Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014413.1 Kokia drynarioides strain JFW-HI SEQ_129451, 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: 119465
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 66 characters in sequence are not A, C, G, or T
Found at i:4256 original size:21 final size:23
Alignment explanation
Indices: 4232--4281 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
4222 ATAAATTTTG
*
4232 ATTTAATCCTT-TAAAAA-TATA
1 ATTTAATCATTGTAAAAATTATA
*
4253 ATTT-ATTATTGTAAAAATTATA
1 ATTTAATCATTGTAAAAATTATA
4275 ATTTAAT
1 ATTTAAT
4282 TTTGACCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 10 0.42
22 8 0.33
23 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTAATCATTGTAAAAATTATA
Found at i:14009 original size:31 final size:31
Alignment explanation
Indices: 13971--14039 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
13961 TTTCACCTCA
13971 AGTCCTTGAAAATTTATCACTTTAATATTTT
1 AGTCCTTGAAAATTTATCACTTTAATATTTT
14002 AGTCCTTGAAAATTTATCACTTTAATATTTT
1 AGTCCTTGAAAATTTATCACTTTAATATTTT
14033 AGTCCTT
1 AGTCCTT
14040 AAACATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.48
Consensus pattern (31 bp):
AGTCCTTGAAAATTTATCACTTTAATATTTT
Found at i:14017 original size:15 final size:16
Alignment explanation
Indices: 13971--14039 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
13961 TTTCACCTCA
13971 AGTCCTTGAA-AATTT
1 AGTCCTTGAATAATTT
* *
13986 A-TCACTTTAATATTTT
1 AGTC-CTTGAATAATTT
14002 AGTCCTTGAA-AATTT
1 AGTCCTTGAATAATTT
* *
14017 A-TCACTTTAATATTTT
1 AGTC-CTTGAATAATTT
14033 AGTCCTT
1 AGTCCTT
14040 AAACATTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.10
15 16 0.38
16 18 0.43
17 4 0.10
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.48
Consensus pattern (16 bp):
AGTCCTTGAATAATTT
Found at i:14041 original size:15 final size:15
Alignment explanation
Indices: 13992--14041 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
13982 ATTTATCACT
13992 TTAATATTTTAGTCC
1 TTAATATTTTAGTCC
*
14007 TTGAA-AATTTA-TCAC
1 TT-AATATTTTAGTC-C
14022 TTTAATATTTTAGTCC
1 -TTAATATTTTAGTCC
14038 TTAA
1 TTAA
14042 ACATTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
14 2 0.07
15 14 0.50
16 10 0.36
17 2 0.07
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (15 bp):
TTAATATTTTAGTCC
Found at i:16635 original size:16 final size:16
Alignment explanation
Indices: 16614--16645 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16604 CTAAATACAC
*
16614 ACAGTAATTAAAATAA
1 ACAGTAATCAAAATAA
16630 ACAGTAATCAAAATAA
1 ACAGTAATCAAAATAA
16646 TCACTCTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.22
Consensus pattern (16 bp):
ACAGTAATCAAAATAA
Found at i:21955 original size:11 final size:11
Alignment explanation
Indices: 21939--21963 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21929 TTGTAAGGCC
21939 TTTTTTCCTTT
1 TTTTTTCCTTT
21950 TTTTTTCCTTT
1 TTTTTTCCTTT
21961 TTT
1 TTT
21964 ATCTTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTCCTTT
Found at i:21988 original size:17 final size:18
Alignment explanation
Indices: 21968--22001 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21958 TTTTTTATCT
21968 TTTAT-AAATAAAATACA
1 TTTATGAAATAAAATACA
*
21985 TTTATGAAGTAAAATAC
1 TTTATGAAATAAAATAC
22002 CCATAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (18 bp):
TTTATGAAATAAAATACA
Found at i:24854 original size:18 final size:18
Alignment explanation
Indices: 24811--24870 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
24801 AATTATTCTG
**
24811 TTGTTAATATTTG-GATA
1 TTGTTAATATTTGTTTTA
24828 TTGTATAATATTTGTTTTA
1 TTGT-TAATATTTGTTTTA
24847 TTGTTAAT-TTTGTTATTA
1 TTGTTAATATTTGTT-TTA
24865 TT-TTAA
1 TTGTTAA
24871 ATACATTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 14 0.37
18 18 0.47
19 6 0.16
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (18 bp):
TTGTTAATATTTGTTTTA
Found at i:26500 original size:23 final size:22
Alignment explanation
Indices: 26474--26524 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
26464 TTGATCTTAT
26474 AAATAAAAAAAGTTAAAAATAAA
1 AAATAAAAAAA-TTAAAAATAAA
* **
26497 AAATATATTAATTAAAAATAAA
1 AAATAAAAAAATTAAAAATAAA
26519 AGAATA
1 A-AATA
26525 TGTTTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (22 bp):
AAATAAAAAAATTAAAAATAAA
Found at i:26512 original size:22 final size:23
Alignment explanation
Indices: 26486--26538 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
26476 ATAAAAAAAG
26486 TTAAAAATAAAA-AATATATTAA
1 TTAAAAATAAAAGAATATATTAA
* *
26508 TTAAAAATAAAAGAATATGTTTA
1 TTAAAAATAAAAGAATATATTAA
26531 -TAAAAATA
1 TTAAAAATA
26539 CATTAATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (23 bp):
TTAAAAATAAAAGAATATATTAA
Found at i:35633 original size:3 final size:3
Alignment explanation
Indices: 35627--35652 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35617 AAAAAATAAA
35627 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
35653 TATTTTCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:50132 original size:31 final size:32
Alignment explanation
Indices: 50094--50165 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 32
50084 GTGCACGAAC
* * *
50094 TTTGATTTAATGTGTAATTTTATATATTAAA-
1 TTTGATTTAATATGTAATTCTATATATGAAAT
50125 TTTGATTT--TATGTAATTCTATATATGAAAT
1 TTTGATTTAATATGTAATTCTATATATGAAAT
50155 TTTGATTTAAT
1 TTTGATTTAAT
50166 CGAATCATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 18 0.51
30 8 0.23
31 8 0.23
32 1 0.03
ACGTcount: A:0.33, C:0.01, G:0.10, T:0.56
Consensus pattern (32 bp):
TTTGATTTAATATGTAATTCTATATATGAAAT
Found at i:53532 original size:22 final size:20
Alignment explanation
Indices: 53483--53532 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
53473 AAGGGTCGAA
*
53483 ATTAAATTGTAATTTTTATG
1 ATTAAAATGTAATTTTTATG
53503 ATAGTAAAATGTAATTTTTAAATG
1 AT--TAAAATGTAATTTTT--ATG
53527 ATTAAA
1 ATTAAA
53533 TCAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
22 18 0.72
24 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (20 bp):
ATTAAAATGTAATTTTTATG
Found at i:53712 original size:16 final size:17
Alignment explanation
Indices: 53691--53722 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53681 TGATCTCTTA
53691 TCTCTCT-TTATTTTAC
1 TCTCTCTATTATTTTAC
53707 TCTCTCTATTATTTTA
1 TCTCTCTATTATTTTA
53723 TTTCATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (17 bp):
TCTCTCTATTATTTTAC
Found at i:55986 original size:24 final size:25
Alignment explanation
Indices: 55950--55997 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
55940 TTCAAAAGTT
* *
55950 ATTTCTTTTAAAATTTGTAATAATA
1 ATTTCTTTTAAAAATTATAATAATA
55975 ATTT-TTTTAAAAATTATAATAAT
1 ATTTCTTTTAAAAATTATAATAAT
55998 TATTGTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTCTTTTAAAAATTATAATAATA
Found at i:56082 original size:120 final size:115
Alignment explanation
Indices: 55874--56100 Score: 247
Period size: 120 Copynumber: 1.9 Consensus size: 115
55864 AGTGAAAGTA
* * * * *
55874 TATAAGAATTATTGTGATGTGATTTGAAATTAATATTAAAATCTAATTAATATATAAATTATTTA
1 TATAAGAATTATTGTGAAGTGATTTGAAAATAATATTAAAATCTAATTAATAGACAAATTATTAA
* * ** * ***
55939 ATTCAAAAGTTATTTCTTTTAAAATTTGTAATAATAATTTTTTTAAAAAT
66 ACTCAAAAGCTAACTATTTTAAAAACAGTAATAATAATTTTTTTAAAAAT
* *
55989 TATAATAATTATTGTGAAGTGATTTGAAAAAAAATATATATTAAAATTTAATTAATAGACAAATT
1 TATAAGAATTATTGTGAAGTGATTTG----AAAATA-ATATTAAAATCTAATTAATAGACAAATT
* * *
56054 GTTAAACTGAAAAGCTAACTATTTTAAAAACAGTGATAATAATTTTT
61 ATTAAACTCAAAAGCTAACTATTTTAAAAACAGTAATAATAATTTTT
56101 AAAATTTTTA
Statistics
Matches: 89, Mismatches: 18, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
115 24 0.27
119 5 0.06
120 60 0.67
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (115 bp):
TATAAGAATTATTGTGAAGTGATTTGAAAATAATATTAAAATCTAATTAATAGACAAATTATTAA
ACTCAAAAGCTAACTATTTTAAAAACAGTAATAATAATTTTTTTAAAAAT
Found at i:56274 original size:15 final size:16
Alignment explanation
Indices: 56256--56289 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
56246 TGATGCGTAA
*
56256 TTTATATTTATC-AAT
1 TTTAAATTTATCAAAT
56271 TTTAAATTTATCAAAT
1 TTTAAATTTATCAAAT
56287 TTT
1 TTT
56290 CATTTCTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTAAATTTATCAAAT
Found at i:84528 original size:4 final size:4
Alignment explanation
Indices: 84521--84586 Score: 71
Period size: 4 Copynumber: 16.2 Consensus size: 4
84511 AAATAAACGG
* * *
84521 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
84571 G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
84587 GTAATATGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
3 3 0.06
4 42 0.79
5 8 0.15
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:84550 original size:25 final size:25
Alignment explanation
Indices: 84521--84585 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
84511 AAATAAACGG
84521 GAAAGAAAGAAAGAAAAGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
* * * *
84546 GAAAGGAAGAAGGAGAGGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
*
84571 G-AAGAAGGAAAGAAA
1 GAAAGAAAGAAAGAAA
84586 GGTAATATGT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (25 bp):
GAAAGAAAGAAAGAAAAGAAAGAAA
Found at i:84671 original size:19 final size:19
Alignment explanation
Indices: 84626--84671 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
84616 GTATGATATC
*
84626 TTTTTAAAATCGTATTTTA
1 TTTTTAAAATCGTATTTAA
**
84645 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCGTATTTAA
84665 TTTTTAA
1 TTTTTAA
84672 CAGATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATCGTATTTAA
Found at i:89581 original size:16 final size:16
Alignment explanation
Indices: 89560--89609 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
89550 TGATGAGGAT
89560 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
89576 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
89591 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
89606 ATTA
1 ATTA
89610 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:90207 original size:9 final size:9
Alignment explanation
Indices: 90191--90236 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
90181 AAACACATTA
90191 CCTTCTTCT
1 CCTTCTTCT
*
90200 CATTCTTCCT
1 CCTTCTT-CT
* *
90210 TCTTCTTCC
1 CCTTCTTCT
90219 CCTTCTTCT
1 CCTTCTTCT
90228 CCTTCTTCT
1 CCTTCTTCT
90237 TTCTTTCTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.02, C:0.43, G:0.00, T:0.54
Consensus pattern (9 bp):
CCTTCTTCT
Found at i:90251 original size:17 final size:17
Alignment explanation
Indices: 90231--90263 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
90221 TTCTTCTCCT
90231 TCTTCTTTCTTTCTTTA
1 TCTTCTTTCTTTCTTTA
*
90248 TCTTTTTTCTTTCTTT
1 TCTTCTTTCTTTCTTT
90264 TTTCCTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTTCTTTCTTTCTTTA
Found at i:93725 original size:2 final size:2
Alignment explanation
Indices: 93718--93746 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
93708 TTTTTCTCAT
93718 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
93747 CTTATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94539 original size:26 final size:29
Alignment explanation
Indices: 94496--94553 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
94486 AATATATAAA
*
94496 TATTACATTTTTAAATATCAAAT-TATAG
1 TATTACATTTTTAAATATCAAATCGATAG
*
94524 TATT-CATTTTT-AATATTAAATCGATAG
1 TATTACATTTTTAAATATCAAATCGATAG
94551 TAT
1 TAT
94554 CTATTTGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 9 0.33
27 14 0.52
28 4 0.15
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (29 bp):
TATTACATTTTTAAATATCAAATCGATAG
Found at i:96503 original size:114 final size:113
Alignment explanation
Indices: 96243--96539 Score: 296
Period size: 114 Copynumber: 2.6 Consensus size: 113
96233 CTGGTGTCTC
* * * * * * *
96243 AACACCCAAACAAATATTTTTAAATTTGAAAAATGTAGTGTC-AGCCATTAGAAGTCAAACACTC
1 AACACCCAAA-AAATATTTTTAAATCTAAAAAAAGTAGTGTCGA-TCATTGGATGACAAACACTC
** ** * * * *
96307 AAAAAATTATTTTTTTATTCGTATTTTTGGGTGTCGACTATTGCTTGCCA
64 AAAAAAAAAAATTTTTATTCATATTTTTGGATGTCGACCATTACTTGCCA
* * * *
96357 AATACCTAAAAAATATTTTTAAATC-AGGAAAAAA-TAGTGTCGATCATTGGATGCCAAACACAC
1 AACACCCAAAAAATATTTTTAAATCTA--AAAAAAGTAGTGTCGATCATTGGATGACAAACACTC
* *
96420 AAAAAAAAAAATTTTTATTCATATTTTTTGGATGTTGGCCATTACTTGCCA
64 AAAAAAAAAAATTTTTATTCATA-TTTTTGGATGTCGACCATTACTTGCCA
* * *
96471 AACACCCAAAAAATATTTTTAAATCTAAAAAAAGT-GATATAGGTCATTGGATGACAAACACTCA
1 AACACCCAAAAAATATTTTTAAATCTAAAAAAAGTAG-TGTCGATCATTGGATGACAAACACTCA
96535 AAAAA
65 AAAAA
96540 TATTTTTAAA
Statistics
Matches: 149, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
113 61 0.41
114 87 0.58
115 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (113 bp):
AACACCCAAAAAATATTTTTAAATCTAAAAAAAGTAGTGTCGATCATTGGATGACAAACACTCAA
AAAAAAAAATTTTTATTCATATTTTTGGATGTCGACCATTACTTGCCA
Found at i:96602 original size:57 final size:56
Alignment explanation
Indices: 96469--96652 Score: 226
Period size: 56 Copynumber: 3.3 Consensus size: 56
96459 CATTACTTGC
* * * * *
96469 CAAACACCCAAAAAATATTTTTAAATCTAAAAAAAGTGATATAGGTCATTGGATGA
1 CAAACACCCAAAAAATATTTTTAAATCTGAAAAAAGTGGTGTAAGTCATTAGATGA
* ** * *
96525 CAAACACTCAAAAAATATTTTTAAATCTGAAAAAAGTGGTGTAAACCATTAAAAGA
1 CAAACACCCAAAAAATATTTTTAAATCTGAAAAAAGTGGTGTAAGTCATTAGATGA
* *
96581 CAAACACCCAAAAAAATATTTTAAAATCTCG-AAAAGGTGGTGTAAGTCATTAGATGA
1 CAAACACCC-AAAAAATATTTTTAAATCT-GAAAAAAGTGGTGTAAGTCATTAGATGA
*
96638 CAAACATCCAAAAAA
1 CAAACACCCAAAAAA
96653 AAAATTTTTA
Statistics
Matches: 108, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
56 60 0.56
57 47 0.44
58 1 0.01
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (56 bp):
CAAACACCCAAAAAATATTTTTAAATCTGAAAAAAGTGGTGTAAGTCATTAGATGA
Found at i:99044 original size:54 final size:54
Alignment explanation
Indices: 98962--99070 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
98952 TGTAAGGGCT
*
98962 TTGGATTTCACCTTTGCTCGCTACCTTGCAAGGCTGGGGAATGGGGGGAATGAA
1 TTGGATTTCACCTTTGCTCGCTACCTTGCAAGGCAGGGGAATGGGGGGAATGAA
99016 TTGGATTTCACCTTTGCTCGCTACCTTGCAAGGCAGGGGAATGGGGGGAATGAA
1 TTGGATTTCACCTTTGCTCGCTACCTTGCAAGGCAGGGGAATGGGGGGAATGAA
99070 T
1 T
99071 GATAGTGTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (54 bp):
TTGGATTTCACCTTTGCTCGCTACCTTGCAAGGCAGGGGAATGGGGGGAATGAA
Found at i:107079 original size:38 final size:38
Alignment explanation
Indices: 107037--107111 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
107027 CCCGTGTGTT
*
107037 CAAGATCCATTCTAAGGATGATGTTTTGATAGAGGTGC
1 CAAGATCCATTCTAAGGATGATATTTTGATAGAGGTGC
*
107075 CAAGATCTATTCTAAGGATGATATTTTGATAGAGGTG
1 CAAGATCCATTCTAAGGATGATATTTTGATAGAGGTG
107112 AATCCAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (38 bp):
CAAGATCCATTCTAAGGATGATATTTTGATAGAGGTGC
Found at i:113687 original size:2 final size:2
Alignment explanation
Indices: 113682--113708 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
113672 ATTAAAAAAT
113682 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
113709 TATTATCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:114266 original size:81 final size:82
Alignment explanation
Indices: 114131--114285 Score: 233
Period size: 81 Copynumber: 1.9 Consensus size: 82
114121 TGGCTCCTTA
* *
114131 AAAATAAAAAATTTTCAATTCAATCTTCTTATAAATAGAAAAACTATAAATTAATATATACTGAA
1 AAAATAAAAAATTTTCAATTAAATCTTCTTATAAATAGAAAAACTATAAATTAATATATAATGAA
*
114196 ATTATACTTAACTCCTC
66 ATTACACTTAACTCCTC
* * *
114213 AAAATAAAAAATTTTCAATTAAAT-TTTTTATAAATA-AAGAAATTATAATTTAATATATAATGA
1 AAAATAAAAAATTTTCAATTAAATCTTCTTATAAATAGAA-AAACTATAAATTAATATATAATGA
114276 AATTACACTT
65 AATTACACTT
114286 TAATATGTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 2 0.03
81 41 0.62
82 23 0.35
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (82 bp):
AAAATAAAAAATTTTCAATTAAATCTTCTTATAAATAGAAAAACTATAAATTAATATATAATGAA
ATTACACTTAACTCCTC
Found at i:114277 original size:23 final size:23
Alignment explanation
Indices: 114246--114291 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
114236 TTTTTTATAA
*
114246 ATAAAGAAATTATAATTTAATAT
1 ATAAAGAAATTACAATTTAATAT
* *
114269 ATAATGAAATTACACTTTAATAT
1 ATAAAGAAATTACAATTTAATAT
114292 GTTAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
ATAAAGAAATTACAATTTAATAT
Found at i:114318 original size:29 final size:31
Alignment explanation
Indices: 114275--114342 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
114265 ATATATAATG
*
114275 AAATTACACTTTAA-TATGTTAAAAATAAAA
1 AAATTATACTTTAATTATGTTAAAAATAAAA
* * *
114305 AAATTATA-TTTAATTTTTTTAAAAATAATA
1 AAATTATACTTTAATTATGTTAAAAATAAAA
114335 AAATTATA
1 AAATTATA
114343 AATTAATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (31 bp):
AAATTATACTTTAATTATGTTAAAAATAAAA
Found at i:114322 original size:81 final size:79
Alignment explanation
Indices: 114127--114355 Score: 242
Period size: 83 Copynumber: 2.8 Consensus size: 79
114117 GCCTTGGCTC
* * * *
114127 CTTAAAAATAAAAAATTTTCAATTCAATCTTCTTATAAATAGAAAAACTATAAATTAATATATAC
1 CTTAAAAATAAAAAATTTT-AATTAAAT-TTTTTATAAATA-AAAAATTATAAATTAATATATAA
* *
114192 TGAAATTATACTTAACT
63 TGAAATTACACTTAAAT
* * *
114209 CCTCAAAATAAAAAATTTTCAATTAAATTTTTTATAAATAAAGAAATTATAATTTAATATATAAT
1 CTTAAAAATAAAAAATTTT-AATTAAATTTTTTATAAATAAA-AAATTATAAATTAATATATAAT
114274 GAAATTACACTTTAATAT
64 GAAATTACAC-TTAA-AT
* * * * * *
114292 GTTAAAAATAAAAAAATTATATTTAATTTTTTTAAAAATAATAAAATTATAAATTAATACATAA
1 CTTAAAAAT-AAAAAATTTTAATTAAATTTTTTATAAATAA-AAAATTATAAATTAATATATAA
114356 CAAACTCATT
Statistics
Matches: 124, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
80 2 0.02
81 39 0.31
82 29 0.23
83 44 0.35
84 10 0.08
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (79 bp):
CTTAAAAATAAAAAATTTTAATTAAATTTTTTATAAATAAAAAATTATAAATTAATATATAATGA
AATTACACTTAAAT
Done.