Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008961.1 Corchorus capsularis cultivar CVL-1 contig08982, 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: 21592
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Found at i:693 original size:15 final size:16
Alignment explanation
Indices: 673--706 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
663 GATTGCTTTC
*
673 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
688 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
704 TTA
1 TTA
707 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:1512 original size:27 final size:27
Alignment explanation
Indices: 1453--1530 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
1443 ATTAGGGTCG
* **
1453 CCCAAGGGCATTTTGGTCATTTTTTGCA
1 CCCAGGGGCATTTTGGTCA-TTTTCACA
1481 CCCAGGGGCATTTTGGTCATTTTCACA
1 CCCAGGGGCATTTTGGTCATTTTCACA
* * *
1508 TCCAGGGGTATTTAGGTCATTTT
1 CCCAGGGGCATTTTGGTCATTTT
1531 GGCATTTAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 26 0.59
28 18 0.41
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTCACA
Found at i:1541 original size:27 final size:27
Alignment explanation
Indices: 1482--1558 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
1472 TTTTTTGCAC
* *
1482 CCAGGGGCATTTTGGTCATTTTCACAT
1 CCAGGGGTATTTAGGTCATTTTCACAT
**
1509 CCAGGGGTATTTAGGTCATTTTGGCAT
1 CCAGGGGTATTTAGGTCATTTTCACAT
** *
1536 TTAGGGGTATCTTAAGTCATTTT
1 CCAGGGGTAT-TTAGGTCATTTT
1559 AAGTTCACTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 31 0.74
28 11 0.26
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (27 bp):
CCAGGGGTATTTAGGTCATTTTCACAT
Found at i:1813 original size:16 final size:16
Alignment explanation
Indices: 1794--1824 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1784 ATACTAACCA
1794 TTAACCATATTAGTTG
1 TTAACCATATTAGTTG
*
1810 TTAATCATATTAGTT
1 TTAACCATATTAGTT
1825 ATATTAAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (16 bp):
TTAACCATATTAGTTG
Found at i:4509 original size:51 final size:51
Alignment explanation
Indices: 4454--4626 Score: 240
Period size: 51 Copynumber: 3.4 Consensus size: 51
4444 GTCATATCAG
* *
4454 ATTTCATCAATAAAAATTGAATCTTTAAGTAGTAAATGACAATTTTTGGTA
1 ATTTCATCAATAAAAATTGAATCTTTAAGTAGAAAATGAAAATTTTTGGTA
* *
4505 ATTTCATCAATAAAATTTGAAATCTTTAAGTAGAAAATGATAATTTTTGGGTA
1 ATTTCATCAATAAAAATTG-AATCTTTAAGTAGAAAATGAAAATTTTT-GGTA
* * * * *
4558 ATTTCATCAAT-AAAATTGAATCTTTAAGTAGCAAGTGAAAAATTTCGATA
1 ATTTCATCAATAAAAATTGAATCTTTAAGTAGAAAATGAAAATTTTTGGTA
4608 ATTTCATCAATAAAAATTG
1 ATTTCATCAATAAAAATTG
4627 GACTTAAAAT
Statistics
Matches: 109, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
50 14 0.13
51 48 0.44
52 32 0.29
53 15 0.14
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.38
Consensus pattern (51 bp):
ATTTCATCAATAAAAATTGAATCTTTAAGTAGAAAATGAAAATTTTTGGTA
Found at i:5636 original size:55 final size:55
Alignment explanation
Indices: 5571--5801 Score: 325
Period size: 55 Copynumber: 4.3 Consensus size: 55
5561 AAAAAAGGGC
* *
5571 AATCAGTAATTAAGTAAAAAGTGATTAATCAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* * *
5626 AATTAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAACCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* *
5681 AATCAGTAATTAAGTAAAAAGAGGTTAATCAAAGTC-----AA-AGTAAT-AGT-
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
*
5728 AATCAGTAATTAAATAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
*
5783 AATCAGTAATCAAGTAAAA
1 AATCAGTAATTAAGTAAAA
5802 GATAGTAATC
Statistics
Matches: 155, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
47 33 0.21
48 3 0.02
49 5 0.03
50 2 0.01
52 2 0.01
53 6 0.04
54 3 0.02
55 101 0.65
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.26
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
Found at i:5689 original size:47 final size:47
Alignment explanation
Indices: 5638--5791 Score: 164
Period size: 47 Copynumber: 3.1 Consensus size: 47
5628 TTAGTAATTA
* *
5638 AGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAACCAGTAAATC
1 AGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATC
* * * * *
5685 AGTAATTAAGTAAAAAGAGGTTAATCAAAGTCAAAGTAATAGTAATCAGTAATTA
1 --------AGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATC
*
5740 AATAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATC
1 AGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATC
5787 AGTAA
1 AGTAA
5792 TCAAGTAAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
47 45 0.53
55 40 0.47
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.25
Consensus pattern (47 bp):
AGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATC
Found at i:5746 original size:102 final size:108
Alignment explanation
Indices: 5571--5801 Score: 330
Period size: 102 Copynumber: 2.2 Consensus size: 108
5561 AAAAAAGGGC
* * * *
5571 AATCAGTAATTAAGTAAAAAGTGATTAATCAGAGTTAAGGTAATAGTAATCAGTAAATTAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAAAGTCAAAGTAATAGTAATCAGTAAATTA-TAA-
*
5636 TAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAACCAGTA
64 TAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAACCAGTA
*
5681 AATCAGTAATTAAGTAAAAAGAGGTTAATCAAAGTCAAAGTAATAGTAATCAGT-AA-T-T-A-A
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAAAGTCAAAGTAATAGTAATCAGTAAATTATAATA
*
5741 A-TAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
66 AGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAACCAGTA
*
5783 AATCAGTAATCAAGTAAAA
1 AATCAGTAATTAAGTAAAA
5802 GATAGTAATC
Statistics
Matches: 113, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
102 57 0.50
103 2 0.02
105 1 0.01
106 1 0.01
108 1 0.01
109 2 0.02
110 49 0.43
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.26
Consensus pattern (108 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAAAGTCAAAGTAATAGTAATCAGTAAATTATAATA
AGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAACCAGTA
Found at i:5823 original size:18 final size:17
Alignment explanation
Indices: 5770--5823 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
5760 AGTCAAGGTA
5770 ATAGTAATCAGTAAAT-
1 ATAGTAATCAGTAAATG
* *
5786 -CAGTAATCAAGTAAAAG
1 ATAGTAATC-AGTAAATG
5803 ATAGTAATCAGTAAATTG
1 ATAGTAATCAGTAAA-TG
5821 ATA
1 ATA
5824 ATTAAGAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 7 0.23
16 6 0.20
17 6 0.20
18 11 0.37
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (17 bp):
ATAGTAATCAGTAAATG
Found at i:5879 original size:72 final size:70
Alignment explanation
Indices: 5758--5901 Score: 184
Period size: 72 Copynumber: 2.0 Consensus size: 70
5748 GAGATTAATC
* * *
5758 AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAGATAGTAATCAGTAAATTGAT
1 AGAGTCAAGGTAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAGATAGTAATCAGTAAATCGAT
5823 AATTA
66 AATTA
* * *
5828 AGAGTCAAGGTAAGAGATTAATCAGTAATTAAAG-AGTCAAGGTAAAA-ATAGTAATCAGTGAAT
1 AGAGTCAAGGTAAGAG--TAATCAGTAAAT-AAGTAATCAA-GTAAAAGATAGTAATCAGTAAAT
5891 CGATAATTA
62 CGATAATTA
5900 AG
1 AG
5902 GGTTAAAGTG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
70 15 0.23
72 41 0.64
73 8 0.12
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (70 bp):
AGAGTCAAGGTAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAGATAGTAATCAGTAAATCGAT
AATTA
Found at i:6160 original size:27 final size:27
Alignment explanation
Indices: 6056--6169 Score: 113
Period size: 27 Copynumber: 4.2 Consensus size: 27
6046 GGAAAAGAAG
*
6056 AAGAGTAAAAAGTGGTAATCAGTAAAA
1 AAGAGTAAAATGTGGTAATCAGTAAAA
* * *
6083 AAGAGTAAAA-GAGAGTAATTAGTAATA
1 AAGAGTAAAATGTG-GTAATCAGTAAAA
** **
6110 AAGAGTAAAAAATGGGGATCAGTAAAA
1 AAGAGTAAAATGTGGTAATCAGTAAAA
* *
6137 AAGAGTAAAATGTGGTATTTAGTAAGAA
1 AAGAGTAAAATGTGGTAATCAGTAA-AA
6165 AAGAG
1 AAGAG
6170 AGTAATTAAT
Statistics
Matches: 69, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
26 2 0.03
27 59 0.86
28 8 0.12
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.20
Consensus pattern (27 bp):
AAGAGTAAAATGTGGTAATCAGTAAAA
Found at i:6168 original size:74 final size:74
Alignment explanation
Indices: 6089--6307 Score: 318
Period size: 74 Copynumber: 3.0 Consensus size: 74
6079 AAAAAAGAGT
*
6089 AAAAGAGAGTAATTAGTAATAAAGAGTAAAAAATGGGGATCAGTAAAAAAGAGTAAAATGTGGTA
1 AAAAGAGAGTAATTAGTAATAAAGAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAATGTGGTA
6154 TTTAGTAAG
66 TTTAGTAAG
* *
6163 AAAAGAGAGTAATTAATAGTAAAGAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAATGTGGTA
1 AAAAGAGAGTAATTAGTAATAAAGAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAATGTGGTA
*
6228 TTCAGTAAG
66 TTTAGTAAG
* * * * *
6237 AAAAG-GGGTAATTAGTAAAAAAGAGTAAAAATATGGTAATCAGT-ACAAAGAGTAAAA-ATGGT
1 AAAAGAGAGTAATTAGTAATAAAGAGTAAAAA-ATGGTGATCAGTAAAAAAGAGTAAAATGTGGT
*
6299 AATTAGTAA
65 ATTTAGTAA
6308 TCAAGAAATA
Statistics
Matches: 131, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
72 11 0.08
73 34 0.26
74 86 0.66
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (74 bp):
AAAAGAGAGTAATTAGTAATAAAGAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAATGTGGTA
TTTAGTAAG
Found at i:6226 original size:27 final size:28
Alignment explanation
Indices: 6183--6241 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
6173 AATTAATAGT
6183 AAAGAGTAAAAAATGGTGA-TCAGTAA-A
1 AAAGAGTAAAAAATGGT-ATTCAGTAAGA
**
6210 AAAGAGTAAAATGTGGTATTCAGTAAGA
1 AAAGAGTAAAAAATGGTATTCAGTAAGA
6238 AAAG
1 AAAG
6242 GGGTAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 1 0.04
27 22 0.79
28 5 0.18
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.20
Consensus pattern (28 bp):
AAAGAGTAAAAAATGGTATTCAGTAAGA
Found at i:6306 original size:25 final size:27
Alignment explanation
Indices: 6243--6307 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 27
6233 TAAGAAAAGG
6243 GGTAATTAGTAAAAAAGAGTAAAAATAT
1 GGTAATTAGT-AAAAAGAGTAAAAATAT
* *
6271 GGTAATCAGTACAAAGAGT-AAAA-AT
1 GGTAATTAGTAAAAAGAGTAAAAATAT
6296 GGTAATTAGTAA
1 GGTAATTAGTAA
6308 TCAAGAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 12 0.36
26 4 0.12
27 8 0.24
28 9 0.27
ACGTcount: A:0.52, C:0.03, G:0.20, T:0.25
Consensus pattern (27 bp):
GGTAATTAGTAAAAAGAGTAAAAATAT
Found at i:7101 original size:2 final size:2
Alignment explanation
Indices: 7094--7118 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7084 ACTATGACCT
7094 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
7119 TGAAATCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8708 original size:67 final size:64
Alignment explanation
Indices: 8637--8886 Score: 342
Period size: 67 Copynumber: 4.0 Consensus size: 64
8627 TGGATACTTC
* *
8637 CTTTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTATTGTTTA
1 CTTTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGTTTA
* *
8701 C---TA---CTTTTACTTCTTGATTAACTTAATTGCTCTGAATTAAGCTAATTACTACTGGTTA
1 CTTTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGTTTA
*
8759 C---T--TCCTTTTACTTCTTGATTAACTTAATTACTCTTAATTAAGCTAATTACTACTGTTGAC
1 CTTTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGTT---
*
8819 TC
63 TA
8821 CTTTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGTTTA
1 CTTTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGTTTA
8885 CT
1 CT
8887 CCTTTTACTG
Statistics
Matches: 166, Mismatches: 10, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
58 53 0.32
59 50 0.30
61 2 0.01
62 2 0.01
64 4 0.02
65 1 0.01
67 54 0.33
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.47
Consensus pattern (64 bp):
CTTTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGTTTA
Found at i:8714 original size:58 final size:58
Alignment explanation
Indices: 8639--8895 Score: 352
Period size: 58 Copynumber: 4.3 Consensus size: 58
8629 GATACTTCCT
*
8639 TTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTATTG
1 TTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTACTG
* * *
8697 TTTACTACTTTTACTTCTTGATTAACTTAATTGCTCTGAATTAAGCTAATTACTACTG
1 TTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTACTG
* *
8755 GTTACTTCCTTTTACTTCTTGATTAACTTAATTACTCTTAATTAAGCTAATTACTACTGTTGACT
1 TTTAC-TCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCT-A--ACTAC---T-ACT
*
8820 CCT
58 --G
*
8823 TTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTG
1 TTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTACTG
8881 TTTACTCCTTTTACT
1 TTTACTCCTTTTACT
8896 GACTTCTCCT
Statistics
Matches: 175, Mismatches: 14, Indels: 20
0.84 0.07 0.10
Matches are distributed among these distances:
58 73 0.42
59 39 0.22
60 4 0.02
61 1 0.01
62 4 0.02
64 4 0.02
65 1 0.01
66 4 0.02
67 41 0.23
68 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.47
Consensus pattern (58 bp):
TTTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTACTG
Found at i:8904 original size:16 final size:16
Alignment explanation
Indices: 8885--8940 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
8875 CTACTGTTTA
8885 CTCCTTTTACTGACTT
1 CTCCTTTTACTGACTT
8901 CTCC-TTT-CT-A---
1 CTCCTTTTACTGACTT
*
8911 CTGCTTTTACTGACTT
1 CTCCTTTTACTGACTT
8927 CTCCTTTCTACTGA
1 CTCCTTT-TACTGA
8941 TTACTTCCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 13
0.67 0.04 0.28
Matches are distributed among these distances:
10 3 0.10
11 3 0.10
12 2 0.06
13 2 0.06
14 2 0.06
15 3 0.10
16 10 0.32
17 6 0.19
ACGTcount: A:0.12, C:0.32, G:0.07, T:0.48
Consensus pattern (16 bp):
CTCCTTTTACTGACTT
Found at i:8919 original size:26 final size:26
Alignment explanation
Indices: 8883--8939 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
8873 TACTACTGTT
*
8883 TACTCCTTTTACTGACTTCTCCTTTC
1 TACTGCTTTTACTGACTTCTCCTTTC
8909 TACTGCTTTTACTGACTTCTCCTTTC
1 TACTGCTTTTACTGACTTCTCCTTTC
8935 TACTG
1 TACTG
8940 ATTACTTCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.12, C:0.32, G:0.07, T:0.49
Consensus pattern (26 bp):
TACTGCTTTTACTGACTTCTCCTTTC
Found at i:9066 original size:25 final size:25
Alignment explanation
Indices: 9011--9059 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
9001 TCTTTGACTG
*
9011 ATTACTTCTCTTACTTTTAGTCTTA
1 ATTACTTCTCTTACTTTTACTCTTA
*
9036 ATTACTTCTTTTACTTTTACTCTT
1 ATTACTTCTCTTACTTTTACTCTT
9060 TTCTACTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTACTTCTCTTACTTTTACTCTTA
Found at i:9115 original size:42 final size:42
Alignment explanation
Indices: 9079--9159 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
9069 TTACTTCTTT
* *
9079 TTTTACTCTTTCACTTCTACTGATTACTTCTTTTACTTTTAC
1 TTTTACTCTTTCACTTCTACTAATTACTCCTTTTACTTTTAC
* *
9121 TTTTATTCTTTTACTTCTACTAATTACTCCTTTTACTTT
1 TTTTACTCTTTCACTTCTACTAATTACTCCTTTTACTTT
9160 CCCTCTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.01, T:0.59
Consensus pattern (42 bp):
TTTTACTCTTTCACTTCTACTAATTACTCCTTTTACTTTTAC
Found at i:9154 original size:36 final size:36
Alignment explanation
Indices: 9034--9221 Score: 174
Period size: 36 Copynumber: 5.2 Consensus size: 36
9024 CTTTTAGTCT
9034 TAATTACTTCTTTTACTTTTACTC--TT--TTCTAC
1 TAATTACTTCTTTTACTTTTACTCTTTTACTTCTAC
*
9066 TAATTACTTC-TTT--TTTTACTCTTTCACTTCTAC
1 TAATTACTTCTTTTACTTTTACTCTTTTACTTCTAC
*
9099 TGATTACTTCTTTTACTTTTACTTTTATTCTTTTACTTCTAC
1 TAATTACTTCTTTTACTTTTAC------TCTTTTACTTCTAC
* ** * *
9141 TAATTACTCCTTTTACTTTCCCTCTTTTTCTTCCAC
1 TAATTACTTCTTTTACTTTTACTCTTTTACTTCTAC
* * *
9177 TGATTACTTCTTTTACTCTTACTCTTTTTCTTCTAC
1 TAATTACTTCTTTTACTTTTACTCTTTTACTTCTAC
*
9213 TGATTACTT
1 TAATTACTT
9222 TTCTTATTTT
Statistics
Matches: 128, Mismatches: 15, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
29 8 0.06
31 4 0.03
32 10 0.08
33 15 0.12
34 3 0.02
36 57 0.45
42 31 0.24
ACGTcount: A:0.16, C:0.24, G:0.02, T:0.58
Consensus pattern (36 bp):
TAATTACTTCTTTTACTTTTACTCTTTTACTTCTAC
Found at i:9172 original size:42 final size:42
Alignment explanation
Indices: 9079--9177 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
9069 TTACTTCTTT
* * * *
9079 TTTTACTCTTTCACTTCTACTGATTACTTCTTTTACTTTTAC
1 TTTTATTCTTTCACTTCTACTAATTACTCCTTTTACTTTCAC
* *
9121 TTTTATTCTTTTACTTCTACTAATTACTCCTTTTACTTTCCC
1 TTTTATTCTTTCACTTCTACTAATTACTCCTTTTACTTTCAC
*
9163 TCTTT-TTCTTCCACT
1 T-TTTATTCTTTCACT
9178 GATTACTTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 45 0.94
43 3 0.06
ACGTcount: A:0.15, C:0.26, G:0.01, T:0.58
Consensus pattern (42 bp):
TTTTATTCTTTCACTTCTACTAATTACTCCTTTTACTTTCAC
Found at i:9187 original size:78 final size:75
Alignment explanation
Indices: 9060--9213 Score: 202
Period size: 78 Copynumber: 2.0 Consensus size: 75
9050 TTTTACTCTT
* * *
9060 TTCTACTAATTACTTCTTTTTTTACTCTTTCACTTCTACTGATTACTTCTTTTACTTTTACT-TT
1 TTCTACTAATTACTCCTTTTTTTACTCTTTCACTTCCACTGATTACTTCTTTTACTCTTACTCTT
*
9124 TATTCTTTTAC
66 T-TTCTTCTAC
* **
9135 TTCTACTAATTACTCCTTTTACTTTCCCTCTTTTTCTTCCACTGATTACTTCTTTTACTCTTACT
1 TTCTACTAATTACTCCTTTT--TTT-ACTCTTTCACTTCCACTGATTACTTCTTTTACTCTTACT
9200 CTTTTTCTTCTAC
63 CTTTTTCTTCTAC
9213 T
1 T
9214 GATTACTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
75 19 0.28
77 3 0.04
78 43 0.63
79 3 0.04
ACGTcount: A:0.16, C:0.25, G:0.01, T:0.58
Consensus pattern (75 bp):
TTCTACTAATTACTCCTTTTTTTACTCTTTCACTTCCACTGATTACTTCTTTTACTCTTACTCTT
TTTCTTCTAC
Found at i:9318 original size:49 final size:48
Alignment explanation
Indices: 9247--9400 Score: 159
Period size: 49 Copynumber: 3.0 Consensus size: 48
9237 CTTTCTACTG
*
9247 ATTACTCTTCCTTTTACTTCTTTAGCTTAATTACTCTGAATTAAACTA
1 ATTACTCTTACTTTTACTTCTTTAGCTTAATTACTCTGAATTAAACTA
*
9295 ATTACTACTTACTCTTT-CTTCTTTAGCTTAATTACTCTGAATTAAGCTATATGCTG
1 ATTACT-CTTACT-TTTACTTCTTTAGCTTAATTACTCTGAATT-A---A-A--CTA
*
9351 ATTACTCTTTCTTTTACTTCTTTTTAG-TCTAATTACTCTGAATTAAACTA
1 ATTACTCTTACTTTTACTTC--TTTAGCT-TAATTACTCTGAATTAAACTA
9401 TTCTGCTATT
Statistics
Matches: 89, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
48 6 0.07
49 31 0.35
50 6 0.07
52 1 0.01
53 2 0.02
54 4 0.04
55 9 0.10
56 10 0.11
57 20 0.22
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (48 bp):
ATTACTCTTACTTTTACTTCTTTAGCTTAATTACTCTGAATTAAACTA
Found at i:9384 original size:57 final size:57
Alignment explanation
Indices: 9310--9456 Score: 165
Period size: 57 Copynumber: 2.6 Consensus size: 57
9300 TACTTACTCT
* * *
9310 TTCTTCTTTAGCTTAATTACTCTGAATTAAGCTA-TATGCTGATTACTCTTTCTTTTAC
1 TTCTT-TTTAGCTTAATTACTCTGAATTAAACTATTATGCT-ATTACTCCTCCTTTTAC
*
9368 TTCTTTTTAG-TCTAATTACTCTGAATTAAACTATTCTGCTATTACTCCTCCTTTTAC
1 TTCTTTTTAGCT-TAATTACTCTGAATTAAACTATTATGCTATTACTCCTCCTTTTAC
** * * *
9425 -TCTTTTTAATTTAATTGCCCAGAATTAAACTA
1 TTCTTTTTAGCTTAATTACTCTGAATTAAACTA
9457 ATTACTGTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
56 27 0.35
57 41 0.53
58 10 0.13
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (57 bp):
TTCTTTTTAGCTTAATTACTCTGAATTAAACTATTATGCTATTACTCCTCCTTTTAC
Found at i:9509 original size:59 final size:59
Alignment explanation
Indices: 9322--9532 Score: 163
Period size: 56 Copynumber: 3.6 Consensus size: 59
9312 CTTCTTTAGC
* * * * *
9322 TTAATTACTCTGAATTAAGCT-ATATGCTGATTA--C-TCTTTCTTTTACTTCTTTTTAGT
1 TTAATTACTCTGAATTAAACTAAT-TACTGTTTACTCTTCTTTCCTTTAC-TCTTTTTAAT
*
9379 CTAATTACTCTGAATTAAACT-ATT-CTGCTATTACTC--C--TCCTTTTACTCTTTTTAAT
1 TTAATTACTCTGAATTAAACTAATTACTG-T-TTACTCTTCTTTCC-TTTACTCTTTTTAAT
* * * * *
9435 TTAATTGCCCAGAATTAAACTAATTACTGTTTACTCTTCTTTCCTTTACTCTTTCTATT
1 TTAATTACTCTGAATTAAACTAATTACTGTTTACTCTTCTTTCCTTTACTCTTTTTAAT
* * * *
9494 TTAATTATTCTGAATTTAACCAATTTACTGATTACTCTT
1 TTAATTACTCTGAATTAAACTAA-TTACTGTTTACTCTT
9533 TTTAATTTTG
Statistics
Matches: 124, Mismatches: 18, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
55 3 0.02
56 35 0.28
57 33 0.27
58 5 0.04
59 31 0.25
60 17 0.14
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (59 bp):
TTAATTACTCTGAATTAAACTAATTACTGTTTACTCTTCTTTCCTTTACTCTTTTTAAT
Found at i:9629 original size:53 final size:53
Alignment explanation
Indices: 9545--10083 Score: 791
Period size: 53 Copynumber: 10.2 Consensus size: 53
9535 TAATTTTGCT
* * *
9545 ACCTATTTACTGA-TTACTCCTTTCACTGCTTAGGTTAATTACTCTGAATTAG
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * *
9597 ACCTGTTTACTAATTTTCTCTTTTTACTGCTTAGGTTAATTACTCTGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * ** * *
9650 ACCTGTTTACTGGTTTAT-AGCTTTTACTTCTTAGTTTAATTACTCTGAATTAA
1 ACCTATTTACTGATTT-TCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
*
9703 ACCTATTTACTAATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * *
9756 ACCTATTTACTGATTTTCCCCTTTTACTACTTAGGTTAATTACTCAGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
9809 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTG-AATTAA
* * *
9863 ACCTATTTACTGATTTTCCCCTTTTACTACTTAGGTT-A--ACTCAGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
*
9913 ACCTATTTACTAATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * *
9966 ACCTATTTACTAATTTTCTCCTTTTATTGCTTAGGTTAATTACTCTGAATTGA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * *
10019 ACCTATTTACTGATTTTCCCCTTTTACTACTTAGGTTAATTACTCGGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
10072 ACCTATTTACTG
1 ACCTATTTACTG
10084 TTTACTCTTT
Statistics
Matches: 438, Mismatches: 42, Indels: 13
0.89 0.09 0.03
Matches are distributed among these distances:
50 40 0.09
51 6 0.01
52 12 0.03
53 338 0.77
54 42 0.10
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (53 bp):
ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
Found at i:10030 original size:263 final size:263
Alignment explanation
Indices: 9545--10095 Score: 856
Period size: 263 Copynumber: 2.1 Consensus size: 263
9535 TAATTTTGCT
* *
9545 ACCTATTTACTGATTACTCCTTTCACTGCTTAGGTTAATTACTCTGAATTAGACCTGTTTACTAA
1 ACCTATTTACTGATTACTCCTTTCACTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTAA
* * * * * ** *
9610 TTTTCTCTTTTTACTGCTTAGGTTAATTACTCTGAATTAAACCTGTTTACTGGTTTATAGCTTTT
66 TTTTCCCCTTTTACTACTTAGGTTAA-TACTCAGAATTAAACCTATTTACTAATTTATACCTTTT
* *
9675 ACTTCTTAGTTTAATTACTCTGAATTAAACCTATTTACTAATTTTCTCCTTTTACTGCTTAGGTT
130 ACTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTAATTTTCTCCTTTTACTGCTTAGGTT
9740 AATTACTCTGAATTAAACCTATTTACTGATTTTCCCCTTTTACTACTTAGGTTAATTACTCAGAA
195 AATTACTCTGAATTAAACCTATTTACTGATTTTCCCCTTTTACTACTTAGGTTAATTACTCAGAA
9805 TTAA
260 TTAA
* *
9809 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAAATTAAACCTATTTACT
1 ACCTATTTACTGA-TTACTCCTTTCACTGCTTAGGTTAATTACTCTG-AATTAAACCTATTTACT
* *
9874 GATTTTCCCCTTTTACTACTTAGGTT-A-ACTCAGAATTAAACCTATTTACTAATTT-TCTCCTT
64 AATTTTCCCCTTTTACTACTTAGGTTAATACTCAGAATTAAACCTATTTACTAATTTAT-ACCTT
*
9936 TTACTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTAATTTTCTCCTTTTATTGCTTAGG
128 TTACTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTAATTTTCTCCTTTTACTGCTTAGG
* *
10001 TTAATTACTCTGAATTGAACCTATTTACTGATTTTCCCCTTTTACTACTTAGGTTAATTACTCGG
193 TTAATTACTCTGAATTAAACCTATTTACTGATTTTCCCCTTTTACTACTTAGGTTAATTACTCAG
10066 AATTAA
258 AATTAA
* *
10072 ACCTATTTACTGTTTACTCTTTTC
1 ACCTATTTACTGATTACTCCTTTC
10096 TTTTCTCTTT
Statistics
Matches: 261, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
262 9 0.03
263 170 0.65
264 13 0.05
265 32 0.12
266 37 0.14
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (263 bp):
ACCTATTTACTGATTACTCCTTTCACTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTAA
TTTTCCCCTTTTACTACTTAGGTTAATACTCAGAATTAAACCTATTTACTAATTTATACCTTTTA
CTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTAATTTTCTCCTTTTACTGCTTAGGTTA
ATTACTCTGAATTAAACCTATTTACTGATTTTCCCCTTTTACTACTTAGGTTAATTACTCAGAAT
TAA
Found at i:13524 original size:34 final size:34
Alignment explanation
Indices: 13472--13536 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
13462 AACTCACTGG
*
13472 AATGGCCCCCTTGTGAGCAACTGAAAACTGCTAT
1 AATGCCCCCCTTGTGAGCAACTGAAAACTGCTAT
13506 AATGCCCCTCCTTG-GAGCAACTGAAAACTGC
1 AATGCCCC-CCTTGTGAGCAACTGAAAACTGC
13537 AAAGTTGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 24 0.83
35 5 0.17
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (34 bp):
AATGCCCCCCTTGTGAGCAACTGAAAACTGCTAT
Found at i:13604 original size:44 final size:44
Alignment explanation
Indices: 13506--13799 Score: 477
Period size: 44 Copynumber: 6.7 Consensus size: 44
13496 AAACTGCTAT
*
13506 AATG-CCCCTCCTTGGAGCAACTGAA-AACTGCAAAGTTGTTGG
1 AATGCCCCCTCCTTGGAGCAACTGAATAACTGAAAAGTTGTTGG
13548 AATGCCCCCTCCTTGGAGCAACTGAA-AATCTGAAAAGTTGTTGG
1 AATGCCCCCTCCTTGGAGCAACTGAATAA-CTGAAAAGTTGTTGG
* * *
13592 AATGCCCTCTCCTTGGAGCAACTGAAGAACTGTAAAGTTGTTGG
1 AATGCCCCCTCCTTGGAGCAACTGAATAACTGAAAAGTTGTTGG
*
13636 AATGCCCCCTCCTTGGAGCAACTGAATAACTGAAAAGTTGTTGA
1 AATGCCCCCTCCTTGGAGCAACTGAATAACTGAAAAGTTGTTGG
* *
13680 AATGCCCCCTCCTTAGAGCAACTGAATAACTGTAAAGTTGTTGG
1 AATGCCCCCTCCTTGGAGCAACTGAATAACTGAAAAGTTGTTGG
*
13724 AATGCCCCCTCCTTGGAGCAACTGAATAACTGAAAAGTTGTTGA
1 AATGCCCCCTCCTTGGAGCAACTGAATAACTGAAAAGTTGTTGG
*
13768 AATGCCCCCTCCTTGGAGCAACTGAAGAACTG
1 AATGCCCCCTCCTTGGAGCAACTGAATAACTG
13800 TTGAAAGATG
Statistics
Matches: 235, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
42 4 0.02
43 23 0.10
44 206 0.88
45 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (44 bp):
AATGCCCCCTCCTTGGAGCAACTGAATAACTGAAAAGTTGTTGG
Found at i:13912 original size:38 final size:38
Alignment explanation
Indices: 13809--13935 Score: 155
Period size: 38 Copynumber: 3.3 Consensus size: 38
13799 GTTGAAAGAT
* * *
13809 GATCTTGATAACTGTTGAAAGACAACATGTTTCCAGTC
1 GATCTTGATAACTGCTGAAAGACGACCTGTTTCCAGTC
* * * *
13847 GAACTTGATAAGTGCTGAAAGACGACCTGTCTCCAGCC
1 GATCTTGATAACTGCTGAAAGACGACCTGTTTCCAGTC
* * *
13885 GATCTTGATAACTGCTGAATGATGACCTGTTTTCAGTC
1 GATCTTGATAACTGCTGAAAGACGACCTGTTTCCAGTC
*
13923 AATCTTGATAACT
1 GATCTTGATAACT
13936 TACTTCGAGA
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 74 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (38 bp):
GATCTTGATAACTGCTGAAAGACGACCTGTTTCCAGTC
Found at i:19687 original size:6 final size:6
Alignment explanation
Indices: 19676--19702 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19666 TTAATTCTGC
19676 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
19703 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Done.