Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010644.1 Corchorus capsularis cultivar CVL-1 contig10665, 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: 65260
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:23 original size:17 final size:17
Alignment explanation
Indices: 1--41 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
*
1 ATATATTTAGATATTAT
1 ATATATATAGATATTAT
18 ATATATATAGATATTAT
1 ATATATATAGATATTAT
35 ATATATA
1 ATATATA
42 ATATATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
ATATATATAGATATTAT
Found at i:421 original size:101 final size:101
Alignment explanation
Indices: 246--469 Score: 385
Period size: 101 Copynumber: 2.2 Consensus size: 101
236 TTTTTGAACT
* * *
246 ATCTTTGCAAAGTATTATTGAAATTTGTCTTCCATTATTGAACTTTGCAAAACATTATTGAAAGA
1 ATCTTTGCATAGCATTATTGAAACTTGTCTTCCATTATTGAACTTTGCAAAACATTATTGAAAGA
311 TTCCCTTCAACTTTTGACTTGTTTTGCTTTTCTCTC
66 TTCCCTTCAACTTTTGACTTGTTTTGCTTTTCTCTC
* * *
347 ATCTTTGCATAGCATTATTGAAGCTTGTCTTCCATTATTGAACTTTGCAGAGCATTATTGAAAGA
1 ATCTTTGCATAGCATTATTGAAACTTGTCTTCCATTATTGAACTTTGCAAAACATTATTGAAAGA
*
412 TTCCCTTCAATTTTTGACTTGTTTTGCTTTTCTCTC
66 TTCCCTTCAACTTTTGACTTGTTTTGCTTTTCTCTC
448 ATCTTTGCATAGCATTATTGAA
1 ATCTTTGCATAGCATTATTGAA
470 CTTTGCATAA
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 116 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (101 bp):
ATCTTTGCATAGCATTATTGAAACTTGTCTTCCATTATTGAACTTTGCAAAACATTATTGAAAGA
TTCCCTTCAACTTTTGACTTGTTTTGCTTTTCTCTC
Found at i:10224 original size:11 final size:11
Alignment explanation
Indices: 10208--10243 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
10198 ATTTGTTCAT
10208 TATTAATTAGA
1 TATTAATTAGA
*
10219 TATTAATTAGC
1 TATTAATTAGA
*
10230 TATTAATTAAA
1 TATTAATTAGA
10241 TAT
1 TAT
10244 ATTATAATGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (11 bp):
TATTAATTAGA
Found at i:15101 original size:30 final size:28
Alignment explanation
Indices: 15035--15086 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
15025 CAATGCACAA
15035 TATAA-TT-TAATCCATTTTATTTATAT
1 TATAACTTATAATCCATTTTATTTATAT
15061 TATAACTTATAATCCATTTTATTTAT
1 TATAACTTATAATCCATTTTATTTAT
15087 CTCTTCAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 5 0.21
27 2 0.08
28 17 0.71
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.56
Consensus pattern (28 bp):
TATAACTTATAATCCATTTTATTTATAT
Found at i:15462 original size:16 final size:16
Alignment explanation
Indices: 15441--15481 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
15431 GTCGGATTGA
15441 TTGGGTTCGAGTCATT
1 TTGGGTTCGAGTCATT
* *
15457 TTGGGTTTGGGTCATT
1 TTGGGTTCGAGTCATT
*
15473 TCGGGTTCG
1 TTGGGTTCG
15482 GGCACCTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.07, C:0.12, G:0.37, T:0.44
Consensus pattern (16 bp):
TTGGGTTCGAGTCATT
Found at i:25874 original size:2 final size:2
Alignment explanation
Indices: 25867--25910 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
25857 TGGGTTTATC
25867 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25907 AT AT
1 AT AT
25911 CTCAAGCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:37262 original size:2 final size:2
Alignment explanation
Indices: 37255--37288 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
37245 TTTTCCTTGG
* *
37255 TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37289 ATGTGATGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:37431 original size:30 final size:30
Alignment explanation
Indices: 37395--37452 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
37385 AGAAGGAGGA
37395 GGAATCGCAAACCCTAATACAAGTAGCATG
1 GGAATCGCAAACCCTAATACAAGTAGCATG
* * *
37425 GGAATCGCAAATCCTACTTCAAGTAGCA
1 GGAATCGCAAACCCTAATACAAGTAGCA
37453 AGGAGAAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (30 bp):
GGAATCGCAAACCCTAATACAAGTAGCATG
Found at i:37598 original size:21 final size:21
Alignment explanation
Indices: 37572--37612 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
37562 TCTTGAAGGC
*
37572 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGATCAA
**
37593 TTGAAGAGTATTGAAGATCA
1 TTGAAGACCATTGAAGATCA
37613 TAAGCCAAGG
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:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGAAGACCATTGAAGATCAA
Found at i:44831 original size:30 final size:30
Alignment explanation
Indices: 44795--44852 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
44785 AGAAAGAGGA
44795 GGAATCGCAAACCCTAATTCAAGTAGCATG
1 GGAATCGCAAACCCTAATTCAAGTAGCATG
* *
44825 GGAATCGCAAATCCTACTTCAAGTAGCA
1 GGAATCGCAAACCCTAATTCAAGTAGCA
44853 AGGAGAAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (30 bp):
GGAATCGCAAACCCTAATTCAAGTAGCATG
Found at i:44998 original size:21 final size:21
Alignment explanation
Indices: 44972--45012 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
44962 TCTTGAAGGC
*
44972 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGATCAA
**
44993 TTGAAGAGTATTGAAGATCA
1 TTGAAGACCATTGAAGATCA
45013 TAAGCTAAGG
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:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGAAGACCATTGAAGATCAA
Found at i:46359 original size:16 final size:16
Alignment explanation
Indices: 46338--46371 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
46328 ACAATTCAGA
*
46338 AAGCAGAAAACCTCTG
1 AAGCAGAAAAACTCTG
46354 AAGCAGAAAAACTCTG
1 AAGCAGAAAAACTCTG
46370 AA
1 AA
46372 ATATTTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAACTCTG
Found at i:46836 original size:5 final size:5
Alignment explanation
Indices: 46826--46852 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
46816 TTGACCCTTG
46826 AATCA AATCA AATCA AATCA AATCA AA
1 AATCA AATCA AATCA AATCA AATCA AA
46853 CTCTCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AATCA
Found at i:48114 original size:94 final size:95
Alignment explanation
Indices: 47943--48135 Score: 298
Period size: 94 Copynumber: 2.0 Consensus size: 95
47933 ATTCACATAA
* *
47943 AATTTGATAGATTGCAGACAAAAGTAAGAGTTCTCACTACTTATAAACAGAAAATAAGATATAGC
1 AATTTGATAAATTGCAGACAAAAGTAAGAGTTCTCACTACTAATAAACAGAAAATAAGATATAGC
* *
48008 TTTTAGTGCTCAAAAAAGAAAGTTGGAATC
66 TTTAAGTGCTCAAAAAAGAAAGGTGGAATC
* *
48038 AATTTGATAAATTGCAGAC-AAAGTAAGAGTTCTCACTACTAATAAACAGAAATTAAGATGTAGC
1 AATTTGATAAATTGCAGACAAAAGTAAGAGTTCTCACTACTAATAAACAGAAAATAAGATATAGC
* * *
48102 TTTAAGTTCTCAAAACAGAAAGGTGGACTC
66 TTTAAGTGCTCAAAAAAGAAAGGTGGAATC
48132 AATT
1 AATT
48136 CGGAACAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
94 71 0.80
95 18 0.20
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (95 bp):
AATTTGATAAATTGCAGACAAAAGTAAGAGTTCTCACTACTAATAAACAGAAAATAAGATATAGC
TTTAAGTGCTCAAAAAAGAAAGGTGGAATC
Found at i:53628 original size:1 final size:1
Alignment explanation
Indices: 53624--53655 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
53614 TTGTCTTTCC
53624 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53656 CCTCTTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:54452 original size:25 final size:24
Alignment explanation
Indices: 54418--54476 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
54408 TTCAAACCCT
*
54418 AAACTTCATTTCTAACAACTTATTC
1 AAACTTCATTTCTAACAA-ATATTC
* *
54443 AAACTTCATTTTTAACAAATCTTC
1 AAACTTCATTTCTAACAAATATTC
54467 AAA-TTCATTT
1 AAACTTCATTT
54477 TCCTTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 7 0.23
24 7 0.23
25 17 0.55
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.42
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATATTC
Found at i:54526 original size:26 final size:25
Alignment explanation
Indices: 54492--54603 Score: 99
Period size: 26 Copynumber: 4.5 Consensus size: 25
54482 CATTTTAATC
54492 ATAAACTAATTAAATACTAATTACTA
1 ATAAACTAATTAAATACTAATT-CTA
* **
54518 ATAAACTAATTAGATACTAATTAAA
1 ATAAACTAATTAAATACTAATTCTA
* *
54543 CATAAACTAA-TAAACTAAGTAATTTTA
1 -ATAAACTAATTAAA-T-ACTAATTCTA
*
54570 ATTAACTAATTAAA-ACTAA-TC--
1 ATAAACTAATTAAATACTAATTCTA
54591 ATAAACTAATTAA
1 ATAAACTAATTAA
54604 TATTAAAAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
21 12 0.17
23 1 0.01
24 4 0.06
25 4 0.06
26 39 0.55
27 11 0.15
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (25 bp):
ATAAACTAATTAAATACTAATTCTA
Found at i:54527 original size:15 final size:13
Alignment explanation
Indices: 54492--54583 Score: 52
Period size: 13 Copynumber: 7.1 Consensus size: 13
54482 CATTTTAATC
54492 ATAAACTAATTAA
1 ATAAACTAATTAA
54505 AT--ACTAATTACTA
1 ATAAACTAATTA--A
*
54518 ATAAACTAATTAG
1 ATAAACTAATTAA
54531 AT--ACTAATTAAA
1 ATAAACTAATT-AA
54543 CATAAACTAA-TAA
1 -ATAAACTAATTAA
* *
54556 ACT-AAGTAATTTTA
1 A-TAAACTAA-TTAA
*
54570 ATTAACTAATTAA
1 ATAAACTAATTAA
54583 A
1 A
54584 ACTAATCATA
Statistics
Matches: 61, Mismatches: 6, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
11 15 0.25
12 7 0.11
13 17 0.28
14 9 0.15
15 13 0.21
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (13 bp):
ATAAACTAATTAA
Found at i:54577 original size:52 final size:51
Alignment explanation
Indices: 54486--54603 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
54476 TTCCTTCATT
* *
54486 TTAATCATAAACTAATTAAATACTAATTACTAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATACTAATTACTAATAAACTAATTA-AAACTAA
* * *
54538 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTACTAATAAACTAATTAAAACTAA
54589 -T---CATAAACTAATTAA
1 TTAAACATAAACTAATTAA
54604 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 10 0.17
48 3 0.05
50 1 0.02
51 10 0.17
52 28 0.48
53 6 0.10
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTACTAATAAACTAATTAAAACTAA
Found at i:59814 original size:33 final size:32
Alignment explanation
Indices: 59777--59857 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
59767 TGTTTCGTCA
* *
59777 CAAACAACACCTAAAGCAGATTTAGTGTCATTG
1 CAAACAACA-CTAAAGCAGATTTAGTATCATCG
** *
59810 CAAACAACACTCAAATTAGGTTTAGTATCATCG
1 CAAACAACACT-AAAGCAGATTTAGTATCATCG
59843 CAAACAACATCTAAA
1 CAAACAACA-CTAAA
59858 AGACTCTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 2 0.05
33 37 0.90
34 2 0.05
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.23
Consensus pattern (32 bp):
CAAACAACACTAAAGCAGATTTAGTATCATCG
Found at i:64731 original size:27 final size:26
Alignment explanation
Indices: 64687--64962 Score: 200
Period size: 26 Copynumber: 10.2 Consensus size: 26
64677 TATTTCTTGA
*
64687 TTACTAATTACCATTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
* * * *
64713 GTACTGATTACCATATTTTGCTTTTT
1 TTACTGATTACCATTTTTTACTCTTT
* *
64739 TTACTGATTACCCCTTTTCTTACTGTTT
1 TTACTGATTA-CCATTTT-TTACTCTTT
* * *
64767 TGACTGAATACCACTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
*
64793 TTACTTAATTACCATTTTTTACTCTCCCTTTT
1 TTAC-TGATTACCATTTTTTA--CT--C-TTT
* * *
64825 TTACTCAATACCA-TTTTTACCCCTTT
1 TTACTGATTACCATTTTTTA-CTCTTT
* *
64851 TTACTGAATACCACTTTTTACTCTTTT
1 TTACTGATTACCATTTTTTACTC-TTT
*
64878 TTACTGATTACCATTTCTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
** *
64904 ATTACCAATTA-C-TCTCTTTAGCT-TTT
1 -TTACTGATTACCAT-TTTTTA-CTCTTT
*
64930 TTACTGATCACCATTTTTTACTCATTT
1 TTACTGATTACCATTTTTTACTC-TTT
64957 CTTACT
1 -TTACT
64963 CTTTTTACTG
Statistics
Matches: 196, Mismatches: 36, Indels: 34
0.74 0.14 0.13
Matches are distributed among these distances:
25 10 0.05
26 75 0.38
27 67 0.34
28 20 0.10
29 3 0.02
30 6 0.03
31 8 0.04
32 7 0.04
ACGTcount: A:0.21, C:0.23, G:0.04, T:0.52
Consensus pattern (26 bp):
TTACTGATTACCATTTTTTACTCTTT
Found at i:64851 original size:58 final size:57
Alignment explanation
Indices: 64764--64874 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 57
64754 TTTCTTACTG
* * * *
64764 TTTTGACTGAATACCACTTTTTACTCTTTTTACTTAATTACCATTTTTTACTCTCCCT
1 TTTTGACTCAATACCACTTTTTACCCTTTTTACTGAA-TACCACTTTTTACTCTCCCT
*
64822 TTTTTACTCAATACCA-TTTTTACCCCTTTTTACTGAATACCACTTTTTACTCT
1 TTTTGACTCAATACCACTTTTTA-CCCTTTTTACTGAATACCACTTTTTACTCT
64875 TTTTTACTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
57 21 0.45
58 26 0.55
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (57 bp):
TTTTGACTCAATACCACTTTTTACCCTTTTTACTGAATACCACTTTTTACTCTCCCT
Found at i:64969 original size:37 final size:37
Alignment explanation
Indices: 64927--64999 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
64917 CTCTTTAGCT
64927 TTTTTACTGATCAC-CATTTT-TTACTCATTTCTTACTC
1 TTTTTACTGATCACTC-TTTTCTTACTC-TTTCTTACTC
* *
64964 TTTTTACTGATTACTCTTTTCTTACTCTTTTTTACT
1 TTTTTACTGATCACTCTTTTCTTACTCTTTCTTACT
65000 GATTACCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.16, C:0.22, G:0.03, T:0.59
Consensus pattern (37 bp):
TTTTTACTGATCACTCTTTTCTTACTCTTTCTTACTC
Found at i:65004 original size:28 final size:27
Alignment explanation
Indices: 64947--65019 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
64937 TCACCATTTT
64947 TTACTCATTTCTTACTCTTTTTACTGA
1 TTACTCATTTCTTACTCTTTTTACTGA
*
64974 TTACTCTTTTCTTACTCTTTTTTACTGA
1 TTACTCATTTCTTACTC-TTTTTACTGA
65002 TTAC-CACTTT-TTACTCTT
1 TTACTCA-TTTCTTACTCTT
65020 CTTCTTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 2 0.05
27 23 0.55
28 17 0.40
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.58
Consensus pattern (27 bp):
TTACTCATTTCTTACTCTTTTTACTGA
Found at i:65013 original size:65 final size:62
Alignment explanation
Indices: 64885--65040 Score: 170
Period size: 65 Copynumber: 2.4 Consensus size: 62
64875 TTTTTACTGA
** *
64885 TTAC-CATTTCTTACTCTTTATTACCAATTACTCTCTTTAGCTTTTTTACTGATCACCATTTT
1 TTACTCATTTCTTACTCTTT-TTACTGATTACTCTCTTTAGCTTTTTTACTGATCACCACTTT
* * *
64947 TTACTCATTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTT
1 TTACTCATTTCTTACTCTTTTTACTGATTACTC-TCT-TTA-GCTTTTTTACTGATCACCACTTT
* **
65012 TTACTCTTCTTCTTTTTCTCTTTTACTGA
1 TTACTCAT-TTCTTACTCT-TTTTACTGA
65041 CTACCATTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
62 15 0.19
63 17 0.22
64 3 0.04
65 27 0.34
66 8 0.10
67 9 0.11
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.56
Consensus pattern (62 bp):
TTACTCATTTCTTACTCTTTTTACTGATTACTCTCTTTAGCTTTTTTACTGATCACCACTTT
Found at i:65016 original size:38 final size:38
Alignment explanation
Indices: 64974--65050 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
64964 TTTTTACTGA
* *
64974 TTACTCTT-TTCTTACTCTTTTTTACTGATTACCACTTT
1 TTACTCTTCTTCTTACTCTCTTTTACTGACTACCA-TTT
**
65012 TTACTCTTCTTCTTTTTCTCTTTTACTGACTACCATTT
1 TTACTCTTCTTCTTACTCTCTTTTACTGACTACCATTT
65050 T
1 T
65051 GCTCTTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 12 0.35
39 22 0.65
ACGTcount: A:0.14, C:0.25, G:0.03, T:0.58
Consensus pattern (38 bp):
TTACTCTTCTTCTTACTCTCTTTTACTGACTACCATTT
Found at i:65091 original size:22 final size:22
Alignment explanation
Indices: 65066--65146 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
65056 TTGAATTTAA
*
65066 TTACTGACTATCATTTTACTCT
1 TTACTGATTATCATTTTACTCT
** *
65088 TTACTGATTATTTTTTTACTTTT
1 TTACTGATTATCATTTTAC-TCT
*
65111 TTATTGATTA-CTATTTTACTC-
1 TTACTGATTATC-ATTTTACTCT
*
65132 TTACTGATTACCATT
1 TTACTGATTATCATT
65147 ACTTTTTGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
21 12 0.26
22 18 0.38
23 17 0.36
ACGTcount: A:0.22, C:0.16, G:0.05, T:0.57
Consensus pattern (22 bp):
TTACTGATTATCATTTTACTCT
Found at i:65118 original size:23 final size:23
Alignment explanation
Indices: 65078--65223 Score: 97
Period size: 21 Copynumber: 6.3 Consensus size: 23
65068 ACTGACTATC
*
65078 ATTTTAC-TCTTTACTGATTATT
1 ATTTTACTTCTTTACTGATTACT
* * *
65100 TTTTTACTTTTTTATTGATTACT
1 ATTTTACTTCTTTACTGATTACT
65123 ATTTTAC-TC-TTACTGATTACCATT
1 ATTTTACTTCTTTACTGATTA-C--T
** *
65147 ACTTTTTGAACTTAATTACTGATTACC
1 A--TTTT--ACTTCTTTACTGATTACT
*
65174 CTTTTAC-T-TTTACTGATTACT
1 ATTTTACTTCTTTACTGATTACT
* *
65195 ATTTTAC-TCTTTACTAATTACC
1 ATTTTACTTCTTTACTGATTACT
65217 ATTTTAC
1 ATTTTAC
65224 CCTTTACAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
21 27 0.28
22 27 0.28
23 20 0.20
24 2 0.02
25 4 0.04
26 4 0.04
28 2 0.02
29 2 0.02
30 10 0.10
ACGTcount: A:0.24, C:0.17, G:0.04, T:0.55
Consensus pattern (23 bp):
ATTTTACTTCTTTACTGATTACT
Found at i:65153 original size:51 final size:50
Alignment explanation
Indices: 65055--65193 Score: 137
Period size: 51 Copynumber: 2.9 Consensus size: 50
65045 CATTTTGCTC
* * *
65055 TTTGAATTTAATTACTGACTATCATTTTACTCTTTACTGATT---ATT-TT
1 TTTGAACTTAATTACTGATTACCATTTTACTC-TTACTGATTACCATTATT
** * *
65102 TTT--ACTTTTTTATTGATTACTATTTTACTCTTACTGATTACCATTACTT
1 TTTGAACTTAATTACTGATTACCATTTTACTCTTACTGATTACCATTA-TT
* *
65151 TTTGAACTTAATTACTGATTACCCTTTTACTTTTACTGATTAC
1 TTTGAACTTAATTACTGATTACCATTTTACTCTTACTGATTAC
65194 TATTTTACTC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
44 9 0.12
45 20 0.28
47 6 0.08
49 5 0.07
51 32 0.44
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.54
Consensus pattern (50 bp):
TTTGAACTTAATTACTGATTACCATTTTACTCTTACTGATTACCATTATT
Found at i:65187 original size:21 final size:21
Alignment explanation
Indices: 65162--65259 Score: 92
Period size: 21 Copynumber: 4.6 Consensus size: 21
65152 TTGAACTTAA
*
65162 TTACTGATTACCCTTTTACTT
1 TTACTGATTACCATTTTACTT
*
65183 TTACTGATTACTATTTTACTCT
1 TTACTGATTACCATTTTACT-T
* *
65205 TTACTAATTACCATTTTACCCT
1 TTACTGATTACCATTTTA-CTT
* *
65227 TTAC-AAATACC-TCTTTACTTT
1 TTACTGATTACCAT-TTTAC-TT
65248 TTACTGATTACC
1 TTACTGATTACC
65260 T
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.03
21 33 0.52
22 27 0.43
23 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.03, T:0.49
Consensus pattern (21 bp):
TTACTGATTACCATTTTACTT
Found at i:65214 original size:22 final size:22
Alignment explanation
Indices: 65162--65230 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
65152 TTGAACTTAA
* * *
65162 TTACTGATTACCCTTTTA-CTT
1 TTACTAATTACCATTTTACCCT
* * *
65183 TTACTGATTACTATTTTACTCT
1 TTACTAATTACCATTTTACCCT
65205 TTACTAATTACCATTTTACCCT
1 TTACTAATTACCATTTTACCCT
65227 TTAC
1 TTAC
65231 AAATACCTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 16 0.40
22 24 0.60
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (22 bp):
TTACTAATTACCATTTTACCCT
Found at i:65249 original size:96 final size:96
Alignment explanation
Indices: 65055--65237 Score: 219
Period size: 96 Copynumber: 1.9 Consensus size: 96
65045 CATTTTGCTC
* * * * * * *
65055 TTTGAATTTAATTACTGACTATCATTTTACTCTTTACTGATTATTTTTTTACTTTTTTATTGATT
1 TTTGAACTTAATTACTGACTACCATTTTACTCTTTACTGATTACTATTTTACTTCTTTACTAATT
* * * *
65120 ACTATTTTACTCTTACTGATTACCATTACTT
66 ACCATTTTACCCTTACTAAATACCATTACTT
* *
65151 TTTGAACTTAATTACTGATTACCCTTTTACT-TTTACTGATTACTATTTTAC-TCTTTACTAATT
1 TTTGAACTTAATTACTGACTACCATTTTACTCTTTACTGATTACTATTTTACTTCTTTACTAATT
65214 ACCATTTTACCCTTTAC-AAATACC
66 ACCATTTTACCC-TTACTAAATACC
65238 TCTTTACTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
94 24 0.33
95 22 0.30
96 27 0.37
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.52
Consensus pattern (96 bp):
TTTGAACTTAATTACTGACTACCATTTTACTCTTTACTGATTACTATTTTACTTCTTTACTAATT
ACCATTTTACCCTTACTAAATACCATTACTT
Done.