Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010902.1 Kokia drynarioides strain JFW-HI SEQ_125870, 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: 271290
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:2475 original size:13 final size:13
Alignment explanation
Indices: 2457--2482 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2447 TAGTTTACTA
2457 AAATTATTATAAT
1 AAATTATTATAAT
2470 AAATTATTATAAT
1 AAATTATTATAAT
2483 TAGGATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATTATAAT
Found at i:6376 original size:49 final size:50
Alignment explanation
Indices: 6298--6399 Score: 152
Period size: 49 Copynumber: 2.1 Consensus size: 50
6288 AAACATGGTA
* * *
6298 GTTATAATTCTTTTTTAGAAAGAATATAATGTTTTTAATATTTTCCATAT
1 GTTACAATTCTTTTTTAGAAAGAATATAATGATTTTAATACTTTCCATAT
* *
6348 GTTACAATTC-TTTTTGGAAAGAATATAATGATTTTAATGCTTTCCATAT
1 GTTACAATTCTTTTTTAGAAAGAATATAATGATTTTAATACTTTCCATAT
6397 GTT
1 GTT
6400 CTCGATAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 38 0.81
50 9 0.19
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (50 bp):
GTTACAATTCTTTTTTAGAAAGAATATAATGATTTTAATACTTTCCATAT
Found at i:14597 original size:15 final size:15
Alignment explanation
Indices: 14577--14674 Score: 124
Period size: 15 Copynumber: 6.5 Consensus size: 15
14567 CAATAGTTCG
14577 CATATAAACAACTCA
1 CATATAAACAACTCA
* ** **
14592 CATATAATCAGTTTG
1 CATATAAACAACTCA
14607 CATATAAACAACTCA
1 CATATAAACAACTCA
*
14622 CATATAAACAACTCG
1 CATATAAACAACTCA
* *
14637 CATATAAATAACTCG
1 CATATAAACAACTCA
14652 CATATAAACAACTCA
1 CATATAAACAACTCA
14667 CATATAAA
1 CATATAAA
14675 TTGTTCAGTG
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 69 1.00
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.24
Consensus pattern (15 bp):
CATATAAACAACTCA
Found at i:14612 original size:30 final size:30
Alignment explanation
Indices: 14560--14658 Score: 128
Period size: 30 Copynumber: 3.3 Consensus size: 30
14550 CATAAGCAGT
*
14560 TCACATACAAT-AGTTCGCATATAAACAAC
1 TCACATATAATCAGTTCGCATATAAACAAC
*
14589 TCACATATAATCAGTTTGCATATAAACAAC
1 TCACATATAATCAGTTCGCATATAAACAAC
* ** *
14619 TCACATATAAACAACTCGCATATAAATAAC
1 TCACATATAATCAGTTCGCATATAAACAAC
*
14649 TCGCATATAA
1 TCACATATAA
14659 ACAACTCACA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
29 10 0.16
30 51 0.84
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.26
Consensus pattern (30 bp):
TCACATATAATCAGTTCGCATATAAACAAC
Found at i:14632 original size:45 final size:45
Alignment explanation
Indices: 14577--14674 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
14567 CAATAGTTCG
** *
14577 CATATAAACAACTCACATAT-AATCAGTTTGCATATAAACAACTCA
1 CATATAAACAACTCACATATAAAT-AACTCGCATATAAACAACTCA
*
14622 CATATAAACAACTCGCATATAAATAACTCGCATATAAACAACTCA
1 CATATAAACAACTCACATATAAATAACTCGCATATAAACAACTCA
14667 CATATAAA
1 CATATAAA
14675 TTGTTCAGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 45 0.94
46 3 0.06
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.24
Consensus pattern (45 bp):
CATATAAACAACTCACATATAAATAACTCGCATATAAACAACTCA
Found at i:14659 original size:30 final size:30
Alignment explanation
Indices: 14574--14674 Score: 139
Period size: 30 Copynumber: 3.4 Consensus size: 30
14564 ATACAATAGT
* **
14574 TCGCATATAAACAACTCACATATAATCAGT
1 TCGCATATAAACAACTCACATATAAACAAC
*
14604 TTGCATATAAACAACTCACATATAAACAAC
1 TCGCATATAAACAACTCACATATAAACAAC
* *
14634 TCGCATATAAATAACTCGCATATAAACAAC
1 TCGCATATAAACAACTCACATATAAACAAC
*
14664 TCACATATAAA
1 TCGCATATAAA
14675 TTGTTCAGTG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.25
Consensus pattern (30 bp):
TCGCATATAAACAACTCACATATAAACAAC
Found at i:21155 original size:56 final size:56
Alignment explanation
Indices: 21069--21230 Score: 234
Period size: 56 Copynumber: 2.9 Consensus size: 56
21059 CATGGCAATC
* *
21069 GAAGACCATGTAGTGTAAGACCTAGTCATGGTGGCTATGCCATCATATGGGAAAAT
1 GAAGACCATATAGTGTAAGACCTAGTCATGGTGGTTATGCCATCATATGGGAAAAT
* * *
21125 GAAGACCATATAGTGTAAGACCTAGTCATGGTAGTTATGTCATCATATGGGGAAAT
1 GAAGACCATATAGTGTAAGACCTAGTCATGGTGGTTATGCCATCATATGGGAAAAT
* * * * *
21181 GAAGACCATACAGTGTAAAACCTAATCATGGTGGTTATGGCACCATATGG
1 GAAGACCATATAGTGTAAGACCTAGTCATGGTGGTTATGCCATCATATGG
21231 AAGCAGATGA
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 95 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (56 bp):
GAAGACCATATAGTGTAAGACCTAGTCATGGTGGTTATGCCATCATATGGGAAAAT
Found at i:21485 original size:87 final size:86
Alignment explanation
Indices: 21335--21551 Score: 285
Period size: 87 Copynumber: 2.5 Consensus size: 86
21325 ATTTCCCAAA
* * *
21335 AAAGTGAAACTTTTGTGGCTAATTCTGTTAAATGGAGCCTCTGTGGTTGATTTTGTTAAAGTGAA
1 AAAGTGAAACTTTTGTGGCTAATTCTATTAAATGAAGCCTCTGTGGCTGATTTTGTTAAAGTGAA
* * *
21400 -TATTTTGTGGTTGATTTTGTT
66 GT-CTTTGTGGCTGATTCTGTT
* * * * *
21421 AAAGTGAAGCTTTTGTGGTTAGTTCTATTAAAGTGAAGTCTTTGTGGCTGATTTTGTTAAAGTGA
1 AAAGTGAAACTTTTGTGGCTAATTCTATTAAA-TGAAGCCTCTGTGGCTGATTTTGTTAAAGTGA
21486 AGTCTTTGTGGCTGATTCTGTT
65 AGTCTTTGTGGCTGATTCTGTT
*
21508 AAAGTGAAACCTTTGTGGCTAATTCTATTAAAATG-AGCCTCTGT
1 AAAGTGAAACTTTTGTGGCTAATTCTATT-AAATGAAGCCTCTGT
21552 AATCCCCAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
86 35 0.32
87 72 0.65
88 4 0.04
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (86 bp):
AAAGTGAAACTTTTGTGGCTAATTCTATTAAATGAAGCCTCTGTGGCTGATTTTGTTAAAGTGAA
GTCTTTGTGGCTGATTCTGTT
Found at i:21526 original size:29 final size:29
Alignment explanation
Indices: 21335--21547 Score: 198
Period size: 29 Copynumber: 7.4 Consensus size: 29
21325 ATTTCCCAAA
* * *
21335 AAAGTGAAACTTTTGTGGCTAATTCTGTT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
* * * *
21364 AAA-TGGAGCCTCTGTGGTTGATTTTGTT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
*** * *
21392 AAAGTGAATATTTTGTGGTTGATTTTGTT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
* * *
21421 AAAGTGAAGCTTTTGTGG-TTAGTTCTATT
1 AAAGTGAAGCCTTTGTGGCTGA-TTCTGTT
* *
21450 AAAGTGAAGTCTTTGTGGCTGATTTTGTT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
*
21479 AAAGTGAAGTCTTTGTGGCTGATTCTGTT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
* * *
21508 AAAGTGAAACCTTTGTGGCTAATTCTATT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
*
21537 AAAATG-AGCCT
1 AAAGTGAAGCCT
21548 CTGTAATCCC
Statistics
Matches: 152, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
28 27 0.18
29 123 0.81
30 2 0.01
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (29 bp):
AAAGTGAAGCCTTTGTGGCTGATTCTGTT
Found at i:21695 original size:19 final size:20
Alignment explanation
Indices: 21657--21696 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
21647 TTTAATTTGT
*
21657 AAATAAATTAATTTATTATA
1 AAATAAATTAATTTACTATA
*
21677 AAAT-AATTAATTTCCTATA
1 AAATAAATTAATTTACTATA
21696 A
1 A
21697 TTTTGAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATAAATTAATTTACTATA
Found at i:29839 original size:16 final size:16
Alignment explanation
Indices: 29818--29848 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29808 ATAATGTGAA
29818 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
29834 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
29849 AGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:30813 original size:38 final size:38
Alignment explanation
Indices: 30757--30841 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
30747 AGTTTTGGTG
* * *
30757 AAATCTGGAAGTGCTCATGTGGCGACAATTGTGGGCGC
1 AAATTTGGAAGTGCTCATGCGGCGACAATTGTAGGCGC
* *
30795 AAATTTGGAAGTGCTCATGCGGCGACAGTTTTAGGCGC
1 AAATTTGGAAGTGCTCATGCGGCGACAATTGTAGGCGC
30833 AAATTTGGA
1 AAATTTGGA
30842 TGTTATTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (38 bp):
AAATTTGGAAGTGCTCATGCGGCGACAATTGTAGGCGC
Found at i:35961 original size:16 final size:17
Alignment explanation
Indices: 35925--35962 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
35915 TCCCTTTATT
35925 TAAA-AATTTATTACCA
1 TAAATAATTTATTACCA
*
35941 TAAATAATTTATTTCCA
1 TAAATAATTTATTACCA
35958 -AAATA
1 TAAATA
35963 TTTGCTTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAATTTATTACCA
Found at i:36373 original size:21 final size:20
Alignment explanation
Indices: 36333--36373 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
36323 TTCTTTAGCT
*
36333 TAGAAAAAATTCTTTTAAAA
1 TAGAAAAAATTCTATTAAAA
*
36353 TAGAAACAATTCCTATTAAAA
1 TAGAAAAAATT-CTATTAAAA
36374 ATTTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.32
Consensus pattern (20 bp):
TAGAAAAAATTCTATTAAAA
Found at i:36886 original size:29 final size:28
Alignment explanation
Indices: 36840--36912 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
36830 ATAATAGCCT
*
36840 AAACTTAAAAATATTTTTTTTGATAAAA
1 AAACTTTAAAATATTTTTTTTGATAAAA
36868 AAACTTTAAAATATTTTTTTTGATAAAA
1 AAACTTTAAAATATTTTTTTTGATAAAA
36896 AAACTTTAAAATATTTT
1 AAACTTTAAAATATTTT
36913 AAATTTAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (28 bp):
AAACTTTAAAATATTTTTTTTGATAAAA
Found at i:38750 original size:84 final size:84
Alignment explanation
Indices: 38609--38776 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
38599 ACGCTAATAA
38609 CTACTAAGTATGTATATTCTTTTTTCATTGAGAACTACTTTCAAGTTAACATTAGAAGTTCAGGG
1 CTACTAAGTATGTATATTCTTTTTTCATTGAGAACTACTTTCAAGTTAACATTAGAAGTTCAGGG
*
38674 AATTAAATAAAACATGAGC
66 AATTAAAAAAAACATGAGC
38693 CTACTAAGTATGTATATTCTTTTTTCATTGAGAACTACTTTCAAGTTAACATTAGAAGTTCAGGG
1 CTACTAAGTATGTATATTCTTTTTTCATTGAGAACTACTTTCAAGTTAACATTAGAAGTTCAGGG
38758 AATTAAAAAAAACATGAGC
66 AATTAAAAAAAACATGAGC
38777 ATCAATGTCA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (84 bp):
CTACTAAGTATGTATATTCTTTTTTCATTGAGAACTACTTTCAAGTTAACATTAGAAGTTCAGGG
AATTAAAAAAAACATGAGC
Found at i:41789 original size:17 final size:17
Alignment explanation
Indices: 41767--41808 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
41757 TACTAGTATC
41767 CGACACGGACACGCCGT
1 CGACACGGACACGCCGT
41784 CGACACGGACACGCCGT
1 CGACACGGACACGCCGT
*
41801 CAACACGG
1 CGACACGG
41809 CTGGATACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.26, C:0.40, G:0.29, T:0.05
Consensus pattern (17 bp):
CGACACGGACACGCCGT
Found at i:47908 original size:23 final size:23
Alignment explanation
Indices: 47882--47969 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
47872 TAAACCTGAC
*
47882 CCGACCCGTTGACTTTGACAGAA
1 CCGAACCGTTGACTTTGACAGAA
* *
47905 CCGAACTGTTGATTTTGACCA-AA
1 CCGAACCGTTGACTTTGA-CAGAA
* *
47928 TCGAACCGTTGACTTTGACTGAA
1 CCGAACCGTTGACTTTGACAGAA
* *
47951 CTGAACCATTGACTTTGAC
1 CCGAACCGTTGACTTTGAC
47970 CGACCATTGA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.02
23 50 0.94
24 2 0.04
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (23 bp):
CCGAACCGTTGACTTTGACAGAA
Found at i:51941 original size:23 final size:23
Alignment explanation
Indices: 51915--51979 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
51905 TGCTGAGCTG
*
51915 AACCATTGATTTTGATCGAACCA
1 AACCATTGACTTTGATCGAACCA
* ***
51938 AACCGTTGACTTTGATCGAATTG
1 AACCATTGACTTTGATCGAACCA
51961 AACCATTGACTTTGATCGA
1 AACCATTGACTTTGATCGA
51980 CCGTTGACCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (23 bp):
AACCATTGACTTTGATCGAACCA
Found at i:52016 original size:14 final size:14
Alignment explanation
Indices: 51978--52016 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
51968 GACTTTGATC
**
51978 GACCGTTGACCGTT
1 GACCGTTGACTATT
*
51992 GATCGTTGACTATT
1 GACCGTTGACTATT
52006 GACCGTTGACT
1 GACCGTTGACT
52017 TTTTTCGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (14 bp):
GACCGTTGACTATT
Found at i:57182 original size:32 final size:32
Alignment explanation
Indices: 57141--57203 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
57131 AATAAATAAT
57141 TTTAGTCAAAATAAAATTAAGAAAATAACAAA
1 TTTAGTCAAAATAAAATTAAGAAAATAACAAA
*
57173 TTTAGTCAAAATAAAATTAATAAAATAACAA
1 TTTAGTCAAAATAAAATTAAGAAAATAACAA
57204 CTTTGAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.27
Consensus pattern (32 bp):
TTTAGTCAAAATAAAATTAAGAAAATAACAAA
Found at i:57189 original size:16 final size:16
Alignment explanation
Indices: 57141--57190 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
57131 AATAAATAAT
57141 TTTAGTCAAAATAAAA
1 TTTAGTCAAAATAAAA
*
57157 TTAAG--AAAATAACAAA
1 TTTAGTCAAAAT-A-AAA
57173 TTTAGTCAAAATAAAA
1 TTTAGTCAAAATAAAA
57189 TT
1 TT
57191 AATAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 5 0.18
15 1 0.04
16 16 0.57
17 1 0.04
18 5 0.18
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (16 bp):
TTTAGTCAAAATAAAA
Found at i:60683 original size:12 final size:12
Alignment explanation
Indices: 60650--60688 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
60640 TTTCCTTCCT
* *
60650 TTTTTCCCTCTA
1 TTTTTCCCTTTC
*
60662 TTTTTTCCTTTC
1 TTTTTCCCTTTC
60674 TTTTTCCCTTTC
1 TTTTTCCCTTTC
60686 TTT
1 TTT
60689 GCCTAATTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTCCCTTTC
Found at i:60819 original size:11 final size:11
Alignment explanation
Indices: 60805--60835 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
60795 TGGGTTTGGG
60805 TAAGGTTTTTA
1 TAAGGTTTTTA
60816 TAAGGTTTTTA
1 TAAGGTTTTTA
*
60827 TAGGGTTTT
1 TAAGGTTTT
60836 ATTTTGGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (11 bp):
TAAGGTTTTTA
Found at i:69947 original size:40 final size:39
Alignment explanation
Indices: 69902--69987 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 39
69892 GATAATGATG
69902 ATTTTAATAATTTTATA-TTTTAAAAAATAATCTTAAAATA
1 ATTTTAATAATTTTATACTTTTAAAAAATAAT-TT-AAATA
*
69942 ATTTTAATAATTTTATACTTTTAAAAAATAATTTTAATA
1 ATTTTAATAATTTTATACTTTTAAAAAATAATTTAAATA
69981 ATTTTAA
1 ATTTTAA
69988 AATCATTTGC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
39 11 0.25
40 19 0.43
41 14 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (39 bp):
ATTTTAATAATTTTATACTTTTAAAAAATAATTTAAATA
Found at i:72562 original size:2 final size:2
Alignment explanation
Indices: 72555--72582 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
72545 CATCTTTCAC
72555 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
72583 TTTGCATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76116 original size:24 final size:23
Alignment explanation
Indices: 76067--76116 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
76057 TAAAGTAGGT
* *
76067 TATATATTATTTTTATAATATTA
1 TATATATGATTTTTATAATATCA
76090 TATATTATGATTTTTACTAAT-TCA
1 TATA-TATGATTTTTA-TAATATCA
76114 TAT
1 TAT
76117 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (23 bp):
TATATATGATTTTTATAATATCA
Found at i:76255 original size:58 final size:58
Alignment explanation
Indices: 76094--76260 Score: 196
Period size: 58 Copynumber: 2.9 Consensus size: 58
76084 ATATTATATA
* * * *
76094 TTATGATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAT
** * *
76154 ACATTA-TTTTATTAAATTTTATTTAATAATAATTATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
*
76211 TTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
76261 AACAATAATC
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
57 20 0.22
58 55 0.60
59 9 0.10
60 7 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
Found at i:85385 original size:25 final size:23
Alignment explanation
Indices: 85344--85389 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
85334 CTAATTAGGG
85344 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
85367 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
85390 TGGATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:90250 original size:24 final size:24
Alignment explanation
Indices: 90219--90266 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
90209 AGGGTTTTAC
90219 ACACCTTTTCTTAATTTTTATTTT
1 ACACCTTTTCTTAATTTTTATTTT
90243 ACACCTTTTCTTAATTTTTATTTT
1 ACACCTTTTCTTAATTTTTATTTT
90267 GACTTTGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (24 bp):
ACACCTTTTCTTAATTTTTATTTT
Found at i:95683 original size:15 final size:14
Alignment explanation
Indices: 95650--95689 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
95640 ACATTTTGGT
95650 TTATTT-ATTTTTC
1 TTATTTAATTTTTC
95663 -TATTTAATTTTATC
1 TTATTTAATTTT-TC
95677 TTATTTAATTTTT
1 TTATTTAATTTTT
95690 TTCTTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.21
13 5 0.21
14 3 0.12
15 11 0.46
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTTAATTTTTC
Found at i:95696 original size:27 final size:27
Alignment explanation
Indices: 95650--95702 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
95640 ACATTTTGGT
*
95650 TTATTTATTTTTCTATTTAATTTTATC
1 TTATTTATTTTTCTATTTAATATTATC
95677 TTATTTAATTTTT-T-TCTTAATATTAT
1 TTATTT-ATTTTTCTAT-TTAATATTAT
95703 AGGTGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.04
27 16 0.70
28 6 0.26
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (27 bp):
TTATTTATTTTTCTATTTAATATTATC
Found at i:98531 original size:21 final size:21
Alignment explanation
Indices: 98505--98548 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
98495 TAGATGCGAG
98505 TATAATTTATCCCATCTCAAA
1 TATAATTTATCCCATCTCAAA
98526 TATAATTTATCCCATCTCAAA
1 TATAATTTATCCCATCTCAAA
98547 TA
1 TA
98549 GCTCATGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (21 bp):
TATAATTTATCCCATCTCAAA
Found at i:101399 original size:26 final size:26
Alignment explanation
Indices: 101370--101506 Score: 121
Period size: 26 Copynumber: 5.3 Consensus size: 26
101360 ATATTGGCTT
* *
101370 ATAAAAGCGAAATATTAAACTAGCTC
1 ATAAGAGCGAAATACTAAACTAGCTC
* *
101396 ATAAGAGCGATATACTATACTAGCTC
1 ATAAGAGCGAAATACTAAACTAGCTC
* * * *
101422 GTAAGAGCGAAATATTGAACTGGCTC
1 ATAAGAGCGAAATACTAAACTAGCTC
* * * * *
101448 GTACGAGTGAAATACTATACTGGCTC
1 ATAAGAGCGAAATACTAAACTAGCTC
* * *
101474 ATAAGAGCGATATACTGAACTGGCTC
1 ATAAGAGCGAAATACTAAACTAGCTC
*
101500 AAAAGAG
1 ATAAGAG
101507 AAATATACTG
Statistics
Matches: 89, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 89 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (26 bp):
ATAAGAGCGAAATACTAAACTAGCTC
Found at i:101431 original size:52 final size:52
Alignment explanation
Indices: 101351--101524 Score: 177
Period size: 52 Copynumber: 3.3 Consensus size: 52
101341 AAGACTCTGA
* * * * * *
101351 AGATATACTATATTGGCTTATAAAAGCGAAATATTAAACTAGCTCATAAGAG
1 AGATATACTATACTAGCTCATAAGAGCGAAATATTGAACTGGCTCATAAGAG
* * * *
101403 CGATATACTATACTAGCTCGTAAGAGCGAAATATTGAACTGGCTCGTACGAG
1 AGATATACTATACTAGCTCATAAGAGCGAAATATTGAACTGGCTCATAAGAG
* * * * * *
101455 TGAAATACTATACTGGCTCATAAGAGCGATATACTGAACTGGCTCAAAAGAG
1 AGATATACTATACTAGCTCATAAGAGCGAAATATTGAACTGGCTCATAAGAG
* * *
101507 AAATATACTGTATTAGCT
1 AGATATACTATACTAGCT
101525 TGTAAGAACG
Statistics
Matches: 97, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
52 97 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (52 bp):
AGATATACTATACTAGCTCATAAGAGCGAAATATTGAACTGGCTCATAAGAG
Found at i:101512 original size:26 final size:26
Alignment explanation
Indices: 101466--101516 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
101456 GAAATACTAT
* **
101466 ACTGGCTCATAAGAGCGATATACTGA
1 ACTGGCTCAAAAGAGAAATATACTGA
101492 ACTGGCTCAAAAGAGAAATATACTG
1 ACTGGCTCAAAAGAGAAATATACTG
101517 TATTAGCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (26 bp):
ACTGGCTCAAAAGAGAAATATACTGA
Found at i:101551 original size:104 final size:104
Alignment explanation
Indices: 101355--101554 Score: 231
Period size: 104 Copynumber: 1.9 Consensus size: 104
101345 CTCTGAAGAT
* * * * **
101355 ATACTATATTGGCTTATAAAAGCGAAATATTAAACTAGCTCATAAGAGCGATATACTATACTAGC
1 ATACTATACTGGCTCATAAAAGCGAAATACTAAACTAGCTCAAAAGAGAAATATACTATACTAGC
* *
101420 TCGTAAGAGCGAAATATTGAACTGGCTCGTACGAGTGAA
66 TCGTAAGAACGAAATACTGAACTGGCTCGTACGAGTGAA
* * * * * *
101459 ATACTATACTGGCTCATAAGAGCGATATACTGAACTGGCTCAAAAGAGAAATATACTGTATTAGC
1 ATACTATACTGGCTCATAAAAGCGAAATACTAAACTAGCTCAAAAGAGAAATATACTATACTAGC
* * *
101524 TTGTAAGAACGATATCCTG-ACTGGGCTCGTA
66 TCGTAAGAACGAAATACTGAACT-GGCTCGTA
101555 TGAGCTAAAT
Statistics
Matches: 78, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
103 3 0.04
104 75 0.96
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (104 bp):
ATACTATACTGGCTCATAAAAGCGAAATACTAAACTAGCTCAAAAGAGAAATATACTATACTAGC
TCGTAAGAACGAAATACTGAACTGGCTCGTACGAGTGAA
Found at i:104417 original size:17 final size:16
Alignment explanation
Indices: 104373--104432 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
104363 AAATTATTTT
104373 TTAAT-TTTTAAATTG
1 TTAATATTTTAAATTG
* *
104388 TTGAA-ATTGTTAACTTT
1 TT-AATATT-TTAAATTG
104405 TTAATTATTTTAAATTG
1 TTAA-TATTTTAAATTG
104422 TTAATATTTTA
1 TTAATATTTTA
104433 CGCTAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
15 2 0.06
16 13 0.36
17 18 0.50
18 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (16 bp):
TTAATATTTTAAATTG
Found at i:105222 original size:44 final size:44
Alignment explanation
Indices: 105137--105230 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
105127 ATAGTAAGCA
* * * *
105137 CACACAGTGTAAATCAGTAGGCATACACAGTGCAAAACAGTAAG
1 CACACAGTGCAAATCAGTAAGCACACACAATGCAAAACAGTAAG
* * * *
105181 CACACAGTGCAAATCAGTAAGCACATATAATGCGAATCAGTAAG
1 CACACAGTGCAAATCAGTAAGCACACACAATGCAAAACAGTAAG
105225 CACACA
1 CACACA
105231 CAGTGCTGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (44 bp):
CACACAGTGCAAATCAGTAAGCACACACAATGCAAAACAGTAAG
Found at i:105248 original size:23 final size:23
Alignment explanation
Indices: 105125--105236 Score: 131
Period size: 23 Copynumber: 5.0 Consensus size: 23
105115 AATGCTGGGA
*
105125 AAAT-AGTAAGCACACACAGTGT
1 AAATCAGTAAGCACACACAGTGC
* *
105147 AAATCAGTAGGCATACACAGTGC
1 AAATCAGTAAGCACACACAGTGC
*
105170 AAAACAGTAAG--CACACAGTGC
1 AAATCAGTAAGCACACACAGTGC
* * *
105191 AAATCAGTAAGCACATATAATGC
1 AAATCAGTAAGCACACACAGTGC
*
105214 GAATCAGTAAGCACACACAGTGC
1 AAATCAGTAAGCACACACAGTGC
105237 TGAATAGTAA
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
21 19 0.26
22 4 0.05
23 50 0.68
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (23 bp):
AAATCAGTAAGCACACACAGTGC
Found at i:112438 original size:23 final size:23
Alignment explanation
Indices: 112406--112513 Score: 128
Period size: 23 Copynumber: 4.7 Consensus size: 23
112396 GCTGGGGAAA
*
112406 CAGTAAGCACAAACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* *
112429 CAGTAGGCACACACTGTGCAAAAT
1 CAGTAAGCACACACAGTGC-AAAT
*
112453 -AGTAAGCACACACAATGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
112475 CAGTAAGCACATATAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
*
112498 TAGTAAGCACACACAG
1 CAGTAAGCACACACAG
112514 CGCTGAAAGT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
22 4 0.06
23 62 0.89
24 4 0.06
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.16
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:112472 original size:46 final size:46
Alignment explanation
Indices: 112407--112512 Score: 142
Period size: 46 Copynumber: 2.3 Consensus size: 46
112397 CTGGGGAAAC
* * *
112407 AGTAAGCACAAACAGTGCAAATCAGTAGGCACACACT-GTGCAAAAT
1 AGTAAGCACACACAATGCAAATCAGTAAGCACACA-TAGTGCAAAAT
* * *
112453 AGTAAGCACACACAATGCAAATCAGTAAGCACATATAGTGCGAATT
1 AGTAAGCACACACAATGCAAATCAGTAAGCACACATAGTGCAAAAT
112499 AGTAAGCACACACA
1 AGTAAGCACACACA
112513 GCGCTGAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 1 0.02
46 52 0.98
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (46 bp):
AGTAAGCACACACAATGCAAATCAGTAAGCACACATAGTGCAAAAT
Found at i:116362 original size:21 final size:21
Alignment explanation
Indices: 116337--116376 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
116327 GATGCTCAGA
* *
116337 AAAAAGAGAAGGAAAAAAATG
1 AAAAAGAAAAAGAAAAAAATG
116358 AAAAAGAAAAAGAAAAAAA
1 AAAAAGAAAAAGAAAAAAA
116377 ATAGGGCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (21 bp):
AAAAAGAAAAAGAAAAAAATG
Found at i:125951 original size:22 final size:22
Alignment explanation
Indices: 125923--125974 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
125913 TCCACTGAGC
125923 AGACATTGAAGCCATTAAGGAG
1 AGACATTGAAGCCATTAAGGAG
125945 AGACATTGAAGCCATTAAGGAG
1 AGACATTGAAGCCATTAAGGAG
*
125967 TGACATTG
1 AGACATTG
125975 GTGATACACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.21
Consensus pattern (22 bp):
AGACATTGAAGCCATTAAGGAG
Found at i:127759 original size:123 final size:123
Alignment explanation
Indices: 127456--127822 Score: 504
Period size: 123 Copynumber: 3.0 Consensus size: 123
127446 TTCTACTATC
* * * *
127456 TTTCCTTTTATTTTAATATCTCATTTTAAAATGGAAATATATATCTTTAGAGAAATATATGGAAG
1 TTTCCTTTTA-TATAATATCTCATATTAAAATGGAAATAT-T-CCTTTAAAGAAATATATGGAAG
* * * * *
127521 ATTTATTAAAACATTATATCCTTTCCAGAAGGATATTATCTTACACG-TTTTAATATTCAT
63 GTTTATTAAAACATTATATCCTTTCCAAAAGGATATTATCTTCCATGTTTTTAATATTCAA
* *
127581 TTTCTTTTTATATAATATCTCATATTAAAATGAAAATATTCCTTTAAAGAAATATATGGAAGGTT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
* * *
127646 TATTAAAACATTATATCATTTCCAAAAGGATATTAACTTCCATGTTTTTTATATTCAA
66 TATTAAAACATTATATCCTTTCCAAAAGGATATTATCTTCCATGTTTTTAATATTCAA
* * *
127704 TTTCCTTTTATACAATATCTAATATTAAAATGGAAATATTCCTTTAAAGAAATATATGAAAGGTT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
** * *
127769 TATTAAAACATTATATCCTTTTTAAAAAGATATTATCTTCCAT-ATTTTAATATT
66 TATTAAAACATTATATCCTTTCCAAAAGGATATTATCTTCCATGTTTTTAATATT
127823 TAACGAAATC
Statistics
Matches: 215, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
122 70 0.33
123 110 0.51
124 26 0.12
125 9 0.04
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (123 bp):
TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
TATTAAAACATTATATCCTTTCCAAAAGGATATTATCTTCCATGTTTTTAATATTCAA
Found at i:131380 original size:72 final size:72
Alignment explanation
Indices: 131294--131451 Score: 289
Period size: 72 Copynumber: 2.2 Consensus size: 72
131284 GAAGAAACGA
*
131294 GGGACTTACTTCTTTTTTATGACATACAAAAAGCTATGTTGCGACAACGCCTGCACGATGACACC
1 GGGACTTACTTCTTTTTTACGACATACAAAAAGCTATGTTGCGACAACGCCTGCACGATGACACC
131359 ACATAAG
66 ACATAAG
*
131366 GGGACTTACTTCTTTTTTGCGACATACAAAAAGCTATGTTGCGACAACGCCTGCACGATGACACC
1 GGGACTTACTTCTTTTTTACGACATACAAAAAGCTATGTTGCGACAACGCCTGCACGATGACACC
131431 ACATAAG
66 ACATAAG
*
131438 GGGACTAACTTCTT
1 GGGACTTACTTCTT
131452 CGTCGCAACA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 83 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (72 bp):
GGGACTTACTTCTTTTTTACGACATACAAAAAGCTATGTTGCGACAACGCCTGCACGATGACACC
ACATAAG
Found at i:137132 original size:21 final size:22
Alignment explanation
Indices: 137102--137142 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
137092 CTGCCTTCTA
*
137102 TGTCGCGACA-CGACTCCTGTG
1 TGTCGAGACATCGACTCCTGTG
137123 TGTCGAGACATCGACTCCTG
1 TGTCGAGACATCGACTCCTG
137143 AATGCGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.17, C:0.32, G:0.27, T:0.24
Consensus pattern (22 bp):
TGTCGAGACATCGACTCCTGTG
Found at i:141199 original size:24 final size:23
Alignment explanation
Indices: 141167--141211 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
141157 GATTTCCTAT
141167 AAGGAGAAATAATGAAGGTGAGAG
1 AAGGAGAAATAA-GAAGGTGAGAG
*
141191 AAGGAGAAATAAGATGGTGAG
1 AAGGAGAAATAAGAAGGTGAG
141212 CAAGAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.38, T:0.13
Consensus pattern (23 bp):
AAGGAGAAATAAGAAGGTGAGAG
Found at i:141771 original size:11 final size:11
Alignment explanation
Indices: 141755--141780 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
141745 AATACAAGCA
141755 TTTTAGTTATG
1 TTTTAGTTATG
141766 TTTTAGTTATG
1 TTTTAGTTATG
141777 TTTT
1 TTTT
141781 TGTACTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (11 bp):
TTTTAGTTATG
Found at i:145376 original size:43 final size:43
Alignment explanation
Indices: 145275--145628 Score: 334
Period size: 43 Copynumber: 8.3 Consensus size: 43
145265 TTATGCATAA
* * * * ** *
145275 AAACACCGCTATATAACATGATCTTTAGCGGC-ACTTTCCAAC
1 AAACGCCGCTATAGAACATGTTCTTTAGCGACGTTTTTCCCAC
* ** *
145317 AAATGTTGCTATAGAACATGGTTC-TTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGAACAT-GTTCTTTAGCGACGTTTTTCCCAC
* * * *
145360 AAACGCCGCTAAAGAACATGTTCTTTACCGACGTTTTTCTCAT
1 AAACGCCGCTATAGAACATGTTCTTTAGCGACGTTTTTCCCAC
* * * * * *
145403 AAACGCAGCTAAACAACATGTTCTTTAGCGGCATTTTCCCCAC
1 AAACGCCGCTATAGAACATGTTCTTTAGCGACGTTTTTCCCAC
* * * * *
145446 AAACACCGTTATAGAGCATGTTCTTTAGCAACATTTTTCCCAC
1 AAACGCCGCTATAGAACATGTTCTTTAGCGACGTTTTTCCCAC
* * *
145489 AAACGCCGCTATAGAACATGTTCTTTAGTGGCATTTTTCCCAC
1 AAACGCCGCTATAGAACATGTTCTTTAGCGACGTTTTTCCCAC
* * * * *
145532 AAACTCCACTATAGAGCATGTTCTTTAGCAATGTTTTTCCCAC
1 AAACGCCGCTATAGAACATGTTCTTTAGCGACGTTTTTCCCAC
* * * *
145575 AAATGCCGCTATAGAGCATGTTCTTTAGTGGCGTTTTTCCCAC
1 AAACGCCGCTATAGAACATGTTCTTTAGCGACGTTTTTCCCAC
*
145618 AAATGCCGCTA
1 AAACGCCGCTA
145629 ACATTAACAT
Statistics
Matches: 253, Mismatches: 56, Indels: 5
0.81 0.18 0.02
Matches are distributed among these distances:
42 25 0.10
43 228 0.90
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGTTCTTTAGCGACGTTTTTCCCAC
Found at i:151963 original size:26 final size:26
Alignment explanation
Indices: 151873--151972 Score: 112
Period size: 26 Copynumber: 3.8 Consensus size: 26
151863 TTTTTAATAA
**
151873 TTAAATAATTAAATATTTGGGTTATT
1 TTAAATAATTAAATATTTAAGTTATT
* *
151899 TTTAATAATTAAATATTTAA-TTAATAAA
1 TTAAATAATTAAATATTTAAGTT-AT--T
* *
151927 TTAAATAATTAAGTATTTAAGTTGTT
1 TTAAATAATTAAATATTTAAGTTATT
151953 TTAAATAATTAAATATTTAA
1 TTAAATAATTAAATATTTAA
151973 ATATTTGGGT
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
25 2 0.03
26 38 0.62
28 19 0.31
29 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (26 bp):
TTAAATAATTAAATATTTAAGTTATT
Found at i:151963 original size:34 final size:34
Alignment explanation
Indices: 151919--152004 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
151909 AAATATTTAA
*
151919 TTAATAAATTAAATAATTAAGTATTTAAGTTGT-T
1 TTAAT-AATTAAATAATTAAATATTTAAGTTGTGT
* **
151953 TTAAATAATTAAATATTTAAATATTTGGGTTGTGT
1 TT-AATAATTAAATAATTAAATATTTAAGTTGTGT
151988 TTAATAATTAAATAATT
1 TTAATAATTAAATAATT
152005 GGGTTATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
34 39 0.87
35 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (34 bp):
TTAATAATTAAATAATTAAATATTTAAGTTGTGT
Found at i:151993 original size:26 final size:26
Alignment explanation
Indices: 151964--152030 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
151954 TAAATAATTA
* *
151964 AATATTTAAATATTTGGGTTGTGTTT
1 AATAATTAAATATTTGGGTTATGTTT
* *
151990 AATAATTAAATAATTGGGTTATTTTT
1 AATAATTAAATATTTGGGTTATGTTT
152016 AATAATTAAATATTT
1 AATAATTAAATATTT
152031 AATTAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (26 bp):
AATAATTAAATATTTGGGTTATGTTT
Found at i:152041 original size:20 final size:21
Alignment explanation
Indices: 152016--152055 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
152006 GGTTATTTTT
152016 AATAATTAAATATTT-AATTA
1 AATAATTAAATATTTGAATTA
152036 AATAATTAAATATTTGAATT
1 AATAATTAAATATTTGAATT
152056 GTTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
AATAATTAAATATTTGAATTA
Found at i:152069 original size:26 final size:26
Alignment explanation
Indices: 151964--152073 Score: 97
Period size: 26 Copynumber: 4.5 Consensus size: 26
151954 TAAATAATTA
* ** *
151964 AATATTTAAATATTTGGGTTGTGTTT
1 AATAATTAAATATTTGAATTGTTTTT
* ** *
151990 AATAATTAAATAATTGGGTTATTTTT
1 AATAATTAAATATTTGAATTGTTTTT
*
152016 AATAATTAAATATTT-AA-----TTA
1 AATAATTAAATATTTGAATTGTTTTT
152036 AATAATTAAATATTTGAATTGTTTTT
1 AATAATTAAATATTTGAATTGTTTTT
152062 AATAATTAAATA
1 AATAATTAAATA
152074 ATTATTTTGT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
20 17 0.25
21 2 0.03
26 50 0.72
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (26 bp):
AATAATTAAATATTTGAATTGTTTTT
Found at i:157226 original size:41 final size:41
Alignment explanation
Indices: 157193--157437 Score: 323
Period size: 41 Copynumber: 6.0 Consensus size: 41
157183 CTTTAGTAGT
157193 GTTTTCCCATAAACGCCGCTAATGCTCTTACCTTTTGCAGC
1 GTTTTCCCATAAACGCCGCTAATGCTCTTACCTTTTGCAGC
* * * * *
157234 ATTTTCTCATAAATGTCGCTAATGCTCTTACCTTTTGCGGC
1 GTTTTCCCATAAACGCCGCTAATGCTCTTACCTTTTGCAGC
* * *
157275 ATTTTCCTATAAACGCCGCTAATGCTCTTACCTTTTGCGGC
1 GTTTTCCCATAAACGCCGCTAATGCTCTTACCTTTTGCAGC
* * *
157316 GTTTTCCCATAAACGTCACTAATGCTCTTACCTTTTACAGC
1 GTTTTCCCATAAACGCCGCTAATGCTCTTACCTTTTGCAGC
157357 GTTTTCCCATAAACGCCGCTAATGCTCTTACCTTTTGC-GAC
1 GTTTTCCCATAAACGCCGCTAATGCTCTTACCTTTTGCAG-C
* * * *
157398 GTTTTTTCCATAAACGCCACTATTGCT-TTACTTTTTGCAG
1 G-TTTTCCCATAAACGCCGCTAATGCTCTTACCTTTTGCAG
157438 ATTTTATGGG
Statistics
Matches: 179, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
40 1 0.01
41 155 0.87
42 23 0.13
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.38
Consensus pattern (41 bp):
GTTTTCCCATAAACGCCGCTAATGCTCTTACCTTTTGCAGC
Found at i:157524 original size:80 final size:81
Alignment explanation
Indices: 157409--157563 Score: 186
Period size: 80 Copynumber: 1.9 Consensus size: 81
157399 TTTTTTCCAT
* * * **
157409 AAACGCCACTATTGCTTTACTTTTTGCAGATTTTATGGGAAAACGCCACTATTACTTTACCTTTT
1 AAACGCCACTATTGCTTTACCTTTTACAGAGTTTATGAAAAAACGCCACTATTACTTTACCTTTT
157474 GCGG-ATTTTACGAAA
66 GCGGCATTTTACGAAA
* * * ** * *
157489 AAACGCCACTATTGTTTTACCTTTTACGGCGTTTATGAAAAAACGCCGTTATTATTTTACTTTTT
1 AAACGCCACTATTGCTTTACCTTTTACAGAGTTTATGAAAAAACGCCACTATTACTTTACCTTTT
*
157554 GTGGCATTTT
66 GCGGCATTTT
157564 CGATCCAAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
80 56 0.92
81 5 0.08
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (81 bp):
AAACGCCACTATTGCTTTACCTTTTACAGAGTTTATGAAAAAACGCCACTATTACTTTACCTTTT
GCGGCATTTTACGAAA
Found at i:157529 original size:40 final size:40
Alignment explanation
Indices: 157409--157563 Score: 157
Period size: 40 Copynumber: 3.9 Consensus size: 40
157399 TTTTTTCCAT
* * * **
157409 AAACGCCACTATTGCTTTACTTTTTGCAGATTTTATGGGA
1 AAACGCCACTATTACTTTACCTTTTGCGGATTTTATGAAA
*
157449 AAACGCCACTATTACTTTACCTTTTGCGGATTTTACGAAA
1 AAACGCCACTATTACTTTACCTTTTGCGGATTTTATGAAA
** * **
157489 AAACGCCACTATTGTTTTACCTTTTACGGCGTTTATGAAA
1 AAACGCCACTATTACTTTACCTTTTGCGGATTTTATGAAA
** * * *
157529 AAACGCCGTTATTATTTTACTTTTTGTGGCATTTT
1 AAACGCCACTATTACTTTACCTTTTGCGG-ATTTT
157564 CGATCCAAAC
Statistics
Matches: 94, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 91 0.97
41 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (40 bp):
AAACGCCACTATTACTTTACCTTTTGCGGATTTTATGAAA
Found at i:159101 original size:47 final size:49
Alignment explanation
Indices: 158994--159101 Score: 112
Period size: 47 Copynumber: 2.2 Consensus size: 49
158984 TCATGCCTAT
* * * *
158994 TATTTTTGTTAACAAAAACCTAATTCGCATGTTAAGCATGTCCATTGTAC
1 TATTTTTG-TAACAAAAACCTAATTCACATGTTAAACATGTCCATTGAAA
* * * * *
159044 TGTTTCTGTAAC-AAAATCTGA-TCACATGTTAAATATGTCCATTGAAA
1 TATTTTTGTAACAAAAACCTAATTCACATGTTAAACATGTCCATTGAAA
159091 TATTTTTGTAA
1 TATTTTTGTAA
159102 TTGTATGTCG
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
47 30 0.64
48 7 0.15
49 4 0.09
50 6 0.13
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (49 bp):
TATTTTTGTAACAAAAACCTAATTCACATGTTAAACATGTCCATTGAAA
Found at i:164767 original size:13 final size:13
Alignment explanation
Indices: 164747--164794 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
164737 TGAGAAGTGC
*
164747 TTTTAAAAAAT-G
1 TTTTAAAAAATAA
164759 TTTTGAAAAAATAA
1 TTTT-AAAAAATAA
*
164773 TTTTAAAAAATAC
1 TTTTAAAAAATAA
*
164786 TTTTGAAAA
1 TTTTAAAAA
164795 GCTTGAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 4 0.13
13 23 0.74
14 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTAAAAAATAA
Found at i:165156 original size:21 final size:20
Alignment explanation
Indices: 165123--165161 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
165113 TTTTCATCTC
165123 AAAAAAATGCTTTTGAAAAAT
1 AAAAAAATGCTTTT-AAAAAT
* *
165144 AAAAAATTTCTTTTAAAA
1 AAAAAAATGCTTTTAAAA
165162 GTTACTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAAAAATGCTTTTAAAAAT
Found at i:165237 original size:17 final size:17
Alignment explanation
Indices: 165215--165251 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
165205 AAGTACTTTC
165215 AAAAACATTACTAAACA
1 AAAAACATTACTAAACA
165232 AAAAACATTACTAAACA
1 AAAAACATTACTAAACA
165249 AAA
1 AAA
165252 CCTAACACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAAACATTACTAAACA
Found at i:183371 original size:9 final size:8
Alignment explanation
Indices: 183354--183398 Score: 54
Period size: 9 Copynumber: 5.1 Consensus size: 8
183344 TCCAAATCAA
183354 ATTCACAT
1 ATTCACAT
183362 ATTCCACAT
1 ATT-CACAT
183371 ATATCACAT
1 AT-TCACAT
183380 ATTTTCACAT
1 A--TTCACAT
183390 ATTCACAT
1 ATTCACAT
183398 A
1 A
183399 ACATTATGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 11 0.33
9 13 0.39
10 8 0.24
11 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (8 bp):
ATTCACAT
Found at i:183379 original size:18 final size:18
Alignment explanation
Indices: 183354--183398 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
183344 TCCAAATCAA
183354 ATTCACATA-TTCCACAT
1 ATTCACATATTTCCACAT
*
183371 ATATCACATATTTTCACAT
1 AT-TCACATATTTCCACAT
183390 ATTCACATA
1 ATTCACATA
183399 ACATTATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 14 0.56
19 9 0.36
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTCACATATTTCCACAT
Found at i:183691 original size:21 final size:21
Alignment explanation
Indices: 183667--183738 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
183657 GGACAAGCCA
183667 CCACATATTTTCCAATAATGG
1 CCACATATTTTCCAATAATGG
** *
183688 CCACATAGTTTTGTAGATAAACT-A
1 CCACATA-TTTTCCA-AT-AA-TGG
*
183712 CCATATATTTTCCAATAATGG
1 CCACATATTTTCCAATAATGG
183733 CCACAT
1 CCACAT
183739 CTTCCTCCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
20 1 0.03
21 14 0.37
22 7 0.18
23 7 0.18
24 8 0.21
25 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (21 bp):
CCACATATTTTCCAATAATGG
Found at i:183866 original size:46 final size:46
Alignment explanation
Indices: 183806--183949 Score: 164
Period size: 46 Copynumber: 3.1 Consensus size: 46
183796 TTATCACTTA
* * * *
183806 TCACATTTTTAGCATTTTTCATGCTCACATATCTC-TTGTTACAATTT
1 TCACA-TTTTAGCATGTATCATGCTCACATATCACATT-TCACAATTT
*
183853 TCACATTTTAGCATGTATCATGCTCACATATCACATTTCACGATTT
1 TCACATTTTAGCATGTATCATGCTCACATATCACATTTCACAATTT
* * * * *
183899 CCACATTTTTGTATGTATCATGCTCACATATCACATATCACATAATT
1 TCACATTTTAGCATGTATCATGCTCACATATCACATTTCACA-ATTT
183946 TCAC
1 TCAC
183950 TTAGGCATGC
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
46 70 0.84
47 13 0.16
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.42
Consensus pattern (46 bp):
TCACATTTTAGCATGTATCATGCTCACATATCACATTTCACAATTT
Found at i:184100 original size:21 final size:21
Alignment explanation
Indices: 184071--184121 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
184061 GAGATGAATT
*
184071 CACACATCATACATCACATAA
1 CACATATCATACATCACATAA
* *
184092 CACTTATCATAGATCACATAA
1 CACATATCATACATCACATAA
184113 CACATATCA
1 CACATATCA
184122 CGTTTTTCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (21 bp):
CACATATCATACATCACATAA
Found at i:184842 original size:19 final size:19
Alignment explanation
Indices: 184820--184858 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
184810 ATGGTACCAA
184820 TGACGATAGTCCACAACGG
1 TGACGATAGTCCACAACGG
* * *
184839 TGACGGTGGTTCACAACGG
1 TGACGATAGTCCACAACGG
184858 T
1 T
184859 TTGATTAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.21
Consensus pattern (19 bp):
TGACGATAGTCCACAACGG
Found at i:187367 original size:15 final size:15
Alignment explanation
Indices: 187347--187381 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
187337 CTAATGCTAC
187347 GAGCACTGAA-GTTGT
1 GAGCACT-AATGTTGT
187362 GAGCACTAATGTTGT
1 GAGCACTAATGTTGT
187377 GAGCA
1 GAGCA
187382 TGCATAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (15 bp):
GAGCACTAATGTTGT
Found at i:192115 original size:18 final size:18
Alignment explanation
Indices: 192092--192140 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
192082 TTAATGAGCC
192092 ATGCTCAAACGAGCCAGT
1 ATGCTCAAACGAGCCAGT
* *
192110 ATGCTCAAACTAGCTAGT
1 ATGCTCAAACGAGCCAGT
192128 ATGCTCAAACGAG
1 ATGCTCAAACGAG
192141 TCAATATTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (18 bp):
ATGCTCAAACGAGCCAGT
Found at i:211008 original size:16 final size:16
Alignment explanation
Indices: 210987--211017 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
210977 ATAATGTGAA
210987 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
211003 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
211018 GGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:211856 original size:26 final size:25
Alignment explanation
Indices: 211827--211875 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
211817 GTAATTTTGG
211827 ACATGTTCATGCAGCGACAATTCTAT
1 ACATGTTCATGCAGCGAC-ATTCTAT
211853 ACATGTTCATGCAGCGACATTCT
1 ACATGTTCATGCAGCGACATTCT
211876 TGTGTCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (25 bp):
ACATGTTCATGCAGCGACATTCTAT
Found at i:212024 original size:37 final size:37
Alignment explanation
Indices: 211978--212048 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
211968 TATTCTTGCA
* *
211978 GTGACAGTTTTGGGTGCAATTTGGAAGTGCTCATTCG
1 GTGACAGTTTTGGGTGCAATCTAGAAGTGCTCATTCG
*
212015 GTGATAGTTTTGGGTGCAATCTAGAAGTGCTCAT
1 GTGACAGTTTTGGGTGCAATCTAGAAGTGCTCAT
212049 GCAACAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.31, T:0.35
Consensus pattern (37 bp):
GTGACAGTTTTGGGTGCAATCTAGAAGTGCTCATTCG
Found at i:214643 original size:30 final size:30
Alignment explanation
Indices: 214599--214683 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
214589 GCATGGACAT
214599 TACGAGCA-TGGAAGTTGCGAGCACTAATGC
1 TACGAGCACT-GAAGTTGCGAGCACTAATGC
* * * **
214629 TGCGAGCACTGAAGTTACTAGCACTAATTT
1 TACGAGCACTGAAGTTGCGAGCACTAATGC
*
214659 TACGAGCACTGAAGTTGTGAGCACT
1 TACGAGCACTGAAGTTGCGAGCACT
214684 GATGTTTTGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 44 0.98
31 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (30 bp):
TACGAGCACTGAAGTTGCGAGCACTAATGC
Found at i:214651 original size:15 final size:15
Alignment explanation
Indices: 214598--214685 Score: 65
Period size: 15 Copynumber: 5.9 Consensus size: 15
214588 AGCATGGACA
214598 TTACGAGCA-TGGAAG
1 TTACGAGCACT-GAAG
*
214613 TTGCGAGCACT-AATG
1 TTACGAGCACTGAA-G
* *
214628 CTGCGAGCACTGAAG
1 TTACGAGCACTGAAG
* *
214643 TTACTAGCACT-AATT
1 TTACGAGCACTGAA-G
214658 TTACGAGCACTGAAG
1 TTACGAGCACTGAAG
**
214673 TTGTGAGCACTGA
1 TTACGAGCACTGA
214686 TGTTTTGAGC
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
14 4 0.07
15 49 0.84
16 5 0.09
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (15 bp):
TTACGAGCACTGAAG
Found at i:214694 original size:15 final size:15
Alignment explanation
Indices: 214662--214696 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
214652 CTAATTTTAC
214662 GAGCACTGAAGTTGT
1 GAGCACTGAAGTTGT
* *
214677 GAGCACTGATGTTTT
1 GAGCACTGAAGTTGT
214692 GAGCA
1 GAGCA
214697 TGGATAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (15 bp):
GAGCACTGAAGTTGT
Found at i:214696 original size:30 final size:30
Alignment explanation
Indices: 214601--214696 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
214591 ATGGACATTA
* * *
214601 CGAGCA-TGGAAGTTGCGAGCACTAATGCTG
1 CGAGCACT-GAAGTTGTGAGCACTAATGTTT
*
214631 CGAGCACTGAAGTTACT-AGCACTAAT-TTT
1 CGAGCACTGAAGTT-GTGAGCACTAATGTTT
*
214660 ACGAGCACTGAAGTTGTGAGCACTGATGTTT
1 -CGAGCACTGAAGTTGTGAGCACTAATGTTT
*
214691 TGAGCA
1 CGAGCA
214697 TGGATAAAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.04
30 48 0.89
31 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (30 bp):
CGAGCACTGAAGTTGTGAGCACTAATGTTT
Found at i:220116 original size:34 final size:34
Alignment explanation
Indices: 220073--220142 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
220063 TGTTGCAAAA
*
220073 ATCCATTCATTCATATAGATAATTTCATACTTAG
1 ATCCATTCATTCATATAGAAAATTTCATACTTAG
220107 ATCCATTCATTCATATAGAAAATTTCATACTTAG
1 ATCCATTCATTCATATAGAAAATTTCATACTTAG
220141 AT
1 AT
220143 TAATTTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (34 bp):
ATCCATTCATTCATATAGAAAATTTCATACTTAG
Found at i:222564 original size:23 final size:23
Alignment explanation
Indices: 222533--222583 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
222523 CATTTCCTAT
222533 CCCTCCATTCCCTTACCGATTTC
1 CCCTCCATTCCCTTACCGATTTC
* *
222556 CCCTTCATTCCCTTGCCGATTTC
1 CCCTCCATTCCCTTACCGATTTC
222579 CCCTC
1 CCCTC
222584 TTGAGAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.10, C:0.49, G:0.06, T:0.35
Consensus pattern (23 bp):
CCCTCCATTCCCTTACCGATTTC
Found at i:234836 original size:24 final size:24
Alignment explanation
Indices: 234786--234841 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
234776 AGTTCTTACG
* * *
234786 TGATTGAATTTAATTATCGATTGAT
1 TGATTG-ATTGAATAATCGATTAAT
*
234811 TGATTGATTGAATAATGGATTAAT
1 TGATTGATTGAATAATCGATTAAT
234835 TGATTGA
1 TGATTGA
234842 AACGTTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.45
Consensus pattern (24 bp):
TGATTGATTGAATAATCGATTAAT
Found at i:239500 original size:17 final size:18
Alignment explanation
Indices: 239464--239505 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
239454 CTAAAATTCA
239464 TTCATTCATATAGATAAT
1 TTCATTCATATAGATAAT
239482 TTCATTC-T-TAGATTAAT
1 TTCATTCATATAGA-TAAT
239499 TTGCATT
1 TT-CATT
239506 AGGGATCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 11 0.50
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (18 bp):
TTCATTCATATAGATAAT
Found at i:254892 original size:106 final size:108
Alignment explanation
Indices: 254771--255013 Score: 300
Period size: 108 Copynumber: 2.3 Consensus size: 108
254761 CTATTATTTA
* * * * * *
254771 TGGAGCCATTTTAAATGGTGTCACCCAATTGA-TTTTTTTA-TT-TTT-TTCTTTATTATATAAT
1 TGGAGACATTTTAAATGGCGCCACCCAATTAATTTTTTTTATTTATTTATTATTTAATATATAAT
* *
254832 ATTTAAATATATATAGTTTAATTTAAATATATATTTTATTTTTTG
66 ATGT-AA-ATATATAGTTTAATTTAAATATATATTTTATTTTTGG
* *
254877 TGGA-ATCATTTTAAATGACGCCACCCAATTAATTTTTTTTATTTATTTATTATTTAATATTTAA
1 TGGAGA-CATTTTAAATGGCGCCACCCAATTAATTTTTTTTATTTATTTATTATTTAATATATAA
*
254941 TATGTAAATATATAGTTTAATTTAAATGTATATTTTATTTTTGG
65 TATGTAAATATATAGTTTAATTTAAATATATATTTTATTTTTGG
* *
254985 TGGAGACATTCTAAATGGCACCA-CCAATT
1 TGGAGACATTTTAAATGGCGCCACCCAATT
255014 CCCGATGATA
Statistics
Matches: 117, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
106 26 0.22
107 14 0.12
108 55 0.47
109 6 0.05
110 16 0.14
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (108 bp):
TGGAGACATTTTAAATGGCGCCACCCAATTAATTTTTTTTATTTATTTATTATTTAATATATAAT
ATGTAAATATATAGTTTAATTTAAATATATATTTTATTTTTGG
Found at i:257205 original size:29 final size:30
Alignment explanation
Indices: 257172--257241 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
257162 TGTGTTTGGA
* *
257172 GTTGATCCTCTAAGTCGGGCTCTACCAT-G
1 GTTGATCCTCCAAGTCGGGCTCCACCATAG
* **
257201 GTTGATCCTCCGAGTCGGGCTCCGTCATAG
1 GTTGATCCTCCAAGTCGGGCTCCACCATAG
257231 GTTGATCCTCC
1 GTTGATCCTCC
257242 GGGTCGAGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.14, C:0.30, G:0.26, T:0.30
Consensus pattern (30 bp):
GTTGATCCTCCAAGTCGGGCTCCACCATAG
Found at i:257236 original size:30 final size:30
Alignment explanation
Indices: 257172--257265 Score: 109
Period size: 30 Copynumber: 3.2 Consensus size: 30
257162 TGTGTTTGGA
** ***
257172 GTTGATCCTCTAAGTCGGGCTCTACCAT-G
1 GTTGATCCTCCGAGTCGGGCTCCGTCATAG
257201 GTTGATCCTCCGAGTCGGGCTCCGTCATAG
1 GTTGATCCTCCGAGTCGGGCTCCGTCATAG
* * *
257231 GTTGATCCTCCGGGTCGAGCTTCGTCATAG
1 GTTGATCCTCCGAGTCGGGCTCCGTCATAG
257261 GTTGA
1 GTTGA
257266 CTTCCACGTC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 23 0.41
30 33 0.59
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.30
Consensus pattern (30 bp):
GTTGATCCTCCGAGTCGGGCTCCGTCATAG
Found at i:259288 original size:23 final size:23
Alignment explanation
Indices: 259261--259308 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
259251 TATTTAAAAA
* *
259261 TAAAATCAAAATTAGAAGGA-AAT
1 TAAAATAAAAATGA-AAGGAGAAT
259284 TAAAATAAAAATGAAAGGAGAAT
1 TAAAATAAAAATGAAAGGAGAAT
259307 TA
1 TA
259309 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.21
Consensus pattern (23 bp):
TAAAATAAAAATGAAAGGAGAAT
Found at i:260738 original size:17 final size:16
Alignment explanation
Indices: 260716--260747 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
260706 AGGTAAATTA
260716 TTTTTAAATTATTTTAT
1 TTTTTAAATT-TTTTAT
260733 TTTTTAAATTTTTTA
1 TTTTTAAATTTTTTA
260748 ATATTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTAAATTTTTTAT
Found at i:260754 original size:17 final size:17
Alignment explanation
Indices: 260713--260754 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
260703 AAAAGGTAAA
260713 TTAT-TTTTAAATTATT
1 TTATATTTTAAATTATT
*
260729 TTATTTTTTAAATT-TT
1 TTATATTTTAAATTATT
260745 TTAATATTTT
1 TT-ATATTTT
260755 CATAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATATTTTAAATTATT
Found at i:260841 original size:40 final size:40
Alignment explanation
Indices: 260796--260875 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
260786 ATTATTTCAT
260796 CAAAATATTAATTTTTTAACTTGAAATGATAACTTGACAC
1 CAAAATATTAATTTTTTAACTTGAAATGATAACTTGACAC
*
260836 CAAAATATTAATTTTTTAACTTGAAATGATGACTTGACAC
1 CAAAATATTAATTTTTTAACTTGAAATGATAACTTGACAC
260876 TTTAGTGACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (40 bp):
CAAAATATTAATTTTTTAACTTGAAATGATAACTTGACAC
Found at i:266756 original size:16 final size:18
Alignment explanation
Indices: 266726--266762 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
266716 TATTTTTATA
*
266726 TTTTTCTTTTCCTTT-TT
1 TTTTTCCTTTCCTTTCTT
266743 TTTTTCCTTT-CTTTCTT
1 TTTTTCCTTTCCTTTCTT
266760 TTT
1 TTT
266763 CATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTCCTTTCCTTTCTT
Found at i:266775 original size:26 final size:26
Alignment explanation
Indices: 266728--266780 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
266718 TTTTTATATT
* *
266728 TTTCTTTTCCTTTTTTTTTTCCTTTC
1 TTTCTTTTCCATTTTTTTTTCCATTC
*
266754 TTTCTTTTTCATTTTTTTTTCCATTC
1 TTTCTTTTCCATTTTTTTTTCCATTC
266780 T
1 T
266781 CTCTCTCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTCTTTTCCATTTTTTTTTCCATTC
Found at i:266778 original size:12 final size:13
Alignment explanation
Indices: 266725--266778 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 13
266715 TTATTTTTAT
266725 ATTTTTCTTTTCC
1 ATTTTTCTTTTCC
*
266738 -TTTTTTTTTTCC
1 ATTTTTCTTTTCC
* *
266750 TTTCTTTCTTTTTC
1 ATT-TTTCTTTTCC
266764 ATTTTT-TTTTCC
1 ATTTTTCTTTTCC
266776 ATT
1 ATT
266779 CTCTCTCTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
12 19 0.56
13 5 0.15
14 10 0.29
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTCTTTTCC
Found at i:267871 original size:40 final size:40
Alignment explanation
Indices: 267823--267937 Score: 117
Period size: 40 Copynumber: 2.9 Consensus size: 40
267813 CACCAGTTTG
*
267823 TGGACAAGCCACCAGTAATGCAAATAAACTGCTAGAAATA
1 TGGACAAGCCACCAGTAATGCAGATAAACTGCTAGAAATA
* ** * * *
267863 TGGGCAAGCCATTAG-AATTGCAGACAAGA-TGCCAGTAATA
1 TGGACAAGCCACCAGTAA-TGCAGATAA-ACTGCTAGAAATA
* *
267903 TGGACAAGCCACCAATAATGCAGATAAACTACTAG
1 TGGACAAGCCACCAGTAATGCAGATAAACTGCTAG
267938 TATTACAAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
39 3 0.05
40 51 0.89
41 3 0.05
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (40 bp):
TGGACAAGCCACCAGTAATGCAGATAAACTGCTAGAAATA
Found at i:268242 original size:17 final size:17
Alignment explanation
Indices: 268220--268264 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
268210 ATCATGCTAT
*
268220 CAATGGCAATAGCCAAA
1 CAATGGCAATAACCAAA
268237 CAATGGCAATAACCAAA
1 CAATGGCAATAACCAAA
*
268254 CAATGACAATA
1 CAATGGCAATA
268265 TCAAATATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.13
Consensus pattern (17 bp):
CAATGGCAATAACCAAA
Done.