAATC
1 ACAAAATGCAATC
10987 ACAAAATGCAATC
1 ACAAAATGCAATC
11000 CAATGAGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (13 bp):
ACAAAATGCAATC
Found at i:21479 original size:2 final size:2
Alignment explanation
Indices: 21472--21518 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
21462 CGACCCCGAA
*
21472 AT AT AT AT AT AT -T AT GT AT AT AT AT AT AT AT AT AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21511 AT AT AT AT
1 AT AT AT AT
21519 GTTTTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:21620 original size:23 final size:23
Alignment explanation
Indices: 21590--21660 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
21580 AGATATGTTT
21590 TACTAATAAATAAAAATACTATA
1 TACTAATAAATAAAAATACTATA
* *
21613 TACTAATAAATAAATATTTACTAATT
1 TACTAATAAATAAA-A-ATACT-ATA
*
21639 TACTAAT-AATATAAATA-TATA
1 TACTAATAAATAAAAATACTATA
21660 T
1 T
21661 TAAAAATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 3 0.08
22 1 0.03
23 16 0.40
24 2 0.05
25 9 0.22
26 9 0.22
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (23 bp):
TACTAATAAATAAAAATACTATA
Found at i:26975 original size:47 final size:47
Alignment explanation
Indices: 26921--27014 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
26911 TTCAAATCGA
26921 TTAGAAAACCCTAGTACCAATTGAATCCAATTTATACCACTTGTCTC
1 TTAGAAAACCCTAGTACCAATTGAATCCAATTTATACCACTTGTCTC
26968 TTAGAAAACCCTAGTACCAATTGAATCCAATTTATACCACTTGTCTC
1 TTAGAAAACCCTAGTACCAATTGAATCCAATTTATACCACTTGTCTC
27015 CAATAGGGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.32
Consensus pattern (47 bp):
TTAGAAAACCCTAGTACCAATTGAATCCAATTTATACCACTTGTCTC
Found at i:28422 original size:30 final size:30
Alignment explanation
Indices: 28388--28459 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
28378 CCGGTTGTGC
** *
28388 CCGGTCTTGTGCAATTGGC-CCATGCCATGG
1 CCGGTCTTGTGCAA-TCCCTCCATGCAATGG
*
28418 CCGGTCTTGTGCGATCCCTCCATGCAATGG
1 CCGGTCTTGTGCAATCCCTCCATGCAATGG
28448 CCGGTCTTGTGC
1 CCGGTCTTGTGC
28460 GATGGCATCC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.11, C:0.32, G:0.29, T:0.28
Consensus pattern (30 bp):
CCGGTCTTGTGCAATCCCTCCATGCAATGG
Found at i:34391 original size:35 final size:36
Alignment explanation
Indices: 34337--34404 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
34327 ATAAAAAATC
* * *
34337 ATAATTTTAAATTACTTTTTTAAAGAAATTGATTAA
1 ATAATTTTAAATAACTTTTTAAAAAAAATTGATTAA
*
34373 ATAA-TTTAAATAATTTTTTAAAAAAAATTGAT
1 ATAATTTTAAATAACTTTTTAAAAAAAATTGAT
34405 CTAGGCATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (36 bp):
ATAATTTTAAATAACTTTTTAAAAAAAATTGATTAA
Done.