Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007742.1 Corchorus capsularis cultivar CVL-1 contig07763, 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: 62251
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:804 original size:12 final size:14
Alignment explanation
Indices: 784--816 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
774 AATGAATTTC
784 TTATATATATGTAA
1 TTATATATATGTAA
798 TTATATATATGTAA
1 TTATATATATGTAA
812 TTATA
1 TTATA
817 AAGATTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TTATATATATGTAA
Found at i:1468 original size:7 final size:7
Alignment explanation
Indices: 1434--1504 Score: 67
Period size: 7 Copynumber: 10.3 Consensus size: 7
1424 GGTTTTTTAA
1434 AATTATT
1 AATTATT
1441 -ATTATT
1 AATTATT
1447 AATTA--
1 AATTATT
*
1452 ATTTAGTT
1 AATTA-TT
1460 AATTATT
1 AATTATT
1467 AATTATT
1 AATTATT
*
1474 TATTATT
1 AATTATT
* *
1481 ATTTTTT
1 AATTATT
1488 AATTATTT
1 AATTA-TT
1496 AATTATT
1 AATTATT
1503 AA
1 AA
1505 ATCATTTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 4 0.08
6 6 0.12
7 30 0.59
8 11 0.22
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (7 bp):
AATTATT
Found at i:1478 original size:11 final size:11
Alignment explanation
Indices: 1462--1496 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1452 ATTTAGTTAA
1462 TTATTAATTAT
1 TTATTAATTAT
1473 TTATT-ATTAT
1 TTATTAATTAT
*
1483 TTTTTAATTAT
1 TTATTAATTAT
1494 TTA
1 TTA
1497 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTAATTAT
Found at i:1503 original size:11 final size:10
Alignment explanation
Indices: 1435--1503 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 10
1425 GTTTTTTAAA
1435 ATTA-TTATT
1 ATTATTTATT
*
1444 ATTAATTAATTT
1 ATT-ATTTA-TT
*
1456 AGTTAATTATT
1 A-TTATTTATT
1467 AATTATTTATT
1 -ATTATTTATT
*
1478 ATTATTTTTT
1 ATTATTTATT
1488 AATTATTTAATT
1 -ATTATTT-ATT
1500 ATTA
1 ATTA
1504 AATCATTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
9 3 0.06
10 10 0.21
11 23 0.49
12 9 0.19
13 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (10 bp):
ATTATTTATT
Found at i:1512 original size:37 final size:37
Alignment explanation
Indices: 1436--1512 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1426 TTTTTTAAAA
*
1436 TTATTATTATTAATTAATTTAGTTAATTATTAATTAT
1 TTATTATTATTAATTAATTTAGTTAATTATTAATCAT
** *
1473 TTATTATTATTTTTTAA-TTATTTAATTATTAAATCAT
1 TTATTATTATTAATTAATTTAGTTAATTATT-AATCAT
1510 TTA
1 TTA
1513 AATAATTGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 12 0.34
37 23 0.66
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (37 bp):
TTATTATTATTAATTAATTTAGTTAATTATTAATCAT
Found at i:1589 original size:30 final size:33
Alignment explanation
Indices: 1554--1625 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
1544 TATTTAATGA
*
1554 TTAATTA-GTTGT-TGTTATTATTATTATT-AT
1 TTAATTATGTAGTATGTTATTATTATTATTAAT
1584 TTAATTATGTAGTAATGTTATTATTATTATTAAT
1 TTAATTATGTAGT-ATGTTATTATTATTATTAAT
1618 TTAATTAT
1 TTAATTAT
1626 TATGAAATAG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
30 7 0.19
31 4 0.11
33 16 0.43
34 10 0.27
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (33 bp):
TTAATTATGTAGTATGTTATTATTATTATTAAT
Found at i:1590 original size:45 final size:44
Alignment explanation
Indices: 1435--1591 Score: 113
Period size: 45 Copynumber: 3.5 Consensus size: 44
1425 GTTTTTTAAA
* * * * * *
1435 ATTATTATTATTAATTAATTTAGTTAATTATTAATTATTTATTATT
1 ATTATT-TTATTATTTAA-TTATTTAATCATTAATTAATTGTTGTT
* *
1481 ATT-TTTTAATTATTTAATTATTAAATCATTTAAATAATTGTATG--
1 ATTATTTT-ATTATTTAATTATTTAATCA-TTAATTAATTGT-TGTT
* ** * *
1525 ATTATTTAAATTATGGAATTATTTAATGATTAATTAGTTGTTGTT
1 ATTATTT-TATTATTTAATTATTTAATCATTAATTAATTGTTGTT
1570 ATTATTATTATTATTTAATTAT
1 ATTATT-TTATTATTTAATTAT
1592 GTAGTAATGT
Statistics
Matches: 85, Mismatches: 18, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
43 2 0.02
44 23 0.27
45 55 0.65
46 5 0.06
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (44 bp):
ATTATTTTATTATTTAATTATTTAATCATTAATTAATTGTTGTT
Found at i:1641 original size:33 final size:34
Alignment explanation
Indices: 1566--1642 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 34
1556 AATTAGTTGT
*
1566 TGTTATTATTATTATT-ATTTAATTATGTAGTAA
1 TGTTATTATTATTATTAATTTAATTATGTAGAAA
1599 TGTTATTATTATTATTAATTTAATTAT-TATGAAA
1 TGTTATTATTATTATTAATTTAATTATGTA-GAAA
1633 TAGTTTATTA
1 T-G-TTATTA
1643 ATTACTTAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
33 18 0.46
34 14 0.36
35 1 0.03
36 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (34 bp):
TGTTATTATTATTATTAATTTAATTATGTAGAAA
Found at i:1773 original size:8 final size:7
Alignment explanation
Indices: 1751--1791 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
1741 ATAGGTTTAA
1751 TAATTAT
1 TAATTAT
1758 TAA--AT
1 TAATTAT
1763 TAATTATT
1 TAATTA-T
1771 TAATTCAT
1 TAATT-AT
1779 TAATTAT
1 TAATTAT
1786 TAATTA
1 TAATTA
1792 ATCAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.17
7 12 0.40
8 12 0.40
9 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (7 bp):
TAATTAT
Found at i:1782 original size:16 final size:15
Alignment explanation
Indices: 1761--1790 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1751 TAATTATTAA
1761 ATTAATTATTTAATTC
1 ATTAATTA-TTAATTC
1777 ATTAATTATTAATT
1 ATTAATTATTAATT
1791 AATCAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAATTATTAATTC
Found at i:3784 original size:16 final size:16
Alignment explanation
Indices: 3765--3827 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
3755 CCGACCCAAG
* *
3765 ACCCGAATGTCCCGCA
1 ACCCGAATGACCCGAA
3781 ACCC-AGATGACCCGAA
1 ACCCGA-ATGACCCGAA
*
3797 ACCCGAGTGACCCGAA
1 ACCCGAATGACCCGAA
*
3813 ACCCGAATAACCCGA
1 ACCCGAATGACCCGA
3828 GAAGTTAACC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 1 0.03
16 38 0.95
17 1 0.03
ACGTcount: A:0.33, C:0.40, G:0.19, T:0.08
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:4720 original size:16 final size:16
Alignment explanation
Indices: 4679--4721 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
4669 GACCCGGTAG
* *
4679 ACCCAAATGACTCGGA
1 ACCCGAATGACTCGAA
*
4695 ACCCGTATGACTCGAA
1 ACCCGAATGACTCGAA
*
4711 ACCTGAATGAC
1 ACCCGAATGAC
4722 CCGAGAAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (16 bp):
ACCCGAATGACTCGAA
Found at i:8556 original size:20 final size:24
Alignment explanation
Indices: 8533--8584 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
8523 TAACAAAAAC
8533 TAATTAA-T-AAAT-ATTATAA-T
1 TAATTAATTAAAATAATTATAATT
8553 TAATTTAATTAAAATAATTATAATT
1 TAA-TTAATTAAAATAATTATAATT
8578 TAATTAA
1 TAATTAA
8585 AAAAACATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.11
21 4 0.15
22 1 0.04
23 4 0.15
24 11 0.41
25 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATTAATTAAAATAATTATAATT
Found at i:14801 original size:2 final size:2
Alignment explanation
Indices: 14794--14828 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
14784 TGAGGATAAG
14794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
14829 AAAGGAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18013 original size:11 final size:11
Alignment explanation
Indices: 17983--18030 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
17973 ATACATGTAT
**
17983 ATTTATAACAA
1 ATTTATAATTA
17994 ATTTATAATTA
1 ATTTATAATTA
18005 ATTTATAATT-
1 ATTTATAATTA
*
18015 ATTTGATAATTT
1 ATTT-ATAATTA
18027 ATTT
1 ATTT
18031 TATATATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 4 0.12
11 25 0.76
12 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
ATTTATAATTA
Found at i:19266 original size:30 final size:31
Alignment explanation
Indices: 19209--19268 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
19199 CTAAACGACT
* *
19209 AAAATGTCAATTTTGTACCAAATCTTTTAAG
1 AAAATGTCAACTTAGTACCAAATCTTTTAAG
* *
19240 AAAATTTCAACTTAGTATCAAA-CTTTTAA
1 AAAATGTCAACTTAGTACCAAATCTTTTAA
19269 TTTCAGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (31 bp):
AAAATGTCAACTTAGTACCAAATCTTTTAAG
Found at i:19487 original size:23 final size:23
Alignment explanation
Indices: 19455--19518 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
19445 TTTTCTTATT
*
19455 TTCTTTTTTCTCTTCCTTTTCTA
1 TTCTTCTTTCTCTTCCTTTTCTA
* * *
19478 TTCTTCTTTCCCTT-TTTTTTTA
1 TTCTTCTTTCTCTTCCTTTTCTA
19500 TTCCTTC-TTCTTCTTCCTT
1 TT-CTTCTTTC-TCTTCCTT
19519 ATTCAAAACC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 11 0.34
23 19 0.59
24 2 0.06
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (23 bp):
TTCTTCTTTCTCTTCCTTTTCTA
Found at i:20746 original size:14 final size:14
Alignment explanation
Indices: 20727--20759 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
20717 CCTCCACGTG
20727 TTATATTATAAAAA
1 TTATATTATAAAAA
20741 TTATATTATAAAAA
1 TTATATTATAAAAA
20755 -TATAT
1 TTATAT
20760 AAATTTCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTATATTATAAAAA
Found at i:22119 original size:94 final size:94
Alignment explanation
Indices: 21988--22175 Score: 324
Period size: 94 Copynumber: 2.0 Consensus size: 94
21978 ACCATCAACT
*
21988 TTACTTAATATGTGTTTCTCTTTTCACATTTAATAAGGGTAAAAAGTACTAAAAAGTTTCTTAAT
1 TTACTTAATATGTGTTTCTCTTTCCACATTTAATAAGGGTAAAAAGTACTAAAAAGTTTCTTAAT
22053 TATCTAAAT-GAGACAGATAATTAGGGACA
66 TATCTAAATGGA-ACAGATAATTAGGGACA
* *
22082 TTACTTAATATGTGTTTCTCTTTCCACATTTAATAAGGGTAAAAAGTAGTCAAAAGTTTCTTAAT
1 TTACTTAATATGTGTTTCTCTTTCCACATTTAATAAGGGTAAAAAGTACTAAAAAGTTTCTTAAT
*
22147 TATCTAAATGGAACAGATAATTTGGGACA
66 TATCTAAATGGAACAGATAATTAGGGACA
22176 AAAAAAGTCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 87 0.98
95 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (94 bp):
TTACTTAATATGTGTTTCTCTTTCCACATTTAATAAGGGTAAAAAGTACTAAAAAGTTTCTTAAT
TATCTAAATGGAACAGATAATTAGGGACA
Found at i:22940 original size:271 final size:271
Alignment explanation
Indices: 22457--22983 Score: 946
Period size: 271 Copynumber: 1.9 Consensus size: 271
22447 AGATCAAAAG
*
22457 AGGAGAAATTATTAGGTGGGACAGTCCCACCACGTCATCTATGGGACCAACCAATAATATTAAGA
1 AGGAGAAATTATTAGATGGGACAGTCCCACCACGTCATCTATGGGACCAACCAATAATATTAAGA
* * *
22522 CAACTCATCAATTTTCTAAAACCATATCTCAATAATATCTCAAATTTGGGGACTTACCCTTAATT
66 CAACTCATCAATTTTCTAAAACCATATCCCAATAATATCTCAAATTTGAGGACTTACCCTTAATA
* *
22587 GATGATTTATTTTAAAAAGGGGCTAAACCTTGAGCTAAAATCGTACCTAAATTTAAGGAGGTCAT
131 GAAGATTTATTTTAAAAAGGGGCTAAACCTTGAGCTAAAATCATACCTAAATTTAAGGAGGTCAT
*
22652 TTGACATGACAAGATTCCATTGGTTAGTCCCATGGATGACGTGGTGGGTCTGTCCCACCTAATAA
196 TTGACATGACAAGATTCCATTGGTTAGTCCCATGGATAACGTGGTGGGTCTGTCCCACCTAATAA
22717 TTTCTCTCAAA
261 TTTCTCTCAAA
* *
22728 AGGAGAAATTATTAGATGGGACGGTCCCACCACGTCATCTATGGGACCAACCAATGATATTAAGA
1 AGGAGAAATTATTAGATGGGACAGTCCCACCACGTCATCTATGGGACCAACCAATAATATTAAGA
22793 CAACTCATCAATTTTCTAAAACCATATCCCAATAATATCTCAAATTTGAGGACTTACCCTTAATA
66 CAACTCATCAATTTTCTAAAACCATATCCCAATAATATCTCAAATTTGAGGACTTACCCTTAATA
* * *
22858 GAAGATTTATTTTAAAAAGGGGCTAAACCTTGGGTTAAAATCATGCCTAAATTTAAGGAGGTCAT
131 GAAGATTTATTTTAAAAAGGGGCTAAACCTTGAGCTAAAATCATACCTAAATTTAAGGAGGTCAT
22923 TTGACATGACAAGATTCCATTGGTTAGTCCCATGGATAACGTGGTGGGTCTGTCCCACCTA
196 TTGACATGACAAGATTCCATTGGTTAGTCCCATGGATAACGTGGTGGGTCTGTCCCACCTA
22984 GTAGCCAATT
Statistics
Matches: 244, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
271 244 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (271 bp):
AGGAGAAATTATTAGATGGGACAGTCCCACCACGTCATCTATGGGACCAACCAATAATATTAAGA
CAACTCATCAATTTTCTAAAACCATATCCCAATAATATCTCAAATTTGAGGACTTACCCTTAATA
GAAGATTTATTTTAAAAAGGGGCTAAACCTTGAGCTAAAATCATACCTAAATTTAAGGAGGTCAT
TTGACATGACAAGATTCCATTGGTTAGTCCCATGGATAACGTGGTGGGTCTGTCCCACCTAATAA
TTTCTCTCAAA
Found at i:28941 original size:2 final size:2
Alignment explanation
Indices: 28934--28967 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28924 AGCAGGTGTA
28934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28968 TGCCATCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33696 original size:41 final size:41
Alignment explanation
Indices: 33633--33717 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
33623 TATGAAACCC
* *
33633 AAACCCTAACAAACAATATAAACCCTAGGTGAGAT-AAAAG
1 AAACCCTAAAAAACAATATAAACCCTAAGTGAGATAAAAAG
33673 AAACCCTCAAAAAAC-ATATTAAACCCTAAGTGAGATAAAAAG
1 AAACCCT-AAAAAACAATA-TAAACCCTAAGTGAGATAAAAAG
33715 AAA
1 AAA
33718 AAACATGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 10 0.25
41 22 0.55
42 8 0.20
ACGTcount: A:0.55, C:0.19, G:0.11, T:0.15
Consensus pattern (41 bp):
AAACCCTAAAAAACAATATAAACCCTAAGTGAGATAAAAAG
Found at i:33957 original size:13 final size:14
Alignment explanation
Indices: 33933--33987 Score: 82
Period size: 13 Copynumber: 4.2 Consensus size: 14
33923 TTGCACTTCA
33933 ATTATT-ATTATT-
1 ATTATTGATTATTG
33945 ATTATTGATTATTG
1 ATTATTGATTATTG
33959 A-TATTGATTATTG
1 ATTATTGATTATTG
33972 ATTATTGA-TATTG
1 ATTATTGATTATTG
33985 ATT
1 ATT
33988 GTTTATATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.15
13 27 0.68
14 7 0.17
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (14 bp):
ATTATTGATTATTG
Found at i:33970 original size:20 final size:20
Alignment explanation
Indices: 33941--33987 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
33931 CAATTATTAT
33941 TATT-ATTATTGATTATTGA
1 TATTGATTATTGATTATTGA
33960 TATTGATTATTGATTATTGA
1 TATTGATTATTGATTATTGA
33980 TATTGATT
1 TATTGATT
33988 GTTTATATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (20 bp):
TATTGATTATTGATTATTGA
Found at i:34877 original size:106 final size:106
Alignment explanation
Indices: 34687--34899 Score: 399
Period size: 106 Copynumber: 2.0 Consensus size: 106
34677 TTTTCTTTCT
34687 ACTGCTTTACTTTGTTTATTGCTGAATAAGGGTATATAGGTTGAGTTCAATATTTGGAAGAAAAG
1 ACTGCTTTACTTTGTTTATTGCTGAATAAGGGTATATAGGTTGAGTTCAATATTTGGAAGAAAAG
*
34752 ATATTTGATACTAATATATTTGATTTTAATGAAATTTAATG
66 ATATTTGATACTAACATATTTGATTTTAATGAAATTTAATG
* *
34793 ACTGCTTTACTTTGTTTATTGCTGAATAAGTGTATATAGGTTTAGTTCAATATTTGGAAGAAAAG
1 ACTGCTTTACTTTGTTTATTGCTGAATAAGGGTATATAGGTTGAGTTCAATATTTGGAAGAAAAG
34858 ATATTTGATACTAACATATTTGATTTTAATGAAATTTAATG
66 ATATTTGATACTAACATATTTGATTTTAATGAAATTTAATG
34899 A
1 A
34900 AGTATCGGTT
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (106 bp):
ACTGCTTTACTTTGTTTATTGCTGAATAAGGGTATATAGGTTGAGTTCAATATTTGGAAGAAAAG
ATATTTGATACTAACATATTTGATTTTAATGAAATTTAATG
Found at i:37498 original size:61 final size:61
Alignment explanation
Indices: 37403--37585 Score: 366
Period size: 61 Copynumber: 3.0 Consensus size: 61
37393 TTTATGAATG
37403 ATGGTGGTCCTAGTAGCTATAGTTGTACCGATAACAGCGAGTAATCATTTTAATTGGATAT
1 ATGGTGGTCCTAGTAGCTATAGTTGTACCGATAACAGCGAGTAATCATTTTAATTGGATAT
37464 ATGGTGGTCCTAGTAGCTATAGTTGTACCGATAACAGCGAGTAATCATTTTAATTGGATAT
1 ATGGTGGTCCTAGTAGCTATAGTTGTACCGATAACAGCGAGTAATCATTTTAATTGGATAT
37525 ATGGTGGTCCTAGTAGCTATAGTTGTACCGATAACAGCGAGTAATCATTTTAATTGGATAT
1 ATGGTGGTCCTAGTAGCTATAGTTGTACCGATAACAGCGAGTAATCATTTTAATTGGATAT
37586 TCCCTCTTGA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 122 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (61 bp):
ATGGTGGTCCTAGTAGCTATAGTTGTACCGATAACAGCGAGTAATCATTTTAATTGGATAT
Found at i:39909 original size:38 final size:38
Alignment explanation
Indices: 39866--39943 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
39856 ATTAATATAT
39866 GAATTTAATGTGGCTATAAGATCCCTAGAATTAAAAAA
1 GAATTTAATGTGGCTATAAGATCCCTAGAATTAAAAAA
*
39904 GAATTTAATGTGGCTATAGGATCCCTAGAATTAAAAAA
1 GAATTTAATGTGGCTATAAGATCCCTAGAATTAAAAAA
39942 GA
1 GA
39944 TGGGCAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (38 bp):
GAATTTAATGTGGCTATAAGATCCCTAGAATTAAAAAA
Found at i:40139 original size:7 final size:7
Alignment explanation
Indices: 40127--40152 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40117 TTGAGACGAG
40127 CCAACAC
1 CCAACAC
40134 CCAACAC
1 CCAACAC
40141 CCAACAC
1 CCAACAC
40148 CCAAC
1 CCAAC
40153 CCAGGTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.58, G:0.00, T:0.00
Consensus pattern (7 bp):
CCAACAC
Found at i:41949 original size:29 final size:29
Alignment explanation
Indices: 41884--41964 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
41874 GCTTAATACC
* **
41884 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAACT-T-TTTTTTGGGA
41915 CAAATTGGCCCCTTAACTTTTTTTTGGGA
1 CAAATTGGCCCCTTAACTTTTTTTTGGGA
* *
41944 CAAATTGACCCATTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
41965 AAAAACGAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 27 0.60
30 1 0.02
31 17 0.38
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTTTTTTTGGGA
Found at i:42957 original size:4 final size:4
Alignment explanation
Indices: 42948--42973 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
42938 ATCAAAAACC
42948 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
42974 TTATGTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:45903 original size:2 final size:2
Alignment explanation
Indices: 45896--45931 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
45886 ACTAAATAAT
45896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45932 CTATCATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46178 original size:43 final size:45
Alignment explanation
Indices: 46122--46216 Score: 149
Period size: 44 Copynumber: 2.2 Consensus size: 45
46112 CCTTATTTCT
*
46122 TTGGTGTTAGTAAAAGGGTGGATTTTAGGAGGG-TTTGCGGGTGG
1 TTGGTGATAGTAAAAGGGTGGATTTTAGGAGGGTTTTGCGGGTGG
*
46166 TTGGTGAT-GTAAAAGGGTGGATTTTGGGAGGGTTTTGCGGGTGG
1 TTGGTGATAGTAAAAGGGTGGATTTTAGGAGGGTTTTGCGGGTGG
*
46210 ATGGTGA
1 TTGGTGA
46217 ATTGGTGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 23 0.49
44 24 0.51
ACGTcount: A:0.18, C:0.02, G:0.46, T:0.34
Consensus pattern (45 bp):
TTGGTGATAGTAAAAGGGTGGATTTTAGGAGGGTTTTGCGGGTGG
Found at i:50013 original size:21 final size:21
Alignment explanation
Indices: 49989--50042 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
49979 AAATTGAGTT
49989 AATTACTTAATTTAATTACCA
1 AATTACTTAATTTAATTACCA
*
50010 AATTACTTAACTTAATTACCA
1 AATTACTTAATTTAATTACCA
* *
50031 ATTTTCTTAATT
1 AATTACTTAATT
50043 GCACCGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTACTTAATTTAATTACCA
Found at i:50063 original size:56 final size:56
Alignment explanation
Indices: 49995--50127 Score: 169
Period size: 56 Copynumber: 2.4 Consensus size: 56
49985 AGTTAATTAC
* * * *
49995 TTAATTTAATTACCAAATTACTTAA-CTTAATTACCAATTTTCTTAATTGCACCGAA
1 TTAAGTTAATTACCAAATTACTTAATC-TAATTACCAAATTGCTTAATTACACCGAA
* * * *
50051 TTAAGTTAATTACCAAGTTACTTAATCTAATTATCAAATTGCTTAATTATACTGAA
1 TTAAGTTAATTACCAAATTACTTAATCTAATTACCAAATTGCTTAATTACACCGAA
*
50107 TTAAGTTGATTACCAAATTAC
1 TTAAGTTAATTACCAAATTAC
50128 CAATTTACTT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
56 65 0.98
57 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (56 bp):
TTAAGTTAATTACCAAATTACTTAATCTAATTACCAAATTGCTTAATTACACCGAA
Found at i:50081 original size:21 final size:21
Alignment explanation
Indices: 50057--50097 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
50047 CGAATTAAGT
*
50057 TAATTACCAAGTTACTTAATC
1 TAATTACCAAATTACTTAATC
* *
50078 TAATTATCAAATTGCTTAAT
1 TAATTACCAAATTACTTAAT
50098 TATACTGAAT
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:0.15, G:0.05, T:0.41
Consensus pattern (21 bp):
TAATTACCAAATTACTTAATC
Found at i:50126 original size:43 final size:43
Alignment explanation
Indices: 50079--50170 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
50069 TACTTAATCT
* * *
50079 AATTATCAAATTGCTTAATTATACTGAATTAAGTTGATTACCA
1 AATTACCAAATTACTTAATTACACTGAATTAAGTTGATTACCA
* * *
50122 AATTACCAATTTACTTAATTACACTGAATTAAGTTGTTTACCC
1 AATTACCAAATTACTTAATTACACTGAATTAAGTTGATTACCA
50165 AATTAC
1 AATTAC
50171 TTAAATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (43 bp):
AATTACCAAATTACTTAATTACACTGAATTAAGTTGATTACCA
Found at i:50170 original size:142 final size:140
Alignment explanation
Indices: 50092--50460 Score: 516
Period size: 142 Copynumber: 2.6 Consensus size: 140
50082 TATCAAATTG
* * * *
50092 CTTAATTATACTGAATTAAGTTGATTACCAAATTACCAATTTACTTAATTACACTGAATTAAGTT
1 CTTAATTACACCGAATTAAGTTGATTACCAGATTACCAATTTACTTAATTACACCGAATTAAGTT
* * *
50157 GTTTACCCAATTACTTAA--ATTTAATCACCAATTTACTTAATTACACCGAATTAAGTTGTTTAC
66 GTTTACCAAATTAC-CAATTATTTAATCACCAATTAACTTAATTA-ACC-AATTAA--TGTTTAC
50220 CAAATTACCAATTTA
126 CAAATTACCAATTTA
50235 CTTAATTACACCGAATTAAGTT-ATTTACCAGATTACCAATTTACTTAATTACACCGAATTAAGT
1 CTTAATTACACCGAATTAAGTTGA-TTACCAGATTACCAATTTACTTAATTACACCGAATTAAGT
*
50299 TGTTTACCAAATTA-C--TTAATTTAATCACCAATTTACTTAATTACACCAAATTAAGTTGTTTA
65 TGTTTACCAAATTACCAATT-ATTTAATCACCAATTAACTTAATTA-ACC-AATTAA--TGTTTA
50361 CCAAATTACCAATTTA
125 CCAAATTACCAATTTA
*
50377 CTTAATTACACCGAATTAAGTTGTTTACCAGATTACCAATTTACTTAATTACACCGAATTAAGTT
1 CTTAATTACACCGAATTAAGTTGATTACCAGATTACCAATTTACTTAATTACACCGAATTAAGTT
50442 GTTTACCAAATTACCAATT
66 GTTTACCAAATTACCAATT
50461 TACTTAATTA
Statistics
Matches: 210, Mismatches: 8, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
142 136 0.65
143 72 0.34
145 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (140 bp):
CTTAATTACACCGAATTAAGTTGATTACCAGATTACCAATTTACTTAATTACACCGAATTAAGTT
GTTTACCAAATTACCAATTATTTAATCACCAATTAACTTAATTAACCAATTAATGTTTACCAAAT
TACCAATTTA
Found at i:50231 original size:43 final size:43
Alignment explanation
Indices: 50183--50313 Score: 244
Period size: 43 Copynumber: 3.0 Consensus size: 43
50173 AAATTTAATC
50183 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
* *
50226 ACCAATTTACTTAATTACACCGAATTAAGTTATTTACCAGATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
50269 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
50312 AC
1 AC
50314 TTAATTTAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (43 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
Found at i:50232 original size:100 final size:100
Alignment explanation
Indices: 50023--50448 Score: 374
Period size: 99 Copynumber: 4.4 Consensus size: 100
50013 TACTTAACTT
* * * * *
50023 AATTACCAATTTTCTTAATTGCACCGAATTAAGTTAATTA-CCAAGTTACTTAATCTAATTATCA
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTATTTACCCAAGTTACTTAATCTAATCACCA
* * *
50087 AATTGCTTAATTATACTGAATTAAGTTGATTACCA
66 AATTACTTAATTACACCGAATTAAGTTGATTACCA
* * *
50122 AATTACCAATTTACTTAATTACACTGAATTAAGTTGTTTACCCAA-TTACTTAAATTTAATCACC
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTATTTACCCAAGTTACTT-AATCTAATCACC
* *
50186 AATTTACTTAATTACACCGAATTAAGTTGTTTACCA
65 AAATTACTTAATTACACCGAATTAAGTTGATTACCA
50222 AATTACCAATTTACTTAATTACACCGAATTAAGTTATTTA-CC-AG-------A--T--T-ACCA
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTATTTACCCAAGTTACTTAATCTAATCACCA
* *
50273 ATTTACTTAATTACACCGAATTAAGTTGTTTACCA
66 AATTACTTAATTACACCGAATTAAGTTGATTACCA
* * * * * * * * * *
50308 AATTA-C--TTAATTTAA-T-CACC-AATTTACTTAATTACACCAAATTAAGTTGTTTACCAAAT
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTATTTAC-CCAAGTT-A---CTTAATCTAAT
* * *
50367 TACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCA
61 CACCAAATTACTTAATTACACCGAATTAAGTTGATTACCA
* *
50407 GATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACC
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTATTTACC
50449 AAATTACCAA
Statistics
Matches: 270, Mismatches: 29, Indels: 51
0.77 0.08 0.15
Matches are distributed among these distances:
80 11 0.04
81 4 0.01
82 3 0.01
83 8 0.03
85 1 0.00
86 44 0.16
87 1 0.00
89 1 0.00
91 1 0.00
94 1 0.00
98 2 0.01
99 86 0.32
100 83 0.31
102 7 0.03
103 1 0.00
104 5 0.02
105 11 0.04
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (100 bp):
AATTACCAATTTACTTAATTACACCGAATTAAGTTATTTACCCAAGTTACTTAATCTAATCACCA
AATTACTTAATTACACCGAATTAAGTTGATTACCA
Found at i:50328 original size:21 final size:18
Alignment explanation
Indices: 50304--50351 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 18
50294 TAAGTTGTTT
50304 ACCAAATTACTTAATTTAATC
1 ACCAAATTACTTAA-TT-A-C
*
50325 ACCAATTTACTTAATTAC
1 ACCAAATTACTTAATTAC
50343 ACCAAATTA
1 ACCAAATTA
50352 AGTTGTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.36
19 1 0.04
20 2 0.08
21 13 0.52
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (18 bp):
ACCAAATTACTTAATTAC
Found at i:50376 original size:43 final size:43
Alignment explanation
Indices: 50325--50509 Score: 327
Period size: 43 Copynumber: 4.3 Consensus size: 43
50315 TAATTTAATC
*
50325 ACCAATTTACTTAATTACACCAAATTAAGTTGTTTACCAAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
*
50368 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAGATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
50411 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
*
50454 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAGATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
*
50497 ACC-ATTTTCTTAA
1 ACCAATTTACTTAA
50510 ATCTTGTCCT
Statistics
Matches: 137, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
42 9 0.07
43 128 0.93
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (43 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
Found at i:54693 original size:1 final size:1
Alignment explanation
Indices: 54687--54715 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
54677 TCCTTTTGGG
54687 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54716 CTGCAAACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:55396 original size:91 final size:90
Alignment explanation
Indices: 55131--55487 Score: 459
Period size: 90 Copynumber: 4.0 Consensus size: 90
55121 CCAGATCACT
* *
55131 CTGAACTGTCCGAAAATGTGCTGCACCGAGCTCACCGAATTCCAACCTTTGAAGAAAT---GCAC
1 CTGAACTGTCTGAAAATCTGCTGCACCGAGCTCACCGAA-TCCAACC-TTGAAGAAATAAGGCAC
* * * * *
55193 CGCATTAACTTGATTTAATGAATGATC
64 CGCCTCAACTTGATTCAACGAATCATC
* * * **
55220 CTGAACTATTTGAAAATCTGCTGCACTGAGCTCACCGAATCTGACCTTGAAGAAATAAGGCACCG
1 CTGAACTGTCTGAAAATCTGCTGCACCGAGCTCACCGAATCCAACCTTGAAGAAATAAGGCACCG
**
55285 CCTCAACTTGATTCGTCGAATCATC
66 CCTCAACTTGATTCAACGAATCATC
* * * *
55310 CCGAACTGTTTGAAAATTTGCTGCACCGAGCTCACCGAATTCCAATCTTGAAGAAATAAGGCACC
1 CTGAACTGTCTGAAAATCTGCTGCACCGAGCTCACCGAA-TCCAACCTTGAAGAAATAAGGCACC
55375 GCCTCAACTTGATTCAACGAATCATC
65 GCCTCAACTTGATTCAACGAATCATC
* **
55401 CTAAACTGTCTGAAAATCTGCTGCACCGAGCTCACCGAATCCAATATTGAAGAAATAAGGCACCG
1 CTGAACTGTCTGAAAATCTGCTGCACCGAGCTCACCGAATCCAACCTTGAAGAAATAAGGCACCG
* *
55466 CCTCAACTTGACTCACCGAATC
66 CCTCAACTTGATTCAACGAATC
55488 CAATTTTGGA
Statistics
Matches: 234, Mismatches: 30, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
87 10 0.04
88 5 0.02
89 34 0.15
90 104 0.44
91 81 0.35
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (90 bp):
CTGAACTGTCTGAAAATCTGCTGCACCGAGCTCACCGAATCCAACCTTGAAGAAATAAGGCACCG
CCTCAACTTGATTCAACGAATCATC
Found at i:55434 original size:181 final size:179
Alignment explanation
Indices: 55133--55476 Score: 501
Period size: 181 Copynumber: 1.9 Consensus size: 179
55123 AGATCACTCT
55133 GAACTGTCCGAAAATGTGCTGCACCGAGCTCACCGAATTCCAACCTTTGAAGAAATGCACCGCAT
1 GAACTGTCCGAAAATGTGCTGCACCGAGCTCACCGAATTCCAACCTTTGAAGAAATGCACCGCAT
* * * * * * * **
55198 TAACTTGATTTAATGAATGATCCTGAACTATTTGAAAATCTGCTGCACTGAGCTCACCGAATCTG
66 CAACTTGATTCAACGAATCATCCTAAACTATCTGAAAATCTGCTGCACCGAGCTCACCGAATCCA
*
55263 ACCTTGAAGAAATAAGGCACCGCCTCAACTTGATTCGTCGAATCATCCC
131 ACATTGAAGAAATAAGGCACCGCCTCAACTTGATTCGTCGAATCATCCC
** * *
55312 GAACTGTTTGAAAATTTGCTGCACCGAGCTCACCGAATTCCAATC-TTGAAGAAATAAGGCACCG
1 GAACTGTCCGAAAATGTGCTGCACCGAGCTCACCGAATTCCAACCTTTGAAGAAAT---GCACCG
* *
55376 CCTCAACTTGATTCAACGAATCATCCTAAACTGTCTGAAAATCTGCTGCACCGAGCTCACCGAAT
63 CATCAACTTGATTCAACGAATCATCCTAAACTATCTGAAAATCTGCTGCACCGAGCTCACCGAAT
*
55441 CCAATATTGAAGAAATAAGGCACCGCCTCAACTTGA
128 CCAACATTGAAGAAATAAGGCACCGCCTCAACTTGA
55477 CTCACCGAAT
Statistics
Matches: 145, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
178 10 0.07
179 41 0.28
181 94 0.65
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (179 bp):
GAACTGTCCGAAAATGTGCTGCACCGAGCTCACCGAATTCCAACCTTTGAAGAAATGCACCGCAT
CAACTTGATTCAACGAATCATCCTAAACTATCTGAAAATCTGCTGCACCGAGCTCACCGAATCCA
ACATTGAAGAAATAAGGCACCGCCTCAACTTGATTCGTCGAATCATCCC
Found at i:55658 original size:35 final size:35
Alignment explanation
Indices: 55608--55674 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
55598 CCACCGTATG
* *
55608 CAACTTTGAAGATGCTGCACCGAGTCATCTGAATC
1 CAACTTCGAAAATGCTGCACCGAGTCATCTGAATC
* *
55643 CAACTTCGAAAATGCTGCCCCGATTCATCTGA
1 CAACTTCGAAAATGCTGCACCGAGTCATCTGA
55675 TTCACCGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (35 bp):
CAACTTCGAAAATGCTGCACCGAGTCATCTGAATC
Found at i:55833 original size:54 final size:55
Alignment explanation
Indices: 55745--55849 Score: 158
Period size: 54 Copynumber: 1.9 Consensus size: 55
55735 ACACTGGGTC
* *
55745 ACTTAAAGATAAAATTAATACCACTGGAGACTTTCTTGATTGACCGTACTGAATT
1 ACTTAAAGATAAAATTAATACCACTGGAAACTTTCTTGATTGACCGCACTGAATT
* * *
55800 ACTTGAAGATAAACTTAA-ACCACTGTAAACTTTCTTGATTGACCGCACTG
1 ACTTAAAGATAAAATTAATACCACTGGAAACTTTCTTGATTGACCGCACTG
55850 GATCACTATG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 29 0.64
55 16 0.36
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Consensus pattern (55 bp):
ACTTAAAGATAAAATTAATACCACTGGAAACTTTCTTGATTGACCGCACTGAATT
Found at i:57048 original size:19 final size:18
Alignment explanation
Indices: 57024--57073 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
57014 TATTCGATTG
*
57024 CTTTTTCTTCTTTTTTTTC
1 CTTTTTCTT-TTTTCTTTC
57043 CTTTTTCTTTTTTCTTT-
1 CTTTTTCTTTTTTCTTTC
57060 CTATTTT-TTTTTTC
1 CT-TTTTCTTTTTTC
57074 AAATGCAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 9 0.31
18 11 0.38
19 9 0.31
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (18 bp):
CTTTTTCTTTTTTCTTTC
Found at i:57670 original size:17 final size:17
Alignment explanation
Indices: 57648--57705 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
57638 TAGGCCAAGG
57648 TTTTTCTTTTCTTCTTC
1 TTTTTCTTTTCTTCTTC
*
57665 TTTTTCTTTTTTTCTTTC
1 TTTTTCTTTTCTTC-TTC
57683 TCTTCTT-TTTTCTTTCTTC
1 T-TT-TTCTTTTC-TTCTTC
57702 TTTT
1 TTTT
57706 CCTTGAGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 14 0.40
18 6 0.17
19 10 0.29
20 5 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTCTTCTTC
Found at i:57679 original size:20 final size:20
Alignment explanation
Indices: 57648--57703 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
57638 TAGGCCAAGG
*
57648 TTTTTCTTTTCTTCTTCTT-
1 TTTTTTTTTTCTTCTTCTTC
57667 TTTCTTTTTTTCTT-TCTCTTC
1 TTT-TTTTTTTCTTCT-TCTTC
*
57688 TTTTTTCTTTCTTCTT
1 TTTTTTTTTTCTTCTT
57704 TTCCTTGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 4 0.13
20 23 0.74
21 4 0.13
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTTCTTCTTCTTC
Found at i:57681 original size:14 final size:15
Alignment explanation
Indices: 57648--57705 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
57638 TAGGCCAAGG
57648 TTTTTCTTTTCTTCTTC
1 TTTTTCTTTT-TT-TTC
57665 TTTTTC-TTTTTTTC
1 TTTTTCTTTTTTTTC
*
57679 TTTCTCTTCTTTTTTC
1 TTTTTCTT-TTTTTTC
57695 TTTCTTCTTTT
1 TTT-TTCTTTT
57706 CCTTGAGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 8 0.22
15 3 0.08
16 15 0.42
17 10 0.28
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTTTTTTC
Found at i:57686 original size:23 final size:26
Alignment explanation
Indices: 57648--57706 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
57638 TAGGCCAAGG
57648 TTTTTCTTTTCTTCTTC-TTTTTCTT
1 TTTTTCTTTTCTTCTTCTTTTTTCTT
57673 TTTTTC-TTTC-TCTTCTTTTTTC-T
1 TTTTTCTTTTCTTCTTCTTTTTTCTT
*
57696 TTCTTCTTTTC
1 TTTTTCTTTTC
57707 CTTGAGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 11 0.35
24 14 0.45
25 6 0.19
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTCTTTTCTTCTTCTTTTTTCTT
Found at i:58385 original size:14 final size:13
Alignment explanation
Indices: 58360--58411 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
58350 TTAAAAACTC
58360 AAAACC-TTTTTG
1 AAAACCATTTTTG
58372 AAAACTCATTTTTG
1 AAAAC-CATTTTTG
* *
58386 GAAACCTTTTCTTG
1 AAAACCATTT-TTG
*
58400 AAAACAATTTTT
1 AAAACCATTTTT
58412 TTGAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 5 0.16
13 7 0.22
14 20 0.62
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (13 bp):
AAAACCATTTTTG
Found at i:61210 original size:65 final size:68
Alignment explanation
Indices: 61130--61263 Score: 166
Period size: 69 Copynumber: 2.0 Consensus size: 68
61120 TTACACTGAG
* * * * *
61130 TTAAGTTAATTACCAAGTTACTTGA-TT-TGA-TAGTTTACTTAATTGCACCGAATTGAGTTAAT
1 TTAAGTTAATTACCAAATTACTTAACTTATGACCAATTTACTTAATTGCACCGAATTAAGTTAAT
61192 TAC
66 TAC
* * *
61195 TTAATTTAATTACCAAATTACTTAACTTAATTACCAATTTTCTTAATTGCACCGAATTAAGTTAA
1 TTAAGTTAATTACCAAATTACTTAACTT-ATGACCAATTTACTTAATTGCACCGAATTAAGTTAA
61260 TTAC
65 TTAC
61264 CAGATTACCA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
65 22 0.39
66 2 0.04
68 2 0.04
69 31 0.54
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (68 bp):
TTAAGTTAATTACCAAATTACTTAACTTATGACCAATTTACTTAATTGCACCGAATTAAGTTAAT
TAC
Found at i:61213 original size:21 final size:21
Alignment explanation
Indices: 61189--61242 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
61179 GAATTGAGTT
61189 AATTACTTAATTTAATTACCA
1 AATTACTTAATTTAATTACCA
*
61210 AATTACTTAACTTAATTACCA
1 AATTACTTAATTTAATTACCA
* *
61231 ATTTTCTTAATT
1 AATTACTTAATT
61243 GCACCGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTACTTAATTTAATTACCA
Found at i:61273 original size:43 final size:43
Alignment explanation
Indices: 61223--61314 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
61213 TACTTAACTT
* *
61223 AATTACCAATTTTCTTAATTGCACCGAATTAAGTTAATTACCA
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTAATTACCA
* **
61266 GATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCA
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTAATTACCA
61309 AATTAC
1 AATTAC
61315 TTAATTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (43 bp):
AATTACCAATTTACTTAATTACACCGAATTAAGTTAATTACCA
Found at i:61312 original size:99 final size:99
Alignment explanation
Indices: 61204--61413 Score: 339
Period size: 99 Copynumber: 2.1 Consensus size: 99
61194 CTTAATTTAA
* * * * *
61204 TTACCAAATTACTTAACTTAATTACCAATTTTCTTAATTGCACCGAATTAAGTTAATTACCAGAT
1 TTACCAAATTACTTAACTTAATCACCAATTTACTCAATTACACCGAATTAAGTTAATTACCAAAT
61269 TACCAATTTACTTAATTACACCGAATTAAGTTGT
66 TACCAATTTACTTAATTACACCGAATTAAGTTGT
* **
61303 TTACCAAATTACTTAATTTAATCACCAATTTACTCAATTACACCGAATTAAGTTGTTTACCAAAT
1 TTACCAAATTACTTAACTTAATCACCAATTTACTCAATTACACCGAATTAAGTTAATTACCAAAT
61368 TACCAATTTACTTAATTACACCGAATTAAGTTGT
66 TACCAATTTACTTAATTACACCGAATTAAGTTGT
*
61402 TTACCAGATTAC
1 TTACCAAATTAC
61414 CATTTTCTTA
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 102 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.38
Consensus pattern (99 bp):
TTACCAAATTACTTAACTTAATCACCAATTTACTCAATTACACCGAATTAAGTTAATTACCAAAT
TACCAATTTACTTAATTACACCGAATTAAGTTGT
Found at i:61374 original size:43 final size:43
Alignment explanation
Indices: 61326--61415 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
61316 TAATTTAATC
61326 ACCAATTTACTCAATTACACCGAATTAAGTTGTTTACCAAATT
1 ACCAATTTACTCAATTACACCGAATTAAGTTGTTTACCAAATT
* *
61369 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAGATT
1 ACCAATTTACTCAATTACACCGAATTAAGTTGTTTACCAAATT
61412 ACCA
1 ACCA
61416 TTTTCTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (43 bp):
ACCAATTTACTCAATTACACCGAATTAAGTTGTTTACCAAATT
Done.