Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006933.1 Corchorus capsularis cultivar CVL-1 contig06954, 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: 57264
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:758 original size:40 final size:40
Alignment explanation
Indices: 698--782 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
688 TTTACACTAC
* *
698 GAACGTGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
1 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATACTT
738 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATACTT
1 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATACTT
*
778 AAACA
1 GAACA
783 AATTAAAACG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (40 bp):
GAACATGTGTGTAATGCAAAATTAACCCATTAAAATACTT
Found at i:2513 original size:50 final size:48
Alignment explanation
Indices: 2426--2520 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 48
2416 AAAAAATATC
* *
2426 AAATTATCAAAAATTAGCATTCTAGTGATTTTTTTTTTTGGCCGGATACT
1 AAATTATCAAAAATTAACATTCTAGTGA-TTTCTTTTTT-GCCGGATACT
2476 AAATTATCAAAAATTACTACATTCTAGTGA-TTCTTTTTTGCCGGA
1 AAATTATCAAAAATTA--ACATTCTAGTGATTTCTTTTTTGCCGGA
2521 ACATTCTAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
49 6 0.15
50 24 0.59
52 11 0.27
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.42
Consensus pattern (48 bp):
AAATTATCAAAAATTAACATTCTAGTGATTTCTTTTTTGCCGGATACT
Found at i:7628 original size:27 final size:26
Alignment explanation
Indices: 7598--7703 Score: 104
Period size: 27 Copynumber: 3.8 Consensus size: 26
7588 TTTTTTAATC
7598 TTTACTTAATACCAATTTTTTTCCTTT
1 TTTACTTAATACC-ATTTTTTTCCTTT
* **
7625 TTTACTTAATACCACTTTTCACCTTTT
1 TTTACTTAATACCATTTTTTTCC-TTT
*
7652 TTTACTTAATACCATTTTTACTTAATGCCATT
1 TTTACTTAATACCA-TTTT--TT--T-CCTTT
7684 TTTACTTAATACCATTTTTT
1 TTTACTTAATACCATTTTTT
7704 ACTCTTTTGC
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
26 7 0.11
27 30 0.46
28 3 0.05
29 2 0.03
30 1 0.02
31 4 0.06
32 16 0.25
33 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTACTTAATACCATTTTTTTCCTTT
Found at i:7706 original size:17 final size:16
Alignment explanation
Indices: 7650--7702 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
7640 TTTTCACCTT
7650 TTTTTACTTAATACCA
1 TTTTTACTTAATACCA
*
7666 TTTTTACTTAATGCCA
1 TTTTTACTTAATACCA
7682 TTTTTACTTAATACCA
1 TTTTTACTTAATACCA
7698 TTTTT
1 TTTTT
7703 TACTCTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTTACTTAATACCA
Found at i:7745 original size:17 final size:18
Alignment explanation
Indices: 7725--7787 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
7715 TCATATCATT
7725 TTTTACTCTTAATACC-A
1 TTTTACTCTTAATACCAA
7742 TTTTACTC-T--TACCAA
1 TTTTACTCTTAATACCAA
**
7757 TTTTTACTCTTAATATCCTT
1 -TTTTACTCTTAATA-CCAA
7777 TTTTACTCTTA
1 TTTTACTCTTA
7788 CCATTTTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 4 0.11
15 1 0.03
16 9 0.24
17 9 0.24
19 13 0.34
20 2 0.05
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTACTCTTAATACCAA
Found at i:7746 original size:59 final size:57
Alignment explanation
Indices: 7623--7767 Score: 143
Period size: 59 Copynumber: 2.5 Consensus size: 57
7613 TTTTTTTCCT
* * * *
7623 TTTTTACTTAATACCACTTTTCACCTTTTTTTACTTAATACCATTTTTACTTAATGCCA
1 TTTTTACTTAATACCAATTTTTA-C-TCTTTTACTTAATACCATTTTTACTTAATACCA
* * * *
7682 TTTTTACTTAATACCATTTTTTACTCTTTTGCTTCATATCATTTTTTACTCTTAATACCA
1 TTTTTACTTAATACCAATTTTTACTCTTTTACTTAATACCA-TTTTTA--CTTAATACCA
7742 -TTTTACTCT--TACCAATTTTTACTCTT
1 TTTTTACT-TAATACCAATTTTTACTCTT
7768 AATATCCTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
57 13 0.18
58 23 0.31
59 28 0.38
60 10 0.14
ACGTcount: A:0.23, C:0.21, G:0.01, T:0.54
Consensus pattern (57 bp):
TTTTTACTTAATACCAATTTTTACTCTTTTACTTAATACCATTTTTACTTAATACCA
Found at i:7788 original size:35 final size:34
Alignment explanation
Indices: 7724--7816 Score: 122
Period size: 33 Copynumber: 2.8 Consensus size: 34
7714 TTCATATCAT
*
7724 TTTTTACTCTTAATA-CC-ATTTTACTCTTACCAA
1 TTTTTACTCTTAATATCCTTTTTTACTCTTACC-A
7757 TTTTTACTCTTAATATCCTTTTTTACTCTTACCA
1 TTTTTACTCTTAATATCCTTTTTTACTCTTACCA
* *
7791 TTTTTACCCTT-CT-TCCTTTTTTACTC
1 TTTTTACTCTTAATATCCTTTTTTACTC
7817 CTTTGCTTAC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
32 13 0.24
33 16 0.29
34 13 0.24
35 13 0.24
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55
Consensus pattern (34 bp):
TTTTTACTCTTAATATCCTTTTTTACTCTTACCA
Found at i:7878 original size:60 final size:58
Alignment explanation
Indices: 7775--7912 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 58
7765 CTTAATATCC
**
7775 TTTTTTACTCTTACCATTTTTACCCTTCTTCCTTTTTTACTCCTTTGCTTACTATCATCATT
1 TTTTTTACTCTTACCA-TTTTACCCTTCTTCCTTTTTTACTCCTTTAATTACTATC--C-TT
* * * *
7837 TTTTTTACCCTTACCATTTTACTCTT-TTTCTTTTTTACTCCTTTAATTAGTATCCTT
1 TTTTTTACTCTTACCATTTTACCCTTCTTCCTTTTTTACTCCTTTAATTACTATCCTT
7894 TTTTTTACTCTTACCATTT
1 TTTTTTACTCTTACCATTT
7913 GATTACCAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 20 0.29
58 1 0.01
60 24 0.35
61 9 0.13
62 15 0.22
ACGTcount: A:0.15, C:0.25, G:0.01, T:0.59
Consensus pattern (58 bp):
TTTTTTACTCTTACCATTTTACCCTTCTTCCTTTTTTACTCCTTTAATTACTATCCTT
Found at i:8126 original size:38 final size:38
Alignment explanation
Indices: 8050--8189 Score: 148
Period size: 38 Copynumber: 3.7 Consensus size: 38
8040 TCTTAGTCCC
*
8050 TTTACTGATTACTATTTTTACCTTAACTCTTAATTATCAAT
1 TTTACTGATTACTA---TTACCTTGACTCTTAATTATCAAT
*
8091 TTTACTGATTACTATTACTTTGACTCTTAATTATCAAT
1 TTTACTGATTACTATTACCTTGACTCTTAATTATCAAT
* * *
8129 TTTACTGATTACTA-T-CCTT--TTACTTGATTA-CTGA-
1 TTTACTGATTACTATTACCTTGACT-CTTAATTATC-AAT
8163 TTTACTGATTACTATTACCTTGACTCT
1 TTTACTGATTACTATTACCTTGACTCT
8190 GATTAATCTC
Statistics
Matches: 86, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
34 16 0.19
35 9 0.10
36 7 0.08
37 3 0.03
38 37 0.43
41 14 0.16
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (38 bp):
TTTACTGATTACTATTACCTTGACTCTTAATTATCAAT
Found at i:8191 original size:29 final size:29
Alignment explanation
Indices: 8159--8248 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
8149 TACTTGATTA
8159 CTGATTTACTGATTACTATTACCTTGACT
1 CTGATTTACTGATTACTATTACCTTGACT
* * * *
8188 CTGATTAATCT-CTT--T-TTA-CTTAATT
1 CTGATTTA-CTGATTACTATTACCTTGACT
* *
8213 ACTGATTTACTGATTACCATTACCTTGGCT
1 -CTGATTTACTGATTACTATTACCTTGACT
8243 CTGATT
1 CTGATT
8249 AATCTCTTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 14
0.65 0.15 0.21
Matches are distributed among these distances:
25 7 0.16
26 12 0.27
27 1 0.02
29 18 0.41
30 6 0.14
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (29 bp):
CTGATTTACTGATTACTATTACCTTGACT
Found at i:8205 original size:55 final size:55
Alignment explanation
Indices: 8146--8416 Score: 317
Period size: 55 Copynumber: 4.8 Consensus size: 55
8136 ATTACTATCC
*
8146 TTTTACTTGATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCT
* *
8201 TTTTACTTAATTACTGATTTACTGATTACCATTACCTTGGCTCTGATTAATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCT
* * * *
8256 TTTTACTTAATTACTGATTTACTGATTATTATTGACTTTGACTCTTAATCTCTGATTACTATCT
1 TTTTACTTAATTACTGATTTACTG---ATTACT-A--TT-AC-CTTGA-CTCTGATTAATCTCT
* * * * *
8320 TTTTACTTAATTACTAATTTACTAATTACCATTACCTCGACTCTGATTGATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCT
* ** *
8375 TGTCCCTTAATTACTGATTTACTGATTACTATCACCTTGACT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
8417 TTTAATTATC
Statistics
Matches: 181, Mismatches: 26, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
55 122 0.67
56 3 0.02
57 2 0.01
58 6 0.03
59 1 0.01
60 1 0.01
61 6 0.03
62 2 0.01
63 3 0.02
64 35 0.19
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.48
Consensus pattern (55 bp):
TTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCT
Found at i:8310 original size:119 final size:119
Alignment explanation
Indices: 8186--8402 Score: 344
Period size: 119 Copynumber: 1.8 Consensus size: 119
8176 ATTACCTTGA
* * * * *
8186 CTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACCATTACCTTGGCTCTGATTAA
1 CTCTGATTAATATCTTTTTACTTAATTACTAATTTACTAATTACCATTACCTCGACTCTGATTAA
* *
8251 TCTCTTTTTACTTAATTACTGATTTACTGATTATTATTGACTTTGACTCTTAAT
66 TCTCTTGTCACTTAATTACTGATTTACTGATTATTATTGACTTTGACTCTTAAT
* *
8305 CTCTGATTACTATCTTTTTACTTAATTACTAATTTACTAATTACCATTACCTCGACTCTGATTGA
1 CTCTGATTAATATCTTTTTACTTAATTACTAATTTACTAATTACCATTACCTCGACTCTGATTAA
*
8370 TCTCTTGTCCCTTAATTACTGATTTACTGATTA
66 TCTCTTGTCACTTAATTACTGATTTACTGATTA
8403 CTATCACCTT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
119 88 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (119 bp):
CTCTGATTAATATCTTTTTACTTAATTACTAATTTACTAATTACCATTACCTCGACTCTGATTAA
TCTCTTGTCACTTAATTACTGATTTACTGATTATTATTGACTTTGACTCTTAAT
Found at i:8424 original size:37 final size:36
Alignment explanation
Indices: 8380--8635 Score: 169
Period size: 37 Copynumber: 7.2 Consensus size: 36
8370 TCTCTTGTCC
* *
8380 CTTAATTACTGATTTACTGATTACTATCACCTTGACT
1 CTTAATTACTTAATTACTGATTACTATCA-CTTGACT
* * * * *
8417 TTTAATTA-TCAATTTTAGTGATTACCATTACTTCGACT
1 CTTAATTACTTAA--TTACTGATTACTATCACTT-GACT
*
8455 CTTAATTACTTAATTAC-GAATTACTATCATTTTGACT
1 CTTAATTACTTAATTACTG-ATTACTATCA-CTTGACT
* * *
8492 CTTAGTTACTTAATTACTGGTTACTATCA-TTTA--
1 CTTAATTACTTAATTACTGATTACTATCACTTGACT
** *
8525 CTTAATTAC-TGGTTACT-ATTAC--T---TTGATT
1 CTTAATTACTTAATTACTGATTACTATCACTTGACT
**
8554 CTTAATTA-TTAATTCACTGATTACTATTTCTTTGACT
1 CTTAATTACTTAATT-ACTGATTACTATCAC-TTGACT
* *
8591 CTTAATTACTTAATTCATTGATTACTATTACTTTGACT
1 CTTAATTACTTAATT-ACTGATTACTATCAC-TTGACT
8629 CTTAATT
1 CTTAATT
8636 GTTAATAGCG
Statistics
Matches: 175, Mismatches: 25, Indels: 37
0.74 0.11 0.16
Matches are distributed among these distances:
27 3 0.02
29 12 0.07
30 3 0.02
31 9 0.05
32 6 0.03
33 9 0.05
35 3 0.02
36 3 0.02
37 63 0.36
38 61 0.35
39 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.48
Consensus pattern (36 bp):
CTTAATTACTTAATTACTGATTACTATCACTTGACT
Found at i:8526 original size:62 final size:62
Alignment explanation
Indices: 8460--8580 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 62
8450 CGACTCTTAA
* * *
8460 TTACTTAATTAC-GAATTACTATCATTTTGACTCTTAGTTACTTAATT-ACTGGTTACTATCAT
1 TTACTTAATTACTG-ATTACTATCACTTTGACTCTTAATTA-TTAATTCACTGATTACTATCAT
* * *
8522 TTACTTAATTACTGGTTACTATTACTTTGATTCTTAATTATTAATTCACTGATTACTAT
1 TTACTTAATTACTGATTACTATCACTTTGACTCTTAATTATTAATTCACTGATTACTAT
8581 TTCTTTGACT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
61 6 0.12
62 44 0.86
63 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (62 bp):
TTACTTAATTACTGATTACTATCACTTTGACTCTTAATTATTAATTCACTGATTACTATCAT
Found at i:8613 original size:38 final size:38
Alignment explanation
Indices: 8522--8635 Score: 178
Period size: 38 Copynumber: 3.1 Consensus size: 38
8512 TTACTATCAT
* *
8522 TTACTTAATT-ACTGGTTACTATTACTTTGATTCTTAA
1 TTACTTAATTCACTGATTACTATTACTTTGACTCTTAA
*
8559 TTA-TTAATTCACTGATTACTATTTCTTTGACTCTTAA
1 TTACTTAATTCACTGATTACTATTACTTTGACTCTTAA
*
8596 TTACTTAATTCATTGATTACTATTACTTTGACTCTTAA
1 TTACTTAATTCACTGATTACTATTACTTTGACTCTTAA
8634 TT
1 TT
8636 GTTAATAGCG
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
36 6 0.09
37 30 0.43
38 34 0.49
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (38 bp):
TTACTTAATTCACTGATTACTATTACTTTGACTCTTAA
Found at i:9184 original size:13 final size:13
Alignment explanation
Indices: 9166--9192 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9156 ACAGAGGATG
9166 AAATAAATCTAAA
1 AAATAAATCTAAA
9179 AAATAAATCTAAA
1 AAATAAATCTAAA
9192 A
1 A
9193 CCCAAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAAATCTAAA
Found at i:10078 original size:23 final size:23
Alignment explanation
Indices: 10052--10113 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
10042 AGCAGAAACA
*
10052 AGAGGAGGAAGAAAGAGAACGAC
1 AGAGGAGGAAGAAAGAGAACAAC
* * *
10075 AGAGGAGAAAGAAAGGGAGCAAC
1 AGAGGAGGAAGAAAGAGAACAAC
*
10098 AGAGGACAGAAGAAAG
1 AGAGGA-GGAAGAAAG
10114 GGAGGAGAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 25 0.78
24 7 0.22
ACGTcount: A:0.53, C:0.08, G:0.39, T:0.00
Consensus pattern (23 bp):
AGAGGAGGAAGAAAGAGAACAAC
Found at i:12850 original size:2 final size:2
Alignment explanation
Indices: 12843--12869 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12833 ATTAGATTAG
12843 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
12870 GTCTAATATC
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:13191 original size:20 final size:19
Alignment explanation
Indices: 13167--13221 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
13157 GAAATCGGAT
13167 TGTATATTATATATATGGA
1 TGTATATTATATATATGGA
*
13186 TCGTATATTATATGTAT-GA
1 T-GTATATTATATATATGGA
*
13205 TATATATATATATATAT
1 TGTATAT-TATATATAT
13222 ATATATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 5 0.16
19 12 0.39
20 14 0.45
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (19 bp):
TGTATATTATATATATGGA
Found at i:13211 original size:2 final size:2
Alignment explanation
Indices: 13189--13230 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
13179 ATATGGATCG
*
13189 TA TA T- TA TA TG TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
13231 ATTGAGGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15367 original size:25 final size:25
Alignment explanation
Indices: 15333--15385 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
15323 ATCAATCAAG
*
15333 AAACCCAAAGACTAAAAATGAAAGA
1 AAACCAAAAGACTAAAAATGAAAGA
* *
15358 AAACCAAAAGACTAAAAGTGAAATA
1 AAACCAAAAGACTAAAAATGAAAGA
15383 AAA
1 AAA
15386 GGCCACATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.66, C:0.13, G:0.11, T:0.09
Consensus pattern (25 bp):
AAACCAAAAGACTAAAAATGAAAGA
Found at i:15474 original size:22 final size:22
Alignment explanation
Indices: 15448--15493 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
15438 AAAGAAACTC
15448 AAGAATTATTCTAAAAAGAGGA
1 AAGAATTATTCTAAAAAGAGGA
*
15470 AAGAATTATTCTAAAGAGAGGA
1 AAGAATTATTCTAAAAAGAGGA
15492 AA
1 AA
15494 TGATTCGGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22
Consensus pattern (22 bp):
AAGAATTATTCTAAAAAGAGGA
Found at i:18178 original size:21 final size:20
Alignment explanation
Indices: 18145--18188 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
18135 GTGGAAAGCA
*
18145 TTATAGCTATTTTAATAACTT
1 TTATAACTATTTTAATAA-TT
* *
18166 TTATAACTTTTTTAGTAATT
1 TTATAACTATTTTAATAATT
18186 TTA
1 TTA
18189 GATTACAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.57
Consensus pattern (20 bp):
TTATAACTATTTTAATAATT
Found at i:18465 original size:21 final size:21
Alignment explanation
Indices: 18439--18480 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
18429 CTTATAATAC
18439 TATAACATTTTTTA-TAACCTT
1 TATAAC-TTTTTTAGTAACCTT
18460 TATAACTTTTTTAGTAACCTT
1 TATAACTTTTTTAGTAACCTT
18481 AAAGAAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.52
Consensus pattern (21 bp):
TATAACTTTTTTAGTAACCTT
Found at i:21792 original size:24 final size:24
Alignment explanation
Indices: 21765--21810 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
21755 AAAAAGTTAC
*
21765 TAAAATCATCCAAGAGCGCTATAA
1 TAAAATCATCCAAGAACGCTATAA
21789 TAAAATCATCCAAGAACGCTAT
1 TAAAATCATCCAAGAACGCTAT
21811 TAAGTTTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (24 bp):
TAAAATCATCCAAGAACGCTATAA
Found at i:21861 original size:21 final size:21
Alignment explanation
Indices: 21828--21871 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
21818 GTGAAAACCA
*
21828 TTATAGCTATTTTAATAACTT
1 TTATAACTATTTTAATAACTT
* * *
21849 TTATAACTTTTTTAGTAATTT
1 TTATAACTATTTTAATAACTT
21870 TT
1 TT
21872 TATTACAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.59
Consensus pattern (21 bp):
TTATAACTATTTTAATAACTT
Found at i:23334 original size:116 final size:117
Alignment explanation
Indices: 23130--23359 Score: 354
Period size: 116 Copynumber: 2.0 Consensus size: 117
23120 CCGATATCGA
* *
23130 CAATTGTTAACTATTATAACCCGTTAGCAGGGCCTTAAGCTAACTATTATAACCCATTACCAGGG
1 CAATTGCTAACTACTATAACCCGTTAGCAGGGCCTTAAGCTAACTATTATAACCCATTACCAGGG
23195 CCGTTTTCCAATTACTATAACCCACTGG-TAGGGCCGATAGAACATGTTCTC
66 CCGTTTTCCAATTACTATAACCCACTGGCTAGGGCCGATAGAACATGTTCTC
** * **
23246 CAATTGCTAACTACTATAACTTGTTAGCAGGGCCTTAAGCTAACTATTATAACCCGTTAGTAGGG
1 CAATTGCTAACTACTATAACCCGTTAGCAGGGCCTTAAGCTAACTATTATAACCCATTACCAGGG
* * * *
23311 TCGTTTTCCAGTTACTATAACCCACTGGCTATGGCCGATAGAATATGTT
66 CCGTTTTCCAATTACTATAACCCACTGGCTAGGGCCGATAGAACATGTT
23360 ATCTGTCGAT
Statistics
Matches: 102, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
116 84 0.82
117 18 0.18
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (117 bp):
CAATTGCTAACTACTATAACCCGTTAGCAGGGCCTTAAGCTAACTATTATAACCCATTACCAGGG
CCGTTTTCCAATTACTATAACCCACTGGCTAGGGCCGATAGAACATGTTCTC
Found at i:28292 original size:77 final size:77
Alignment explanation
Indices: 28165--28319 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
28155 GAATTTGCCT
*
28165 AACTTATAAATTTTATTAGAGAATAAATTTTGTGTGGTGGAGGAGCAAAATGAATCAAACTAGTA
1 AACTTAGAAATTTTATTAGAGAATAAATTTTGTGTGGTGGAGGAGCAAAATGAATCAAACTAGTA
28230 AATTTGGGTCAA
66 AATTTGGGTCAA
28242 AACTTAGAAATTTTATTAGAGAATAAATTTTGTGTGGTGGAGGAGCAAAATGAATCAAACTAGTA
1 AACTTAGAAATTTTATTAGAGAATAAATTTTGTGTGGTGGAGGAGCAAAATGAATCAAACTAGTA
28307 AATTTGGGTCAA
66 AATTTGGGTCAA
28319 A
1 A
28320 TTGAAGGAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (77 bp):
AACTTAGAAATTTTATTAGAGAATAAATTTTGTGTGGTGGAGGAGCAAAATGAATCAAACTAGTA
AATTTGGGTCAA
Found at i:34396 original size:8 final size:8
Alignment explanation
Indices: 34381--34593 Score: 60
Period size: 8 Copynumber: 27.4 Consensus size: 8
34371 AAAAAAGTAA
34381 AAATA-AT
1 AAATAGAT
* *
34388 AGATAAAT
1 AAATAGAT
*
34396 AAAAAGAT
1 AAATAGAT
34404 AAATAGAT
1 AAATAGAT
* *
34412 ATATAGAC
1 AAATAGAT
*
34420 AAAAAGAT
1 AAATAGAT
34428 AAATAAGTATGT
1 AAAT-AG-A--T
*
34440 AAATAAAT
1 AAATAGAT
* *
34448 ATATATAT
1 AAATAGAT
* *
34456 ATATATAT
1 AAATAGAT
34464 AAATA-A-
1 AAATAGAT
*
34470 AGAATAGCT
1 A-AATAGAT
*
34479 TAATAGAT
1 AAATAGAT
*
34487 AATTAGA-
1 AAATAGAT
*
34494 AGGATAGAT
1 A-AATAGAT
34503 AAATA-AT
1 AAATAGAT
*
34510 -AGTAG-T
1 AAATAGAT
34516 AAATAGAT
1 AAATAGAT
34524 -AATAGTACT
1 AAATAG-A-T
34533 AAATAGAT
1 AAATAGAT
34541 -AATA-AT
1 AAATAGAT
34547 AAATA-AT
1 AAATAGAT
* *
34554 -AAT-TAC
1 AAATAGAT
34560 AAATAGAT
1 AAATAGAT
*
34568 AAGA-AAAT
1 AA-ATAGAT
*
34576 GAATAG-T
1 AAATAGAT
34583 AAATAGAT
1 AAATAGAT
34591 AAA
1 AAA
34594 ACAAAAAAAA
Statistics
Matches: 151, Mismatches: 32, Indels: 45
0.66 0.14 0.20
Matches are distributed among these distances:
6 11 0.07
7 41 0.27
8 80 0.53
9 6 0.04
10 7 0.05
11 1 0.01
12 5 0.03
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.27
Consensus pattern (8 bp):
AAATAGAT
Found at i:34527 original size:17 final size:17
Alignment explanation
Indices: 34505--34569 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
34495 GGATAGATAA
*
34505 ATAATAGTAGTAAATAG
1 ATAATAGTACTAAATAG
34522 ATAATAGTACTAAATAG
1 ATAATAGTACTAAATAG
34539 ATAATA--A-TAAATA-
1 ATAATAGTACTAAATAG
34552 ATAAT--TAC-AAATAG
1 ATAATAGTACTAAATAG
34566 ATAA
1 ATAA
34570 GAAAATGAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
13 11 0.25
14 10 0.23
15 1 0.02
17 22 0.50
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.29
Consensus pattern (17 bp):
ATAATAGTACTAAATAG
Found at i:34547 original size:27 final size:27
Alignment explanation
Indices: 34517--34569 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
34507 AATAGTAGTA
*
34517 AATAGATAAT-AGTACTAAATAGATAAT
1 AATAAATAATAAGTAC-AAATAGATAAT
*
34544 AATAAATAATAATTACAAATAGATAA
1 AATAAATAATAAGTACAAATAGATAA
34570 GAAAATGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (27 bp):
AATAAATAATAAGTACAAATAGATAAT
Found at i:34637 original size:22 final size:22
Alignment explanation
Indices: 34496--34649 Score: 80
Period size: 22 Copynumber: 6.6 Consensus size: 22
34486 TAATTAGAAG
*
34496 GATAGATAAATAATAGT-AGTA
1 GATAGATAAATAATAGTAAATA
* * *
34517 AATAGAT-AATAGTACTAAATA
1 GATAGATAAATAATAGTAAATA
* *
34538 GATAATAATAAATAATAATTACAAATA
1 GAT-A-GATAAATAAT-AGT--AAATA
34565 GATAAGA-AAATGAATAGTAAATA
1 GAT-AGATAAAT-AATAGTAAATA
* * * *
34588 GATAAAACAAAAAAAACTAAGTAGATA
1 GAT---AGATAAATAA-T-AGTAAATA
*
34615 GATAGATAGATAATAGTAAATA
1 GATAGATAAATAATAGTAAATA
34637 GATAGATAAATAA
1 GATAGATAAATAA
34650 AATAATTTAA
Statistics
Matches: 101, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
20 7 0.07
21 11 0.11
22 20 0.20
23 11 0.11
24 11 0.11
25 13 0.13
26 8 0.08
27 20 0.20
ACGTcount: A:0.60, C:0.03, G:0.13, T:0.25
Consensus pattern (22 bp):
GATAGATAAATAATAGTAAATA
Found at i:36394 original size:1 final size:1
Alignment explanation
Indices: 36390--36415 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
36380 GGTTTTTTCC
36390 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
36416 CCTTCCTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:39101 original size:17 final size:16
Alignment explanation
Indices: 39056--39120 Score: 59
Period size: 17 Copynumber: 4.2 Consensus size: 16
39046 ATTTATTTTC
39056 TTATCTATTT-GTA-A
1 TTATCTATTTAGTATA
39070 TTAT-TATTTA-T-TA
1 TTATCTATTTAGTATA
39083 TTATCTATTTAGTACTA
1 TTATCTATTTAGTA-TA
* *
39100 TTATCTAATTAATACTA
1 TTATCTATTTAGTA-TA
39117 TTAT
1 TTAT
39121 TTATCTATCT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
13 11 0.26
14 10 0.23
15 1 0.02
17 21 0.49
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (16 bp):
TTATCTATTTAGTATA
Found at i:39101 original size:20 final size:20
Alignment explanation
Indices: 39078--39128 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 20
39068 AATTATTATT
*
39078 TATTATTATCTATTTAGTAC
1 TATTATTATCTATTTAATAC
*
39098 ---TATTATCTAATTAATAC
1 TATTATTATCTATTTAATAC
39115 TATTATTTATCTAT
1 TATTA-TTATCTAT
39129 CTTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 7
0.71 0.09 0.21
Matches are distributed among these distances:
17 15 0.62
20 2 0.08
21 7 0.29
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (20 bp):
TATTATTATCTATTTAATAC
Found at i:39178 original size:4 final size:4
Alignment explanation
Indices: 39169--39322 Score: 73
Period size: 4 Copynumber: 38.5 Consensus size: 4
39159 TATTAAGCTA
* * * *
39169 TTAT TTAT TTAT TTAT TTAT TTAT TTAT ATAT ATAT ATAT ATAT ATT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT
* * * * * * * * *
39217 CTGT TTAC ATAC TTAT TTAT CTAT TTGT TTAT ATAT CTAT TTAT CTT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT
* * * * * *
39265 TTAT TTAT CTA- TTAT TTTT TTAT AGTTAT CTA- TTAC TTAA TTAT ATAT
1 TTAT TTAT TTAT TTAT TTAT TTAT --TTAT TTAT TTAT TTAT TTAT TTAT
39313 TTAT TTAT TT
1 TTAT TTAT TT
39323 TAATCTTAAT
Statistics
Matches: 116, Mismatches: 26, Indels: 16
0.73 0.16 0.10
Matches are distributed among these distances:
3 7 0.06
4 102 0.88
5 3 0.03
6 4 0.03
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (4 bp):
TTAT
Found at i:39308 original size:21 final size:21
Alignment explanation
Indices: 39269--39309 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39259 ATCTTTTTAT
* **
39269 TTATCTATTATTTTTTTATAG
1 TTATCTATTACTTAATTATAG
39290 TTATCTATTACTTAATTATA
1 TTATCTATTACTTAATTATA
39310 TATTTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATCTATTACTTAATTATAG
Done.