Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011346.1 Kokia drynarioides strain JFW-HI SEQ_126326, 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: 114985
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 219 characters in sequence are not A, C, G, or T
Found at i:7664 original size:4 final size:4
Alignment explanation
Indices: 7655--7681 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
7645 ACCAAGGGTT
7655 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
7682 GGAAGTACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:9600 original size:13 final size:15
Alignment explanation
Indices: 9571--9605 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
9561 CAATCGTAAA
9571 TTTATTAAAATATAT
1 TTTATTAAAATATAT
*
9586 TTTATAAAAATAT-T
1 TTTATTAAAATATAT
9600 TTTATT
1 TTTATT
9606 TTTATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATTAAAATATAT
Found at i:23707 original size:3 final size:3
Alignment explanation
Indices: 23699--23749 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
23689 ACATCTCCGT
* *
23699 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC -TC TTT TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
23745 TTC TT
1 TTC TT
23750 TTATTACCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:24782 original size:2 final size:2
Alignment explanation
Indices: 24775--24799 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24765 CGTAGGGGAG
24775 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
24800 ATTATCCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25369 original size:16 final size:16
Alignment explanation
Indices: 25345--25389 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
25335 TAAAAGAAAC
25345 AAAATTAAAAATAAAAG
1 AAAA-TAAAAATAAAAG
*
25362 AAAATAAAATTAAAAG
1 AAAATAAAAATAAAAG
25378 -AAATAGAAAATA
1 AAAATA-AAAATA
25390 GGGAAGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.18
Consensus pattern (16 bp):
AAAATAAAAATAAAAG
Found at i:25370 original size:22 final size:22
Alignment explanation
Indices: 25330--25389 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
25320 CGATCTAAGC
*
25330 AAAAATAAAAG-AAACAAAATT
1 AAAAATAAAAGAAAATAAAATT
25351 AAAAATAAAAGAAAATAAAATT
1 AAAAATAAAAGAAAATAAAATT
*
25373 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
25390 GGGAAGTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAAAATT
Found at i:26007 original size:19 final size:19
Alignment explanation
Indices: 25985--26029 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
25975 TTATATTAGG
25985 ATTTAATATTTAATATAT-T
1 ATTTAATATTTAA-ATATGT
* *
26004 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
26023 ATTTAAT
1 ATTTAAT
26030 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:28613 original size:30 final size:30
Alignment explanation
Indices: 28576--28654 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 30
28566 TTATTATAAC
28576 TTATTTAAATATTTTAATATATGAAATATTAA
1 TTATTTAAATATTTTAATA-AT-AAATATTAA
*
28608 -T-TTTAAATATTTTTAAGTAATTAATATTAA
1 TTATTTAAATA-TTTTAA-TAATAAATATTAA
28638 TTATTTAAA-ATTTTAAT
1 TTATTTAAATATTTTAAT
28655 TAGATTATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
29 1 0.02
30 22 0.52
31 11 0.26
32 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (30 bp):
TTATTTAAATATTTTAATAATAAATATTAA
Found at i:33980 original size:131 final size:132
Alignment explanation
Indices: 33746--34010 Score: 514
Period size: 131 Copynumber: 2.0 Consensus size: 132
33736 TCCACACATG
*
33746 TAACAAAAAAGGGATAGTTTCTCATATTGATATTTCGCATAAGCCGATCTTTCTTGACCAAATAC
1 TAACAAAAAAGGGATAGTTTCTCATATTGATATTTCGCATAAGCAGATCTTTCTTGACCAAATAC
33811 TATTAGCTTCTTCCTTTTCAATAGCTTTCTCACATTCAATTCTACTTTTATTCGCATATAT-TTT
66 TATTAGCTTCTTCCTTTTCAATAGCTTTCTCACATTCAATTCTACTTTTATTCGCATATATATTT
33875 TT
131 TT
33877 TAACAAAAAAGGGATAGTTTCTCATATTGATATTTCGCATAAGCAGATCTTTCTTGACCAAATAC
1 TAACAAAAAAGGGATAGTTTCTCATATTGATATTTCGCATAAGCAGATCTTTCTTGACCAAATAC
33942 TATTAGCTTCTTCCTTTTCAATAGCTTTCTCACATTCAATTCTACTTTTATTCGCATATATATTT
66 TATTAGCTTCTTCCTTTTCAATAGCTTTCTCACATTCAATTCTACTTTTATTCGCATATATATTT
34007 TT
131 TT
34009 TA
1 TA
34011 CCCATTATGT
Statistics
Matches: 132, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
131 125 0.95
132 7 0.05
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (132 bp):
TAACAAAAAAGGGATAGTTTCTCATATTGATATTTCGCATAAGCAGATCTTTCTTGACCAAATAC
TATTAGCTTCTTCCTTTTCAATAGCTTTCTCACATTCAATTCTACTTTTATTCGCATATATATTT
TT
Found at i:37837 original size:58 final size:59
Alignment explanation
Indices: 37714--37825 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
37704 TTTTGTGGCC
* * *
37714 CAATTCGATGCTTGATCTTGACAATTTTTTCTAATTTGATATCTAAGCTTTTTTTCATT
1 CAATTTGATACTTGAACTTGACAATTTTTTCTAATTTGATATCTAAGCTTTTTTTCATT
* *
37773 CAATTTGATACTTGAACTTGACACTTTTTT-TAATTTGGTA-CTTAAG-TTTTTTT
1 CAATTTGATACTTGAACTTGACAATTTTTTCTAATTTGATATC-TAAGCTTTTTTT
37826 AGGTTCAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 8 0.17
58 13 0.28
59 26 0.55
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.52
Consensus pattern (59 bp):
CAATTTGATACTTGAACTTGACAATTTTTTCTAATTTGATATCTAAGCTTTTTTTCATT
Found at i:37849 original size:58 final size:59
Alignment explanation
Indices: 37730--37850 Score: 133
Period size: 58 Copynumber: 2.1 Consensus size: 59
37720 GATGCTTGAT
* *
37730 CTTGACAATTTTTTCTAATTTGATATCTAAGCTTTTTTTCATTCAATTTGATACTTGAA
1 CTTGACAATTTTTTCTAATTTGATATCTAAGCTTTTTTTCATTCAATTTGATACCTAAA
* * * *
37789 CTTGACACTTTTTT-TAATTTGGTA-CTTAAG-TTTTTTT-AGGTTCAATTTGGTGCCTAAA
1 CTTGACAATTTTTTCTAATTTGATATC-TAAGCTTTTTTTCA--TTCAATTTGATACCTAAA
37847 CTTG
1 CTTG
37851 TCAAATGATT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
56 1 0.02
57 8 0.15
58 31 0.58
59 13 0.25
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.50
Consensus pattern (59 bp):
CTTGACAATTTTTTCTAATTTGATATCTAAGCTTTTTTTCATTCAATTTGATACCTAAA
Found at i:39184 original size:25 final size:24
Alignment explanation
Indices: 39146--39196 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
39136 CGAAGTACTT
* *
39146 AACAGAAGCGCATAAATGCTTGGGA
1 AACAAAAGCACATAAATGC-TGGGA
*
39171 AACAAAAGCACATAAGTGCTGGGA
1 AACAAAAGCACATAAATGCTGGGA
39195 AA
1 AA
39197 TAGTAGGCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.45, C:0.16, G:0.25, T:0.14
Consensus pattern (24 bp):
AACAAAAGCACATAAATGCTGGGA
Found at i:42231 original size:28 final size:27
Alignment explanation
Indices: 42171--42231 Score: 63
Period size: 28 Copynumber: 2.2 Consensus size: 27
42161 TTTGGGTAAA
*
42171 ATATATTTATTTTTTAGGGATAAATTT
1 ATATATTTATTTTTTAAGGATAAATTT
*
42198 -TAATATTATATTTTTTAATG-TAATATTT
1 AT-ATATT-TATTTTTTAAGGATAA-ATTT
42226 ATATAT
1 ATATAT
42232 AAATTTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
26 1 0.04
27 8 0.29
28 18 0.64
29 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (27 bp):
ATATATTTATTTTTTAAGGATAAATTT
Found at i:44926 original size:22 final size:23
Alignment explanation
Indices: 44895--44942 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
44885 ATTTAAGATT
*
44895 TAAAGATTAAATTGATAAAAAAA
1 TAAAGATTAAAATGATAAAAAAA
*
44918 TAAA-ATTAAAATGATAAAAGAA
1 TAAAGATTAAAATGATAAAAAAA
44940 TAA
1 TAA
44943 TTGTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (23 bp):
TAAAGATTAAAATGATAAAAAAA
Found at i:45537 original size:45 final size:45
Alignment explanation
Indices: 45473--45563 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
45463 ATACAAATAA
45473 AAATAACTCCGATTCTTCCATCCTTTTTCTTTCCCCTTACCAAAC
1 AAATAACTCCGATTCTTCCATCCTTTTTCTTTCCCCTTACCAAAC
45518 AAATAACTCCGATTCTTCCATCCTTTTTCTTTCCCCTTACCAAAC
1 AAATAACTCCGATTCTTCCATCCTTTTTCTTTCCCCTTACCAAAC
45563 A
1 A
45564 CAACATATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.25, C:0.35, G:0.02, T:0.37
Consensus pattern (45 bp):
AAATAACTCCGATTCTTCCATCCTTTTTCTTTCCCCTTACCAAAC
Found at i:47001 original size:224 final size:224
Alignment explanation
Indices: 46611--47056 Score: 793
Period size: 224 Copynumber: 2.0 Consensus size: 224
46601 CAAGGAAAAG
*
46611 TAATTATATGAAAATTAAGAATGTATATTTATGAAAATATCACGTAATTAATGTAGAAATAAGTT
1 TAATTATATGAAAATTAAGAATGTATATCTATGAAAATATCACGTAATTAATGTAGAAATAAGTT
* * * *
46676 TTATGAGAACTAAATTGTACACAATTAGCGCTTAAACCATCCAAAAACAAAAACAGTTGTTGAAT
66 TCACGAGAACTAAATTGTACACAATTAACGCTTAAACCAACCAAAAACAAAAACAGTTGTTGAAT
*
46741 AATTATTAGAAGTCATTAGTACTGAGTGCATGATTTGGAAGTGTTCAATCATTTATAAATAAATT
131 AATTATTAGAAGTCATTAGTACTGAGTGCATGATTTGAAAGTGTTCAATCATTTATAAATAAATT
46806 GATCAAATAAAAGAAGGGCCGACTAGAAA
196 GATCAAATAAAAGAAGGGCCGACTAGAAA
46835 TAATTATATGAAAATTAAGAATGTATATCTATGAAAATATCACGTAATTAATGTAGAAATAAGTT
1 TAATTATATGAAAATTAAGAATGTATATCTATGAAAATATCACGTAATTAATGTAGAAATAAGTT
* * *
46900 TCACGAGAACTAAATTGTATACAATTAACGCTTAAACCAACCAAAAACAAAAATAGTTGTTGGAT
66 TCACGAGAACTAAATTGTACACAATTAACGCTTAAACCAACCAAAAACAAAAACAGTTGTTGAAT
*
46965 AATTATTAGAAGTCATTAGTAGTGAGTGCATGATTTGAAAGTGTTCAATCATTTATAAATAAATT
131 AATTATTAGAAGTCATTAGTACTGAGTGCATGATTTGAAAGTGTTCAATCATTTATAAATAAATT
*
47030 GATCAAATAAAAGAGGGGCCGACTAGA
196 GATCAAATAAAAGAAGGGCCGACTAGA
47057 CTGAAGAAAA
Statistics
Matches: 211, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
224 211 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.30
Consensus pattern (224 bp):
TAATTATATGAAAATTAAGAATGTATATCTATGAAAATATCACGTAATTAATGTAGAAATAAGTT
TCACGAGAACTAAATTGTACACAATTAACGCTTAAACCAACCAAAAACAAAAACAGTTGTTGAAT
AATTATTAGAAGTCATTAGTACTGAGTGCATGATTTGAAAGTGTTCAATCATTTATAAATAAATT
GATCAAATAAAAGAAGGGCCGACTAGAAA
Found at i:49564 original size:220 final size:221
Alignment explanation
Indices: 49179--49605 Score: 660
Period size: 220 Copynumber: 1.9 Consensus size: 221
49169 TGGTTGAGTA
* *
49179 GGTGGGAGTGTGATGCCCATCCTACATCAGATGTGAGTGTGATTGTTAAAGATCCATATAAAGGT
1 GGTGGGAGTGTGATGCCCATCCTACATCAGATGTGAGTGTGATTATTAAAGATCCATAAAAAGGT
* *
49244 CGAAGTCCATCATTACTAGCAACAGGAGCATAAGCTTTTTACATCACATTGTTTTGGTCCATAAA
66 CAAAGTCCATCATTACTAGCAACAGGAGCATAAGCTTTTTACATCACATGGTTTTGGTCCATAAA
* * *
49309 AGTCACTGGACTAGTGGTGCTTTTAGTGAGATGAACCATATTGAAACAATTCCCCTGAGCAATAG
131 AGTCACTGGACTAGGGGTGCTTTGAGTGAGATGAACCATACTGAAACAATTCCCCTGAGCAATAG
* *
49374 GCTTTTTTGCACTGGGCATCACACTG
196 CCTTTTCTGCACTGGGCATCACACTG
* *
49400 GGTGGGAGTGTGATGTCCA-CACTACTTCAGATGTGAGTGTGATTATT-AAGATCCATAAAAAGG
1 GGTGGGAGTGTGATGCCCATC-CTACATCAGATGTGAGTGTGATTATTAAAGATCCATAAAAAGG
* *
49463 TCAAAGTCCATCATTACTAGCAACTGGAGCATAAGCTTTTTACATCACGTGGTTTTGGTCCATAA
65 TCAAAGTCCATCATTACTAGCAACAGGAGCATAAGCTTTTTACATCACATGGTTTTGGTCCATAA
* * ** * *
49528 AAGTCACTGGACTAGGGGTGGTTTGAGTGCGATGAACCATACTGAAACGGTTTCCCTGAGCAGTA
130 AAGTCACTGGACTAGGGGTGCTTTGAGTGAGATGAACCATACTGAAACAATTCCCCTGAGCAATA
49593 GCCTTTTCTGCAC
195 GCCTTTTCTGCAC
49606 ACATCACCCC
Statistics
Matches: 186, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
220 144 0.77
221 42 0.23
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (221 bp):
GGTGGGAGTGTGATGCCCATCCTACATCAGATGTGAGTGTGATTATTAAAGATCCATAAAAAGGT
CAAAGTCCATCATTACTAGCAACAGGAGCATAAGCTTTTTACATCACATGGTTTTGGTCCATAAA
AGTCACTGGACTAGGGGTGCTTTGAGTGAGATGAACCATACTGAAACAATTCCCCTGAGCAATAG
CCTTTTCTGCACTGGGCATCACACTG
Found at i:53800 original size:17 final size:17
Alignment explanation
Indices: 53759--53800 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
53749 TAGATAAGTA
*
53759 CCAACACC-AAATAACC
1 CCAACACCTAAAAAACC
**
53775 CCAGGACCTAAAAAACC
1 CCAACACCTAAAAAACC
53792 CCAACACCT
1 CCAACACCT
53801 TTATTTTCTA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.45, C:0.43, G:0.05, T:0.07
Consensus pattern (17 bp):
CCAACACCTAAAAAACC
Found at i:54352 original size:44 final size:44
Alignment explanation
Indices: 54287--54412 Score: 225
Period size: 44 Copynumber: 2.9 Consensus size: 44
54277 AAATGCCTTC
* *
54287 AGAGCATAAGGCTTATTTATCCCCAAACAAGTTAACATGCGTTA
1 AGAGCATAAGTCATATTTATCCCCAAACAAGTTAACATGCGTTA
*
54331 AGAGCATAAGTCATATGTATCCCCAAACAAGTTAACATGCGTTA
1 AGAGCATAAGTCATATTTATCCCCAAACAAGTTAACATGCGTTA
54375 AGAGCATAAGTCATATTTATCCCCAAACAAGTTAACAT
1 AGAGCATAAGTCATATTTATCCCCAAACAAGTTAACAT
54413 TGTTCTCCCT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 78 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (44 bp):
AGAGCATAAGTCATATTTATCCCCAAACAAGTTAACATGCGTTA
Found at i:57203 original size:10 final size:10
Alignment explanation
Indices: 57179--57213 Score: 56
Period size: 9 Copynumber: 3.7 Consensus size: 10
57169 TTGCTAAGTC
57179 TTTTAAAAC-
1 TTTTAAAACT
57188 TTTTAAAACT
1 TTTTAAAACT
57198 TTTTAAAA-T
1 TTTTAAAACT
57207 TTTTAAA
1 TTTTAAA
57214 TTTTATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTTAAAACT
Found at i:57214 original size:8 final size:9
Alignment explanation
Indices: 57179--57217 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
57169 TTGCTAAGTC
*
57179 TTTTAAAAC
1 TTTTAAAAT
57188 TTTTAAAACT
1 TTTTAAAA-T
57198 TTTTAAAAT
1 TTTTAAAAT
57207 TTTT-AAAT
1 TTTTAAAAT
57215 TTT
1 TTT
57218 ATATTAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.25
9 13 0.46
10 8 0.29
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:73319 original size:10 final size:9
Alignment explanation
Indices: 73297--73472 Score: 87
Period size: 10 Copynumber: 19.0 Consensus size: 9
73287 TGAAAAAATA
*
73297 AAAAATAAT
1 AAAAATTAT
*
73306 AAAAGTTAT
1 AAAAATTAT
73315 AAAAATTAT
1 AAAAATTAT
*
73324 -TAAATT-T
1 AAAAATTAT
73331 AAAAA-TATT
1 AAAAATTA-T
* *
73340 TAAATTTATT
1 AAAAATTA-T
*
73350 AAAAATTAG
1 AAAAATTAT
*
73359 AAAAAATAT
1 AAAAATTAT
73368 -AAAATATAT
1 AAAAAT-TAT
* *
73377 AGAAATATAG
1 AAAAAT-TAT
73387 AATAAATTAT
1 AA-AAATTAT
*
73397 -AAAATTTT
1 AAAAATTAT
*
73405 AAAAAATCAT
1 -AAAAATTAT
73415 AAGAAAATTAT
1 -A-AAAATTAT
73426 AGAAAATGTA-
1 A-AAAAT-TAT
73436 AAGAAA-TAT
1 AA-AAATTAT
*
73445 AAAAATCAT
1 AAAAATTAT
73454 AAAAATTTAT
1 AAAAA-TTAT
73464 AAAAATTAT
1 AAAAATTAT
73473 TGTACTAAAA
Statistics
Matches: 129, Mismatches: 23, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
7 2 0.02
8 23 0.18
9 44 0.34
10 47 0.36
11 13 0.10
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:73327 original size:19 final size:17
Alignment explanation
Indices: 73297--73357 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 17
73287 TGAAAAAATA
* *
73297 AAAAATAATAAAAGTTAT
1 AAAAATTATTAAA-TTAT
73315 AAAAATTATTAAATT-T
1 AAAAATTATTAAATTAT
73331 AAAAA-TATTTAAATTTATT
1 AAAAATTA-TTAAA-TTA-T
73350 AAAAATTA
1 AAAAATTA
73358 GAAAAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 2 0.06
16 11 0.31
17 4 0.11
18 11 0.31
19 6 0.17
20 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAAATTATTAAATTAT
Found at i:73372 original size:28 final size:29
Alignment explanation
Indices: 73331--73421 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
73321 TATTAAATTT
*
73331 AAAAATATTTAAATTTATTAAAAAT-TAGA
1 AAAAATA-TAAAATTTATTAAAAATATAGA
* *
73360 AAAAATATAAAATATA-TAGAAATATAGA
1 AAAAATATAAAATTTATTAAAAATATAGA
* *
73388 ATAAATTATAAAATTT-TAAAAAATCATAAGA
1 A-AAAATATAAAATTTATTAAAAAT-AT-AGA
73419 AAA
1 AAA
73422 TTATAGAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
27 6 0.12
28 12 0.24
29 24 0.48
30 4 0.08
31 4 0.08
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAATATAAAATTTATTAAAAATATAGA
Found at i:73456 original size:19 final size:19
Alignment explanation
Indices: 73406--73469 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
73396 TAAAATTTTA
73406 AAAAATCAT-AAGAAAATTAT
1 AAAAATCATAAAG-AAA-TAT
*
73426 AGAAAAT-GTAAAGAAATAT
1 A-AAAATCATAAAGAAATAT
*
73445 AAAAATCATAAA-AATTTAT
1 AAAAATCATAAAGAA-ATAT
73464 AAAAAT
1 AAAAAT
73470 TATTGTACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 7 0.19
19 17 0.46
20 5 0.14
21 8 0.22
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (19 bp):
AAAAATCATAAAGAAATAT
Found at i:74355 original size:14 final size:15
Alignment explanation
Indices: 74328--74356 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
74318 AAGTTGTGAT
74328 AATTATACATTTAAA
1 AATTATACATTTAAA
74343 AATTATA-ATTTAAA
1 AATTATACATTTAAA
74357 GAAGTTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTATACATTTAAA
Found at i:74398 original size:17 final size:18
Alignment explanation
Indices: 74365--74399 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
74355 AAGAAGTTGT
74365 AATAATTAGACATTTAAA
1 AATAATTAGACATTTAAA
74383 AATAATTAGA-ATTTAAA
1 AATAATTAGACATTTAAA
74400 TAACAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
AATAATTAGACATTTAAA
Found at i:74407 original size:18 final size:18
Alignment explanation
Indices: 74368--74408 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
74358 AAGTTGTAAT
*
74368 AATTAGACATTTAAAAAT
1 AATTAGACATTTAAAAAC
74386 AATTAGA-ATTTAAATAAC
1 AATTAGACATTTAAA-AAC
74404 AATTA
1 AATTA
74409 TTAGTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
AATTAGACATTTAAAAAC
Found at i:76785 original size:23 final size:24
Alignment explanation
Indices: 76749--76802 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
76739 GACTCAAATA
76749 TAAAATGATCTAAA-T-AAATAATC
1 TAAAATGATCTAAACTAAAATAA-C
* *
76772 TAAAATGCTGTAAACCTAAAATAAC
1 TAAAATGATCTAAA-CTAAAATAAC
76797 TAAAAT
1 TAAAAT
76803 AAAAAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 12 0.46
25 8 0.31
26 6 0.23
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (24 bp):
TAAAATGATCTAAACTAAAATAAC
Found at i:76946 original size:23 final size:23
Alignment explanation
Indices: 76902--76947 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
76892 TGATCAGTTA
* * *
76902 AATTAGTCATATATGTTTTTTTT
1 AATTAGTCAAATAGGTTATTTTT
*
76925 AATTAGTTAAATAGGTTATTTTT
1 AATTAGTCAAATAGGTTATTTTT
76948 TTTAAGATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
AATTAGTCAAATAGGTTATTTTT
Found at i:77817 original size:15 final size:15
Alignment explanation
Indices: 77783--77815 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
77773 AAATGTTATG
77783 TTTTTGATAAAAATA
1 TTTTTGATAAAAATA
77798 TTTTTG-T-AAAATA
1 TTTTTGATAAAAATA
77811 TTTTT
1 TTTTT
77816 TTATCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 1 0.06
15 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TTTTTGATAAAAATA
Found at i:79826 original size:2 final size:2
Alignment explanation
Indices: 79819--79848 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
79809 CCAGTTGTAA
79819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79849 TGTTTTCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87787 original size:28 final size:28
Alignment explanation
Indices: 87736--87789 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
87726 CCTTCATCTT
*
87736 TTAGGATCAAATAAATTTTTTTGGAGAA
1 TTAGGATCAAATAAATTTTATTGGAGAA
87764 TTAGGATCAAAT-AATTTTAATTGGAG
1 TTAGGATCAAATAAATTTT-ATTGGAG
87790 GTGTTCGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (28 bp):
TTAGGATCAAATAAATTTTATTGGAGAA
Found at i:87987 original size:25 final size:25
Alignment explanation
Indices: 87949--88012 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
87939 TATATTTTTT
87949 AAAA-ATATAAAATATTTTTTTTCA
1 AAAAGATATAAAATATTTTTTTTCA
87973 AAAAGATATAAAATATTTTTTTTCA
1 AAAAGATATAAAATATTTTTTTTCA
87998 AAAAGATATAAAATA
1 AAAAGATATAAAATA
88013 AGATTGATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
24 4 0.10
25 35 0.90
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (25 bp):
AAAAGATATAAAATATTTTTTTTCA
Found at i:88048 original size:29 final size:29
Alignment explanation
Indices: 88015--88073 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
88005 ATAAAATAAG
88015 ATTGATAGAAAATGAAACGGAATCAGACA
1 ATTGATAGAAAATGAAACGGAATCAGACA
*
88044 ATTGATAGAAAATGAAATGGAATCAGACA
1 ATTGATAGAAAATGAAACGGAATCAGACA
88073 A
1 A
88074 GAAGGGAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.53, C:0.08, G:0.20, T:0.19
Consensus pattern (29 bp):
ATTGATAGAAAATGAAACGGAATCAGACA
Found at i:90390 original size:25 final size:25
Alignment explanation
Indices: 90328--90394 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
90318 TATTCTGTCG
* *
90328 ATCACGTTAGTTTTTAATAGTAAAA
1 ATCAAGTTAATTTTTAATAGTAAAA
* *
90353 AT-AAATAAATTTTTAATAG-AAATA
1 ATCAAGTTAATTTTTAATAGTAAA-A
*
90377 ATCAAGTTACTTTTTAAT
1 ATCAAGTTAATTTTTAAT
90395 TTAATGTATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
23 3 0.09
24 16 0.48
25 14 0.42
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (25 bp):
ATCAAGTTAATTTTTAATAGTAAAA
Found at i:92963 original size:30 final size:29
Alignment explanation
Indices: 92593--92963 Score: 273
Period size: 30 Copynumber: 12.4 Consensus size: 29
92583 ATACGAGGTC
* * * *
92593 AAAATGTGATTTTTAGGAAGGTTTAGGGGTC
1 AAAATGT-AATTTTAGAAAAGTTTA-GGGTT
* * * *
92624 AAAATGTGATTTTAGACAAGTTCGAGGGTC
1 AAAATGTAATTTTAGAAAAGTT-TAGGGTT
*
92654 AAAATGTAA-TTT-GGAAAGCTTTAAGGGTT
1 AAAATGTAATTTTAGAAAAG-TTT-AGGGTT
* * *
92683 AAAATGCATTTTTAG-AATGTTTAAGGGTT
1 AAAATGTAATTTTAGAAAAGTTT-AGGGTT
* * *
92712 AAAATGCAATTTTGGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTAGAAAAGTTTA-GGGTT
* *
92742 AAAATGTAATTTTAGAGAAGTTTGGGAGTT
1 AAAATGTAATTTTAGAAAAGTTTAGG-GTT
* *
92772 AAAATGTAACTTTGGAAAAGTTTGAGGGTT
1 AAAATGTAATTTTAGAAAAGTTT-AGGGTT
* * *
92802 AAAATGTAATTTTTGAGAAGTTTGATGGTT
1 AAAATGTAATTTTAGAAAAGTTT-AGGGTT
* * *
92832 GAAATGTAATTTTGGAAATGTTTGAGGGTT
1 AAAATGTAATTTTAGAAAAGTTT-AGGGTT
* * *
92862 AAAATGTAATTTTTGAGAAGTTTTAAGGTT
1 AAAATGTAATTTTAGAAAAG-TTTAGGGTT
* * *
92892 AAAATGTGATTTT-GAAAAGGTTTGGGGTC
1 AAAATGTAATTTTAGAAAA-GTTTAGGGTT
* * *
92921 AAAATATAATTTTAGAAAAATTTAGGGATC
1 AAAATGTAATTTTAGAAAAGTTTAGGG-TT
*
92951 AAAATGTGATTTT
1 AAAATGTAATTTT
92964 TAAAGAAAAA
Statistics
Matches: 275, Mismatches: 52, Indels: 27
0.78 0.15 0.08
Matches are distributed among these distances:
28 4 0.01
29 70 0.25
30 187 0.68
31 14 0.05
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGTT
Found at i:95950 original size:25 final size:24
Alignment explanation
Indices: 95922--96075 Score: 110
Period size: 25 Copynumber: 6.5 Consensus size: 24
95912 ACACTAACGC
95922 GCTCTCTGTTATTAGCACTGTATGT
1 GCTCTCTGTTATTAGCACT-TATGT
* *
95947 GCTCT-T-TGATTAGCACTTTGTGT
1 GCTCTCTGTTATTAGCAC-TTATGT
*
95970 GCTCTCTG--ATTAGTACTT-TGT
1 GCTCTCTGTTATTAGCACTTATGT
95991 GTACTCTCTG-T-TTAG-A-TTATGTGT
1 G--CTCTCTGTTATTAGCACTTA--TGT
* *
96015 GCTCTCTGTTGTCCAGCACTTATGT
1 GCTCTCTGTTAT-TAGCACTTATGT
* *
96040 GCTCTCTGTTGTCCAGCACTTATGT
1 GCTCTCTGTTAT-TAGCACTTATGT
96065 GCTCTCTGTTA
1 GCTCTCTGTTA
96076 GTACTTTGGT
Statistics
Matches: 110, Mismatches: 5, Indels: 28
0.77 0.03 0.20
Matches are distributed among these distances:
21 6 0.05
22 10 0.09
23 37 0.34
24 8 0.07
25 45 0.41
26 1 0.01
27 3 0.03
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (24 bp):
GCTCTCTGTTATTAGCACTTATGT
Found at i:95951 original size:23 final size:23
Alignment explanation
Indices: 95932--95982 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
95922 GCTCTCTGTT
95932 ATTAGCACTGTATGTGCTCTTTG
1 ATTAGCACTGTATGTGCTCTTTG
* * *
95955 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTGTATGTGCTCTTTG
95978 ATTAG
1 ATTAG
95983 TACTTTGTGT
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:0.18, C:0.18, G:0.22, T:0.43
Consensus pattern (23 bp):
ATTAGCACTGTATGTGCTCTTTG
Found at i:95987 original size:23 final size:22
Alignment explanation
Indices: 95944--96022 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
95934 TAGCACTGTA
*
95944 TGTGCTCTTTGATTAGCACTTTG
1 TGTGCTCTCTGATTAG-ACTTTG
95967 TGTGCTCTCTGATTAGTACTTTG
1 TGTGCTCTCTGATTAG-ACTTTG
* *
95990 TGTACTCTCTGTTTAGA-TTATG
1 TGTGCTCTCTGATTAGACTT-TG
96012 TGTGCTCTCTG
1 TGTGCTCTCTG
96023 TTGTCCAGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
21 2 0.04
22 13 0.26
23 35 0.70
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.48
Consensus pattern (22 bp):
TGTGCTCTCTGATTAGACTTTG
Found at i:97284 original size:21 final size:22
Alignment explanation
Indices: 97245--97353 Score: 62
Period size: 23 Copynumber: 4.8 Consensus size: 22
97235 TATACGGAAC
*
97245 GAACAGAGAGTAC-CAAAGTACT
1 GAACAGAGAGCACAC-AAGTACT
* *
97267 -AACAGAGAGCACATAAGTGCT
1 GAACAGAGAGCACACAAGTACT
*
97288 GGGCAACAGAGAGCACACACAGTGCT
1 --G-AACAGAGAGCACACA-AGTACT
* *
97314 AAACAGAGAGTACACAATGTAC-
1 GAACAGAGAGCACACAA-GTACT
* *
97336 AAATCAGAGAGCATACAA
1 GAA-CAGAGAGCACACAA
97354 AGTGCCAATC
Statistics
Matches: 70, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
21 17 0.24
22 4 0.06
23 29 0.41
25 14 0.20
26 6 0.09
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (22 bp):
GAACAGAGAGCACACAAGTACT
Found at i:97318 original size:23 final size:23
Alignment explanation
Indices: 97292--97384 Score: 82
Period size: 23 Copynumber: 4.0 Consensus size: 23
97282 AGTGCTGGGC
97292 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
97315 AACAGAGAGTACACA-ATGTAC-A
1 AACAGAGAGCACACACA-GTGCTA
* * *
97337 AATCAGAGAGCATACAAAGTGCCA
1 AA-CAGAGAGCACACACAGTGCTA
* * *
97361 ATCAGAGAACACACACAATGCTA
1 AACAGAGAGCACACACAGTGCTA
97384 A
1 A
97385 TAATAGAGAG
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
22 4 0.07
23 48 0.87
24 3 0.05
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:97352 original size:25 final size:25
Alignment explanation
Indices: 97317--97396 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 25
97307 CAGTGCTAAA
97317 CAGAGAG--TACACAATGTACAAAT
1 CAGAGAGCATACACAATGTACAAAT
* *
97340 CAGAGAGCATACA-AA-GTGCCAAT
1 CAGAGAGCATACACAATGTACAAAT
* *
97363 CAGAGAACACACACAATGCTA-ATAAT
1 CAGAGAGCATACACAATG-TACA-AAT
97389 -AGAGAGCA
1 CAGAGAGCA
97397 CGAGATGTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
23 24 0.55
24 4 0.09
25 12 0.27
26 4 0.09
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (25 bp):
CAGAGAGCATACACAATGTACAAAT
Found at i:104490 original size:216 final size:213
Alignment explanation
Indices: 104155--105120 Score: 1169
Period size: 216 Copynumber: 4.5 Consensus size: 213
104145 ACTGCTAAGT
* * * * *
104155 CCATCTTAGATTCCATATTCAAAGTAATAC-CTTCAATTTTACCAATTCTCTCACCATTTTCCTC
1 CCATCTTAGACTCCATATTCAAAATAGTACAC-TCAATTTTACCAATTCCCTCACCTTTTTCCTC
* * * * * *
104219 GGCACCACTATTTTCTTCCTCCTCCAGCTTAACACTGTGAGGAACTTCGCTTTTGGAACTAAACT
65 AGCACCA--GTTTTCTTCCTCTTCCAACTTAACACTGTG-GGAACTTCACTTTTGGAACTGAACT
* * * * *
104284 CTAAAGGAGCTAATTCAGTTCTAGTTTCACTTTCACTAGCAGGAGCTTCCAATGGAGGTGAAGCC
127 CTAAAGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCTTCCAATGGAGGAGAAGCC
** *
104349 TTTTCTAAATCAGGAAGTAAAG
192 TTTTCTGTATCAGGAACTAAAG
* * * **
104371 CCAT-TGTAGACTCCATATTCGAAGTAGTACACTCAAATTTACCAATTCTTTCACCTTTTTCCTC
1 CCATCT-TAGACTCCATATTCAAAATAGTACACTCAATTTTACCAATTCCCTCACCTTTTTCCTC
* * * *
104435 AGCACTAGTTTCTCCTTCCTCTTCCAACTTAACACTCTGGGAATCTTCACTTTTGGAACCGGACT
65 AGCACCAGTTT-T-CTTCCTCTTCCAACTTAACACTGTGGGAA-CTTCACTTTTGGAACTGAACT
* * *
104500 CTAAAGAAGCTAATTCAGTTGTAATTTCACTTTCAATGGCAGAAGCTTCCAGTGGAGGAGAAGCC
127 CTAAAGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCTTCCAATGGAGGAGAAGCC
*
104565 TTTTCTTTATCAGGAACTAAAG
192 TTTTCTGTATCAGGAACTAAAG
* * * * *
104587 CTATCTTAGACTCCGTATTCAAAATAGTATACTCAATTTTACGAATTCCCTCACCTTCTTCCTCA
1 CCATCTTAGACTCCATATTCAAAATAGTACACTCAATTTTACCAATTCCCTCACCTTTTTCCTCA
*
104652 GCACCAGTATTTTCTTCCTCTTCCAACTTAACACACTG-GGGAACTTCACTTTTGGAACTGGACT
66 GCACCAG--TTTTCTTCCTCTTCCAACTT-A-ACACTGTGGGAACTTCACTTTTGGAACTGAACT
* * * *
104716 CTGAAGGAGCTAATTCAGTAGTAATTTCACTTTCAATAGCAAAAGCTTCCAGTGGAGGAGAAGCC
127 CTAAAGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCTTCCAATGGAGGAGAAGCC
104781 TTTTCTGTATCAGGAACTAAAG
192 TTTTCTGTATCAGGAACTAAAG
*
104803 CCATCTTAGACTCTGCAT-TT-GAAATAGTACACTCAATTTTACCAATTCCCTCACCTTTTTCCT
1 CCATCTTAGACTC--CATATTCAAAATAGTACACTCAATTTTACCAATTCCCTCACCTTTTTCCT
104866 CAGCACCAGCATTTTCTTCCTCTTCCAACTTAACACTGTGGGTAACTTCACTTTTGGAACTGAAC
64 CAGCACCAG--TTTTCTTCCTCTTCCAACTTAACACTGTGGG-AACTTCACTTTTGGAACTGAAC
* * ** * *
104931 TCTGAAGGAGCTAATTCAGTTGTAATTGCACTTTCAATAGCAGAAAATT-CAAGTGGAAGCGAAG
126 TCTAAAGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCTTCCAA-TGGAGGAGAAG
*
104995 CCTTTTCTGTATCAAGAACTAAAG
190 CCTTTTCTGTATCAGGAACTAAAG
* * * *
105019 CCA---TAGACTCCGTATTTAAAATATTACACTCAATTTTACC-ATATCCCTCACCATTTTCCTC
1 CCATCTTAGACTCCATATTCAAAATAGTACACTCAATTTTACCAAT-TCCCTCACCTTTTTCCTC
* *
105080 AGCACCAGCGTTTTCTTCTTCGTCCAACTTAACACTGTGGG
65 AGCACCA--GTTTTCTTCCTCTTCCAACTTAACACTGTGGG
105121 GAACGCAACT
Statistics
Matches: 661, Mismatches: 69, Indels: 43
0.86 0.09 0.06
Matches are distributed among these distances:
211 2 0.00
212 4 0.01
213 81 0.12
214 9 0.01
215 13 0.02
216 531 0.80
217 11 0.02
218 10 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (213 bp):
CCATCTTAGACTCCATATTCAAAATAGTACACTCAATTTTACCAATTCCCTCACCTTTTTCCTCA
GCACCAGTTTTCTTCCTCTTCCAACTTAACACTGTGGGAACTTCACTTTTGGAACTGAACTCTAA
AGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCTTCCAATGGAGGAGAAGCCTTTT
CTGTATCAGGAACTAAAG
Found at i:108930 original size:15 final size:15
Alignment explanation
Indices: 108883--108933 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
108873 TTACCTCAAG
* *
108883 TTACATTTTAGTTAT
1 TTACGTTTTAATTAT
* * *
108898 TTATGTTTGAAATA-
1 TTACGTTTTAATTAT
108912 TTACGTTTTAATTAT
1 TTACGTTTTAATTAT
108927 TTACGTT
1 TTACGTT
108934 ATCATGTTGT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.57
Consensus pattern (15 bp):
TTACGTTTTAATTAT
Found at i:112113 original size:17 final size:17
Alignment explanation
Indices: 112091--112126 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
112081 AATTGAAGAA
112091 AAAAAGAAAGAAAAAAG
1 AAAAAGAAAGAAAAAAG
*
112108 AAAAAGAAAGAAAGAAG
1 AAAAAGAAAGAAAAAAG
112125 AA
1 AA
112127 GGAAGAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAG
Found at i:112142 original size:16 final size:15
Alignment explanation
Indices: 112121--112150 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
112111 AAGAAAGAAA
112121 GAAGAAGGAAGAAGGG
1 GAAGAAGG-AGAAGGG
112137 GAAGAAGGAGAAGG
1 GAAGAAGGAGAAGG
112151 AAAAAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GAAGAAGGAGAAGGG
Found at i:112541 original size:20 final size:21
Alignment explanation
Indices: 112499--112541 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
112489 TAATTTACTT
112499 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
112520 TAATTTTATTTTGTTA-TTAG
1 TAATTTAATTTTGTTAGTTAG
112540 TA
1 TA
112542 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Found at i:113051 original size:16 final size:16
Alignment explanation
Indices: 113006--113055 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
112996 TAAACCTAAC
113006 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
*
113022 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
113036 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
113052 TAAT
1 TAAT
113056 ATCCCATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.11
14 8 0.29
15 2 0.07
16 12 0.43
17 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:113121 original size:30 final size:29
Alignment explanation
Indices: 113087--113181 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
113077 AAATGGTACA
113087 AAATAAATATTTATTTTGTACTATTTTAGT
1 AAATAAATA-TTATTTTGTACTATTTTAGT
* * * *
113117 AAAT-AATGA-TGTGTGGATACTATTTTGGT
1 AAATAAAT-ATTATTTTG-TACTATTTTAGT
* *
113146 ATATAAATATATATTTTGTACCATTTTAGT
1 AAATAAATAT-TATTTTGTACTATTTTAGT
113176 AAATAA
1 AAATAA
113182 CACATTTTGG
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 4 0.08
29 18 0.37
30 23 0.47
31 4 0.08
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (29 bp):
AAATAAATATTATTTTGTACTATTTTAGT
Found at i:114422 original size:4 final size:4
Alignment explanation
Indices: 114413--114486 Score: 78
Period size: 4 Copynumber: 17.8 Consensus size: 4
114403 TATTTTCTTC
* * *
114413 TTCT TTCTT TTCT CTCC TTC- TTCAT TTCT TCCT TTCT TTCT TTCTT TTCT
1 TTCT TTC-T TTCT TTCT TTCT TTC-T TTCT TTCT TTCT TTCT TTC-T TTCT
114463 TTCT TTCTT TTCT TTCT TTCT TTC
1 TTCT TTC-T TTCT TTCT TTCT TTC
114487 CTGTTTATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
3 3 0.05
4 42 0.70
5 15 0.25
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:114434 original size:17 final size:16
Alignment explanation
Indices: 114400--114486 Score: 79
Period size: 17 Copynumber: 5.3 Consensus size: 16
114390 AACACATTAC
*
114400 CTTTATTTTCTT-CTT
1 CTTTCTTTTCTTCCTT
114415 CTTTCTTTTCTCTCCTT
1 CTTTCTTTTCT-TCCTT
*
114432 C-TTCATTTCTTCCTTT
1 CTTTCTTTTCTTCC-TT
* *
114448 CTTTCTTTCTTTTCTTT
1 CTTTCTTT-TCTTCCTT
*
114465 CTTTCTTTTCTTTCTTT
1 CTTTCTTTTC-TTCCTT
114482 CTTTC
1 CTTTC
114487 CTGTTTATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
15 13 0.22
16 13 0.22
17 30 0.50
18 4 0.07
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (16 bp):
CTTTCTTTTCTTCCTT
Found at i:114463 original size:13 final size:13
Alignment explanation
Indices: 114413--114485 Score: 89
Period size: 13 Copynumber: 5.8 Consensus size: 13
114403 TATTTTCTTC
114413 TTCTTTCTTTTCT
1 TTCTTTCTTTTCT
* *
114426 CTCCTTC--TTCAT
1 TTCTTTCTTTTC-T
*
114438 TTC-TTCCTTTCT
1 TTCTTTCTTTTCT
114450 TTCTTTCTTTTCT
1 TTCTTTCTTTTCT
114463 TTCTTTCTTTTCT
1 TTCTTTCTTTTCT
114476 TTCTTTCTTT
1 TTCTTTCTTT
114486 CCTGTTTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
11 6 0.12
12 7 0.13
13 39 0.75
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.71
Consensus pattern (13 bp):
TTCTTTCTTTTCT
Done.