Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012130.1 Kokia drynarioides strain JFW-HI SEQ_127129, 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: 116386
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:1376 original size:43 final size:43
Alignment explanation
Indices: 1294--1378 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
1284 ATTAACATGT
* *
1294 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
1337 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
1379 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:2010 original size:45 final size:45
Alignment explanation
Indices: 1946--2074 Score: 195
Period size: 45 Copynumber: 2.9 Consensus size: 45
1936 GCATAGCTCA
1946 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* *
1991 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGTAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** ** *
2036 TCAAGGAAAGGATATCAGGTTGAGTTTGACGAGCCACCG
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCG
2075 TGATACTCTA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.19
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:2364 original size:14 final size:13
Alignment explanation
Indices: 2347--2414 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 13
2337 CATTAAACCC
2347 TAAAACCTAAA-T
1 TAAAACCTAAACT
2359 TATAAACCCTAAACT
1 TA-AAA-CCTAAACT
*
2374 TAAAACCTTAAACCG
1 TAAAACC-TAAA-CT
2389 T-AAACACTAAACT
1 TAAAAC-CTAAACT
*
2402 TGAAACTCTAAAC
1 TAAAAC-CTAAAC
2415 CGTAAACACT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 2 0.04
13 7 0.15
14 31 0.67
15 6 0.13
ACGTcount: A:0.50, C:0.24, G:0.03, T:0.24
Consensus pattern (13 bp):
TAAAACCTAAACT
Found at i:2392 original size:28 final size:28
Alignment explanation
Indices: 2361--2425 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
2351 ACCTAAATTA
*
2361 TAAACCCTAAACTTAAAAC-CTTAAACCG
1 TAAACACTAAACTTAAAACTC-TAAACCG
*
2389 TAAACACTAAACTTGAAACTCTAAACCG
1 TAAACACTAAACTTAAAACTCTAAACCG
2417 TAAACACTA
1 TAAACACTA
2426 GATTGATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.48, C:0.26, G:0.05, T:0.22
Consensus pattern (28 bp):
TAAACACTAAACTTAAAACTCTAAACCG
Found at i:2421 original size:14 final size:14
Alignment explanation
Indices: 2382--2425 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2372 CTTAAAACCT
2382 TAAACCGTAAACAC
1 TAAACCGTAAACAC
* *
2396 TAAA-CTTGAAACTC
1 TAAACCGT-AAACAC
2410 TAAACCGTAAACAC
1 TAAACCGTAAACAC
2424 TA
1 TA
2426 GATTGATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 2 0.08
14 20 0.83
15 2 0.08
ACGTcount: A:0.48, C:0.25, G:0.07, T:0.20
Consensus pattern (14 bp):
TAAACCGTAAACAC
Found at i:5716 original size:21 final size:22
Alignment explanation
Indices: 5690--5742 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
5680 AAACACATTA
5690 CCTTTCTTTCCTCTC-CTTCTT
1 CCTTTCTTTCCTCTCTCTTCTT
* *
5711 CCTTTCTTT-CTTTCTTTTCTT
1 CCTTTCTTTCCTCTCTCTTCTT
*
5732 TCTTTCTTTCC
1 CCTTTCTTTCC
5743 CGTTTATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 22 0.81
22 1 0.04
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (22 bp):
CCTTTCTTTCCTCTCTCTTCTT
Found at i:5721 original size:4 final size:4
Alignment explanation
Indices: 5691--5741 Score: 57
Period size: 4 Copynumber: 12.2 Consensus size: 4
5681 AACACATTAC
* * *
5691 CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT CTTTT CTTT CTTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT
5741 C
1 C
5742 CCGTTTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 32 0.82
5 7 0.18
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:5729 original size:13 final size:13
Alignment explanation
Indices: 5691--5741 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
5681 AACACATTAC
*
5691 CTTTCTTTCCTCT
1 CTTTCTTTCCTTT
*
5704 CCTTC-TTCCTTT
1 CTTTCTTTCCTTT
*
5716 CTTTCTTTCTTTT
1 CTTTCTTTCCTTT
5729 CTTTCTTT-CTTT
1 CTTTCTTTCCTTT
5741 C
1 C
5742 CCGTTTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
12 14 0.44
13 18 0.56
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
CTTTCTTTCCTTT
Found at i:5868 original size:2 final size:2
Alignment explanation
Indices: 5861--5886 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5851 AATAAAATAA
5861 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
5887 GGCACAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6107 original size:9 final size:9
Alignment explanation
Indices: 6087--6117 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
6077 TTTTTATTTT
6087 AAATATATAA
1 AAATA-ATAA
6097 AAATAATAA
1 AAATAATAA
6106 AAATAATAA
1 AAATAATAA
6115 AAA
1 AAA
6118 AACACGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAATAA
Found at i:18005 original size:161 final size:161
Alignment explanation
Indices: 17740--18062 Score: 619
Period size: 161 Copynumber: 2.0 Consensus size: 161
17730 TGTGATGACA
*
17740 AACTCTCAATTTCGCGACAAGACCTAATCAATGAGTTACATCGCAGCAAGGAACCTTCGGAGTCA
1 AACTCTCAATTTCGCGACAAGACCTAATCAATGAGTTACATCGCAACAAGGAACCTTCGGAGTCA
17805 CGACTCGATATTTTGAATTCTTTACAGTTTTGTCCTAATTTGACCTTGAGTTAGTAATAAAGATT
66 CGACTCGATATTTTGAATTCTTTACAGTTTTGTCCTAATTTGACCTTGAGTTAGTAATAAAGATT
17870 TTGTAAGCTCGTATAAGACCCAAAAATGATT
131 TTGTAAGCTCGTATAAGACCCAAAAATGATT
*
17901 AACTCTCAATTTCGCGACAAGACCTAATCAATGAGTTACATCGTAACAAGGAACCTTCGGAGTCA
1 AACTCTCAATTTCGCGACAAGACCTAATCAATGAGTTACATCGCAACAAGGAACCTTCGGAGTCA
*
17966 CGACTCGATATTTTGAATTCTTTACAGTTTTGTCCTAATTTGACCTTGAGTTAGTAATAAAGCTT
66 CGACTCGATATTTTGAATTCTTTACAGTTTTGTCCTAATTTGACCTTGAGTTAGTAATAAAGATT
18031 TTGTAAGCTCGTATAAGACCCAAAAATGATT
131 TTGTAAGCTCGTATAAGACCCAAAAATGATT
18062 A
1 A
18063 CGAATTGTAT
Statistics
Matches: 159, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 159 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (161 bp):
AACTCTCAATTTCGCGACAAGACCTAATCAATGAGTTACATCGCAACAAGGAACCTTCGGAGTCA
CGACTCGATATTTTGAATTCTTTACAGTTTTGTCCTAATTTGACCTTGAGTTAGTAATAAAGATT
TTGTAAGCTCGTATAAGACCCAAAAATGATT
Found at i:33940 original size:29 final size:30
Alignment explanation
Indices: 33887--33945 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
33877 ACAAGACCAG
*
33887 TGTGCATTATTATATATGAACTTTT-ATTT
1 TGTGCATTATTATACATGAACTTTTGATTT
33916 TGTGCAATT-TTATACAT-AACGTTTTGATTT
1 TGTGC-ATTATTATACATGAAC-TTTTGATTT
33946 GATTGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 3 0.12
29 16 0.62
30 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53
Consensus pattern (30 bp):
TGTGCATTATTATACATGAACTTTTGATTT
Found at i:56636 original size:18 final size:18
Alignment explanation
Indices: 56610--56647 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
56600 ATGCATATCA
56610 TTTAATTGTCAT-TGCATT
1 TTTAATTGTC-TCTGCATT
*
56628 TTTATTTGTCTCTGCATT
1 TTTAATTGTCTCTGCATT
56646 TT
1 TT
56648 ACTCATTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.61
Consensus pattern (18 bp):
TTTAATTGTCTCTGCATT
Found at i:60840 original size:13 final size:15
Alignment explanation
Indices: 60809--60840 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
60799 ACAACTGATA
60809 ATATCAGTGAGACTG
1 ATATCAGTGAGACTG
60824 ATATCA-TGAGA-TG
1 ATATCAGTGAGACTG
60837 ATAT
1 ATAT
60841 AAATCGAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 5 0.29
15 6 0.35
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (15 bp):
ATATCAGTGAGACTG
Found at i:70241 original size:26 final size:28
Alignment explanation
Indices: 70211--70268 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 28
70201 CTCGAATATT
70211 TTATGT-TATAAAAAAT-ATTATAT-TAA
1 TTATGTGT-TAAAAAATAATTATATATAA
*
70237 TTATGTGTTAAATAATAATTATATATAA
1 TTATGTGTTAAAAAATAATTATATATAA
70265 TTAT
1 TTAT
70269 TTTTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 13 0.46
27 8 0.29
28 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (28 bp):
TTATGTGTTAAAAAATAATTATATATAA
Found at i:70323 original size:21 final size:23
Alignment explanation
Indices: 70273--70328 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
70263 AATTATTTTT
70273 ATATT-AAATAATTAATCCAATA
1 ATATTAAAATAATTAATCCAATA
* *
70295 ACAGTTAAAATTATT-ATCCAA-A
1 ATA-TTAAAATAATTAATCCAATA
70317 ATATTAAAATAA
1 ATATTAAAATAA
70329 ACTTACCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 8 0.29
22 5 0.18
23 8 0.29
24 7 0.25
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (23 bp):
ATATTAAAATAATTAATCCAATA
Found at i:77095 original size:32 final size:33
Alignment explanation
Indices: 77056--77118 Score: 110
Period size: 32 Copynumber: 1.9 Consensus size: 33
77046 TGTAAAATAC
77056 ATAATGCAAGACATAA-TTAAAAATGCAAACAA
1 ATAATGCAAGACATAATTTAAAAATGCAAACAA
*
77088 ATAATGCAAGACATAATTTAAAGATGCAAAC
1 ATAATGCAAGACATAATTTAAAAATGCAAAC
77119 TTAATAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.56, C:0.13, G:0.11, T:0.21
Consensus pattern (33 bp):
ATAATGCAAGACATAATTTAAAAATGCAAACAA
Found at i:88268 original size:120 final size:119
Alignment explanation
Indices: 88078--88505 Score: 452
Period size: 125 Copynumber: 3.5 Consensus size: 119
88068 AAATGGTGTA
* * * ** *
88078 GGCCATTGCATGGCCGACACCCCT-TTTAATCTGATAAAAAAATCAAAATTTTGGGTGTTGGCCA
1 GGCCA-TGCATGGCCGACACTCCTATTT-ATTTGATAAAAAAATCAAATTTTTTTGTGTT-GCTA
* *
88142 TGCAATGGTCGACACCCCCTTTTTGTTAAATAAAAAA-TTCAATTTTTTTTTGTATT
63 TGCAATGGTCGACACCCCCTTTTTGTCAAATAAAAAATTTAAATTTTTTTTTGTATT
* *
88198 GGTCATGTCATGGCCGACACTCCTATTTATTTGATAAAAAAATCCAATTTTTTTGTGTTGACTAT
1 GGCCATG-CATGGCCGACACTCCTATTTATTTGATAAAAAAATCAAATTTTTTTGTGTTG-CTAT
* *
88263 GCAAT-GTACGACACCCCCTTTTT-TCAAATAAAAAATTTTAAAATTTTTTTGGTATT
64 GCAATGGT-CGACACCCCCTTTTTGTCAAATAAAAAA-TTTAAATTTTTTTTTGTATT
* * *
88319 GGCCATGAAATGGCCGACACTCACTATTTATTTGATAAAAAAATCAAATTTTTTAGTGTTGGTCA
1 GGCCATG-CATGGCCGACACTC-CTATTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGCT-A
* ** * * * *
88384 TGTAATGACCGACACTCCCTTTTTGTCAGATAAAAAAAATTTAAAATTTTTTTTTATGTT
63 TGCAATGGTCGACACCCCCTTTTTGTCA-A-ATAAAAAATTT-AAATTTTTTTTTGTATT
* * *
88444 GACCATGCAATGGTCGACAC-CCTTTATTTATTTGATAAAAAAATCAATTTTTTTTGTGTTGC
1 GGCCATGC-ATGGCCGACACTCC--TATTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGC
88506 CCATGTAATG
Statistics
Matches: 259, Mismatches: 33, Indels: 27
0.81 0.10 0.08
Matches are distributed among these distances:
119 16 0.06
120 68 0.26
121 39 0.15
122 56 0.22
123 4 0.02
124 5 0.02
125 71 0.27
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (119 bp):
GGCCATGCATGGCCGACACTCCTATTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGCTATGC
AATGGTCGACACCCCCTTTTTGTCAAATAAAAAATTTAAATTTTTTTTTGTATT
Found at i:88485 original size:125 final size:122
Alignment explanation
Indices: 88078--88524 Score: 441
Period size: 120 Copynumber: 3.7 Consensus size: 122
88068 AAATGGTGTA
* * * **
88078 GGCCATTGC-ATGGCCGACACCCCTT-TTAATCTGATAAAAAAATCAAAATTTTGGGTGTTGGCC
1 GGCCA-TGCAATGGCCGACA-CCCTTATTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGGCC
** * * * *
88141 ATGCAATGGTCGACACCCCCTTTTTGTTAA-ATAAAAAA-TT-CAATTTTTTTTTGTATT
64 ATGCAATGACCGACACCCCCTTTTTGTCAATAAAAAAAATTTAAAATTTTTTTTTAT-TT
* * * *
88198 GGTCATGTC-ATGGCCGACACTCC-TATTTATTTGATAAAAAAATCCAATTTTTTTGTGTTGACT
1 GGCCATG-CAATGGCCGACAC-CCTTATTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGGCC
* *
88261 ATGCAATGTA-CGACACCCCCTTTTT-TCAA-ATAAAAAATTTTAAAATTTTTTTGGTA-TT
64 ATGCAATG-ACCGACACCCCCTTTTTGTCAATA-AAAAAAATTTAAAATTTTTTT-TTATTT
* * *
88319 GGCCATGAAATGGCCGACACTCAC-TATTTATTTGATAAAAAAATCAAATTTTTTAGTGTTGGTC
1 GGCCATGCAATGGCCGACAC-C-CTTATTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGGCC
* *
88383 ATGTAATGACCGACACTCCCTTTTTGTCAGATAAAAAAAATTTAAAATTTTTTTTTATGTT
64 ATGCAATGACCGACACCCCCTTTTTGTCA-ATAAAAAAAATTTAAAATTTTTTTTTAT-TT
* * * *
88444 GACCATGCAATGGTCGACACCCTTTATTTATTTGATAAAAAAATCAATTTTTTTTGTGTTGCCCA
1 GGCCATGCAATGGCCGACACCC-TTATTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGGCCA
* *
88509 TGTAATGACTGACACC
65 TGCAATGACCGACACC
88525 AACTTTTCCT
Statistics
Matches: 273, Mismatches: 36, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
119 8 0.03
120 75 0.27
121 24 0.09
122 66 0.24
123 7 0.03
124 22 0.08
125 71 0.26
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (122 bp):
GGCCATGCAATGGCCGACACCCTTATTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGGCCAT
GCAATGACCGACACCCCCTTTTTGTCAATAAAAAAAATTTAAAATTTTTTTTTATTT
Found at i:88523 original size:60 final size:61
Alignment explanation
Indices: 88091--88524 Score: 246
Period size: 60 Copynumber: 7.1 Consensus size: 61
88081 CATTGCATGG
* * ** ** * *
88091 CCGACACCCCTT-TTAATCTGATAAAAAAAT-CAAAATTTTGGGTGTTGGCCATGCAATGG
1 CCGACACCCCTTATTTATTTGATAAAAAAATACAATTTTTTTTGTGTTGGCCATGTAATGA
* * ** * * * * *
88150 TCGACACCCCCTT-TTTGTTAAAT-AAAAAATTCAATTTTTTTTTGTATTGGTCATGTCATGG
1 CCGACA-CCCCTTATTTATTTGATAAAAAAATACAA-TTTTTTTTGTGTTGGCCATGTAATGA
* * * * *
88211 CCGACACTCC-TATTTATTTGATAAAAAAATCCAA-TTTTTTTGTGTTGACTATGCAATGTA
1 CCGACACCCCTTATTTATTTGATAAAAAAATACAATTTTTTTTGTGTTGGCCATGTAATG-A
*** * * * * * *
88271 -CGACACCCCCTT-TTT-TCAAATAAAAAATTTTAAAATTTTTTTGGTATTGGCCATGAAATGG
1 CCGACA-CCCCTTATTTATTTGATAAAAAA--ATACAATTTTTTTTGTGTTGGCCATGTAATGA
* * * *
88332 CCGACACTCAC-TATTTATTTGATAAAAAAAT-CAAATTTTTTAGTGTTGGTCATGTAATGA
1 CCGACAC-CCCTTATTTATTTGATAAAAAAATACAATTTTTTTTGTGTTGGCCATGTAATGA
* ** * * * *
88392 CCGACACTCCCTT-TTTGTCAGATAAAAAAAATTTAAAATTTTTTTTTATGTTGACCATGCAATG
1 CCGACAC-CCCTTATTTATTTGAT-AAAAAAA--TACAA-TTTTTTTTGTGTTGGCCATGTAATG
*
88456 G
61 A
* * *
88457 TCGACACCCTTTATTTATTTGATAAAAAAAT-CAATTTTTTTTGTGTTGCCCATGTAATGA
1 CCGACACCCCTTATTTATTTGATAAAAAAATACAATTTTTTTTGTGTTGGCCATGTAATGA
*
88517 CTGACACC
1 CCGACACC
88525 AACTTTTCCT
Statistics
Matches: 277, Mismatches: 76, Indels: 43
0.70 0.19 0.11
Matches are distributed among these distances:
59 45 0.16
60 97 0.35
61 50 0.18
62 30 0.11
63 10 0.04
64 13 0.05
65 32 0.12
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (61 bp):
CCGACACCCCTTATTTATTTGATAAAAAAATACAATTTTTTTTGTGTTGGCCATGTAATGA
Found at i:89343 original size:17 final size:17
Alignment explanation
Indices: 89323--89377 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
89313 AAAAAATAAT
89323 AATTAGAATATACAAGA
1 AATTAGAATATACAAGA
*
89340 AATTAGAA-AT--TA-A
1 AATTAGAATATACAAGA
* *
89353 AATTAAAATATACAGGA
1 AATTAGAATATACAAGA
89370 AATTAGAA
1 AATTAGAA
89378 ATTAAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
13 8 0.28
14 3 0.10
16 2 0.07
17 16 0.55
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.25
Consensus pattern (17 bp):
AATTAGAATATACAAGA
Found at i:89357 original size:30 final size:30
Alignment explanation
Indices: 89323--89420 Score: 126
Period size: 30 Copynumber: 3.3 Consensus size: 30
89313 AAAAAATAAT
*
89323 AATTAGAATATACAAGAAATTAGAAATTAA
1 AATTAAAATATACAAGAAATTAGAAATTAA
*
89353 AATTAAAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAAGAAATTAGAAATTAA
* * *
89383 ATTTAAAATA-AAAACGAAATTACAAATTAA
1 AATTAAAATATACAA-GAAATTAGAAATTAA
*
89413 ATTTAAAA
1 AATTAAAA
89421 AGTAAACAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (30 bp):
AATTAAAATATACAAGAAATTAGAAATTAA
Found at i:91999 original size:84 final size:85
Alignment explanation
Indices: 91748--92218 Score: 653
Period size: 84 Copynumber: 5.5 Consensus size: 85
91738 TAAATTTAAA
* * * *
91748 ATTTAATAAAAATTGTAATATAATAGTAA-TTTTTAATTTGAATATTAAAATTTGGTAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
** *
91812 TATTGTCACGTCAATACATT
66 TATTGTCAAATCAACACATT
* *
91832 ATTTGATAAAAATTTTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
* *
91897 TATTGTTAATTCAACACATT
66 TATTGTCAAATCAACACATT
* * *
91917 ATTTGATAAAAATTATAATATAATAATAATTTTTTT-TTAAAATATTAAAATTTGGTAAACAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
91981 TATTGTCAAATCAACACATT
66 TATTGTCAAATCAACACATT
* **
92001 GTTTGATAAAAATTGTAATATAATAATAATAAATTTTTTTATTTAAATATTAAAATTTAATAAAT
1 ATTTGATAAAAATTGT-A-AT-ATAATAAT-AATTTTTTTATTTAAATATTAAAATTTGGTAAAT
* *
92066 AATATATTATCAAATCAACACATT
62 AATGTATTGTCAAATCAACACATT
* * *
92090 ATTTAAT-AAAATTGTAATATAATAATAATTCTTTTATTT-AATATTAAAATTTGGTAAAAAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
92153 TATTGTCAAATCAACACATT
66 TATTGTCAAATCAACACATT
* *
92173 ATTTGATATAAATTGAAATATAATAATAATCTTTTTTATTTAAATA
1 ATTTGATAAAAATTGTAATATAATAATAAT-TTTTTTATTTAAATA
92219 ATGTTAAATT
Statistics
Matches: 342, Mismatches: 36, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
83 45 0.13
84 115 0.34
85 101 0.30
86 8 0.02
87 9 0.03
88 17 0.05
89 47 0.14
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.44
Consensus pattern (85 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
TATTGTCAAATCAACACATT
Found at i:92155 original size:172 final size:170
Alignment explanation
Indices: 91748--92218 Score: 691
Period size: 169 Copynumber: 2.8 Consensus size: 170
91738 TAAATTTAAA
* * * *
91748 ATTTAATAAAAATTGTAATATAATAGTAATTTTTAATTTGAATATTAAAATTTGGTAAATAATGT
1 ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGGTAAAAAATGT
** * *
91813 ATTGTCACGTCAATACATTATTTGATAAAAATT-TTAATATAATAATAATTTTTTTATTTAAATA
66 ATTGTCAAATCAACACATTATTTGATAAAAATTGTAAATATAATAATAATTTTTTTATTTAAATA
* * * * *
91877 TTAAAATTTGATAAATAATGTATTGTTAATTCAACACATT
131 TTAAAATTTAATAAATAATATATTATCAAATCAACACATT
* * *
91917 ATTTGATAAAAATTATAATATAATAATAATTTTTT-TTTAAAATATTAAAATTTGGTAAACAATG
1 ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTT-AAATATTAAAATTTGGTAAAAAATG
*
91981 TATTGTCAAATCAACACATTGTTTGATAAAAATTGTAATATAATAATAATAAATTTTTTTATTTA
65 TATTGTCAAATCAACACATTATTTGATAAAAATTGTAA-AT-ATAATAAT-AATTTTTTTATTTA
92046 AATATTAAAATTTAATAAATAATATATTATCAAATCAACACATT
127 AATATTAAAATTTAATAAATAATATATTATCAAATCAACACATT
92090 ATTTAAT-AAAATTGTAATATAATAATAATTCTTTTATTT-AATATTAAAATTTGGTAAAAAATG
1 ATTTAATAAAAATTGTAATATAATAATAATT-TTTTATTTAAATATTAAAATTTGGTAAAAAATG
*
92153 TATTGTCAAATCAACACATTATTTGATATAAATTG-AAATATAATAATAATCTTTTTTATTTAAA
65 TATTGTCAAATCAACACATTATTTGATAAAAATTGTAAATATAATAATAAT-TTTTTTATTTAAA
92217 TA
129 TA
92219 ATGTTAAATT
Statistics
Matches: 273, Mismatches: 21, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
168 6 0.02
169 107 0.39
170 4 0.01
171 4 0.01
172 86 0.32
173 63 0.23
174 3 0.01
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.44
Consensus pattern (170 bp):
ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGGTAAAAAATGT
ATTGTCAAATCAACACATTATTTGATAAAAATTGTAAATATAATAATAATTTTTTTATTTAAATA
TTAAAATTTAATAAATAATATATTATCAAATCAACACATT
Found at i:96341 original size:61 final size:62
Alignment explanation
Indices: 96220--96435 Score: 230
Period size: 60 Copynumber: 3.5 Consensus size: 62
96210 GTTATGACCG
* * *
96220 ACACCAAAATAATTTGAAATTTTTTTATCTGACAAAAA--GAAGGTATCAGCCATTGCATGGCCA
1 ACACCAAAAAAATTTGAAA-TTTTTTATCTGACAAAAAGGGAA--TGTCGGCCATTGCATGGCCA
*
96283 ACACCAAAAAAATTTGAAATTTTTTATCTGA-AAAAAGGGAATGTCGGCCGTTGCATGGCCA
1 ACACCAAAAAAATTTGAAATTTTTTATCTGACAAAAAGGGAATGTCGGCCATTGCATGGCCA
* ** * * * * ** *
96344 ACA-CTAAAAAATTTGATTTTTTTTATCAGATAAATAGGG-GTGTCGATCATGGCATGGCCA
1 ACACCAAAAAAATTTGAAATTTTTTATCTGACAAAAAGGGAATGTCGGCCATTGCATGGCCA
96404 ACACCAAAAAAA-TTG-AATTTTTTATCTGACAA
1 ACACCAAAAAAATTTGAAATTTTTTATCTGACAA
96436 TAATTTGATT
Statistics
Matches: 130, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
59 13 0.10
60 45 0.35
61 39 0.30
62 12 0.09
63 21 0.16
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (62 bp):
ACACCAAAAAAATTTGAAATTTTTTATCTGACAAAAAGGGAATGTCGGCCATTGCATGGCCA
Found at i:98386 original size:6 final size:6
Alignment explanation
Indices: 98375--98446 Score: 67
Period size: 6 Copynumber: 12.2 Consensus size: 6
98365 TATAATTTAT
** * **
98375 TTTAAA TTTAAA TTTAAA TTTATCT TTTAAT TTTAAA TTT-GC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA
*
98423 TTTAAA TTT-AA TTAAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
98447 GGATTTAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.13
6 42 0.79
7 4 0.08
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:98392 original size:12 final size:12
Alignment explanation
Indices: 98375--98446 Score: 67
Period size: 11 Copynumber: 6.1 Consensus size: 12
98365 TATAATTTAT
98375 TTTAAATTTAAA
1 TTTAAATTTAAA
**
98387 TTTAAATTTATCT
1 TTTAAATTTA-AA
*
98400 TTTAATTTTAAA
1 TTTAAATTTAAA
**
98412 TTT-GCTTTAAA
1 TTTAAATTTAAA
98423 TTTAAATTT-AA
1 TTTAAATTTAAA
*
98434 TTAAAATTTAAA
1 TTTAAATTTAAA
98446 T
1 T
98447 GGATTTAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
11 19 0.40
12 19 0.40
13 9 0.19
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:98406 original size:18 final size:18
Alignment explanation
Indices: 98381--98446 Score: 73
Period size: 17 Copynumber: 3.7 Consensus size: 18
98371 TTATTTTAAA
*
98381 TTTAAATTTAAATTTATC
1 TTTAAATTTAAATTTAGC
*
98399 TTTTAATTTTAAATTT-GC
1 -TTTAAATTTAAATTTAGC
*
98417 TTTAAATTTAAATTTA-A
1 TTTAAATTTAAATTTAGC
*
98434 TTAAAATTTAAAT
1 TTTAAATTTAAAT
98447 GGATTTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 26 0.63
18 1 0.02
19 14 0.34
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTAAATTTAAATTTAGC
Found at i:98409 original size:47 final size:47
Alignment explanation
Indices: 98353--98443 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
98343 TTGATTCAAA
* * *
98353 TTTATTTTTAAATATAATTT-ATTTTAAATTTAAATTTAAATTTATCT
1 TTTAATTTTAAATATAATTTAAATTTAAATTT-AATTAAAATTTATCT
* **
98400 TTTAATTTTAAATTTGCTTTAAATTTAAATTTAATTAAAATTTA
1 TTTAATTTTAAATATAATTTAAATTTAAATTTAATTAAAATTTA
98444 AATGGATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
47 27 0.73
48 10 0.27
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (47 bp):
TTTAATTTTAAATATAATTTAAATTTAAATTTAATTAAAATTTATCT
Found at i:99177 original size:3 final size:3
Alignment explanation
Indices: 99171--99196 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
99161 AATGCTTTAA
99171 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
99197 AATATAATAC
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:100390 original size:59 final size:58
Alignment explanation
Indices: 100263--100711 Score: 363
Period size: 59 Copynumber: 7.5 Consensus size: 58
100253 CCTTGGAGGT
* * * *
100263 CCCT-AAACTGTCAAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATGCTATTTTTGA
1 CCCTCAAACT-TCCAAAAATTCTATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGA
*
100322 CCC-CAAAACTTCCAAAAA-TCTTATTTTTGACCCCGAACCTTCCAAAAATTCCATTTTT-A
1 CCCTC-AAACTTCCAAAAATTC-TATTTTT-ACCCCGAA-CTTCCAAAAATCCCATTTTTGA
* *
100381 CCCTCAAACTTTCAAAAATTCTATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCTATTTTT-ACCCC-GAACTTCCAAAAATCCCATTTTTGA
* * * * *
100441 CCC-CAAAACTTCTAAAAATTTTGTTTTTACCCCCGAACTTCTAAAAATCTCATTTTT-A
1 CCCTC-AAACTTCCAAAAATTCTATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGA
* ** * * * * *
100499 ACCTCGAAACTTTTAAAAAATTCCATTTTCACCCCAAACTTCTAAAAATCCCATTTTTAAA
1 CCCTC-AAAC-TTCCAAAAATTCTATTTTTACCCCGAACTTCCAAAAATCCCATTTTT-GA
* *
100560 CCCT-AAACTTCCAAAAATTCTATTTTTACCCCCGAACTAAAAATGCCAAAAATGCTATTTTTGA
1 CCCTCAAACTTCCAAAAATTCTATTTTTA-CCCCGAACT-----T-CCAAAAATCCCATTTTTGA
* * * ** * *
100624 CCCTAAAACTTCCAAAAATCCCATTTTTAACCCTAAAACTTCTAAAAATCCCATTTTTTA
1 CCCTCAAACTTCCAAAAATTCTATTTTT-ACCC-CGAACTTCCAAAAATCCCATTTTTGA
* * *
100684 TCCTGAAACTTCCAAAAATTCCATTTTT
1 CCCTCAAACTTCCAAAAATTCTATTTTT
100712 TGCCCCTGAA
Statistics
Matches: 319, Mismatches: 46, Indels: 49
0.77 0.11 0.12
Matches are distributed among these distances:
58 21 0.07
59 134 0.42
60 110 0.34
61 5 0.02
64 6 0.02
65 38 0.12
66 5 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
CCCTCAAACTTCCAAAAATTCTATTTTTACCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:100427 original size:89 final size:89
Alignment explanation
Indices: 100267--100742 Score: 362
Period size: 89 Copynumber: 5.3 Consensus size: 89
100257 GGAGGTCCCT
* * * * * *
100267 AAACTGTCAAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATGCTATTTTTGACCCCAAAACT
1 AAACT-TCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCTATTTTTAACCCCAAAACT
* *
100332 TCCAAAAATCTTATTTTTGACCCCG
65 TCCAAAAATCTCATTTTTGACCCCA
*
100357 AACCTTCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCTATTTTTAACCCCAAAACTT
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCTATTTTTAACCCCAAAACTT
*
100422 CCAAAAATCCCATTTTTGACCCCA
66 CCAAAAATCTCATTTTTGACCCCA
* *** * * * *
100446 AAACTTCTAAAAATTTTGTTTTTACCCCCGAAC-TTCTAAAAA-TCTCATTTTTAACCTCGAAAC
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTTC-AAAAATTCT-ATTTTTAACCCCAAAAC
** *
100509 TTTTAAAAAAT-TCCA-TTTTCACCCC-
64 -TTCCAAAAATCT-CATTTTTGACCCCA
* * * *
100534 AAACTTCTAAAAATCCCATTTTTAAACCCT-AAACTTCCAAAAATTCTATTTTTACCCCCGAACT
1 AAACTTCCAAAAATTCCATTTTT--ACCCTCAAACTTTCAAAAATTCTATTTTTA-ACCC---C-
* * *
100598 AAAAATGCCAAAAATGCT-ATTTTTGACCCTA
59 AAAACTTCCAAAAAT-CTCATTTTTGACCCCA
* * * * * * **
100629 AAACTTCCAAAAATCCCATTTTTAACCCTAAAAC-TTCTAAAAATCCCATTTTTTATCCTGAAAC
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCAAACTTTC-AAAAATTCTATTTTTAACCCCAAAAC
*
100693 TTCCAAAAAT-TCCATTTTTTG-CCCCT
64 TTCCAAAAATCT-CA-TTTTTGACCCCA
* *
100719 GAA-TGTCTAAAAATTCCATTTTTA
1 AAACT-TCCAAAAATTCCATTTTTA
100743 AACCCTGGAT
Statistics
Matches: 308, Mismatches: 55, Indels: 47
0.75 0.13 0.11
Matches are distributed among these distances:
88 26 0.08
89 147 0.48
90 59 0.19
91 6 0.02
93 9 0.03
94 21 0.07
95 40 0.13
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (89 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCTATTTTTAACCCCAAAACTT
CCAAAAATCTCATTTTTGACCCCA
Found at i:100712 original size:30 final size:30
Alignment explanation
Indices: 100267--100741 Score: 296
Period size: 30 Copynumber: 15.8 Consensus size: 30
100257 GGAGGTCCCT
*
100267 AAACTGTCAAAAAATTCCA-TTTTTACCCCCG
1 AAACT-TCCAAAAATTCCATTTTTTA-CCCCG
* * * *
100298 -AACTTCCAAAAATGCTATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTTACCCCG
* *
100327 AAACTTCCAAAAA-TCTTATTTTTGACCCCG
1 AAACTTCCAAAAATTC-CATTTTTTACCCCG
*
100357 AACCTTCCAAAAATTCCA-TTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTTACCC-CG
* * * *
100386 AAACTTTCAAAAATTCTATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTTACCCCG
* * *
100416 AAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTTACCCCG
* *
100446 AAACTTCTAAAAATT--TTGTTTTTACCCCCG
1 AAACTTCCAAAAATTCCAT-TTTTTA-CCCCG
* * *
100476 -AACTTCTAAAAA-TCTCATTTTTAACCTCG
1 AAACTTCCAAAAATTC-CATTTTTTACCCCG
** *
100505 AAACTTTTAAAAAATTCCA-TTTTCACCCC-
1 AAAC-TTCCAAAAATTCCATTTTTTACCCCG
* * * * *
100534 AAACTTCTAAAAATCCCATTTTTAAACCCT
1 AAACTTCCAAAAATTCCATTTTTTACCCCG
*
100564 AAACTTCCAAAAATTCTA-TTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTTA-CCCCG
* * * **
100594 -AACTAAAAATGCCAAAAATGCTATTTTTGACCCTA
1 AAACT-----T-CCAAAAATTCCATTTTTTACCCCG
* * **
100629 AAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTTACCCCG
* * * *
100659 AAACTTCTAAAAATCCCATTTTTTATCCTG
1 AAACTTCCAAAAATTCCATTTTTTACCCCG
*
100689 AAACTTCCAAAAATTCCATTTTTTGCCCCTG
1 AAACTTCCAAAAATTCCATTTTTTACCCC-G
*
100720 -AA-TGTCTAAAAATTCCATTTTT
1 AAACT-TCCAAAAATTCCATTTTT
100742 AAACCCTGGA
Statistics
Matches: 358, Mismatches: 58, Indels: 57
0.76 0.12 0.12
Matches are distributed among these distances:
28 13 0.04
29 82 0.23
30 223 0.62
31 14 0.04
32 2 0.01
34 1 0.00
35 14 0.04
36 9 0.03
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTTACCCCG
Found at i:112038 original size:27 final size:27
Alignment explanation
Indices: 112002--112061 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
111992 AATTTTCAAC
*
112002 TAATGATTGTTTCCTTTGATCCTCTTTT
1 TAAT-ATTGTTTCCTTTGATCCTCTTCT
*
112030 TAATATTGTTTCTTTTGATCCTCTTCT
1 TAATATTGTTTCCTTTGATCCTCTTCT
112057 TAATA
1 TAATA
112062 GAATTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.18, C:0.17, G:0.08, T:0.57
Consensus pattern (27 bp):
TAATATTGTTTCCTTTGATCCTCTTCT
Found at i:112907 original size:206 final size:206
Alignment explanation
Indices: 112550--113401 Score: 1208
Period size: 206 Copynumber: 4.1 Consensus size: 206
112540 AAACGACGCA
*
112550 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCAAAGCGAGCAAAAT
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGCAAAAT
* *
112615 CTTCGAACCTCAGCTTCTTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCC
66 CTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCC
* *
112680 TGATGAGATACTAATAAGTGAATCAAATTCGTCTTCCTGAT-AAGATACAGAGAAGCGGATTGAA
131 TGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAA-ATACAGAGAAGCGGATTGAA
112744 ACAAGCGATGCG
195 ACAAGCGATGCG
*
112756 GTTATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGCAAAAT
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGCAAAAT
* * * *
112821 CTTTGAACCCCAGCTTCTTGATGAGACACCGAGAAGCAAGTCAAAGCAATAAACGGTTAGCTTCC
66 CTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCC
* * *
112886 TGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAA
131 TGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGATTGAAA
*
112951 CAAGTGATGCG
196 CAAGCGATGCG
112962 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGCAAAAT
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGCAAAAT
* * *
113027 CTTCAAACCCCAGCTTCCTGATGAGACACCGAGAAACAGGTCGAAGCAATAAACGGTTAGCTTCT
66 CTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCC
* *
113092 TGATGAGATACTAAGAAGTGAATCAAATTCGTCTTCTTGATGAAATACAGAGAAGCGGATTGAAA
131 TGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGATTGAAA
* *
113157 CAAACGACGCG
196 CAAGCGATGCG
* * * *
113168 GTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC-GA-TGAAC-AAAT
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGCAAAAT
* * * * * **
113230 CTTCTAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAACGAATAGCTTC
66 CTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAAT-AAACGGTTAGCTTC
* *** * * * * * * * **
113295 CTGATGAAATACGGGGAAGTAAACCAAAATCATCTTCCTAATGAAACAAAGAGAAGTGGATCAAA
130 CTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGATTGAA
* **
113360 ACAAGTGATATG
195 ACAAGCGATGCG
* *
113372 GTCTTCTTCCGGATGAGATACTGAGAAGAA
1 GTCATCTTCCTGATGAGATACTGAGAAGAA
113402 AGTCAAGTCA
Statistics
Matches: 582, Mismatches: 62, Indels: 6
0.90 0.10 0.01
Matches are distributed among these distances:
203 48 0.08
204 98 0.17
205 1 0.00
206 434 0.75
207 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (206 bp):
GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGCAAAAT
CTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCC
TGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGATTGAAA
CAAGCGATGCG
Found at i:113813 original size:17 final size:17
Alignment explanation
Indices: 113776--113816 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
113766 TATTTTTTTT
** *
113776 AAATTTAAATTTGCTTT
1 AAATTTAAATTTAATTA
113793 AAATTTAAATTTAATTA
1 AAATTTAAATTTAATTA
113810 AAATTTA
1 AAATTTA
113817 CTTAATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATTTAAATTTAATTA
Found at i:114495 original size:3 final size:3
Alignment explanation
Indices: 114489--114559 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
114479 ATAAATGCTT
* * * * *
114489 TAA TAA TAA TAA TAA TAT TAT TAA AAA TAA -ATA TAA TAC TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* *
114534 CAT TAA TTAA TAA TAA TAA TAA TAA T
1 TAA TAA -TAA TAA TAA TAA TAA TAA T
114560 GAGTAAAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 1 0.02
3 48 0.91
4 4 0.08
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:114496 original size:31 final size:31
Alignment explanation
Indices: 114437--114498 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
114427 GTATTAATGA
* * **
114437 CATTAATAATAGTAAATGGTTTTTTAATAAT
1 CATTAATAATAATAAATGCTTTAATAATAAT
114468 CATTAATAATAATAAATGCTTTAATAATAAT
1 CATTAATAATAATAAATGCTTTAATAATAAT
114499 AATAATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (31 bp):
CATTAATAATAATAAATGCTTTAATAATAAT
Found at i:114517 original size:21 final size:21
Alignment explanation
Indices: 114472--114526 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
114462 AATAATCATT
*
114472 AATAATAATAA-ATGCTTTAAT
1 AATAATAATAATAT-CTTTAAA
114493 AATAATAATAATAT-TATTAAA
1 AATAATAATAATATCT-TTAAA
114514 AATAA-ATATAATA
1 AATAATA-ATAATA
114527 CTAATGACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AATAATAATAATATCTTTAAA
Found at i:115659 original size:29 final size:30
Alignment explanation
Indices: 115609--115859 Score: 192
Period size: 30 Copynumber: 8.5 Consensus size: 30
115599 GAAGGTCCCT
* *
115609 AAACTATCCAAAAATTCCATTTTT-ACCCCC
1 AAACT-TCCAAAAATACCATTTTTAACCCCA
* * **
115639 GAACTTCCAAAAAAAATATTTTTAACCCCA
1 AAACTTCCAAAAATACCATTTTTAACCCCA
115669 AAACTTCCAAAAATACCATTTTTAACCCCA
1 AAACTTCCAAAAATACCATTTTTAACCCCA
* *
115699 AAACTTCTAAAAATTCCATTTTT-ACCCTC-
1 AAACTTCCAAAAATACCATTTTTAACCC-CA
* * * * *
115728 GAACTTCTAAAAATCCCATTTTTAACCTCG
1 AAACTTCCAAAAATACCATTTTTAACCCCA
* * *
115758 AAACTTCTAAAAAAATCCATTTTT-A-CCCT
1 AAACTTCCAAAAATA-CCATTTTTAACCCCA
* * * * *
115787 GAAGTTCTAAAAAT-CTCATTTTTAACCTCG
1 AAACTTCCAAAAATAC-CATTTTTAACCCCA
* ** *
115817 AAACTTTCAAAAATTTCATTTTT-ACCCCC
1 AAACTTCCAAAAATACCATTTTTAACCCCA
115846 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
115860 GCCAAAAATG
Statistics
Matches: 179, Mismatches: 33, Indels: 19
0.77 0.14 0.08
Matches are distributed among these distances:
27 1 0.01
28 7 0.04
29 71 0.40
30 92 0.51
31 8 0.04
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.32
Consensus pattern (30 bp):
AAACTTCCAAAAATACCATTTTTAACCCCA
Found at i:115711 original size:59 final size:57
Alignment explanation
Indices: 115609--115859 Score: 231
Period size: 59 Copynumber: 4.2 Consensus size: 57
115599 GAAGGTCCCT
* *
115609 AAACTATCCAAAAATTCCATTTTTACCCCCG-AACTTCCAAAAAAAAT-ATTTTTAACCCC
1 AAACT-TCCAAAAA-TCCATTTTTAACCCCGAAACTT-CTAAAAAAATCATTTTT-ACCCC
* *
115668 AAAACTTCCAAAAATACCATTTTTAACCCCAAAACTTCT-AAAAATTCCATTTTTACCCTC
1 -AAACTTCCAAAAAT-CCATTTTTAACCCCGAAACTTCTAAAAAAAT-CATTTTTACCC-C
* * * *
115728 GAACTTCTAAAAATCCCATTTTTAACCTCGAAACTTCTAAAAAAATCCATTTTTACCCT
1 AAACTTCCAAAAAT-CCATTTTTAACCCCGAAACTTCTAAAAAAAT-CATTTTTACCCC
* * * * **
115787 GAAGTTCTAAAAATCTCATTTTTAACCTCGAAACTT-TCAAAAATTTCATTTTTACCCCC
1 AAACTTCCAAAAATC-CATTTTTAACCCCGAAACTTCT-AAAAAAATCATTTTTA-CCCC
115846 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
115860 GCCAAAAATG
Statistics
Matches: 164, Mismatches: 18, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
58 17 0.10
59 112 0.68
60 35 0.21
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.32
Consensus pattern (57 bp):
AAACTTCCAAAAATCCATTTTTAACCCCGAAACTTCTAAAAAAATCATTTTTACCCC
Found at i:115947 original size:29 final size:31
Alignment explanation
Indices: 115872--116083 Score: 146
Period size: 29 Copynumber: 7.2 Consensus size: 31
115862 CAAAAATGTT
* * * *
115872 ATTTTTGA-CCTAAAAATTTCCAAAAATCCC
1 ATTTTTGACCCTCAAAACTTCTAAAAATTCC
* *
115902 ATTTTTGACCC-CAAAACTTTTGAAAATTCC
1 ATTTTTGACCCTCAAAACTTCTAAAAATTCC
* *
115932 ATTTTT-ACCCTC-AAACTTATAAAAATCCC
1 ATTTTTGACCCTCAAAACTTCTAAAAATTCC
* * *
115961 ATTTTTGA-TCTCGAAACTTCAAAAAATTCC
1 ATTTTTGACCCTCAAAACTTCTAAAAATTCC
* *
115991 ATTTTT-TCCCTC-GAA-TGTCTAAAAATTCC
1 ATTTTTGACCCTCAAAACT-TCTAAAAATTCC
**
116020 ATTTTTG-CCC-CCGAA-TGTCTAAAAATTCC
1 ATTTTTGACCCTCAAAACT-TCTAAAAATTCC
**
116049 ATTTTTG-CCC-CCGAA-TGTCTAAAAATTCC
1 ATTTTTGACCCTCAAAACT-TCTAAAAATTCC
116078 ATTTTT
1 ATTTTT
116084 AAACCCCGAA
Statistics
Matches: 157, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.01
29 101 0.64
30 52 0.33
31 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (31 bp):
ATTTTTGACCCTCAAAACTTCTAAAAATTCC
Found at i:115968 original size:59 final size:59
Alignment explanation
Indices: 115893--116083 Score: 181
Period size: 59 Copynumber: 3.3 Consensus size: 59
115883 AAAAATTTCC
***
115893 AAAAATCCCATTTTTGACCCCAAAACTTTTGAAAATTCCATTTTTACCCTCAAACT-TAT
1 AAAAATCCCATTTTTGACCCCAAAACTTCAAAAAATTCCATTTTTACCCTCAAA-TGTAT
* * * * * *
115952 AAAAATCCCATTTTTGATCTCGAAACTTCAAAAAATTCCATTTTTTCCCTCGAATGTCT
1 AAAAATCCCATTTTTGACCCCAAAACTTCAAAAAATTCCATTTTTACCCTCAAATGTAT
* ** * * * * *
116011 AAAAATTCCATTTTTG-CCCCCGAA-TGTCTAAAAATTCCATTTTTGCCCCCGAATGTCT
1 AAAAATCCCATTTTTGACCCCAAAACT-TCAAAAAATTCCATTTTTACCCTCAAATGTAT
*
116069 AAAAATTCCATTTTT
1 AAAAATCCCATTTTT
116084 AAACCCCGAA
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
57 1 0.01
58 49 0.43
59 63 0.56
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (59 bp):
AAAAATCCCATTTTTGACCCCAAAACTTCAAAAAATTCCATTTTTACCCTCAAATGTAT
Done.