Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014335.1 Corchorus capsularis cultivar CVL-1 contig14356, 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: 95591
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:366 original size:21 final size:20
Alignment explanation
Indices: 316--368 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
306 ACTAGCGCTG
316 GGCGCCCATGTGCTATGCTT
1 GGCGCCCATGTGCTATGCTT
336 GGCGCCCATGTGCTATGCTT
1 GGCGCCCATGTGCTATGCTT
356 GGCGCCCCATGTG
1 GGCG-CCCATGTG
369 GTTTGCCTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 24 0.75
21 8 0.25
ACGTcount: A:0.09, C:0.32, G:0.32, T:0.26
Consensus pattern (20 bp):
GGCGCCCATGTGCTATGCTT
Found at i:1519 original size:26 final size:26
Alignment explanation
Indices: 1481--1531 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1471 AGGACGGTAA
* *
1481 AAATAGAATTTTTCTAAATAAAATAG
1 AAATAGAAATTTTCTAAACAAAATAG
*
1507 AAATTGAAATTTTCTAAACAAAATA
1 AAATAGAAATTTTCTAAACAAAATA
1532 TATTTTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (26 bp):
AAATAGAAATTTTCTAAACAAAATAG
Found at i:2449 original size:20 final size:20
Alignment explanation
Indices: 2424--2463 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2414 ACGTAGAATA
2424 ACGTTAACGTGCTATATTTT
1 ACGTTAACGTGCTATATTTT
2444 ACGTTAACGTGCTATATTTT
1 ACGTTAACGTGCTATATTTT
2464 GATGACGTTT
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:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (20 bp):
ACGTTAACGTGCTATATTTT
Found at i:7146 original size:29 final size:29
Alignment explanation
Indices: 7068--7144 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
7058 GGCCCAAACT
* *
7068 AACACCTGGTCCTTCTTTTTGCATCAGCC
1 AACACCTGGCCCTTCTTTTTGCATCAACC
* *
7097 AACACCTGGCCCTTCTCTTTGTATCAACC
1 AACACCTGGCCCTTCTTTTTGCATCAACC
7126 AACACCTGGCCC-TCTTTTT
1 AACACCTGGCCCTTCTTTTT
7145 TGCAACACCT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 6 0.14
29 37 0.86
ACGTcount: A:0.18, C:0.36, G:0.12, T:0.34
Consensus pattern (29 bp):
AACACCTGGCCCTTCTTTTTGCATCAACC
Found at i:9308 original size:23 final size:23
Alignment explanation
Indices: 9278--9324 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
9268 GAGTTTTCTT
9278 AACTGTTTTTTTGTTACATTCAA
1 AACTGTTTTTTTGTTACATTCAA
9301 AACTGTTTTTTTGTTACATTCAA
1 AACTGTTTTTTTGTTACATTCAA
9324 A
1 A
9325 TCTCATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (23 bp):
AACTGTTTTTTTGTTACATTCAA
Found at i:11899 original size:36 final size:36
Alignment explanation
Indices: 11852--11922 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
11842 TCTCGATGAA
*
11852 TGTGTTAAATTTATGGGTGTTGATTGTGATGGTTTC
1 TGTGTTAAATTTATGGGTGTTCATTGTGATGGTTTC
*
11888 TGTGTTAAATTTATGGGTGTTCATTGTTATGGTTT
1 TGTGTTAAATTTATGGGTGTTCATTGTGATGGTTT
11923 ATAGCCTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.17, C:0.03, G:0.28, T:0.52
Consensus pattern (36 bp):
TGTGTTAAATTTATGGGTGTTCATTGTGATGGTTTC
Found at i:14819 original size:17 final size:17
Alignment explanation
Indices: 14787--14834 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
14777 CATATCACAT
* *
14787 GACTAGTAACGGTTTAG
1 GACTAGTAATGTTTTAG
* *
14804 GACTAGTCATGTTTTAT
1 GACTAGTAATGTTTTAG
*
14821 TACTAGTAATGTTT
1 GACTAGTAATGTTT
14835 CTCAAATCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (17 bp):
GACTAGTAATGTTTTAG
Found at i:22737 original size:396 final size:396
Alignment explanation
Indices: 21999--22793 Score: 1527
Period size: 396 Copynumber: 2.0 Consensus size: 396
21989 ACAATACTAA
21999 AGCCTAATGCTCATCGATTTCAAGTAAGGTGAACAACTTGGAATCGATGGGAATATTCTTGGTGA
1 AGCCTAATGCTCATCGATTTCAAGTAAGGTGAACAACTTGGAATCGATGGGAATATTCTTGGTGA
22064 TGTCGACTTCAATGCCTTCCAAAAGTTCTTCAATGGACTCTAAACCTCCAAGATGAGATCTTACA
66 TGTCGACTTCAATGCCTTCCAAAAGTTCTTCAATGGACTCTAAACCTCCAAGATGAGATCTTACA
22129 AAGCCCAATAAAGATTCCTTGAACCTTTTAGCCCGAGCCCTAGTCATTGGACCTTGCGGAATGGC
131 AAGCCCAATAAAGATTCCTTGAACCTTTTAGCCCGAGCCCTAGTCATTGGACCTTGCGGAATGGC
*
22194 TAAAGGATCAAAAGGTCGGTCTTGTCCGGATGGCCCAATCGATGTCCGGTTGTGGCCGGTTGGTG
196 TAAAGGATCAAAAGGTCGGTCTTGTCCGGATGGCCCAATCAATGTCCGGTTGTGGCCGGTTGGTG
22259 CGCCAAGCGATGGCCGGTTATGGCCGGATGCCCCATGCGATGTCGCATGCGATGGCCGGTCATGT
261 CGCCAAGCGATGGCCGGTTATGGCCGGATGCCCCATGCGATGTCGCATGCGATGGCCGGTCATGT
* * * *
22324 GGCCGGTGTTGCGCGGCTTCTCCAAGCAATGGCTGGTCACTTGTGCTTCCATGTCCATGGTCCTT
326 GGCCGATGTTACGCGGCTTCTCCAAGCAATGGCCGGTCACTTGTGCTTCCATGTCCATGCTCCTT
22389 CAAGCT
391 CAAGCT
22395 AGCCTAATGCTCATCGATTTCAAGTAAGGTGAACAACTTGGAATCGATGGGAATATTCTTGGTGA
1 AGCCTAATGCTCATCGATTTCAAGTAAGGTGAACAACTTGGAATCGATGGGAATATTCTTGGTGA
22460 TGTCGACTTCAATGCCTTCCAAAAGTTCTTCAATGGACTCTAAACCTCCAAGATGAGATCTTACA
66 TGTCGACTTCAATGCCTTCCAAAAGTTCTTCAATGGACTCTAAACCTCCAAGATGAGATCTTACA
* *
22525 AAGCCCAATAAAGCTTCCTTGAACCTTTTAGCCCGAGCCCTAGTCATTGGACCTTGCGGAATGGT
131 AAGCCCAATAAAGATTCCTTGAACCTTTTAGCCCGAGCCCTAGTCATTGGACCTTGCGGAATGGC
22590 TAAAGGATCAAAAGGTCGGTCTTGTCCGGATGGCCCAATCAATGTCCGGTTGTGGCCGGTTGGTG
196 TAAAGGATCAAAAGGTCGGTCTTGTCCGGATGGCCCAATCAATGTCCGGTTGTGGCCGGTTGGTG
22655 CGCCAAGCGATGGCCGGTTATGGCCGGATGCCCCATGCGATGTCGCATGCGATGGCCGGTCATGT
261 CGCCAAGCGATGGCCGGTTATGGCCGGATGCCCCATGCGATGTCGCATGCGATGGCCGGTCATGT
22720 GGCCGATGTTACGCGGCTTCTCCAAGCAATGGCCGGTCACTTGTGCTTCCATGTCCATGCTCCTT
326 GGCCGATGTTACGCGGCTTCTCCAAGCAATGGCCGGTCACTTGTGCTTCCATGTCCATGCTCCTT
22785 CAAGCT
391 CAAGCT
22791 AGC
1 AGC
22794 ATCCATGACA
Statistics
Matches: 392, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
396 392 1.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (396 bp):
AGCCTAATGCTCATCGATTTCAAGTAAGGTGAACAACTTGGAATCGATGGGAATATTCTTGGTGA
TGTCGACTTCAATGCCTTCCAAAAGTTCTTCAATGGACTCTAAACCTCCAAGATGAGATCTTACA
AAGCCCAATAAAGATTCCTTGAACCTTTTAGCCCGAGCCCTAGTCATTGGACCTTGCGGAATGGC
TAAAGGATCAAAAGGTCGGTCTTGTCCGGATGGCCCAATCAATGTCCGGTTGTGGCCGGTTGGTG
CGCCAAGCGATGGCCGGTTATGGCCGGATGCCCCATGCGATGTCGCATGCGATGGCCGGTCATGT
GGCCGATGTTACGCGGCTTCTCCAAGCAATGGCCGGTCACTTGTGCTTCCATGTCCATGCTCCTT
CAAGCT
Found at i:28046 original size:5 final size:5
Alignment explanation
Indices: 28031--28061 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
28021 TCTGGTCGAA
28031 ATTTT -TTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
28062 ATTTTTCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
ATTTT
Found at i:28056 original size:15 final size:14
Alignment explanation
Indices: 28031--28067 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
28021 TCTGGTCGAA
28031 ATTTTTTTTATTTT
1 ATTTTTTTTATTTT
28045 ATTTTATTTTATTTT
1 ATTTT-TTTTATTTT
28060 ATATTTTT
1 AT-TTTTT
28068 CGATATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 13 0.62
16 3 0.14
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTTTTTATTTT
Found at i:28168 original size:8 final size:8
Alignment explanation
Indices: 28140--28173 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
28130 GAATCAGCTA
28140 TGAATTTT
1 TGAATTTT
*
28148 TGAAGTTTC
1 TGAA-TTTT
28157 TGAATTTT
1 TGAATTTT
28165 TGAATTTT
1 TGAATTTT
28173 T
1 T
28174 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:39065 original size:17 final size:17
Alignment explanation
Indices: 39043--39077 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39033 GTTTGGAAGT
39043 AGGAAAATACTAGGGAA
1 AGGAAAATACTAGGGAA
**
39060 AGGAAAATTTTAGGGAA
1 AGGAAAATACTAGGGAA
39077 A
1 A
39078 TTTAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.29, T:0.17
Consensus pattern (17 bp):
AGGAAAATACTAGGGAA
Found at i:39152 original size:12 final size:12
Alignment explanation
Indices: 39135--39165 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39125 TTTGGTGTTG
*
39135 AGGAAAATACTA
1 AGGAAAATACCA
39147 AGGAAAATACCA
1 AGGAAAATACCA
39159 AGGAAAA
1 AGGAAAA
39166 CATTTTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.10, G:0.19, T:0.10
Consensus pattern (12 bp):
AGGAAAATACCA
Found at i:41004 original size:8 final size:8
Alignment explanation
Indices: 40931--41028 Score: 64
Period size: 8 Copynumber: 12.6 Consensus size: 8
40921 ATAACTAAGT
40931 AATAGATA
1 AATAGATA
40939 AATACG-TA
1 AATA-GATA
40947 AATAGA-A
1 AATAGATA
40954 AATA-AGTA
1 AATAGA-TA
40962 AA-AG-TA
1 AATAGATA
* *
40968 GATACATA
1 AATAGATA
40976 GAA-AGATA
1 -AATAGATA
*
40984 AATAGGTA
1 AATAGATA
* *
40992 TATAGATT
1 AATAGATA
41000 AATAGATA
1 AATAGATA
* *
41008 TATTGATA
1 AATAGATA
41016 AATAGATA
1 AATAGATA
41024 AATAG
1 AATAG
41029 GTAGGTAAAC
Statistics
Matches: 67, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
6 4 0.06
7 10 0.15
8 51 0.76
9 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.27
Consensus pattern (8 bp):
AATAGATA
Found at i:41082 original size:27 final size:26
Alignment explanation
Indices: 41033--41096 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
41023 AAATAGGTAG
41033 GTAAACTAAA-AAACAAAAGAT-AATA
1 GTAAA-TAAATAAACAAAAGATAAATA
* *
41058 GCTGAATAAATAAATAAAAGGATAAATA
1 G-TAAATAAATAAACAAAA-GATAAATA
41086 GTAAATAAATA
1 GTAAATAAATA
41097 TAGATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 5 0.16
26 10 0.31
27 12 0.38
28 5 0.16
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20
Consensus pattern (26 bp):
GTAAATAAATAAACAAAAGATAAATA
Found at i:48734 original size:21 final size:21
Alignment explanation
Indices: 48710--48754 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
48700 ATTTACTGGA
* *
48710 TTGCTAAACACTGTCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
48731 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
48752 TTG
1 TTG
48755 ACGCCTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.31, G:0.11, T:0.40
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:49055 original size:65 final size:65
Alignment explanation
Indices: 48986--49119 Score: 148
Period size: 65 Copynumber: 2.1 Consensus size: 65
48976 CCACTTGGGA
* *
48986 GGCTTCGCCA-CGGCAAGCCGCCCTCA-TGGGGCGGCTTCA-ACATGGGCAGGCCGCCCCAGTGA
1 GGCTTCACCATCGGCAAGCCGCCC-CACTGGGGCGACTT-AGACA-GGGCAGGCCGCCCCAGTGA
49048 GGC
63 GGC
* * * * * *
49051 GGCTTCACCATGGGCAGGCCGCCCCACTGGGGCGACTTAGCCAGGGCAGGCCGTCCCGGTGGGGC
1 GGCTTCACCATCGGCAAGCCGCCCCACTGGGGCGACTTAGACAGGGCAGGCCGCCCCAGTGAGGC
49116 GGCT
1 GGCT
49120 CGACTATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
65 35 0.60
66 23 0.40
ACGTcount: A:0.13, C:0.36, G:0.38, T:0.13
Consensus pattern (65 bp):
GGCTTCACCATCGGCAAGCCGCCCCACTGGGGCGACTTAGACAGGGCAGGCCGCCCCAGTGAGGC
Found at i:49114 original size:32 final size:33
Alignment explanation
Indices: 48997--49116 Score: 129
Period size: 33 Copynumber: 3.7 Consensus size: 33
48987 GCTTCGCCAC
* * *
48997 GGCAAGCCGCCCTCA-TGGGGCGGCTTCAACATG
1 GGCAGGCCGCCC-CAGTGGGGCGACTTCACCATG
* *
49030 GGCAGGCCGCCCCAGTGAGGCGGCTTCACCATG
1 GGCAGGCCGCCCCAGTGGGGCGACTTCACCATG
*
49063 GGCAGGCCGCCCCACTGGGGCGACTT-AGCCA-G
1 GGCAGGCCGCCCCAGTGGGGCGACTTCA-CCATG
* *
49095 GGCAGGCCGTCCCGGTGGGGCG
1 GGCAGGCCGCCCCAGTGGGGCG
49117 GCTCGACTAT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
32 23 0.30
33 53 0.70
ACGTcount: A:0.14, C:0.35, G:0.39, T:0.12
Consensus pattern (33 bp):
GGCAGGCCGCCCCAGTGGGGCGACTTCACCATG
Found at i:49237 original size:33 final size:33
Alignment explanation
Indices: 49194--49274 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
49184 CGGTGCTGTA
49194 CCCCTGGGGCGGCACTACCATAGCCAT-G-CCGCC
1 CCCCTGGGGCGGCACTACCAT-G-CATAGACCGCC
* * *
49227 TCCCTGGGGCGGCCCTACCATGGATAGACCGCC
1 CCCCTGGGGCGGCACTACCATGCATAGACCGCC
49260 CCCCTGGGGCGGCAC
1 CCCCTGGGGCGGCAC
49275 CGGTACTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 2 0.05
32 2 0.05
33 37 0.90
ACGTcount: A:0.14, C:0.43, G:0.31, T:0.12
Consensus pattern (33 bp):
CCCCTGGGGCGGCACTACCATGCATAGACCGCC
Found at i:49443 original size:63 final size:64
Alignment explanation
Indices: 49339--49485 Score: 208
Period size: 63 Copynumber: 2.3 Consensus size: 64
49329 AAAAGGCCTT
* * *
49339 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTGGGGCGGC-AAG-CGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGAGCCGTCCTAGT-GGGAGGCTAAGCCGTGGCAGA
* ** *
49402 GCCGTCCTAGTGGGGTGGCTAGCCGTGGCAGAGCCGTCCTAGTGGGAGGCTCCGCCGTGGTAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGAGCCGTCCTAGTGGGAGGCTAAGCCGTGGCAGA
49466 GCCGTCCTAGTGGGGAGGCT
1 GCCGTCCTAGTGGGGAGGCT
49486 CCGCGTGGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
62 6 0.08
63 42 0.56
64 27 0.36
ACGTcount: A:0.13, C:0.27, G:0.44, T:0.16
Consensus pattern (64 bp):
GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGAGCCGTCCTAGTGGGAGGCTAAGCCGTGGCAGA
Found at i:49493 original size:32 final size:32
Alignment explanation
Indices: 49339--49485 Score: 208
Period size: 32 Copynumber: 4.6 Consensus size: 32
49329 AAAAGGCCTT
* *
49339 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
* *
49371 GCCGTCCTAGTGGGGCGGCAAG-CGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
*
49402 GCCGTCCTAGTGGGGTGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
* *
49434 GCCGTCCTAGT-GGGAGGCTCCGCCGTGGTAGA
1 GCCGTCCTAGTGGGGAGGCT-AGCCGTGGCAGA
49466 GCCGTCCTAGTGGGGAGGCT
1 GCCGTCCTAGTGGGGAGGCT
49486 CCGCGTGGCT
Statistics
Matches: 105, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
31 36 0.34
32 61 0.58
33 8 0.08
ACGTcount: A:0.13, C:0.27, G:0.44, T:0.16
Consensus pattern (32 bp):
GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
Found at i:50459 original size:15 final size:13
Alignment explanation
Indices: 50439--50484 Score: 67
Period size: 12 Copynumber: 3.5 Consensus size: 13
50429 CTGATTTACT
50439 TTTATTATTTACTTA
1 TTTATTA-TTA-TTA
50454 TTTATTATTATTA
1 TTTATTATTATTA
50467 -TTATTATTATTA
1 TTTATTATTATTA
50479 TTTATT
1 TTTATT
50485 TTTTTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.40
13 8 0.27
14 3 0.10
15 7 0.23
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:50461 original size:3 final size:3
Alignment explanation
Indices: 50440--50480 Score: 55
Period size: 3 Copynumber: 12.7 Consensus size: 3
50430 TGATTTACTT
50440 TTA TTA TTTA CTTA TTTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
50481 TATTTTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 26 0.74
4 9 0.26
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:52774 original size:30 final size:31
Alignment explanation
Indices: 52738--52805 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
52728 AACAATCTAC
*
52738 CAATCAATTAACAA-ATAATTGCAATTC-AAT
1 CAATCAATTAACAATAT-ATGGCAATTCAAAT
*
52768 CAATCAA-TAGCAATATATGGCAATTCAAAT
1 CAATCAATTAACAATATATGGCAATTCAAAT
52798 CAA-CAATT
1 CAATCAATT
52806 GAAAGATAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.28
Consensus pattern (31 bp):
CAATCAATTAACAATATATGGCAATTCAAAT
Found at i:55178 original size:19 final size:19
Alignment explanation
Indices: 55150--55188 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
55140 AGATGACAAG
*
55150 ACACAAATCATCAGCCAAA
1 ACACAAATCATAAGCCAAA
*
55169 ACACACATCATAAGCCAAA
1 ACACAAATCATAAGCCAAA
55188 A
1 A
55189 GAAAGAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.31, G:0.05, T:0.10
Consensus pattern (19 bp):
ACACAAATCATAAGCCAAA
Found at i:60558 original size:30 final size:30
Alignment explanation
Indices: 60522--60587 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
60512 ACATCGCAGG
*
60522 GGCCATCGCACGAGCCATCTGGCCACAACC
1 GGCCATCGCACGAGCCATCCGGCCACAACC
*
60552 GGCCATCGCACGGGCCATCCGGCCACAACC
1 GGCCATCGCACGAGCCATCCGGCCACAACC
*
60582 GACCAT
1 GGCCAT
60588 TCGACCCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.44, G:0.24, T:0.09
Consensus pattern (30 bp):
GGCCATCGCACGAGCCATCCGGCCACAACC
Found at i:73149 original size:22 final size:22
Alignment explanation
Indices: 73123--73166 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
73113 TGTCCTGCGC
*
73123 AACAACTTCTGTCCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
* *
73145 AACAAGTTCTGGGCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
73167 TCCTGAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
AACAACTTCTGGCCCGAAGTTG
Found at i:73150 original size:52 final size:52
Alignment explanation
Indices: 73068--73171 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
73058 AGGTTTTTCC
*
73068 CGCAACAACTTCTGTCCCGAAGTTGTACAAGTTCTGGGCCAAAGTTGTCCTG
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCAAAGTTGTCCTG
*
73120 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCAAAGTTGTCCTG
73172 AAATTCTTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (52 bp):
CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCAAAGTTGTCCTG
Found at i:73500 original size:22 final size:20
Alignment explanation
Indices: 73467--73507 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
73457 TTTCCTTTTT
*
73467 CTTTCTTTAATTTTTGATTC
1 CTTTCTTTAATTTTCGATTC
73487 CTTTACTTTCAATTTTCGATT
1 CTTT-CTTT-AATTTTCGATT
73508 TCAATTGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.61
Consensus pattern (20 bp):
CTTTCTTTAATTTTCGATTC
Found at i:76354 original size:13 final size:13
Alignment explanation
Indices: 76336--76361 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76326 TTATTATTTC
76336 TTGAATTTAGTTT
1 TTGAATTTAGTTT
76349 TTGAATTTAGTTT
1 TTGAATTTAGTTT
76362 ACTTGCATTT
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:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
TTGAATTTAGTTT
Found at i:77543 original size:21 final size:20
Alignment explanation
Indices: 77504--77548 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
77494 AATTATCAAT
* *
77504 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
77524 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
77545 TAAA
1 TAAA
77549 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:80031 original size:22 final size:21
Alignment explanation
Indices: 79988--80031 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
79978 TGGCTTTTCT
* *
79988 TTTCATTTTTTTTTTCATATA
1 TTTCATTTTTTTTTACAAATA
80009 TTTCAGTTTTTTTTTACAAATA
1 TTTCA-TTTTTTTTTACAAATA
80031 T
1 T
80032 AAAAAGCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTCATTTTTTTTTACAAATA
Found at i:80663 original size:15 final size:15
Alignment explanation
Indices: 80643--80673 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
80633 GTATGTCGCA
80643 ACGTCCAGGTCCGGT
1 ACGTCCAGGTCCGGT
80658 ACGTCCAGGTCCGGT
1 ACGTCCAGGTCCGGT
80673 A
1 A
80674 GGTACCGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.19
Consensus pattern (15 bp):
ACGTCCAGGTCCGGT
Found at i:85405 original size:21 final size:19
Alignment explanation
Indices: 85367--85405 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
85357 TCTCTCTTTC
*
85367 TTTTGGCTTATGATGTGTG
1 TTTTGGCTGATGATGTGTG
*
85386 TTTTGGCTGATGATATGTG
1 TTTTGGCTGATGATGTGTG
85405 T
1 T
85406 CCTGTCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.05, G:0.31, T:0.51
Consensus pattern (19 bp):
TTTTGGCTGATGATGTGTG
Found at i:86531 original size:69 final size:68
Alignment explanation
Indices: 86330--86750 Score: 522
Period size: 70 Copynumber: 6.2 Consensus size: 68
86320 GGAAATGAAC
* * * *
86330 TTGGCTTATGGAAAAG-CC--CTGCTTGGATGGAACCAAGGC-TAAACTAACTCATA-GTGAAAC
1 TTGGCTTGTGGAAAAGCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATG-GAAAC
86390 GAGT
65 GAGT
* * * *
86394 TTGGCTAT-TGGAAAAGCCCT--TGC-T-GATGGAACCAAGGC-TAAATTGACTCGTGTGGAAAT
1 TTGGCT-TGTGGAAAAGCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
86453 GAGT
65 GAGT
*
86457 ATGGCTTGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCC-TGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
86522 GAGT
65 GAGT
* * * *
86526 TTGGCTTGCGGAAAAGCCCCTGAATACTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAG-CCCTG-CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
*
86591 TGAGT
64 CGAGT
86596 TTGGCTTGTGGAAAAGCCGCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCC-CTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
86661 GAGT
65 GAGT
* * *
86665 TTGGCTTGTGGAAAAGCCCCTGAATACTTGGATGGAACCAAGGCTTGAACTTACTCGTATGGAAA
1 TTGGCTTGTGGAAAAG-CCCTG-CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
86730 CGAGT
64 CGAGT
* *
86735 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
86751 TCGAAGCATT
Statistics
Matches: 315, Mismatches: 26, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
62 1 0.00
63 48 0.15
64 17 0.05
65 6 0.02
66 3 0.01
67 1 0.00
68 14 0.04
69 101 0.32
70 124 0.39
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (68 bp):
TTGGCTTGTGGAAAAGCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACG
AGT
Found at i:86602 original size:139 final size:138
Alignment explanation
Indices: 86317--86750 Score: 588
Period size: 139 Copynumber: 3.2 Consensus size: 138
86307 ATTGACTTCA
** * *
86317 TATGGAAATGAACTTGGCTTATGGAAAAG-CC--CTGCTTGGATGGAACCAAGGC-TAAACTAAC
1 TATGGAAATGAGTTTGGCTTATGGAAAAGCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGAC
* * *
86378 TCATA-GTGAAACGAGTTTGGCTAT-TGGAAAAG-CCCT---TGC-T-GATGGAACCAAGGC-TA
66 TCGTATG-GAAACGAGTTTGGCT-TGTGGAAAAGCCCCTGAATACTTGGATGGAACCAAGGCTTG
*
86434 AATTGACTCG
129 AACTGACTCG
* * *
86444 TGTGGAAATGAGTATGGCTTGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGCTTGAACTGA
1 TATGGAAATGAGTTTGGCTTATGGAAAAGCCC-TGCTGCTTGGATGGAACCAAGGCTTGAACTGA
* *
86509 CTCGTATGGAAACGAGTTTGGCTTGCGGAAAAGCCCCTGAATACTTGGATGGAACCAAAGCTTGA
65 CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATACTTGGATGGAACCAAGGCTTGA
86574 ACTGACTCG
130 ACTGACTCG
*
86583 TATGGAAATGAGTTTGGCTTGTGGAAAAGCCGCTGCTGCTTGGATGGAACCAAGGCTTGAACTGA
1 TATGGAAATGAGTTTGGCTTATGGAAAAGCC-CTGCTGCTTGGATGGAACCAAGGCTTGAACTGA
86648 CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATACTTGGATGGAACCAAGGCTTGA
65 CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATACTTGGATGGAACCAAGGCTTGA
*
86713 ACTTACTCG
130 ACTGACTCG
* *
86722 TATGGAAACGAGTTTGACTTATGGAAAAG
1 TATGGAAATGAGTTTGGCTTATGGAAAAG
86751 TCGAAGCATT
Statistics
Matches: 271, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
127 24 0.09
128 2 0.01
131 22 0.08
132 33 0.12
133 5 0.02
136 2 0.01
137 1 0.00
138 13 0.05
139 168 0.62
140 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (138 bp):
TATGGAAATGAGTTTGGCTTATGGAAAAGCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGAC
TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATACTTGGATGGAACCAAGGCTTGAA
CTGACTCG
Found at i:88965 original size:44 final size:44
Alignment explanation
Indices: 88917--89059 Score: 214
Period size: 44 Copynumber: 3.2 Consensus size: 44
88907 CACAACTTTG
*
88917 GAAAACCATTTTATCAAAACCTTTTTAAAACCATGACTCTTTTT
1 GAAAACCATTTTATCAAAACCTTTTAAAAACCATGACTCTTTTT
*
88961 GAAAAACCGTTTTTATCAAAACCTTTTAAAAACCATGACTCTTTTT
1 G-AAAACC-ATTTTATCAAAACCTTTTAAAAACCATGACTCTTTTT
* * *
89007 GAAAACCATTTTATCAAAATCTTTTGAGAACCATGACTCTTTTT
1 GAAAACCATTTTATCAAAACCTTTTAAAAACCATGACTCTTTTT
*
89051 TAAAACCAT
1 GAAAACCAT
89060 CGTTGATTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 42 0.47
45 12 0.13
46 36 0.40
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (44 bp):
GAAAACCATTTTATCAAAACCTTTTAAAAACCATGACTCTTTTT
Found at i:90382 original size:21 final size:21
Alignment explanation
Indices: 90349--90410 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
90339 TGACCGGCCA
*
90349 CATGCCCGGCCATCACCATTG
1 CATGCCCGGCCATCACCATCG
* *
90370 CATGACCGCCCATCACCATCG
1 CATGCCCGGCCATCACCATCG
90391 CATGCCCGGCCATCATCCAT
1 CATGCCCGGCCATCA-CCAT
90411 GCACAACCGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 31 0.89
22 4 0.11
ACGTcount: A:0.21, C:0.45, G:0.16, T:0.18
Consensus pattern (21 bp):
CATGCCCGGCCATCACCATCG
Done.