Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008421.1 Corchorus capsularis cultivar CVL-1 contig08442, 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: 34657
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--39 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40 CACACACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2761 original size:29 final size:31
Alignment explanation
Indices: 2728--2791 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
2718 TATATCAGAA
*
2728 GATTAATCCCATTATCA-TT-TGGATTGGG-T
1 GATTAATCACATTAT-ATTTGTGGATTGGGAT
*
2757 GATTAATCAGATTATATTTGTGGATTGGGAT
1 GATTAATCACATTATATTTGTGGATTGGGAT
2788 GATT
1 GATT
2792 TGGAAATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 15 0.50
30 9 0.30
31 5 0.17
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (31 bp):
GATTAATCACATTATATTTGTGGATTGGGAT
Found at i:7469 original size:27 final size:27
Alignment explanation
Indices: 7412--7475 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
7402 GTATCCCAGC
* * *
7412 TATTTCCGGCAGGATATGTAAGCAACG
1 TATTTCCGGCAGGATACGTAACCAACA
* * *
7439 TATTTCTGGCAGGATACGTACCCCACA
1 TATTTCCGGCAGGATACGTAACCAACA
7466 TATTTCCGGC
1 TATTTCCGGC
7476 GGGGTTCCTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (27 bp):
TATTTCCGGCAGGATACGTAACCAACA
Found at i:9057 original size:82 final size:82
Alignment explanation
Indices: 8920--9083 Score: 310
Period size: 82 Copynumber: 2.0 Consensus size: 82
8910 TTCTATCGCA
*
8920 TATGCAATGAAATAAAGTGGGTTTTAAACTGCTTCGTCTCCACCCTTTATGTGTTCATGCCATTG
1 TATGCAATGAAATAAAGTGGGTTTTAAACTGCTTCGTCTCCACCCTTTATGTGTTCACGCCATTG
8985 ATTCCTTCAATAAGAAC
66 ATTCCTTCAATAAGAAC
*
9002 TATGCAATGAAATGAAGTGGGTTTTAAACTGCTTCGTCTCCACCCTTTATGTGTTCACGCCATTG
1 TATGCAATGAAATAAAGTGGGTTTTAAACTGCTTCGTCTCCACCCTTTATGTGTTCACGCCATTG
9067 ATTCCTTCAATAAGAAC
66 ATTCCTTCAATAAGAAC
9084 AATGTAAGAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (82 bp):
TATGCAATGAAATAAAGTGGGTTTTAAACTGCTTCGTCTCCACCCTTTATGTGTTCACGCCATTG
ATTCCTTCAATAAGAAC
Found at i:14204 original size:24 final size:22
Alignment explanation
Indices: 14177--14221 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
14167 CCCACTTCTA
14177 ATGGTGAGCATTCTACCTCATTTG
1 ATGGTGAGCATTCT-CC-CATTTG
*
14201 ATGGTGAGTATTCTCCCATTT
1 ATGGTGAGCATTCTCCCATTT
14222 TTTATGGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 2 0.10
24 13 0.65
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (22 bp):
ATGGTGAGCATTCTCCCATTTG
Found at i:14393 original size:19 final size:19
Alignment explanation
Indices: 14369--14407 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
14359 TTCGCGGTCA
14369 TTGGGAGCGTACTACCGCT
1 TTGGGAGCGTACTACCGCT
14388 TTGGGAGCGTACTACCGCT
1 TTGGGAGCGTACTACCGCT
14407 T
1 T
14408 CGCGGTCATT
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:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (19 bp):
TTGGGAGCGTACTACCGCT
Found at i:14501 original size:27 final size:27
Alignment explanation
Indices: 14427--14501 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 27
14417 TGGGCGCACT
* *
14427 CCCTCTTTCGATGGTGGGCGCACGACG
1 CCCTCTTCCGATGGTGGGCGTACGACG
* * *** *
14454 TCCTCTCCCGACAATGGGCGTACGGCG
1 CCCTCTTCCGATGGTGGGCGTACGACG
*
14481 CCCTCTTGCGATGGTGGGCGT
1 CCCTCTTCCGATGGTGGGCGT
14502 GTGGCGCTTT
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.11, C:0.33, G:0.33, T:0.23
Consensus pattern (27 bp):
CCCTCTTCCGATGGTGGGCGTACGACG
Found at i:14595 original size:26 final size:26
Alignment explanation
Indices: 14556--14719 Score: 157
Period size: 28 Copynumber: 5.9 Consensus size: 26
14546 GATGGTTGGC
* *
14556 GTACGGCGCCCTCTTCGAAGATGGAT
1 GTACGGCGCTCTCTTCCAAGATGGAT
*
14582 GTACGGTGCTCTCTTCCAAGATGGCGGAT
1 GTACGGCGCTCTCTTCCAAGAT---GGAT
* *
14611 GTACGACGCTCTCTTGCAAGATGGCGGAT
1 GTACGGCGCTCTCTTCCAAGAT---GGAT
14640 GTACGGCGCTCTCTTCCAAGATGTGGAT
1 GTACGGCGCTCTCTTCCAAGA--TGGAT
**
14668 GTATAGCGCTCTCTTCCAAGATGTGGAT
1 GTACGGCGCTCTCTTCCAAGA--TGGAT
* *
14696 GTATGGCGCTCTTTTCCAAGATGG
1 GTACGGCGCTCTCTTCCAAGATGG
14720 TGGATGTACA
Statistics
Matches: 121, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
26 22 0.18
28 49 0.40
29 49 0.40
31 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (26 bp):
GTACGGCGCTCTCTTCCAAGATGGAT
Found at i:14676 original size:28 final size:29
Alignment explanation
Indices: 14540--14727 Score: 199
Period size: 29 Copynumber: 6.7 Consensus size: 29
14530 CGACACCCTT
* * *
14540 TTCCAAGATGGTTGG-CGTACGGCGCCCTC
1 TTCCAAGATGG-TGGATGTATGGCGCTCTC
* * *
14569 TTCGAAGA---TGGATGTACGGTGCTCTC
1 TTCCAAGATGGTGGATGTATGGCGCTCTC
* * *
14595 TTCCAAGATGGCGGATGTACGACGCTCTC
1 TTCCAAGATGGTGGATGTATGGCGCTCTC
* * *
14624 TTGCAAGATGGCGGATGTACGGCGCTCTC
1 TTCCAAGATGGTGGATGTATGGCGCTCTC
*
14653 TTCCAAGAT-GTGGATGTATAGCGCTCTC
1 TTCCAAGATGGTGGATGTATGGCGCTCTC
*
14681 TTCCAAGAT-GTGGATGTATGGCGCTCTT
1 TTCCAAGATGGTGGATGTATGGCGCTCTC
14709 TTCCAAGATGGTGGATGTA
1 TTCCAAGATGGTGGATGTA
14728 CAATGCTCTC
Statistics
Matches: 138, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
25 3 0.02
26 18 0.13
28 51 0.37
29 66 0.48
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (29 bp):
TTCCAAGATGGTGGATGTATGGCGCTCTC
Found at i:14899 original size:29 final size:29
Alignment explanation
Indices: 14860--15021 Score: 162
Period size: 29 Copynumber: 5.6 Consensus size: 29
14850 TTGCCATCTT
* ** * *
14860 GAGGGTGTACTACCACTTTATGAGCTTTA
1 GAGGGAGTACTACCACTTCGTGAACTTTG
* *
14889 GAGGGAGTACTACCACTTGGTGAACTTGG
1 GAGGGAGTACTACCACTTCGTGAACTTTG
**
14918 GAGGGAGTACTACCACTTCGTGGTCTTTG
1 GAGGGAGTACTACCACTTCGTGAACTTTG
* * *
14947 AAGGGAGTACTATCACTTCGGGAACTTTG
1 GAGGGAGTACTACCACTTCGTGAACTTTG
* * **
14976 GAGGGAGTACTACCACCTCTTGCTCTTTG
1 GAGGGAGTACTACCACTTCGTGAACTTTG
*
15005 GGGGGATGTACTACCAC
1 GAGGGA-GTACTACCAC
15022 CCTTTTTTTT
Statistics
Matches: 109, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
29 99 0.91
30 10 0.09
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (29 bp):
GAGGGAGTACTACCACTTCGTGAACTTTG
Found at i:15679 original size:28 final size:28
Alignment explanation
Indices: 15642--15801 Score: 202
Period size: 28 Copynumber: 5.8 Consensus size: 28
15632 ATTTGGACTC
* *
15642 TATCTTGGCTGTATGCCTTTGGAAATCT
1 TATCTAGGCTGTATGCCTTTGGAAATTT
15670 TATCTAGGCTGTATGCCTTTGGAAATTT
1 TATCTAGGCTGTATGCCTTTGGAAATTT
* * *
15698 T-TGTATGGCCGTATGCC-TTGAGGAATTT
1 TATCTA-GGCTGTATGCCTTTG-GAAATTT
* *
15726 TATCTAGGCTGTATGCCTTTAGAGATTT
1 TATCTAGGCTGTATGCCTTTGGAAATTT
*
15754 TATCT--GCTGCATGCCTTTGGAAATTT
1 TATCTAGGCTGTATGCCTTTGGAAATTT
15780 TATCTAGGCTGTATGCCTTTGG
1 TATCTAGGCTGTATGCCTTTGG
15802 GGTAGGCTGT
Statistics
Matches: 112, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
26 23 0.21
27 6 0.05
28 78 0.70
29 5 0.04
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (28 bp):
TATCTAGGCTGTATGCCTTTGGAAATTT
Found at i:15809 original size:20 final size:20
Alignment explanation
Indices: 15784--15823 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
15774 AAATTTTATC
15784 TAGGCTGTATGCCTTTGGGG
1 TAGGCTGTATGCCTTTGGGG
15804 TAGGCTGTATGCCTTTGGGG
1 TAGGCTGTATGCCTTTGGGG
15824 GTTGCCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.40, T:0.35
Consensus pattern (20 bp):
TAGGCTGTATGCCTTTGGGG
Found at i:15945 original size:58 final size:58
Alignment explanation
Indices: 15878--16034 Score: 190
Period size: 58 Copynumber: 2.7 Consensus size: 58
15868 TCTCGCACGT
* * * * * * *
15878 GTGGAGGATGCCCATTGGGACGTGTGATCGAGGGTTGCTCGGTCTT-CTTATTGCATGA
1 GTGGGGGATGCCCACTGGGACATGTGACCGAGGGATGCTCGCT-TTACTTATTACATGA
*
15936 GTGGGGGATGCCCACTGGGTCATGTGACCGAGGGATGCTCGCTTTACTTATTACATGA
1 GTGGGGGATGCCCACTGGGACATGTGACCGAGGGATGCTCGCTTTACTTATTACATGA
* * * *
15994 GTGGGGGATGCCCGCTTGGCCATGCGACCGAGGGATGCTCG
1 GTGGGGGATGCCCACTGGGACATGTGACCGAGGGATGCTCG
16035 ATCGTTATTG
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
57 2 0.02
58 84 0.98
ACGTcount: A:0.16, C:0.21, G:0.37, T:0.26
Consensus pattern (58 bp):
GTGGGGGATGCCCACTGGGACATGTGACCGAGGGATGCTCGCTTTACTTATTACATGA
Found at i:19605 original size:16 final size:17
Alignment explanation
Indices: 19584--19621 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
19574 GCACAAAGAG
19584 ATAAAAT-AATGAA-TAA
1 ATAAAATAAAT-AACTAA
19600 ATAAAATAAATAACTAA
1 ATAAAATAAATAACTAA
19617 ATAAA
1 ATAAA
19622 TAAGAAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAAATAAATAACTAA
Found at i:19654 original size:22 final size:21
Alignment explanation
Indices: 19615--19655 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
19605 ATAAATAACT
* *
19615 AAATAAATAAGAAGTGAAATG
1 AAATAAACAAGAAATGAAATG
19636 AAATAAAGCAAGAAATGAAA
1 AAATAAA-CAAGAAATGAAA
19656 GGAGCACCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.66, C:0.02, G:0.17, T:0.15
Consensus pattern (21 bp):
AAATAAACAAGAAATGAAATG
Found at i:25920 original size:70 final size:70
Alignment explanation
Indices: 25807--25943 Score: 274
Period size: 70 Copynumber: 2.0 Consensus size: 70
25797 TGATCTAGTA
25807 GCTCCCAAGTTTCCCCAATCTCATATCTAATCATCTGTAGGCAAGTCAAAGTAAGTCTGGGTGAG
1 GCTCCCAAGTTTCCCCAATCTCATATCTAATCATCTGTAGGCAAGTCAAAGTAAGTCTGGGTGAG
25872 CATGT
66 CATGT
25877 GCTCCCAAGTTTCCCCAATCTCATATCTAATCATCTGTAGGCAAGTCAAAGTAAGTCTGGGTGAG
1 GCTCCCAAGTTTCCCCAATCTCATATCTAATCATCTGTAGGCAAGTCAAAGTAAGTCTGGGTGAG
25942 CA
66 CA
25944 ACACATGCTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (70 bp):
GCTCCCAAGTTTCCCCAATCTCATATCTAATCATCTGTAGGCAAGTCAAAGTAAGTCTGGGTGAG
CATGT
Found at i:26400 original size:34 final size:34
Alignment explanation
Indices: 26357--26691 Score: 556
Period size: 34 Copynumber: 10.0 Consensus size: 34
26347 TAGTAGGGCC
* *
26357 GTCTTCCAGTTATTATCACAACCCACTGGACAGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
* *
26391 GTCTTCCAGTTATTATCACCACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
26425 GTC-TCCAGTTATTATCTCAACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
26458 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
26492 GTC-TCCAGTTATTATCTCAACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
*
26525 GTCTTCCAGTTATTATCACAACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
*
26559 GTC-TCCAGTTATTATTTCAACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
*
26592 GTCTTCCAGTTATTATCACAACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
26626 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
*
26660 GTCTTCCAATTATTA--T-AACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
26691 G
1 G
26692 CCGATAAAAC
Statistics
Matches: 287, Mismatches: 11, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
31 16 0.06
32 1 0.00
33 95 0.33
34 175 0.61
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (34 bp):
GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
Found at i:26469 original size:67 final size:67
Alignment explanation
Indices: 26361--26691 Score: 578
Period size: 67 Copynumber: 5.0 Consensus size: 67
26351 AGGGCCGTCT
* * *
26361 TCCAGTTATTATCACAACCCACTGGACAGGGTCTTCCAGTTATTATCACCACCCACTGGGCAGGG
1 TCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGGG
26426 TC
66 TC
*
26428 TCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCTCAACCCACTGGGCAGGG
1 TCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGGG
26493 TC
66 TC
26495 TCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGGG
1 TCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGGG
26560 TC
66 TC
*
26562 TCCAGTTATTATTTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGGG
1 TCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGGG
26627 TC
66 TC
*
26629 TTCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAATTATTAT---AACCCACTGGGCAGG
1 -TCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGG
26691 G
65 G
26692 CCGATAAAAC
Statistics
Matches: 255, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
65 16 0.06
67 195 0.76
68 44 0.17
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (67 bp):
TCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGGG
TC
Found at i:26533 original size:101 final size:102
Alignment explanation
Indices: 26357--26691 Score: 565
Period size: 101 Copynumber: 3.3 Consensus size: 102
26347 TAGTAGGGCC
* * *
26357 GTCTTCCAGTTATTATCACAACCCACTGGACAGGGTCTTCCAGTTATTATCACCACCCACTGGGC
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGC
26422 AGGGTC-TCCAGTTATTATCTCAACCCACTGGGCAGG
66 AGGGTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
*
26458 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGGGTC-TCCAGTTATTATCTCAACCCACTGGGC
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGC
*
26522 AGGGTCTTCCAGTTATTATCACAACCCACTGGGCAGG
66 AGGGTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
*
26559 GTC-TCCAGTTATTATTTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGC
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGC
26623 AGGGTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
66 AGGGTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
*
26660 GTCTTCCAATTATTA--T-AACCCACTGGGCAGGG
1 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGGG
26692 CCGATAAAAC
Statistics
Matches: 222, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
99 16 0.07
100 64 0.29
101 132 0.59
102 10 0.05
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (102 bp):
GTCTTCCAGTTATTATCTCAACCCACTGGGCAGGGTCTTCCAGTTATTATCACAACCCACTGGGC
AGGGTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
Found at i:33667 original size:201 final size:201
Alignment explanation
Indices: 33322--34303 Score: 1552
Period size: 201 Copynumber: 4.9 Consensus size: 201
33312 ATGCTTCCAT
* *
33322 AAAATTTATATAATACACCATCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
*
33387 GTTGACATGTGTACCCTTAGGGAGTATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
66 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
* *
33452 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATTATATAACAATCC
131 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTATATAATAATCC
33517 TATAAG
196 TATAAG
* * *
33523 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCATACTACACGTGCGGAGTTTAACTTTAAGG
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
* *
33588 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAGTATTTAATTATGAAATAGGGTATG
66 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
*
33653 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
131 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTATATAATAATCC
33718 TATAAG
196 TATAAG
* * *
33724 AAAATTTATACAATACAACGTTAGTGGAGTTTAGCAGATTGCACGTGCGGGGTTTAAC-TTAAGG
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
*
33788 GTTGACATGTGTACCCTTAGGG---A-GTA-T-GTATT-AATATTTAATTATGAAATGGGGTATG
66 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
* * * * *
33846 TGTTAACTTCTTAACCTGCTTATGGAGTCCAAAATTTACACTGACAGTGTCTTGTATAATATTTC
131 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTATATAATAATCC
33911 TATAAG
196 TATAAG
* * * * * *
33917 AAAAATTATACAATATACCGTCAATGGAGTTTAGCAGACTGCACGTGCGGGGTTCAATTTTAAAG
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
* * **
33982 GTTGACAAGTGTA-CCTTCTGGGAATATGTATTAATATTAAATATTTAATTATGAAATAAGGTAT
66 GTTGACATGTGTACCCTT-AGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTAT
*
34046 GTGTTAACTTCTTAACCCGCTTATGGAGTTCAAAATTTACACTGACAGTGTATTATATAATAATC
130 GTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTATATAATAATC
34111 CTATAAG
195 CTATAAG
* * * *
34118 AAAATTTATACAATATACCGTCAGTGGAGTTTAGCAGATTGCATGTGCGGGGTTTAACTTTAAGA
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
* *
34183 GTTAACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGTATG
66 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
34248 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTA-TATAT
131 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTATAT
34304 TACACCGTCA
Statistics
Matches: 714, Mismatches: 57, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
193 145 0.20
194 24 0.03
195 1 0.00
196 3 0.00
197 2 0.00
198 3 0.00
199 1 0.00
200 37 0.05
201 494 0.69
202 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (201 bp):
AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTATATAATAATCC
TATAAG
Found at i:34058 original size:394 final size:396
Alignment explanation
Indices: 33322--34657 Score: 1935
Period size: 394 Copynumber: 3.4 Consensus size: 396
33312 ATGCTTCCAT
* *
33322 AAAATTTATATAATACACCATCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
33387 GTTGACATGTGTACCCTTAGGGAGTATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
66 GTTGACATGTGTACCCTTAGGGA--ATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
* * *
33452 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATTATATAACAATCC
129 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGT-TTGTATAA-TAT-C
* * * *
33517 TATAAGAAAATTTATACAATACACCGTCAGTGGAGTTTAGCATACTACACGTGCGGAGTTTAACT
191 TATAAGAAAAATTATACAATA-ACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACT
* *
33582 TTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAGTATTTAATTATGAAATAG
255 TTAAGGGTTGACATGTGTACCCTTCGGGAATATGTATTAATATTAAATATTTAATTATGAAATAG
33647 GGTATGTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAA
320 GGTATGTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAA
33712 TAATCCTATAAG
385 TAATCCTATAAG
* * *
33724 AAAATTTATACAATACAACGTTAGTGGAGTTTAGCAGATTGCACGTGCGGGGTTTAAC-TTAAGG
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
*
33788 GTTGACATGTGTACCCTTAGGG-A-GTA-T-GTATT-AATATTTAATTATGAAATGGGGTATGTG
66 GTTGACATGTGTACCCTTAGGGAATGTATTAATATTAAATATTTAATTATGAAATGGGGTATGTG
*
33848 TTAACTTCTTAACCTGCTTATGGAGTCCAAAATTTACACTGACAGTGTCTTGTATAATATTTCTA
131 TTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGT-TTGTATAATA--TCTA
* * *
33913 TAAGAAAAATTATACAATATACCGTCAATGGAGTTTAGCAGACTGCACGTGCGGGGTTCAATTTT
193 TAAGAAAAATTATACAATA-ACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTT
* * *
33978 AAAGGTTGACAAGTGTA-CCTTCTGGGAATATGTATTAATATTAAATATTTAATTATGAAATAAG
257 AAGGGTTGACATGTGTACCCTTC-GGGAATATGTATTAATATTAAATATTTAATTATGAAATAGG
* *
34042 GTATGTGTTAACTTCTTAACCCGCTTATGGAGTTCAAAATTTACACTGACAGTGTATTATATAAT
321 GTATGTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAAT
34107 AATCCTATAAG
386 AATCCTATAAG
* * * *
34118 AAAATTTATACAATATACCGTCAGTGGAGTTTAGCAGATTGCATGTGCGGGGTTTAACTTTAAGA
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
* *
34183 GTTAACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGTATG
66 GTTGACATGTGTACCCTTAGGG-A-ATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
34248 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACA--G--TG-----TA--TAT
129 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTTTGTATAATATCTAT
*
34302 -------A-T-TAC----ACCGTCAGTGGAGTTTAACAGACTGCACGTGCGGGGTTTAACTTTAA
194 AAGAAAAATTATACAATAACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAA
* * * *
34354 GGGTTGACATGTTTACCCTTAC-GGAGTATGTATTAATATTAAATATTTAATTATGAAATGGGGA
259 GGGTTGACATGTGTACCCTT-CGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGT
34418 ATGTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAA
323 ATGTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAA
34483 TCCTATAAG
388 TCCTATAAG
* *
34492 AAAATTTATACGATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
34557 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGATAT
66 GTTGACATGTGTACCCTTAGGG-A-ATGTATTAATATTAAATATTTAATTATGAAATGGGG-TAT
* * *
34622 GTGTCAACTTCTTAACCCGTTTGTGGAGTCCAAAAT
128 GTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAAT
Statistics
Matches: 861, Mismatches: 59, Indels: 55
0.88 0.06 0.06
Matches are distributed among these distances:
374 283 0.33
375 40 0.05
376 1 0.00
379 3 0.00
380 1 0.00
381 1 0.00
388 3 0.00
392 2 0.00
393 5 0.01
394 323 0.38
395 31 0.04
396 1 0.00
397 5 0.01
398 2 0.00
399 3 0.00
400 2 0.00
401 32 0.04
402 123 0.14
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (396 bp):
AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
GTTGACATGTGTACCCTTAGGGAATGTATTAATATTAAATATTTAATTATGAAATGGGGTATGTG
TTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTTTGTATAATATCTATAA
GAAAAATTATACAATAACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
GTTGACATGTGTACCCTTCGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGTATG
TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
TATAAG
Found at i:34424 original size:173 final size:173
Alignment explanation
Indices: 34134--34472 Score: 588
Period size: 173 Copynumber: 2.0 Consensus size: 173
34124 TATACAATAT
* * *
34134 ACCGTCAGTGGAGTTTAGCAGATTGCATGTGCGGGGTTTAACTTTAAGAGTTAACATGTGTACCC
1 ACCGTCAGTGGAGTTTAACAGACTGCACGTGCGGGGTTTAACTTTAAGAGTTAACATGTGTACCC
* *
34199 TTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGTATGTGTTAACTTCTTAACC
66 TTACGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGAATGTGTTAACTTCTTAACC
34264 CGCTTATGGAGTCCAAAATTTACACTGACAGTGTATATATTAC
131 CGCTTATGGAGTCCAAAATTTACACTGACAGTGTATATATTAC
* * *
34307 ACCGTCAGTGGAGTTTAACAGACTGCACGTGCGGGGTTTAACTTTAAGGGTTGACATGTTTACCC
1 ACCGTCAGTGGAGTTTAACAGACTGCACGTGCGGGGTTTAACTTTAAGAGTTAACATGTGTACCC
* *
34372 TTACGGAGTATGTATTAATATTAAATATTTAATTATGAAATGGGGAATGTGTTAACTTCTTAACC
66 TTACGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGAATGTGTTAACTTCTTAACC
34437 CGCTTATGGAGTCCAAAATTTACACTGACAGTGTAT
131 CGCTTATGGAGTCCAAAATTTACACTGACAGTGTAT
34473 TGTATAATAA
Statistics
Matches: 156, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
173 156 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (173 bp):
ACCGTCAGTGGAGTTTAACAGACTGCACGTGCGGGGTTTAACTTTAAGAGTTAACATGTGTACCC
TTACGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGAATGTGTTAACTTCTTAACC
CGCTTATGGAGTCCAAAATTTACACTGACAGTGTATATATTAC
Done.