Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1246672 original size:17 final size:17
Alignment explanation
Indices: 1246652--1246685 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1246642 TGCCATTATC
1246652 GAGCCGCAACCATTGTT
1 GAGCCGCAACCATTGTT
*
1246669 GAGCTGCAACCATTGTT
1 GAGCCGCAACCATTGTT
1246686 ATATTCGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (17 bp):
GAGCCGCAACCATTGTT
Found at i:1246925 original size:25 final size:24
Alignment explanation
Indices: 1246897--1246968 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 24
1246887 TTATTGTTTA
*
1246897 AAATATTTAAAAATTAATTTTATAT
1 AAATATTT-AAAATTAAATTTATAT
*
1246922 AAATATTT-ATATTAAATTTATAT
1 AAATATTTAAAATTAAATTTATAT
*
1246945 AATATATTT-ATATT-AATTTATAT
1 AA-ATATTTAAAATTAAATTTATAT
1246968 A
1 A
1246969 GTAATCTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 25 0.57
24 11 0.25
25 8 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATATTTAAAATTAAATTTATAT
Found at i:1246929 original size:13 final size:11
Alignment explanation
Indices: 1246911--1246968 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
1246901 ATTTAAAAAT
1246911 TAAT-TTTATA
1 TAATATTTATA
1246921 TAAATATTTATA
1 T-AATATTTATA
1246933 TTAA-ATTTATA
1 -TAATATTTATA
1246944 TAATATATT-TA
1 TAATAT-TTATA
*
1246955 TATTAATTTATA
1 TAAT-ATTTATA
1246967 TA
1 TA
1246969 GTAATCTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
10 4 0.10
11 19 0.47
12 16 0.40
13 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TAATATTTATA
Found at i:1246941 original size:23 final size:24
Alignment explanation
Indices: 1246909--1246968 Score: 97
Period size: 23 Copynumber: 2.6 Consensus size: 24
1246899 ATATTTAAAA
*
1246909 ATTAATTTTATATAA-ATATTTAT
1 ATTAAATTTATATAATATATTTAT
1246932 ATTAAATTTATATAATATATTTAT
1 ATTAAATTTATATAATATATTTAT
1246956 ATT-AATTTATATA
1 ATTAAATTTATATA
1246969 GTAATCTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 24 0.69
24 11 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTAAATTTATATAATATATTTAT
Found at i:1248229 original size:6 final size:6
Alignment explanation
Indices: 1248220--1248244 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1248210 CCTCCTGCGA
1248220 CGCCTC CGCCTC CGCCTC CGCCTC C
1 CGCCTC CGCCTC CGCCTC CGCCTC C
1248245 AAAAAACCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.16, T:0.16
Consensus pattern (6 bp):
CGCCTC
Found at i:1251642 original size:31 final size:31
Alignment explanation
Indices: 1251581--1251646 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1251571 GATATTCCTT
**
1251581 ATTGAAATGCATCTATTTCCACTATTAAATG
1 ATTGAAATGCATCTATTTCCACTAGGAAATG
**
1251612 ATTGAAATGCATCTATTTGTA-TAAGGAAATG
1 ATTGAAATGCATCTATTTCCACT-AGGAAATG
1251643 ATTG
1 ATTG
1251647 GCTGGCACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (31 bp):
ATTGAAATGCATCTATTTCCACTAGGAAATG
Found at i:1253147 original size:39 final size:40
Alignment explanation
Indices: 1253088--1253218 Score: 117
Period size: 39 Copynumber: 3.4 Consensus size: 40
1253078 TCTTATGATA
** * *
1253088 TCTCAGGGGCAAAGCCAAAATTA-GAAGTTTCTTGCAATG
1 TCTCAGGGGCAAAGAGAAAATTATGAAGATTCCTGCAATG
* * *
1253127 TGTCAGGGGCAAAGAGAAAA-TATGAAGATTCCTGTAATT
1 TCTCAGGGGCAAAGAGAAAATTATGAAGATTCCTGCAATG
* * *
1253166 TCTCAGGGCCAAAGAGAAAATCTA--AAGATTCCTGTAATT
1 TCTCAGGGGCAAAGAGAAAAT-TATGAAGATTCCTGCAATG
* *
1253205 TATCAGGGCCAAAG
1 TCTCAGGGGCAAAG
1253219 GGAATATCAG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
38 2 0.03
39 75 0.95
41 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (40 bp):
TCTCAGGGGCAAAGAGAAAATTATGAAGATTCCTGCAATG
Found at i:1253235 original size:39 final size:39
Alignment explanation
Indices: 1253129--1253218 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 39
1253119 TTGCAATGTG
* * * *
1253129 TCAGGGGCAAAGAGAAAATATGAAGATTCCTGTAATTTC
1 TCAGGGCCAAAGAGAAAATCTAAAGATTCCTGTAATTTA
1253168 TCAGGGCCAAAGAGAAAATCTAAAGATTCCTGTAATTTA
1 TCAGGGCCAAAGAGAAAATCTAAAGATTCCTGTAATTTA
1253207 TCAGGGCCAAAG
1 TCAGGGCCAAAG
1253219 GGAATATCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (39 bp):
TCAGGGCCAAAGAGAAAATCTAAAGATTCCTGTAATTTA
Found at i:1253249 original size:78 final size:78
Alignment explanation
Indices: 1253054--1253249 Score: 198
Period size: 78 Copynumber: 2.5 Consensus size: 78
1253044 TGAGACTTCT
* * * * *
1253054 GGGCCAAAAGGAAAATCAGAAGATTCTTATGATATCTCAGGGGCAAAGCCAAAATTAGAAGTTTC
1 GGGCCAAAGGGAAAATCAGAAGATTCTTGTGATATCTCAGGGCCAAAGACAAAATTAGAAGATTC
* *
1253119 TTGCAATGTGTCA
66 CTGCAATGTATCA
* * * * * *
1253132 GGGGCAAAGAGAAAAT-ATGAAGATTCCTGTAATTTCTCAGGGCCAAAGAGAAAATCTA-AAGAT
1 GGGCCAAAGGGAAAATCA-GAAGATTCTTGTGATATCTCAGGGCCAAAGACAAAAT-TAGAAGAT
* *
1253195 TCCTGTAATTTATCA
64 TCCTGCAATGTATCA
* * *
1253210 GGGCCAAAGGGAATATCAGAGGATTCTTGTGATAACTCAG
1 GGGCCAAAGGGAAAATCAGAAGATTCTTGTGATATCTCAG
1253250 TTCTGATAAC
Statistics
Matches: 92, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
77 1 0.01
78 88 0.96
79 3 0.03
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (78 bp):
GGGCCAAAGGGAAAATCAGAAGATTCTTGTGATATCTCAGGGCCAAAGACAAAATTAGAAGATTC
CTGCAATGTATCA
Found at i:1257121 original size:18 final size:18
Alignment explanation
Indices: 1257098--1257135 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1257088 CGAGCTCGGC
*
1257098 ATGGCATTGGC-ATTGGCA
1 ATGGCAATGGCGA-TGGCA
1257116 ATGGCAATGGCGATGGCA
1 ATGGCAATGGCGATGGCA
1257134 AT
1 AT
1257136 CCTGTACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (18 bp):
ATGGCAATGGCGATGGCA
Found at i:1257476 original size:2 final size:2
Alignment explanation
Indices: 1257469--1257507 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1257459 CTAGTTGAGA
1257469 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
1257508 AAGCATGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1259221 original size:26 final size:26
Alignment explanation
Indices: 1259172--1259221 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1259162 TTTTGCTTTA
*
1259172 TTTAAAGTAAAATATTATTTTTTTGT
1 TTTAAAGTAAAATATTATTATTTTGT
*
1259198 TTTAAA-TAAAATTTTAATTATTTT
1 TTTAAAGTAAAATATT-ATTATTTT
1259222 AAAATTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTAAAGTAAAATATTATTATTTTGT
Found at i:1261133 original size:99 final size:99
Alignment explanation
Indices: 1261030--1261233 Score: 345
Period size: 99 Copynumber: 2.1 Consensus size: 99
1261020 TGTGTTTTGT
* * * * *
1261030 TGTCATAATCATATTTAACGTTTTTTATATTTGTATAGGCTTTGTTATGTTAATAATTGATATTA
1 TGTCATAAGCATATTTAACGTATTTTATATTTATATAGGCTTTGATACGTTAATAATTGATATTA
1261095 TATAAATTTTGAGATACGTATTCGTGTCATGTCA
66 TATAAATTTTGAGATACGTATTCGTGTCATGTCA
1261129 TGTCATAAGCATATTTAACGTATTTTATATTTATATAGGCTTTGATACGTTAATAATTGATATTA
1 TGTCATAAGCATATTTAACGTATTTTATATTTATATAGGCTTTGATACGTTAATAATTGATATTA
* *
1261194 TATAGATTTTGAGATATGTATTCGTGTCATGTCA
66 TATAAATTTTGAGATACGTATTCGTGTCATGTCA
1261228 TGTCAT
1 TGTCAT
1261234 GTATTAAGTG
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (99 bp):
TGTCATAAGCATATTTAACGTATTTTATATTTATATAGGCTTTGATACGTTAATAATTGATATTA
TATAAATTTTGAGATACGTATTCGTGTCATGTCA
Found at i:1265147 original size:23 final size:23
Alignment explanation
Indices: 1265121--1265183 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1265111 AAAATAATAT
1265121 ATTAA-ATTTAAAATATTTTTTAA
1 ATTAATATTTAAAATATTTTTT-A
* *
1265144 ATTAATAATT-AAATAATTTTTA
1 ATTAATATTTAAAATATTTTTTA
*
1265166 ATCAATATTTATAAATAT
1 ATTAATATTTA-AAATAT
1265184 CATTAAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 9 0.28
23 15 0.47
24 8 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTAATATTTAAAATATTTTTTA
Found at i:1265916 original size:4 final size:4
Alignment explanation
Indices: 1265907--1265933 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1265897 CGAATAAATT
1265907 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1265934 TTCTCAGCCC
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:1266617 original size:12 final size:13
Alignment explanation
Indices: 1266600--1266628 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1266590 GATATTGCAT
1266600 TTTTTTTTTC-AA
1 TTTTTTTTTCTAA
1266612 TTTTTTTTTCTAA
1 TTTTTTTTTCTAA
1266625 TTTT
1 TTTT
1266629 ACTTCTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCTAA
Found at i:1268585 original size:24 final size:22
Alignment explanation
Indices: 1268558--1268640 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 22
1268548 TAATTTAATT
1268558 TAAAATTTAAAATTTATTTATTAA
1 TAAAATTTAAAATTT-TTTA-TAA
*
1268582 TAAAAATTTTAAAATTTTTTTATAT
1 T-AAAA-TTTAAAA-TTTTTTATAA
* *
1268607 TAATATTTATATATTTTTTATAA
1 TAAAATTTA-AAATTTTTTATAA
*
1268630 TTAAATTTAAA
1 TAAAATTTAAA
1268641 TAAAATATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
22 1 0.02
23 20 0.42
24 6 0.12
25 7 0.15
26 11 0.23
27 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAAAATTTAAAATTTTTTATAA
Found at i:1268663 original size:84 final size:84
Alignment explanation
Indices: 1268501--1268665 Score: 185
Period size: 84 Copynumber: 2.0 Consensus size: 84
1268491 TTCATGGGTT
* * * *
1268501 AAATTTGAAAATTTTTTTATTTAAATTTAATAAATTTATATTGAGTTTAATTTAATTTAAAATTT
1 AAATTTGAAAATTTTTTTATTTAAATTTAATAAATTTATATTGAATTAAATTTAATATAAAATAT
*
1268566 AAAATTTATTTATTAATAA
66 AAAATTTAATTATTAATAA
* * *
1268585 AAATTTTAAAATTTTTTTATATTAATATTT-ATATATTT-T-TTATAATTAAATTTAA-ATAAAA
1 AAATTTGAAAATTTTTTTAT-TTAA-ATTTAATAAATTTATATT-GAATTAAATTTAATATAAAA
*
1268646 TATAAATTTTAAATTATTAA
63 TATAAAATTT-AATTATTAA
1268666 ATAGTGATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
83 15 0.22
84 38 0.56
85 11 0.16
86 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (84 bp):
AAATTTGAAAATTTTTTTATTTAAATTTAATAAATTTATATTGAATTAAATTTAATATAAAATAT
AAAATTTAATTATTAATAA
Found at i:1271567 original size:15 final size:15
Alignment explanation
Indices: 1271547--1271580 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1271537 CGTATTTATA
*
1271547 AAATTTTATTATTTT
1 AAATTTTATTACTTT
1271562 AAATTTTATTACTTT
1 AAATTTTATTACTTT
1271577 AAAT
1 AAAT
1271581 ATTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
AAATTTTATTACTTT
Found at i:1274560 original size:18 final size:17
Alignment explanation
Indices: 1274526--1274579 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 17
1274516 AGTGAAAATT
1274526 TTAAATTATTAATTTAAA
1 TTAAATTATTAA-TTAAA
*
1274544 TTAATTTGATTAATTAAA
1 TTAAATT-ATTAATTAAA
1274562 TTAAATTATTTAATTAAA
1 TTAAATTA-TTAATTAAA
1274580 AATAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 26 0.81
19 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TTAAATTATTAATTAAA
Found at i:1274587 original size:15 final size:16
Alignment explanation
Indices: 1274564--1274601 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1274554 TAATTAAATT
* *
1274564 AAATTATTTAATTA-A
1 AAATAATTTAAATATA
1274579 AAATAATTTAAATATA
1 AAATAATTTAAATATA
1274595 AAATAAT
1 AAATAAT
1274602 ATATTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATAATTTAAATATA
Found at i:1274611 original size:19 final size:18
Alignment explanation
Indices: 1274568--1274638 Score: 71
Period size: 17 Copynumber: 4.1 Consensus size: 18
1274558 TAAATTAAAT
1274568 TATTTAAT-TAAA-AATA
1 TATTTAATATAAATAATA
1274584 -ATTTAAATATAAAATAATA
1 TATTT-AATAT-AAATAATA
* *
1274603 TATTTAATAAAAAT-ATG
1 TATTTAATATAAATAATA
1274620 TATTTAA-ATAAATAATA
1 TATTTAATATAAATAATA
1274637 TA
1 TA
1274639 ATTTTTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
15 4 0.09
16 8 0.18
17 14 0.31
18 7 0.16
19 8 0.18
20 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (18 bp):
TATTTAATATAAATAATA
Found at i:1274648 original size:19 final size:18
Alignment explanation
Indices: 1274570--1274648 Score: 58
Period size: 19 Copynumber: 4.4 Consensus size: 18
1274560 AATTAAATTA
*
1274570 TTTAATTAAAA-ATA-AT
1 TTTAATAAAAATATATAT
*
1274586 TTAAATATAAAATA-ATAT
1 TTTAATA-AAAATATATAT
*
1274604 ATTTAATAAAAATATGTAT
1 -TTTAATAAAAATATATAT
*
1274623 TTAAATAAATAATATA-ATT
1 TTTAATAAA-AATATATA-T
1274642 TTTAATA
1 TTTAATA
1274649 TATATCATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
16 5 0.10
17 5 0.10
18 18 0.37
19 21 0.43
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (18 bp):
TTTAATAAAAATATATAT
Found at i:1274724 original size:6 final size:6
Alignment explanation
Indices: 1274683--1274713 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1274673 TCTCGTTAAG
1274683 TAAATT TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT T
1274714 TTTTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:1275890 original size:2 final size:2
Alignment explanation
Indices: 1275883--1275910 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1275873 TCTCACTCAC
1275883 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1275911 GCTGCCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1278371 original size:42 final size:43
Alignment explanation
Indices: 1278279--1278371 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 43
1278269 GCATGAAATT
**
1278279 AATTTTGAATTTATTCTTTCCCTTTGCTTCTTATTTTTGAGAA
1 AATTTTGAATTTATTCTTTCCCTTTGCTTCTTATTTTCAAGAA
* * *
1278322 AAATTTGAA-TTATTCTTT-CCTTTCTCTTCTTATTTTCAAGGA
1 AATTTTGAATTTATTCTTTCCCTTT-GCTTCTTATTTTCAAGAA
1278364 AATTTTGA
1 AATTTTGA
1278372 TGGTTATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
41 5 0.12
42 30 0.70
43 8 0.19
ACGTcount: A:0.24, C:0.14, G:0.09, T:0.54
Consensus pattern (43 bp):
AATTTTGAATTTATTCTTTCCCTTTGCTTCTTATTTTCAAGAA
Found at i:1279028 original size:20 final size:22
Alignment explanation
Indices: 1279003--1279042 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1278993 TTATTTTACT
1279003 TTTTA-TTAA-TATAAAAATTA
1 TTTTATTTAATTATAAAAATTA
1279023 TTTTATTTAATTATAAAAAT
1 TTTTATTTAATTATAAAAAT
1279043 ATAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTATTTAATTATAAAAATTA
Found at i:1281307 original size:9 final size:9
Alignment explanation
Indices: 1281295--1281320 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1281285 TTTTTAATTA
1281295 TATTAAAAG
1 TATTAAAAG
1281304 TATTAAAAG
1 TATTAAAAG
1281313 TATTAAAA
1 TATTAAAA
1281321 TTTTAGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (9 bp):
TATTAAAAG
Found at i:1282461 original size:19 final size:20
Alignment explanation
Indices: 1282430--1282470 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1282420 AAAATATTCA
1282430 TAAATAAAATTAAA-ATTTT
1 TAAATAAAATTAAACATTTT
1282449 TAAA-AAAATTTAAACATTTT
1 TAAATAAAA-TTAAACATTTT
1282469 TA
1 TA
1282471 TTTAAATCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 9 0.45
20 7 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATAAAATTAAACATTTT
Found at i:1284320 original size:20 final size:20
Alignment explanation
Indices: 1284295--1284333 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1284285 CGAAATATTT
1284295 TTGAATC-GATAAAAAATCGA
1 TTGAATCTG-TAAAAAATCGA
1284315 TTGAATCTGTAAAAAATCG
1 TTGAATCTGTAAAAAATCG
1284334 TTAGAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (20 bp):
TTGAATCTGTAAAAAATCGA
Found at i:1285204 original size:57 final size:56
Alignment explanation
Indices: 1285119--1285284 Score: 284
Period size: 57 Copynumber: 3.0 Consensus size: 56
1285109 TTATAAAAAT
1285119 AAAAAAT-AATTTTTT-TTGATATTTAACAATAATTCAAAATTTGAAATTAAATTA
1 AAAAAATAAATTTTTTATTGATATTTAACAATAATTCAAAATTTGAAATTAAATTA
1285173 AAAAAATAAATTTTTTTATTGATATTTAACAATAATTCAAAATTTGAAATTAAATTA
1 AAAAAATAAA-TTTTTTATTGATATTTAACAATAATTCAAAATTTGAAATTAAATTA
*
1285230 AAAAAATAAAATTTTTTATTGATATTTAGCAATAATTCAAAATTTG-AATTAAATT
1 AAAAAAT-AAATTTTTTATTGATATTTAACAATAATTCAAAATTTGAAATTAAATT
1285285 GAACTCAATT
Statistics
Matches: 107, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
54 7 0.07
55 2 0.02
56 15 0.14
57 80 0.75
58 3 0.03
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (56 bp):
AAAAAATAAATTTTTTATTGATATTTAACAATAATTCAAAATTTGAAATTAAATTA
Found at i:1286084 original size:2 final size:2
Alignment explanation
Indices: 1286077--1286126 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1286067 TTAAAAGTCT
* *
1286077 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1286119 TG TA TA TA
1 TA TA TA TA
1286127 GTAGCCCGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1286195 original size:11 final size:11
Alignment explanation
Indices: 1286179--1286206 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1286169 GGGTAATTTT
1286179 TTTATCATTAA
1 TTTATCATTAA
1286190 TTTATCATTAA
1 TTTATCATTAA
1286201 TTTATC
1 TTTATC
1286207 CTTATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTATCATTAA
Found at i:1286445 original size:28 final size:27
Alignment explanation
Indices: 1286395--1286461 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
1286385 TACATTTGCA
*
1286395 TAAATAAAATATAAATTGAATAATCAAAT
1 TAAAT-AAATATAAATTGAATAA-AAAAT
1286424 TAAATAAATATAAATT-ATATAAAAAAT
1 TAAATAAATATAAATTGA-ATAAAAAAT
*
1286451 TATA-AAATATA
1 TAAATAAATATA
1286462 TAAAATTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 7 0.20
27 8 0.23
28 15 0.43
29 5 0.14
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (27 bp):
TAAATAAATATAAATTGAATAAAAAAT
Found at i:1286679 original size:33 final size:33
Alignment explanation
Indices: 1286638--1286705 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1286628 TAACTTTATA
1286638 AATATTTTTACAATACCCAAATGTCTAAACTCT
1 AATATTTTTACAATACCCAAATGTCTAAACTCT
1286671 AATATTTTTACAATACCCAAATGTCTAAACTCT
1 AATATTTTTACAATACCCAAATGTCTAAACTCT
1286704 AA
1 AA
1286706 GTTGAAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (33 bp):
AATATTTTTACAATACCCAAATGTCTAAACTCT
Found at i:1289987 original size:15 final size:15
Alignment explanation
Indices: 1289963--1290036 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
1289953 ACCATGATTT
1289963 TTTA-ATAATTTATA
1 TTTATATAATTTATA
*
1289977 TTTGTATAATTTATA
1 TTTATATAATTTATA
* *
1289992 TATATATATATATCATA
1 TTTATATA-AT-TTATA
1290009 TTT-TAT-ATTT-TA
1 TTTATATAATTTATA
*
1290021 TTTATATAAATTATA
1 TTTATATAATTTATA
1290036 T
1 T
1290037 AAATTGATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
12 5 0.11
13 4 0.09
14 8 0.17
15 19 0.40
16 5 0.11
17 6 0.13
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (15 bp):
TTTATATAATTTATA
Found at i:1290204 original size:20 final size:19
Alignment explanation
Indices: 1290175--1290229 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
1290165 TTTTACATGA
1290175 TAAA-TATAATTATATTAT
1 TAAAGTATAATTATATTAT
*
1290193 TAAATTTATAATTA-ATTTAT
1 TAAA-GTATAATTATA-TTAT
1290213 TAAAGTATTAATTATAT
1 TAAAGTA-TAATTATAT
1290230 AAAAAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.13
19 3 0.10
20 23 0.74
21 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAAAGTATAATTATATTAT
Found at i:1290469 original size:18 final size:18
Alignment explanation
Indices: 1290446--1290499 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
1290436 TTAATTAATT
1290446 TATTTTTAATATAAATAA
1 TATTTTTAATATAAATAA
* *
1290464 TATTTTTAATATATAT-T
1 TATTTTTAATATAAATAA
1290481 TCATTATTTAATATAAATA
1 T-ATT-TTTAATATAAATA
1290500 TAAATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 18 0.60
19 11 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTTTAATATAAATAA
Found at i:1290494 original size:37 final size:33
Alignment explanation
Indices: 1290433--1290499 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 33
1290423 GTTTTTTAGT
1290433 TTTTTAATTAATTTATTTTTAATATAAATAATA
1 TTTTTAATTAATTTATTTTTAATATAAATAATA
1290466 TTTTTAATATATATTTCATTATTTAATATAAATA
1 TTTTTAAT-TA-ATTT-ATT-TTTAATATAAATA
1290500 TAAATATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 8 0.27
34 2 0.07
35 4 0.13
36 3 0.10
37 13 0.43
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTTTAATTAATTTATTTTTAATATAAATAATA
Found at i:1290507 original size:19 final size:19
Alignment explanation
Indices: 1290450--1290507 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
1290440 TTAATTTATT
* *
1290450 TTTAATATAAATA-ATATT
1 TTTAATATAAATATAAATA
* * * *
1290468 TTTAATATATATTTCATTA
1 TTTAATATAAATATAAATA
1290487 TTTAATATAAATATAAATA
1 TTTAATATAAATATAAATA
1290506 TT
1 TT
1290508 ATTTATTTAT
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAATATAAATATAAATA
Found at i:1290515 original size:26 final size:27
Alignment explanation
Indices: 1290484--1290541 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
1290474 ATATATTTCA
1290484 TTATTTAATATAAATATAA-ATATT-AT
1 TTATTTAATATAAATA-AATATATTAAT
* *
1290510 TTATTTATTATATATAAATATATTAAT
1 TTATTTAATATAAATAAATATATTAAT
1290537 TTATT
1 TTATT
1290542 ATCATTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 19 0.68
27 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTATTTAATATAAATAAATATATTAAT
Found at i:1290518 original size:30 final size:31
Alignment explanation
Indices: 1290471--1290531 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
1290461 TAATATTTTT
1290471 AATATATATTTCATTATT-TAATATAAATATA
1 AATATATATTTCATTATTAT-ATATAAATATA
1290502 AATAT-TATTT-ATTTATTATATATAAATATA
1 AATATATATTTCA-TTATTATATATAAATATA
1290532 TTAATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 1 0.04
30 21 0.75
31 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
AATATATATTTCATTATTATATATAAATATA
Found at i:1290538 original size:23 final size:24
Alignment explanation
Indices: 1290497--1290543 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1290487 TTTAATATAA
*
1290497 ATATAAATATTATTTATTTATTAT
1 ATATAAATATTATTAATTTATTAT
1290521 ATATAAATA-TATTAATTTATTAT
1 ATATAAATATTATTAATTTATTAT
1290544 CATTAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATAAATATTATTAATTTATTAT
Found at i:1290600 original size:24 final size:24
Alignment explanation
Indices: 1290573--1290632 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1290563 TTTTTACTAT
1290573 TATTATTATAATTAAATTTAAATA
1 TATTATTATAATTAAATTTAAATA
* * * * *
1290597 TATTTTTATTATTAATTTTAATTT
1 TATTATTATAATTAAATTTAAATA
1290621 TATTATTATAAT
1 TATTATTATAAT
1290633 ATTTAATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTATTATAATTAAATTTAAATA
Found at i:1290626 original size:21 final size:21
Alignment explanation
Indices: 1290600--1290666 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
1290590 TTAAATATAT
1290600 TTTTATTAT--TAAT-TTTAA
1 TTTTATTATGATAATATTTAA
*
1290618 TTTTATTATTATAATATTTAA
1 TTTTATTATGATAATATTTAA
1290639 TTTTATTATGATAATATTTAA
1 TTTTATTATGATAATATTTAA
*
1290660 TCTTATT
1 TTTTATT
1290667 GATACCACTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 9 0.20
20 4 0.09
21 31 0.70
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (21 bp):
TTTTATTATGATAATATTTAA
Found at i:1290775 original size:10 final size:10
Alignment explanation
Indices: 1290760--1290784 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1290750 GGGCTCTACC
1290760 CGGATGCGAT
1 CGGATGCGAT
1290770 CGGATGCGAT
1 CGGATGCGAT
1290780 CGGAT
1 CGGAT
1290785 AGTTAGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (10 bp):
CGGATGCGAT
Found at i:1294639 original size:31 final size:31
Alignment explanation
Indices: 1294581--1294646 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1294571 TTTAAATATA
*
1294581 AAAAATAAATAAAATTAACTTAAAAATTATT
1 AAAAATAAATAAAATTAACATAAAAATTATT
* *
1294612 AAAAATAAATAAAATTTAA-ATAGAAATTCTT
1 AAAAATAAATAAAA-TTAACATAAAAATTATT
1294643 AAAA
1 AAAA
1294647 TTTAATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (31 bp):
AAAAATAAATAAAATTAACATAAAAATTATT
Found at i:1297245 original size:17 final size:17
Alignment explanation
Indices: 1297219--1297256 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1297209 TCTTGTTTAA
1297219 TTATAGATAAATT-TTTT
1 TTATAGAT-AATTATTTT
*
1297236 TTATATATAATTATTTT
1 TTATAGATAATTATTTT
1297253 TTAT
1 TTAT
1297257 TTTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTATAGATAATTATTTT
Found at i:1297267 original size:18 final size:17
Alignment explanation
Indices: 1297228--1297270 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1297218 ATTATAGATA
1297228 AATT-TTTTTTATATAT
1 AATTATTTTTTATATAT
* *
1297244 AATTATTTTTTATTTTT
1 AATTATTTTTTATATAT
1297261 AATTTATTTT
1 AA-TTATTTT
1297271 AATAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 12 0.52
18 7 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
AATTATTTTTTATATAT
Found at i:1297817 original size:2 final size:2
Alignment explanation
Indices: 1297810--1297834 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1297800 TACTTTTCAA
1297810 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
1297835 ATTACTCCTC
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:1299415 original size:17 final size:17
Alignment explanation
Indices: 1299388--1299458 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
1299378 AAATCATACC
1299388 TCTTAATTAAATATATAT
1 TCTT-ATTAAATATATAT
*
1299406 TCTTATTAAATATTTAT
1 TCTTATTAAATATATAT
* * *
1299423 T-ATATTTAATATTTAT
1 TCTTATTAAATATATAT
*
1299439 TTTTATTAAAATTATATAT
1 TCTTATT-AAA-TATATAT
1299458 T
1 T
1299459 TAATATTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
16 14 0.32
17 17 0.39
18 6 0.14
19 7 0.16
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TCTTATTAAATATATAT
Found at i:1299433 original size:16 final size:16
Alignment explanation
Indices: 1299409--1299467 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
1299399 TATATATTCT
*
1299409 TATTAAATATTTATTA
1 TATTTAATATTTATTA
1299425 TATTTAATATTTATT-
1 TATTTAATATTTATTA
* *
1299440 TTTATTAA-AATTA-TA
1 TAT-TTAATATTTATTA
1299455 TATTTAATATTTA
1 TATTTAATATTTA
1299468 AATTTTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
14 5 0.14
15 12 0.34
16 18 0.51
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTAATATTTATTA
Found at i:1299459 original size:30 final size:33
Alignment explanation
Indices: 1299397--1299477 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
1299387 CTCTTAATTA
* *
1299397 AATATATATTCTTATTAAATATTTATTATATTT
1 AATATTTATTTTTATTAAATATTTATTATATTT
1299430 AATATTTATTTTTATTAAA-A-TTA-TATATTT
1 AATATTTATTTTTATTAAATATTTATTATATTT
1299460 AATATTTAAATTTTTATT
1 AATATTT--ATTTTTATT
1299478 TTAATACAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 14 0.32
31 3 0.07
32 10 0.23
33 17 0.39
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (33 bp):
AATATTTATTTTTATTAAATATTTATTATATTT
Found at i:1299480 original size:37 final size:38
Alignment explanation
Indices: 1299410--1299490 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 38
1299400 ATATATTCTT
*
1299410 ATTAAATATTTATTATATTTAATATTTATTTTTATTAAA
1 ATTAAATATTTA-TATATTTAATATTTATTTTTAATAAA
* * *
1299449 ATTATATATTTA-ATATTTAA-ATTTTTATTTTAATACA
1 ATTAAATATTTATATATTTAATATTTAT-TTTTAATAAA
1299486 ATTAA
1 ATTAA
1299491 TCGATCCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
36 5 0.14
37 20 0.56
39 11 0.31
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (38 bp):
ATTAAATATTTATATATTTAATATTTATTTTTAATAAA
Found at i:1300297 original size:38 final size:38
Alignment explanation
Indices: 1300241--1300315 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
1300231 ATTAATATTT
* *
1300241 AATAATAAAAAATATTTTTATTTAAATTTAATTATAAA
1 AATAATAAAAAATATTTTTATTGAAATTTAATAATAAA
* *
1300279 AATAA-AAAATAATTTTTTTATTGATATTTAATAATAA
1 AATAATAAAA-AATATTTTTATTGAAATTTAATAATAA
1300316 TTCAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 4 0.12
38 28 0.88
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
AATAATAAAAAATATTTTTATTGAAATTTAATAATAAA
Found at i:1300376 original size:11 final size:12
Alignment explanation
Indices: 1300347--1300379 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1300337 AACTCAATTT
1300347 AAATTTAAATAA
1 AAATTTAAATAA
1300359 AAATTTAAA-AA
1 AAATTTAAATAA
*
1300370 AATTTTAAAT
1 AAATTTAAAT
1300380 TGTAATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATTTAAATAA
Found at i:1300804 original size:20 final size:20
Alignment explanation
Indices: 1300769--1300809 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1300759 TATATTATAT
1300769 AAGATATATTTAAAAAATAAA
1 AAGATATATTTAAAAAA-AAA
1300790 AAGATA-ATTTTAAAAAAAAA
1 AAGATATA-TTTAAAAAAAAA
1300810 GAGACATAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
AAGATATATTTAAAAAAAAA
Found at i:1301236 original size:2 final size:2
Alignment explanation
Indices: 1301229--1301271 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1301219 CTCAAGTATG
1301229 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1301271 T
1 T
1301272 GCTTAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1301513 original size:226 final size:227
Alignment explanation
Indices: 1301251--1301698 Score: 774
Period size: 227 Copynumber: 2.0 Consensus size: 227
1301241 TATATATATA
*
1301251 TATATATATATATATATATATGCTTAAAAATTAATAACAAATACTGATTTTTTT-TAAATTTTTA
1 TATATATATATATATATATATGCTTAAAAATTAATAACAAATACTGATTTTTTTAAAAATTTTTA
1301315 ATTAAATTATAAATGAATTTTTCATGTTGATATAACAAATATTCTACAAAAAATACTTATATAAA
66 ATTAAATTATAAATGAATTTTTCATGTTGATATAACAAATATTCTACAAAAAATACTTATATAAA
* *
1301380 TTGAGTAAAACTTTTAAACTCGACATCATAATTTTGATACTTGTTAATAACTTTACGAATGCGTA
131 TTGAGTAAAACTTTTAAACTCGACACCATAATTTTGATACTTGTTAATAACTTTACGAATACGT-
1301445 AATAAAACATAAATTAAATAATCAAATACTGAT
195 AATAAAACATAAATTAAATAATCAAATACTGAT
1301478 TATATATATATATA-ATATATGCTTAAAAATTAATAACAAATACTGATTTTTTTAAAAATTTTTA
1 TATATATATATATATATATATGCTTAAAAATTAATAACAAATACTGATTTTTTTAAAAATTTTTA
* ** *
1301542 ATTAAATTATAAATGAATTTTTCATGTTGATATTACAAATATTCTATGAAAAATTCTTATATAAA
66 ATTAAATTATAAATGAATTTTTCATGTTGATATAACAAATATTCTACAAAAAATACTTATATAAA
* * * *
1301607 TTGAGTAAAACTTTTAAACTCGACACCATAATTTTGATGCTTGTTAATAACTTTATGAGTATGTA
131 TTGAGTAAAACTTTTAAACTCGACACCATAATTTTGATACTTGTTAATAACTTTACGAATACGTA
1301672 ATAAAACATAAATTAAATAATCAAATA
196 ATAAAACATAAATTAAATAATCAAATA
1301699 AAATAAATAT
Statistics
Matches: 209, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
226 67 0.32
227 142 0.68
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.40
Consensus pattern (227 bp):
TATATATATATATATATATATGCTTAAAAATTAATAACAAATACTGATTTTTTTAAAAATTTTTA
ATTAAATTATAAATGAATTTTTCATGTTGATATAACAAATATTCTACAAAAAATACTTATATAAA
TTGAGTAAAACTTTTAAACTCGACACCATAATTTTGATACTTGTTAATAACTTTACGAATACGTA
ATAAAACATAAATTAAATAATCAAATACTGAT
Found at i:1301712 original size:28 final size:27
Alignment explanation
Indices: 1301679--1301743 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
1301669 GTAATAAAAC
1301679 ATAAATTAAATAATCAAA-TAAAATAAAT
1 ATAAATTAAATAA--AAATTAAAATAAAT
* *
1301707 ATAAATTATATAAAAATTAAAATATAT
1 ATAAATTAAATAAAAATTAAAATAAAT
1301734 ATATAATTAA
1 ATA-AATTAA
1301744 GTCATTGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 12 0.38
28 17 0.53
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
ATAAATTAAATAAAAATTAAAATAAAT
Found at i:1305642 original size:26 final size:26
Alignment explanation
Indices: 1305591--1305643 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1305581 AAATATATTT
*
1305591 ATTTAAAATTTTATTTAATTTATTAA
1 ATTTAAAATTTTATTTAATCTATTAA
*
1305617 ATTTAAAAGTTTTATTTAA-CTGTTAA
1 ATTTAAAA-TTTTATTTAATCTATTAA
1305643 A
1 A
1305644 ATATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTTAAAATTTTATTTAATCTATTAA
Found at i:1305697 original size:30 final size:29
Alignment explanation
Indices: 1305663--1305719 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
1305653 AATATTTTTA
*
1305663 TAATAATATTTATATATTTA-TAATTAAATT
1 TAATAAAATTT-T-TATTTATTAATTAAATT
1305693 TAATAAAATTTTTATTTATTAATTAAA
1 TAATAAAATTTTTATTTATTAATTAAA
1305720 AATTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 9 0.36
30 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TAATAAAATTTTTATTTATTAATTAAATT
Found at i:1306204 original size:20 final size:20
Alignment explanation
Indices: 1306179--1306216 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1306169 ATATAATAAA
1306179 TATAATT-ATATTATTAAATT
1 TATAATTAAT-TTATTAAATT
1306199 TATAATTAATTTATTAAA
1 TATAATTAATTTATTAAA
1306217 ATAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATTAATTTATTAAATT
Found at i:1306223 original size:20 final size:19
Alignment explanation
Indices: 1306176--1306229 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
1306166 CATATATAAT
1306176 AAATATAATTATATTATTA
1 AAATATAATTATATTATTA
*
1306195 AATTTATAATTA-ATTTATTA
1 AA-ATATAATTATA-TTATTA
*
1306215 AAATAATAATAATAT
1 AAAT-ATAATTATAT
1306230 AAAAATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 4 0.14
20 23 0.82
21 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATATAATTATATTATTA
Found at i:1306248 original size:14 final size:15
Alignment explanation
Indices: 1306211--1306252 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1306201 TAATTAATTT
1306211 ATTAAAATAATAATA
1 ATTAAAATAATAATA
*
1306226 ATATAAAAATTATAA-A
1 AT-T-AAAATAATAATA
1306242 ATTAAAATAAT
1 ATTAAAATAAT
1306253 TTTATACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 7 0.30
15 3 0.13
16 4 0.17
17 9 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATTAAAATAATAATA
Found at i:1306597 original size:26 final size:26
Alignment explanation
Indices: 1306565--1306619 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
1306555 TTTATATTCT
1306565 ATTATTTAATATAAATATAA-ATATTA
1 ATTATTTAATATAAATA-AATATATTA
* *
1306591 ATTATTTATTATATATAAATATATTA
1 ATTATTTAATATAAATAAATATATTA
1306617 ATT
1 ATT
1306620 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTATTTAATATAAATAAATATATTA
Found at i:1306727 original size:24 final size:21
Alignment explanation
Indices: 1306700--1306752 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
1306690 TTTTAATATT
*
1306700 ATTATTATAATATCCAATTTTATC
1 ATTATTATAATA---AATTTCATC
**
1306724 ATTAAAATAATAAATTTCATC
1 ATTATTATAATAAATTTCATC
1306745 ATTATTAT
1 ATTATTAT
1306753 TATTTTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 14 0.58
24 10 0.42
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATTATAATAAATTTCATC
Found at i:1307343 original size:21 final size:22
Alignment explanation
Indices: 1307319--1307360 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1307309 AAATAATCAC
1307319 TTAAAAT-ATAA-ATATATATTT
1 TTAAAATAATAATATA-ATATTT
1307340 TTAAAATAATAATATAATATT
1 TTAAAATAATAATATAATATT
1307361 AACACATGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 9 0.47
23 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAATAATAATATAATATTT
Found at i:1308880 original size:16 final size:17
Alignment explanation
Indices: 1308859--1308900 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1308849 GTTAAAACTA
*
1308859 AATAAAATAAAAT-AAT
1 AATAAAAAAAAATAAAT
1308875 AATAAAGCAAAAAATAAAT
1 AATAAA--AAAAAATAAAT
1308894 AATAAAA
1 AATAAAA
1308901 GCTTAAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 6 0.27
17 1 0.05
18 6 0.27
19 9 0.41
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (17 bp):
AATAAAAAAAAATAAAT
Found at i:1310716 original size:16 final size:17
Alignment explanation
Indices: 1310685--1310719 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1310675 TTTTAAAATT
*
1310685 TTTTATTTATATTTAAA
1 TTTTATTCATATTTAAA
1310702 TTTTATTCA-ATTTAAA
1 TTTTATTCATATTTAAA
1310718 TT
1 TT
1310720 AAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATTCATATTTAAA
Found at i:1312074 original size:16 final size:15
Alignment explanation
Indices: 1312053--1312082 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1312043 TTGTTACACT
1312053 TAGAATAGCAATATAG
1 TAGAATAG-AATATAG
1312069 TAGAATAGAATATA
1 TAGAATAGAATATA
1312083 AAGTTAACAT
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:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:1314793 original size:80 final size:82
Alignment explanation
Indices: 1314672--1314827 Score: 289
Period size: 80 Copynumber: 1.9 Consensus size: 82
1314662 AATCTGTAAA
1314672 AAAAAAAACAAATTAGATGTATCTAATTGAATATTACAATAACAAGCAGCAAATGTGATTTAAAA
1 AAAAAAAACAAATTAGATGTATCTAATTGAATATTACAATAACAAGCAGCAAATGTGATTTAAAA
1314737 AACTGTGAAACCAATGC
66 AACTGTGAAACCAATGC
*
1314754 AAAAAAAA-AAATTAGATGTATC-AATTGAATATTATAATAACAAGCAGCAAATGTGATTTAAAA
1 AAAAAAAACAAATTAGATGTATCTAATTGAATATTACAATAACAAGCAGCAAATGTGATTTAAAA
1314817 AACTGTGAAAC
66 AACTGTGAAAC
1314828 TAATTTTTTT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
80 51 0.70
81 14 0.19
82 8 0.11
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (82 bp):
AAAAAAAACAAATTAGATGTATCTAATTGAATATTACAATAACAAGCAGCAAATGTGATTTAAAA
AACTGTGAAACCAATGC
Found at i:1315959 original size:72 final size:73
Alignment explanation
Indices: 1315833--1316017 Score: 284
Period size: 73 Copynumber: 2.5 Consensus size: 73
1315823 GGTTGGACCG
* *
1315833 ATTTTTTATTTAAATTAAAATATAGAATAAATTTTTTATTTGGGTAGACTATTAT-TTTTTCATT
1 ATTTTTTATTTAGATTAAAATATGGAATAAATTTTTTATTTGGGTAGACTATTATATTTTTCATT
1315897 AATTAATA
66 AATTAATA
* *
1315905 ATTTTTTATTTAGATTAAAATATGGAATAAATTTTTTATTTGGTTAGA-TCATTATATTTTTTAT
1 ATTTTTTATTTAGATTAAAATATGGAATAAATTTTTTATTTGGGTAGACT-ATTATATTTTTCAT
1315969 TAATTAATA
65 TAATTAATA
* * *
1315978 ATTTTTTATTTAGATTAAAATATGAAATCAATTTCTTATT
1 ATTTTTTATTTAGATTAAAATATGGAATAAATTTTTTATT
1316018 AATTTAAATT
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
71 1 0.01
72 50 0.48
73 53 0.51
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.54
Consensus pattern (73 bp):
ATTTTTTATTTAGATTAAAATATGGAATAAATTTTTTATTTGGGTAGACTATTATATTTTTCATT
AATTAATA
Found at i:1315995 original size:24 final size:23
Alignment explanation
Indices: 1315894--1315995 Score: 59
Period size: 30 Copynumber: 4.2 Consensus size: 23
1315884 TTATTTTTTC
1315894 ATTAATTAATAATTTTTTATTTAG
1 ATTAATTAATAATTTTTTATTT-G
1315918 ATTAAAATATGGAATAAATTTTTTATTTG
1 ATT--AAT-T--AAT-AATTTTTTATTTG
* * * *
1315947 GTTAGA-TCATTA-TATTT-TTT-
1 ATTA-ATTAATAATTTTTTATTTG
1315967 ATTAATTAATAATTTTTTATTTAG
1 ATTAATTAATAATTTTTTATTT-G
1315991 ATTAA
1 ATTAA
1315996 AATATGAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 24
0.64 0.09 0.27
Matches are distributed among these distances:
19 1 0.02
20 7 0.12
21 7 0.12
22 7 0.12
23 1 0.02
24 10 0.17
26 4 0.07
27 2 0.03
28 1 0.02
29 6 0.10
30 12 0.21
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (23 bp):
ATTAATTAATAATTTTTTATTTG
Found at i:1316093 original size:16 final size:16
Alignment explanation
Indices: 1316068--1316110 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1316058 ATATATTTTG
1316068 ATTAATATTAACTTATTT
1 ATTAA-ATTAA-TTATTT
*
1316086 -TTAAATTAATTTTTT
1 ATTAAATTAATTATTT
1316101 ATTAAATTAA
1 ATTAAATTAA
1316111 AATATTAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
16 14 0.61
17 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTAAATTAATTATTT
Found at i:1316315 original size:16 final size:16
Alignment explanation
Indices: 1316259--1316375 Score: 126
Period size: 16 Copynumber: 7.2 Consensus size: 16
1316249 CCCGAAACCG
*
1316259 ACCCGAACTCGAGTCCGA
1 ACCCGAA-T-GAGCCCGA
* * *
1316277 ACCCGAATAAGTCCAA
1 ACCCGAATGAGCCCGA
1316293 ACCCGAATGAGCCCGA
1 ACCCGAATGAGCCCGA
* *
1316309 ACTCGAATGAGCTCGA
1 ACCCGAATGAGCCCGA
* * *
1316325 ACCTGAACGAGTCCGA
1 ACCCGAATGAGCCCGA
1316341 ACCCGAATGAGCCCGA
1 ACCCGAATGAGCCCGA
*
1316357 ACCCGAATGAGCTCGA
1 ACCCGAATGAGCCCGA
1316373 ACC
1 ACC
1316376 TAAACAAGCT
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
16 75 0.90
17 1 0.01
18 7 0.08
ACGTcount: A:0.32, C:0.34, G:0.22, T:0.11
Consensus pattern (16 bp):
ACCCGAATGAGCCCGA
Found at i:1316338 original size:48 final size:48
Alignment explanation
Indices: 1316285--1316408 Score: 178
Period size: 48 Copynumber: 2.6 Consensus size: 48
1316275 GAACCCGAAT
* *
1316285 AAGTCCAAACCCGAATGAGCCCGAACTCGAATGAGCTCGAACCTGAAC
1 AAGTCCAAACCCGAATGAGCCCGAACCCGAATGAGCTCGAACCTAAAC
* *
1316333 GAGTCCGAACCCGAATGAGCCCGAACCCGAATGAGCTCGAACCTAAAC
1 AAGTCCAAACCCGAATGAGCCCGAACCCGAATGAGCTCGAACCTAAAC
* *
1316381 AAG-CTCAAACCTGAACGAGCCCGAACCC
1 AAGTC-CAAACCCGAATGAGCCCGAACCC
1316409 AAACAAACTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 1 0.01
48 66 0.99
ACGTcount: A:0.35, C:0.34, G:0.21, T:0.10
Consensus pattern (48 bp):
AAGTCCAAACCCGAATGAGCCCGAACCCGAATGAGCTCGAACCTAAAC
Found at i:1316385 original size:16 final size:16
Alignment explanation
Indices: 1316366--1316414 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
1316356 AACCCGAATG
1316366 AGCTCGAACCTAAACA
1 AGCTCGAACCTAAACA
* * *
1316382 AGCTCAAACCTGAACG
1 AGCTCGAACCTAAACA
* *
1316398 AGCCCGAACCCAAACA
1 AGCTCGAACCTAAACA
1316414 A
1 A
1316415 ACTTGAACTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.43, C:0.35, G:0.14, T:0.08
Consensus pattern (16 bp):
AGCTCGAACCTAAACA
Found at i:1316406 original size:32 final size:32
Alignment explanation
Indices: 1316318--1316440 Score: 111
Period size: 32 Copynumber: 3.8 Consensus size: 32
1316308 AACTCGAATG
* * **
1316318 AGCTCGAACCTGAACGAGTCCGAACCCGAATG
1 AGCTCGAACCTGAACGAGCCCGAACCCAAACA
* * * * *
1316350 AGCCCGAACCCGAATGAGCTCGAACCTAAACA
1 AGCTCGAACCTGAACGAGCCCGAACCCAAACA
*
1316382 AGCTCAAACCTGAACGAGCCCGAACCCAAACA
1 AGCTCGAACCTGAACGAGCCCGAACCCAAACA
* * * **
1316414 AACTTGAACTTGAACTTGCCCGAACCC
1 AGCTCGAACCTGAACGAGCCCGAACCC
1316441 GAACCTGCCC
Statistics
Matches: 70, Mismatches: 21, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.35, C:0.34, G:0.19, T:0.12
Consensus pattern (32 bp):
AGCTCGAACCTGAACGAGCCCGAACCCAAACA
Found at i:1322416 original size:7 final size:8
Alignment explanation
Indices: 1322397--1322424 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1322387 TAAGAACCAA
1322397 AAAAAATT
1 AAAAAATT
1322405 AAAAAATT
1 AAAAAATT
1322413 AAAAAATT
1 AAAAAATT
1322421 AAAA
1 AAAA
1322425 TATTTTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:1322432 original size:26 final size:27
Alignment explanation
Indices: 1322403--1322455 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1322393 CCAAAAAAAA
1322403 TTAA-AAAATTAAAAAATTAAAA-TATT
1 TTAATAAAATT-AAAAATTAAAAGTATT
* *
1322429 TTAATGATATTAAAAATTAAAAGTATT
1 TTAATAAAATTAAAAATTAAAAGTATT
1322456 AAAATTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
TTAATAAAATTAAAAATTAAAAGTATT
Found at i:1323627 original size:27 final size:28
Alignment explanation
Indices: 1323597--1323652 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1323587 AATAAGATTA
1323597 AAATTT-AAATTTTTAAAATTTTTATTT
1 AAATTTAAAATTTTTAAAATTTTTATTT
*
1323624 AAATTTAAAATTTTTTAAATTTTTATTT
1 AAATTTAAAATTTTTAAAATTTTTATTT
1323652 A
1 A
1323653 TAAAGTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
AAATTTAAAATTTTTAAAATTTTTATTT
Found at i:1324134 original size:2 final size:2
Alignment explanation
Indices: 1324127--1324171 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1324117 TACTTTTCAA
1324127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1324169 AT A
1 AT A
1324172 AAATGACTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1324737 original size:20 final size:20
Alignment explanation
Indices: 1324705--1324745 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1324695 TATATTATAT
1324705 AAGATATATTTAAAAAATAAA
1 AAGATATATTTAAAAAA-AAA
1324726 AAGATA-ATTTAAAAAAAAA
1 AAGATATATTTAAAAAAAAA
1324745 A
1 A
1324746 GACATAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
AAGATATATTTAAAAAAAAA
Found at i:1325059 original size:2 final size:2
Alignment explanation
Indices: 1325052--1325092 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1325042 TTAAAAGTCT
1325052 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
1325093 GTTTGTTTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1325188 original size:2 final size:2
Alignment explanation
Indices: 1325181--1325225 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1325171 CTCAAGTATG
1325181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1325223 TA T
1 TA T
1325226 GCTTAAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1328803 original size:13 final size:14
Alignment explanation
Indices: 1328787--1328820 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1328777 AATTTTTTTA
1328787 AAAAAAAATT-AAT
1 AAAAAAAATTAAAT
*
1328800 AAAATAAATTAAAT
1 AAAAAAAATTAAAT
1328814 AAAAAAA
1 AAAAAAA
1328821 TATAAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAAAAATTAAAT
Found at i:1328821 original size:13 final size:13
Alignment explanation
Indices: 1328788--1328827 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
1328778 ATTTTTTTAA
1328788 AAAAAAATT-AAT
1 AAAAAAATTAAAT
1328800 AAAATAAATTAAAT
1 AAAA-AAATTAAAT
1328814 AAAAAAATATAAAT
1 AAAAAAAT-TAAAT
1328828 CAAACAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.16
13 9 0.36
14 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAAAAATTAAAT
Found at i:1329377 original size:26 final size:26
Alignment explanation
Indices: 1329326--1329378 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1329316 AAATATATTT
*
1329326 ATTTAAAATTTTATTTAATTTATTAA
1 ATTTAAAATTTTATTTAATCTATTAA
*
1329352 ATTTAAAAGTTTTATTTAA-CTGTTAA
1 ATTTAAAA-TTTTATTTAATCTATTAA
1329378 A
1 A
1329379 ATATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTTAAAATTTTATTTAATCTATTAA
Found at i:1329432 original size:30 final size:29
Alignment explanation
Indices: 1329398--1329454 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
1329388 AATATTTTTA
*
1329398 TAATAATATTTATATATTTA-TAATTAAATT
1 TAATAAAATTT-T-TATTTATTAATTAAATT
1329428 TAATAAAATTTTTATTTATTAATTAAA
1 TAATAAAATTTTTATTTATTAATTAAA
1329455 AATTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 9 0.36
30 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TAATAAAATTTTTATTTATTAATTAAATT
Found at i:1329905 original size:20 final size:20
Alignment explanation
Indices: 1329880--1329917 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1329870 GTACTATAAG
1329880 TATAATT-ATATTATTAAATT
1 TATAATTAAT-TTATTAAATT
1329900 TATAATTAATTTATTAAA
1 TATAATTAATTTATTAAA
1329918 ATATTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATTAATTTATTAAATT
Found at i:1330263 original size:63 final size:63
Alignment explanation
Indices: 1330183--1330328 Score: 163
Period size: 63 Copynumber: 2.3 Consensus size: 63
1330173 TAATATAACT
* * * * *
1330183 AATATTTTTATTATATATTTTATTATTTGATATGATTATAATTA-TAAGTAATTATTCA-ATATA
1 AATATATTTATT-TATATTTTATTATTTAATATAAATATAAATATTAAGTAATTATT-ATATATA
* * *
1330246 AATATAATTTATTTATATTCTATTATTTAATATAAATATAAATATTAATTATTTATTATATATA
1 AATAT-ATTTATTTATATTTTATTATTTAATATAAATATAAATATTAAGTAATTATTATATATA
*
1330310 AATATATTAATTTA-ATTTT
1 AATATATTTATTTATATTTT
1330329 TTTAATCATT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
62 4 0.06
63 40 0.57
64 26 0.37
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (63 bp):
AATATATTTATTTATATTTTATTATTTAATATAAATATAAATATTAAGTAATTATTATATATA
Found at i:1330299 original size:26 final size:26
Alignment explanation
Indices: 1330267--1330321 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
1330257 TTTATATTCT
1330267 ATTATTTAATATAAATATAA-ATATTA
1 ATTATTTAATATAAATA-AATATATTA
* *
1330293 ATTATTTATTATATATAAATATATTA
1 ATTATTTAATATAAATAAATATATTA
1330319 ATT
1 ATT
1330322 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTATTTAATATAAATAAATATATTA
Found at i:1330429 original size:27 final size:24
Alignment explanation
Indices: 1330382--1330457 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 24
1330372 AATATAAATT
*
1330382 TTATTATTAATTTTAAT-ATTATTA
1 TTATAATTAATTTT-ATCATTATTA
1330406 TTATAATACTTAATTTTATCATTA-TA
1 TTAT-A-A-TTAATTTTATCATTATTA
*
1330432 --ATAATTAATTTAATCATTATTA
1 TTATAATTAATTTTATCATTATTA
1330454 TTAT
1 TTAT
1330458 TTTTAATCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
21 14 0.33
22 3 0.07
23 1 0.02
24 8 0.19
26 5 0.12
27 12 0.28
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATAATTAATTTTATCATTATTA
Found at i:1331045 original size:21 final size:22
Alignment explanation
Indices: 1331021--1331062 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1331011 AAATAATCAC
1331021 TTAAAAT-ATAA-ATATATATTT
1 TTAAAATAATAATATA-ATATTT
1331042 TTAAAATAATAATATAATATT
1 TTAAAATAATAATATAATATT
1331063 AACACATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 9 0.47
23 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAATAATAATATAATATTT
Found at i:1332582 original size:16 final size:17
Alignment explanation
Indices: 1332561--1332602 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1332551 GTTAAAACTA
*
1332561 AATAAAATAAAAT-AAT
1 AATAAAAAAAAATAAAT
1332577 AATAAAGCAAAAAATAAAT
1 AATAAA--AAAAAATAAAT
1332596 AATAAAA
1 AATAAAA
1332603 GCTTAAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 6 0.27
17 1 0.05
18 6 0.27
19 9 0.41
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (17 bp):
AATAAAAAAAAATAAAT
Found at i:1334419 original size:16 final size:17
Alignment explanation
Indices: 1334388--1334422 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1334378 TTTTAAAATT
*
1334388 TTTTATTTATATTTAAA
1 TTTTATTCATATTTAAA
1334405 TTTTATTCA-ATTTAAA
1 TTTTATTCATATTTAAA
1334421 TT
1 TT
1334423 AAAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATTCATATTTAAA
Found at i:1335778 original size:16 final size:15
Alignment explanation
Indices: 1335757--1335786 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1335747 TTGTTACACT
1335757 TAGAATAGCAATATAG
1 TAGAATAG-AATATAG
1335773 TAGAATAGAATATA
1 TAGAATAGAATATA
1335787 AAGTTAACAT
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:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:1338497 original size:82 final size:84
Alignment explanation
Indices: 1338372--1338531 Score: 288
Period size: 82 Copynumber: 1.9 Consensus size: 84
1338362 TCAAATCTGT
1338372 AAAAAAAAAACAAATTAGATGTATCTAATTGAATATTACAATAACAAGCAGCAAATGTGATTTAA
1 AAAAAAAAAACAAATTAGATGTATCTAATTGAATATTACAATAACAAGCAGCAAATGTGATTTAA
1338437 AAAACTGTGAAACCAATGC
66 AAAACTGTGAAACCAATGC
* *
1338456 AAAAAAAAAA-AAATTAGATGTATC-AATTGAATATTATAATAACAAGCAGTAAATGTGATTTAA
1 AAAAAAAAAACAAATTAGATGTATCTAATTGAATATTACAATAACAAGCAGCAAATGTGATTTAA
1338519 AAAACTGTGAAAC
66 AAAACTGTGAAAC
1338532 TAATTTTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
82 50 0.68
83 14 0.19
84 10 0.14
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (84 bp):
AAAAAAAAAACAAATTAGATGTATCTAATTGAATATTACAATAACAAGCAGCAAATGTGATTTAA
AAAACTGTGAAACCAATGC
Found at i:1339675 original size:73 final size:73
Alignment explanation
Indices: 1339547--1339732 Score: 268
Period size: 73 Copynumber: 2.5 Consensus size: 73
1339537 GGTTGGACCG
* * *
1339547 ATTTTTTATTTAAATTAAAATATAGAATAAATTTTTTATTTGGTTGGACTATTATGTT-TTTCAT
1 ATTTTTTATTTAGATTAAAATATAGAATAAATTTTTTATTTGGTTAGACTATTATGTTGTCT-AT
1339611 TAATTAATA
65 TAATTAATA
* * * *
1339620 ATTTTTTATTTAGGTTAAAATATAAAATAAATTTCTTATTTGGTTAGA-TCGTTATGTTGTCTAT
1 ATTTTTTATTTAGATTAAAATATAGAATAAATTTTTTATTTGGTTAGACT-ATTATGTTGTCTAT
*
1339684 TAATTAATG
65 TAATTAATA
1339693 ATTTTTTATTTAGATTAAAATATAGAATAAATTTTTTATT
1 ATTTTTTATTTAGATTAAAATATAGAATAAATTTTTTATT
1339733 AATTTAAATT
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
72 1 0.01
73 97 0.97
74 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (73 bp):
ATTTTTTATTTAGATTAAAATATAGAATAAATTTTTTATTTGGTTAGACTATTATGTTGTCTATT
AATTAATA
Found at i:1339757 original size:17 final size:17
Alignment explanation
Indices: 1339720--1339758 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1339710 AAATATAGAA
**
1339720 TAAATTTTTTATTAATT
1 TAAATTTTTTATTAACG
*
1339737 TAAATTTTTTATTCACG
1 TAAATTTTTTATTAACG
1339754 TAAAT
1 TAAAT
1339759 ATTTCATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (17 bp):
TAAATTTTTTATTAACG
Found at i:1340022 original size:16 final size:16
Alignment explanation
Indices: 1340003--1340095 Score: 89
Period size: 16 Copynumber: 5.8 Consensus size: 16
1339993 GAATAAGCCT
1340003 GAACCCGAACGAGTCC
1 GAACCCGAACGAGTCC
* *
1340019 GAACTCGAATGAG-CTC
1 GAACCCGAACGAGTC-C
** *
1340035 GAACTTGAACGAGTCT
1 GAACCCGAACGAGTCC
* * *
1340051 GAACCTGAATGAGCCC
1 GAACCCGAACGAGTCC
1340067 GAACCCGAACGAGTCC
1 GAACCCGAACGAGTCC
*
1340083 GAACCTGAACGAG
1 GAACCCGAACGAG
1340096 CTCAAATCTG
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
15 1 0.02
16 60 0.97
17 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.26, T:0.13
Consensus pattern (16 bp):
GAACCCGAACGAGTCC
Found at i:1340045 original size:32 final size:32
Alignment explanation
Indices: 1339987--1340096 Score: 132
Period size: 32 Copynumber: 3.4 Consensus size: 32
1339977 ACTCGAGCTT
* * *
1339987 GAACCCGAATAAGCCTGAACCCGAACGAGTCC
1 GAACCTGAATGAGCCCGAACCCGAACGAGTCC
* ** *
1340019 GAA-CTCGAATGAGCTCGAACTTGAACGAGTCT
1 GAACCT-GAATGAGCCCGAACCCGAACGAGTCC
1340051 GAACCTGAATGAGCCCGAACCCGAACGAGTCC
1 GAACCTGAATGAGCCCGAACCCGAACGAGTCC
*
1340083 GAACCTGAACGAGC
1 GAACCTGAATGAGC
1340097 TCAAATCTGA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
31 1 0.02
32 61 0.95
33 2 0.03
ACGTcount: A:0.33, C:0.30, G:0.25, T:0.13
Consensus pattern (32 bp):
GAACCTGAATGAGCCCGAACCCGAACGAGTCC
Found at i:1340054 original size:48 final size:48
Alignment explanation
Indices: 1340001--1340095 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
1339991 CCGAATAAGC
* * * *
1340001 CTGAACCCGAACGAGTCCGAACTCGAATGAG-CTCGAACTTGAACGAGT
1 CTGAACCCGAACGAGCCCGAACCCGAACGAGTC-CGAACCTGAACGAGT
* *
1340049 CTGAACCTGAATGAGCCCGAACCCGAACGAGTCCGAACCTGAACGAG
1 CTGAACCCGAACGAGCCCGAACCCGAACGAGTCCGAACCTGAACGAG
1340096 CTCAAATCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.32, C:0.29, G:0.25, T:0.14
Consensus pattern (48 bp):
CTGAACCCGAACGAGCCCGAACCCGAACGAGTCCGAACCTGAACGAGT
Found at i:1340140 original size:48 final size:48
Alignment explanation
Indices: 1340034--1340140 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
1340024 CGAATGAGCT
* * * *
1340034 CGAACTTGAACGAGTCTGAACCTGAATGAGCCCGAACCCGAACGAGTC
1 CGAACTTGAACGAGTCTAAACCTGAATGAGCCCGAACCCAAACAACTC
* *
1340082 CGAACCTGAACGAG-CTCAAATCTGAATGAGCCCGAACCCAAACAAACT-
1 CGAACTTGAACGAGTCT-AAACCTGAATGAGCCCGAACCCAAAC-AACTC
*
1340130 TGAACTTGAAC
1 CGAACTTGAAC
1340141 TTGCCCGAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
47 2 0.04
48 45 0.92
49 2 0.04
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.15
Consensus pattern (48 bp):
CGAACTTGAACGAGTCTAAACCTGAATGAGCCCGAACCCAAACAACTC
Found at i:1346129 original size:7 final size:8
Alignment explanation
Indices: 1346110--1346137 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1346100 TAAGAACCAG
1346110 AAAAAATT
1 AAAAAATT
1346118 AAAAAATT
1 AAAAAATT
1346126 AAAAAATT
1 AAAAAATT
1346134 AAAA
1 AAAA
1346138 TATTTTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:1346145 original size:26 final size:27
Alignment explanation
Indices: 1346116--1346168 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1346106 CCAGAAAAAA
1346116 TTAA-AAAATTAAAAAATTAAAA-TATT
1 TTAATAAAATT-AAAAATTAAAAGTATT
* *
1346142 TTAATGATATTAAAAATTAAAAGTATT
1 TTAATAAAATTAAAAATTAAAAGTATT
1346169 AAAATTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
TTAATAAAATTAAAAATTAAAAGTATT
Found at i:1347328 original size:21 final size:21
Alignment explanation
Indices: 1347303--1347343 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1347293 TATTTATAAA
1347303 TAAAATTTAAATTTAAATTTT
1 TAAAATTTAAATTTAAATTTT
**
1347324 TAAAATTTTTATTTAAATTT
1 TAAAATTTAAATTTAAATTT
1347344 AATTCAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAAATTTAAATTTAAATTTT
Found at i:1347842 original size:2 final size:2
Alignment explanation
Indices: 1347835--1347873 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1347825 TACTTTTCAA
1347835 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
1347874 ATGACTCCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1348762 original size:2 final size:2
Alignment explanation
Indices: 1348755--1348781 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1348745 TTAAAAGTCT
1348755 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
1348782 GTTTGTTTAG
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:1348879 original size:2 final size:2
Alignment explanation
Indices: 1348874--1348913 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1348864 AGTACGTGTG
1348874 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1348914 CTTAAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1349127 original size:28 final size:27
Alignment explanation
Indices: 1349094--1349158 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
1349084 GTAATAAAAC
1349094 ATAAATTAAATAATCAAA-TAAAATAAAT
1 ATAAATTAAATAA--AAATTAAAATAAAT
* *
1349122 ATAAATTATATAAAAATTAAAATATAT
1 ATAAATTAAATAAAAATTAAAATAAAT
1349149 ATATAATTAA
1 ATA-AATTAA
1349159 GTCATTGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 12 0.38
28 17 0.53
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
ATAAATTAAATAAAAATTAAAATAAAT
Found at i:1353102 original size:21 final size:22
Alignment explanation
Indices: 1353073--1353116 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1353063 AAACTCGTTA
1353073 ATTTATTTAA-ATATATTAAAAT
1 ATTTATTTAATAT-TATTAAAAT
*
1353095 ATTT-TTTAATATTTTTAAAAT
1 ATTTATTTAATATTATTAAAAT
1353116 A
1 A
1353117 AATTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTATTTAATATTATTAAAAT
Found at i:1353122 original size:20 final size:21
Alignment explanation
Indices: 1353099--1353145 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1353089 TAAAATATTT
* *
1353099 TTTAATATTTTTA-AAATAAA
1 TTTAATATATATATAAATAAA
*
1353119 TTT-ATATATATATAATTAAA
1 TTTAATATATATATAAATAAA
1353139 TTTAATA
1 TTTAATA
1353146 AAATTTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.32
20 12 0.55
21 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATATATATATAAATAAA
Found at i:1353510 original size:34 final size:34
Alignment explanation
Indices: 1353466--1353532 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1353456 GGAGAAAAGG
* *
1353466 TAATATTTTATATATATATATATTCATA-ATTTTT
1 TAATAATTTATATATATATA-ATTAATATATTTTT
*
1353500 TAATAATTTATATTTATATAATTAATATATTTT
1 TAATAATTTATATATATATAATTAATATATTTT
1353533 ATTTATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (34 bp):
TAATAATTTATATATATATAATTAATATATTTTT
Found at i:1353526 original size:22 final size:22
Alignment explanation
Indices: 1353499--1353550 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1353489 TCATAATTTT
1353499 TTAATA-ATTTATATTTATATAA
1 TTAATATATTT-TATTTATATAA
1353521 TTAATATATTTTATTTATATAA
1 TTAATATATTTTATTTATATAA
*
1353543 ATAATATA
1 TTAATATA
1353551 AATGAAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAATATATTTTATTTATATAA
Found at i:1353712 original size:32 final size:32
Alignment explanation
Indices: 1353670--1353736 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
1353660 AAAATTTCTT
* * **
1353670 ATATTTATAATA-AATATAATTATATTATTAAA
1 ATATTAATAATATAA-AAAATTATAAAATTAAA
1353702 ATATTAATAATATAAAAAATTATAAAATTAAA
1 ATATTAATAATATAAAAAATTATAAAATTAAA
1353734 ATA
1 ATA
1353737 ATTTTATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
ATATTAATAATATAAAAAATTATAAAATTAAA
Found at i:1353982 original size:18 final size:17
Alignment explanation
Indices: 1353946--1354029 Score: 102
Period size: 18 Copynumber: 4.9 Consensus size: 17
1353936 TTTTTTTAAT
1353946 TTTTTAAT-TAATT-TA
1 TTTTTAATATAATTATA
1353961 TTTTTAATATAATTAATA
1 TTTTTAATATAATT-ATA
*
1353979 TTTTTAATATATATTTTA
1 TTTTTAATATA-ATTATA
1353997 TTATTTAATATAATTATA
1 TT-TTTAATATAATTATA
*
1354015 ATTTTAA-ATAATTAT
1 TTTTTAATATAATTAT
1354030 TAAACATAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
15 8 0.13
16 13 0.21
17 5 0.08
18 23 0.38
19 12 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTAATATAATTATA
Found at i:1354018 original size:16 final size:16
Alignment explanation
Indices: 1353963--1354029 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 16
1353953 TTAATTTATT
*
1353963 TTTAATATAATTAATATT
1 TTTAATATAATT-ATA-A
*
1353981 TTTAATATATATTTTATTA
1 TTTAATATA-A--TTATAA
1354000 TTTAATATAATTATAA
1 TTTAATATAATTATAA
1354016 TTTTAA-ATAATTAT
1 -TTTAATATAATTAT
1354030 TAAACATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
16 13 0.31
17 5 0.12
18 10 0.24
19 10 0.24
20 2 0.05
21 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAATATAATTATAA
Found at i:1354156 original size:40 final size:40
Alignment explanation
Indices: 1354076--1354156 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
1354066 AATATAAATA
* **
1354076 TTAATTATTTATTATATATAAATATATTAATTTAATTTTT
1 TTAATTATTTATTATATATAAATAAATTAACATAATTTTT
*
1354116 TTAATT-TTTATTATTATATAATTAAATTAAACATAATTTTT
1 TTAATTATTTATTA-TATATAAATAAATT-AACATAATTTTT
1354157 ATTATTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 7 0.20
40 18 0.51
41 10 0.29
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (40 bp):
TTAATTATTTATTATATATAAATAAATTAACATAATTTTT
Done.