Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 83 of 210
Found at i:28771077 original size:25 final size:23
Alignment explanation
Indices: 28771030--28771075 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28771020 ATACATTTGA
*
28771030 TTTTATAATATATATATGCATAT
1 TTTTATAATATATATATACATAT
* *
28771053 TTTTATAATCTATATATATATAT
1 TTTTATAATATATATATACATAT
28771076 ATATATACGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTATAATATATATATACATAT
Found at i:28772487 original size:21 final size:21
Alignment explanation
Indices: 28772457--28772610 Score: 87
Period size: 21 Copynumber: 7.3 Consensus size: 21
28772447 ACAGAAACCT
*
28772457 ATAAGGGTTGAACGGAAGCTC
1 ATAAGAGTTGAACGGAAGCTC
* * * *
28772478 GTAAGAGTTGAACGAAAACCC
1 ATAAGAGTTGAACGGAAGCTC
* **
28772499 ATAAG-GGTGAAATAGAAGCTC
1 ATAAGAGTTG-AACGGAAGCTC
* * * *
28772520 AAAAGAGTTGAACGAAAACCC
1 ATAAGAGTTGAACGGAAGCTC
* * *
28772541 ATAAGGGTTAAACAGAAGCTC
1 ATAAGAGTTGAACGGAAGCTC
* *
28772562 GA-AAAAGTTGAACGGAAACTC
1 -ATAAGAGTTGAACGGAAGCTC
* * *
28772583 ATAAGGGTTAAACAGAAGCTC
1 ATAAGAGTTGAACGGAAGCTC
*
28772604 ATGAGAG
1 ATAAGAG
28772611 CTAAACAAAA
Statistics
Matches: 91, Mismatches: 38, Indels: 8
0.66 0.28 0.06
Matches are distributed among these distances:
20 4 0.04
21 83 0.91
22 4 0.04
ACGTcount: A:0.44, C:0.14, G:0.26, T:0.16
Consensus pattern (21 bp):
ATAAGAGTTGAACGGAAGCTC
Found at i:28772497 original size:42 final size:42
Alignment explanation
Indices: 28772451--28772603 Score: 216
Period size: 42 Copynumber: 3.6 Consensus size: 42
28772441 AGCTAAACAG
* * * *
28772451 AAACCTATAAGGGTTGAACGGAAGCTCGTAAGAGTTGAACGA
1 AAACCCATAAGGGTTAAACAGAAGCTCGAAAGAGTTGAACGA
* * *
28772493 AAACCCATAAGGGTGAAATAGAAGCTCAAAAGAGTTGAACGA
1 AAACCCATAAGGGTTAAACAGAAGCTCGAAAGAGTTGAACGA
* *
28772535 AAACCCATAAGGGTTAAACAGAAGCTCGAAAAAGTTGAACGG
1 AAACCCATAAGGGTTAAACAGAAGCTCGAAAGAGTTGAACGA
*
28772577 AAACTCATAAGGGTTAAACAGAAGCTC
1 AAACCCATAAGGGTTAAACAGAAGCTC
28772604 ATGAGAGCTA
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 98 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACAGAAGCTCGAAAGAGTTGAACGA
Found at i:28778654 original size:15 final size:16
Alignment explanation
Indices: 28778634--28778669 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
28778624 GGTTATTGGT
28778634 TGGGTTAGGG-TTTTG
1 TGGGTTAGGGCTTTTG
28778649 TGGGTTAGGGCTTTTG
1 TGGGTTAGGGCTTTTG
28778665 -GGGTT
1 TGGGTT
28778670 TATTGGGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.06, C:0.03, G:0.47, T:0.44
Consensus pattern (16 bp):
TGGGTTAGGGCTTTTG
Found at i:28784641 original size:3 final size:3
Alignment explanation
Indices: 28784633--28784663 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
28784623 CTGCTTTTGA
28784633 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
28784664 CCTGCATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:28795022 original size:21 final size:22
Alignment explanation
Indices: 28794998--28795100 Score: 76
Period size: 21 Copynumber: 5.0 Consensus size: 22
28794988 TGAACGAAAA
*
28794998 CTCATAATG-GTTAAATTGAAG
1 CTCATAATGAGTTAAACTGAAG
*
28795019 CTCA-AAAGAGTTAAACTGCAA-
1 CTCATAATGAGTTAAACTG-AAG
* * * *
28795040 CCCAGAA-GGGTTAAACTGAAA
1 CTCATAATGAGTTAAACTGAAG
28795061 CTCAT-ATGAGTT-AACTGAAG
1 CTCATAATGAGTTAAACTGAAG
* *
28795081 CTCATAA-GAGCTAAAATGAA
1 CTCATAATGAGTTAAACTGAA
28795101 AACAAACACG
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
20 22 0.34
21 39 0.60
22 4 0.06
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (22 bp):
CTCATAATGAGTTAAACTGAAG
Found at i:28802475 original size:59 final size:60
Alignment explanation
Indices: 28802372--28802489 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 60
28802362 GGCACTCAAA
* * * * *
28802372 CTTTCAGTAGAATCTAGAGATTATATCTCACCGAGGACAGTATCAAACTTATT-AAAGAG
1 CTTTCAATAGAATCTAGAGATTAAATCTCACCAAAGACAATATCAAACTTATTGAAAGAG
* *
28802431 CTTTCAATATAATTTAGAGATTAAA-CTCTACCAAAGACAATATCAAACTTATTGAAAGA
1 CTTTCAATAGAATCTAGAGATTAAATCTC-ACCAAAGACAATATCAAACTTATTGAAAGA
28802490 TGTCGACTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 3 0.06
59 42 0.84
60 5 0.10
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.30
Consensus pattern (60 bp):
CTTTCAATAGAATCTAGAGATTAAATCTCACCAAAGACAATATCAAACTTATTGAAAGAG
Found at i:28803225 original size:21 final size:21
Alignment explanation
Indices: 28803199--28803239 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28803189 TTTGACTATG
* *
28803199 CTTTCTTCTTCCTTTTTAATT
1 CTTTCTTCTACCTTTATAATT
28803220 CTTTCTTCTACCTTTATAAT
1 CTTTCTTCTACCTTTATAAT
28803240 GTTTAACGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (21 bp):
CTTTCTTCTACCTTTATAATT
Found at i:28805696 original size:295 final size:295
Alignment explanation
Indices: 28805166--28805744 Score: 1158
Period size: 295 Copynumber: 2.0 Consensus size: 295
28805156 TTATAATTTC
28805166 TTTATTTGTAAGAGGACTGAATTTAATTCTATTTCATTATGCGGGTCAAAGTGTGATTTCACTAT
1 TTTATTTGTAAGAGGACTGAATTTAATTCTATTTCATTATGCGGGTCAAAGTGTGATTTCACTAT
28805231 ATATTAATTCATAGTTTATCTATTTATAGGAAGACTAAATTGAAAAAAAAATCATTTTTGGGGAC
66 ATATTAATTCATAGTTTATCTATTTATAGGAAGACTAAATTGAAAAAAAAATCATTTTTGGGGAC
28805296 CAAGTCCCTAGAGGTGTTTAACCGGTTAACCGACCCGAACTAACATTAACCGAACTTTTTAAACC
131 CAAGTCCCTAGAGGTGTTTAACCGGTTAACCGACCCGAACTAACATTAACCGAACTTTTTAAACC
28805361 CTTATCCGTTGATCGAACGGAAATTTTTTCAAAAAAAATTAATTGATCAAACTTTTTCGGTTAAT
196 CTTATCCGTTGATCGAACGGAAATTTTTTCAAAAAAAATTAATTGATCAAACTTTTTCGGTTAAT
28805426 TCGATTTGTTTTTTTTTTTTTTTTTTTTAAAAATT
261 TCGATTTGTTTTTTTTTTTTTTTTTTTTAAAAATT
28805461 TTTATTTGTAAGAGGACTGAATTTAATTCTATTTCATTATGCGGGTCAAAGTGTGATTTCACTAT
1 TTTATTTGTAAGAGGACTGAATTTAATTCTATTTCATTATGCGGGTCAAAGTGTGATTTCACTAT
28805526 ATATTAATTCATAGTTTATCTATTTATAGGAAGACTAAATTGAAAAAAAAATCATTTTTGGGGAC
66 ATATTAATTCATAGTTTATCTATTTATAGGAAGACTAAATTGAAAAAAAAATCATTTTTGGGGAC
28805591 CAAGTCCCTAGAGGTGTTTAACCGGTTAACCGACCCGAACTAACATTAACCGAACTTTTTAAACC
131 CAAGTCCCTAGAGGTGTTTAACCGGTTAACCGACCCGAACTAACATTAACCGAACTTTTTAAACC
28805656 CTTATCCGTTGATCGAACGGAAATTTTTTCAAAAAAAATTAATTGATCAAACTTTTTCGGTTAAT
196 CTTATCCGTTGATCGAACGGAAATTTTTTCAAAAAAAATTAATTGATCAAACTTTTTCGGTTAAT
28805721 TCGATTTGTTTTTTTTTTTTTTTT
261 TCGATTTGTTTTTTTTTTTTTTTT
28805745 GTTAAAACAG
Statistics
Matches: 284, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
295 284 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (295 bp):
TTTATTTGTAAGAGGACTGAATTTAATTCTATTTCATTATGCGGGTCAAAGTGTGATTTCACTAT
ATATTAATTCATAGTTTATCTATTTATAGGAAGACTAAATTGAAAAAAAAATCATTTTTGGGGAC
CAAGTCCCTAGAGGTGTTTAACCGGTTAACCGACCCGAACTAACATTAACCGAACTTTTTAAACC
CTTATCCGTTGATCGAACGGAAATTTTTTCAAAAAAAATTAATTGATCAAACTTTTTCGGTTAAT
TCGATTTGTTTTTTTTTTTTTTTTTTTTAAAAATT
Found at i:28811072 original size:14 final size:13
Alignment explanation
Indices: 28811043--28811086 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
28811033 TATTTACAAA
28811043 TTTAAATTTTAGTT
1 TTTAAATTTTA-TT
28811057 TTTAAATTTTTATT
1 TTTAAA-TTTTATT
*
28811071 TTCTAAAATTTATT
1 TT-TAAATTTTATT
28811085 TT
1 TT
28811087 GATAGCCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (13 bp):
TTTAAATTTTATT
Found at i:28811352 original size:10 final size:10
Alignment explanation
Indices: 28811337--28811378 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
28811327 TTATATTCAC
28811337 AATAATTTTT
1 AATAATTTTT
28811347 AATAATTTATT
1 AATAATTT-TT
*
28811358 -ATAATTCTT
1 AATAATTTTT
*
28811367 AACAATTTTT
1 AATAATTTTT
28811377 AA
1 AA
28811379 ATATTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 2 0.07
10 23 0.85
11 2 0.07
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (10 bp):
AATAATTTTT
Found at i:28819921 original size:16 final size:17
Alignment explanation
Indices: 28819889--28819922 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28819879 ACTCTAACAT
28819889 GATGTTGAATATCTTTG
1 GATGTTGAATATCTTTG
28819906 GATGTTGAAT-TCTTTG
1 GATGTTGAATATCTTTG
28819922 G
1 G
28819923 GAAATGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.47
Consensus pattern (17 bp):
GATGTTGAATATCTTTG
Found at i:28835317 original size:17 final size:18
Alignment explanation
Indices: 28835289--28835322 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28835279 AGAATTCATC
*
28835289 TTATTATAGATTTAAATA
1 TTATTATAGATTGAAATA
28835307 TTATTAT-GATTGAAAT
1 TTATTATAGATTGAAAT
28835323 TTTTTCGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
TTATTATAGATTGAAATA
Found at i:28836305 original size:151 final size:150
Alignment explanation
Indices: 28835921--28836497 Score: 838
Period size: 150 Copynumber: 3.8 Consensus size: 150
28835911 TTATATTTGA
* *
28835921 GCCATTTGTTCGTA-TTTTTCCCCGAATTTTATTACTTT-AAAAAATATACTATTTTTTAATTTT
1 GCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTT
* * * **
28835984 CTAATTTTACATTATTTTAGTAGATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTATTTAA
66 ATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAA
28836049 ATTAAAAAAAACT-TTATTTCG
131 ATT--AAAAAACTCTTATTTCG
* * *
28836070 GCCCTTTGTTCGTATTTTTTT-CTGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTT
1 GCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTT
* * * * * *
28836134 ATTATTTTAGATTATTTTAGTACATTATGCTTGAAATTTATTAATTTACTGTATTTTTTAAATAA
66 ATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAA
*
28836199 ATTAAAAAACTCTTATTTTG
131 ATTAAAAAACTCTTATTTCG
28836219 GCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTTAAAAAAATATACTATTTTCTAATTT
1 GCCATTTGTTCGTATTTTTTTCCCGAATTTTATTAC-TTTAAAAAAATATACTATTTTCTAATTT
28836284 TATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATA
65 TATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATA
*
28836349 AATTTAAAAAAATCCTTATTTCG
130 AA-TTAAAAAACT-CTTATTTCG
* ** * *
28836372 ACCATTTGTTCGTATTTTTTTTTCTAGATTTTATTACTTTCAATAAAAATATATTATTTTCTAAT
1 GCCATTTGTTCGTATTTTTTTCCCGA-ATTTTATTACTTT-AA-AAAAATATACTATTTTCTAAT
*
28836437 TTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTT
63 TTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTT
28836498 NNNNNNNNNN
Statistics
Matches: 384, Mismatches: 34, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
148 8 0.02
149 55 0.14
150 98 0.26
151 89 0.23
152 9 0.02
153 33 0.09
154 12 0.03
155 80 0.21
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (150 bp):
GCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTT
ATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAA
ATTAAAAAACTCTTATTTCG
Found at i:28837249 original size:151 final size:150
Alignment explanation
Indices: 28836902--28837428 Score: 785
Period size: 151 Copynumber: 3.5 Consensus size: 150
28836892 NNNNNNNNNN
28836902 TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTTATGTTTG-AATGTATTCATTTAGT
1 TATTTTCTAATTTTATTATTTTACATTATTTTAGTACA-TTATGTTTGAAATGTATTCATTTAGT
* **
28836966 GTGTTTTTTAAATAAATTTTAAAAAAAAACCATTATTTCGGCCCTTTGTACGTATTTTTTCCCCA
65 GTGTTTTTTAAATAAA-TTT--AAAAAAACCATTATTTTGGCCCTTTGTTTGTATTTTTT-CCCA
* *
28837031 TATTTTATTACTTTAAAAAATATAA
126 GATTTTATTACTTTAAAAAATATAC
*
28837056 TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATGTAGTG
1 TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTG
* * *
28837121 TGTTTTTTAAATAAATTTAAAAAAACCCATTATTTTGGCCTTTTATTTGTATTTTTTCTCAGATT
66 TGTTTTTTAAATAAATTTAAAAAAA-CCATTATTTTGGCCCTTTGTTTGTATTTTTTCCCAGATT
28837186 TTATTACTTTAAAAAATATAC
130 TTATTACTTTAAAAAATATAC
* * * * *
28837207 TATTTTATAATTTTATTATTTTAGATTATTTTAGTACATTATGCTTGAAATGTATTAATTTACTG
1 TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTG
* *
28837272 TATTTTTTAAATAAA-TT--AAAAACCATTATTTTGGCCCTTTGTTTGTATTTCTTTCCCCGAAT
66 TGTTTTTTAAATAAATTTAAAAAAACCATTATTTTGGCCCTTTGTTTGTATTT-TTTCCCAG-AT
28837334 TTTATTACTTTTAAAAAATATAC
129 TTTATTAC-TTTAAAAAATATAC
*
28837357 TATTTTCTAA-TTTATTATTTTATATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTG
1 TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTG
28837421 TGTTTTTT
66 TGTTTTTT
28837429 TATTGAAAGT
Statistics
Matches: 342, Mismatches: 26, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
147 26 0.08
148 11 0.03
149 67 0.20
150 25 0.07
151 106 0.31
152 26 0.08
153 12 0.04
154 69 0.20
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.53
Consensus pattern (150 bp):
TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTG
TGTTTTTTAAATAAATTTAAAAAAACCATTATTTTGGCCCTTTGTTTGTATTTTTTCCCAGATTT
TATTACTTTAAAAAATATAC
Found at i:28838231 original size:147 final size:147
Alignment explanation
Indices: 28837874--28838422 Score: 810
Period size: 147 Copynumber: 3.7 Consensus size: 147
28837864 TATATTTCAA
* * * * *
28837874 GCATAATGTACTAAAATAATATAAAATAATAAAATTAGAAAATATTATATTTTTTAAAGGAATAA
1 GCATAATGTACTAAAATAATACAAAATTAGAAAATTAGAAAATAGTATATTTTTTAAAGTAATAA
* ** *
28837939 AATCTGGGGAAAAAATACGAACAAAGGGCCAAAATAAGATTTTTTTTTTAAATTTATTTAAAAAA
66 AATCTGGGGAAAAAATACGAACAAAGGGCCGAAATAAG--GGTTTTTTTAAATTTATTTGAAAAA
* *
28838004 CACACTAAATGAATACATTT
129 CACAGTAAATTAATACA-TT
* *
28838024 CAAACATAATGTACTAAAATAATATAAAATTAGAAAATTAGAAAATAGTATATTTTTTAAAGTAA
1 ---GCATAATGTACTAAAATAATACAAAATTAGAAAATTAGAAAATAGTATATTTTTTAAAGTAA
* * *
28838089 TAAAATTTGGGGGAAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTGAAAA
63 TAAAATCTGGGGAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTGAAAA
28838154 ACACAGTAAATTAATACATT
128 ACACAGTAAATTAATACATT
*
28838174 GCATAATGTACTAAAATAATGCAAAATTAGAAAATTAGAAAATAGTATATTTTTTAAAGTAATAA
1 GCATAATGTACTAAAATAATACAAAATTAGAAAATTAGAAAATAGTATATTTTTTAAAGTAATAA
* * *
28838239 AATTTGGGGGAAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTGAAAAACA
66 AATCTGGGGAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTGAAAAACA
28838304 CAGTAAATTAATACATT
131 CAGTAAATTAATACATT
*
28838321 GCATAATGTACTAAAATAATGCAAAATTAGAAAATTAGAAAATAGTATATTTTTTAAAAGTAATA
1 GCATAATGTACTAAAATAATACAAAATTAGAAAATTAGAAAATAGTATATTTTTT-AAAGTAATA
* * * *
28838386 AAATCTGAGAAAAAAATACGAACAAAAGGCTGAAATA
65 AAATCTGGGGAAAAAATACGAACAAAGGGCCGAAATA
28838423 CAAACATGTT
Statistics
Matches: 371, Mismatches: 24, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
147 199 0.54
148 39 0.11
150 2 0.01
151 37 0.10
153 94 0.25
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (147 bp):
GCATAATGTACTAAAATAATACAAAATTAGAAAATTAGAAAATAGTATATTTTTTAAAGTAATAA
AATCTGGGGAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTGAAAAACA
CAGTAAATTAATACATT
Found at i:28839221 original size:17 final size:17
Alignment explanation
Indices: 28839199--28839231 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28839189 TTAATCACTT
28839199 TAATATTAAATTTAATC
1 TAATATTAAATTTAATC
28839216 TAATATTAAATTTAAT
1 TAATATTAAATTTAAT
28839232 ATTAAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATATTAAATTTAATC
Found at i:28842121 original size:22 final size:24
Alignment explanation
Indices: 28842071--28842121 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
28842061 TTGCAATGCT
28842071 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
28842096 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
28842117 TTTAT
1 TTTAT
28842122 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:28842264 original size:14 final size:15
Alignment explanation
Indices: 28842242--28842318 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
28842232 CAATCAAACA
28842242 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
28842256 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
28842271 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
28842291 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
28842305 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
28842319 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:28842283 original size:20 final size:20
Alignment explanation
Indices: 28842258--28842297 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28842248 AATATTTTCC
*
28842258 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28842278 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
28842298 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28842303 original size:34 final size:35
Alignment explanation
Indices: 28842246--28842312 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28842236 CAAACACCAG
*
28842246 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
28842281 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28842313 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28842319 original size:14 final size:14
Alignment explanation
Indices: 28842281--28842320 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28842271 ACAGAAAAGT
*
28842281 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
28842295 AAATCATTTTACGG
1 AAAACATTTTACAG
28842309 AAAACATTTTAC
1 AAAACATTTTAC
28842321 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:28843745 original size:28 final size:28
Alignment explanation
Indices: 28843713--28843769 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28843703 TGAATCAAAT
28843713 GTTCACTTTGAATCTTTTACGGGTTACG
1 GTTCACTTTGAATCTTTTACGGGTTACG
28843741 GTTCACTTTGAATCTTTTACGGGTTACG
1 GTTCACTTTGAATCTTTTACGGGTTACG
28843769 G
1 G
28843770 ACTTGTATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.42
Consensus pattern (28 bp):
GTTCACTTTGAATCTTTTACGGGTTACG
Found at i:28848702 original size:43 final size:43
Alignment explanation
Indices: 28848641--28848814 Score: 348
Period size: 43 Copynumber: 4.0 Consensus size: 43
28848631 ATGTTGGTAG
28848641 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
1 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
28848684 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
1 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
28848727 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
1 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
28848770 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
1 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
28848813 TC
1 TC
28848815 ATGATGACTT
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 131 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (43 bp):
TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
Found at i:28849739 original size:82 final size:83
Alignment explanation
Indices: 28849637--28849802 Score: 325
Period size: 82 Copynumber: 2.0 Consensus size: 83
28849627 TCATTGGACA
28849637 TCCACATTATATATATAATAAAAAATAAAAAAAAAGTTATTATTTAATGTTATAAAAGTTTACGA
1 TCCACATTATATATATAATAAAAAATAAAAAAAAAGTTATTATTTAATGTTATAAAAGTTTACGA
28849702 AATTAAAAGTGATCTGAT
66 AATTAAAAGTGATCTGAT
28849720 TCCACATTAT-TATATAATAAAAAATAAAAAAAAAGTTATTATTTAATGTTATAAAAGTTTACGA
1 TCCACATTATATATATAATAAAAAATAAAAAAAAAGTTATTATTTAATGTTATAAAAGTTTACGA
28849784 AATTAAAAGTGATCTGAT
66 AATTAAAAGTGATCTGAT
28849802 T
1 T
28849803 TGATTAAAAT
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 73 0.88
83 10 0.12
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (83 bp):
TCCACATTATATATATAATAAAAAATAAAAAAAAAGTTATTATTTAATGTTATAAAAGTTTACGA
AATTAAAAGTGATCTGAT
Found at i:28852759 original size:19 final size:19
Alignment explanation
Indices: 28852737--28852782 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
28852727 AAAGTTATAG
28852737 AAAAATATAT-AAATTATTA-
1 AAAAATA-ATGAAA-TATTAT
*
28852756 AAAAGTAATGAAATATTAT
1 AAAAATAATGAAATATTAT
28852775 AAAAATAA
1 AAAAATAA
28852783 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAAATAATGAAATATTAT
Found at i:28859384 original size:3 final size:3
Alignment explanation
Indices: 28859376--28859408 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28859366 TTATTTAAAA
28859376 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
28859409 TCATTTTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28860958 original size:14 final size:14
Alignment explanation
Indices: 28860939--28860966 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28860929 AGTTTCAGTC
28860939 GGCCCAGAATACAA
1 GGCCCAGAATACAA
28860953 GGCCCAGAATACAA
1 GGCCCAGAATACAA
28860967 AATCAGTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.21, T:0.07
Consensus pattern (14 bp):
GGCCCAGAATACAA
Found at i:28862212 original size:22 final size:21
Alignment explanation
Indices: 28862143--28862216 Score: 55
Period size: 22 Copynumber: 3.4 Consensus size: 21
28862133 TTAGTCTTTT
*
28862143 TTTTAATTTTT-TTATTAATTAA
1 TTTTCATTTTTATT-TTAATT-A
* *
28862165 TTTTCATTTTTATTTTGTATTT
1 TTTTCATTTTTATTTT-AATTA
28862187 TTTTC-TTTTTCATATTTAATTA
1 TTTTCATTTTT-AT-TTTAATTA
28862209 TTTT-ATTT
1 TTTTCATTT
28862217 AAATCTATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
21 5 0.12
22 29 0.69
23 8 0.19
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (21 bp):
TTTTCATTTTTATTTTAATTA
Found at i:28862587 original size:15 final size:15
Alignment explanation
Indices: 28862567--28862596 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28862557 TATGCCATTA
28862567 TTGTATTTATTATTG
1 TTGTATTTATTATTG
*
28862582 TTGTATTTGTTATTG
1 TTGTATTTATTATTG
28862597 CGACATCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (15 bp):
TTGTATTTATTATTG
Found at i:28874489 original size:44 final size:43
Alignment explanation
Indices: 28874438--28875164 Score: 454
Period size: 44 Copynumber: 16.6 Consensus size: 43
28874428 GATCGCATCT
*
28874438 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * * *
28874482 AGTCTTATC-CTCCTGAAGTTGCAGT-AAGGCAGGCTAAAGATGGTA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
*
28874527 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
28874571 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAAAGATAGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * *
28874616 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGA-TTA-AAGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * *
28874659 TAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAA-AATCA
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * * * * * *
28874702 CAGATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T-CGCATCT
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * *
28874744 AGTCTTATCTCTCTGAAGTTACAGTGGAGCAGACTAAGTAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* *
28874788 AGTCTTATCTTCCC-GACGTTGCAGT-GAGGCAGACTGAAGATGGCGA
1 AGTCTTATC-TCCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGC-A
* *
28874834 A-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-TTA-AAGCCAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * *
28874876 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AACCA
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * * * * * * *
28874919 CAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGA-TCA-CATCG
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * * * *
28874962 GGTCTTATCTCCCTGAAATTGTAGTGGAGTAGACTAAGTAAGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* *
28875006 AGTCTTATC-CTCCTGAAGTTACAGT-GAGACAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAG-CAGACT-AAGA-AGCA
* * * *
28875051 AATCTTATCTACCTGAAGTTGCAGTGGAGCAGATTAA-AACCAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* * * ** *
28875094 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGAAG-CA
*
28875140 ATTC-TATCTCCCTGAAGTTGCAGTG
1 AGTCTTATCTCCCTGAAGTTGCAGTG
28875165 AAGCGGGTTA
Statistics
Matches: 543, Mismatches: 91, Indels: 98
0.74 0.12 0.13
Matches are distributed among these distances:
40 22 0.04
41 38 0.07
42 14 0.03
43 32 0.06
44 285 0.52
45 139 0.26
46 13 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:28874544 original size:45 final size:44
Alignment explanation
Indices: 28874440--28874654 Score: 192
Period size: 45 Copynumber: 4.8 Consensus size: 44
28874430 TCGCATCTAG
* * *
28874440 TCTTAT-CTCCCTGAAGTTGCAGTGGAGTAGACT-AAG-TAAGCAAG
1 TCTTATCCT-CCTGAAGTTGCAGTAG-GCAGACTAAAGAT-AGCAAA
* * *
28874484 TCTTATCCTCCTGAAGTTGCAGTAAGGCAGGCTAAAGATGGTAAA
1 TCTTATCCTCCTGAAGTTGCAGT-AGGCAGACTAAAGATAGCAAA
* *
28874529 TCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCAAG
1 TCTTATCCT-CCTGAAGTTGCAGTAG-GCAGACTAAAGAT-AGCAAA
28874573 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATAGCAAA
1 TCTTATCCTCCTGAAGTTGCAGT-AGGCAGACTAAAGATAGCAAA
* * *
28874618 TCTTAT-CTCCCTGAAATTGCAGTGGAGCAGATTAAAG
1 TCTTATCCT-CCTGAAGTTGCAGTAG-GCAGACTAAAG
28874655 CCGATAATCC
Statistics
Matches: 142, Mismatches: 16, Indels: 25
0.78 0.09 0.14
Matches are distributed among these distances:
43 1 0.01
44 64 0.45
45 75 0.53
46 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
TCTTATCCTCCTGAAGTTGCAGTAGGCAGACTAAAGATAGCAAA
Found at i:28874839 original size:217 final size:218
Alignment explanation
Indices: 28874529--28875132 Score: 933
Period size: 217 Copynumber: 2.8 Consensus size: 218
28874519 AGATGGTAAA
*
28874529 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAATCAAGTCTTATCCTCCTGAAGTTGCA
* * * *
28874594 GTGAGGCAGACTAAAGATAGCAAATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCCGA
66 GTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
* * * *
28874659 TAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTT
131 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTT
* *
28874724 ACAG-AGAGCAGATCGCATCTAG
196 ACAGTAGAGCAGATCACATCGAG
* * * * *
28874746 TCTTATCTCTCTGAAGTTACAGTGGAGCAGACTAAGTAATCAAGTCTTATCTTCCCGACGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAATCAAGTCTTATCCTCCTGAAGTTGCA
* *
28874811 GTGAGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAA
66 GTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
28874876 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTT
131 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTT
* * *
28874941 GCAGTAGAGTAGATCACATCGGG
196 ACAGTAGAGCAGATCACATCGAG
* * * *
28874964 TCTTATCTCCCTGAAATTGTAGTGGAGTAGACTAAGTAAGT-AAGTCTTATCCTCCTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA-TCAAGTCTTATCCTCCTGAAGTTGC
* * *
28875028 AGTGAGACAGACTGAAGATGGCAAATCTTATCTACCTGAAGTTGCAGTGGAGCAGATTAAAACCA
65 AGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA
28875093 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
130 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
28875133 GCCGATAATT
Statistics
Matches: 350, Mismatches: 35, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
217 182 0.52
218 167 0.48
219 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (218 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAATCAAGTCTTATCCTCCTGAAGTTGCA
GTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTT
ACAGTAGAGCAGATCACATCGAG
Found at i:28875120 original size:89 final size:88
Alignment explanation
Indices: 28874440--28875214 Score: 450
Period size: 89 Copynumber: 8.9 Consensus size: 88
28874430 TCGCATCTAG
* * * *
28874440 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA-AGTCTTATC-CTCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCATAATCTTATCTC-CCTGAAGTTG
* * *
28874503 CAGTAAG-GCAGGCTAAAGATGGTAAA
63 CAGTGAGAGCAGACT-AAGATGGCAAA
* * *
28874529 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA-AGTCTTATC-CTCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCATAATCTTATCTC-CCTGAAGTTG
*
28874592 CAGTGAG-GCAGACTAAAGATAGCAAA
63 CAGTGAGAGCAGACT-AAGATGGCAAA
* * * *
28874618 TCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAGGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-ATAATCTTATCTCCCTGAAGTTGCA
* * * ** *
28874683 GTG-GAGCGGATTAAAATCACAGA
65 GTGAGAGCAGACTAAGATGGCAAA
* * * *** * * * *
28874706 TCTTATCTCTCTGAAGTTACAG-AGAGCAGA-TCGCATC-TAGTCTTATCTCTCTGAAGTTACAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAATCTTATCTCCCTGAAGTTGCAG
*
28874768 TG-GAGCAGACTAAGTAAT--CAAG
66 TGAGAGCAGACTAAG--ATGGCAAA
* * ** *
28874790 TCTTATCTTCCC-GACGTTGCAGT-GAGGCAGACTGAAGATGGC-GAATCTTATCTCCCTGAAGT
1 TCTTATC-TCCCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-ACCATAATCTTATCTCCCTGAAGT
* * *
28874852 TGCAGTG-GAGTAGATTAA-A-GCCAATAA
61 TGCAGTGAGAGCAGACTAAGATGGC-A-AA
* * * *
28874879 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATA-ATCTTATCTCCCTGAAGTTGCA
* * * *
28874944 GT-AGAGTAGA-TCACATCGG---G
65 GTGAGAGCAGACTAAGAT-GGCAAA
* * * * *
28874964 TCTTATCTCCCTGAAATTGTAGTGGAGTAGACTAAGTAA--GTAAGTCTTATC-CTCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCATAA-TCTTATCTC-CCTGAAGTT
*
28875026 ACAGTGAGA-CAGACTGAAGATGGCAAA
62 GCAGTGAGAGCAGACT-AAGATGGCAAA
* *
28875053 TCTTATCTACCTGAAGTTGCAGTGGAGCAGATTAAAACCAATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-ATAATCTTATCTCCCTGAAGTTGCA
* *
28875118 GTG-GAGCAGATTAA-A-GCCGATAA
65 GTGAGAGCAGACTAAGATGGC-A-AA
* * * * * *
28875141 T-TCTATCTCCCTGAAGTTGCAGTGAAGCGGGTTAAAACCTTAGATCTTACCTCTCT-AGAGTTG
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATA-ATCTTATCTCCCTGA-AGTTG
28875204 CA--GAGAGCAGA
63 CAGTGAGAGCAGA
28875215 TCGCATCTAA
Statistics
Matches: 544, Mismatches: 96, Indels: 94
0.74 0.13 0.13
Matches are distributed among these distances:
84 52 0.10
85 60 0.11
86 15 0.03
87 34 0.06
88 122 0.22
89 253 0.47
90 8 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAATCTTATCTCCCTGAAGTTGCAG
TGAGAGCAGACTAAGATGGCAAA
Found at i:28875160 original size:218 final size:218
Alignment explanation
Indices: 28874443--28875163 Score: 936
Period size: 218 Copynumber: 3.3 Consensus size: 218
28874433 CATCTAGTCT
* * *
28874443 TATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA-AG-TCTTATC-CTCCTGAAGTTGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCACAGATCTTATCTCT-CTGAAGTTGCA
* * * * *
28874505 GTA-AGGCAGGCTAAAGATGGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG
63 GTAGA-GCA-GAT-CACATCG--AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG
* * * *
28874569 CAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATAGCAAATCTTATCTCCCTGAAA
123 TAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAG
*
28874634 TTGCAGTGGAGCAGATTAAAGCCGATAATCC
188 TTGCAGTGGAGCAGATTAAAGCCAATAATCC
* * * *
28874665 TATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAG-A
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
* * * *
28874729 GAGCAGATCGCATCTAGTCTTATCTCTCTGAAGTTACAGTGGAGCAGACTAAGTAA-TCAAGTCT
66 GAGCAGATCACATCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGT-AAGTCT
* * * *
28874793 TATCTTCCCGACGTTGCAGTGAGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGT
130 TATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGT
*
28874858 GGAGTAGATTAAAGCCAATAATCC
195 GGAGCAGATTAAAGCCAATAATCC
*
28874882 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
* * * * *
28874947 GAGTAGATCACATCGGGTCTTATCTCCCTGAAATTGTAGTGGAGTAGACTAAGTAAGTAAGTCTT
66 GAGCAGATCACATCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCTT
* * *
28875012 ATCCTCCTGAAGTTACAGTGAGACAGACTGAAGATGGCAAATCTTATCTACCTGAAGTTGCAGTG
131 ATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTG
*
28875077 GAGCAGATTAAAACCAATAATCC
196 GAGCAGATTAAAGCCAATAATCC
* * *
28875100 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA-AT-TCTATCTCCCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-ACAGATCT-TATCTCTCTGAAGTTGCAG
28875163 T
64 T
28875164 GAAGCGGGTT
Statistics
Matches: 438, Mismatches: 52, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
217 183 0.42
218 189 0.43
219 5 0.01
220 6 0.01
221 6 0.01
222 47 0.11
223 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (218 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
GAGCAGATCACATCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCTT
ATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTG
GAGCAGATTAAAGCCAATAATCC
Found at i:28875205 original size:88 final size:87
Alignment explanation
Indices: 28875056--28875215 Score: 198
Period size: 88 Copynumber: 1.8 Consensus size: 87
28875046 TGGCAAATCT
* * *
28875056 TATCTACCTGAAGTTGCAGTGGAGCAGATTAAAACCAATAATCCTATCTCCCTGAAGTTGCAGTG
1 TATCTACCTGAAGTTGCAGTGAAGCAGATTAAAACCAATAATCCTACCTCCCTGAAGTTGCAG-A
28875121 GAGCAGATTAAAGCCGATAATTC
65 GAGCAGATTAAAGCCGATAATTC
* * * * * *
28875144 TATCTCCCTGAAGTTGCAGTGAAGCGGGTTAAAACC-TTAGATCTTACCTCTCT-AGAGTTGCAG
1 TATCTACCTGAAGTTGCAGTGAAGCAGATTAAAACCAATA-ATCCTACCTCCCTGA-AGTTGCAG
28875207 AGAGCAGAT
64 AGAGCAGAT
28875216 CGCATCTAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
87 11 0.18
88 50 0.82
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (87 bp):
TATCTACCTGAAGTTGCAGTGAAGCAGATTAAAACCAATAATCCTACCTCCCTGAAGTTGCAGAG
AGCAGATTAAAGCCGATAATTC
Found at i:28875228 original size:24 final size:24
Alignment explanation
Indices: 28875201--28875247 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
28875191 CTCTCTAGAG
28875201 TTGCAGAGAGCAGATCGCATCTAA
1 TTGCAGAGAGCAGATCGCATCTAA
* *
28875225 TTGCAGAGATCAGATTGCATCTA
1 TTGCAGAGAGCAGATCGCATCTA
28875248 GTCTTTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (24 bp):
TTGCAGAGAGCAGATCGCATCTAA
Found at i:28876971 original size:132 final size:132
Alignment explanation
Indices: 28876819--28877074 Score: 512
Period size: 132 Copynumber: 1.9 Consensus size: 132
28876809 ATATAAAGGG
28876819 ATATATATGTATATAAATTATAGAATATAAAAATATTTATATATATGTTCGTATGTATATAAAAT
1 ATATATATGTATATAAATTATAGAATATAAAAATATTTATATATATGTTCGTATGTATATAAAAT
28876884 AAGTTACTATAAAGACATGTAAATGCATCATGTATATGTGCATGTATAGGTATATATAGGTGTGC
66 AAGTTACTATAAAGACATGTAAATGCATCATGTATATGTGCATGTATAGGTATATATAGGTGTGC
28876949 AA
131 AA
28876951 ATATATATGTATATAAATTATAGAATATAAAAATATTTATATATATGTTCGTATGTATATAAAAT
1 ATATATATGTATATAAATTATAGAATATAAAAATATTTATATATATGTTCGTATGTATATAAAAT
28877016 AAGTTACTATAAAGACATGTAAATGCATCATGTATATGTGCATGTATAGGTATATATAG
66 AAGTTACTATAAAGACATGTAAATGCATCATGTATATGTGCATGTATAGGTATATATAG
28877075 AGAATAAAAT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 124 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (132 bp):
ATATATATGTATATAAATTATAGAATATAAAAATATTTATATATATGTTCGTATGTATATAAAAT
AAGTTACTATAAAGACATGTAAATGCATCATGTATATGTGCATGTATAGGTATATATAGGTGTGC
AA
Found at i:28877209 original size:18 final size:18
Alignment explanation
Indices: 28877168--28877215 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
28877158 TTTAATAGTA
* *
28877168 ATAATAATAATAATAATG
1 ATAATAATAAAAATAATC
* *
28877186 ACAATAATAAAAATTATC
1 ATAATAATAAAAATAATC
*
28877204 ATAATACTAAAA
1 ATAATAATAAAA
28877216 TAACGAACAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (18 bp):
ATAATAATAAAAATAATC
Found at i:28878951 original size:11 final size:10
Alignment explanation
Indices: 28878925--28878950 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28878915 AGGGGAGAGC
28878925 TTTTTTGAAG
1 TTTTTTGAAG
28878935 TTTTTTGAAG
1 TTTTTTGAAG
28878945 TTTTTT
1 TTTTTT
28878951 TTAAAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (10 bp):
TTTTTTGAAG
Found at i:28879507 original size:21 final size:21
Alignment explanation
Indices: 28879483--28879533 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
28879473 ATACGCATAT
28879483 TTTTTTAATGTAATGTAATTA
1 TTTTTTAATGTAATGTAATTA
* *
28879504 TTTTTT-ATTTTATGTAATTA
1 TTTTTTAATGTAATGTAATTA
28879524 TTTTTATAAT
1 TTTTT-TAAT
28879534 CTATCTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 17 0.65
21 7 0.27
22 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (21 bp):
TTTTTTAATGTAATGTAATTA
Found at i:28883261 original size:23 final size:22
Alignment explanation
Indices: 28883229--28883290 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
28883219 GCCCGGCCCG
* *
28883229 TTTTTAATTATAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
28883253 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
28883275 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
28883291 TTGTTATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 16 0.46
23 14 0.40
24 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:28883285 original size:16 final size:16
Alignment explanation
Indices: 28883264--28883320 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
28883254 TTTTATTAAA
*
28883264 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
28883280 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
28883296 ATCAAAATTAATTGTT
1 ATTAAAATTAATTGTT
28883312 ATTAAAATT
1 ATTAAAATT
28883321 CTATCAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:28884286 original size:6 final size:6
Alignment explanation
Indices: 28884275--28884311 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
28884265 GTTAAGGATG
*
28884275 GGGGAA GGGGAA GGGGAA AGGGAA GGGGAA GGGGAA G
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA G
28884312 AGAAAGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:28884318 original size:18 final size:18
Alignment explanation
Indices: 28884279--28884319 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28884269 AGGATGGGGG
*
28884279 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGA
28884297 AAGGGGAAGGGG-AAGAGA
1 AAGGGGAAGGGGAAAG-GA
28884315 AAGGG
1 AAGGG
28884320 AAGATCGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAAGGA
Found at i:28885597 original size:16 final size:16
Alignment explanation
Indices: 28885576--28885606 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28885566 TTATAGTCCT
*
28885576 ATTACAGCCTTATTCC
1 ATTACAACCTTATTCC
28885592 ATTACAACCTTATTC
1 ATTACAACCTTATTC
28885607 AATTCTAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACAACCTTATTCC
Found at i:28892283 original size:37 final size:37
Alignment explanation
Indices: 28892233--28892358 Score: 119
Period size: 37 Copynumber: 3.3 Consensus size: 37
28892223 ACACTCGCTA
*
28892233 GATTTAAAATCGCGACTGTCATTTTTACGGTTCAATT
1 GATTTAAGATCGCGACTGTCATTTTTACGGTTCAATT
* * * *
28892270 GATTTAAGATCGCGA-TGTTTGATATTCTAACAGTTCGATT
1 GATTTAAGATCGCGACTG--TCAT-TT-TTACGGTTCAATT
* * * * *
28892310 GATTTAACATCGCAACTGTCATTTTTTCGGTTGACTT
1 GATTTAAGATCGCGACTGTCATTTTTACGGTTCAATT
28892347 GATTTAAGATCG
1 GATTTAAGATCG
28892359 TGACCTTCGA
Statistics
Matches: 69, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
36 2 0.03
37 32 0.46
38 5 0.07
39 5 0.07
40 23 0.33
41 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.40
Consensus pattern (37 bp):
GATTTAAGATCGCGACTGTCATTTTTACGGTTCAATT
Found at i:28892412 original size:77 final size:77
Alignment explanation
Indices: 28892233--28892378 Score: 211
Period size: 77 Copynumber: 1.9 Consensus size: 77
28892223 ACACTCGCTA
* * ** *
28892233 GATTTAAAATCGCGACTGTCATTTTTACGGTTCAATTGATTTAAGATCGCGATGTTTGATATTCT
1 GATTTAACATCGCAACTGTCATTTTTACGGTTCAATTGATTTAAGATCGCGACCTTCGATATTCT
28892298 AACAGTTCGATT
66 AACAGTTCGATT
* * * *
28892310 GATTTAACATCGCAACTGTCATTTTTTCGGTTGACTTGATTTAAGATCGTGACCTTCGATATTCT
1 GATTTAACATCGCAACTGTCATTTTTACGGTTCAATTGATTTAAGATCGCGACCTTCGATATTCT
28892375 AACA
66 AACA
28892379 TTTTGCTTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 60 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (77 bp):
GATTTAACATCGCAACTGTCATTTTTACGGTTCAATTGATTTAAGATCGCGACCTTCGATATTCT
AACAGTTCGATT
Found at i:28893652 original size:36 final size:38
Alignment explanation
Indices: 28893605--28893699 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 38
28893595 GTCTCCAAAT
* *
28893605 TCACATTTCAATTCAATTTCACTTTTTCA-CTTTCAA-
1 TCACAATTCAATTCAATTTCACTTTTCCATCTTTCAAG
* *
28893641 TCACAATTCAATTCAAAATTCACTTTTCCATTTTTCAAG
1 TCACAATTCAATTC-AATTTCACTTTTCCATCTTTCAAG
*
28893680 TCATTATATTCAATTCAATT
1 TCA-CA-ATTCAATTCAATT
28893700 CCAGACATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 13 0.27
37 13 0.27
38 6 0.12
39 3 0.06
40 4 0.08
41 9 0.19
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (38 bp):
TCACAATTCAATTCAATTTCACTTTTCCATCTTTCAAG
Found at i:28896563 original size:42 final size:42
Alignment explanation
Indices: 28896499--28896596 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
28896489 GATCTCGGTA
* * *
28896499 TCGCACACCTAGTGCCTATTATTCAACATTGTCATTTTAATT
1 TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAATT
* *
28896541 TCGCACACTTAGTGCCCGTTATTCAACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAATT
28896583 TCGCACACTTAGTG
1 TCGCACACTTAGTG
28896597 TCATTCCTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAATT
Found at i:28896711 original size:2 final size:2
Alignment explanation
Indices: 28896704--28896735 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28896694 ATTCAGCTAC
28896704 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28896736 TTGCATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28901648 original size:20 final size:19
Alignment explanation
Indices: 28901609--28901647 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28901599 TATTTTAAAA
28901609 TATTTGTACATTTTAATTT
1 TATTTGTACATTTTAATTT
*
28901628 TATTATGTATATTTT-ATTT
1 TATT-TGTACATTTTAATTT
28901647 T
1 T
28901648 TTTCTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (19 bp):
TATTTGTACATTTTAATTT
Found at i:28908009 original size:31 final size:29
Alignment explanation
Indices: 28907974--28908078 Score: 110
Period size: 31 Copynumber: 3.6 Consensus size: 29
28907964 GACATAAGTA
28907974 TAAATATG-GAAAAGTTTCGTGGCATAAATTG
1 TAAATATGCGAAAAGTTT-GTGGCAT-AA-TG
*
28908005 TAAATATGCGAAAAG-TTATGGCATAA-G
1 TAAATATGCGAAAAGTTTGTGGCATAATG
* *
28908032 TAAATATGCAAAAAGTTTTGTGGCATAAGTA
1 TAAATATGCGAAAAG-TTTGTGGCATAA-TG
28908063 TAAATATG-GAAAAGTT
1 TAAATATGCGAAAAGTT
28908079 GAAGTGAAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
27 15 0.23
29 14 0.22
30 11 0.17
31 18 0.28
32 6 0.09
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (29 bp):
TAAATATGCGAAAAGTTTGTGGCATAATG
Found at i:28908038 original size:27 final size:27
Alignment explanation
Indices: 28908004--28908078 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
28907994 GGCATAAATT
28908004 GTAAATATGCGAAAAGTTATGGCATAA
1 GTAAATATGCGAAAAGTTATGGCATAA
* *
28908031 GTAAATATGCAAAAAGTTTTGTGGCATAA
1 GTAAATATGCGAAAAG--TTATGGCATAA
28908060 GTATAAATATG-GAAAAGTT
1 G--TAAATATGCGAAAAGTT
28908079 GAAGTGAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 15 0.37
28 2 0.05
29 11 0.27
30 5 0.12
31 8 0.20
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.29
Consensus pattern (27 bp):
GTAAATATGCGAAAAGTTATGGCATAA
Found at i:28908365 original size:11 final size:11
Alignment explanation
Indices: 28908351--28908392 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
28908341 TAAATATTAC
28908351 TTTATTAATAT
1 TTTATTAATAT
*
28908362 TTTAATGAGATAT
1 TTT-ATTA-ATAT
28908375 TTTATTAATAT
1 TTTATTAATAT
28908386 TTTATTA
1 TTTATTA
28908393 TAAATAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:28927618 original size:17 final size:18
Alignment explanation
Indices: 28927576--28927618 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
28927566 TTAATATGGT
*
28927576 TATATATAAAATTATAAA
1 TATATATTAAATTATAAA
28927594 TA-ATTATTAAA-TATAAA
1 TATA-TATTAAATTATAAA
28927611 TATATATT
1 TATATATT
28927619 TAAAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATATTAAATTATAAA
Found at i:28928065 original size:17 final size:17
Alignment explanation
Indices: 28928032--28928064 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28928022 AAAAAGTATT
*
28928032 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
28928049 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
28928065 AGTATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:28929993 original size:17 final size:17
Alignment explanation
Indices: 28929971--28930006 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28929961 CGATTGCATG
28929971 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
28929988 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
28930005 TT
1 TT
28930007 CCCTTTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTCTATTGCTGTTTAT
Found at i:28931347 original size:23 final size:23
Alignment explanation
Indices: 28931319--28931642 Score: 477
Period size: 23 Copynumber: 14.1 Consensus size: 23
28931309 GATTTGTTCT
*
28931319 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
28931342 GAAATTGTTATGATTGTCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
*
28931365 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
* *
28931388 GAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
*
28931411 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
* *
28931434 GAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
*
28931457 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
* *
28931480 GAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
*
28931503 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
* *
28931526 GAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
*
28931549 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
* *
28931572 GAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
*
28931595 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
* *
28931618 GAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTATGATTGTCTGCTG
28931641 GA
1 GA
28931643 GAAAATTGGA
Statistics
Matches: 266, Mismatches: 35, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 266 1.00
ACGTcount: A:0.20, C:0.09, G:0.30, T:0.42
Consensus pattern (23 bp):
GAAATTGTTATGATTGTCTGCTG
Found at i:28931370 original size:46 final size:46
Alignment explanation
Indices: 28931319--28931642 Score: 630
Period size: 46 Copynumber: 7.0 Consensus size: 46
28931309 GATTTGTTCT
* *
28931319 GAAATTGTTTTGATTGTCTGCTGGAAATTGTTATGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
28931365 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
28931411 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
28931457 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
28931503 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
28931549 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
28931595 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
28931641 GA
1 GA
28931643 GAAAATTGGA
Statistics
Matches: 276, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 276 1.00
ACGTcount: A:0.20, C:0.09, G:0.30, T:0.42
Consensus pattern (46 bp):
GAAATTGTTTTGATTGTCTGCTGGAAATTGGTATGATTGGCTGCTG
Found at i:28938114 original size:16 final size:16
Alignment explanation
Indices: 28938090--28938157 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
28938080 GATTTGCTAT
* *
28938090 TACAGCTCTAATTCAA
1 TACACCTCTAATCCAA
28938106 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
28938122 TAAACCTCTAATCCAA
1 TACACCTCTAATCCAA
28938138 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28938154 TACA
1 TACA
28938158 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.40, C:0.32, G:0.01, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28944713 original size:261 final size:261
Alignment explanation
Indices: 28944249--28944726 Score: 642
Period size: 261 Copynumber: 1.8 Consensus size: 261
28944239 ACCAACTCAG
* ** *
28944249 TTAAAATGTATAAAAATATAAAATAAAACTTTAATAAAGTGGTAAATTAAATGTTTTACTAATGT
1 TTAAAATATATAAAAATATAAAATAAAACTTTAATAAAGTGGTAAATTAAAAATTTTACTAATGC
* * * * * * ** *
28944314 AGTTGACGTGGGTTCAAATCCCAATATATGTATATTTTTATTGGATTTGTTTTAAAGTGAAAAGA
66 AATTGACGTAGGTTCAAATACCAATATATGCATAGTTTTAATCAATTTGTTTTAAAGTGAAAAAA
** * *
28944379 CTAAAATACTCTTGAATAACATTACTTATTTTAATTACGAAAGGGCATTCTCGTAACTTCCTAAC
131 CTAAAATACTCTCAAATAACATTACTTATTTTAATTACGAAAGGACATTCTCATAACTTCCTAAC
*
28944444 TGAGTTGGTGACCCTGTTGAGGGTTACATAAACTCGATTAGAGATAATAAGGCGTGCATAATAAA
196 TGAGTTGGTGACCCAGTTGAGGGTTACATAAACTCGATTAGAGATAATAAGGCGTGCATAATAAA
28944509 A
261 A
* * * *
28944510 TTAAAATATATAAAAATATCAAAATAAAATTTTAGTTGAA-TGGTAAATTAAAAATTTTATTAAT
1 TTAAAATATATAAAAATAT-AAAATAAAACTTTA-ATAAAGTGGTAAATTAAAAATTTTACTAAT
* *
28944574 GCAATTGATGTAGGTTTAAATACCAATATATGCAT-GTTTTAATCAACTTT-TTTTAAAGTGAAA
64 GCAATTGACGTAGGTTCAAATACCAATATATGCATAGTTTTAATCAA-TTTGTTTTAAAGTGAAA
* *
28944637 AAACTAAAATA-TCCTCAAATAATATTACTTATTTTAATTAC-AGAAGGACATTCTCATAAGTTC
128 AAACTAAAATACT-CTCAAATAACATTACTTATTTTAATTACGA-AAGGACATTCTCATAACTTC
28944700 CTAACTGAGTTGGTGACCCAGTTGAGG
191 CTAACTGAGTTGGTGACCCAGTTGAGG
28944727 ATGACACCAA
Statistics
Matches: 186, Mismatches: 26, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
260 2 0.01
261 116 0.62
262 65 0.35
263 3 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (261 bp):
TTAAAATATATAAAAATATAAAATAAAACTTTAATAAAGTGGTAAATTAAAAATTTTACTAATGC
AATTGACGTAGGTTCAAATACCAATATATGCATAGTTTTAATCAATTTGTTTTAAAGTGAAAAAA
CTAAAATACTCTCAAATAACATTACTTATTTTAATTACGAAAGGACATTCTCATAACTTCCTAAC
TGAGTTGGTGACCCAGTTGAGGGTTACATAAACTCGATTAGAGATAATAAGGCGTGCATAATAAA
A
Found at i:28945062 original size:308 final size:295
Alignment explanation
Indices: 28944497--28945287 Score: 813
Period size: 308 Copynumber: 2.6 Consensus size: 295
28944487 ATAATAAGGC
* * *
28944497 GTGCATAATAAAATTAAAATATATAAAAATATCAAAATAAAATTTTAGTTGAATGGTAAATTAAA
1 GTGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAATTTTAGTTGAGTGGTAAATTAAA
* * * * *
28944562 AATTTTATTAATGCAATTGATGTAGGTTTAAATACCAATATATGCATGTTTTAATCAACTTTTTT
66 AGTTTTATTAATGCAATTGGTGTGGGTTCAAATACCAATATATGCATATTTTAATCAAC-TTTTT
* * *
28944627 TAAAGTGAAAAAACTAAAATATCCTCAAATAATATTACTTATTTTAATTACAGAAGGACATTCTC
130 TAAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTATTTCAATTACAAAAGGACATTCTC
* * *
28944692 ATAAGTTCCTAACTGAGTTGGTGACCCAGTTGAGGATGACACCAACTCAATTAGGAGTTTTATTA
195 ATAACTTCCTAACTAAGTTGGTGACCCAGTTGAGGATGACACCAACTCAATAAGGAGTTTTATTA
*
28944757 ATAGTGTGTATATATATATACAAATACA-CAACCAATAAAGTTCATGGAGT
260 ATA----G--TATATATATACAAAT-CATCAA--AATAAA----A--AAGT
* *
28944807 GTGCATAATAAAATTAAAATGTATAAAAATATTAAAGTAAAACTTTAGATT-AGTGGTAAATTAA
1 GTGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAATTTTAG-TTGAGTGGTAAATTAA
* * ** * * * * **
28944871 ATGTTCTAAAAATGCAATTGGTGTGGGTTCAAATATC-ATCATGTGTATATTTTTATTGA-TTTT
65 AAGTTTTATTAATGCAATTGGTGTGGGTTCAAATACCAAT-ATATGCATATTTTAATCAACTTTT
*** *
28944934 TTAAAGTGAAAATGTTAAAATACCCTCGAATAATATTACTTATTTCAATTACAAAAGGACATTCT
129 TTAAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTATTTCAATTACAAAAGGACATTCT
* * * * * * *
28944999 CGTAACTTCCTAACTAAGTTGGTGACCCGGTTGAGGGTGACGCCAACTTAGTCAATG-GTTTTAT
194 CATAACTTCCTAACTAAGTTGGTGACCCAGTTGAGGATGACACCAACTCAAT-AAGGAGTTTTAT
* ** *
28945063 TAATAGTATATATATACAACTCATGGAGATAAAAAAGT
258 TAATAGTATATATATACAAATCATCAAAATAAAAAAGT
* **
28945101 GTGCATAATAAAGTTAAAATGTATAAAAATATTAAAATAAAATTTTAGTTGAGTGAAAAATTAAA
1 GTGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAATTTTAGTTGAGTGGTAAATTAAA
* * ** ****
28945166 AGTTTTATTAATGCAATTGGTGTGGGTTCAAAT-CCTACTGTATGCATATTTTTTTTGTTTTTTT
66 AGTTTTATTAATGCAATTGGTGTGGGTTCAAATACC-AATATATGCATA-TTTTAAT-CAACTTT
* * * *
28945230 TTTAAAGTGAAAAAACTAAAATATCTTCAAATAATATTAATTATATT-AATTACGAAAG
128 TTTAAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTAT-TTCAATTACAAAAG
28945288 AGTATTCTCG
Statistics
Matches: 403, Mismatches: 67, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
293 3 0.01
294 95 0.24
295 7 0.02
296 2 0.00
297 50 0.12
298 2 0.00
300 5 0.01
301 2 0.00
302 15 0.04
304 1 0.00
308 118 0.29
309 4 0.01
310 97 0.24
311 2 0.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (295 bp):
GTGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAATTTTAGTTGAGTGGTAAATTAAA
AGTTTTATTAATGCAATTGGTGTGGGTTCAAATACCAATATATGCATATTTTAATCAACTTTTTT
AAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTATTTCAATTACAAAAGGACATTCTCA
TAACTTCCTAACTAAGTTGGTGACCCAGTTGAGGATGACACCAACTCAATAAGGAGTTTTATTAA
TAGTATATATATACAAATCATCAAAATAAAAAAGT
Found at i:28945911 original size:16 final size:17
Alignment explanation
Indices: 28945880--28945912 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28945870 CATTTCATAA
*
28945880 ATTTTTATAATATTAAT
1 ATTTTAATAATATTAAT
28945897 ATTTTAATAAT-TTAAT
1 ATTTTAATAATATTAAT
28945913 TCCCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAATAATATTAAT
Found at i:28947267 original size:18 final size:18
Alignment explanation
Indices: 28947240--28947277 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28947230 ACTCCAAGGC
28947240 GACGACGAAGATGAAGAT
1 GACGACGAAGATGAAGAT
* *
28947258 GACGATGAAGATGGAGAT
1 GACGACGAAGATGAAGAT
28947276 GA
1 GA
28947278 TGAAGATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.37, T:0.13
Consensus pattern (18 bp):
GACGACGAAGATGAAGAT
Found at i:28965378 original size:78 final size:78
Alignment explanation
Indices: 28965253--28965406 Score: 308
Period size: 78 Copynumber: 2.0 Consensus size: 78
28965243 TAAAATTTAA
28965253 GAGGGGGGGGGGGGCAAAGCTTCATCACAAAATTAAGAGCCAAGAACAAGCAAGAAAATGATATG
1 GAGGGGGGGGGGGGCAAAGCTTCATCACAAAATTAAGAGCCAAGAACAAGCAAGAAAATGATATG
28965318 GAAAACCACAGAG
66 GAAAACCACAGAG
28965331 GAGGGGGGGGGGGGCAAAGCTTCATCACAAAATTAAGAGCCAAGAACAAGCAAGAAAATGATATG
1 GAGGGGGGGGGGGGCAAAGCTTCATCACAAAATTAAGAGCCAAGAACAAGCAAGAAAATGATATG
28965396 GAAAACCACAG
66 GAAAACCACAG
28965407 GCATACATGG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.44, C:0.16, G:0.31, T:0.10
Consensus pattern (78 bp):
GAGGGGGGGGGGGGCAAAGCTTCATCACAAAATTAAGAGCCAAGAACAAGCAAGAAAATGATATG
GAAAACCACAGAG
Found at i:28970654 original size:22 final size:22
Alignment explanation
Indices: 28970629--28970671 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28970619 TATGTATGTC
* *
28970629 ATATTTAAATTTATTTTGATTT
1 ATATCTAAATATATTTTGATTT
*
28970651 ATATCTAGATATATTTTGATT
1 ATATCTAAATATATTTTGATT
28970672 ACCACTCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (22 bp):
ATATCTAAATATATTTTGATTT
Found at i:28973145 original size:20 final size:20
Alignment explanation
Indices: 28973122--28973189 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
28973112 CCTTGATCCT
*
28973122 TGTCTAAATACAACGAATCG
1 TGTCTCAATACAACGAATCG
* *** *
28973142 TGTCTCAAGACCTTG-ATCCT
1 TGTCTCAATACAACGAAT-CG
28973162 TGTCTCAATACAACGAATCG
1 TGTCTCAATACAACGAATCG
28973182 TGTCTCAA
1 TGTCTCAA
28973190 GACCTTGGAT
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (20 bp):
TGTCTCAATACAACGAATCG
Found at i:28973157 original size:40 final size:40
Alignment explanation
Indices: 28973109--28973196 Score: 167
Period size: 40 Copynumber: 2.2 Consensus size: 40
28973099 CTATGTCTGG
28973109 AGACCTTGATCCTTGTCTAAATACAACGAATCGTGTCTCA
1 AGACCTTGATCCTTGTCTAAATACAACGAATCGTGTCTCA
*
28973149 AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
1 AGACCTTGATCCTTGTCTAAATACAACGAATCGTGTCTCA
28973189 AGACCTTG
1 AGACCTTG
28973197 GATCGAATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (40 bp):
AGACCTTGATCCTTGTCTAAATACAACGAATCGTGTCTCA
Found at i:28973201 original size:20 final size:20
Alignment explanation
Indices: 28973138--28973201 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
28973128 AATACAACGA
28973138 ATCGTGTCTCAAGACCTT-G
1 ATCGTGTCTCAAGACCTTGG
* * *** *
28973157 ATCCTTGTCTCAATACAACGA
1 AT-CGTGTCTCAAGACCTTGG
28973178 ATCGTGTCTCAAGACCTTGG
1 ATCGTGTCTCAAGACCTTGG
28973198 ATCG
1 ATCG
28973202 AATTTGATTG
Statistics
Matches: 31, Mismatches: 12, Indels: 3
0.67 0.26 0.07
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
ATCGTGTCTCAAGACCTTGG
Found at i:28974064 original size:40 final size:39
Alignment explanation
Indices: 28973944--28974074 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 39
28973934 TTTGGATTAA
* * *
28973944 AAACGCCGCAAAAGGTAAAGTATTAGCG-GTATTTTTGCAT
1 AAACGCCGCAAAAAGTAAAGCAATAGCGCGT-TTTTT-CAT
* * ** *
28973984 AAATGCCAC-AAAAGATAAAGCAATAGCGGCAATTTCTCAT
1 AAACGCCGCAAAAAG-TAAAGCAATAGC-GCGTTTTTTCAT
28974024 AAACGCCGCAAAAAGTAAAGCAATAGCGACGTTTTTTCAT
1 AAACGCCGCAAAAAGTAAAGCAATAGCG-CGTTTTTTCAT
28974064 -AACGCCGCAAA
1 AAACGCCGCAAA
28974075 TTTTTTCTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 11
0.75 0.13 0.11
Matches are distributed among these distances:
39 16 0.22
40 47 0.64
41 10 0.14
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.21
Consensus pattern (39 bp):
AAACGCCGCAAAAAGTAAAGCAATAGCGCGTTTTTTCAT
Found at i:28976626 original size:181 final size:174
Alignment explanation
Indices: 28976319--28976669 Score: 488
Period size: 181 Copynumber: 2.0 Consensus size: 174
28976309 TATATATATA
* *
28976319 TTTATCTATTTAACCAGCTTTCAGCGACTAATATTTTTTTCAGCTTGCACATGTGTCTTGTGAGC
1 TTTATCTATTTAACCAGCTTTCAGCAACTAATATTTTTTTCAGCTTGCACACGTGTCTTGTGAGC
* * * *
28976384 ACTTGAATTCATCAAAAGACATTACAGAAGAAATTCTTTTATCATGTTCTTGGTTGCATCACCTA
66 ACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATGTTCTCGGTAGCATCACCTA
* * * *
28976449 TTAAGGAAACATATATTTCCTTAGTATGTCTCTCAATAAGGCATTTCT
131 TTAA-G-AA-A-ACATTTCATTAGCATGTCTCTCAATAAAGCATTTCT
* * *
28976497 TTTATCTATTTAACCAGCTTTCTGCAAGTAA-ATTTTTCCTTCATCTTGCAGGCACGTGTCTTGT
1 TTTATCTATTTAACCAGCTTTCAGCAACTAATATTTTT--TTCAGCTTGCA--CACGTGTCTTGT
* *
28976561 GAGTACATGAATTCATCTAAAGACATTACAAAAGAAATTCTTTTATCATGTTCTCGGTAGCATCA
62 GAGCACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATGTTCTCGGTAGCATCA
28976626 CCTATTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCAT
127 CCTATTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCAT
28976670 CTTTTTTTGG
Statistics
Matches: 154, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
177 34 0.22
178 29 0.19
179 12 0.08
180 1 0.01
181 78 0.51
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (174 bp):
TTTATCTATTTAACCAGCTTTCAGCAACTAATATTTTTTTCAGCTTGCACACGTGTCTTGTGAGC
ACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATGTTCTCGGTAGCATCACCTA
TTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCATTTCT
Found at i:28978701 original size:22 final size:21
Alignment explanation
Indices: 28978671--28978730 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
28978661 ACACTCCATG
28978671 ATGCACACAAGTGCCAAATATAA
1 ATGC-CACAAGTGCCAAATA-AA
* *
28978694 ATGCCACAAGCGCC-AATAGA
1 ATGCCACAAGTGCCAAATAAA
*
28978714 ATGTACACAAGTGCCAA
1 ATG-CCACAAGTGCCAA
28978731 TCTTCCTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.13
21 13 0.42
22 10 0.32
23 4 0.13
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.15
Consensus pattern (21 bp):
ATGCCACAAGTGCCAAATAAA
Found at i:28992306 original size:22 final size:22
Alignment explanation
Indices: 28992278--28992321 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28992268 AACATGAGAA
* *
28992278 GGAAAAGATTCATATAGGTCAT
1 GGAAAAGATTCACATAAGTCAT
*
28992300 GGAAAAGCTTCACATAAGTCAT
1 GGAAAAGATTCACATAAGTCAT
28992322 CCTTTGGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (22 bp):
GGAAAAGATTCACATAAGTCAT
Found at i:29001994 original size:177 final size:178
Alignment explanation
Indices: 29001674--29002038 Score: 524
Period size: 177 Copynumber: 2.1 Consensus size: 178
29001664 TTGAATTACT
* *
29001674 CAATTTAGTCCTTAAAATCAGGACAAACATAACTTTCAATTTAAAGCCTCGAATTAAAATCTCAT
1 CAATTTAGTCCTTAAAATCAGGACAAACATAACTTTCAATTTAAAGCCTCGAATTAAAATCTAAC
* * * * *
29001739 TTCACCAAAACTCATTAGGGACCCTCTATTTTGTATCCCTACCAAATATATTTGACAATTTTGTA
66 TTCACCAAAACTCATTAAGGACCATCTATTTTGTATCCCTACAAAAAATATATGACAATTTTGTA
*
29001804 TTTTATTCAATTTGGTCCCTAATATATGAAACTAACAATTAAG-TTGTA
131 TTTTATTCAATTTGGTCCCTAATATACGAAACTAACAATTAAGCTT-TA
** **
29001852 CAATTTAGTACC-TAAAATTGGGACATGCATAACTTTCAATTTAAAGCCTCGAATTAAAATCTAA
1 CAATTTAGT-CCTTAAAATCAGGACAAACATAACTTTCAATTTAAAGCCTCGAATTAAAATCTAA
*
29001916 CTTCACC-AAACTCATTAAGGATCATCTATTTTGTATCCCTACAAAAAA-ATAATGACAATTTT-
65 CTTCACCAAAACTCATTAAGGACCATCTATTTTGTATCCCTACAAAAAATAT-ATGACAATTTTG
* *
29001978 TCATTTTATTCAATTTGGTCTCTAATATACGAAACTAACAATTAGGCTTTA
129 T-ATTTTATTCAATTTGGTCCCTAATATACGAAACTAACAATTAAGCTTTA
29002029 CAATTTAGTC
1 CAATTTAGTC
29002039 ATTTTCTTAA
Statistics
Matches: 168, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
176 4 0.02
177 98 0.58
178 64 0.38
179 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (178 bp):
CAATTTAGTCCTTAAAATCAGGACAAACATAACTTTCAATTTAAAGCCTCGAATTAAAATCTAAC
TTCACCAAAACTCATTAAGGACCATCTATTTTGTATCCCTACAAAAAATATATGACAATTTTGTA
TTTTATTCAATTTGGTCCCTAATATACGAAACTAACAATTAAGCTTTA
Found at i:29002280 original size:3 final size:3
Alignment explanation
Indices: 29002267--29002296 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
29002257 ACGGAGGTGA
*
29002267 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
29002297 TTTCATCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:29003854 original size:144 final size:143
Alignment explanation
Indices: 29003590--29003880 Score: 510
Period size: 144 Copynumber: 2.0 Consensus size: 143
29003580 TTATTTAGAC
* *
29003590 CTTTAGTCCATTTCTTTGCTTGTAATGACTTTTCATCCTTTTAGTTTAATGTATTTTAGTTTCTT
1 CTTTAGTCCATTTCTTTGCTTGTAATGACTTTTCAACCTTTTAGTTTAATGTATTTTAATTTCTT
* *
29003655 TTAATTTAATCTGTTAAAGACTTCAACTTTTATGTTTCTTCTTCTCTATTTTGTTGTTGGATACC
66 TTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTCTTCTCTATTTTGTTGTTGGATACC
29003720 TCTCATTACTTTT
131 TCTCATTACTTTT
*
29003733 CTTTGAGTCCATTTCTTTGCTTGTACTGACTTTTCAACCTTTTAGTTTAATGTATTTTAATTTCT
1 CTTT-AGTCCATTTCTTTGCTTGTAATGACTTTTCAACCTTTTAGTTTAATGTATTTTAATTTCT
*
29003798 TTTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTGTTCTCTATTTTGTTGTTGGATAC
65 TTTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTCTTCTCTATTTTGTTGTTGGATAC
*
29003863 CTCTGATTACTTTT
130 CTCTCATTACTTTT
29003877 CTTT
1 CTTT
29003881 TCTGTTTTCT
Statistics
Matches: 140, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
143 4 0.03
144 136 0.97
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (143 bp):
CTTTAGTCCATTTCTTTGCTTGTAATGACTTTTCAACCTTTTAGTTTAATGTATTTTAATTTCTT
TTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTCTTCTCTATTTTGTTGTTGGATACC
TCTCATTACTTTT
Found at i:29004394 original size:33 final size:33
Alignment explanation
Indices: 29004357--29004423 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
29004347 TTTCATAACT
29004357 TTGCACGTTGTACAATTTAGTCCTCGATAGCTA
1 TTGCACGTTGTACAATTTAGTCCTCGATAGCTA
29004390 TTGCACGTTGTACAATTTAGTCCTCGATAGCTA
1 TTGCACGTTGTACAATTTAGTCCTCGATAGCTA
29004423 T
1 T
29004424 CTCGTAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (33 bp):
TTGCACGTTGTACAATTTAGTCCTCGATAGCTA
Found at i:29005269 original size:24 final size:24
Alignment explanation
Indices: 29005183--29005269 Score: 66
Period size: 24 Copynumber: 3.6 Consensus size: 24
29005173 GGCTTAGAAT
**
29005183 TAGTCTTAAAATTACCCTTTAGGAC
1 TAGTCTTAAAATTAAAC-TTAGGAC
* * ** ** *
29005208 TAGTTTTAGAATTAGGCTTACAAT
1 TAGTCTTAAAATTAAACTTAGGAC
* *
29005232 TAGTCTCAATATTAAACTTAGGAC
1 TAGTCTTAAAATTAAACTTAGGAC
29005256 TAGTCTTAAAATTA
1 TAGTCTTAAAATTA
29005270 GGTCTAGGAT
Statistics
Matches: 44, Mismatches: 18, Indels: 1
0.70 0.29 0.02
Matches are distributed among these distances:
24 31 0.70
25 13 0.30
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (24 bp):
TAGTCTTAAAATTAAACTTAGGAC
Found at i:29005315 original size:13 final size:13
Alignment explanation
Indices: 29005299--29005349 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
29005289 GAACTTAATT
29005299 TTAGAACTTAGGA
1 TTAGAACTTAGGA
* *
29005312 TTAG-ACTTAAGC
1 TTAGAACTTAGGA
* *
29005324 TAAGAGCTTAGGA
1 TTAGAACTTAGGA
*
29005337 TTAGGACTTAGGA
1 TTAGAACTTAGGA
29005350 CTTAAAACTC
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (13 bp):
TTAGAACTTAGGA
Found at i:29006937 original size:22 final size:22
Alignment explanation
Indices: 29006909--29006950 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
29006899 GTAGTTAAGT
29006909 GACCATATGTCTCAAGACATAG
1 GACCATATGTCTCAAGACATAG
29006931 GACCATATGTCTCAAGACAT
1 GACCATATGTCTCAAGACAT
29006951 GAAAGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (22 bp):
GACCATATGTCTCAAGACATAG
Found at i:29008287 original size:19 final size:20
Alignment explanation
Indices: 29008263--29008316 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
29008253 GCAATTAAGC
29008263 CTAGAAATTTTGGTATAGG-
1 CTAGAAATTTTGGTATAGGA
* *
29008282 CTAGAAATTTTAGTATCGGA
1 CTAGAAATTTTGGTATAGGA
*
29008302 TTA-AAATTTTGGTAT
1 CTAGAAATTTTGGTAT
29008317 TGCTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 28 0.93
20 2 0.07
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (20 bp):
CTAGAAATTTTGGTATAGGA
Found at i:29014179 original size:21 final size:21
Alignment explanation
Indices: 29014136--29014249 Score: 113
Period size: 21 Copynumber: 5.5 Consensus size: 21
29014126 TCGAAAACTG
* * *
29014136 AACAGAAGCTCATGATAGCTA
1 AACAGAAGCTCATAAGAGTTA
29014157 AACAGAAGCTCATAAGAGTTA
1 AACAGAAGCTCATAAGAGTTA
* * * * *
29014178 AATAGAAACACATAAGGGTTG
1 AACAGAAGCTCATAAGAGTTA
* *
29014199 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGTTA
* *
29014220 AACAGAAACTCATAA-AGTTG
1 AACAGAAGCTCATAAGAGTTA
29014240 AACAGAAGCT
1 AACAGAAGCT
29014250 TGTGAGAGCT
Statistics
Matches: 73, Mismatches: 20, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
20 12 0.16
21 61 0.84
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGTTA
Found at i:29014258 original size:41 final size:42
Alignment explanation
Indices: 29014157--29014306 Score: 140
Period size: 42 Copynumber: 3.6 Consensus size: 42
29014147 ATGATAGCTA
* * * *
29014157 AACAGAAGCTCATAAGAGTTAAATAGAAACACATAAGGGTTG
1 AACAGAAGCTCGTAAGAGCTAAACAGAAACACATAAGAGTTG
*
29014199 AACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAA-AGTTG
1 AACAGAAGCTCGTAAGAGCTAAACAGAAACACATAAGAGTTG
* * * * **** * *
29014240 AACAGAAGCTTGTGAGAGCTGAACAAAAATTTGTATGAGTTA
1 AACAGAAGCTCGTAAGAGCTAAACAGAAACACATAAGAGTTG
* *
29014282 AACGGAAGCTCGTAAGAGCTTAACA
1 AACAGAAGCTCGTAAGAGCTAAACA
29014307 TAAAGTAAAA
Statistics
Matches: 89, Mismatches: 18, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
41 32 0.36
42 57 0.64
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTAAACAGAAACACATAAGAGTTG
Found at i:29014264 original size:21 final size:20
Alignment explanation
Indices: 29014197--29014264 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
29014187 ACATAAGGGT
29014197 TGAACAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCGT-AGAGC
* * * * *
29014218 TAAACAGAAACTCATAAAGT
1 TGAACAGAAGCTCGTAGAGC
*
29014238 TGAACAGAAGCTTGTGAGAGC
1 TGAACAGAAGCTCGT-AGAGC
29014259 TGAACA
1 TGAACA
29014265 AAAATTTGTA
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.18
Consensus pattern (20 bp):
TGAACAGAAGCTCGTAGAGC
Found at i:29016478 original size:18 final size:18
Alignment explanation
Indices: 29016455--29016502 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
29016445 AAAAAGCCTA
*
29016455 ACACAATATTTTTTTTTG
1 ACACAATATTTTTTTCTG
*
29016473 ACACAAT-TTTTTATCTG
1 ACACAATATTTTTTTCTG
29016490 ACA-AATATTTTTT
1 ACACAATATTTTTT
29016503 AAAATTTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 3 0.12
17 16 0.62
18 7 0.27
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.52
Consensus pattern (18 bp):
ACACAATATTTTTTTCTG
Found at i:29026215 original size:28 final size:29
Alignment explanation
Indices: 29026162--29026217 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
29026152 TAAATATTGA
*
29026162 AATTTATGATTTAAAATAAATTAATAATAT
1 AATTTAT-ATTTAAAATAAATAAATAATAT
29026192 AATTTAT-TTTAAATATAAA-AAATAAT
1 AATTTATATTTAAA-ATAAATAAATAAT
29026218 TTTTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 12 0.50
29 5 0.21
30 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (29 bp):
AATTTATATTTAAAATAAATAAATAATAT
Found at i:29026261 original size:78 final size:78
Alignment explanation
Indices: 29026201--29026359 Score: 255
Period size: 78 Copynumber: 2.0 Consensus size: 78
29026191 TAATTTATTT
* *
29026201 TAAATATAAAAAATAATTTTTTTAATTTTCTAATTAAATTGGTGTTAACATCAACCAAATTTTAT
1 TAAAAATAAAAAATAATTTTTTTAATTTTCTAATTAAATTGGTGTTAACATCAACCAAATTTAAT
*
29026266 TTAATAATATAGA
66 ATAATAATATAGA
* * *
29026279 TAAAAATATAAAATAATTTTTTTAATTTTCTAATTAAATTGTTGTTAACATCAACCAAATTTTAT
1 TAAAAATAAAAAATAATTTTTTTAATTTTCTAATTAAATTGGTGTTAACATCAACCAAATTTAAT
*
29026344 TTAATAATATAGA
66 ATAATAATATAGA
29026357 TAA
1 TAA
29026360 TCTAGTGCAG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (78 bp):
TAAAAATAAAAAATAATTTTTTTAATTTTCTAATTAAATTGGTGTTAACATCAACCAAATTTAAT
ATAATAATATAGA
Found at i:29029122 original size:26 final size:26
Alignment explanation
Indices: 29029083--29029156 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
29029073 AGATTAGTTG
*
29029083 AAAACTATAAAAAAAATTATTAT-TATA
1 AAAATTAT-AAAAAAATTATTATGTA-A
* * **
29029110 AAAATTATTAAAAAATCAAAATGGTAA
1 AAAATTATAAAAAAATTATTAT-GTAA
29029137 AAAATTATAAAAAAATTATT
1 AAAATTATAAAAAAATTATT
29029157 TGAATTTTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
26 10 0.28
27 24 0.67
28 2 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (26 bp):
AAAATTATAAAAAAATTATTATGTAA
Found at i:29036766 original size:3 final size:3
Alignment explanation
Indices: 29036758--29036794 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
29036748 CAAAAAGGAA
29036758 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29036795 TTATTATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29046809 original size:28 final size:26
Alignment explanation
Indices: 29046763--29046825 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
29046753 ATTTTATTTC
29046763 TCAAAAACACTGCTAAACACCAAACTTT
1 TCAAAAACACTGCTAAACA--AAACTTT
* * *
29046791 TCAAAAACACTTCTCAACAATACTTT
1 TCAAAAACACTGCTAAACAAAACTTT
*
29046817 TCAAGAACA
1 TCAAAAACA
29046826 TTGTTACCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 14 0.45
28 17 0.55
ACGTcount: A:0.46, C:0.27, G:0.03, T:0.24
Consensus pattern (26 bp):
TCAAAAACACTGCTAAACAAAACTTT
Found at i:29056849 original size:72 final size:73
Alignment explanation
Indices: 29056731--29056878 Score: 289
Period size: 72 Copynumber: 2.0 Consensus size: 73
29056721 TGTTTTTTTT
29056731 TTAGTTTGAATTAATTTTGTATAATTTGGAAATATTATTAATTCAACATGTCTATATCTATATAT
1 TTAGTTTGAATTAATTTTGTATAATTTGGAAATATTATTAATTCAACATGTCTATATCTATATAT
29056796 GTATTATA
66 GTATTATA
29056804 TTAGTTTGAA-TAATTTTGTATAATTTGGAAATATTATTAATTCAACATGTCTATATCTATATAT
1 TTAGTTTGAATTAATTTTGTATAATTTGGAAATATTATTAATTCAACATGTCTATATCTATATAT
29056868 GTATTATA
66 GTATTATA
29056876 TTA
1 TTA
29056879 TAAATTTTTT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 65 0.87
73 10 0.13
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.49
Consensus pattern (73 bp):
TTAGTTTGAATTAATTTTGTATAATTTGGAAATATTATTAATTCAACATGTCTATATCTATATAT
GTATTATA
Found at i:29056878 original size:39 final size:39
Alignment explanation
Indices: 29056762--29056884 Score: 107
Period size: 39 Copynumber: 3.3 Consensus size: 39
29056752 TAATTTGGAA
29056762 ATATTATTAATTCAACATGTCTATATCTATATATGTATT
1 ATATTATTAATTCAACATGTCTATATCTATATATGTATT
* * * * * * * *
29056801 ATATTAGT--TTGAATA-AT-T-T-TGTATAATTTGGA-A
1 ATATTATTAATTCAACATGTCTATATCTAT-ATATGTATT
29056834 ATATTATTAATTCAACATGTCTATATCTATATATGTATT
1 ATATTATTAATTCAACATGTCTATATCTATATATGTATT
*
29056873 ATATTATAAATT
1 ATATTATTAATT
29056885 TTTTTACCTT
Statistics
Matches: 59, Mismatches: 17, Indels: 16
0.64 0.18 0.17
Matches are distributed among these distances:
33 11 0.19
34 6 0.10
35 6 0.10
36 2 0.03
37 6 0.10
38 6 0.10
39 22 0.37
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (39 bp):
ATATTATTAATTCAACATGTCTATATCTATATATGTATT
Found at i:29057197 original size:23 final size:23
Alignment explanation
Indices: 29057153--29057197 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
29057143 TTTATTAAAA
* * *
29057153 ATAATGAAATTATAAATGAATAC
1 ATAATAAAATTACAAATAAATAC
*
29057176 ATAATAAAATTACATATAAATA
1 ATAATAAAATTACAAATAAATA
29057198 TCTTAAAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (23 bp):
ATAATAAAATTACAAATAAATAC
Found at i:29062636 original size:16 final size:16
Alignment explanation
Indices: 29062615--29062647 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29062605 ACTATTGATG
29062615 CTACTCATAACATTAA
1 CTACTCATAACATTAA
29062631 CTACTCATAACATTAA
1 CTACTCATAACATTAA
29062647 C
1 C
29062648 CAAGTTGAAA
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:0.42, C:0.27, G:0.00, T:0.30
Consensus pattern (16 bp):
CTACTCATAACATTAA
Found at i:29076452 original size:22 final size:22
Alignment explanation
Indices: 29076426--29076473 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
29076416 AATTATGATC
*
29076426 ATTACTTTAATTGCACT-ATTTA
1 ATTACTATAATT-CACTGATTTA
*
29076448 ATTACTATAATTCATTGATTTA
1 ATTACTATAATTCACTGATTTA
29076470 ATTA
1 ATTA
29076474 TTAATTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTACTATAATTCACTGATTTA
Found at i:29078675 original size:20 final size:21
Alignment explanation
Indices: 29078636--29078676 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
29078626 GTAATTATAT
*
29078636 TAATTAAATGAAATAAAAATA
1 TAATTAAATGAAACAAAAATA
*
29078657 TAATTAACT-AAACAAAAATA
1 TAATTAAATGAAACAAAAATA
29078677 ATTACACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
TAATTAAATGAAACAAAAATA
Found at i:29079506 original size:15 final size:15
Alignment explanation
Indices: 29079481--29079515 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29079471 GACTCTATTT
*
29079481 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
29079495 TAATTAATATTAAGA
1 TAATTAATATTAAGA
29079510 TAATTA
1 TAATTA
29079516 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:29081003 original size:66 final size:66
Alignment explanation
Indices: 29080933--29081065 Score: 187
Period size: 66 Copynumber: 2.0 Consensus size: 66
29080923 GCTTAGGTAC
* *
29080933 AAACTTTGCTCTAAAAACATGTTCCTCTCGATGAACAAAATAAGTGCTCTC-TCTAATTTGTACA
1 AAACTTTGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTC-CATCTAATTTGTACA
29080997 CA
65 CA
* * * * *
29080999 AAACTTTGGTCTAAATACATATTTCTTTCGATAAACAAAATAAGTGCTCCATTTAATTTGTACAC
1 AAACTTTGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTCCATCTAATTTGTACAC
29081064 A
66 A
29081065 A
1 A
29081066 TTAAATAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 58 0.98
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (66 bp):
AAACTTTGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTCCATCTAATTTGTACAC
A
Found at i:29084853 original size:1 final size:1
Alignment explanation
Indices: 29084847--29084881 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
29084837 ATCATCTTTC
29084847 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29084882 GCATTTGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29089156 original size:19 final size:19
Alignment explanation
Indices: 29089132--29089176 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
29089122 AGGAATTAGG
29089132 AAATTTTGAACTAATCTTC
1 AAATTTTGAACTAATCTTC
29089151 AAATTTTGAACTAATCTTC
1 AAATTTTGAACTAATCTTC
29089170 AAATTTT
1 AAATTTT
29089177 TCAGGAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (19 bp):
AAATTTTGAACTAATCTTC
Found at i:29094872 original size:34 final size:32
Alignment explanation
Indices: 29094751--29094880 Score: 127
Period size: 34 Copynumber: 3.9 Consensus size: 32
29094741 TTTTTAAAAA
* *
29094751 TAAATCAGGGTTTATAGTTTTT-TAAAATTAAT
1 TAAATTAGGGTTTA-AGTTTTTAAAAAATTAAT
* *
29094783 TAAATTAGGTTTTAAGGGTTTTAAATAAATTAAT
1 TAAATTAGGGTTTAA-GTTTTTAAA-AAATTAAT
* *
29094817 TAAATTAAGGTCTAGAGTTTTTAAGAAAATTAAT
1 TAAATTAGGGTTTA-AGTTTTTAA-AAAATTAAT
* *
29094851 TAAATTAGGGTTTAATTTTTTTAAACAATT
1 TAAATTAGGGTTTAA-GTTTTTAAAAAATT
29094881 TTGTGTTTAG
Statistics
Matches: 80, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
31 1 0.01
32 17 0.21
33 7 0.09
34 53 0.66
35 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (32 bp):
TAAATTAGGGTTTAAGTTTTTAAAAAATTAAT
Found at i:29095116 original size:126 final size:126
Alignment explanation
Indices: 29094967--29095614 Score: 847
Period size: 126 Copynumber: 5.2 Consensus size: 126
29094957 TTTGTTTTTT
* * * * * *
29094967 TTTTTCTATAGTAGTTTCAGAAAAATTAATTTTGAGAAGACGATTCTTAAAAAATAGTGTCGAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAA
* * * *
29095032 ATGCTAT-AAGTAAGATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
66 ACGCT-TCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
* *
29095093 TTTTTCTACAGTTGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAA
* * *
29095158 AAGCTTCAAGCAAGATGCATTGTCAGCAAAATTACTGAAAAATGCTCCCACGTAGACGCTC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
** * * * *
29095219 TTTTTCTATGGTAGTTCTTGAAAAAATGATTTTGAGAAGACAATTCTGAAAAATTAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAA
* * * * *
29095284 ACGCTTCAAGCAAGATGCACTGTCAGTAAAAATACTGAAAAATGCTCCCACATGGACGCTC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
*
29095345 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGAC-AGTTCTGAAAAAATAGTGTC-AA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGA-TTCTGAAAAAATAGTGTCAAA
* * * * *
29095408 AACGCTTCAAACAGGATGCATTGTCAGCAAAATTATTG-AAAAAGCTCCTACGTAGACGCTC
65 AACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
* * * *
29095469 TTTTTGTACAATAGTTCCTGAAAAAATAATATTT-AGAAGACGGTTCTGAAAAAATAGTGTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAAT-TTTGAGAAGACGATTCTGAAAAAATAGTGTCAAA
* * * * * * *
29095533 AATGCTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACACTC
65 AACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
29095595 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
29095615 CTTGGCCTTA
Statistics
Matches: 457, Mismatches: 59, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
124 70 0.15
125 73 0.16
126 314 0.69
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
Found at i:29105674 original size:19 final size:18
Alignment explanation
Indices: 29105647--29105682 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29105637 GTTTAGCAAT
29105647 GCTTAAAAAAACACTTTTG
1 GCTT-AAAAAACACTTTTG
*
29105666 GCTTGAAAAACACTTTT
1 GCTTAAAAAACACTTTT
29105683 TGAAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
GCTTAAAAAACACTTTTG
Found at i:29106394 original size:13 final size:13
Alignment explanation
Indices: 29106378--29106456 Score: 54
Period size: 13 Copynumber: 6.2 Consensus size: 13
29106368 TTATTTTTCC
29106378 AAAGCACTTTTTA
1 AAAGCACTTTTTA
*
29106391 AAAG--CTTTTCA
1 AAAGCACTTTTTA
** * *
29106402 AAAATACTTCTAA
1 AAAGCACTTTTTA
* **
29106415 AAATCACTTTTCC
1 AAAGCACTTTTTA
29106428 AAAGCACTTTTTA
1 AAAGCACTTTTTA
* *
29106441 AAAACACTTCTTA
1 AAAGCACTTTTTA
29106454 AAA
1 AAA
29106457 ACAATGCTAA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
11 9 0.18
13 41 0.82
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.34
Consensus pattern (13 bp):
AAAGCACTTTTTA
Found at i:29106410 original size:50 final size:50
Alignment explanation
Indices: 29106347--29106443 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
29106337 AAACCAAATA
* * * *
29106347 TTTCAAAAGTACTTCTCAAAATTATTTTTCCAAAGCACTTTTTAAAAGCT
1 TTTCAAAAATACTTCTAAAAATCACTTTTCCAAAGCACTTTTTAAAAGCT
29106397 TTTCAAAAATACTTCTAAAAATCACTTTTCCAAAGCACTTTTTAAAA
1 TTTCAAAAATACTTCTAAAAATCACTTTTCCAAAGCACTTTTTAAAA
29106444 ACACTTCTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (50 bp):
TTTCAAAAATACTTCTAAAAATCACTTTTCCAAAGCACTTTTTAAAAGCT
Found at i:29107244 original size:22 final size:22
Alignment explanation
Indices: 29107218--29107267 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
29107208 ATTGGGTTGA
* *
29107218 CGTTGTGACGTTGAGGGTTCCT
1 CGTTGCGACGTCGAGGGTTCCT
29107240 CGTTGCGACGTCGAGGGTTCCT
1 CGTTGCGACGTCGAGGGTTCCT
29107262 CGTTGC
1 CGTTGC
29107268 AACATACTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.08, C:0.24, G:0.36, T:0.32
Consensus pattern (22 bp):
CGTTGCGACGTCGAGGGTTCCT
Found at i:29112057 original size:16 final size:16
Alignment explanation
Indices: 29112008--29112060 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
29111998 AAAGAAATTT
*
29112008 AAAAATAAAATATTCA
1 AAAAATAATATATTCA
* *
29112024 AAAAATAATA-AGT-G
1 AAAAATAATATATTCA
*
29112038 AAAAATGATATATTCA
1 AAAAATAATATATTCA
29112054 AAAAATA
1 AAAAATA
29112061 CTATGTCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
14 9 0.32
15 4 0.14
16 15 0.54
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAAATAATATATTCA
Found at i:29114873 original size:46 final size:46
Alignment explanation
Indices: 29114820--29114954 Score: 234
Period size: 46 Copynumber: 2.9 Consensus size: 46
29114810 GTTCATAGGC
* *
29114820 GTGTAGCTAAAGCTATCACTTATCACTTTATCACTTGATCAGATAA
1 GTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
*
29114866 GTGTAGCTAAAGCTACCACTTATCACTTTGTCAGTTGATCAGATAA
1 GTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
*
29114912 GTGTAGCTAAAGCTACCACTTATCACTTTGTCACTAGATCAGA
1 GTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
29114955 AGTACTCAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 84 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (46 bp):
GTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
Found at i:29115063 original size:19 final size:21
Alignment explanation
Indices: 29115023--29115069 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
29115013 TTTTATTTTC
29115023 ATTTCATCAATAAATATATAT
1 ATTTCATCAATAAATATATAT
*
29115044 ATTTCATC-ATACAT-TATAT
1 ATTTCATCAATAAATATATAT
*
29115063 AATTCAT
1 ATTTCAT
29115070 GAAATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 5 0.21
21 8 0.33
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTCATCAATAAATATATAT
Found at i:29117109 original size:13 final size:13
Alignment explanation
Indices: 29117091--29117120 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29117081 AAAAAATTCT
29117091 AAAATTATGATAA
1 AAAATTATGATAA
*
29117104 AAAATTATTATAA
1 AAAATTATGATAA
29117117 AAAA
1 AAAA
29117121 CTAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAATTATGATAA
Found at i:29123149 original size:22 final size:21
Alignment explanation
Indices: 29123124--29123174 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
29123114 ATTAATTAAC
29123124 AATTGTATAAATTTACTTTTAT
1 AATTGTATAAA-TTACTTTTAT
* *
29123146 AATTTTATAAATTGCTTTTAT
1 AATTGTATAAATTACTTTTAT
*
29123167 -GTTGTATA
1 AATTGTATA
29123175 TCTTCAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 6 0.24
21 9 0.36
22 10 0.40
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (21 bp):
AATTGTATAAATTACTTTTAT
Found at i:29124647 original size:2 final size:2
Alignment explanation
Indices: 29124640--29124666 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29124630 TTAGAAAGTA
29124640 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
29124667 CTTCTGAAAT
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:29127932 original size:41 final size:41
Alignment explanation
Indices: 29127870--29127960 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
29127860 CCATTTAGAG
*
29127870 TCAGATTCAGCCACTTCTACAATCCTAAAAGGTCCTAACAA
1 TCAGGTTCAGCCACTTCTACAATCCTAAAAGGTCCTAACAA
29127911 TCAGGTTCAGCCACTTCTACAATCCTAAAAGGTCCTAACAA
1 TCAGGTTCAGCCACTTCTACAATCCTAAAAGGTCCTAACAA
29127952 TCAGGTTCA
1 TCAGGTTCA
29127961 ATTAGGTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.25
Consensus pattern (41 bp):
TCAGGTTCAGCCACTTCTACAATCCTAAAAGGTCCTAACAA
Found at i:29131553 original size:2 final size:2
Alignment explanation
Indices: 29131546--29131585 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29131536 CTAAGAATTT
29131546 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29131586 ATAAGTAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29137374 original size:45 final size:45
Alignment explanation
Indices: 29137323--29137426 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
29137313 TCTAATTTAT
**
29137323 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACATGTGCCAATTAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTGCCAATTAAA
* * *
29137368 ATTACAAAGTTTGTTCCAAGTTTGTTTCAACACCTGTCATTTAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTGCCAATTAAA
29137413 ATTACAAAGTTTGT
1 ATTACAAAGTTTGT
29137427 ATTTTTGCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (45 bp):
ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTGCCAATTAAA
Found at i:29143976 original size:60 final size:54
Alignment explanation
Indices: 29143853--29143980 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 54
29143843 ATACATTATT
* * *
29143853 TTATATATATTTATTGAAATATTTTGATTAATTGATTTATAATTTCATAAATTTA
1 TTATATAT-TTTTTTGAAATATTTTGATTAATTGATGTATAATTACATAAATTTA
29143908 TTATATATTTTTNNNNNNTTGAAATATTTTGATTAATTGATGTATAATTACATAAATTTA
1 TTATATATTTTT------TTGAAATATTTTGATTAATTGATGTATAATTACATAAATTTA
29143968 TTATATATTTTTT
1 TTATATATTTTTT
29143981 AGTACCACGA
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
54 4 0.06
55 8 0.12
60 52 0.81
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.54
Consensus pattern (54 bp):
TTATATATTTTTTTGAAATATTTTGATTAATTGATGTATAATTACATAAATTTA
Found at i:29159146 original size:44 final size:44
Alignment explanation
Indices: 29159096--29159231 Score: 121
Period size: 44 Copynumber: 3.1 Consensus size: 44
29159086 AAATTCTAGC
*
29159096 CTTGTCTCCCTGAGTGGCAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTCCCTGAGTGGCAGTGGAGTAGGTTGAAAATAACAGAT
* * * *** * * * * *
29159140 CTTGTCTACCTGTATTGACAGCAAAGTAGATCGAAGATACCAG-C
1 CTTGTCTCCCTG-AGTGGCAGTGGAGTAGGTTGAAAATAACAGAT
* **
29159184 CTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAACAGAT
1 CTTGTCTCCCTGAGTGGCAGTGGAGTAGGTTGAAAATAACAGAT
29159228 CTTG
1 CTTG
29159232 CCTTCCTGTA
Statistics
Matches: 65, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
43 19 0.29
44 25 0.38
45 21 0.32
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (44 bp):
CTTGTCTCCCTGAGTGGCAGTGGAGTAGGTTGAAAATAACAGAT
Found at i:29159259 original size:88 final size:88
Alignment explanation
Indices: 29159093--29159264 Score: 238
Period size: 88 Copynumber: 2.0 Consensus size: 88
29159083 GTGAAATTCT
* ** * * *
29159093 AGCCTTGTCTCCCTGAGTGGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTACCTGTATTGA
1 AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGCCTACCTGTATAGA
*
29159158 CAGCAAAGTAGATCGAAGATACC
66 CAGCAAAGCAGATCGAAGATACC
*
29159181 AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGCCTTCCTGTACTAG
1 AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGCCTACCTGTA-TAG
**
29159246 -CAGTGAAGCAGATCGAAGA
65 ACAGCAAAGCAGATCGAAGA
29159265 CATTAGTCTT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 71 0.97
89 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (88 bp):
AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGCCTACCTGTATAGA
CAGCAAAGCAGATCGAAGATACC
Found at i:29159333 original size:50 final size:50
Alignment explanation
Indices: 29159271--29159388 Score: 157
Period size: 50 Copynumber: 2.4 Consensus size: 50
29159261 AAGACATTAG
* *
29159271 TCTTATCGCCCTGACATTGCAATGGAA-AAGATTGAAGCCACAACGGTGAA
1 TCTTATCTCCCTGACATTGCAA-CGAAGAAGATTGAAGCCACAACGGTGAA
* * * *
29159321 TCTTATTTCCCTGACGTTGCAACGAAGCAGATTGAAGCCACGACGGTGAA
1 TCTTATCTCCCTGACATTGCAACGAAGAAGATTGAAGCCACAACGGTGAA
*
29159371 TCTTATCTCCCTGGCATT
1 TCTTATCTCCCTGACATT
29159389 AAGGCCTGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 3 0.05
50 55 0.95
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (50 bp):
TCTTATCTCCCTGACATTGCAACGAAGAAGATTGAAGCCACAACGGTGAA
Done.