Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold180
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: 544442
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 40629 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:132733 original size:226 final size:227
Alignment explanation
Indices: 132312--132761 Score: 674
Period size: 226 Copynumber: 2.0 Consensus size: 227
132302 AAAGCTCATT
* *
132312 TAATCTTTAACTTAAAACTTATGCCCATCTAAACCTAAAAGCTTATATAAACTCAATTAGGACAA
1 TAATCTTTAACTTAAAACTCATGCCCATCTAAACCTAAAAGCTCATATAAACTCAATTA-GACAA
* * **
132377 AAAAAAAGCGAAATAAAGAAAAACTAAAATCTTCAGTTTGTAAGTATGCTTATAATTTATAGTAT
65 AAAAAAAGCGAAATAAAAAAAAACTAAAATCTTCAGTTTGTAAGTATACTTATAATTTATAAAAT
* * * *
132442 TGTTACTTTTAATAATAGTTTTACAATCATAAAGAGTTAGTAAAATTTCATTTATAATAATATTT
130 TGTTACCTTTAATAATAATTTTACAATCATAAAGAGTTAATAAAATTACATTTATAATAATATTT
* *
132507 ATTTTGATATTAATTTGTAGGTTTTATTTATAA
195 ATTTTGATATTAATTTGTAAGTTTGATTTATAA
* * * *
132540 TAAT-TTTAA-TTAAAAGCTCATGTCTATCTAAACCTAAAAGCTCATGTAAACTTAATTA-A-AA
1 TAATCTTTAACTTAAAA-CTCATGCCCATCTAAACCTAAAAGCTCATATAAACTCAATTAGACAA
132601 CAAAAAAAGCGAAATTAAAAAAAAACTAAAATCTTCAGTTTGTAAGTATACTTATAATTTATAAA
65 -AAAAAAAGCGAAA-TAAAAAAAAACTAAAATCTTCAGTTTGTAAGTATACTTATAATTTATAAA
* *
132666 ATTTTTACCTTTAATAATAATTTTACAATTATAAAGAGTTAATAAAATTACATTTATAATAATAT
128 ATTGTTACCTTTAATAATAATTTTACAATCATAAAGAGTTAATAAAATTACATTTATAATAATAT
132731 TTATTTTGATATTAATTTGTAAGTTTGATTT
193 TTATTTTGATATTAATTTGTAAGTTTGATTT
132762 TTTAACGTTG
Statistics
Matches: 201, Mismatches: 18, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
224 2 0.01
225 14 0.07
226 140 0.70
227 41 0.20
228 4 0.02
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (227 bp):
TAATCTTTAACTTAAAACTCATGCCCATCTAAACCTAAAAGCTCATATAAACTCAATTAGACAAA
AAAAAAGCGAAATAAAAAAAAACTAAAATCTTCAGTTTGTAAGTATACTTATAATTTATAAAATT
GTTACCTTTAATAATAATTTTACAATCATAAAGAGTTAATAAAATTACATTTATAATAATATTTA
TTTTGATATTAATTTGTAAGTTTGATTTATAA
Found at i:133609 original size:15 final size:16
Alignment explanation
Indices: 133560--133611 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
133550 GTTCAGGTTA
* **
133560 TTTCAGGTTCGAGTTT
1 TTTCAAGTTCGAACTT
*
133576 TTTCAAGTTCGGACTT
1 TTTCAAGTTCGAACTT
133592 TTTCAAGTTCGAACTT
1 TTTCAAGTTCGAACTT
133608 TTTC
1 TTTC
133612 GGGTTTGGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (16 bp):
TTTCAAGTTCGAACTT
Found at i:136162 original size:20 final size:20
Alignment explanation
Indices: 136104--136163 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
136094 TTTAAATATT
* *
136104 AAATTATTTTTTTAAATTTA
1 AAATAATTTTTATAAATTTA
136124 AAA-AATTAATTTCAT--ATTTA
1 AAATAATT--TTT-ATAAATTTA
136144 AAATAATTTTTATAAATTTA
1 AAATAATTTTTATAAATTTA
136164 TTAAATTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 2 0.06
19 6 0.19
20 16 0.50
21 7 0.22
22 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATAATTTTTATAAATTTA
Found at i:136746 original size:26 final size:28
Alignment explanation
Indices: 136702--136757 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
136692 AACTTTATGC
* *
136702 ATGTTTTATATTAGTTTCA-AACTTTAA
1 ATGTATTATATTAGATTCACAACTTTAA
*
136729 ATGTATTA-ATTAGATTCACAATTTTAA
1 ATGTATTATATTAGATTCACAACTTTAA
136756 AT
1 AT
136758 TTTGTATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (28 bp):
ATGTATTATATTAGATTCACAACTTTAA
Found at i:136851 original size:21 final size:20
Alignment explanation
Indices: 136811--136851 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
136801 TTTGATAAAG
**
136811 TAATATTTATTTTATTTGAA
1 TAATATTTATTTTACATGAA
136831 TAATATTTATTTTTACATGAA
1 TAATATTTA-TTTTACATGAA
136852 AAAATGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (20 bp):
TAATATTTATTTTACATGAA
Found at i:137562 original size:22 final size:22
Alignment explanation
Indices: 137532--137574 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
137522 ACTTGACTAT
*
137532 ATTTAAAAAGATTAAAAAATTA
1 ATTTAAAAAAATTAAAAAATTA
*
137554 ATTTTAAAAAATTAAAAAATT
1 ATTTAAAAAAATTAAAAAATT
137575 TTATTATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATTTAAAAAAATTAAAAAATTA
Found at i:140300 original size:17 final size:17
Alignment explanation
Indices: 140268--140299 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
140258 TTTCAATTGA
140268 GAAAAAAAACTAAAAAG
1 GAAAAAAAACTAAAAAG
140285 GAAAAAAAA-TAAAAA
1 GAAAAAAAACTAAAAA
140300 ATAGAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.81, C:0.03, G:0.09, T:0.06
Consensus pattern (17 bp):
GAAAAAAAACTAAAAAG
Found at i:140891 original size:49 final size:49
Alignment explanation
Indices: 140836--140930 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 49
140826 TTTTTATATC
* * *
140836 ATTTTTCATGTCTTAAGTATTTTT-T-ATATCATTTCATGTATTTTTAGCT
1 ATTTTTCATGACTTAAGGATTTTTATGATAT--TTTCATGCATTTTTAGCT
*
140885 ATTTTTCATGACTTAGGGATTTTTATGATATTTTCATGCATTTTTA
1 ATTTTTCATGACTTAAGGATTTTTATGATATTTTCATGCATTTTTA
140931 TGTCATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 35 0.88
50 1 0.03
51 4 0.10
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (49 bp):
ATTTTTCATGACTTAAGGATTTTTATGATATTTTCATGCATTTTTAGCT
Found at i:141084 original size:49 final size:48
Alignment explanation
Indices: 141030--141161 Score: 149
Period size: 48 Copynumber: 2.7 Consensus size: 48
141020 ACATTTCATG
* * * *
141030 CATTTTTATGTTATTTTAGTTATTTTCTATGATTTAAGAGGTATTATGA
1 CATTTTTATGTCATTTTAGTCATTTTCAATGACTT-AGAGGTATTATGA
* * * * *
141079 TATTTTTTTATCGTTTTAGTCATTTTCAATGACTTAGGGGTATTATGA
1 CATTTTTATGTCATTTTAGTCATTTTCAATGACTTAGAGGTATTATGA
*
141127 CATTTTTCTGTCATTTTAGTCATTCTT-AATGACTT
1 CATTTTTATGTCATTTTAGTCATT-TTCAATGACTT
141162 GGGGGGTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
48 40 0.58
49 29 0.42
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.54
Consensus pattern (48 bp):
CATTTTTATGTCATTTTAGTCATTTTCAATGACTTAGAGGTATTATGA
Found at i:141144 original size:48 final size:49
Alignment explanation
Indices: 141030--141180 Score: 153
Period size: 49 Copynumber: 3.1 Consensus size: 49
141020 ACATTTCATG
* * * * *
141030 CATTTTTATGTTATTTTAGTTATTTTCTATGATTTAAGAGGTATTATGA
1 CATTTTTATGTCATTTTAGTCATTTTCAATGACTTAAGGGGTATTATGA
* * * *
141079 TATTTTTTTATCGTTTTAGTCATTTTCAATGACTT-AGGGGTATTATGA
1 CATTTTTATGTCATTTTAGTCATTTTCAATGACTTAAGGGGTATTATGA
* ** * *
141127 CATTTTTCTGTCATTTTAGTCATTCTT-AATGACTTGGGGGGTTTTATGT
1 CATTTTTATGTCATTTTAGTCATT-TTCAATGACTTAAGGGGTATTATGA
141176 CATTT
1 CATTT
141181 CATGAATTTT
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
48 40 0.48
49 44 0.52
ACGTcount: A:0.22, C:0.09, G:0.17, T:0.53
Consensus pattern (49 bp):
CATTTTTATGTCATTTTAGTCATTTTCAATGACTTAAGGGGTATTATGA
Found at i:141281 original size:58 final size:58
Alignment explanation
Indices: 141197--141589 Score: 258
Period size: 58 Copynumber: 6.8 Consensus size: 58
141187 TTTTTATTTT
* * * * * *
141197 ATTTGGGTTATTTTTCATGATTTAGGGAATTTTTATGTAATTTTATGGATGTT-GGATC
1 ATTTAGGTCATTTTTCATGATCTAGGG-ACTTTTATGCAATTTTATGAATGTTAGGATC
* * * *
141255 ATTTAGGTCATTTTTCATAATCTAGGGATTTTTATGCAATTTCAAGAATGTTGAGG-TC
1 ATTTAGGTCATTTTTCATGATCTAGGGACTTTTATGCAATTTTATGAATGTT-AGGATC
* * * ** * * *
141313 ATTTAAGCCATTTTTCATGGTCTAGGGACTTGGATGCAATTTTAAGAATGTTAGGGTT
1 ATTTAGGTCATTTTTCATGATCTAGGGACTTTTATGCAATTTTATGAATGTTAGGATC
* * * * * * *
141371 ATTTAAGTCATTTTTTAGGATCTAGGGGA-TTTTGTGCAATTTTATAAATGTT-GATATT
1 ATTTAGGTCATTTTTCATGATCTA-GGGACTTTTATGCAATTTTATGAATGTTAG-GATC
* * * ** * * * *
141429 ATTTAGGTCATTTTAT-ATAATTTAAGGACTTCAATGTAATTTTATAAATATTAGGGTC
1 ATTTAGGTCATTTT-TCATGATCTAGGGACTTTTATGCAATTTTATGAATGTTAGGATC
* * * * * * *
141487 ATTTAGGTCATTTTT-ATGATATAAGGACTTTTATGTAATGTTATGTATATTGGGATC
1 ATTTAGGTCATTTTTCATGATCTAGGGACTTTTATGCAATTTTATGAATGTTAGGATC
* * * * * * * *
141544 ATTTAAGCCATTTTTTATAATTTAGAGACTTTTTTACAATTTTATG
1 ATTTAGGTCATTTTTCATGATCTAGGGACTTTTATGCAATTTTATG
141590 CATCTCAAAA
Statistics
Matches: 266, Mismatches: 60, Indels: 18
0.77 0.17 0.05
Matches are distributed among these distances:
57 75 0.28
58 183 0.69
59 8 0.03
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (58 bp):
ATTTAGGTCATTTTTCATGATCTAGGGACTTTTATGCAATTTTATGAATGTTAGGATC
Found at i:141537 original size:57 final size:57
Alignment explanation
Indices: 141429--141564 Score: 157
Period size: 57 Copynumber: 2.4 Consensus size: 57
141419 TGTTGATATT
* *
141429 ATTTAGGTCATTTTATATAATTTAAGGACTTCAATGTAATTTTATAAATATTAGGG-TC
1 ATTTAGGTCATTTT-TATAATATAAGGACTTCAATGTAATGTTATAAATATT-GGGATC
* ** **
141487 ATTTAGGTCATTTTTATGATATAAGGACTTTTATGTAATGTTATGTATATTGGGATC
1 ATTTAGGTCATTTTTATAATATAAGGACTTCAATGTAATGTTATAAATATTGGGATC
* *
141544 ATTTAAGCCATTTTTTATAAT
1 ATTTAGGTCA-TTTTTATAAT
141565 TTAGAGACTT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
56 3 0.05
57 40 0.61
58 23 0.35
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (57 bp):
ATTTAGGTCATTTTTATAATATAAGGACTTCAATGTAATGTTATAAATATTGGGATC
Found at i:144943 original size:28 final size:27
Alignment explanation
Indices: 144878--144959 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
144868 TCACTTAATT
*
144878 AATATAAAATA-TTAAAATTAAAAATTT
1 AATATAAAATATTTAAAATTAAAAA-TA
* *
144905 AAT-TAATATATGTTAAAATTTAAAATA
1 AATATAAAATAT-TTAAAATTAAAAATA
*
144932 AATATAAAATATTTTTAAAATTCAAAAT
1 AATATAAAATA--TTTAAAATTAAAAAT
144960 GACTCATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
26 6 0.13
27 7 0.16
28 18 0.40
29 13 0.29
30 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (27 bp):
AATATAAAATATTTAAAATTAAAAATA
Found at i:151697 original size:71 final size:72
Alignment explanation
Indices: 151533--151723 Score: 192
Period size: 71 Copynumber: 2.7 Consensus size: 72
151523 TTCAACTTGA
* * * * * *
151533 TTCTTATGGATCAATCTATTTTCTACACA-AAATGTAAGTTGCAA-TTTCAAGGGCTTAAATGAT
1 TTCTTATGGATCAATCTATTTTATACACAGTAA-GAAAATAGCAATTTTCAAGGGCTTAAAGGAT
*
151596 CAATCTAT
65 CAATCCAT
** * * *
151604 TTCTTATGGAT-AGATCCGTTTTATACATAGTAAGCAAATGGCAATTTTCAAGGG-TTAAAGGAT
1 TTCTTATGGATCA-ATCTATTTTATACACAGTAAGAAAATAGCAATTTTCAAGGGCTTAAAGGAT
* *
151667 CGATCCGT
65 CAATCCAT
*
151675 TTCTTATGGATCAATCTATTTTATACGCAGTAAGAAAATAGCAACTTTT
1 TTCTTATGGATCAATCTATTTTATACACAGTAAGAAAATAGCAA-TTTT
151724 AGGAATTAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
70 1 0.01
71 80 0.82
72 16 0.16
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (72 bp):
TTCTTATGGATCAATCTATTTTATACACAGTAAGAAAATAGCAATTTTCAAGGGCTTAAAGGATC
AATCCAT
Found at i:152288 original size:63 final size:65
Alignment explanation
Indices: 152183--152353 Score: 148
Period size: 65 Copynumber: 2.7 Consensus size: 65
152173 TGTTGTAACA
** * * * * * * * **
152183 AAAAAATATAACAATTCAAACCTTCCAAATCCTAACCGACAAAAAAATAATTG-A-TGCTATAAT
1 AAAAAATATAACACCTCGAGCCTTCCTAACCCTAATCTACAAAAAAATAAGTGTAGTAATATAAT
* * **** **
152246 AAAAAATATAGCACCTTGAGCCTTCCTAACCCTAATCTACAAAGTGTTTGGTGTAGTAATATAAT
1 AAAAAATATAACACCTCGAGCCTTCCTAACCCTAATCTACAAAAAAATAAGTGTAGTAATATAAT
*
152311 AAAAAATATAACACCTCGAGCCTTCCTAACCTTAATCTACAAA
1 AAAAAATATAACACCTCGAGCCTTCCTAACCCTAATCTACAAA
152354 GTATTTGGTA
Statistics
Matches: 84, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
63 36 0.43
64 1 0.01
65 47 0.56
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.26
Consensus pattern (65 bp):
AAAAAATATAACACCTCGAGCCTTCCTAACCCTAATCTACAAAAAAATAAGTGTAGTAATATAAT
Found at i:152377 original size:59 final size:65
Alignment explanation
Indices: 152240--152369 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
152230 TAATTGATGC
* * *
152240 TATAATAAAAAATATAGCACCTTGAGCCTTCCTAACCCTAATCTACAAAGTGTTTGGTGTAGTAA
1 TATAATAAAAAATATAACACCTCGAGCCTTCCTAACCCTAATCTACAAAGTATTTGGTGTAGTAA
* *
152305 TATAATAAAAAATATAACACCTCGAGCCTTCCTAACCTTAATCTACAAAGTATTTGGTATAGTAA
1 TATAATAAAAAATATAACACCTCGAGCCTTCCTAACCCTAATCTACAAAGTATTTGGTGTAGTAA
152370 CAAAAATACA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (65 bp):
TATAATAAAAAATATAACACCTCGAGCCTTCCTAACCCTAATCTACAAAGTATTTGGTGTAGTAA
Found at i:153655 original size:93 final size:91
Alignment explanation
Indices: 153510--153692 Score: 226
Period size: 93 Copynumber: 2.0 Consensus size: 91
153500 TTCTCCATTA
* * * *
153510 ACAAGACTCGAAATTGAGACATTGCTTAAGAGACACCGAACTCCTTATCACTCAACCCA-ATATG
1 ACAAGACTCGAAACTGAGACATTGCTTAAAAGACACCGAACTCCTTACCACTCAACCCAGAAAT-
*
153574 CATTGGTAAAACATTTATTTCATTGAATC
65 -ATTGGTAAAACATGTA-TTCATTGAATC
* * * *
153603 ACAAGACTCGAAACTGAGACCTTGCTTAAAAGACACC-AAGTTTCTTACCACTCGACCCAGGAAA
1 ACAAGACTCGAAACTGAGACATTGCTTAAAAGACACCGAA-CTCCTTACCACTCAACCCA-GAAA
153667 TATTGGTAAAACATGTATTCATTGAA
64 TATTGGTAAAACATGTATTCATTGAA
153693 CAGTGAGAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
92 11 0.14
93 64 0.82
95 3 0.04
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (91 bp):
ACAAGACTCGAAACTGAGACATTGCTTAAAAGACACCGAACTCCTTACCACTCAACCCAGAAATA
TTGGTAAAACATGTATTCATTGAATC
Found at i:157058 original size:19 final size:20
Alignment explanation
Indices: 157024--157061 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
157014 AATTATTCAT
157024 ATTTAAATATATTTTATTTG
1 ATTTAAATATATTTTATTTG
*
157044 ATTTAATTA-ATTTTATTT
1 ATTTAAATATATTTTATTT
157062 AAAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
ATTTAAATATATTTTATTTG
Found at i:160639 original size:2 final size:2
Alignment explanation
Indices: 160632--160658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
160622 CTTTGCATAC
160632 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 A
160659 ATTGTAAACC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:163561 original size:22 final size:22
Alignment explanation
Indices: 163514--163583 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
163504 CAAGTTACAA
* * *
163514 ATATAATTTTTATTA-AATGTAA
1 ATATTATTTTTATTATAA-ATAC
163536 ATATTATTTTTATTATAAATAC
1 ATATTATTTTTATTATAAATAC
* **
163558 ATATTAATTTTATTATACCTAC
1 ATATTATTTTTATTATAAATAC
163580 ATAT
1 ATAT
163584 AGTTATTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 39 0.95
23 2 0.05
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (22 bp):
ATATTATTTTTATTATAAATAC
Found at i:164697 original size:20 final size:21
Alignment explanation
Indices: 164672--164719 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
164662 TCTTGTAATA
*
164672 TTTTTTCGA-TTTTACTTTAT
1 TTTTTTCGAGTTTTACATTAT
* *
164692 TTTTTT-TAGTTTTGCATTAT
1 TTTTTTCGAGTTTTACATTAT
164712 TTTTTTCG
1 TTTTTTCG
164720 TTAAATTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.71
Consensus pattern (21 bp):
TTTTTTCGAGTTTTACATTAT
Found at i:166862 original size:32 final size:31
Alignment explanation
Indices: 166826--166885 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
166816 GAAATCAAAT
*
166826 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAAAAGCTCTAGAAAAAT-ATAA-AATATGA
*
166858 ACAAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAAGCTCTAGAAAAATATAAAATA
166886 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 4 0.16
32 13 0.52
33 8 0.32
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (31 bp):
ACAAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:167184 original size:13 final size:13
Alignment explanation
Indices: 167166--167191 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
167156 AATTTTTTTG
167166 TGTATCGATACAT
1 TGTATCGATACAT
167179 TGTATCGATACAT
1 TGTATCGATACAT
167192 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:169760 original size:13 final size:13
Alignment explanation
Indices: 169742--169766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
169732 ATAATCCCCC
169742 TGTATCGATACAT
1 TGTATCGATACAT
169755 TGTATCGATACA
1 TGTATCGATACA
169767 AAGAAAAATG
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:171847 original size:15 final size:15
Alignment explanation
Indices: 171827--171857 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
171817 ATTTCGTTTG
*
171827 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
171842 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
171857 G
1 G
171858 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:173689 original size:21 final size:21
Alignment explanation
Indices: 173660--173704 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
173650 AAGTTTTTAT
*
173660 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
173680 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
173702 TTT
1 TTT
173705 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:178098 original size:89 final size:88
Alignment explanation
Indices: 177938--178394 Score: 396
Period size: 89 Copynumber: 5.2 Consensus size: 88
177928 TATAATGGAG
* * * *
177938 TCTGATACCCCATGCATC-GATCACACCTTTCAAGTTCCAAGAAATTTATTAAGCATTAGACAAA
1 TCTGATACCCCATGCATCTG-TCACATCTTTCAGGTTTCAAGAAATTTATTAAGCATTAGTCAAA
178002 TATTTTCTGTCATGTCAAAAGGAA
65 TATTTTCTGTCATGTCAAAAGGAA
* * * * *
178026 TCTGATACCTCCATGCATTTGTCACTTCTTTCAGGTTTCAAGATATTTATTAGGCATTAGTTAAA
1 TCTGATACC-CCATGCATCTGTCACATCTTTCAGGTTTCAAGAAATTTATTAAGCATTAGTCAAA
* *
178091 TATTTTCTGTAACGTCAGAAA-GAA
65 TATTTTCTGTCATGTCA-AAAGGAA
* * *
178115 TCTAATACCCTCATGCATCTGTCACATCTTTTAGG-TTCTAAGATATTTATTAAGCATTAGTCAA
1 TCTGATACCC-CATGCATCTGTCACATCTTTCAGGTTTC-AAGAAATTTATTAAGCATTAGTCAA
* * *
178179 ATATTTCCTGTCTTGTCAGAAA-AAA
64 ATATTTTCTGTCATGTCA-AAAGGAA
* *** * *** *
178204 TCTGATACCTCAATGCATCTGTTGTATCTTT-TGGATTTCAAGAAATACCTTAGGCATTAGTCAA
1 TCTGATACC-CCATGCATCTGTCACATCTTTCAGG-TTTCAAGAAATTTATTAAGCATTAGTCAA
* * ** *
178268 ATATTTCCTATTGTATCAAAAGGAA
64 ATATTTTCTGTCATGTCAAAAGGAA
* * * ** *
178293 TCTGATA---C-TGTATCTATTACATCTTTTGGGTTCCAAGAAA-TTATTAAGCATTAGTCAAAT
1 TCTGATACCCCATGCATCTGTCACATCTTTCAGGTTTCAAGAAATTTATTAAGCATTAGTCAAAT
*
178353 ATCTTT-TGTCGTGTCAAAAGGAA
66 AT-TTTCTGTCATGTCAAAAGGAA
*
178376 TCTAATACCCCTATGCATC
1 TCTGATACCCC-ATGCATC
178395 ATCATATCTT
Statistics
Matches: 298, Mismatches: 55, Indels: 32
0.77 0.14 0.08
Matches are distributed among these distances:
83 38 0.13
84 25 0.08
85 2 0.01
86 1 0.00
88 23 0.08
89 201 0.67
90 8 0.03
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (88 bp):
TCTGATACCCCATGCATCTGTCACATCTTTCAGGTTTCAAGAAATTTATTAAGCATTAGTCAAAT
ATTTTCTGTCATGTCAAAAGGAA
Found at i:179185 original size:21 final size:21
Alignment explanation
Indices: 179147--179187 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
179137 CTAAGTAAAA
179147 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
179168 ATAC-TATTGATATTAATACA
1 ATACGTATTG-TATCAATACA
179188 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:179256 original size:20 final size:19
Alignment explanation
Indices: 179227--179297 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
179217 ACCCTGAAAA
*
179227 GTATCAATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
179247 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
179266 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
179287 GTATCGATACA
1 GTATCGATACA
179298 GGACATTGGC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 4 0.10
20 34 0.85
21 2 0.05
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:179350 original size:53 final size:53
Alignment explanation
Indices: 179267--179403 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
179257 AAATTGCATA
*
179267 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
179321 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
179374 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
179404 TTGGAAGTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:179446 original size:10 final size:10
Alignment explanation
Indices: 179427--179457 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
179417 AATCTCATTT
*
179427 TCACTGTTCA
1 TCACTATTCA
179437 TCACTATTCA
1 TCACTATTCA
179447 TCACTATTCA
1 TCACTATTCA
179457 T
1 T
179458 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (10 bp):
TCACTATTCA
Found at i:179471 original size:22 final size:22
Alignment explanation
Indices: 179445--179499 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
179435 CATCACTATT
179445 CATCACTATTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
*
179467 CATCA-TTTTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
*
179488 CATCACTGTTCA
1 CATCACTATTCA
179500 CACTGTTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (22 bp):
CATCACTATTCATGTATCGATA
Found at i:179594 original size:13 final size:13
Alignment explanation
Indices: 179576--179601 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
179566 ACATATTTGT
179576 GTGTATCGATACA
1 GTGTATCGATACA
179589 GTGTATCGATACA
1 GTGTATCGATACA
179602 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:182274 original size:21 final size:21
Alignment explanation
Indices: 182250--182294 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
182240 TTCATCGTAC
* *
182250 TAAAATTAAACTTAGTTATAA
1 TAAAATTAAACTTAATCATAA
*
182271 TAAAATTAAATTTAATCATAA
1 TAAAATTAAACTTAATCATAA
182292 TAA
1 TAA
182295 TAAATTACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAATTAAACTTAATCATAA
Found at i:182395 original size:18 final size:18
Alignment explanation
Indices: 182362--182396 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
182352 ACATAAGAAT
* *
182362 AAAAAAAACTATCAAAAC
1 AAAAAAAACCAACAAAAC
182380 AAAAAAAACCAACAAAA
1 AAAAAAAACCAACAAAA
182397 AAAGTACATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.17, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAAAACCAACAAAAC
Found at i:182947 original size:2 final size:2
Alignment explanation
Indices: 182940--182986 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
182930 AATCCACTTT
182940 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
182982 TA TA T
1 TA TA T
182987 TATTAATCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:183245 original size:20 final size:19
Alignment explanation
Indices: 183220--183261 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
183210 AAAAATACAT
183220 AAAAATTAAATTATAAACAA
1 AAAAATTAAA-TATAAACAA
* *
183240 AAAAATTATATGTAAACAA
1 AAAAATTAAATATAAACAA
183259 AAA
1 AAA
183262 TTCTAAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAATTAAATATAAACAA
Found at i:183871 original size:29 final size:26
Alignment explanation
Indices: 183805--183871 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
183795 CCCAACTGAA
* *
183805 AAAATAAAAAAAACATTTTAAAAAATT
1 AAAATAAAAAAAA-AATTTAAAAAAAT
*
183832 AAAA-AATAAAAAAATTATAAAAAAACT
1 AAAATAAAAAAAAAATT-TAAAAAAA-T
*
183859 AAAATAAACAAAA
1 AAAATAAAAAAAA
183872 TTTTTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 3 0.09
26 14 0.44
27 9 0.28
28 6 0.19
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.19
Consensus pattern (26 bp):
AAAATAAAAAAAAAATTTAAAAAAAT
Found at i:184992 original size:20 final size:20
Alignment explanation
Indices: 184967--185012 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
184957 GTTTATTTTA
*
184967 TTTTTATAAT-TTTTCTAGTT
1 TTTTTAAAATATTTTCTA-TT
*
184987 TTTTTAAAATATTTTTTATT
1 TTTTTAAAATATTTTCTATT
185007 TTTTTA
1 TTTTTA
185013 GTTAGGAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTTAAAATATTTTCTATT
Found at i:185359 original size:21 final size:21
Alignment explanation
Indices: 185335--185422 Score: 65
Period size: 21 Copynumber: 4.1 Consensus size: 21
185325 TAATTTTAAA
185335 ATATAATTTGTTTTATAATTT
1 ATATAATTTGTTTTATAATTT
* *
185356 ATATATTTTATTTT-T-ATTT
1 ATATAATTTGTTTTATAATTT
* * *
185375 TTATAAGTAT-TATTATAATCTT
1 ATATAA-TTTGTTTTATAAT-TT
185397 GAAATATAATTTGTTTTATAATTT
1 ---ATATAATTTGTTTTATAATTT
185421 AT
1 AT
185423 TGTTATGACT
Statistics
Matches: 50, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
19 11 0.22
20 4 0.08
21 16 0.32
22 2 0.04
24 4 0.08
25 13 0.26
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (21 bp):
ATATAATTTGTTTTATAATTT
Found at i:185370 original size:65 final size:65
Alignment explanation
Indices: 185296--185422 Score: 236
Period size: 65 Copynumber: 2.0 Consensus size: 65
185286 TGAAAGTATG
*
185296 TTTTATTTTTATTTTTATAAGTATTATTATAATTTTAAAATATAATTTGTTTTATAATTTATATA
1 TTTTATTTTTATTTTTATAAGTATTATTATAATCTTAAAATATAATTTGTTTTATAATTTATATA
*
185361 TTTTATTTTTATTTTTATAAGTATTATTATAATCTTGAAATATAATTTGTTTTATAATTTAT
1 TTTTATTTTTATTTTTATAAGTATTATTATAATCTTAAAATATAATTTGTTTTATAATTTAT
185423 TGTTATGACT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (65 bp):
TTTTATTTTTATTTTTATAAGTATTATTATAATCTTAAAATATAATTTGTTTTATAATTTATATA
Found at i:185653 original size:20 final size:18
Alignment explanation
Indices: 185615--185654 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
185605 CAACATAGAA
185615 TTTTTTTTAAATATGATT
1 TTTTTTTTAAATATGATT
*
185633 TTTTTATTTATAATTTGATT
1 TTTTT-TTTA-AATATGATT
185653 TT
1 TT
185655 AATATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 4 0.21
20 10 0.53
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTTTTAAATATGATT
Found at i:189273 original size:89 final size:88
Alignment explanation
Indices: 188892--189281 Score: 255
Period size: 89 Copynumber: 4.4 Consensus size: 88
188882 TTAAAACTTG
* * * * * * * * * * *
188892 AAAGATGTGATAAATGCATAGGGGTATCAAATTCCTTCTTACATGAAAGAAAATATTTAACTAAT
1 AAAGATGTGACAGATGAATAAGGATATCAGATTCTTTCTGACACGATAG-AAATATTTGACTAAT
* ** * * *
188957 GCTTAACGAATTTCTTAGAACTCG
65 GCCTAATAAATTTCTTAAAACCCA
* * ** * * * * *
188981 AAAGATATAACAGATTCATAAAGG-TATCAAATTCTTACTGATATGACAAGAAATATTTGACTAA
1 AAAGATGTGACAGATGAAT-AAGGATATCAGATTCTTTCTGACACGA-TAGAAATATTTGACTAA
* * * *
189045 TGCCTATTAAATTTTTTGAAACTCA
64 TGCCTAATAAATTTCTTAAAACCCA
* * * * * * *
189070 AAAGATATGAGAAAT-ACACAAGGGTATCAGATTCTTTCTGACACGATAGAAACATTTAACTAAT
1 AAAGATGTGACAGATGA-ATAAGGATATCAGATTCTTTCTGACACGATAGAAATATTTGACTAAT
* *
189134 GCCTAATAAATTTCTCGAAAACCAA
65 GCCTAATAAATTTCT-TAAAACCCA
* * * **
189159 AAAGATGTAACAGTTGCATGGGGATATCAGATTACTTT-TGACACGATAGAAAATATTTGACTAA
1 AAAGATGTGACAGATGAATAAGGATATCAGATT-CTTTCTGACACGATAG-AAATATTTGACTAA
* * *
189223 TACCTAATAAATTCCTTAAAACCCG
64 TGCCTAATAAATTTCTTAAAACCCA
* *
189248 AAAGATGTGATAGATGAATAAGGATATCAAATTC
1 AAAGATGTGACAGATGAATAAGGATATCAGATTC
189282 CATTATAAAT
Statistics
Matches: 232, Mismatches: 61, Indels: 17
0.75 0.20 0.05
Matches are distributed among these distances:
88 33 0.14
89 163 0.70
90 36 0.16
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.30
Consensus pattern (88 bp):
AAAGATGTGACAGATGAATAAGGATATCAGATTCTTTCTGACACGATAGAAATATTTGACTAATG
CCTAATAAATTTCTTAAAACCCA
Found at i:191654 original size:20 final size:20
Alignment explanation
Indices: 191607--191652 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
191597 AAAAATAACG
*
191607 AAAAAAATAATGTAAAACTA
1 AAAAAAATAAAGTAAAACTA
191627 AAAAAAATAAAGTAAAA-TA
1 AAAAAAATAAAGTAAAACTA
191646 AAAAAAA
1 AAAAAAA
191653 ATTACAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.15
Consensus pattern (20 bp):
AAAAAAATAAAGTAAAACTA
Found at i:199770 original size:15 final size:15
Alignment explanation
Indices: 199750--199778 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
199740 AATACAACAC
199750 AAAAATTAGGAGAAT
1 AAAAATTAGGAGAAT
199765 AAAAATTAGGAGAA
1 AAAAATTAGGAGAA
199779 ATGAGTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (15 bp):
AAAAATTAGGAGAAT
Found at i:202167 original size:32 final size:32
Alignment explanation
Indices: 202126--202191 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
202116 TTTCATCTCC
202126 AAGCATCTATACGAAAACAGCAGAAAATATAT
1 AAGCATCTATACGAAAACAGCAGAAAATATAT
202158 AAGCATCTATACGAAAACAGCAGAAAATATAT
1 AAGCATCTATACGAAAACAGCAGAAAATATAT
202190 AA
1 AA
202192 ACGTCAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.18
Consensus pattern (32 bp):
AAGCATCTATACGAAAACAGCAGAAAATATAT
Found at i:208932 original size:16 final size:15
Alignment explanation
Indices: 208907--208937 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
208897 GTTTGCCCTT
208907 TTCTTTTCTTTTCTC
1 TTCTTTTCTTTTCTC
208922 TTCTCTTTCTTTTCTC
1 TTCT-TTTCTTTTCTC
208938 ATCCGTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCTTTTCTTTTCTC
Found at i:211505 original size:14 final size:15
Alignment explanation
Indices: 211486--211514 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
211476 ATTTCAACAT
211486 AAAAAAAA-GAAAAA
1 AAAAAAAAGGAAAAA
211500 AAAAAAAAGGAAAAA
1 AAAAAAAAGGAAAAA
211515 TGAAGATACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGGAAAAA
Found at i:212959 original size:41 final size:41
Alignment explanation
Indices: 212914--212997 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
212904 AACAAATTAT
*
212914 ATTCGCTATTGACCAAGTAGCTTTTACATACACGAACATGA
1 ATTCGCTATTGACCAAGTAGCTTTGACATACACGAACATGA
212955 ATTCGCTATTGACCAAGTAGCTTTGACATACACGAACATGA
1 ATTCGCTATTGACCAAGTAGCTTTGACATACACGAACATGA
212996 AT
1 AT
212998 GGTAATTTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (41 bp):
ATTCGCTATTGACCAAGTAGCTTTGACATACACGAACATGA
Found at i:213698 original size:2 final size:2
Alignment explanation
Indices: 213693--213728 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
213683 ATATATATAT
213693 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
213729 CTTGAATTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:213994 original size:42 final size:42
Alignment explanation
Indices: 213947--214030 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
213937 CATATCTTCG
213947 ATGAAGACCTAGAAATTCTCAGCTCCTAGCCAACCATAATAC
1 ATGAAGACCTAGAAATTCTCAGCTCCTAGCCAACCATAATAC
213989 ATGAAGACCTAGAAATTCTCAGCTCCTAGCCAACCATAATAC
1 ATGAAGACCTAGAAATTCTCAGCTCCTAGCCAACCATAATAC
214031 GACAAACCCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (42 bp):
ATGAAGACCTAGAAATTCTCAGCTCCTAGCCAACCATAATAC
Found at i:215788 original size:2 final size:2
Alignment explanation
Indices: 215781--215815 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
215771 TTTGCACAAA
215781 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 A
215816 GATCAGTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:223288 original size:11 final size:11
Alignment explanation
Indices: 223262--223300 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
223252 AAACAGGGAG
223262 AAGAAAGAGAAA
1 AAGAAAGAG-AA
223274 AAGAAACG-GAA
1 AAGAAA-GAGAA
223285 AAGAAAGAGAA
1 AAGAAAGAGAA
223296 AAGAA
1 AAGAA
223301 TTAAGAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 16 0.64
12 7 0.28
13 1 0.04
ACGTcount: A:0.72, C:0.03, G:0.26, T:0.00
Consensus pattern (11 bp):
AAGAAAGAGAA
Found at i:228839 original size:7 final size:7
Alignment explanation
Indices: 228827--228859 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
228817 TGTGAATGAC
228827 TTATTAA
1 TTATTAA
228834 TTATTAA
1 TTATTAA
228841 TTATT-A
1 TTATTAA
*
228847 TAATTAA
1 TTATTAA
228854 TTATTA
1 TTATTA
228860 GTTACTGTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTATTAA
Found at i:229950 original size:79 final size:79
Alignment explanation
Indices: 229839--230045 Score: 245
Period size: 79 Copynumber: 2.6 Consensus size: 79
229829 GAGATAATAA
* * * * * *
229839 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
229904 -TTAGAAAAAAAAAT
65 TTTAGAAAAAAAAAC
* * *
229918 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* * * *
229983 TTTGGAAATAAAGC
66 TTAGAAAAAAAAAC
* * *
229997 CGGGGTTGAAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
230046 GAAATAACGA
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
78 1 0.01
79 106 0.99
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:230053 original size:28 final size:27
Alignment explanation
Indices: 229997--230068 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
229987 GAAATAAAGC
* *
229997 CGGGGTTGAAGTATTCCCTCGGAAGTAA
1 CGGGGTTGGAGTA-TCCCTCGGAAATAA
230025 CGGGGTTGGAGTATCCC-CGATGAAATAA
1 CGGGGTTGGAGTATCCCTCG--GAAATAA
*
230053 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
230069 TTGATTGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 33 0.85
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCGGAAATAA
Found at i:230163 original size:52 final size:51
Alignment explanation
Indices: 230081--230214 Score: 207
Period size: 52 Copynumber: 2.6 Consensus size: 51
230071 GATTGTGAAA
230081 AAAATTGGTGTTTTTGAAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAGG
1 AAAATTGGTG-TTTTGAAAATAAAATCGGAGCTGGAGTATCCCCGATTAAA-G
* *
230134 AAAATTGGTGTTTT-AGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAG
1 AAAATTGGTGTTTTGA-AAATAAAATCGGAGCTGGAGTATCCCCGATTAAAG
*
230185 AAAATTAGTGTTTTGAAAATAAAATCGGAG
1 AAAATTGGTGTTTTGAAAATAAAATCGGAG
230215 ATTGAATTTC
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
51 29 0.38
52 37 0.49
53 10 0.13
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (51 bp):
AAAATTGGTGTTTTGAAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAG
Found at i:230209 original size:51 final size:52
Alignment explanation
Indices: 230081--230231 Score: 209
Period size: 51 Copynumber: 2.9 Consensus size: 52
230071 GATTGTGAAA
*
230081 AAAATTGGTGTTTTTGAAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAGG
1 AAAATTGGTG-TTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG
*
230134 AAAATTGGTGTTTT-AGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA-G
1 AAAATTGGTGTTTTGA-AAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG
* * *
230185 AAAATTAGTGTTTTGAAAATAAAATCGGAGATT-GAATTTCCCCGATT
1 AAAATTGGTGTTTTGAAAATAAAATCGGAG-TTGGAGTATCCCCGATT
230232 GCGGAGAGTT
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
51 41 0.46
52 39 0.43
53 10 0.11
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (52 bp):
AAAATTGGTGTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG
Found at i:232589 original size:13 final size:13
Alignment explanation
Indices: 232571--232597 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
232561 AAAATTTCCA
232571 AATGTATGGATAC
1 AATGTATGGATAC
232584 AATGTATGGATAC
1 AATGTATGGATAC
232597 A
1 A
232598 CAGAAAAATG
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:0.07, G:0.22, T:0.30
Consensus pattern (13 bp):
AATGTATGGATAC
Found at i:234137 original size:17 final size:17
Alignment explanation
Indices: 234111--234148 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
234101 ATTACACATT
234111 AAAT-GAGATAGTTTCA
1 AAATAGAGATAGTTTCA
234127 AAATAGAGATAGTTTCA
1 AAATAGAGATAGTTTCA
234144 AAATA
1 AAATA
234149 AAGAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (17 bp):
AAATAGAGATAGTTTCA
Found at i:234159 original size:17 final size:17
Alignment explanation
Indices: 234116--234152 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
234106 ACATTAAATG
*
234116 AGATAGTTTCAAAATAG
1 AGATAGTTTCAAAATAA
234133 AGATAGTTTCAAAATAA
1 AGATAGTTTCAAAATAA
234150 AGA
1 AGA
234153 ATATTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27
Consensus pattern (17 bp):
AGATAGTTTCAAAATAA
Found at i:238681 original size:12 final size:12
Alignment explanation
Indices: 238654--238712 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
238644 TTAGATAAAA
238654 ATATT-TTT-TT
1 ATATTATTTATT
*
238664 AAATTATTTATT
1 ATATTATTTATT
238676 ATATTATTATTATT
1 ATATTA-T-TTATT
238690 AATATTATTTATT
1 -ATATTATTTATT
* *
238703 TTAATATTTA
1 ATATTATTTA
238713 AATTATTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 4 0.10
11 3 0.08
12 15 0.38
13 6 0.15
14 6 0.15
15 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTATTTATT
Found at i:238730 original size:15 final size:17
Alignment explanation
Indices: 238661--238724 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
238651 AAAATATTTT
*
238661 TTTAAATTA-TTTATTA
1 TTTAAATTATTTTAATA
238677 TATT--ATTATTATTAATA
1 T-TTAAATTATT-TTAATA
*
238694 -TT-ATTTATTTTAATA
1 TTTAAATTATTTTAATA
238709 TTTAAATTATTTTAAT
1 TTTAAATTATTTTAAT
238725 TTAAATGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
15 12 0.31
16 9 0.23
17 18 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAATTATTTTAATA
Found at i:239891 original size:23 final size:25
Alignment explanation
Indices: 239856--239901 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
239846 AATAAAAATT
239856 AGCCATCAA-TTTTGACAAACAACA
1 AGCCATCAATTTTTGACAAACAACA
239880 AGCCAT-AATTTTTGACAAACAA
1 AGCCATCAATTTTTGACAAACAA
239902 AAAGGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (25 bp):
AGCCATCAATTTTTGACAAACAACA
Found at i:239925 original size:27 final size:27
Alignment explanation
Indices: 239887--239954 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
239877 ACAAGCCATA
239887 ATTTTTGACAAACAAAAAGGAACCACC
1 ATTTTTGACAAACAAAAAGGAACCACC
* * *
239914 ATTTTTGACAAATACAAAGTAACCACC
1 ATTTTTGACAAACAAAAAGGAACCACC
*
239941 ATTGTTGACAAACA
1 ATTTTTGACAAACA
239955 CATGGTGGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.24
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGGAACCACC
Found at i:239973 original size:24 final size:25
Alignment explanation
Indices: 239942--239999 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
239932 GTAACCACCA
*
239942 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
239966 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
239992 TTGTTGAC
1 TTGTTGAC
240000 TAGCCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:241716 original size:13 final size:13
Alignment explanation
Indices: 241698--241724 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
241688 TCAAAGTAAC
241698 ATGAAAAACCATA
1 ATGAAAAACCATA
241711 ATGAAAAACCATA
1 ATGAAAAACCATA
241724 A
1 A
241725 ACAGAATAAG
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:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (13 bp):
ATGAAAAACCATA
Found at i:242520 original size:24 final size:25
Alignment explanation
Indices: 242492--242560 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
242482 ACGTTGCGAT
242492 CAAGCTGGAATAGCCCAGTTGACT-
1 CAAGCTGGAATAGCCCAGTTGACTC
* * *
242516 GAAGCTGGAATAGCCCACTTGGCTC
1 CAAGCTGGAATAGCCCAGTTGACTC
*
242541 CAAG-TGGAATAGCTCAGTTG
1 CAAGCTGGAATAGCCCAGTTG
242561 CCTAGAGCGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 35 0.92
25 3 0.08
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (25 bp):
CAAGCTGGAATAGCCCAGTTGACTC
Found at i:242868 original size:19 final size:20
Alignment explanation
Indices: 242846--242885 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
242836 TTAAATAAGG
*
242846 ATATATAAT-GTAAATCAAA
1 ATATAAAATAGTAAATCAAA
*
242865 ATATAAAATAGTATATCAAA
1 ATATAAAATAGTAAATCAAA
242885 A
1 A
242886 CATGCAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (20 bp):
ATATAAAATAGTAAATCAAA
Found at i:243097 original size:36 final size:36
Alignment explanation
Indices: 243057--243179 Score: 142
Period size: 36 Copynumber: 3.2 Consensus size: 36
243047 TTTGATAAAA
243057 AATTTATATATTAAAATATATATAATATAAATTATT
1 AATTTATATATTAAAATATATATAATATAAATTATT
243093 AATTTATATA--AAAATATGAATATAATATAAATTATT
1 AATTTATATATTAAAATAT--ATATAATATAAATTATT
*
243129 AAAATGTAAATAATATATTAAAATGTATATAATATAAATTATT
1 --AAT-T---T-ATATATTAAAATATATATAATATAAATTATT
243172 AATTTATA
1 AATTTATA
243180 AAAATATGAA
Statistics
Matches: 75, Mismatches: 1, Indels: 22
0.77 0.01 0.22
Matches are distributed among these distances:
34 7 0.09
36 30 0.40
37 1 0.01
38 3 0.04
39 1 0.01
40 1 0.01
41 3 0.04
42 1 0.01
43 22 0.29
45 6 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (36 bp):
AATTTATATATTAAAATATATATAATATAAATTATT
Found at i:243141 original size:19 final size:20
Alignment explanation
Indices: 243119--243164 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
243109 TGAATATAAT
243119 ATAAAT-TATTAAAATGTAA
1 ATAAATATATTAAAATGTAA
*
243138 AT-AATATATTAAAATGTAT
1 ATAAATATATTAAAATGTAA
243157 AT-AATATA
1 ATAAATATA
243165 AATTATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
ATAAATATATTAAAATGTAA
Found at i:244851 original size:17 final size:18
Alignment explanation
Indices: 244818--244853 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
244808 TTCGATTATG
244818 ATTATAATTTCTCAAATA
1 ATTATAATTTCTCAAATA
244836 ATTATAATTT-TCAAATA
1 ATTATAATTTCTCAAATA
244853 A
1 A
244854 ATAAAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATAATTTCTCAAATA
Found at i:245119 original size:13 final size:13
Alignment explanation
Indices: 245101--245125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
245091 TTCAGCTTTT
245101 AAATAAAATTTAA
1 AAATAAAATTTAA
245114 AAATAAAATTTA
1 AAATAAAATTTA
245126 TCATAATTAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATAAAATTTAA
Found at i:247124 original size:16 final size:16
Alignment explanation
Indices: 247035--247130 Score: 59
Period size: 16 Copynumber: 5.6 Consensus size: 16
247025 AAATTTATTG
247035 AAATTATATTTATATTAA
1 AAATTATA--TATATTAA
* *
247053 ATAATAAAATACTAATTAA
1 A-AATTATATA-T-ATTAA
* *
247072 AATAATATTTATATTAA
1 AA-ATTATATATATTAA
* *
247089 ATAATTACAAATTATT-A
1 A-AATTATATA-TATTAA
247106 AAATTATATATATTAA
1 AAATTATATATATTAA
247122 AAATTATAT
1 AAATTATAT
247131 TTATACTTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
15 4 0.07
16 17 0.29
17 14 0.24
18 9 0.15
19 15 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTATATATATTAA
Found at i:247209 original size:24 final size:25
Alignment explanation
Indices: 247163--247217 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
247153 AGTATATATC
*
247163 AAAATTATAGTTACTAAATAATAATA
1 AAAATTATAGTTACTAAACAATAA-A
247189 AAAATTATA-TTA-TAAACAATAAA
1 AAAATTATAGTTACTAAACAATAAA
247212 AAAATT
1 AAAATT
247218 GAGAAGAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 7 0.25
24 9 0.32
25 3 0.11
26 9 0.32
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAATTATAGTTACTAAACAATAAA
Found at i:249862 original size:16 final size:15
Alignment explanation
Indices: 249826--249864 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
249816 TTTCAATTCA
249826 AATATTTTTTATATT
1 AATATTTTTTATATT
**
249841 CGTATTTTTATATATT
1 AATATTTTT-TATATT
249857 AATATTTT
1 AATATTTT
249865 ATTGTCACTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (15 bp):
AATATTTTTTATATT
Found at i:250219 original size:22 final size:21
Alignment explanation
Indices: 250194--250240 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
250184 TTCATAAATT
250194 AAATAAATCTTATTAATAATAA
1 AAATAAATCTTATT-ATAATAA
*
250216 AAAT--ATTTTATTATAATAA
1 AAATAAATCTTATTATAATAA
*
250235 TAATAA
1 AAATAA
250241 TATAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
22 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATAAATCTTATTATAATAA
Found at i:293077 original size:17 final size:18
Alignment explanation
Indices: 293055--293092 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
293045 TTTAAAAAAT
* *
293055 ATTAAA-AAAATTGAGAA
1 ATTAAAGAAAAATAAGAA
293072 ATTAAAGAAAAATAAGAA
1 ATTAAAGAAAAATAAGAA
293090 ATT
1 ATT
293093 TCAAGGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (18 bp):
ATTAAAGAAAAATAAGAA
Found at i:293974 original size:3 final size:3
Alignment explanation
Indices: 293968--293999 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
293958 AGAACAATGA
293968 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
294000 ATAAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:295773 original size:14 final size:14
Alignment explanation
Indices: 295754--295824 Score: 63
Period size: 14 Copynumber: 4.9 Consensus size: 14
295744 GTTATTTTAG
*
295754 ATATTAACATAAAA
1 ATATTAAAATAAAA
295768 ATATTAAAAT-AAA
1 ATATTAAAATAAAA
*
295781 ATATAAAAATAATATA
1 ATATTAAAATAA-A-A
*
295797 TTATTAAATATAAAA
1 ATATTAAA-ATAAAA
* *
295812 ATAATATAATAAA
1 ATATTAAAATAAA
295825 TATGATAAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
13 12 0.26
14 15 0.33
15 7 0.15
16 8 0.17
17 4 0.09
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATTAAAATAAAA
Found at i:295783 original size:13 final size:13
Alignment explanation
Indices: 295754--295799 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
295744 GTTATTTTAG
*
295754 ATATTAACATAAAA
1 ATATTAAAAT-AAA
295768 ATATTAAAATAAA
1 ATATTAAAATAAA
* *
295781 ATATAAAAATAAT
1 ATATTAAAATAAA
295794 ATATTA
1 ATATTA
295800 TTAAATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 19 0.68
14 9 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
ATATTAAAATAAA
Found at i:295832 original size:23 final size:21
Alignment explanation
Indices: 295762--295824 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
295752 AGATATTAAC
* *
295762 ATAAAAATATTAAAATAAAAT
1 ATAAAAATAATATAATAAAAT
*
295783 ATAAAAATAATATATTATTAAAT
1 ATAAAAATAATATA--ATAAAAT
295806 ATAAAAATAATATAATAAA
1 ATAAAAATAATATAATAAA
295825 TATGATAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.44
23 20 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAAAATAATATAATAAAAT
Found at i:297798 original size:19 final size:19
Alignment explanation
Indices: 297774--297810 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
297764 TTTTTTTAAA
297774 AATAATATTTTATAAATTT
1 AATAATATTTTATAAATTT
* *
297793 AATAATTTTTTTTAAATT
1 AATAATATTTTATAAATT
297811 ATAAGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATAATATTTTATAAATTT
Found at i:298606 original size:15 final size:14
Alignment explanation
Indices: 298588--298629 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
298578 TTTATATTAA
298588 TATTATTTTTATAAT
1 TATT-TTTTTATAAT
298603 TATTTGTATTT-TAAT
1 TATTT-T-TTTATAAT
298618 TATTTTTTTATA
1 TATTTTTTTATA
298630 TTGTGTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.12
14 4 0.17
15 14 0.58
16 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (14 bp):
TATTTTTTTATAAT
Found at i:300799 original size:2 final size:2
Alignment explanation
Indices: 300787--300821 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
300777 TACCTTGCAG
*
300787 TA TA AA 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 T
300822 CATTATAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:302697 original size:6 final size:6
Alignment explanation
Indices: 302686--302723 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
302676 GATTAAATAT
* *
302686 AATTAA AATTAA AATTAA AATTAA ATTTAA ATTTAA AA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AA
302724 ATTTGAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AATTAA
Found at i:303994 original size:24 final size:24
Alignment explanation
Indices: 303950--303996 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
303940 GACCTTGTCT
*
303950 GAAAATAGTGAAAATCCAAAAGTA
1 GAAAATAGTGAAAATCAAAAAGTA
*
303974 GAAAATATTGTAAAA-CAAAAAGT
1 GAAAATAGTG-AAAATCAAAAAGT
303997 CGTGAGCGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (24 bp):
GAAAATAGTGAAAATCAAAAAGTA
Found at i:304618 original size:5 final size:5
Alignment explanation
Indices: 304608--304633 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
304598 ATAAACTTTC
304608 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
304634 TAAAGACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:307410 original size:9 final size:9
Alignment explanation
Indices: 307396--307450 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
307386 ATCATACAAC
307396 ATTTAAAAA
1 ATTTAAAAA
307405 ATTT-AAAA
1 ATTTAAAAA
*
307413 ATAT-AAAA
1 ATTTAAAAA
*
307421 ATATAAAAAA
1 AT-TTAAAAA
*
307431 ATTAAAAAA
1 ATTTAAAAA
*
307440 AATTAAAAA
1 ATTTAAAAA
307449 AT
1 AT
307451 AAAATAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
8 13 0.34
9 19 0.50
10 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:307430 original size:10 final size:10
Alignment explanation
Indices: 307409--307466 Score: 52
Period size: 9 Copynumber: 6.0 Consensus size: 10
307399 TAAAAAATTT
307409 AAAAATAT--
1 AAAAATATAA
307417 AAAAATATAA
1 AAAAATATAA
307427 AAAAAT-TAA
1 AAAAATATAA
*
307436 AAAAA-ATTA
1 AAAAATATAA
*
307445 AAAAATAAAA
1 AAAAATATAA
307455 TAAATAATATAA
1 -AAA-AATATAA
307467 TATCCAATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 8 0.20
9 15 0.38
10 8 0.20
11 3 0.08
12 6 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAAATATAA
Found at i:307437 original size:8 final size:8
Alignment explanation
Indices: 307398--307454 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
307388 CATACAACAT
307398 TTAAAAAA
1 TTAAAAAA
*
307406 TTTAAAAA
1 TTAAAAAA
307414 TATAAAAATA
1 T-TAAAAA-A
*
307424 TAAAAAAA
1 TTAAAAAA
307432 TTAAAAAAAA
1 TT--AAAAAA
307442 TTAAAAAA
1 TTAAAAAA
307450 -TAAAA
1 TTAAAA
307455 TAAATAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
7 5 0.12
8 16 0.39
9 10 0.24
10 10 0.24
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
TTAAAAAA
Found at i:307438 original size:26 final size:26
Alignment explanation
Indices: 307400--307459 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
307390 TACAACATTT
* *
307400 AAAAAATTTAAAAATA-TAAAAATATA
1 AAAAAATTAAAAAAAATTAAAAA-ATA
307426 AAAAAATTAAAAAAAATTAAAAAATA
1 AAAAAATTAAAAAAAATTAAAAAATA
307452 AAATAAAT
1 AAA-AAAT
307460 AATATAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (26 bp):
AAAAAATTAAAAAAAATTAAAAAATA
Found at i:307459 original size:9 final size:8
Alignment explanation
Indices: 307408--307461 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
307398 TTAAAAAATT
*
307408 TAAAAATA
1 TAAAAAAA
*
307416 TAAAAATA
1 TAAAAAAA
307424 TAAAAAAA
1 TAAAAAAA
307432 TTAAAAAAAA
1 -T-AAAAAAA
*
307442 TTAAAAAA
1 TAAAAAAA
307450 TAAAATAAA
1 TAAAA-AAA
307459 TAA
1 TAA
307462 TATAATATCC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
8 25 0.62
9 8 0.20
10 7 0.17
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
TAAAAAAA
Found at i:310254 original size:6 final size:6
Alignment explanation
Indices: 310239--310274 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
310229 GCAAAAATGT
*
310239 TAATTG TAATTA TAATTA TAATTA TAATTA TAATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
310275 AGAGATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:311754 original size:20 final size:20
Alignment explanation
Indices: 311729--311785 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
311719 AAGAATTGAA
311729 GAGGGATACAAGAGAGAGAT
1 GAGGGATACAAGAGAGAGAT
*
311749 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGAGAT
311769 GAGGGATACAAGAGAGA
1 GAGGGATACAAGAGAGA
311786 AGGGAGCTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.44, C:0.05, G:0.42, T:0.09
Consensus pattern (20 bp):
GAGGGATACAAGAGAGAGAT
Found at i:311940 original size:24 final size:27
Alignment explanation
Indices: 311867--311937 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
311857 AAACAAGCCT
* *
311867 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
311895 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
311922 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
311938 AATGGGTGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:316342 original size:20 final size:20
Alignment explanation
Indices: 316317--316373 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
316307 AAGAATTGAA
316317 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
316337 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
* *
316357 GGGGGATATAAGAGAGG
1 GAGGGATACAAGAGAGG
316374 AGGGAGCCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.04, G:0.47, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:316516 original size:27 final size:27
Alignment explanation
Indices: 316455--316525 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
316445 AAACAAGCCT
* *
316455 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
316483 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
*
316510 CCATTTTTTACAAACA
1 CCATTTTTGACAAACA
316526 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:317464 original size:32 final size:33
Alignment explanation
Indices: 317423--317507 Score: 84
Period size: 32 Copynumber: 2.6 Consensus size: 33
317413 TCAAGGTTAG
* *
317423 ATTTGAATTTTTTTTAATTTTAAAT-ATTTTGA
1 ATTTAAATTTTTTTTAATTTTAAATAATTTTAA
* **
317455 ATTTAAATTTTATTT-GGTTTAAATAATTTTAA
1 ATTTAAATTTTTTTTAATTTTAAATAATTTTAA
*
317487 ATATTAATTTTTTTTTTAATT
1 AT-TTAA-ATTTTTTTTAATT
317508 CGAATTCTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
31 7 0.17
32 21 0.52
33 4 0.10
34 7 0.17
35 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (33 bp):
ATTTAAATTTTTTTTAATTTTAAATAATTTTAA
Found at i:322433 original size:2 final size:2
Alignment explanation
Indices: 322426--322453 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
322416 GTTTTCTTTA
322426 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
322454 TAAAAGGAAA
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:323764 original size:2 final size:2
Alignment explanation
Indices: 323757--323784 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
323747 TAATTGATTT
323757 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
323785 AACCGAATCG
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:339801 original size:18 final size:18
Alignment explanation
Indices: 339780--339819 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
339770 AAAAAAATAA
339780 TATAATATATTAT-AAATT
1 TATAAT-TATTATAAAATT
*
339798 TATAATTATTTTAAAATT
1 TATAATTATTATAAAATT
339816 TATA
1 TATA
339820 TAATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAATTATTATAAAATT
Found at i:339877 original size:26 final size:27
Alignment explanation
Indices: 339822--339885 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
339812 AATTTATATA
* **
339822 ATATAAATAATTATCATACTAAAATTT
1 ATATAAATAATTATAATACTAAAAAAT
339849 ATATAAAT-ATTATAATA-TAATAAAAT
1 ATATAAATAATTATAATACTAA-AAAAT
*
339875 ATATAATTAAT
1 ATATAAATAAT
339886 ACACAAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 3 0.10
26 18 0.58
27 10 0.32
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATAAATAATTATAATACTAAAAAAT
Found at i:339879 original size:17 final size:17
Alignment explanation
Indices: 339853--339886 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
339843 AAATTTATAT
339853 AAATATTATAATATAATA
1 AAATATTATAAT-TAATA
339871 AAATA-TATAATTAATA
1 AAATATTATAATTAATA
339887 CACAAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATTATAATTAATA
Found at i:341351 original size:15 final size:16
Alignment explanation
Indices: 341313--341364 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
341303 TTAATTACTA
341313 TTAATATAAATATAAT
1 TTAATATAAATATAAT
341329 TCTAATATATAAT-T-AT
1 T-TAATATA-AATATAAT
341345 TTAATAT-AATATAACT
1 TTAATATAAATATAA-T
341361 TTAA
1 TTAA
341365 CATTTTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.10
14 1 0.03
15 7 0.23
16 9 0.29
17 8 0.26
18 3 0.10
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATATAAATATAAT
Found at i:341523 original size:27 final size:27
Alignment explanation
Indices: 341477--341566 Score: 103
Period size: 27 Copynumber: 3.3 Consensus size: 27
341467 AATACATATT
*
341477 TTATTATAAATTTTAATTTTATTATTACA
1 TTATTATTAATTTTAATTTTATTA-TA-A
*
341506 TTA-T-TTAATTTTACTTTTATTATAA
1 TTATTATTAATTTTAATTTTATTATAA
* *
341531 TTATTATTACTTTTAATTTTATTAAAA
1 TTATTATTAATTTTAATTTTATTATAA
*
341558 TTAATATTA
1 TTATTATTA
341567 CTGTACATTC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.08
26 3 0.06
27 42 0.79
28 1 0.02
29 3 0.06
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATTATTAATTTTAATTTTATTATAA
Found at i:341890 original size:17 final size:18
Alignment explanation
Indices: 341848--341890 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
341838 TAACTTTATT
341848 TTTAATATAATAAATAAAA
1 TTTAATATAATAAAT-AAA
341867 TTT--TATAATAAAT-AA
1 TTTAATATAATAAATAAA
341882 TTTAATATA
1 TTTAATATA
341891 TTATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.23
17 14 0.64
19 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAATATAATAAATAAA
Found at i:342095 original size:21 final size:21
Alignment explanation
Indices: 342069--342134 Score: 96
Period size: 21 Copynumber: 3.0 Consensus size: 21
342059 ATTCAATCTC
342069 ATTATTATAATATTTAATTTT
1 ATTATTATAATATTTAATTTT
*
342090 ATTATTATAATAATTAATTTT
1 ATTATTATAATATTTAATTTT
*
342111 ATTATCATAATTATTTTAATTTT
1 ATTATTATAA-TA-TTTAATTTT
342134 A
1 A
342135 CTTAAATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 29 0.73
22 2 0.05
23 9 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTATAATATTTAATTTT
Found at i:343078 original size:29 final size:28
Alignment explanation
Indices: 343035--343122 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
343025 TAATTATTAT
343035 AATTATA-T-ATATTAAATAATAAAATAA
1 AATTATATTCATATT-AATAATAAAATAA
* * *
343062 AATTATATTCATGTTAATAAT-GATTAA
1 AATTATATTCATATTAATAATAAAATAA
343089 AATTATATTCATATTAA-AATAAGTAATAA
1 AATTATATTCATATTAATAATAA--AATAA
343118 AATTA
1 AATTA
343123 ATAAAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
26 3 0.06
27 27 0.54
28 7 0.14
29 13 0.26
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (28 bp):
AATTATATTCATATTAATAATAAAATAA
Found at i:343198 original size:20 final size:19
Alignment explanation
Indices: 343154--343201 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
343144 AAGTAAATTA
*
343154 ATAAAATAAATATGAAAAAT
1 ATAAAA-AAATATGAAAAAG
*
343174 TTAAAAAAATATGAAGAAAG
1 ATAAAAAAATATGAA-AAAG
343194 ATAAAAAA
1 ATAAAAAA
343202 GAAGAATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
ATAAAAAAATATGAAAAAG
Found at i:343992 original size:24 final size:21
Alignment explanation
Indices: 343938--343995 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
343928 AATGTTAATT
343938 TTAATTTTATTATTATAATAA
1 TTAATTTTATTATTATAATAA
343959 TTAATTTTATTATTATAATAA
1 TTAATTTTATTATTATAATAA
*
343980 TTAATTTCATTATTAT
1 TTAATTTTATTATTAT
343996 CATTATTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAATTTTATTATTATAATAA
Found at i:343992 original size:39 final size:38
Alignment explanation
Indices: 343949--344025 Score: 86
Period size: 39 Copynumber: 2.0 Consensus size: 38
343939 TAATTTTATT
343949 ATTATAATAATTAATTTT-ATTATTA-TAATAATTAATTTC
1 ATTATAATAATT-ATTTTAATT-TTATTAA-AATTAATTTC
* *
343988 ATTATTATCATTATTTTCAATTTTATTAAAATTAATTT
1 ATTATAATAATTATTTT-AATTTTATTAAAATTAATTT
344026 TAATAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
38 5 0.15
39 22 0.67
40 6 0.18
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (38 bp):
ATTATAATAATTATTTTAATTTTATTAAAATTAATTTC
Found at i:345814 original size:21 final size:21
Alignment explanation
Indices: 345788--345832 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
345778 TATTCGAGCG
345788 TTAACTCTATAGACTCTTTCC
1 TTAACTCTATAGACTCTTTCC
*
345809 TTAACTCTATATACTCTTTCC
1 TTAACTCTATAGACTCTTTCC
345830 TTA
1 TTA
345833 GAAACTCCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAACTCTATAGACTCTTTCC
Found at i:349840 original size:2 final size:2
Alignment explanation
Indices: 349833--349862 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
349823 ATAATTTAAA
349833 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
349863 TCAGGTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351297 original size:177 final size:177
Alignment explanation
Indices: 350955--351309 Score: 455
Period size: 177 Copynumber: 2.0 Consensus size: 177
350945 TAAAGTCACA
* * *
350955 ACACTTGGAGAAATTGGTGACTCCTTCCACATCCCATGTACCGTCCTTATTCTTCTGGGTAAAGA
1 ACACTTGGAGAAATTGGTGACTCCTTCCACATCCCATGTACCGTCCTTATGCTGCTGGGCAAAGA
* * * * *
351020 ATATAATCTAATGGGAATTCATAGAGAGGGCTTTGAATTTAGATTATTTGTTATTAGCAGATTTA
66 ACAGAATCTAATGGGAATTCACAGAGAGGGCTTTGAATTTAGACTAGTTGTTATTAGCAGATTTA
* *
351085 TATGCAATAAACTTTAACGCATTAATTGTTTTAGGCAATTGATTCTT
131 TATGCAATAAACTTTAACGAATTAACTGTTTTAGGCAATTGATTCTT
* * *** *
351132 ACACTTGGTG-AATTGGTGACTTCTTCCACATGTTATGTACTGTCCTTATAGC-GCTGGGCAAAG
1 ACACTTGGAGAAATTGGTGACTCCTTCCACATCCCATGTACCGTCCTTAT-GCTGCTGGGCAAAG
* *
351195 AACAGAATCTAATGGGAATTCGCAGAGAGGGCTGTTGAATTTAGACTAGTTGTTATTAGCATATT
65 AACAGAATCTAATGGGAATTCACAGAGAGGGCT-TTGAATTTAGACTAGTTGTTATTAGCAGATT
*** * *
351260 TATATTTTATAAA-TTTGAATGAATTAACTGTTTTAGGCAGTTGATTCTT
129 TATATGCAATAAACTTT-AACGAATTAACTGTTTTAGGCAATTGATTCTT
351309 A
1 A
351310 TTTTCTTGCC
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
176 75 0.49
177 77 0.51
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.37
Consensus pattern (177 bp):
ACACTTGGAGAAATTGGTGACTCCTTCCACATCCCATGTACCGTCCTTATGCTGCTGGGCAAAGA
ACAGAATCTAATGGGAATTCACAGAGAGGGCTTTGAATTTAGACTAGTTGTTATTAGCAGATTTA
TATGCAATAAACTTTAACGAATTAACTGTTTTAGGCAATTGATTCTT
Found at i:352738 original size:16 final size:16
Alignment explanation
Indices: 352717--352749 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
352707 TCAGTGGTCT
352717 AGCTGATATTTGAATG
1 AGCTGATATTTGAATG
352733 AGCTGATATTTGAATG
1 AGCTGATATTTGAATG
352749 A
1 A
352750 TATGCCTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (16 bp):
AGCTGATATTTGAATG
Found at i:359645 original size:26 final size:26
Alignment explanation
Indices: 359596--359645 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
359586 GTCAGCTCGA
*
359596 TAATTAATAAATCAAACTCGATTCAT
1 TAATTAATAAATCAAACTCAATTCAT
* *
359622 TAATTAATAAGTCAAACTTAATTC
1 TAATTAATAAATCAAACTCAATTC
359646 TATCTAATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (26 bp):
TAATTAATAAATCAAACTCAATTCAT
Found at i:368884 original size:16 final size:17
Alignment explanation
Indices: 368853--368887 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
368843 AAGGAAGATG
*
368853 AAGAAGAAAGAAAGAAA
1 AAGAAGAAAAAAAGAAA
368870 AAGAA-AAAAAAAGAAA
1 AAGAAGAAAAAAAGAAA
368886 AA
1 AA
368888 ATATGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAAAAGAAA
Found at i:368895 original size:10 final size:10
Alignment explanation
Indices: 368859--368888 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
368849 GATGAAGAAG
*
368859 AAAGAAAGAA
1 AAAGAAAAAA
368869 AAAGAAAAAA
1 AAAGAAAAAA
368879 AAAGAAAAAA
1 AAAGAAAAAA
368889 TATGAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:375384 original size:36 final size:35
Alignment explanation
Indices: 375304--375384 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
375294 TCAAAATGAC
* * *
375304 AAAAAAAAAAGTCAAAAGCAAAAGCACAAAAAATG
1 AAAACAAAAAGTCAAAAGCAAAAGCAAAAAAAAGG
* *
375339 AAAAGAAAAAGTGCAAAAGCAAAA-TAAAAAAAAGG
1 AAAACAAAAAGT-CAAAAGCAAAAGCAAAAAAAAGG
375374 AACAACAAAAA
1 AA-AACAAAAA
375385 TAAAAAAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 21 0.54
36 18 0.46
ACGTcount: A:0.73, C:0.10, G:0.12, T:0.05
Consensus pattern (35 bp):
AAAACAAAAAGTCAAAAGCAAAAGCAAAAAAAAGG
Done.