Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014987.1 Corchorus capsularis cultivar CVL-1 contig15008, 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: 83042
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:19033 original size:9 final size:8
Alignment explanation
Indices: 19003--19031 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
18993 CTGTTTTTGC
19003 TTTTTGTT
1 TTTTTGTT
19011 TTTTTGTT
1 TTTTTGTT
19019 TTTTTGTT
1 TTTTTGTT
19027 TTTTT
1 TTTTT
19032 TGGCAAGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (8 bp):
TTTTTGTT
Found at i:19481 original size:54 final size:54
Alignment explanation
Indices: 19420--19524 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
19410 GAGAATTTTC
* *
19420 ATCTCATCATCTAACTCACAAACAGTTTTAGGAAGCAAATTTGCATAAAAATTA
1 ATCTCATCATCTAACTCACAAACAGTTTTAGGAAGCAAATCTACATAAAAATTA
* * *
19474 ATCTCATCATCTAACTCACGAACGGTTTTAGGAAGCGAATCTACATAAAAA
1 ATCTCATCATCTAACTCACAAACAGTTTTAGGAAGCAAATCTACATAAAAA
19525 GTTACCTTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (54 bp):
ATCTCATCATCTAACTCACAAACAGTTTTAGGAAGCAAATCTACATAAAAATTA
Found at i:20344 original size:60 final size:60
Alignment explanation
Indices: 20257--20415 Score: 241
Period size: 60 Copynumber: 2.6 Consensus size: 60
20247 GTTAATTGCT
* * * *
20257 CAAATAAGAGCCTAATGTT-TGCCAAAATGCTCAAATAAGAG-CTCAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGAGTC-CAATCTTTTAATTTGAC
*
20317 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGAGTCCGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGAGTCCAATCTTTTAATTTGAC
20377 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAG
20416 GGCCTGGTGT
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
60 90 0.98
61 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGAGTCCAATCTTTTAATTTGAC
Found at i:20355 original size:31 final size:31
Alignment explanation
Indices: 20317--20420 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
20307 TTAATTTGGC
20317 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * * **
20348 CAAATAAGAGTCCGATC-TT-T-TAATTTGAC-
1 CAAATAAG-GGCCTAACGTTATCGAAAATG-CT
20377 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
20408 CAAATAAGGGCCT
1 CAAATAAGGGCCT
20421 GGTGTCAGTT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
28 5 0.09
29 14 0.25
30 4 0.07
31 27 0.49
32 5 0.09
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:20483 original size:31 final size:30
Alignment explanation
Indices: 20448--20551 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 30
20438 CGCGTGAGAC
20448 AGACCCTTATTTGAGCATTTTGACAAACGTT
1 AGACCCTTATTTGAGCATTTTGACAAA-GTT
** *
20479 AGACCCTTATTTG-GCCAAATT--CAAAGATG
1 AGACCCTTATTTGAG-CATTTTGACAAAG-TT
*
20508 AGGCCCTTATTTGAGCATTTTGACAAATGTT
1 AGACCCTTATTTGAGCATTTTGACAAA-GTT
*
20539 AGGCCCTTATTTG
1 AGACCCTTATTTG
20552 GCTAAATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
28 1 0.02
29 21 0.35
30 2 0.03
31 35 0.58
32 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (30 bp):
AGACCCTTATTTGAGCATTTTGACAAAGTT
Found at i:20515 original size:29 final size:29
Alignment explanation
Indices: 20482--20580 Score: 87
Period size: 29 Copynumber: 3.3 Consensus size: 29
20472 AAACGTTAGA
20482 CCCTTATTTGGCCAAATTCAAAGATGAGG
1 CCCTTATTTGGCCAAATTCAAAGATGAGG
** *
20511 CCCTTATTTGAG-CATTTTGACAAATG-TTAGG
1 CCCTTATTTG-GCCAAATT--CAAA-GATGAGG
* *
20542 CCCTTATTTGGCTAAATTAAAAGATCG-GG
1 CCCTTATTTGGCCAAATTCAAAGAT-GAGG
20571 CCCTTATTTG
1 CCCTTATTTG
20581 AGCATTTTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
28 1 0.02
29 30 0.55
30 2 0.04
31 21 0.38
32 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTCAAAGATGAGG
Found at i:20524 original size:60 final size:59
Alignment explanation
Indices: 20451--20611 Score: 227
Period size: 60 Copynumber: 2.7 Consensus size: 59
20441 GTGAGACAGA
*
20451 CCCTTATTTGAGCATTTTGACAAACGTTAGACCCTTATTTGGCCAAATTCAAAGAT-GAGG
1 CCCTTATTTGAGCATTTTGACAAACGTTAG-CCCTTATTTGGCCAAATTAAAAGATCG-GG
* *
20511 CCCTTATTTGAGCATTTTGACAAATGTTAGGCCCTTATTTGGCTAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTGACAAACGTTA-GCCCTTATTTGGCCAAATTAAAAGATCGGG
*
20571 CCCTTATTTGAGCATTTTGGA-AAACATTATGCCCTTATTTG
1 CCCTTATTTGAGCATTTT-GACAAACGTTA-GCCCTTATTTG
20612 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
60 88 0.96
61 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (59 bp):
CCCTTATTTGAGCATTTTGACAAACGTTAGCCCTTATTTGGCCAAATTAAAAGATCGGG
Found at i:25049 original size:50 final size:50
Alignment explanation
Indices: 24974--25074 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
24964 ATGGTGTAAG
24974 TAGGAATTGTATTAGTAGAAATAATCATATTAGCAATGCATTTGCTTGTT
1 TAGGAATTGTATTAGTAGAAATAATCATATTAGCAATGCATTTGCTTGTT
25024 TAGGAATTGTATTAGTAGAAATAATCATATTAGCAATGCATTTGCTTGTT
1 TAGGAATTGTATTAGTAGAAATAATCATATTAGCAATGCATTTGCTTGTT
25074 T
1 T
25075 TTACTTCCGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.41
Consensus pattern (50 bp):
TAGGAATTGTATTAGTAGAAATAATCATATTAGCAATGCATTTGCTTGTT
Found at i:29031 original size:2 final size:2
Alignment explanation
Indices: 29024--29049 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29014 ACAAATTGTA
29024 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29050 CCCCTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34022 original size:23 final size:24
Alignment explanation
Indices: 33975--34024 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
33965 AACCACGGAG
* *
33975 AATATTTTCATCTGTATAGTAACA
1 AATATTTTCATCGGTACAGTAACA
33999 AATATTTT-ATCGGTACAGTAACA
1 AATATTTTCATCGGTACAGTAACA
34022 AAT
1 AAT
34025 CTAACACGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (24 bp):
AATATTTTCATCGGTACAGTAACA
Found at i:34123 original size:17 final size:17
Alignment explanation
Indices: 34101--34135 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
34091 TTCCGGTGAA
34101 AAAAAAAAAAACAGAAC
1 AAAAAAAAAAACAGAAC
34118 AAAAAAAAAAACAGAAC
1 AAAAAAAAAAACAGAAC
34135 A
1 A
34136 CGTAGTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAACAGAAC
Found at i:41965 original size:1 final size:1
Alignment explanation
Indices: 41959--42001 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
41949 ACTACTAAGT
* * *
41959 AAAAAAAAAAAAAAGAAAAAAAAAGAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
42002 GGGTACTAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:41977 original size:9 final size:9
Alignment explanation
Indices: 41959--42000 Score: 68
Period size: 9 Copynumber: 4.7 Consensus size: 9
41949 ACTACTAAGT
41959 AAAAAA-AA
1 AAAAAAGAA
41967 AAAAAAGAAA
1 AAAAAAG-AA
41977 AAAAAAGAA
1 AAAAAAGAA
41986 AAAAAAGAA
1 AAAAAAGAA
41995 AAAAAA
1 AAAAAA
42001 AGGGTACTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 6 0.19
9 17 0.53
10 9 0.28
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:41977 original size:10 final size:10
Alignment explanation
Indices: 41959--42002 Score: 74
Period size: 10 Copynumber: 4.6 Consensus size: 10
41949 ACTACTAAGT
41959 AAAAA-AAAA
1 AAAAAGAAAA
41968 AAAAAGAAAA
1 AAAAAGAAAA
41978 AAAAAG-AAA
1 AAAAAGAAAA
41987 AAAAAGAAAA
1 AAAAAGAAAA
41997 AAAAAG
1 AAAAAG
42003 GGTACTAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.42
10 19 0.58
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:41987 original size:19 final size:19
Alignment explanation
Indices: 41959--42002 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
41949 ACTACTAAGT
41959 AAAAAA-AAAAAAAAGAAA
1 AAAAAAGAAAAAAAAGAAA
41977 AAAAAAGAAAAAAAAGAAA
1 AAAAAAGAAAAAAAAGAAA
41996 AAAAAAG
1 AAAAAAG
42003 GGTACTAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAAAAAGAAA
Found at i:53121 original size:3 final size:3
Alignment explanation
Indices: 53113--53139 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53103 CTTTTTCCAT
53113 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
53140 AAGAAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:60907 original size:11 final size:11
Alignment explanation
Indices: 60883--60917 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
60873 TTGACAGCGC
60883 AACAAAAACAA
1 AACAAAAACAA
* *
60894 AACGAAAACGA
1 AACAAAAACAA
60905 AACAAAAACAA
1 AACAAAAACAA
60916 AA
1 AA
60918 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:65916 original size:2 final size:2
Alignment explanation
Indices: 65909--65944 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
65899 GGTAAATCGA
65909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65945 CAAGTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68769 original size:15 final size:15
Alignment explanation
Indices: 68749--68805 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
68739 GTGAGTTTTC
68749 TTTGTAATTTATTTG
1 TTTGTAATTTATTTG
* *
68764 TTTGT-A-TGAGTTTTC
1 TTTGTAATTTA--TTTG
68779 TTTGTAATTTATTTG
1 TTTGTAATTTATTTG
68794 TTTGTATATTTA
1 TTTGTA-ATTTA
68806 GTATATTGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
13 2 0.06
14 1 0.03
15 22 0.67
16 6 0.18
17 2 0.06
ACGTcount: A:0.19, C:0.02, G:0.14, T:0.65
Consensus pattern (15 bp):
TTTGTAATTTATTTG
Found at i:68776 original size:30 final size:30
Alignment explanation
Indices: 68740--68800 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
68730 TCATGGAATG
68740 TGAGTTTTCTTTGTAATTTATTTGTTTGTA
1 TGAGTTTTCTTTGTAATTTATTTGTTTGTA
68770 TGAGTTTTCTTTGTAATTTATTTGTTTGTA
1 TGAGTTTTCTTTGTAATTTATTTGTTTGTA
68800 T
1 T
68801 ATTTAGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.03, G:0.16, T:0.64
Consensus pattern (30 bp):
TGAGTTTTCTTTGTAATTTATTTGTTTGTA
Found at i:68871 original size:2 final size:2
Alignment explanation
Indices: 68864--68890 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
68854 ATTTATGTAA
68864 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 A
68891 CACACATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68995 original size:24 final size:24
Alignment explanation
Indices: 68941--68996 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
68931 CTGAACGCGT
*
68941 TTAAA-TAAAAAAAATTGAAATAA
1 TTAAATTAAAAAAAATTGAAAGAA
68964 TTGAAATTAATAAAAAATT-AAAGAA
1 TT-AAATTAA-AAAAAATTGAAAGAA
68989 TTAAATTA
1 TTAAATTA
68997 TTATATTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.07
24 9 0.31
25 10 0.34
26 8 0.28
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (24 bp):
TTAAATTAAAAAAAATTGAAAGAA
Found at i:70528 original size:25 final size:26
Alignment explanation
Indices: 70485--70534 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
70475 GAAACTGTAG
*
70485 AAATTGAATTTTTCTAAATAAAATAA
1 AAATTGAAGTTTTCTAAATAAAATAA
70511 AAATTG-AGTTTTCTAAATAAAATA
1 AAATTGAAGTTTTCTAAATAAAATA
70535 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (26 bp):
AAATTGAAGTTTTCTAAATAAAATAA
Found at i:71709 original size:350 final size:351
Alignment explanation
Indices: 70949--72346 Score: 1919
Period size: 351 Copynumber: 4.0 Consensus size: 351
70939 ATTGTCAAGT
* * * * * * *
70949 CAGATGTCTTGAAATCTAAATTTGATACTT-TTAGACTTAATTTGTTACTGTAGAAGCCCAAAGA
1 CAGATGTCTTGAAATCTAAATCTGATA-TTCTTAAACCTAATTCGTTAATATGGAAGCCCAAAGA
* * * * * *
71013 AGGATTCCGAGTCCAATCAGTAATTATGATGAAGTAATTATTCAGCTCTGATGCAGCATTGTTAA
65 AGGAGTCCAAATCCAATCAGTAATTATGATGCAGTAATGATTCAGCGCTGATGCAGCATTGTTAA
* * * * * * **
71078 ATCCTATTCGAATGAGGAATTCACAAGAGCAGTTTTTGAAGAAAATTCATAATTTTTGATCCGAA
130 ATCCTATTCAAAAGAGGACTTCACAATAGCAGTTTTGGAAGAAAATTCATAACTTTTGATCTAAA
* * * *
71143 GTTCAGAAAAATACAAATGAGGTACCGTTTGAAAGAGAATTCCAAGATCTACAACTTTTATGTTT
195 GCTCAGAAAAATGCAAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTTT
* * ** * *
71208 GCCACGAGACCTAATTCTAGAGTTCCAGTGGACGATTTTGCCCTTGAAATTTTTGGACAGAATTG
260 ACCTCGAGACCTAATTCTTCAGTTCCGGTGGACGATTTTGCCCTTGAAATTTCTGGACAGAATTG
*
71273 ATCTTCTCCTGAACCGGCTTGGAGAGC
325 ATCTTCTCCTAAACCGGCTTGGAGAGC
* * * * * *
71300 CAGATGTCTTGGAGTCTGAATCTGATATTCTTAAACCCAATTCATTAATATGTAAGCCCAAAGAA
1 CAGATGTCTTGAAATCTAAATCTGATATTCTTAAACCTAATTCGTTAATATGGAAGCCCAAAGAA
* * * * * *
71365 GAAGTCCAAATCCAATTAGTAATTATGATGTAGTTATGATTCAGAC-CTAATGCAGCATTTTTAA
66 GGAGTCCAAATCCAATCAGTAATTATGATGCAGTAATGATTCAG-CGCTGATGCAGCATTGTTAA
* *
71429 GTCCTATTCAAAAGAGGACTTCACAATAGCAGTTTTGGAAGAAAATTCATAACTTCTGATCTAAA
130 ATCCTATTCAAAAGAGGACTTCACAATAGCAGTTTTGGAAGAAAATTCATAACTTTTGATCTAAA
** ** ** * *
71494 GCTCAGATTAATGCAAATGAGGTACTATTGGAAAGAGGATTCCAAGATCTACATTTTTTAT-ATC
195 GCTCAGAAAAATGCAAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTTT
*
71558 ACCTCGAGACCTAATTCTAT-AGTTCCGGTGGACGATTTTGCCCTTGAAATTTTTGGACAGAATT
260 ACCTCGAGACCTAATTCT-TCAGTTCCGGTGGACGATTTTGCCCTTGAAATTTCTGGACAGAATT
*
71622 GATCTTCTCCTAAACTGGCTTGGAGAGC
324 GATCTTCTCCTAAACCGGCTTGGAGAGC
* *
71650 CAGAAGTCTTGAAGTCTAAATCTGATATTCTTAAACCTAATTCGTTAATATGGAAGCCCAAAGAA
1 CAGATGTCTTGAAATCTAAATCTGATATTCTTAAACCTAATTCGTTAATATGGAAGCCCAAAGAA
*
71715 GGAGTCCAAATCCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGATGCAGCATTGTTAAA
66 GGAGTCCAAATCCAATCAGTAATTATGATGCAGTAATGATTCAGCGCTGATGCAGCATTGTTAAA
** * * *
71780 TGTTATTCAAAAGAGGACTTCACAATAACAGTTTTGGAAGAAAATTCATAACTTTTTATCTAGAG
131 TCCTATTCAAAAGAGGACTTCACAATAGCAGTTTTGGAAGAAAATTCATAACTTTTGATCTAAAG
* * *
71845 CTCAAAAAAATGCAAATGAGGTACCGTTGGAAAGAAGATTCTAAGATCTACAACTTTTATGTTTA
196 CTCAGAAAAATGCAAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTTTA
71910 CCTCGAGACCTAATTCTTCAGTTCCGGTGGACGATTTTGCCCTTGAAATTTCTGGACAGAATTGA
261 CCTCGAGACCTAATTCTTCAGTTCCGGTGGACGATTTTGCCCTTGAAATTTCTGGACAGAATTGA
*
71975 TCTCCTCCTAAACCGGCTTGGAGAGC
326 TCTTCTCCTAAACCGGCTTGGAGAGC
* * **
72001 CAGATGTCTTGAAATCTAAATCTGATATTCTTAAA-CTCGATTCGTTAATATGGAAACTTAAAGA
1 CAGATGTCTTGAAATCTAAATCTGATATTCTTAAACCT-AATTCGTTAATATGGAAGCCCAAAGA
* * * * *
72065 AGGAGTCCAAATCCAATTAGTAATTATGATGCGGTAATGGTTCAGCGCTGATGTAGCATTGCTAA
65 AGGAGTCCAAATCCAATCAGTAATTATGATGCAGTAATGATTCAGCGCTGATGCAGCATTGTTAA
* * * * * *
72130 ATCCTATTCAAAAAAGAACTTC-CAAATAGCAGTTTTGGAAAAAAATTTATAACTTTTTATCTAG
130 ATCCTATTCAAAAGAGGACTTCAC-AATAGCAGTTTTGGAAGAAAATTCATAACTTTTGATCTAA
* *
72194 AGCTCAG-AAAATGCAAATGAGGTACCGTTGAAAAGAGGATTCGAAGATCTACAACTTTTATGTT
194 AGCTCAGAAAAATGCAAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTT
*
72258 TACCTCGAGACCTAATTCTTCAGTTCCGGTGGACGATTTTGCCCTTGAAATTTCAGGACAGAATT
259 TACCTCGAGACCTAATTCTTCAGTTCCGGTGGACGATTTTGCCCTTGAAATTTCTGGACAGAATT
*
72323 GATCTTCTCCTAAACCGACTTGGA
324 GATCTTCTCCTAAACCGGCTTGGA
72347 AAATGTTTTA
Statistics
Matches: 929, Mismatches: 110, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
349 1 0.00
350 457 0.49
351 470 0.51
352 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (351 bp):
CAGATGTCTTGAAATCTAAATCTGATATTCTTAAACCTAATTCGTTAATATGGAAGCCCAAAGAA
GGAGTCCAAATCCAATCAGTAATTATGATGCAGTAATGATTCAGCGCTGATGCAGCATTGTTAAA
TCCTATTCAAAAGAGGACTTCACAATAGCAGTTTTGGAAGAAAATTCATAACTTTTGATCTAAAG
CTCAGAAAAATGCAAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTTTA
CCTCGAGACCTAATTCTTCAGTTCCGGTGGACGATTTTGCCCTTGAAATTTCTGGACAGAATTGA
TCTTCTCCTAAACCGGCTTGGAGAGC
Found at i:72297 original size:701 final size:701
Alignment explanation
Indices: 70949--72346 Score: 1975
Period size: 701 Copynumber: 2.0 Consensus size: 701
70939 ATTGTCAAGT
* * * * * * *
70949 CAGATGTCTTGAAATCTAAATTTGATACTTTTAGACTTAATTTGTTACTGTAGAAGCCCAAAGAA
1 CAGAAGTCTTGAAATCTAAATCTGATACTTTTAAACCTAATTCGTTAATATAGAAGCCCAAAGAA
* * * * *
71014 GGATTCCGAGTCCAATCAGTAATTATGATGAAGTAATTATTCAGCTCTGATGCAGCATTGTTAAA
66 GGAGTCCAAATCCAATCAGTAATTATGATGAAGTAATGATTCAGCCCTGATGCAGCATTGTTAAA
* * * * *
71079 TCCTATTCGAATGAGGAATTCACAAGAGCAGTTTTTGAAGAAAATTCATAATTTTTGATCCGAAG
131 TCCTATTCAAAAGAGGAATTCACAAGAACAGTTTTGGAAGAAAATTCATAATTTTTGATCAGAAG
* * * *
71144 TTCAGAAAAATACAAATGAGGTACCGTTTGAAAGAGAATTCCAAGATCTACAACTTTTATGTTTG
196 CTCAAAAAAATACAAATGAGGTACCGTTGGAAAGAGAATTCCAAGATCTACAACTTTTATGTTTA
* *
71209 CCACGAGACCTAATTCTAGAGTTCCAGTGGACGATTTTGCCCTTGAAATTTTTGGACAGAATTGA
261 CCACGAGACCTAATTCTACAGTTCCAGTGGACGATTTTGCCCTTGAAATTTCTGGACAGAATTGA
* * * * *
71274 TCTTCTCCTGAACCGGCTTGGAGAGCCAGATGTCTTGGAGTCTGAATCTGATATTCTTAAACCCA
326 TCTCCTCCTAAACCGGCTTGGAGAGCCAGATGTCTTGAAATCTAAATCTGATATTCTTAAACCCA
* * * *
71339 ATTCATTAATATGTAAGCCCAAAGAAGAAGTCCAAATCCAATTAGTAATTATGATGTAGTTATGA
391 ATTCATTAATATGGAAACCCAAAGAAGAAGTCCAAATCCAATTAGTAATTATGATGCAGTAATGA
** * * *
71404 TTCAGACCTAATGCAGCATTTTTAAGTCCTATTCAAAAGAGGACTTCACAATAGCAGTTTTGGAA
456 TTCAGACCTAATGCAGCATTGCTAAATCCTATTCAAAAAAGAACTTCACAATAGCAGTTTTGGAA
* * * *
71469 GAAAATTCATAACTTCTGATCTAAAGCTCAGATTAATGCAAATGAGGTACTATTGGAAAGAGGAT
521 AAAAATTCATAACTTCTGATCTAAAGCTCAGATAAATGCAAATGAGGTACCATTGAAAAGAGGAT
**
71534 TCCAAGATCTACATTTTTTATATCACCTCGAGACCTAATTCTATAGTTCCGGTGGACGATTTTGC
586 TCCAAGATCTACAACTTTTATATCACCTCGAGACCTAATTCTATAGTTCCGGTGGACGATTTTGC
** * *
71599 CCTTGAAATTTTTGGACAGAATTGATCTTCTCCTAAACTGGCTTGGAGAGC
651 CCTTGAAATTTCAGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAGC
* *
71650 CAGAAGTCTTGAAGTCTAAATCTGATA-TTCTTAAACCTAATTCGTTAATATGGAAGCCCAAAGA
1 CAGAAGTCTTGAAATCTAAATCTGATACTT-TTAAACCTAATTCGTTAATATAGAAGCCCAAAGA
*
71714 AGGAGTCCAAATCCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGATGCAGCATTGTTAA
65 AGGAGTCCAAATCCAATCAGTAATTATGATGAAGTAATGATTCAGCCCTGATGCAGCATTGTTAA
** * *
71779 ATGTTATTCAAAAGAGGACTTCACAATAACAGTTTTGGAAGAAAATTCATAACTTTTT-ATCTAG
130 ATCCTATTCAAAAGAGGAATTCACAAGAACAGTTTTGGAAGAAAATTCATAA-TTTTTGATC-AG
* *
71843 -AGCTCAAAAAAATGCAAATGAGGTACCGTTGGAAAGA-AGATTCTAAGATCTACAACTTTTATG
193 AAGCTCAAAAAAATACAAATGAGGTACCGTTGGAAAGAGA-ATTCCAAGATCTACAACTTTTATG
* * *
71906 TTTACCTCGAGACCTAATTCTTCAGTTCCGGTGGACGATTTTGCCCTTGAAATTTCTGGACAGAA
257 TTTACCACGAGACCTAATTCTACAGTTCCAGTGGACGATTTTGCCCTTGAAATTTCTGGACAGAA
71971 TTGATCTCCTCCTAAACCGGCTTGGAGAGCCAGATGTCTTGAAATCTAAATCTGATATTCTTAAA
322 TTGATCTCCTCCTAAACCGGCTTGGAGAGCCAGATGTCTTGAAATCTAAATCTGATATTCTTAAA
* * * ** * *
72036 CTCGATTCGTTAATATGGAAACTTAAAGAAGGAGTCCAAATCCAATTAGTAATTATGATGCGGTA
387 CCCAATTCATTAATATGGAAACCCAAAGAAGAAGTCCAAATCCAATTAGTAATTATGATGCAGTA
* * *
72101 ATGGTTCAG-CGCTGATGTAGCATTGCTAAATCCTATTCAAAAAAGAACTTC-CAAATAGCAGTT
452 ATGATTCAGAC-CTAATGCAGCATTGCTAAATCCTATTCAAAAAAGAACTTCAC-AATAGCAGTT
* * * * *
72164 TTGGAAAAAAATTTATAACTTTTTATCTAGAGCTCAGA-AAATGCAAATGAGGTACCGTTGAAAA
515 TTGGAAAAAAATTCATAACTTCTGATCTAAAGCTCAGATAAATGCAAATGAGGTACCATTGAAAA
* * *
72228 GAGGATTCGAAGATCTACAACTTTTATGTTTACCTCGAGACCTAATTCT-TCAGTTCCGGTGGAC
580 GAGGATTCCAAGATCTACAACTTTTAT-ATCACCTCGAGACCTAATTCTAT-AGTTCCGGTGGAC
72292 GATTTTGCCCTTGAAATTTCAGGACAGAATTGATCTTCTCCTAAACCGACTTGGA
643 GATTTTGCCCTTGAAATTTCAGGACAGAATTGATCTTCTCCTAAACCGACTTGGA
72347 AAATGTTTTA
Statistics
Matches: 612, Mismatches: 77, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
700 52 0.08
701 554 0.91
702 6 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (701 bp):
CAGAAGTCTTGAAATCTAAATCTGATACTTTTAAACCTAATTCGTTAATATAGAAGCCCAAAGAA
GGAGTCCAAATCCAATCAGTAATTATGATGAAGTAATGATTCAGCCCTGATGCAGCATTGTTAAA
TCCTATTCAAAAGAGGAATTCACAAGAACAGTTTTGGAAGAAAATTCATAATTTTTGATCAGAAG
CTCAAAAAAATACAAATGAGGTACCGTTGGAAAGAGAATTCCAAGATCTACAACTTTTATGTTTA
CCACGAGACCTAATTCTACAGTTCCAGTGGACGATTTTGCCCTTGAAATTTCTGGACAGAATTGA
TCTCCTCCTAAACCGGCTTGGAGAGCCAGATGTCTTGAAATCTAAATCTGATATTCTTAAACCCA
ATTCATTAATATGGAAACCCAAAGAAGAAGTCCAAATCCAATTAGTAATTATGATGCAGTAATGA
TTCAGACCTAATGCAGCATTGCTAAATCCTATTCAAAAAAGAACTTCACAATAGCAGTTTTGGAA
AAAAATTCATAACTTCTGATCTAAAGCTCAGATAAATGCAAATGAGGTACCATTGAAAAGAGGAT
TCCAAGATCTACAACTTTTATATCACCTCGAGACCTAATTCTATAGTTCCGGTGGACGATTTTGC
CCTTGAAATTTCAGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAGC
Found at i:74951 original size:149 final size:149
Alignment explanation
Indices: 74681--74978 Score: 569
Period size: 149 Copynumber: 2.0 Consensus size: 149
74671 AAAGATAAAG
* *
74681 ATATACACTAAGTTTGAATGTGCATTTTCTAACTTTTTTGGGTTAAAATGTGTGTTAAGGACCAT
1 ATATACACTAAGTTTAAACGTGCATTTTCTAACTTTTTTGGGTTAAAATGTGTGTTAAGGACCAT
*
74746 TTCCCAAGTCTAGGAAGGTGTACATGGCGGTGGCCCAGCCATGAAGATGCAAATGGCCCATTTCA
66 TTCCCAAGTCTAGGAAGGTGTACATGGCGGTGGCCCAGCCACGAAGATGCAAATGGCCCATTTCA
74811 AAGCATTCTTTTCTTTTTC
131 AAGCATTCTTTTCTTTTTC
74830 ATATACACTAAGTTTAAACGTGCATTTTCTAACTTTTTTGGGTTAAAATGTGTGTTAAGGACCAT
1 ATATACACTAAGTTTAAACGTGCATTTTCTAACTTTTTTGGGTTAAAATGTGTGTTAAGGACCAT
74895 TTCCCAAGTCTAGGAAGGTGTACATGGCGGTGGCCCAGCCACGAAGATGCAAATGGCCCATTTCA
66 TTCCCAAGTCTAGGAAGGTGTACATGGCGGTGGCCCAGCCACGAAGATGCAAATGGCCCATTTCA
74960 AAGCATTCTTTTCTTTTTC
131 AAGCATTCTTTTCTTTTTC
74979 TTTTCCTCTT
Statistics
Matches: 146, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 146 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (149 bp):
ATATACACTAAGTTTAAACGTGCATTTTCTAACTTTTTTGGGTTAAAATGTGTGTTAAGGACCAT
TTCCCAAGTCTAGGAAGGTGTACATGGCGGTGGCCCAGCCACGAAGATGCAAATGGCCCATTTCA
AAGCATTCTTTTCTTTTTC
Found at i:80928 original size:21 final size:21
Alignment explanation
Indices: 80902--80947 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
80892 CTATGTTATT
80902 TTAGATCACATTGATCATTCA
1 TTAGATCACATTGATCATTCA
80923 TTAGATCACATTGATCATTCA
1 TTAGATCACATTGATCATTCA
80944 TTAG
1 TTAG
80948 TTTGGTAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (21 bp):
TTAGATCACATTGATCATTCA
Found at i:81246 original size:3 final size:3
Alignment explanation
Indices: 81238--81286 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
81228 ATATCAAAAT
* * *
81238 ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA AAA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
81286 A
1 A
81287 AATTTGTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:82350 original size:333 final size:334
Alignment explanation
Indices: 81796--82449 Score: 811
Period size: 331 Copynumber: 1.9 Consensus size: 334
81786 AAAAAAAAGC
* * * * ** *
81796 AAGGTTATTGAATTAGTTGTTAGTACTATACATCTTTTATGATCATTATAGGTTTTTTAATAACT
1 AAGGTCATTGAATTAGTTGATAGTACCATACATCTTTTATAAAAATTATAGGTTTTTCAATAACT
*
81861 TTTGAGAAAAAAAAAGGGTAAATATTCACCATTGATGAAAGTTTACTCATGTTATTAAGAATATA
66 TTTGAGAAAAAAAAAGGGTAAATATTCACCATTGATGAAA--TTACTAATG-T-TT---AATATA
* * *
81926 AGGATTAGTAAATACAATTTTAATTTACTTTTATAGCTTTTTTAGTAAACTTAAGTAATAAAATT
124 AGGATTAGTAAATACAATTTTAATTAACTTTTATAGCTGTTTCAGTAAACTTAAGTAATAAAATT
** * * * *
81991 GGTAACTTTTATTAATGATGAAAAGTTGCTAAACTTAATAAGAACGTGTAAGGTTATTTCAATCT
189 GGTAACTTCCATTAATGATGAAAAGTTACTAAAATTAATAAGAA--TGTAAGATTACTTCAATCT
* *
82056 AGATAGTACTATAAAGTTTTCCATAACCTTTATAACCTTTTAAGTAATCTTAGGTAAGAAAATCA
252 AGATAGAACTATAAAGTTTTCCATAACCTTTATAA-C-TTTAAGTAATCTTAGATAAGAAAATCA
82121 GTACTTTACCTTTATAATAT
315 GTACTTTACCTTTATAATAT
* * * *
82141 AAGGTCATTGAATTAGTTGATATTACCATACCTTTTTTATAAAAATTATAGGTTTTTCAGTAACT
1 AAGGTCATTGAATTAGTTGATAGTACCATACATCTTTTATAAAAATTATAGGTTTTTCAATAACT
* * *
82206 TTTGAG-AGAAAAAA-GGTAAATATTTACCATTGATG-AA-TACTAATG-TT-AT-TAAGGATTG
66 TTTGAGAAAAAAAAAGGGTAAATATTCACCATTGATGAAATTACTAATGTTTAATATAAGGATTA
* *
82264 GTAAATATAATTTTAA-TAACTTTTATAGGTGTTTCAGTAGATCACTTAAGTAATAAAATTGGTA
131 GTAAATACAATTTTAATTAACTTTTATAGCTGTTTCAGTA-A--ACTTAAGTAATAAAATTGGTA
* * * * *
82328 ACTTCCATTATTGATTAAAAGTTACTAAAATTAATAAGGATGTAAGATTACTTGAATGTAGATAG
193 ACTTCCATTAATGATGAAAAGTTACTAAAATTAATAAGAATGTAAGATTACTTCAATCTAGATAG
* *
82393 AACTGTAATGTTTTCCATAACCTTTATAACTTTAAGTAATCTTAGATAAGAAAATCA
258 AACTATAAAGTTTTCCATAACCTTTATAACTTTAAGTAATCTTAGATAAGAAAATCA
82450 ATAACCAATA
Statistics
Matches: 271, Mismatches: 35, Indels: 22
0.83 0.11 0.07
Matches are distributed among these distances:
329 26 0.10
330 20 0.07
331 71 0.26
332 2 0.01
333 54 0.20
336 2 0.01
339 7 0.03
342 2 0.01
343 20 0.07
344 7 0.03
345 60 0.22
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (334 bp):
AAGGTCATTGAATTAGTTGATAGTACCATACATCTTTTATAAAAATTATAGGTTTTTCAATAACT
TTTGAGAAAAAAAAAGGGTAAATATTCACCATTGATGAAATTACTAATGTTTAATATAAGGATTA
GTAAATACAATTTTAATTAACTTTTATAGCTGTTTCAGTAAACTTAAGTAATAAAATTGGTAACT
TCCATTAATGATGAAAAGTTACTAAAATTAATAAGAATGTAAGATTACTTCAATCTAGATAGAAC
TATAAAGTTTTCCATAACCTTTATAACTTTAAGTAATCTTAGATAAGAAAATCAGTACTTTACCT
TTATAATAT
Done.