Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1428
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: 125228
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:898 original size:177 final size:177
Alignment explanation
Indices: 602--955 Score: 667
Period size: 177 Copynumber: 2.0 Consensus size: 177
592 AAGGTATGAT
602 GCATGGACGAGAGTTCGAAGGCGTAATATAATTGTGTCGAATAAGGATGGGATTATTGCTCCAGT
1 GCATGGACGAGAGTTCGAAGGCGTAATATAATTGTGTCGAATAAGGATGGGATTATTGCTCCAGT
667 AATCATTCGACCAGAACTAGTGATGCCTTCCGAGATAGACTCGATCAAATCTGAGGTT-CAAGAG
66 AATCATTCGACCAGAACTAGTGATGCCTTCCGAGATAGACTCGATCAAATCTGAGGTTAC-AGAG
731 AATAGAAAGGATTAAATGATGAGAATCAACAATTGCATGAAGAGGTGG
130 AATAGAAAGGATTAAATGATGAGAATCAACAATTGCATGAAGAGGTGG
*
779 GCATGGACGAGAGTTCGAAGGCGTAATATAATTGTGTCTAATAAGGATGGGATTATTGCTCCAGT
1 GCATGGACGAGAGTTCGAAGGCGTAATATAATTGTGTCGAATAAGGATGGGATTATTGCTCCAGT
844 AATCATTCGACCAGAACTAGTGATGCCTTCCGAGATAGACTCCGATC-AATCTGAGGTTACAGAG
66 AATCATTCGACCAGAACTAGTGATGCCTTCCGAGATAGACT-CGATCAAATCTGAGGTTACAGAG
908 AATAGAAAGGATTAAATGATGAGAATCAACAATTGCATGAAGAGGTGG
130 AATAGAAAGGATTAAATGATGAGAATCAACAATTGCATGAAGAGGTGG
956 CCCACTTGAG
Statistics
Matches: 174, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
177 168 0.97
178 6 0.03
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (177 bp):
GCATGGACGAGAGTTCGAAGGCGTAATATAATTGTGTCGAATAAGGATGGGATTATTGCTCCAGT
AATCATTCGACCAGAACTAGTGATGCCTTCCGAGATAGACTCGATCAAATCTGAGGTTACAGAGA
ATAGAAAGGATTAAATGATGAGAATCAACAATTGCATGAAGAGGTGG
Found at i:5208 original size:31 final size:30
Alignment explanation
Indices: 5147--5213 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
5137 TAAAATACAA
* *
5147 AATTTATTATTTTTAATATATATTTTATTT
1 AATTTATTATTTTTAATATATAATTAATTT
5177 AATTTATTTATTTTTAA-ATAATAATTAATTT
1 AATTTA-TTATTTTTAATAT-ATAATTAATTT
*
5208 AGTTTA
1 AATTTA
5214 AATAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (30 bp):
AATTTATTATTTTTAATATATAATTAATTT
Found at i:6418 original size:24 final size:23
Alignment explanation
Indices: 6390--6435 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
6380 TAAAAATACG
* *
6390 ATATAAATACATGAATATATTAAA
1 ATATAAATAAATAAATA-ATTAAA
*
6414 ATATAGATAAATAAATAATTAA
1 ATATAAATAAATAAATAATTAA
6436 CGTGTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
ATATAAATAAATAAATAATTAAA
Found at i:6596 original size:22 final size:21
Alignment explanation
Indices: 6570--6626 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 21
6560 TATAAAAATA
6570 TATATAAAATAA-ATAA-ATTAT
1 TATATAAAA-AATATAATATT-T
6591 TAATATATAAAAATATAATATTT
1 T-ATATA-AAAAATATAATATTT
6614 TATATAAAAAATA
1 TATATAAAAAATA
6627 ATACAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 8 0.25
22 12 0.38
23 9 0.28
24 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TATATAAAAAATATAATATTT
Found at i:6637 original size:20 final size:20
Alignment explanation
Indices: 6559--6637 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 20
6549 ATATACGTAC
6559 ATATAAAAATATATATAAAAT
1 ATATAAAAATATA-ATAAAAT
* *
6580 A-A-ATAAAT-T-AT-TAAT
1 ATATAAAAATATAATAAAAT
***
6595 ATATAAAAATATAATATTTT
1 ATATAAAAATATAATAAAAT
6615 ATATAAAAA-ATAATACAAAT
1 ATATAAAAATATAATA-AAAT
6635 ATA
1 ATA
6638 AATGCATAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
15 4 0.09
16 3 0.07
17 5 0.11
18 2 0.05
19 13 0.30
20 16 0.36
21 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATAAAAATATAATAAAAT
Found at i:6893 original size:2 final size:2
Alignment explanation
Indices: 6886--6913 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6876 TTATAACTTC
6886 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
6914 GAGAAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7200 original size:20 final size:22
Alignment explanation
Indices: 7158--7206 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
7148 TATCTATATT
*
7158 TATTTATCAATATTTATACTTTA
1 TATTTATCAATA-TTATAATTTA
7181 TATTTAT-AATA-TATAATTTA
1 TATTTATCAATATTATAATTTA
7201 TATTTA
1 TATTTA
7207 AAATTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 14 0.56
22 4 0.16
23 7 0.28
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTTATCAATATTATAATTTA
Found at i:7215 original size:20 final size:20
Alignment explanation
Indices: 7169--7215 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7159 ATTTATCAAT
* *
7169 ATTTATACTTTATATTTATA
1 ATTTATAATTTATATTTAAA
*
7189 ATATATAATTTATATTTAAA
1 ATTTATAATTTATATTTAAA
7209 ATTTATA
1 ATTTATA
7216 TATAATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTATAATTTATATTTAAA
Found at i:7227 original size:33 final size:33
Alignment explanation
Indices: 7167--7229 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
7157 TTATTTATCA
* * *
7167 ATATTTATACTTTATATTTATAATATATAATTT
1 ATATTTAAAATTTATATTAATAATATATAATTT
7200 ATATTTAAAATTTATATATAAT-ATATATAA
1 ATATTTAAAATTTATAT-TAATAATATATAA
7230 AAATATGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (33 bp):
ATATTTAAAATTTATATTAATAATATATAATTT
Found at i:7242 original size:18 final size:18
Alignment explanation
Indices: 7215--7256 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
7205 TAAAATTTAT
* *
7215 ATAT-AATATATATAAAA
1 ATATGAATATAAAAAAAA
7232 ATATGAATATAAAAAAAA
1 ATATGAATATAAAAAAAA
*
7250 ATTTGAA
1 ATATGAA
7257 CTCATTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (18 bp):
ATATGAATATAAAAAAAA
Found at i:15475 original size:128 final size:129
Alignment explanation
Indices: 15220--15485 Score: 363
Period size: 128 Copynumber: 2.1 Consensus size: 129
15210 CCCTATGATT
* * * * * ***
15220 TAAACAAATATGAATCGTTTTTCATCTTTTATATTCCTATGGGTATCCGTAGGGGTATAAAAGAT
1 TAAATAAATATGAATCATTTTTAATCTTTTATATTCCAATGGATATCAACAGGGGTATAAAAGAT
* *
15285 TTCAAAAACTTTTCGTATCTTTTCGGGTTTCCATCAAGGTACGAAATAATTTTTTTC-CAAAAA
66 TTCAAAAACTTTTCGTATCTTTTCGGGTTTCCATCAAGGTACAAAATAATTTTTTTCAAAAAAA
* *
15348 TAAATAAATATTAATCATTTTTAATTTTTTATATTCCAATGGATATCAACAGGGGTATAAAAGAT
1 TAAATAAATATGAATCATTTTTAATCTTTTATATTCCAATGGATATCAACAGGGGTATAAAAGAT
* * * * *
15413 TTCAAAAACTTTTTGTATCTTTTTGGGTTTCCATTAAGGTACAAAATGATTTTTTTTAAAAAAA
66 TTCAAAAACTTTTCGTATCTTTTCGGGTTTCCATCAAGGTACAAAATAATTTTTTTCAAAAAAA
*
15477 TAATTAAAT
1 TAAATAAAT
15486 TAACTCTCAT
Statistics
Matches: 119, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
128 106 0.89
129 13 0.11
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (129 bp):
TAAATAAATATGAATCATTTTTAATCTTTTATATTCCAATGGATATCAACAGGGGTATAAAAGAT
TTCAAAAACTTTTCGTATCTTTTCGGGTTTCCATCAAGGTACAAAATAATTTTTTTCAAAAAAA
Found at i:16617 original size:32 final size:32
Alignment explanation
Indices: 16574--16639 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
16564 AACTTACGTG
*
16574 TTCCACGGGCTTCCATGGAGTGCGTGAGAGAT
1 TTCCACAGGCTTCCATGGAGTGCGTGAGAGAT
16606 TTCCACAGGCTTCCATGGAGTGCGTGAGAGAT
1 TTCCACAGGCTTCCATGGAGTGCGTGAGAGAT
16638 TT
1 TT
16640 TTATTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.20, C:0.21, G:0.32, T:0.27
Consensus pattern (32 bp):
TTCCACAGGCTTCCATGGAGTGCGTGAGAGAT
Found at i:25129 original size:46 final size:46
Alignment explanation
Indices: 25052--25145 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
25042 TAAAATATTT
* *
25052 TTAGCATTTTGTCGATTCTTTAAGAAGTGTTAAAAATTTCAAAACC
1 TTAGCATTTTGTCGATTCTTTAAGAAATGTTAAAAATATCAAAACC
*
25098 TTAGCATTTTGTCGATTCTTTGAGAAATGTTAAAAATATCAAAACC
1 TTAGCATTTTGTCGATTCTTTAAGAAATGTTAAAAATATCAAAACC
25144 TT
1 TT
25146 TCATATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (46 bp):
TTAGCATTTTGTCGATTCTTTAAGAAATGTTAAAAATATCAAAACC
Found at i:26243 original size:136 final size:136
Alignment explanation
Indices: 25999--26272 Score: 485
Period size: 136 Copynumber: 2.0 Consensus size: 136
25989 TGCACATAGT
* * *
25999 ATTCAGCAAAAATGTTAATAGAATAACATGTGAAATAATGTTATAAAATAATTCACACAAAGTGA
1 ATTCAGCAAAAATGTTAATACAACAACAAGTGAAATAATGTTATAAAATAATTCACACAAAGTGA
* *
26064 CAACACAGAAAAGGAGCGACAATCGAAATATATCTCACATTTGTCTTCGATTATCGAAAAAATAA
66 CAACACAGAAAAAGAGCGACAATCGAAATATATCTCACATTTGTCTTCGATTATCAAAAAAATAA
26129 CCGAAA
131 CCGAAA
*
26135 ATTCAGCAAAAATGTTAGTACAACAACAAGTGAAATAATGTTATAAAATAATTCACACAAAGTGA
1 ATTCAGCAAAAATGTTAATACAACAACAAGTGAAATAATGTTATAAAATAATTCACACAAAGTGA
26200 CAACACAGAAAAAGAGCGACAATCGAAATATATCTCACATTTGTCTTCGATTATCAAAAAAATAA
66 CAACACAGAAAAAGAGCGACAATCGAAATATATCTCACATTTGTCTTCGATTATCAAAAAAATAA
*
26265 TCGAAA
131 CCGAAA
26271 AT
1 AT
26273 AGGGGATAGC
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
136 131 1.00
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (136 bp):
ATTCAGCAAAAATGTTAATACAACAACAAGTGAAATAATGTTATAAAATAATTCACACAAAGTGA
CAACACAGAAAAAGAGCGACAATCGAAATATATCTCACATTTGTCTTCGATTATCAAAAAAATAA
CCGAAA
Found at i:28268 original size:20 final size:20
Alignment explanation
Indices: 28243--28280 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28233 GTAAAAACCC
*
28243 AGAATGTATCGATACATTGA
1 AGAATGCATCGATACATTGA
28263 AGAATGCATCGATACATT
1 AGAATGCATCGATACATT
28281 TGGGTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (20 bp):
AGAATGCATCGATACATTGA
Found at i:28312 original size:36 final size:36
Alignment explanation
Indices: 28265--28335 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
28255 TACATTGAAG
28265 AATGCATCGATACATTTGGGTACTTTTCCATACTTC
1 AATGCATCGATACATTTGGGTACTTTTCCATACTTC
28301 AATGCATCGATACATTTGGGTACTTTTCCATACTT
1 AATGCATCGATACATTTGGGTACTTTTCCATACTT
28336 TTCGCATTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
AATGCATCGATACATTTGGGTACTTTTCCATACTTC
Found at i:28974 original size:28 final size:29
Alignment explanation
Indices: 28865--29263 Score: 483
Period size: 29 Copynumber: 13.8 Consensus size: 29
28855 TTTTTTAAAA
* *
28865 AAAATAGTGCCACTAACTTGTGTGGGCTTTG
1 AAAAGAGTGCCACTGAC-T-TGTGGGCTTTG
*
28896 AAAAGAGTTGCCACCGACTCATGTGGGCTTTG
1 AAAAGAG-TGCCACTGACT--TGTGGGCTTTG
*
28928 AAAAGAGTGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
28957 AAAAG-GTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
28985 AAAAGAGTGCCACTAACTTGAGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
29014 -AAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGAGTGCCACTGACTT--GTGGGCTTTG
* *
29044 AAAA-TGTGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
29072 AAAGGA-TGCCACTTAC---TAGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
29097 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
29126 -AAAGGGTGCCACTGACTCGTGGGTTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
29154 AAAA-TGTGCTACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
29182 AAAAGAATGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
29211 AAAAGAGTGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
29240 AAAAGAGTGCCACTGATTTGTGGG
1 AAAAGAGTGCCACTGACTTGTGGG
29264 TGCCATTGAC
Statistics
Matches: 318, Mismatches: 37, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.04
26 9 0.03
28 113 0.36
29 117 0.37
30 21 0.07
31 19 0.06
32 26 0.08
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (29 bp):
AAAAGAGTGCCACTGACTTGTGGGCTTTG
Found at i:28989 original size:57 final size:57
Alignment explanation
Indices: 28865--30046 Score: 1357
Period size: 57 Copynumber: 20.5 Consensus size: 57
28855 TTTTTTAAAA
* * *
28865 AAAATAGTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCGACTCATGTGGGCTTTG
1 AAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAG-G-TGCCACTGACT--TGTGGGCTTTG
*
28928 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
28985 AAAAGAGTGCCACTAACTTGAGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTT--GTGGGCTTTG
* * * *
29044 AAAA-TGTGCCACTAACTTGTGGGCTTTG-AAAGGATGCCACTTAC---TAGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTG
* * *
29097 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTCGTGGGTTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
* * * *
29154 AAAA-TGTGCTACTAACTTGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTG
*
29211 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGA-TT-T--G---TG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTG
* *
29262 ----G-GTGCCATTGACTTGCATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTG--TGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
* *
29316 AAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCATGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTG--TGGGCTTTG
* *
29375 -AAAGGGTGTCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
* * * * *
29431 AAAAGAATGCCACTGATTTATGGGCTTTGAAAAAAGTGCCATTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
29489 AAAAGAGTTGCCACTGACTTGTGTGGGCTTTGAAAAGAATGCCACTGACTTGTGTGGGCTTTA
1 AAAAGAG-TGCCACTGAC-T-TGTGGGCTTTGAAAAG-GTGCCACTGAC-T-TGTGGGCTTTG
29552 AAAAGAGTGCCACTGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACT--TGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTG
* * *
29612 -AAAGGGTGCCACTGATTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCATGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTG--TGGGCTTTG
* * *
29670 -AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGTGTACCACTGACTTGTGGGCTTTA
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTG
* * *
29726 AAAAGAGTACCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTGACTTGTGGGTTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTG
* * * *
29784 CAAAGAGTTACCACCGACTCGTGTGGGCTTTGCAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAG-TGCCACTGACT--TGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTG
* * * *
29845 AAATGAGTGCCACTGACTTGTGAGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
* ** ** * * *
29902 AAAAGAGTGCCACCGACTCATGTTCTTTGAAAAGGTGCCACCGACTCGTGTGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
* *
29959 AAAAGAGTGCCATTGACTTGTGGGCTTTGAAAAGAGTGCCATTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTG
*
30017 -AAAGGGTGCCACTGACTTGTGGGCTTTGAA
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAA
30047 GAGATGAACG
Statistics
Matches: 975, Mismatches: 100, Indels: 94
0.83 0.09 0.08
Matches are distributed among these distances:
46 12 0.01
47 11 0.01
48 15 0.02
49 1 0.00
51 3 0.00
53 12 0.01
54 34 0.03
55 4 0.00
56 57 0.06
57 315 0.32
58 255 0.26
59 79 0.08
60 25 0.03
61 79 0.08
62 40 0.04
63 33 0.03
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (57 bp):
AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
Found at i:29329 original size:29 final size:29
Alignment explanation
Indices: 29263--30046 Score: 969
Period size: 29 Copynumber: 26.9 Consensus size: 29
29253 TGATTTGTGG
* *
29263 GTGCCATTGACTTGCATGGGCTTTG-AAAGG
1 GTGCCACTGACTTG--TGGGCTTTGAAAAGA
29293 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
29322 GTGCCACTGATTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
29350 GTGCCACTGACTTGCATGGGCTTTG-AAAGG
1 GTGCCACTGACTTG--TGGGCTTTGAAAAGA
*
29380 GTGTCACTGACTTGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
29408 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
29437 ATGCCACTGATTTATGGGCTTTGAAAAAA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
29466 GTGCCATTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
29495 GTTGCCACTGACTTGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGAC-T-TGTGGGCTTTGAAAAGA
* *
29527 ATGCCACTGACTTGTGTGGGCTTTAAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAAGA
29558 GTGCCACTGACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGACT--TGTGGGCTTTGAAAAGA
*
29589 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
29617 GTGCCACTGATTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
29645 GTGCCACTGACTTGCATGGGCTTTG-AAAGG
1 GTGCCACTGACTTG--TGGGCTTTGAAAAGA
*
29675 GTGCCACTGACTTGTGGGCTTTG-AAAGT
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
29703 GTACCACTGACTTGTGGGCTTTAAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
29732 GTACCACTGACTTGTGGGCTTTAAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
29761 GTGCCACTGACTTGTGGGTTTTGCAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
29790 GTTACCACCGACTCGTGTGGGCTTTGCAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
*
29822 GTGCCACTGACTTGTGGGCTTTGAAATGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
29851 GTGCCACTGACTTGTGAGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
29879 GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* ** **
29908 GTGCCACCGACTCATGTTCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
29936 GTGCCACCGACTCGTGTGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
29965 GTGCCATTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
29994 GTGCCATTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
30022 GTGCCACTGACTTGTGGGCTTTGAA
1 GTGCCACTGACTTGTGGGCTTTGAA
30047 GAGATGAACG
Statistics
Matches: 677, Mismatches: 59, Indels: 37
0.88 0.08 0.05
Matches are distributed among these distances:
28 216 0.32
29 262 0.39
30 87 0.13
31 78 0.12
32 34 0.05
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:29479 original size:86 final size:86
Alignment explanation
Indices: 29279--30046 Score: 938
Period size: 86 Copynumber: 8.8 Consensus size: 86
29269 TTGACTTGCA
* *
29279 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTT
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT
* *
29343 TGAAAGGGTGCCACTGACTTG
66 TGAAAGAGTGCCACTGATTTG
* *
29364 CATGGGCTTTG-AAAGGGTGTCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGC
1 --TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
29427 TTTGAAAAGAATGCCACTGATTTA
64 TTTG-AAAGAGTGCCACTGATTTG
* *
29451 TGGGCTTTGAAAAAAGTGCCATTGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGTGGG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGAC-T-TGTGGG
*
29516 CTTTGAAAAGAATGCCACTGACTTGTG
63 CTTTG-AAAGAGTGCCACTGA-TT-TG
*
29543 TGGGCTTTAAAAAGAGTGCCACTGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TGGGCTTTGAAAAGAGTGCCACTGACT--TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
29608 TTTGAAAGGGTGCCACTGATTTG
64 TTTGAAAGAGTGCCACTGATTTG
* *
29631 TGGGCTTTG-AAAGGGTGCCACTGACTTGCATGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG--TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
29694 TTTGAAAGTGTACCACTGACTTG
64 TTTGAAAGAGTGCCACTGATTTG
* * * *
29717 TGGGCTTTAAAAAGAGTACCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTGACTTGTGGGTTT
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT
* * *
29782 TGCAAAGAGTTACCACCGACTCGTG
66 TG-AAAGAG-TGCCACTGA-T-TTG
* * *
29807 TGGGCTTTGCAAAGAGTGCCACTGACTTGTGGGCTTTGAAATGAGTGCCACTGACTTGTGAGCTT
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT
* * *
29872 TGAAAGGGTGCCACTAACTTG
66 TGAAAGAGTGCCACTGATTTG
* ** ** * * *
29893 TGGGCTTTGAAAAGAGTGCCACCGACTCATGTTCTTTGAAAAG-GTGCCACCGACTCGTGTGCTT
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT
* *
29957 TGAAAAGAGTGCCATTGACTTG
66 TG-AAAGAGTGCCACTGATTTG
* *
29979 TGGGCTTTGAAAAGAGTGCCATTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTT
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT
30043 TGAA
66 TGAA
30047 GAGATGAACG
Statistics
Matches: 594, Mismatches: 67, Indels: 42
0.84 0.10 0.06
Matches are distributed among these distances:
85 45 0.08
86 234 0.39
87 104 0.18
88 34 0.06
89 8 0.01
90 102 0.17
91 13 0.02
92 26 0.04
93 10 0.02
94 18 0.03
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (86 bp):
TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT
TGAAAGAGTGCCACTGATTTG
Found at i:30167 original size:15 final size:15
Alignment explanation
Indices: 30147--30177 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30137 TTACCTGAAT
*
30147 GACGCAGGGTTTGTA
1 GACGCAGGATTTGTA
30162 GACGCAGGATTTGTA
1 GACGCAGGATTTGTA
30177 G
1 G
30178 GGCTTGAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.39, T:0.26
Consensus pattern (15 bp):
GACGCAGGATTTGTA
Found at i:31319 original size:20 final size:20
Alignment explanation
Indices: 31295--31343 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
31285 TTTTTCTTAG
* *
31295 TTTTTCATTTTTTT-TTTTG
1 TTTTTTATTTTTTTGTTTTA
*
31314 TTTTTTGTTTTTTTGTTTTA
1 TTTTTTATTTTTTTGTTTTA
31334 TTTTTT-TTTT
1 TTTTTTATTTT
31344 GGTGTAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.04, C:0.02, G:0.06, T:0.88
Consensus pattern (20 bp):
TTTTTTATTTTTTTGTTTTA
Found at i:31326 original size:15 final size:14
Alignment explanation
Indices: 31302--31342 Score: 64
Period size: 15 Copynumber: 2.8 Consensus size: 14
31292 TAGTTTTTCA
31302 TTTTTTTTTTTGTT
1 TTTTTTTTTTTGTT
31316 TTTTGTTTTTTTGTT
1 TTTT-TTTTTTTGTT
31331 TTATTTTTTTTT
1 TT-TTTTTTTTT
31343 TGGTGTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.16
15 19 0.76
16 2 0.08
ACGTcount: A:0.02, C:0.00, G:0.07, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTTTGTT
Found at i:45172 original size:20 final size:20
Alignment explanation
Indices: 45147--45218 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
45137 GAATGTATCG
*
45147 TGTATCGATACATTGAAGAA
1 TGTATCGATACATTAAAGAA
* *
45167 TGTATCGATACATTCATA-CA
1 TGTATCGATACATT-AAAGAA
45187 TGTATCGATACATTAAAGAA
1 TGTATCGATACATTAAAGAA
*
45207 TATATCGATACA
1 TGTATCGATACA
45219 GTTGGATACT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 2 0.05
20 41 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATTAAAGAA
Found at i:45857 original size:153 final size:151
Alignment explanation
Indices: 45588--45865 Score: 332
Period size: 153 Copynumber: 1.8 Consensus size: 151
45578 GGTAATCATC
* * *
45588 GGATCACTTTTATGCCAAAGGTTCACTTTTAGGATAGGTTCATCCTTTCACATCATTTTCGTGTT
1 GGATCACTTTTATGCCAAAGCTGCACATTTAGGATAGGTTCATCCTTTCACATCATTTTCGTGTT
* * * *
45653 TTAAGGTTATTAAGATACTTTCACATCAAAGGTATATCGAAGGGTATTTTGGTCATTTTTCCATA
66 TTAAAGTTATCAAGATACTTTCACATCAAAGGTATATCGAAGGGCATTTTGGTAATTTTTCCATA
45718 ATCGAATCCTAGGTCACCATT
131 ATCGAATCCTAGGTCACCATT
* * *
45739 GGATCACTTTTATGCGAAAGCTGCACATTTAGGATAGGTTTGA-CCTTTTTCA-ATC-TTTTTGT
1 GGATCACTTTTATGCCAAAGCTGCACATTTAGGATAGG-TTCATCC--TTTCACATCATTTTCGT
* * * *
45801 GCTCTTTAAAGTTATCGAGATACTTTCATATCGAAA-GTATA-CGCGATGGCATTTTGGTAATTT
63 G-T-TTTAAAGTTATCAAGATACTTTCACATC-AAAGGTATATCG-AAGGGCATTTTGGTAATTT
45864 TT
124 TT
45866 TCTCAACCAA
Statistics
Matches: 106, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
151 43 0.41
152 9 0.08
153 51 0.48
154 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (151 bp):
GGATCACTTTTATGCCAAAGCTGCACATTTAGGATAGGTTCATCCTTTCACATCATTTTCGTGTT
TTAAAGTTATCAAGATACTTTCACATCAAAGGTATATCGAAGGGCATTTTGGTAATTTTTCCATA
ATCGAATCCTAGGTCACCATT
Found at i:47685 original size:23 final size:23
Alignment explanation
Indices: 47659--47702 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
47649 GTCCTTTAGG
*
47659 TCATGTTCCATGATCTAGGGACT
1 TCATCTTCCATGATCTAGGGACT
*
47682 TCATCTTTCATGATCTAGGGA
1 TCATCTTCCATGATCTAGGGA
47703 TTTTGAGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
TCATCTTCCATGATCTAGGGACT
Found at i:47783 original size:58 final size:58
Alignment explanation
Indices: 47682--47925 Score: 178
Period size: 58 Copynumber: 4.2 Consensus size: 58
47672 TCTAGGGACT
* * * *
47682 TCATCTTTCATGATCTAGGGATTTTGAGAT--AATTTTATGAATTTTGATGTCATTTAAG
1 TCATTTTTCATGATCTAGGAACTTT-A-ATGCAATTTTATAAATTTTGATGTCATTTAAG
* * * * *
47740 TAATTTTTCATGATATAGGAACTTTAATGCAATTTTATAAATTTTGAAGTAATTTAGG
1 TCATTTTTCATGATCTAGGAACTTTAATGCAATTTTATAAATTTTGATGTCATTTAAG
* * ** * * * *
47798 CCATTTTTCATGACCTAGGAACTTTTGTGCAAATATAT-AATGTTGGA-GTCATTTAGG
1 TCATTTTTCATGATCTAGGAACTTTAATGCAATTTTATAAAT-TTTGATGTCATTTAAG
* * * * * *
47855 TTA-TTTTCAATGATCCAGAAACTTTCATGCAATTTTATACATTTT-TTAGAT-ATTTAAG
1 TCATTTTTC-ATGATCTAGGAACTTTAATGCAATTTTATAAATTTTGAT-G-TCATTTAAG
47913 TCATTTTTCATGA
1 TCATTTTTCATGA
47926 CTTAGAAATT
Statistics
Matches: 144, Mismatches: 33, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
56 7 0.05
57 38 0.26
58 93 0.65
59 6 0.04
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (58 bp):
TCATTTTTCATGATCTAGGAACTTTAATGCAATTTTATAAATTTTGATGTCATTTAAG
Found at i:49978 original size:19 final size:21
Alignment explanation
Indices: 49951--50001 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
49941 ATATTTATAT
*
49951 TTTATATATAT-TTA-AATTA
1 TTTAAATATATGTTATAATTA
*
49970 TTTAAATATAATGTTATAATTT
1 TTTAAATAT-ATGTTATAATTA
49992 TTTAAATATA
1 TTTAAATATA
50002 CAGATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.30
20 2 0.07
21 4 0.15
22 13 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAAATATATGTTATAATTA
Found at i:50823 original size:24 final size:23
Alignment explanation
Indices: 50765--50823 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
50755 TTATAAATTT
*
50765 TTAT-ATTTCATATTATAATTTTA
1 TTATAATTT-ATATTATAATTTAA
**
50788 TTATCTTATTATATTATAATTTAA
1 TTATAAT-TTATATTATAATTTAA
50812 TTAATAATTTAT
1 TT-ATAATTTAT
50824 GTTGGTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 4 0.14
24 20 0.69
25 5 0.17
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATAATTTATATTATAATTTAA
Found at i:51212 original size:16 final size:15
Alignment explanation
Indices: 51181--51245 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
51171 TTTTGATCGA
51181 TTTTAAATATAATTT
1 TTTTAAATATAATTT
*
51196 TTTTAAATTTGAATTT
1 TTTTAAATAT-AATTT
*
51212 TAATTTATAATATTATTT
1 T--TTTA-AATATAATTT
* *
51230 TATTAAAAAT-ATTT
1 TTTTAAATATAATTT
51244 TT
1 TT
51246 ATTTTAAGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 5 0.12
15 13 0.32
16 9 0.22
18 9 0.22
19 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTTAAATATAATTT
Found at i:51754 original size:16 final size:16
Alignment explanation
Indices: 51725--51775 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
51715 AATATTTTTC
* *
51725 ATAATATAATATAATT
1 ATAATAAAAAATAATT
51741 ATAATAAAAAATAA-T
1 ATAATAAAAAATAATT
* * *
51756 ATTATTAAAAATATTT
1 ATAATAAAAAATAATT
51772 ATAA
1 ATAA
51776 GTCAAGTCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATAAAAAATAATT
Found at i:52222 original size:20 final size:20
Alignment explanation
Indices: 52199--52270 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 20
52189 TTATAATTAA
52199 ATTTAAATAAAAATTTTATT
1 ATTTAAATAAAAATTTTATT
* *
52219 ATTTAAGTAAAAATTTAAATAT
1 ATTTAAATAAAAATTT-TAT-T
52241 ATTTAAAAAATAAAAATTTT-TT
1 ATTT---AAATAAAAATTTTATT
*
52263 ATCTAAAT
1 ATTTAAAT
52271 TTAGTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
19 4 0.10
20 15 0.36
21 2 0.05
22 9 0.21
23 1 0.02
25 11 0.26
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (20 bp):
ATTTAAATAAAAATTTTATT
Found at i:53217 original size:2 final size:2
Alignment explanation
Indices: 53206--53244 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
53196 TTTCAAATTT
*
53206 TA TA -A TA TA TA TA TA TA TA AA 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
53245 GAATTTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:53727 original size:21 final size:21
Alignment explanation
Indices: 53689--53728 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53679 ATATATAATA
**
53689 TTAAAAAATAAATTTTAAATT
1 TTAAAAAATAAAAATTAAATT
*
53710 TTAAAAATTAAAAATTAAA
1 TTAAAAAATAAAAATTAAA
53729 AAAAAGTGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAAAAATAAAAATTAAATT
Found at i:54093 original size:21 final size:21
Alignment explanation
Indices: 54069--54109 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
54059 ATTTGTAGTA
54069 ATATTTATTTTAAAAATAATG
1 ATATTTATTTTAAAAATAATG
*
54090 ATATTTATTTTAAATATAAT
1 ATATTTATTTTAAAAATAAT
54110 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATATTTATTTTAAAAATAATG
Found at i:54114 original size:19 final size:19
Alignment explanation
Indices: 54067--54114 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
54057 TTATTTGTAG
54067 TAAT-ATTTATTTTAAAAA
1 TAATAATTTATTTTAAAAA
*
54085 TAATGATATTTATTTTAAATA
1 TAAT-A-ATTTATTTTAAAAA
54106 TAATAATTT
1 TAATAATTT
54115 TTTATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.15
19 4 0.15
20 1 0.04
21 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATAATTTATTTTAAAAA
Found at i:54156 original size:54 final size:52
Alignment explanation
Indices: 54090--54257 Score: 180
Period size: 54 Copynumber: 3.1 Consensus size: 52
54080 AAAAATAATG
54090 ATATTTATTTTAAATATAATAATTTTTTATTTAATAATTAAATTTTTATATAAAA
1 ATATTTATTTTAAA-ATAATAA-TTTTTATTTAATAATTAAATTTTTATA-AAAA
* * *
54145 ATATTTA-TTTAAAGAAAATAATTTTTATCTT-ATAATTAACTTTTAATAAAAA
1 ATATTTATTTTAAA-ATAATAATTTTTAT-TTAATAATTAAATTTTTATAAAAA
* * *
54197 ATTATTTATTTTGAAAATTATGAA-TTTCATTTAATAATTAAATTTTTATGAAAAT
1 A-TATTTATTTT-AAAATAAT-AATTTTTATTTAATAATTAAATTTTTAT-AAAAA
54252 ATATTT
1 ATATTT
54258 TTAACACCTA
Statistics
Matches: 96, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
52 5 0.05
53 30 0.31
54 44 0.46
55 17 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (52 bp):
ATATTTATTTTAAAATAATAATTTTTATTTAATAATTAAATTTTTATAAAAA
Found at i:54203 original size:53 final size:54
Alignment explanation
Indices: 54090--54242 Score: 154
Period size: 53 Copynumber: 2.8 Consensus size: 54
54080 AAAAATAATG
* * *
54090 ATATTTATTTTAAATATAATAATTTTTTATTTAATAATTAAATTTTTATATAAAA
1 ATATTTA-TTTAAAGAAAATAATTTTTTATTTAATAATTAAATTTTAATATAAAA
*
54145 ATATTTATTTAAAGAAAATAA-TTTTTATCTT-ATAATTAACTTTTAATA-AAAA
1 ATATTTATTTAAAGAAAATAATTTTTTAT-TTAATAATTAAATTTTAATATAAAA
* * * *
54197 ATTATTTATTT--TGAAAATTATGAATTTCATTTAATAATTAAATTTT
1 A-TATTTATTTAAAGAAAATAAT--TTTTTATTTAATAATTAAATTTT
54243 TATGAAAATA
Statistics
Matches: 83, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
51 7 0.08
52 5 0.06
53 33 0.40
54 31 0.37
55 7 0.08
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (54 bp):
ATATTTATTTAAAGAAAATAATTTTTTATTTAATAATTAAATTTTAATATAAAA
Found at i:55706 original size:18 final size:18
Alignment explanation
Indices: 55683--55725 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
55673 TTTTTAAAGG
55683 TATAATAAAAATAAAAAA
1 TATAATAAAAATAAAAAA
*
55701 TATAATTAAAATAAAAAA
1 TATAATAAAAATAAAAAA
*
55719 TAAAATA
1 TATAATA
55726 TGTAATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TATAATAAAAATAAAAAA
Found at i:61995 original size:3 final size:3
Alignment explanation
Indices: 61987--62027 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
61977 TTGTCGTAGT
61987 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
62028 TTAATTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:63476 original size:15 final size:15
Alignment explanation
Indices: 63439--63479 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
63429 TAGGTAAATA
63439 GGTGGTGGATGCACG
1 GGTGGTGGATGCACG
* * *
63454 AGTTGTGGATGCATG
1 GGTGGTGGATGCACG
63469 GGTGGTGGATG
1 GGTGGTGGATG
63480 GACAAGATCA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.15, C:0.07, G:0.51, T:0.27
Consensus pattern (15 bp):
GGTGGTGGATGCACG
Found at i:65151 original size:13 final size:13
Alignment explanation
Indices: 65135--65165 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
65125 ATAATTCATC
65135 ATGTATCGATACA
1 ATGTATCGATACA
65148 ATGTATCGATACA
1 ATGTATCGATACA
65161 ATGTA
1 ATGTA
65166 CCATGTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:65268 original size:13 final size:13
Alignment explanation
Indices: 65250--65276 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
65240 TACTATGAAC
65250 ATGTATCGATACA
1 ATGTATCGATACA
65263 ATGTATCGATACA
1 ATGTATCGATACA
65276 A
1 A
65277 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:71766 original size:21 final size:21
Alignment explanation
Indices: 71724--71766 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
71714 CTTGTTTTTC
* *
71724 TTAGCTAATTCATTATTTTCA
1 TTAGCTAATTCATTAATATCA
71745 TTAGCTAACTTC-TTAATATCA
1 TTAGCTAA-TTCATTAATATCA
71766 T
1 T
71767 CTTGCAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (21 bp):
TTAGCTAATTCATTAATATCA
Found at i:74005 original size:13 final size:13
Alignment explanation
Indices: 73987--74017 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
73977 ACAATTCATC
*
73987 ATGTATCGATACA
1 ATGTATCAATACA
74000 ATGTATCAATACA
1 ATGTATCAATACA
74013 ATGTA
1 ATGTA
74018 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:74106 original size:19 final size:19
Alignment explanation
Indices: 74063--74117 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
74053 TGCCAGTTTT
* **
74063 ATGTATTGATACAATTGTCC
1 ATGTATCGATACAA-TGAAC
74083 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
74102 ATGTATCGATACAATG
1 ATGTATCGATACAATG
74118 TATCAATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:78446 original size:28 final size:27
Alignment explanation
Indices: 78414--78503 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 27
78404 AATATTTTTT
78414 ATACCATAAACTAATTACCCAAAAACTA
1 ATACCATAAACTAATTACCCAAAAA-TA
* **
78442 ATACCCTAAACCTAATTCAACATAATAAATA
1 ATACCATAAA-CTAATT--ACCCAA-AAATA
*
78473 ATTACTATAAACTAATTACCCAAAAATA
1 A-TACCATAAACTAATTACCCAAAAATA
78501 ATA
1 ATA
78504 ATAAATAACT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
27 2 0.04
28 15 0.30
29 10 0.20
31 13 0.26
32 10 0.20
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (27 bp):
ATACCATAAACTAATTACCCAAAAATA
Found at i:79430 original size:33 final size:33
Alignment explanation
Indices: 79393--79473 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
79383 TTTTCACAAT
* *
79393 TTGTATTGATACATTATTCATCGTATCGATACA
1 TTGTATCGATACATTATTCATCATATCGATACA
* *
79426 TTGTATCGATACATTGTTCATTATATCGATACA
1 TTGTATCGATACATTATTCATCATATCGATACA
79459 TTGTATCGATACATT
1 TTGTATCGATACATT
79474 CTGGGTTTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (33 bp):
TTGTATCGATACATTATTCATCATATCGATACA
Found at i:79433 original size:13 final size:13
Alignment explanation
Indices: 79415--79473 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
79405 ATTATTCATC
79415 GTATCGATACATT
1 GTATCGATACATT
79428 GTATCGATACATT
1 GTATCGATACATT
79441 G--T---T-CATT
1 GTATCGATACATT
*
79448 ATATCGATACATT
1 GTATCGATACATT
79461 GTATCGATACATT
1 GTATCGATACATT
79474 CTGGGTTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
7 4 0.11
8 1 0.03
9 1 0.03
11 1 0.03
12 1 0.03
13 30 0.79
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:79452 original size:20 final size:20
Alignment explanation
Indices: 79424--79462 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
79414 CGTATCGATA
*
79424 CATTGTATCGATACATTGTT
1 CATTATATCGATACATTGTT
79444 CATTATATCGATACATTGT
1 CATTATATCGATACATTGT
79463 ATCGATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (20 bp):
CATTATATCGATACATTGTT
Found at i:81955 original size:28 final size:28
Alignment explanation
Indices: 81923--81996 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
81913 TTTCACAATT
*
81923 GGGGATACTCCAACCCCGTTATTTCAT-C
1 GGGGATACTCCAACCCCGTTATTT-ATGA
* * *
81951 GGGGATACTTCAATCCCGTTATTTTTGA
1 GGGGATACTCCAACCCCGTTATTTATGA
81979 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
81997 GCTTTATATC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTATGA
Found at i:81988 original size:107 final size:107
Alignment explanation
Indices: 81872--82151 Score: 364
Period size: 108 Copynumber: 2.6 Consensus size: 107
81862 TTTCTTAATC
* * *
81872 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATTGGGGATACTCCAAC
* * **
81937 CCCGTTATT-TCATCGGGGATACTTCAATCCCGTTATTTTTGA
66 CCCGTT-TTGTCATCGGAGATACTCCAATCCCGTTATTTTCAA
** * ** * * *
81979 GGGGATACTCCAACCCCGGCTTTATATCTAAAATATTGATTTTTTCATAATTGGGGGTACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATA-CCAATTTTTCACAATTGGGGATACTCCAA
82044 CCCCGTTTTGTCATCGGAGATACTCCAATCCCGTTATTTTCAA
65 CCCCGTTTTGTCATCGGAGATACTCCAATCCCGTTATTTTCAA
* * * *
82087 AGGGATACTTCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATGCTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATTGGGGATACTCCAAC
82152 TCTGATTTTA
Statistics
Matches: 144, Mismatches: 27, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
107 54 0.38
108 90 0.62
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATTGGGGATACTCCAAC
CCCGTTTTGTCATCGGAGATACTCCAATCCCGTTATTTTCAA
Found at i:82068 original size:28 final size:27
Alignment explanation
Indices: 82036--82109 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
82026 TAATTGGGGG
**
82036 TACTCCAACCCCGTTTTGTCATCGGAGA
1 TACTCCAACCCCGTTTTGTCAAAGG-GA
* *
82064 TACTCCAATCCCGTTATTTTCAAAGGGA
1 TACTCCAACCCCGTT-TTGTCAAAGGGA
*
82092 TACTTCAACCCCGATTTT
1 TACTCCAACCCCG-TTTT
82110 ATTTCTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
28 29 0.76
29 9 0.24
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (27 bp):
TACTCCAACCCCGTTTTGTCAAAGGGA
Found at i:82159 original size:51 final size:51
Alignment explanation
Indices: 82088--82202 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 51
82078 TATTTTCAAA
* * * * * *
82088 GGGATACTTCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCG
1 GGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTCTCACAATCG
*
82139 GGGATGCTCCAACTCTGATTTTATTTCCAAAACACCAATTTCTCACAATCG
1 GGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTCTCACAATCG
82190 GGGATACTCCAAC
1 GGGATACTCCAAC
82203 CCCATTATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTCTCACAATCG
Found at i:82351 original size:79 final size:79
Alignment explanation
Indices: 82138--82515 Score: 363
Period size: 79 Copynumber: 4.8 Consensus size: 79
82128 TTTCACAATC
* * * * *
82138 GGGGATGCTCCAA-CTCTGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCTC-GATTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACTCCAA
82202 CCCCATTA-TTTC-A
65 CCCCATTATTTTCGA
* * *** * * * * *
82215 TGGGGATACTCTAACATCGGCGTTA-TTTCTAAAGCATCGATTTTCCACAAT-AGGGGATACTCC
1 -GGGGATACTCCAACCTCGATTTTATTTTC-AAAACACCAATTTTTCATAATCA-GGGATACTCC
*
82278 AACCCCGTTATTTTCGA
63 AACCCCATTATTTTCGA
* *
82295 GGGGATACTCAAACCTCGATTTTATTTTCAAAACACCAATTTTTTATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACTCCAAC
** *
82360 CCTGTTATTTCCGA
66 CCCATTATTTTCGA
* * * * *
82374 GGGAATACTCCAACCCCGATTTTATTTTTTAAAATACCAATTTTTTTATAATCAGGGATACTCCA
1 GGGGATACTCCAACCTCGATTTTA-TTTTCAAAACACCAA-TTTTTCATAATCAGGGATACTCCA
* *
82439 ACCCTATTATTTTCAA
64 ACCCCATTATTTTCGA
* * * *
82455 GGGGATACTCCAACCCCGATTTTA-TTTCTAGAACACCGATTTTTCATAATCGGGGATACTC
1 GGGGATACTCCAACCTCGATTTTATTTTC-AAAACACCAATTTTTCATAATCAGGGATACTC
82516 TAGCCCGTTG
Statistics
Matches: 248, Mismatches: 42, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
77 3 0.01
78 50 0.20
79 109 0.44
80 26 0.10
81 60 0.24
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACTCCAAC
CCCATTATTTTCGA
Found at i:82448 original size:26 final size:28
Alignment explanation
Indices: 82419--82470 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
82409 ACCAATTTTT
82419 TTATAATC-A-GGGATACTCCAACCCTA
1 TTATAATCAAGGGGATACTCCAACCCTA
**
82445 TTATTTTCAAGGGGATACTCCAACCC
1 TTATAATCAAGGGGATACTCCAACCC
82471 CGATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 1 0.05
28 15 0.68
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (28 bp):
TTATAATCAAGGGGATACTCCAACCCTA
Found at i:83699 original size:36 final size:34
Alignment explanation
Indices: 83628--83715 Score: 101
Period size: 35 Copynumber: 2.6 Consensus size: 34
83618 AATTTAAAAC
*
83628 TTATAATATTTTATTTTATTAAATTAAATTATTA
1 TTATAATATTTTATTTTATTAAAATAAATTATTA
83662 TTATAAGTATTTTATTTT-TATAAAAT-AATTATT-
1 TTATAA-TATTTTATTTTAT-TAAAATAAATTATTA
* *
83695 TTATTATAATTATATTTTATT
1 TTATAAT-ATTTTATTTTATT
83716 TAAGTAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
32 1 0.02
33 15 0.32
34 15 0.32
35 16 0.34
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (34 bp):
TTATAATATTTTATTTTATTAAAATAAATTATTA
Found at i:84351 original size:14 final size:14
Alignment explanation
Indices: 84328--84357 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
84318 CCACCATCAA
84328 TCTTTCTTTTCTTT
1 TCTTTCTTTTCTTT
*
84342 TCTTTTTTTTCTTT
1 TCTTTCTTTTCTTT
84356 TC
1 TC
84358 CATCACCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TCTTTCTTTTCTTT
Found at i:85700 original size:21 final size:20
Alignment explanation
Indices: 85675--85714 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
85665 ATATAAATTT
*
85675 TAATAACATAATATTTTTAAA
1 TAATAAAATAA-ATTTTTAAA
85696 TAATAAAATAAATTTTTAA
1 TAATAAAATAAATTTTTAA
85715 TTCAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATAAAATAAATTTTTAAA
Found at i:86197 original size:2 final size:2
Alignment explanation
Indices: 86143--86183 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
86133 ATCCCCCCTG
* *
86143 TC TC TC TC TC TC TC TC TC TC TT TC TC TT TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
86184 ATCGATCGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:87575 original size:38 final size:38
Alignment explanation
Indices: 87533--87618 Score: 145
Period size: 38 Copynumber: 2.3 Consensus size: 38
87523 GTGATTATTA
* *
87533 GGTGATATTCCATTTCTCTTTATTCCCCCTTGTTTTTT
1 GGTGATATTCCATATCTCCTTATTCCCCCTTGTTTTTT
*
87571 GGTGATATTCCATATCTCCTTATTGCCCCTTGTTTTTT
1 GGTGATATTCCATATCTCCTTATTCCCCCTTGTTTTTT
87609 GGTGATATTC
1 GGTGATATTC
87619 AGTCTCATTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.13, C:0.22, G:0.14, T:0.51
Consensus pattern (38 bp):
GGTGATATTCCATATCTCCTTATTCCCCCTTGTTTTTT
Found at i:90896 original size:14 final size:14
Alignment explanation
Indices: 90879--90917 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
90869 TAAATAGAAT
*
90879 TTTAAAAATATATA
1 TTTAAAAATATAAA
90893 TTTAAAAATGATAAA
1 TTTAAAAAT-ATAAA
*
90908 TTAAAAAATA
1 TTTAAAAATA
90918 AGTGAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TTTAAAAATATAAA
Found at i:91732 original size:30 final size:30
Alignment explanation
Indices: 91696--91760 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
91686 TGAGATTTTT
* * *
91696 TTTGTCAATTTTTTAATTAAATTAATTTCA
1 TTTGTCAATTCTGTAACTAAATTAATTTCA
91726 TTTGTCAATTCTGTAACTAAATTAATTTCA
1 TTTGTCAATTCTGTAACTAAATTAATTTCA
91756 TTTGT
1 TTTGT
91761 GATTAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTGTCAATTCTGTAACTAAATTAATTTCA
Found at i:95038 original size:19 final size:19
Alignment explanation
Indices: 94995--95038 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
94985 TCGTAGTTAT
94995 TTTTTTAAAAGAATGATAG
1 TTTTTTAAAAGAATGATAG
** * *
95014 CGTTTTAAGAGAGTGATAG
1 TTTTTTAAAAGAATGATAG
95033 TTTTTT
1 TTTTTT
95039 TTAAATATGA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.45
Consensus pattern (19 bp):
TTTTTTAAAAGAATGATAG
Found at i:95665 original size:75 final size:75
Alignment explanation
Indices: 95520--95666 Score: 199
Period size: 75 Copynumber: 2.0 Consensus size: 75
95510 GAGTTTATTA
* * *
95520 CACCAGGCAGAAACCAATGCTGTTTGGCATTCATTACACCTCCCTCTTCAAATAGAAACAATCTT
1 CACCAGGCAGAAACCAATGCTATTTAGCATTCATTACACCTCCCTCTTCAAAAAGAAACAATCTT
*
95585 TGTCCCATTG
66 AGTCCCATTG
* * *
95595 CACCAGGCAGAAACCAATGTTATTTAGTATTCATTGCACCTCCCTCTTCAAACAAG-AACAAT-T
1 CACCAGGCAGAAACCAATGCTATTTAGCATTCATTACACCTCCCTCTTCAAA-AAGAAACAATCT
95658 TGAGTCCCA
65 T-AGTCCCA
95667 ACCAAGTAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
74 2 0.03
75 59 0.94
76 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (75 bp):
CACCAGGCAGAAACCAATGCTATTTAGCATTCATTACACCTCCCTCTTCAAAAAGAAACAATCTT
AGTCCCATTG
Found at i:96298 original size:19 final size:18
Alignment explanation
Indices: 96264--96305 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 18
96254 ACATCTTGAA
96264 AAAAATATATTTTTTTAT
1 AAAAATATATTTTTTTAT
96282 AAAAATTATTATATTTTTTA-
1 AAAAA-TA-TAT-TTTTTTAT
96302 AAAA
1 AAAA
96306 CAGTTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.24
19 2 0.10
20 7 0.33
21 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAAATATATTTTTTTAT
Found at i:96722 original size:20 final size:19
Alignment explanation
Indices: 96675--96722 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
96665 AAAAATTATC
96675 AAATAT-TTTTTTATTTTA
1 AAATATATTTTTTATTTTA
96693 AAAT-TAATTTTTTATTTTTA
1 AAATAT-ATTTTTTA-TTTTA
96713 AAATATATTT
1 AAATATATTT
96723 AAAAATATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.04
18 4 0.15
19 7 0.27
20 13 0.50
21 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AAATATATTTTTTATTTTA
Found at i:97310 original size:29 final size:29
Alignment explanation
Indices: 97259--97314 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
97249 TATGTACACG
* * * *
97259 ATGGTTGAGTGGAAAGTTGAAAAAAAACA
1 ATGGTTAAGTGAAAAATTAAAAAAAAACA
97288 ATGGTTAAGTGAAAAATTAAAAAAAAA
1 ATGGTTAAGTGAAAAATTAAAAAAAAA
97315 ATATCTCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.21, T:0.21
Consensus pattern (29 bp):
ATGGTTAAGTGAAAAATTAAAAAAAAACA
Found at i:97487 original size:52 final size:55
Alignment explanation
Indices: 97421--97526 Score: 146
Period size: 52 Copynumber: 2.0 Consensus size: 55
97411 AATTATTCTT
* * *
97421 TTATTAATTCACCAATTAATTAACTATATA-TATA-A-AATAGAATTTATCATGC
1 TTATAAATTCACCAACTAACTAACTATATAGTATATACAATAGAATTTATCATGC
*
97473 TTATAAATTCACCAACTAACTAACTATATATGTATATACATTAGAATTTATCAT
1 TTATAAATTCACCAACTAACTAACTATATA-GTATATACAATAGAATTTATCAT
97527 ACTCACTTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
52 27 0.59
54 4 0.09
55 1 0.02
56 14 0.30
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (55 bp):
TTATAAATTCACCAACTAACTAACTATATAGTATATACAATAGAATTTATCATGC
Found at i:98473 original size:20 final size:21
Alignment explanation
Indices: 98450--98488 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
98440 ATTCAATCAA
98450 TAAAATTAT-TTAAAAATATT
1 TAAAATTATATTAAAAATATT
*
98470 TAAAATTATATTAATAATA
1 TAAAATTATATTAAAAATA
98489 AAACTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATTATATTAAAAATATT
Found at i:98483 original size:11 final size:10
Alignment explanation
Indices: 98450--98483 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
98440 ATTCAATCAA
98450 TAAAATTATT
1 TAAAATTATT
*
98460 TAAAAATATT
1 TAAAATTATT
98470 TAAAATTATAT
1 TAAAATTAT-T
98481 TAA
1 TAA
98484 TAATAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAAAATTATT
Found at i:99140 original size:22 final size:21
Alignment explanation
Indices: 99115--99189 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 21
99105 TATAGATATA
99115 TATTTTTGTAAAAAAAATTATC
1 TATTTTT-TAAAAAAAATTATC
**
99137 TATTTATTTTTAAAAAATTATC
1 TATTT-TTTAAAAAAAATTATC
*
99159 TATTTATCT--AAAAAATCTATC
1 TATTT-TTTAAAAAAAAT-TATC
99180 TATATTTTTA
1 TAT-TTTTTA
99190 TTTTATAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.16
21 9 0.20
22 27 0.60
23 2 0.04
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (21 bp):
TATTTTTTAAAAAAAATTATC
Found at i:99172 original size:21 final size:21
Alignment explanation
Indices: 99126--99182 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
99116 ATTTTTGTAA
*
99126 AAAAAATTATCTATTTATTTTT
1 AAAAAATTATCTATTTA-TTCT
99148 AAAAAATTATCTATTTA-TCT
1 AAAAAATTATCTATTTATTCT
99168 AAAAAATCTATCTAT
1 AAAAAAT-TATCTAT
99183 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 9 0.27
21 7 0.21
22 17 0.52
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAAAATTATCTATTTATTCT
Found at i:99667 original size:13 final size:13
Alignment explanation
Indices: 99649--99681 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
99639 ATTTAATAAT
99649 TTATATTTTTATA
1 TTATATTTTTATA
99662 TTATATTTTTATA
1 TTATATTTTTATA
*
99675 TTTTATT
1 TTATATT
99682 ATAATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATATTTTTATA
Found at i:99673 original size:21 final size:22
Alignment explanation
Indices: 99642--99698 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
99632 TTGATAAATT
99642 TAATA-ATTTATATTTTTA-TA
1 TAATATATTTATATTTTTATTA
* *
99662 TTATATTTTTATA-TTTTATTA
1 TAATATATTTATATTTTTATTA
99683 TAATATATTTATATTT
1 TAATATATTTATATTT
99699 AAAATATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.30
21 19 0.63
22 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TAATATATTTATATTTTTATTA
Found at i:99689 original size:15 final size:15
Alignment explanation
Indices: 99671--99719 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
99661 ATTATATTTT
99671 TATATTTTATTATAA
1 TATATTTTATTATAA
99686 TATATTTATATT-TAA
1 TATATTT-TATTATAA
* *
99701 AATA-TTTAATA-AA
1 TATATTTTATTATAA
99714 TATATT
1 TATATT
99720 AATATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 8 0.29
14 3 0.11
15 13 0.46
16 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTTTATTATAA
Found at i:104215 original size:31 final size:31
Alignment explanation
Indices: 104155--104216 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
104145 TGTAGTTCAT
* *
104155 TCTTCTAGACCAAGGATATCGATGGAAATCA
1 TCTTCTAGAACAAGGATATCGATGAAAATCA
* * *
104186 TCTTCTAGAACAGGGATGTTGATGAAAATCA
1 TCTTCTAGAACAAGGATATCGATGAAAATCA
104217 AAATAATAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (31 bp):
TCTTCTAGAACAAGGATATCGATGAAAATCA
Found at i:108887 original size:22 final size:22
Alignment explanation
Indices: 108862--108905 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
108852 AATAAAAACT
*
108862 TGACCATAATCATTTATCACAA
1 TGACCATAATCATTGATCACAA
*
108884 TGACCATAATTATTGATCACAA
1 TGACCATAATCATTGATCACAA
108906 ACTGCTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (22 bp):
TGACCATAATCATTGATCACAA
Found at i:112270 original size:13 final size:13
Alignment explanation
Indices: 112252--112277 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
112242 ACAAAGATCC
112252 ATGTATCGATACA
1 ATGTATCGATACA
112265 ATGTATCGATACA
1 ATGTATCGATACA
112278 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:112273 original size:33 final size:33
Alignment explanation
Indices: 112231--112297 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
112221 AAAATTTCCA
***
112231 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
112264 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
112297 A
1 A
112298 TTTCCTTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:112341 original size:19 final size:18
Alignment explanation
Indices: 112317--112384 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
112307 TATTAGCTAA
112317 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
112336 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
112351 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
112368 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
112385 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:112357 original size:13 final size:13
Alignment explanation
Indices: 112339--112363 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
112329 ACAATACTTA
112339 TGTATCGATACAT
1 TGTATCGATACAT
112352 TGTATCGATACA
1 TGTATCGATACA
112364 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:112361 original size:32 final size:32
Alignment explanation
Indices: 112320--112382 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
112310 TAGCTAATTA
*
112320 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
112352 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
112383 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:113278 original size:153 final size:151
Alignment explanation
Indices: 113011--113288 Score: 330
Period size: 153 Copynumber: 1.8 Consensus size: 151
113001 GGTAATCATC
* * *
113011 GGATCACTTTTATGCCAAAGGTTCACTTTTAGGATAGGTTCATCCTTTCACATCATTTTCATGTT
1 GGATCACTTTTATGCCAAAGCTGCACATTTAGGATAGGTTCATCCTTTCACATCATTTTCATGTT
* * * *
113076 TTAAGGTTATTAAGATACTTTCACATCAAAAGTATATCGAAGGGTATTTTGGTCATTTTTCCATA
66 TTAAAGTTATCAAGATACTTTCACATCAAAAGTATATCGAAGGGCATTTTGGTAATTTTTCCATA
113141 ATCGAATCCTAGGTCGCCATT
131 ATCGAATCCTAGGTCGCCATT
* * **
113162 GGATCACTTTTATGCGAAAGCTGCACATTTAGGATAGGTTTGA-CCTTTTTCA-ATC-TTTTTGT
1 GGATCACTTTTATGCCAAAGCTGCACATTTAGGATAGG-TTCATCC--TTTCACATCATTTTCAT
* * * * *
113224 GCTCTTTAAAGTTATCGAGATACTTTCATATCGAAAGTATA-CGCGATGGCATTTTGGTAATTTT
63 G-T-TTTAAAGTTATCAAGATACTTTCACATCAAAAGTATATCG-AAGGGCATTTTGGTAATTTT
113288 T
125 T
113289 TCTCAACCAA
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
151 42 0.40
152 9 0.09
153 54 0.51
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (151 bp):
GGATCACTTTTATGCCAAAGCTGCACATTTAGGATAGGTTCATCCTTTCACATCATTTTCATGTT
TTAAAGTTATCAAGATACTTTCACATCAAAAGTATATCGAAGGGCATTTTGGTAATTTTTCCATA
ATCGAATCCTAGGTCGCCATT
Found at i:115105 original size:23 final size:23
Alignment explanation
Indices: 115079--115122 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
115069 GTCCTTTAGG
*
115079 TCATGTTCCATGATCTAGGGACT
1 TCATCTTCCATGATCTAGGGACT
*
115102 TCATCTTTCATGATCTAGGGA
1 TCATCTTCCATGATCTAGGGA
115123 TTTTGAGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
TCATCTTCCATGATCTAGGGACT
Found at i:115203 original size:58 final size:57
Alignment explanation
Indices: 115102--115346 Score: 201
Period size: 58 Copynumber: 4.2 Consensus size: 57
115092 TCTAGGGACT
* * * *
115102 TCATCTTTCATGATCTAGGGATTTTGAGAT--AATTTTATGAATTTTGATGTCATTTAAG
1 TCATTTTTCATGATCTAGGAACTTT-A-ATGCAATTTTATAAATTTTGA-GTCATTTAAG
* * *
115160 TAATTTTTCATGATATAGGAACTTTAATGCAATTTTATAAATTTTGAAGTAATTTAAG
1 TCATTTTTCATGATCTAGGAACTTTAATGCAATTTTATAAATTTTG-AGTCATTTAAG
* * ** * * * * *
115218 CCATTTTTCATGACCTAGGAACTTTTGTGCAAATATATATATGTTGGAGTCATTTAGG
1 TCATTTTTCATGATCTAGGAACTTTAATGCAATTTTATAAAT-TTTGAGTCATTTAAG
* * * * *
115276 TTA-TTTTCAATGATCCAGAAACTTTCATGCAATTTTATACATTTTTGAGAT-ATTTAAG
1 TCATTTTTC-ATGATCTAGGAACTTTAATGCAATTTTATA-AATTTTGAG-TCATTTAAG
115334 TCATTTTTCATGA
1 TCATTTTTCATGA
115347 CTTAAAAATT
Statistics
Matches: 146, Mismatches: 33, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
56 2 0.01
57 6 0.04
58 127 0.87
59 11 0.08
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.44
Consensus pattern (57 bp):
TCATTTTTCATGATCTAGGAACTTTAATGCAATTTTATAAATTTTGAGTCATTTAAG
Found at i:118220 original size:24 final size:24
Alignment explanation
Indices: 118196--118252 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
118186 TATATTTTTA
118196 TATATTCATATTATTATTTTATTAT
1 TATATT-ATATTATTATTTTATTAT
* * *
118221 TTTATTATATTATAATTTAATTAAT
1 TATATTATATTATTATTTTATT-AT
118246 TAT-TTAT
1 TATATTAT
118253 GCTGCTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TATATTATATTATTATTTTATTAT
Found at i:118233 original size:8 final size:8
Alignment explanation
Indices: 118185--118233 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
118175 TTATAAATTT
*
118185 TTATATTT
1 TTATATTA
118193 TTATA-TA
1 TTATATTA
118200 TTCATATTA
1 TT-ATATTA
*
118209 TTATTTTA
1 TTATATTA
*
118217 TTATTTTA
1 TTATATTA
118225 TTATATTA
1 TTATATTA
118233 T
1 T
118234 AATTTAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
7 3 0.08
8 29 0.81
9 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (8 bp):
TTATATTA
Found at i:118233 original size:16 final size:16
Alignment explanation
Indices: 118168--118249 Score: 57
Period size: 16 Copynumber: 5.3 Consensus size: 16
118158 TATTAATAAT
*
118168 TTATT-TTTTA-TAAA
1 TTATTATTTTATTATA
*
118182 TTTTTATATTT-TTATA
1 TTATTAT-TTTATTATA
* *
118198 -TATTCATATTATTATT
1 TTATT-ATTTTATTATA
118214 TTATTATTTTATTATA
1 TTATTATTTTATTATA
* *
118230 TTATAATTTAATTA-A
1 TTATTATTTTATTATA
118245 TTATT
1 TTATT
118250 TATGCTGCTA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
14 4 0.08
15 11 0.21
16 33 0.63
17 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTATTTTATTATA
Found at i:118640 original size:16 final size:15
Alignment explanation
Indices: 118609--118673 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
118599 TTTTGATCGA
118609 TTTTAAATATAATTT
1 TTTTAAATATAATTT
*
118624 TTTTAAATTTGAATTT
1 TTTTAAATAT-AATTT
*
118640 TAATTTATAATATTATTT
1 T--TTTA-AATATAATTT
* *
118658 TATTAAAAAT-ATTT
1 TTTTAAATATAATTT
118672 TT
1 TT
118674 ATTTTAAGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 5 0.12
15 13 0.32
16 9 0.22
18 9 0.22
19 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTTAAATATAATTT
Found at i:119181 original size:16 final size:16
Alignment explanation
Indices: 119152--119202 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
119142 AATATTTTTC
* *
119152 ATAATACAATATAATT
1 ATAATAAAAAATAATT
119168 ATAATAAAAAATAA-T
1 ATAATAAAAAATAATT
* * *
119183 ATTATTAAAAATATTT
1 ATAATAAAAAATAATT
119199 ATAA
1 ATAA
119203 GTCAAGTCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATAAAAAATAATT
Found at i:120656 original size:2 final size:2
Alignment explanation
Indices: 120645--120683 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
120635 TTTCAAATTT
*
120645 TA TA -A TA TA TA TA TA TA TA AA 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
120684 GAATTTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:121166 original size:21 final size:21
Alignment explanation
Indices: 121128--121167 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
121118 ATATATAATA
**
121128 TTAAAAAATAAATTTTAAATT
1 TTAAAAAATAAAAATTAAATT
*
121149 TTAAAAATTAAAAATTAAA
1 TTAAAAAATAAAAATTAAA
121168 AAAAAGTGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAAAAATAAAAATTAAATT
Found at i:121532 original size:21 final size:21
Alignment explanation
Indices: 121508--121548 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
121498 ATTTGTAGTA
121508 ATATTTATTTTAAAAATAATG
1 ATATTTATTTTAAAAATAATG
*
121529 ATATTTATTTTAAATATAAT
1 ATATTTATTTTAAAAATAAT
121549 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATATTTATTTTAAAAATAATG
Found at i:121553 original size:19 final size:19
Alignment explanation
Indices: 121506--121553 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
121496 TTATTTGTAG
121506 TAAT-ATTTATTTTAAAAA
1 TAATAATTTATTTTAAAAA
*
121524 TAATGATATTTATTTTAAATA
1 TAAT-A-ATTTATTTTAAAAA
121545 TAATAATTT
1 TAATAATTT
121554 TTTATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.15
19 4 0.15
20 1 0.04
21 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATAATTTATTTTAAAAA
Found at i:121673 original size:53 final size:51
Alignment explanation
Indices: 121557--121695 Score: 131
Period size: 53 Copynumber: 2.6 Consensus size: 51
121547 ATAATTTTTT
* *
121557 ATTTAATAATTAAATTTTTATATAAAAA-TATTTATTTAAAGAAAATAATTTTT
1 ATTTAATAATTAAA-TTTTA-ATAAAAATTATTTATTT-AAGAAAATAAATTTC
* *
121610 ATCTT-ATAATTAACTTTTAATAAAAATTATTTATTT-TGAAAATTATGAATTTC
1 AT-TTAATAATTAAATTTTAATAAAAATTATTTATTTAAGAAAA-TA--AATTTC
* *
121663 ATTTAATAATTAAATTTTTATGAAAATATATTT
1 ATTTAATAATTAAATTTTAATAAAAAT-TATTT
121696 TTAACACCTA
Statistics
Matches: 72, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
50 5 0.07
51 9 0.12
52 16 0.22
53 35 0.49
54 7 0.10
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (51 bp):
ATTTAATAATTAAATTTTAATAAAAATTATTTATTTAAGAAAATAAATTTC
Found at i:123144 original size:18 final size:18
Alignment explanation
Indices: 123121--123163 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
123111 TTTTTAAAGG
123121 TATAATAAAAATAAAAAA
1 TATAATAAAAATAAAAAA
*
123139 TATAATTAAAATAAAAAA
1 TATAATAAAAATAAAAAA
*
123157 TAAAATA
1 TATAATA
123164 TGTAATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TATAATAAAAATAAAAAA
Done.