Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 101 of 135
Found at i:34655801 original size:25 final size:25
Alignment explanation
Indices: 34655742--34655801 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
34655732 ATAGCCAATC
* *
34655742 CTTTGGCCCAACCATGAAACCAAAG
1 CTTTGACCCAACCATAAAACCAAAG
* *
34655767 -TTTGACCCAACCTTAAAACCTAAG
1 CTTTGACCCAACCATAAAACCAAAG
34655791 CTTTGACCCAA
1 CTTTGACCCAA
34655802 TCAACCCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 20 0.67
25 10 0.33
ACGTcount: A:0.35, C:0.32, G:0.12, T:0.22
Consensus pattern (25 bp):
CTTTGACCCAACCATAAAACCAAAG
Found at i:34655908 original size:23 final size:23
Alignment explanation
Indices: 34655849--34655909 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
34655839 TTGACCCAAT
34655849 ACTCGAATCGACCCGAACCCGTTG
1 ACTCG-ATCGACCCGAACCCGTTG
*
34655873 ACTCGACCTGACCC-AACCCGTTG
1 ACTCGATC-GACCCGAACCCGTTG
*
34655896 ACTTTGATCGACCC
1 AC-TCGATCGACCC
34655910 CTTGACCGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.20
Consensus pattern (23 bp):
ACTCGATCGACCCGAACCCGTTG
Found at i:34660721 original size:12 final size:12
Alignment explanation
Indices: 34660704--34660744 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
34660694 GTTTAACGAC
34660704 ATAAAATAAAAG
1 ATAAAATAAAAG
*
34660716 ATAAAATAAAAT
1 ATAAAATAAAAG
34660728 AGT-AAATAAAAG
1 A-TAAAATAAAAG
34660740 A-AAAA
1 ATAAAA
34660745 GCTTGAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 3 0.12
12 21 0.84
13 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:34676524 original size:15 final size:16
Alignment explanation
Indices: 34676504--34676536 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34676494 TTTATTTTAT
*
34676504 TTTGTT-TTTACTTAA
1 TTTGTTATTTACCTAA
34676519 TTTGTTATTTACCTAA
1 TTTGTTATTTACCTAA
34676535 TT
1 TT
34676537 CCATTTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTGTTATTTACCTAA
Found at i:34687545 original size:17 final size:18
Alignment explanation
Indices: 34687523--34687565 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
34687513 ATAGTTTCCA
34687523 TGCATTTTTA-TTGTCAT
1 TGCATTTTTATTTGTCAT
34687540 TGCATTTTTATTTTGTCAT
1 TGCATTTTTA-TTTGTCAT
34687559 TGCATTT
1 TGCATTT
34687566 CTTTTGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.42
19 14 0.58
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (18 bp):
TGCATTTTTATTTGTCAT
Found at i:34687570 original size:17 final size:16
Alignment explanation
Indices: 34687523--34687572 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 16
34687513 ATAGTTTCCA
34687523 TGCATTTTTATTGTCAT
1 TGCATTTTT-TTGTCAT
34687540 TGCATTTTTATTTTGTCAT
1 TGCA--TTT-TTTTGTCAT
34687559 TGCATTTCTTTTGT
1 TGCATTT-TTTTGT
34687573 TAATTTAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 13 0.45
19 14 0.48
20 2 0.07
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (16 bp):
TGCATTTTTTTGTCAT
Found at i:34688169 original size:23 final size:21
Alignment explanation
Indices: 34688141--34688196 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
34688131 CAATCACTTG
*
34688141 AAAAAAGAAAATGAGAAAAAGA
1 AAAAAAGAAAAAGAG-AAAAGA
34688163 AAGAAAA-ACAAAAGAGAAAAGA
1 AA-AAAAGA-AAAAGAGAAAAGA
*
34688185 AAAGAAGAAAAA
1 AAAAAAGAAAAA
34688197 ATGTTTGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 7 0.24
22 12 0.41
23 10 0.34
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAAAGAAAAAGAGAAAAGA
Found at i:34704178 original size:17 final size:17
Alignment explanation
Indices: 34704158--34704212 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
34704148 ATTGTCCCTA
*
34704158 CATTATTAATGTCATTG
1 CATTATTATTGTCATTG
* **
34704175 CATTTTTATTGTCGCTG
1 CATTATTATTGTCATTG
34704192 CATCTA-TATTGTCATTG
1 CAT-TATTATTGTCATTG
34704209 CATT
1 CATT
34704213 TCCATATATA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 1 0.03
17 28 0.93
18 1 0.03
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (17 bp):
CATTATTATTGTCATTG
Found at i:34707227 original size:15 final size:16
Alignment explanation
Indices: 34707207--34707247 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
34707197 GGCAACCCAA
34707207 TTTTATTTTTATTTC-
1 TTTTATTTTTATTTCT
*
34707222 TTTTATTTCT-TTTCT
1 TTTTATTTTTATTTCT
34707237 TTTTATTTTTA
1 TTTTATTTTTA
34707248 ATATTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATTTTTATTTCT
Found at i:34707252 original size:24 final size:23
Alignment explanation
Indices: 34707206--34707289 Score: 62
Period size: 24 Copynumber: 3.4 Consensus size: 23
34707196 AGGCAACCCA
*
34707206 ATTTTATTTTTATTTCTTTTATTT
1 ATTTTATTTTTATTT-TTATATTT
* *
34707230 CTTTTCTTTTTATTTTTAATATTT
1 ATTTTATTTTTATTTTT-ATATTT
* *
34707254 ATTTATTTTCTTTATTTTAAT-TCTT
1 ATTT-TATT-TTTATTTTTATAT-TT
34707279 ATTTTCATTTT
1 ATTTT-ATTTT
34707290 ATGTTCAGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
23 2 0.04
24 25 0.52
25 13 0.27
26 8 0.17
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (23 bp):
ATTTTATTTTTATTTTTATATTT
Found at i:34709231 original size:23 final size:25
Alignment explanation
Indices: 34709205--34709250 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
34709195 TCAACTAGGG
34709205 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
34709228 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
34709251 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:34711083 original size:3 final size:3
Alignment explanation
Indices: 34711077--34711102 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34711067 AGAAAGTGAA
34711077 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
34711103 TGAGATGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:34713360 original size:12 final size:12
Alignment explanation
Indices: 34713345--34713375 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34713335 TTAGAAGTAG
34713345 TTTTCTTCTCGA
1 TTTTCTTCTCGA
*
34713357 TTTTCTTCTTGA
1 TTTTCTTCTCGA
34713369 TTTTCTT
1 TTTTCTT
34713376 TAAGGAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.19, G:0.06, T:0.68
Consensus pattern (12 bp):
TTTTCTTCTCGA
Found at i:34719404 original size:39 final size:39
Alignment explanation
Indices: 34719358--34719432 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
34719348 GGGACCCCTA
*
34719358 TTCTGGAAATTGAA-ACACAAACCCTTT-CTAAAAAAAAAG
1 TTCTGGAAA-TCAATACA-AAACCCTTTCCTAAAAAAAAAG
*
34719397 TTCTGGAAATCAATACAAACCCCTTTCCTAAAAAAA
1 TTCTGGAAATCAATACAAAACCCTTTCCTAAAAAAA
34719433 TTAATATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 11 0.34
39 21 0.66
ACGTcount: A:0.47, C:0.21, G:0.08, T:0.24
Consensus pattern (39 bp):
TTCTGGAAATCAATACAAAACCCTTTCCTAAAAAAAAAG
Found at i:34720857 original size:28 final size:30
Alignment explanation
Indices: 34720804--34720864 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
34720794 GCTTATAGGT
*
34720804 CCCTAAACTATTCATAAATTATA-TTTTGA
1 CCCTAAACTATTCATAAATTACATTTTTGA
*
34720833 CCCTAAACT-TTCCA-AAATTCCATTTTTGA
1 CCCTAAACTATT-CATAAATTACATTTTTGA
34720862 CCC
1 CCC
34720865 CGGTTTCACC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (30 bp):
CCCTAAACTATTCATAAATTACATTTTTGA
Found at i:34720890 original size:30 final size:31
Alignment explanation
Indices: 34720846--34721242 Score: 114
Period size: 30 Copynumber: 13.5 Consensus size: 31
34720836 TAAACTTTCC
*
34720846 AAAATT-CCATTTTTGACCCCGGTTTCACCA
1 AAAATTACCATTTTTGACCCCGATTTCACCA
* *
34720876 AAAATTACCA-TTTTGCCCCCGAACTTT--TC-
1 AAAATTACCATTTTTGACCCCG-A-TTTCACCA
* * *
34720905 AAAA-TCCCATTTTTAACCCCGATTTCACTA
1 AAAATTACCATTTTTGACCCCGATTTCACCA
* * * *
34720935 AAAATTACCA-TTTT-ACCCCTAAACTT--GCT
1 AAAATTACCATTTTTGACCCC--GATTTCACCA
*
34720964 AAAATT-CCATTTTTGACCTCGATTTCACCA
1 AAAATTACCATTTTTGACCCCGATTTCACCA
34720994 AAAATTACCA-TTTT-ACCCCTGAACTTT--CC-
1 AAAATTACCATTTTTGACCCC-G-A-TTTCACCA
* ** *
34721023 AAAA-T-CTCATTTTTAACCTAGGTTTCACCA
1 AAAATTAC-CATTTTTGACCCCGATTTCACCA
* *
34721053 AAAATTACCATTTTAG-CCCCAAAATTT--CC-
1 AAAATTACCATTTTTGACCCC--GATTTCACCA
* * * **
34721082 AAAAGT-CTA-TTTTAACATCGATTTCACCA
1 AAAATTACCATTTTTGACCCCGATTTCACCA
* *
34721111 AAAATT---ATTTTTTACCCCCCAAACTTT--CC-
1 AAAATTACCATTTTTGA--CCCC-GA-TTTCACCA
* *
34721140 AAAAGT-CCATTTTTGACCCCGGTTTCACCA
1 AAAATTACCATTTTTGACCCCGATTTCACCA
*
34721170 AAAATTACCA-TTTTG-CCCTCGAGCTTT---CT
1 AAAATTACCATTTTTGACCC-CGA--TTTCACCA
*
34721199 AAAA-TCCCATTTTTGACCCCGATTTCACCA
1 AAAATTACCATTTTTGACCCCGATTTCACCA
*
34721229 ATAATTA-CATTTTT
1 AAAATTACCATTTTT
34721243 ACCTCTGGAA
Statistics
Matches: 263, Mismatches: 52, Indels: 104
0.63 0.12 0.25
Matches are distributed among these distances:
26 4 0.02
27 17 0.06
28 29 0.11
29 80 0.30
30 84 0.32
31 33 0.13
32 16 0.06
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (31 bp):
AAAATTACCATTTTTGACCCCGATTTCACCA
Found at i:34720915 original size:59 final size:59
Alignment explanation
Indices: 34720826--34721241 Score: 430
Period size: 59 Copynumber: 7.1 Consensus size: 59
34720816 CATAAATTAT
* * * *
34720826 ATTTTGACCCTAAACTTTCCAAAATTCCATTTTTGACCCCGGTTTCACCAAAAATTACC
1 ATTTTGCCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACC
* * * *
34720885 ATTTTGCCCCCGAACTTTTCAAAATCCCATTTTTAACCCCGATTTCACTAAAAATTACC
1 ATTTTGCCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACC
* * * * * *
34720944 ATTTTACCCCTAAACTTGCTAAAATTCCATTTTTGACCTCGATTTCACCAAAAATTACC
1 ATTTTGCCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACC
* ** * * ** *
34721003 ATTTTACCCCTGAACTTTCCAAAATCTCATTTTTAACCTAGGTTTCACCAAAAATTACC
1 ATTTTGCCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACC
* * * ** *
34721062 ATTTTAG-CCCCAAAATTTCCAAAAGT-CTA-TTTTAACATCGATTTCACCAAAAATTA-T
1 ATTTT-GCCCCCAAACTTTCCAAAA-TCCCATTTTTGACCCCGATTTCACCAAAAATTACC
* * *
34721119 TTTTTACCCCCCAAACTTTCCAAAAGT-CCATTTTTGACCCCGGTTTCACCAAAAATTACC
1 ATTTT-GCCCCCAAACTTTCCAAAA-TCCCATTTTTGACCCCGATTTCACCAAAAATTACC
* * * * *
34721179 ATTTTGCCCTCGAGCTTTCTAAAATCCCATTTTTGACCCCGATTTCACCAATAATTA-C
1 ATTTTGCCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACC
34721237 ATTTT
1 ATTTT
34721242 TACCTCTGGA
Statistics
Matches: 298, Mismatches: 53, Indels: 13
0.82 0.15 0.04
Matches are distributed among these distances:
57 5 0.02
58 51 0.17
59 237 0.80
60 5 0.02
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (59 bp):
ATTTTGCCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACC
Found at i:34721034 original size:118 final size:116
Alignment explanation
Indices: 34720833--34721241 Score: 482
Period size: 118 Copynumber: 3.5 Consensus size: 116
34720823 TATATTTTGA
* *
34720833 CCCTAAACTTTCCAAAATTCCATTTTTGACCCCGGTTTCACCAAAAATTACCATTTTGCCCCCGA
1 CCCTAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTA-CATTTTACCCCCGA
* * *
34720898 ACTTTTCAAAATCCCATTTTTAACCCCGATTTCACTAAAAATTACCATTTTAC
65 ACTTTCCAAAAT-CCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTAC
* * * *
34720951 CCCTAAACTTGCTAAAATTCCATTTTTGACCTCGATTTCACCAAAAATTACCATTTTACCCCTGA
1 CCCTAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTA-CATTTTACCCCCGA
**
34721016 ACTTTCCAAAATCTCATTTTTAACCTAGGTTTCACCAAAAATTACCATTTTAGC
65 ACTTTCCAAAATC-CATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTA-C
* * * * ** ** *
34721070 CCC-AAAATTTCCAAAAGTCTA-TTTTAACATCGATTTCACCAAAAATTATTTTTTACCCCCCAA
1 CCCTAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACATTTTA-CCCCCGA
* *
34721133 ACTTTCCAAAAGTCCATTTTTGACCCCGGTTTCACCAAAAATTACCATTTT-G
65 ACTTTCCAAAA-TCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTAC
* * * * *
34721185 CCCTCGAGCTTTCTAAAATCCCATTTTTGACCCCGATTTCACCAATAATTACATTTT
1 CCCT-AAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACATTTT
34721242 TACCTCTGGA
Statistics
Matches: 245, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
115 3 0.01
116 5 0.02
117 87 0.36
118 146 0.60
119 4 0.02
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (116 bp):
CCCTAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACATTTTACCCCCGAA
CTTTCCAAAATCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTAC
Found at i:34721168 original size:176 final size:176
Alignment explanation
Indices: 34720833--34721241 Score: 497
Period size: 176 Copynumber: 2.3 Consensus size: 176
34720823 TATATTTTGA
* *
34720833 CCCTAAACTTTCCAAAAT-TCCATTTTTGACCCCGGTTTCACCAAAAATTACCATTTTGCCCCCG
1 CCCTGAACTTTCCAAAATCT-CATTTTTGACCCCGGTTTCACCAAAAATTACCATTTTGCCCCCA
* * * * *
34720897 AACTTTTCAAAATCCCATTTTTAACCCCGATTTCACTAAAAATTACCATTTTACCCCTAAACTTG
65 AAATTTCCAAAATCCCATTTTTAACACCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTG
* * *
34720962 CTAAAATTCCATTTTTGACCTCGATTTCACCAAAAATTACCATTTTAC
130 CCAAAAGTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTT-C
* **
34721010 CCCTGAACTTTCCAAAATCTCATTTTTAACCTAGGTTTCACCAAAAATTACCATTTTAG-CCCCA
1 CCCTGAACTTTCCAAAATCTCATTTTTGACCCCGGTTTCACCAAAAATTACCATTTT-GCCCCCA
* * **
34721074 AAATTTCCAAAAGT-CTA-TTTTAACATCGATTTCACCAAAAATTA-TTTTTTACCCCCCAAACT
65 AAATTTCCAAAA-TCCCATTTTTAACACCGATTTCACCAAAAATTACCATTTTA-CCCCCAAACT
* * *
34721136 TTCCAAAAGTCCATTTTTGACCCCGGTTTCACCAAAAATTACCATTTTG
128 TGCCAAAAGTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTC
* * * * *
34721185 CCCTCGAGCTTTCTAAAATCCCATTTTTGACCCCGATTTCACCAATAATTA-CATTTT
1 CCCT-GAACTTTCCAAAATCTCATTTTTGACCCCGGTTTCACCAAAAATTACCATTTT
34721242 TACCTCTGGA
Statistics
Matches: 199, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
175 15 0.08
176 114 0.57
177 67 0.34
178 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (176 bp):
CCCTGAACTTTCCAAAATCTCATTTTTGACCCCGGTTTCACCAAAAATTACCATTTTGCCCCCAA
AATTTCCAAAATCCCATTTTTAACACCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTGC
CAAAAGTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTC
Found at i:34733703 original size:200 final size:200
Alignment explanation
Indices: 34733359--34734267 Score: 1331
Period size: 200 Copynumber: 4.5 Consensus size: 200
34733349 CAAAACGGTA
*
34733359 AGGCGGTAATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAAACACGAGCAAAT
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTC-AACACGAGCAAAT
* *
34733424 CTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAACAATAAAA-AGGTTAGCTTC
65 CTTCGAACCCAGCTTCATGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATA-GTTAGCTTC
* * * *
34733488 CTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCTAGAGAAGCGAATCAAA
129 CTGACGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATCAAA
*
34733553 GCAAGC-G
194 ACAA-CAG
* * * *
34733560 AGGCGGTCATCTTCCTGATGAGATACAGGGTAGAACACCAACTCAGCACTCAACACGAGCAAATC
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAACACGAGCAAATC
* *
34733625 TTCGAACCCAGCTTCATGATGAGACATTGAGAAGTAGGTCGAAACAATAAAATAGTTAGCTTCCT
66 TTCGAACCCAGCTTCATGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATAGTTAGCTTCCT
* * * * *
34733690 GATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTAAGGAGATCCAGAGAAGCGAATCAAAAA
131 GACGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATCAAAAC
34733755 AAGC-G
196 AA-CAG
* * * *
34733760 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCACTCAACATGAGCAAATT
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAACACGAGCAAATC
* *
34733825 TTCGAACCCAGCTT-ACTGATGAGACACTGAGAAGCAGGTCAAAACAATAAAATGGTTAGCTTCC
66 TTCGAACCCAGCTTCA-TGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATAGTTAGCTTCC
** *
34733889 TGACGAGATACAGAGAAGTGGACCAAATTTATCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
130 TGACGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATCAAAA
34733954 CAACAG
195 CAACAG
* * * * *
34733960 AGGCGGTCACCTTCCTGATGAGATACAGAGAAGAATACCAACCCAACGCTCAATACGAGCAAATT
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAACACGAGCAAATC
* *
34734025 TTCGAACCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCCT
66 TTCGAACCCAGCTTCATGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATAGTTAGCTTCCT
* *
34734090 GACGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAAC
131 GACGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATCAAAAC
34734155 AACAG
196 AACAG
* * * * **
34734160 AGGCGGTCACCTTCCTGAGGAGATACAGAGAAGGATACCAACTCAACGCTCAAGGCGAGCAAATC
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAACACGAGCAAATC
* * *
34734225 TTCAAACCCAGCTTCTTGATGAGACACTGAGAAGCATGTCGAA
66 TTCGAACCCAGCTTCATGATGAGACACTGAGAAGCAGGTCGAA
34734268 GTCAAAGAAA
Statistics
Matches: 657, Mismatches: 47, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
199 2 0.00
200 608 0.93
201 47 0.07
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.19
Consensus pattern (200 bp):
AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAACACGAGCAAATC
TTCGAACCCAGCTTCATGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATAGTTAGCTTCCT
GACGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCAAATCAAAAC
AACAG
Found at i:34734651 original size:16 final size:17
Alignment explanation
Indices: 34734630--34734669 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
34734620 TTGAATTAAT
34734630 TTTAAATTT-ATTCAAA
1 TTTAAATTTGATTCAAA
* *
34734646 TTTAAATTTGTTTTAAA
1 TTTAAATTTGATTCAAA
34734663 TTTAAAT
1 TTTAAAT
34734670 ACATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTGATTCAAA
Found at i:34734663 original size:17 final size:16
Alignment explanation
Indices: 34734625--34734669 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
34734615 TAAGTTTGAA
*
34734625 TTAATTTTAAATTTAT
1 TTAAATTTAAATTTAT
* *
34734641 TCAAATTTAAATTTGTT
1 TTAAATTTAAATTT-AT
34734658 TTAAATTTAAAT
1 TTAAATTTAAAT
34734670 ACATTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:34735730 original size:18 final size:18
Alignment explanation
Indices: 34735707--34735741 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34735697 TTGAAATGTT
34735707 CAGATCTGGTTCAAAAAC
1 CAGATCTGGTTCAAAAAC
*
34735725 CAGATCTGGTTTAAAAA
1 CAGATCTGGTTCAAAAA
34735742 TGAAATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (18 bp):
CAGATCTGGTTCAAAAAC
Found at i:34736511 original size:29 final size:29
Alignment explanation
Indices: 34736473--34736681 Score: 105
Period size: 29 Copynumber: 7.1 Consensus size: 29
34736463 ATAAATTATA
34736473 TTTTAACCCCAAACTTTCCAAAATTCCAT
1 TTTTAACCCCAAACTTTCCAAAATTCCAT
*
34736502 TTTTAACCCC--AGTTTCACCAAAAATTACCA-
1 TTTTAACCCCAAACTTT--CC-AAAATT-CCAT
** *
34736532 TTTTGCCCCCAAACTTTCCAAAATCCCAT
1 TTTTAACCCCAAACTTTCCAAAATTCCAT
* * **
34736561 TTTTGACCTC--GGTTTCATCAAAAATTACCA-
1 TTTTAACCCCAAACTTTC--C-AAAATT-CCAT
34736591 TTTT-ACCACCAAACTTTCCAAAATTCCAT
1 TTTTAACC-CCAAACTTTCCAAAATTCCAT
* **
34736620 TTTTTACCCC--GGTTTCACTAAAAATTACCA-
1 TTTTAACCCCAAACTTTC-C--AAAATT-CCAT
* * *
34736650 TTTTACCCCCAAACTTTCCAAAACTCTAT
1 TTTTAACCCCAAACTTTCCAAAATTCCAT
34736679 TTT
1 TTT
34736682 GACCTCAGTT
Statistics
Matches: 136, Mismatches: 21, Indels: 46
0.67 0.10 0.23
Matches are distributed among these distances:
27 12 0.09
28 9 0.07
29 49 0.36
30 44 0.32
31 10 0.07
32 12 0.09
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (29 bp):
TTTTAACCCCAAACTTTCCAAAATTCCAT
Found at i:34736561 original size:59 final size:59
Alignment explanation
Indices: 34736472--34736828 Score: 452
Period size: 59 Copynumber: 6.1 Consensus size: 59
34736462 CATAAATTAT
* * * *
34736472 ATTTTAACCCCAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCACCAAAAATTACC
1 ATTTTACCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGGTTTCACCAAAAATTACC
* * *
34736531 ATTTTGCCCCCAAACTTTCCAAAATCCCATTTTTGACCTCGGTTTCATCAAAAATTACC
1 ATTTTACCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGGTTTCACCAAAAATTACC
* * * *
34736590 ATTTTACCACCAAACTTTCCAAAATTCCATTTTTTACCCCGGTTTCACTAAAAATTACC
1 ATTTTACCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGGTTTCACCAAAAATTACC
* * *
34736649 ATTTTACCCCCAAACTTTCCAAAA-CTC-TATTTTGACCTCAGTTTCACCAAAAATTACC
1 ATTTTACCCCCAAACTTTCCAAAATCCCAT-TTTTGACCCCGGTTTCACCAAAAATTACC
** * *
34736707 ATTTTACCCCTGAACTTTCCAAAAGT-CTATTTTTAACCCCGGTTTCACCAAAAATTACC
1 ATTTTACCCCCAAACTTTCCAAAA-TCCCATTTTTGACCCCGGTTTCACCAAAAATTACC
* * * * * *
34736766 ATTTTACCCTCGAGCTTTCTAAAATCCCATTTTTGACCTCGATTTCACCAAAAATTA-C
1 ATTTTACCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGGTTTCACCAAAAATTACC
34736824 ATTTT
1 ATTTT
34736829 TAGCCCCGAA
Statistics
Matches: 257, Mismatches: 36, Indels: 11
0.85 0.12 0.04
Matches are distributed among these distances:
57 1 0.00
58 55 0.21
59 200 0.78
60 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (59 bp):
ATTTTACCCCCAAACTTTCCAAAATCCCATTTTTGACCCCGGTTTCACCAAAAATTACC
Found at i:34736681 original size:118 final size:117
Alignment explanation
Indices: 34736472--34736828 Score: 522
Period size: 117 Copynumber: 3.0 Consensus size: 117
34736462 CATAAATTAT
* *
34736472 ATTTTAACCCCAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCACCAAAAATTACCATTTTG
1 ATTTT-ACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTA
*
34736537 CCCCCAAACTTTCCAAAATCCCATTTTTGACCTCGGTTTCATCAAAAATTACC
65 CCCCCAAACTTTCCAAAATCCCATTTTTGACCTCGGTTTCACCAAAAATTACC
* *
34736590 ATTTTACCACCAAACTTTCCAAAATTCCATTTTTTACCCCGGTTTCACTAAAAATTACCATTTTA
1 ATTTTACC-CCAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTA
* *
34736655 CCCCCAAACTTTCCAAAA-CTC-TATTTTGACCTCAGTTTCACCAAAAATTACC
65 CCCCCAAACTTTCCAAAATCCCAT-TTTTGACCTCGGTTTCACCAAAAATTACC
* * *
34736707 ATTTTACCCCTGAACTTTCCAAAAGTCTATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTA
1 ATTTTACCCC-AAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTA
* * * * *
34736772 CCCTCGAGCTTTCTAAAATCCCATTTTTGACCTCGATTTCACCAAAAATTA-C
65 CCCCCAAACTTTCCAAAATCCCATTTTTGACCTCGGTTTCACCAAAAATTACC
34736824 ATTTT
1 ATTTT
34736829 TAGCCCCGAA
Statistics
Matches: 215, Mismatches: 19, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
116 3 0.01
117 109 0.51
118 102 0.47
119 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (117 bp):
ATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTAC
CCCCAAACTTTCCAAAATCCCATTTTTGACCTCGGTTTCACCAAAAATTACC
Found at i:34740073 original size:29 final size:30
Alignment explanation
Indices: 34740025--34740081 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
34740015 ATTTACACAT
34740025 TTTATTTTTACCTCTTTTTC-TTTTTTTAC
1 TTTATTTTTACCTCTTTTTCATTTTTTTAC
*
34740054 TTTATTTTTTCCT-TTGTTTCATTTTTTT
1 TTTATTTTTACCTCTT-TTTCATTTTTTT
34740082 CTTCTTATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.75
Consensus pattern (30 bp):
TTTATTTTTACCTCTTTTTCATTTTTTTAC
Found at i:34745314 original size:17 final size:16
Alignment explanation
Indices: 34745271--34745344 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
34745261 GAGACTATTG
*
34745271 AGAAGAAAGAAAAAAA
1 AGAAAAAAGAAAAAAA
34745287 AGAAAAAAGAAAATAAA
1 AGAAAAAAGAAAA-AAA
* * *
34745304 GGAAAATAGAAATAAGA
1 AGAAAAAAGAAA-AAAA
* *
34745321 A-AATAAAGAAAAATA
1 AGAAAAAAGAAAAAAA
*
34745336 ATAAAAAAG
1 AGAAAAAAG
34745345 TTAAAAATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
15 4 0.09
16 26 0.57
17 15 0.33
18 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (16 bp):
AGAAAAAAGAAAAAAA
Found at i:34745314 original size:24 final size:24
Alignment explanation
Indices: 34745276--34745344 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
34745266 TATTGAGAAG
*
34745276 AAAGAAAAAAAAGAAAAAAGAAAAT
1 AAAG-AAAAATAGAAAAAAGAAAAT
* *
34745301 AAAGGAAAATAGAAATAAGAAAAT
1 AAAGAAAAATAGAAAAAAGAAAAT
*
34745325 AAAGAAAAATAATAAAAAAG
1 AAAGAAAAAT-AGAAAAAAG
34745345 TTAAAAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 26 0.70
25 11 0.30
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (24 bp):
AAAGAAAAATAGAAAAAAGAAAAT
Found at i:34745528 original size:29 final size:30
Alignment explanation
Indices: 34745459--34745548 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 30
34745449 TAATGACACC
* * *
34745459 ATGATCAAAACATAATAAATCGTTAAA-ATTA
1 ATGATCAAAACGTAATAAA--ATTAAAGTTTA
* * *
34745490 GTGATCAAAATGTAA-CAAATTAAAGTTTA
1 ATGATCAAAACGTAATAAAATTAAAGTTTA
34745519 ATGATCAAAACGTAATAAAATTAAAGTTTA
1 ATGATCAAAACGTAATAAAATTAAAGTTTA
34745549 GTGACCTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 5 0.10
29 16 0.33
30 15 0.31
31 12 0.25
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (30 bp):
ATGATCAAAACGTAATAAAATTAAAGTTTA
Found at i:34748167 original size:4 final size:4
Alignment explanation
Indices: 34748158--34748186 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
34748148 AATCCTCCCC
34748158 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
34748187 CCCACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:34760576 original size:25 final size:25
Alignment explanation
Indices: 34760538--34760585 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
34760528 CTTTTATATT
*
34760538 ATTGACTTTAATCA-TGAAAGTATC
1 ATTGACTTTAATCACTCAAAGTATC
*
34760562 ATTGAGCTTTTATCACTCAAAGTA
1 ATTGA-CTTTAATCACTCAAAGTA
34760586 CGGTGTGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 8 0.40
26 7 0.35
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (25 bp):
ATTGACTTTAATCACTCAAAGTATC
Found at i:34761372 original size:13 final size:14
Alignment explanation
Indices: 34761354--34761397 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
34761344 ATATTAATTT
34761354 ATTTA-TAAATTAA
1 ATTTATTAAATTAA
*
34761367 ATTTATTAAATAAA
1 ATTTATTAAATTAA
34761381 ATATTATTAGAATTAA
1 AT-TTATTA-AATTAA
34761397 A
1 A
34761398 ATATTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 5 0.19
14 9 0.35
15 6 0.23
16 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTTATTAAATTAA
Found at i:34761399 original size:17 final size:16
Alignment explanation
Indices: 34761359--34761404 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 16
34761349 AATTTATTTA
34761359 TAAATT-AAAT-TTAT
1 TAAATTAAAATATTAT
34761373 TAAA-TAAAATATTAT
1 TAAATTAAAATATTAT
34761388 TAGAATTAAAATATTAT
1 TA-AATTAAAATATTAT
34761405 ATAAGATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 8 0.29
15 6 0.21
16 2 0.07
17 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TAAATTAAAATATTAT
Found at i:34762982 original size:9 final size:8
Alignment explanation
Indices: 34762968--34763029 Score: 56
Period size: 9 Copynumber: 7.5 Consensus size: 8
34762958 TATTTTTTAA
34762968 ATAAAAAT
1 ATAAAAAT
34762976 CATAAAAAT
1 -ATAAAAAT
34762985 CATAAAAATT
1 -ATAAAAA-T
* *
34762995 CTACAAAT
1 ATAAAAAT
34763003 A-AAAAATT
1 ATAAAAA-T
34763011 ATAAAAAT
1 ATAAAAAT
34763019 A-AAAAAT
1 ATAAAAAT
34763026 ATAA
1 ATAA
34763030 CATATATTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
7 11 0.24
8 7 0.16
9 26 0.58
10 1 0.02
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:34763009 original size:16 final size:16
Alignment explanation
Indices: 34762966--34763029 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 16
34762956 TGTATTTTTT
*
34762966 AAAT-AAAAATCATAA
1 AAATAAAAAATTATAA
* *
34762981 AAATCATAAAAATTCTAC
1 AAAT-A-AAAAATTATAA
34762999 AAATAAAAAATTATAA
1 AAATAAAAAATTATAA
34763015 AAATAAAAAA-TATAA
1 AAATAAAAAATTATAA
34763030 CATATATTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 9 0.22
16 19 0.46
17 1 0.02
18 12 0.29
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAAAATTATAA
Found at i:34763162 original size:9 final size:9
Alignment explanation
Indices: 34762968--34763168 Score: 58
Period size: 10 Copynumber: 21.8 Consensus size: 9
34762958 TATTTTTTAA
*
34762968 ATAAAAATC
1 ATAAAAATT
*
34762977 ATAAAAATC
1 ATAAAAATT
34762986 ATAAAAATT
1 ATAAAAATT
* *
34762995 CTACAAA-T
1 ATAAAAATT
34763003 A-AAAAATT
1 ATAAAAATT
34763011 ATAAAAA-T
1 ATAAAAATT
34763019 A-AAAAA-T
1 ATAAAAATT
*
34763026 AT-AACATAT
1 ATAAAAAT-T
* *
34763035 ATTACAAATAC
1 A-TAAAAAT-T
*
34763046 AAAAAAATT
1 ATAAAAATT
* *
34763055 ATATAAAGTC
1 ATA-AAAATT
34763065 AT-AAAATAT
1 ATAAAAAT-T
* *
34763074 AAAAAAATC
1 ATAAAAATT
*
34763083 ATTAAAACTT
1 A-TAAAAATT
* *
34763093 ATGAACATT
1 ATAAAAATT
34763102 AT-AAAATGT
1 ATAAAAAT-T
*
34763111 AAAAAAATT
1 ATAAAAATT
*
34763120 CTAAAATAATT
1 AT-AAA-AATT
**
34763131 ATAACAAGCT
1 ATAA-AAATT
34763141 ATAAAAAATTT
1 AT-AAAAA-TT
34763152 ATAAAAATT
1 ATAAAAATT
34763161 ATTAAAAA
1 A-TAAAAA
34763169 AGTCATATAT
Statistics
Matches: 139, Mismatches: 34, Indels: 37
0.66 0.16 0.18
Matches are distributed among these distances:
7 14 0.10
8 13 0.09
9 46 0.33
10 50 0.36
11 16 0.12
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (9 bp):
ATAAAAATT
Found at i:34769009 original size:23 final size:23
Alignment explanation
Indices: 34768976--34769020 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
34768966 AGTGAAAAGA
*
34768976 ACAAAACGAAAATGAGT-AGAAAT
1 ACAAAAAGAAAA-GAGTAAGAAAT
34768999 ACAAAAAGAAAAGAGTAAGAAA
1 ACAAAAAGAAAAGAGTAAGAAA
34769021 AAGTGTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.67, C:0.07, G:0.18, T:0.09
Consensus pattern (23 bp):
ACAAAAAGAAAAGAGTAAGAAAT
Found at i:34776279 original size:19 final size:19
Alignment explanation
Indices: 34776253--34776305 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
34776243 GCGGAAGGAA
34776253 GAGCATATTGGCTCGTTTT
1 GAGCATATTGGCTCGTTTT
* *
34776272 GGGCATATTGGCTC-ATTT
1 GAGCATATTGGCTCGTTTT
*
34776290 GAGCATACTGGCTCGT
1 GAGCATATTGGCTCGT
34776306 AAGAGCATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (19 bp):
GAGCATATTGGCTCGTTTT
Found at i:34781513 original size:10 final size:10
Alignment explanation
Indices: 34781498--34781528 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
34781488 CTTCGGAAGG
34781498 AATTCGGGTA
1 AATTCGGGTA
34781508 AATTCGGGTA
1 AATTCGGGTA
*
34781518 AATTCGAGTA
1 AATTCGGGTA
34781528 A
1 A
34781529 GGTTTCTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (10 bp):
AATTCGGGTA
Found at i:34784529 original size:19 final size:19
Alignment explanation
Indices: 34784492--34784529 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
34784482 TACCTGTGTA
*
34784492 TTGTCTTTGTTTTGTAGAT
1 TTGTCTTTGTTTTGAAGAT
34784511 TTGT-TTTGTTGTTGAAGAT
1 TTGTCTTTGTT-TTGAAGAT
34784530 CGGATCCCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.13, C:0.03, G:0.24, T:0.61
Consensus pattern (19 bp):
TTGTCTTTGTTTTGAAGAT
Found at i:34790003 original size:13 final size:14
Alignment explanation
Indices: 34789985--34790014 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34789975 GTCAACACAA
34789985 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
34789998 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
34790012 TCA
1 TCA
34790015 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:34791557 original size:11 final size:12
Alignment explanation
Indices: 34791531--34791585 Score: 67
Period size: 12 Copynumber: 4.4 Consensus size: 12
34791521 ATAGTAAACA
34791531 TTTT-TTTTCTT
1 TTTTCTTTTCTT
34791542 CTTTTCTTTTCTT
1 -TTTTCTTTTCTT
34791555 TTTTCTTTTCTT
1 TTTTCTTTTCTT
*
34791567 TTTCTCATTTTCCT
1 TTT-TC-TTTTCTT
34791581 TTTTC
1 TTTTC
34791586 AAGTGACTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
12 19 0.49
13 11 0.28
14 9 0.23
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:34791560 original size:17 final size:17
Alignment explanation
Indices: 34791531--34791569 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
34791521 ATAGTAAACA
34791531 TTTTTTTTCTTCTTTTC
1 TTTTTTTTCTTCTTTTC
34791548 TTTTCTTTT-TTCTTTTC
1 TTTT-TTTTCTTCTTTTC
34791565 TTTTT
1 TTTTT
34791570 CTCATTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.76
18 4 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTTCTTCTTTTC
Found at i:34792354 original size:24 final size:24
Alignment explanation
Indices: 34792314--34792361 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
34792304 ACCCTCGTCT
34792314 TTGTGCTTCTTCTTCTTTTTATCC
1 TTGTGCTTCTTCTTCTTTTTATCC
*
34792338 TTGTGCCTTTTTC-TCTTTTTATCC
1 TTGTG-CTTCTTCTTCTTTTTATCC
34792362 GTCGTACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.04, C:0.25, G:0.08, T:0.62
Consensus pattern (24 bp):
TTGTGCTTCTTCTTCTTTTTATCC
Found at i:34794538 original size:15 final size:15
Alignment explanation
Indices: 34794515--34794544 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34794505 TTGAAACAAC
*
34794515 ACAAGTAAAAGTAAA
1 ACAAATAAAAGTAAA
34794530 ACAAATAAAAGTAAA
1 ACAAATAAAAGTAAA
34794545 TAGAAAAATG
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:0.70, C:0.07, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAAATAAAAGTAAA
Found at i:34802038 original size:36 final size:36
Alignment explanation
Indices: 34801998--34802084 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
34801988 TCTCCCAATT
34801998 GACCCAAAGGTCATGATGCTCATTTTACTCCCTGTC
1 GACCCAAAGGTCATGATGCTCATTTTACTCCCTGTC
* *
34802034 GACCCGAAGGTCATGATGCTCATTTTACTCCCTGTT
1 GACCCAAAGGTCATGATGCTCATTTTACTCCCTGTC
*
34802070 GACTCAAAGGTCATG
1 GACCCAAAGGTCATG
34802085 TCTGTTACTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (36 bp):
GACCCAAAGGTCATGATGCTCATTTTACTCCCTGTC
Found at i:34811416 original size:30 final size:30
Alignment explanation
Indices: 34811382--34811438 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
34811372 TTTGTTTCAG
*
34811382 GTTCT-ATATTATTATTATCTTCTAATACTT
1 GTTCTAAT-TTATTATTAACTTCTAATACTT
*
34811412 GTTCTAATTTTTTATTAACTTCTAATA
1 GTTCTAATTTATTATTAACTTCTAATA
34811439 GCATACCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (30 bp):
GTTCTAATTTATTATTAACTTCTAATACTT
Found at i:34817153 original size:35 final size:36
Alignment explanation
Indices: 34817064--34817162 Score: 164
Period size: 36 Copynumber: 2.8 Consensus size: 36
34817054 TCTTTATTCG
34817064 TTTACTCCTTGTTGACCCAAAGGTCATGATGCTCAT
1 TTTACTCCTTGTTGACCCAAAGGTCATGATGCTCAT
* * *
34817100 TTTACTCCCTATTAACCCAAAGGTCATGATGCTCA-
1 TTTACTCCTTGTTGACCCAAAGGTCATGATGCTCAT
34817135 TTTACTCCTTGTTGACCCAAAGGTCATG
1 TTTACTCCTTGTTGACCCAAAGGTCATG
34817163 CCTGTTACCA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 25 0.44
36 32 0.56
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.34
Consensus pattern (36 bp):
TTTACTCCTTGTTGACCCAAAGGTCATGATGCTCAT
Found at i:34818730 original size:25 final size:25
Alignment explanation
Indices: 34818696--34818743 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
34818686 CTCTGTGTTA
34818696 GTGTGCAGGTGATTAGGTGCATTTG
1 GTGTGCAGGTGATTAGGTGCATTTG
*
34818721 GTGTGCAGGTGATTGGGTGCATT
1 GTGTGCAGGTGATTAGGTGCATT
34818744 ACATTATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.15, C:0.08, G:0.42, T:0.35
Consensus pattern (25 bp):
GTGTGCAGGTGATTAGGTGCATTTG
Found at i:34827373 original size:7 final size:8
Alignment explanation
Indices: 34827357--34827384 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
34827347 CAAGTGTGGA
34827357 TTTTATTT
1 TTTTATTT
34827365 TTTTATTT
1 TTTTATTT
34827373 TTTTATTT
1 TTTTATTT
34827381 TTTT
1 TTTT
34827385 TGCCTGCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTATTT
Found at i:34829497 original size:24 final size:23
Alignment explanation
Indices: 34829457--34829503 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
34829447 TATTACAAGC
*
34829457 AAAAAAAAATTAGTATTAAAAAT
1 AAAAAAAAATCAGTATTAAAAAT
* *
34829480 AAAAATAAAATCATTATTATAAAT
1 AAAAA-AAAATCAGTATTAAAAAT
34829504 TCGGGTCAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAAAAATCAGTATTAAAAAT
Found at i:34831267 original size:18 final size:18
Alignment explanation
Indices: 34831233--34831268 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
34831223 TTATTCTCAA
34831233 TATTACAAAATATAAAAT
1 TATTACAAAATATAAAAT
34831251 TATTA-AAAATATCAAAAT
1 TATTACAAAATAT-AAAAT
34831269 GAATCTAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
TATTACAAAATATAAAAT
Found at i:34832442 original size:30 final size:30
Alignment explanation
Indices: 34832408--34832472 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
34832398 TAACTTAACA
* * * *
34832408 AACAAGTATCTCTAGAATAGTAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
*
34832438 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
34832468 AACAA
1 AACAA
34832473 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.23
Consensus pattern (30 bp):
AACAAATACCTCTAAAATAATAACAAAATT
Found at i:34840049 original size:25 final size:27
Alignment explanation
Indices: 34839996--34840076 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 27
34839986 TGAAAACCTT
34839996 TTAGATTTTTAATATAATTTTTAGAATA
1 TTAGATTTTT-ATATAATTTTTAGAATA
34840024 TTAGATTTTT-TAT-ATTTTTA-ACATA
1 TTAGATTTTTATATAATTTTTAGA-ATA
* * *
34840049 TT--TTTTTTATA-AATTTTTAAAAAA
1 TTAGATTTTTATATAATTTTTAGAATA
34840073 TTAG
1 TTAG
34840077 CTGTTTTTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
23 5 0.11
24 14 0.31
25 13 0.29
26 3 0.07
28 10 0.22
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (27 bp):
TTAGATTTTTATATAATTTTTAGAATA
Found at i:34840065 original size:49 final size:50
Alignment explanation
Indices: 34840001--34840102 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 50
34839991 ACCTTTTAGA
* * * *
34840001 TTTTTAATATAATTTTTAGAATATTAGAT-TTTTTATATTTTTAACATATT
1 TTTTTAATATAATTTTTAAAAAATTAGATGTTTTTAGAATTTTAA-ATATT
* *
34840051 TTTTTTATA-AATTTTTAAAAAATTAGCTGTTTTTAGAATTTTAAATATT
1 TTTTTAATATAATTTTTAAAAAATTAGATGTTTTTAGAATTTTAAATATT
34840100 TTT
1 TTT
34840103 AGATTTTTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 24 0.53
50 21 0.47
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (50 bp):
TTTTTAATATAATTTTTAAAAAATTAGATGTTTTTAGAATTTTAAATATT
Found at i:34840150 original size:10 final size:10
Alignment explanation
Indices: 34840135--34840205 Score: 58
Period size: 10 Copynumber: 7.3 Consensus size: 10
34840125 ATTTTTGAAG
*
34840135 AATTCTTTGT
1 AATTCTTTAT
34840145 AATTCTTTAT
1 AATTCTTTAT
*
34840155 AATTCTTAAT
1 AATTCTTTAT
*
34840165 -ATT-TTTAA
1 AATTCTTTAT
* **
34840173 AAATAATTAT
1 AATTCTTTAT
34840183 AATTACTTTAT
1 AATT-CTTTAT
34840194 AATT-TTTAT
1 AATTCTTTAT
34840203 AAT
1 AAT
34840206 ATTATGTATT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
8 3 0.06
9 13 0.27
10 24 0.50
11 8 0.17
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (10 bp):
AATTCTTTAT
Found at i:34842513 original size:29 final size:29
Alignment explanation
Indices: 34842481--34842931 Score: 289
Period size: 29 Copynumber: 15.3 Consensus size: 29
34842471 AAATGCGATA
* *
34842481 TTTGGATGCTCGGGGGTAAAAATGTAATT
1 TTTGGAAGTTCGGGGGTAAAAATGTAATT
* * *
34842510 TTTGGACA--TCTAGGGGT-AACATGGTAACT
1 TTTGGA-AGTTC-GGGGGTAAAAAT-GTAATT
* ** * *
34842539 TTTGAAAACTCGAGGGAAAAAATGTAATT
1 TTTGGAAGTTCGGGGGTAAAAATGTAATT
* *
34842568 TTTGGACA-TCCGAGGGT-AAAATGCTAATT
1 TTTGGA-AGTTCGGGGGTAAAAATG-TAATT
* * * *
34842597 TTTGGATGTTCGGGGGCAAAAAAGTGATT
1 TTTGGAAGTTCGGGGGTAAAAATGTAATT
* **
34842626 TTTGCAAAGTT-TAGGGTAAAAAATG-ATATT
1 TTTG-GAAGTTCGGGGGT-AAAAATGTA-ATT
* ** *
34842656 TTTAGAAGTTCAAGGGTAAAAATGTGATT
1 TTTGGAAGTTCGGGGGTAAAAATGTAATT
34842685 TTTGGAAAGTTC-GGGGTCAAAAATG--ATAT
1 TTTGG-AAGTTCGGGGGT-AAAAATGTAAT-T
**
34842714 TTTGGAAGTTTAGGGGTAAAAA-GATAATT
1 TTTGGAAGTTCGGGGGTAAAAATG-TAATT
* * *
34842743 TTTGGAAGTTCGGGAGCAAAAATGTGATT
1 TTTGGAAGTTCGGGGGTAAAAATGTAATT
* *
34842772 TTTGGAAATTCGAGGGT-AAAATGGTAATT
1 TTTGGAAGTTCGGGGGTAAAAAT-GTAATT
** * *
34842801 TTTTAAAGTTTGAGGGGTAAAAATGTGATT
1 TTTGGAAGTTCG-GGGGTAAAAATGTAATT
*
34842831 TTTGGAAGTTTGAGGGGT-AAAATGGTAATT
1 TTTGGAAGTTCG-GGGGTAAAAAT-GTAATT
34842861 TTTGTGAAGTTCGGGGGTAAAAATGTAATT
1 TTTG-GAAGTTCGGGGGTAAAAATGTAATT
* * * *
34842891 TTTGTGAAGTTTGGGGGTCAAAATATGATT
1 TTTG-GAAGTTCGGGGGTAAAAATGTAATT
34842921 TTTGGAGAGTT
1 TTTGGA-AGTT
34842932 TAAGGACCTT
Statistics
Matches: 334, Mismatches: 58, Indels: 59
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.00
28 30 0.09
29 158 0.47
30 128 0.38
31 17 0.05
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (29 bp):
TTTGGAAGTTCGGGGGTAAAAATGTAATT
Found at i:34842686 original size:59 final size:58
Alignment explanation
Indices: 34842614--34842735 Score: 163
Period size: 59 Copynumber: 2.1 Consensus size: 58
34842604 GTTCGGGGGC
*
34842614 AAAAAAGTGATTTTTGCAAAGTTTAGGGTAAAAAATGATATTTTTAGAAGTTCAAGGGT
1 AAAAAAGTGATTTTTGCAAAGTTCAGGGTAAAAAATGATA-TTTTAGAAGTTCAAGGGT
* * * * * * *
34842673 AAAAATGTGATTTTTGGAAAGTTCGGGGTCAAAAATGATATTTTGGAAGTTTAGGGGT
1 AAAAAAGTGATTTTTGCAAAGTTCAGGGTAAAAAATGATATTTTAGAAGTTCAAGGGT
34842731 AAAAA
1 AAAAA
34842736 GATAATTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 20 0.36
59 35 0.64
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (58 bp):
AAAAAAGTGATTTTTGCAAAGTTCAGGGTAAAAAATGATATTTTAGAAGTTCAAGGGT
Found at i:34849336 original size:91 final size:88
Alignment explanation
Indices: 34849146--34849382 Score: 226
Period size: 91 Copynumber: 2.6 Consensus size: 88
34849136 CCCTCAATTT
* * * * * * * *
34849146 TTTTCAAAAAAAGCAATTAAGCCCTTGCTTTTATTTTGCATTCACTTGGATATTTGAACTTTCAA
1 TTTTCAAAAAAAGTAATTAAGCCCTTACTTTTATTTTTCACTCAATTGGGTACTTAAACTTTCAA
* * *
34849211 AATATGTCAAAAAAGCCCTTAAA
66 AATATATCAAAAAAACCCTCAAA
** * *
34849234 TTTAAAAAAAAAAAAGTAATTAAGCCCCTACTTTTATTTTTCACTCAATTGGGTGCTTAAACTTT
1 TTT---TCAAAAAAAGTAATTAAGCCCTTACTTTTATTTTTCACTCAATTGGGTACTTAAACTTT
*
34849299 CAAAATGTATCAAAAAAACCCTCAAA
63 CAAAATATATCAAAAAAACCCTCAAA
* *
34849325 GCTTTTCAAAAAAA-TCAATTAAGCCTTTGA-TTTTTTTTTTGCACTCAATTGGGTACTT
1 --TTTTCAAAAAAAGT-AATTAAGCCCTT-ACTTTTATTTTT-CACTCAATTGGGTACTT
34849383 GAACCGCCCC
Statistics
Matches: 119, Mismatches: 22, Indels: 13
0.77 0.14 0.08
Matches are distributed among these distances:
88 3 0.03
89 1 0.01
90 26 0.22
91 86 0.72
93 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (88 bp):
TTTTCAAAAAAAGTAATTAAGCCCTTACTTTTATTTTTCACTCAATTGGGTACTTAAACTTTCAA
AATATATCAAAAAAACCCTCAAA
Found at i:34850738 original size:2 final size:2
Alignment explanation
Indices: 34850733--34850763 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34850723 TTTGAAAAAT
34850733 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34850764 TAAATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34855479 original size:20 final size:20
Alignment explanation
Indices: 34855442--34855491 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
34855432 TAGTTTCTAA
*
34855442 ATAAATTATATATTATTTTG
1 ATAAATTATATATAATTTTG
34855462 ATAAA-TATATTATAA-TTT-
1 ATAAATTATA-TATAATTTTG
*
34855480 ATATATTATATA
1 ATAAATTATATA
34855492 CATGCAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.23
19 11 0.42
20 9 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAAATTATATATAATTTTG
Found at i:34856407 original size:10 final size:10
Alignment explanation
Indices: 34856394--34856465 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 10
34856384 AATTATTAAC
34856394 ATTTATAAAA
1 ATTTATAAAA
34856404 ATTTATAAAATA
1 ATTTAT-AAA-A
*
34856416 ATTTTTTTAAAA
1 A--TTTATAAAA
*
34856428 A-TTATCAAA
1 ATTTATAAAA
*
34856437 ATAT-TAAAA
1 ATTTATAAAA
*
34856446 AGTTATAAAA
1 ATTTATAAAA
34856456 A-TTATAAAA
1 ATTTATAAAA
34856465 A
1 A
34856466 CAATAAAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
9 22 0.45
10 13 0.27
11 3 0.06
12 4 0.08
13 3 0.06
14 4 0.08
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (10 bp):
ATTTATAAAA
Found at i:34856464 original size:8 final size:9
Alignment explanation
Indices: 34856423--34856480 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
34856413 ATAATTTTTT
34856423 TAAAAATTA
1 TAAAAATTA
34856432 TCAAAATATTA
1 T-AAAA-ATTA
*
34856443 -AAAAGTTA
1 TAAAAATTA
34856451 TAAAAATTA
1 TAAAAATTA
**
34856460 TAAAAACAA
1 TAAAAATTA
34856469 TAAAAAGTTA
1 TAAAAA-TTA
34856479 TA
1 TA
34856481 TAATTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
8 3 0.08
9 25 0.64
10 7 0.18
11 4 0.10
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:34856465 original size:19 final size:18
Alignment explanation
Indices: 34856422--34856457 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34856412 AATAATTTTT
*
34856422 TTAAAAATTATCAAAATA
1 TTAAAAATTATAAAAATA
34856440 TTAAAAAGTTATAAAAAT
1 TTAAAAA-TTATAAAAAT
34856458 TATAAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
TTAAAAATTATAAAAATA
Found at i:34856465 original size:28 final size:28
Alignment explanation
Indices: 34856423--34856480 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
34856413 ATAATTTTTT
* * *
34856423 TAAAAATTATCAAAATATTAAAAAGTTA
1 TAAAAATTATAAAAACAATAAAAAGTTA
34856451 TAAAAATTATAAAAACAATAAAAAGTTA
1 TAAAAATTATAAAAACAATAAAAAGTTA
34856479 TA
1 TA
34856481 TAATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (28 bp):
TAAAAATTATAAAAACAATAAAAAGTTA
Found at i:34859515 original size:25 final size:24
Alignment explanation
Indices: 34859451--34859517 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 24
34859441 TCTTTAGATT
34859451 TTTTAATTTTTATATTTTTAAAAATA
1 TTTT-ATTTTTA-ATTTTTAAAAATA
* * *
34859477 TTTT-TTTTGAATTTTTATAATTA
1 TTTTATTTTTAATTTTTAAAAATA
34859500 TTTTGATTTTTAATTTTT
1 TTTT-ATTTTTAATTTTT
34859518 GAAATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 15 0.43
24 5 0.14
25 11 0.31
26 4 0.11
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (24 bp):
TTTTATTTTTAATTTTTAAAAATA
Found at i:34861502 original size:24 final size:22
Alignment explanation
Indices: 34861474--34861517 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
34861464 CATAATTTCA
*
34861474 TATACTATTATCAATTCACAATTT
1 TATACCATT-TCAATTC-CAATTT
34861498 TATACCATTTCAATTCCAAT
1 TATACCATTTCAATTCCAAT
34861518 CATACATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.43
Consensus pattern (22 bp):
TATACCATTTCAATTCCAATTT
Found at i:34866585 original size:14 final size:13
Alignment explanation
Indices: 34866549--34866594 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
34866539 TCGGGACAAC
*
34866549 TTCTTTTTCTT-T
1 TTCTTTTCCTTCT
34866561 TTCTGTTTCCTTCT
1 TTCT-TTTCCTTCT
34866575 ATTCTTTTCCTTC-
1 -TTCTTTTCCTTCT
34866588 TTCTTTT
1 TTCTTTT
34866595 ATTTTCTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 11 0.37
13 6 0.20
14 9 0.30
15 4 0.13
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.72
Consensus pattern (13 bp):
TTCTTTTCCTTCT
Found at i:34872601 original size:18 final size:18
Alignment explanation
Indices: 34872543--34872610 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
34872533 CATAGTCTGT
*
34872543 TGTGACTGCAT-TCGAGCA
1 TGTGACTGCATCT-GAGTA
** *
34872561 TGTGGTTGCA-CTGATTA
1 TGTGACTGCATCTGAGTA
*
34872578 TATGACTGCATCTGAGTA
1 TGTGACTGCATCTGAGTA
34872596 TGTGACTGCATCTGA
1 TGTGACTGCATCTGA
34872611 TCAGGCTGCG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
17 10 0.26
18 29 0.74
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (18 bp):
TGTGACTGCATCTGAGTA
Found at i:34881155 original size:27 final size:27
Alignment explanation
Indices: 34881117--34881181 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
34881107 GAAAAAATTA
34881117 CCACGTCAGCATCGTTAGTCCCTTCGG
1 CCACGTCAGCATCGTTAGTCCCTTCGG
34881144 CCACGTCAGCATCGTTAGTCCCTTCGG
1 CCACGTCAGCATCGTTAGTCCCTTCGG
34881171 CCACGTCAGCA
1 CCACGTCAGCA
34881182 AGACCGTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.17, C:0.38, G:0.22, T:0.23
Consensus pattern (27 bp):
CCACGTCAGCATCGTTAGTCCCTTCGG
Found at i:34885983 original size:12 final size:12
Alignment explanation
Indices: 34885949--34886044 Score: 79
Period size: 12 Copynumber: 8.2 Consensus size: 12
34885939 ATTGCTGTTC
*
34885949 TTTGCTG-TTTT
1 TTTGCTGCTATT
* *
34885960 TTTACTGTTATT
1 TTTGCTGCTATT
*
34885972 TTTGTTGCTATT
1 TTTGCTGCTATT
*
34885984 TTTGCTGTTATT
1 TTTGCTGCTATT
* *
34885996 TTTGTTGCTGTT
1 TTTGCTGCTATT
* **
34886008 TTTGTTATTA-T
1 TTTGCTGCTATT
34886019 TTTGCTGCTATT
1 TTTGCTGCTATT
*
34886031 TTTGCTGCTGTT
1 TTTGCTGCTATT
34886043 TT
1 TT
34886045 GGTTATTATT
Statistics
Matches: 66, Mismatches: 17, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
11 14 0.21
12 52 0.79
ACGTcount: A:0.07, C:0.09, G:0.17, T:0.67
Consensus pattern (12 bp):
TTTGCTGCTATT
Found at i:34885991 original size:24 final size:24
Alignment explanation
Indices: 34885958--34886037 Score: 108
Period size: 24 Copynumber: 3.4 Consensus size: 24
34885948 CTTTGCTGTT
*
34885958 TTTTTACTGTTATTTTTGTTGCTA
1 TTTTTGCTGTTATTTTTGTTGCTA
*
34885982 TTTTTGCTGTTATTTTTGTTGCTG
1 TTTTTGCTGTTATTTTTGTTGCTA
* * *
34886006 TTTTTGTTATTA-TTTTGCTGCTA
1 TTTTTGCTGTTATTTTTGTTGCTA
34886029 TTTTTGCTG
1 TTTTTGCTG
34886038 CTGTTTTGGT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 16 0.33
24 32 0.67
ACGTcount: A:0.09, C:0.09, G:0.16, T:0.66
Consensus pattern (24 bp):
TTTTTGCTGTTATTTTTGTTGCTA
Found at i:34885998 original size:36 final size:36
Alignment explanation
Indices: 34885934--34886044 Score: 100
Period size: 35 Copynumber: 3.1 Consensus size: 36
34885924 TTTTTTACTG
* *
34885934 TTTTGATTGCTGTTCTTTGCTGTT-TTTTTACTGTTAT
1 TTTTG-TTGCTATT-TTTGCTGTTATTTTTACTGCTAT
** *
34885971 TTTTGTTGCTATTTTTGCTGTTATTTTTGTTGCTGT
1 TTTTGTTGCTATTTTTGCTGTTATTTTTACTGCTAT
** * * *
34886007 TTTTGTTATTA-TTTTGCTGCTATTTTTGCTGCTGT
1 TTTTGTTGCTATTTTTGCTGTTATTTTTACTGCTAT
34886042 TTT
1 TTT
34886045 GGTTATTATT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
35 34 0.53
36 25 0.39
37 5 0.08
ACGTcount: A:0.07, C:0.10, G:0.17, T:0.66
Consensus pattern (36 bp):
TTTTGTTGCTATTTTTGCTGTTATTTTTACTGCTAT
Found at i:34886022 original size:35 final size:35
Alignment explanation
Indices: 34885983--34886057 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
34885973 TTGTTGCTAT
* * *
34885983 TTTTGCTGTTATTTTTGTTGCTGTTTTTGTTATTA
1 TTTTGCTGCTATTTTTGCTGCTGTTTTGGTTATTA
34886018 TTTTGCTGCTATTTTTGCTGCTGTTTTGGTTATTA
1 TTTTGCTGCTATTTTTGCTGCTGTTTTGGTTATTA
34886053 TTTTG
1 TTTTG
34886058 GTTGTTTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.08, C:0.08, G:0.19, T:0.65
Consensus pattern (35 bp):
TTTTGCTGCTATTTTTGCTGCTGTTTTGGTTATTA
Found at i:34887883 original size:90 final size:90
Alignment explanation
Indices: 34887730--34887910 Score: 326
Period size: 90 Copynumber: 2.0 Consensus size: 90
34887720 CACATTTTTT
* * *
34887730 AGTGAATTTAGCTAAACAATTAAATGACAAGAAAAATTTAAATATATGTTTGTTTCATTTAAAAT
1 AGTGAATTTAGCTAAACAATTAAAAGACAAGAAAAATTCAAATATATGTTTGTTTCATGTAAAAT
34887795 AGCTTTTTTGAAATATTTTCAGGAA
66 AGCTTTTTTGAAATATTTTCAGGAA
*
34887820 AGTGAATTTAGCTAAACAATTAAAAGACAAGAAAAATTCAAATGTATGTTTGTTTCATGTAAAAT
1 AGTGAATTTAGCTAAACAATTAAAAGACAAGAAAAATTCAAATATATGTTTGTTTCATGTAAAAT
34887885 AGCTTTTTTGAAATATTTTCAGGAA
66 AGCTTTTTTGAAATATTTTCAGGAA
34887910 A
1 A
34887911 TCTGTCAAAC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (90 bp):
AGTGAATTTAGCTAAACAATTAAAAGACAAGAAAAATTCAAATATATGTTTGTTTCATGTAAAAT
AGCTTTTTTGAAATATTTTCAGGAA
Found at i:34898337 original size:18 final size:18
Alignment explanation
Indices: 34898293--34898340 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
34898283 ACTCAAGTTC
* *
34898293 CTTTGTTTTCTTTTCTTG
1 CTTTGTTTGCTTTTCTTA
*
34898311 CTTTATTTGCTTTTCTTA
1 CTTTGTTTGCTTTTCTTA
*
34898329 TTTTGTTTGCTT
1 CTTTGTTTGCTT
34898341 GAGGACAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.04, C:0.15, G:0.10, T:0.71
Consensus pattern (18 bp):
CTTTGTTTGCTTTTCTTA
Found at i:34905354 original size:16 final size:16
Alignment explanation
Indices: 34905333--34905364 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
34905323 AAACTATCAA
34905333 TGCACCTTCTAATGAC
1 TGCACCTTCTAATGAC
34905349 TGCACCTTCTAATGAC
1 TGCACCTTCTAATGAC
34905365 AGTGACTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.31
Consensus pattern (16 bp):
TGCACCTTCTAATGAC
Found at i:34905836 original size:512 final size:513
Alignment explanation
Indices: 34904858--34905852 Score: 1221
Period size: 512 Copynumber: 1.9 Consensus size: 513
34904848 CACAAGATTA
* *
34904858 TGATCGCGCTATGAACGTCACAACAAATATGTGCAAGCGTATACTGACGATGCAAGTATAGTAGA
1 TGATCACGCTATGAACGTCACAACAAATATGTGCAAGCGTACACTGACGATGCAAGTATAGTAGA
* * * * * * *
34904923 CAGATGTGAATCTGTCGGATATTGATCCCACGAGGATGGATGTTTGTTGTCTATTAATGTTGTCG
66 CAAAAGTGAATCTATCGGATATCGATCCCAC-AGGATGGACGTCTGTTGTCTATAAATGTTGTCG
*
34904988 CAATGAATAAGTAAATGCAATAAAATTGTGAGATTGATTGTCGAAGCAATAATGTGAAAATAAAG
130 CAATGAATAAGTAAATGCAATAAAATTGTGAGAATGATTGTCGAAGCAATAATGTGAAAATAAAG
* * * * *
34905053 ATGAAATGCAATAATAATGAAATGGAGTCCTCATCGTGAATACTGAACAGAATACTAACTGTGCG
195 ATGAAATGCAATAATAATAAAATGGAGTCCACAACGTGAATAATGAACAGAAAACTAACTGTGCG
* * * * * **
34905118 ACTCGCAAGGTTTAAAATAATAGGTGATTATCGTCGCAAATAAGTACAATGAATGTCTTACCAAA
260 ACTCACAAGGTTAAAAATAACACGTAATTATCGTCGCAAATAAGTACAATGAACATCTTACCAAA
* * * *
34905183 CTTGGCTTCTCTATTCGATCTAAGATTTAAATATGCATTTTAACCTCACCTTCTAGTGATGGCAA
325 CTTGGCTTCTCTATTAGATCTAAGATTTAAATATGCA-TCTAACCTCACCTTCCAGTGATAGCAA
* ** * * *
34905248 TGTAACACATTCAAAAACAAGTGGATTAAATTCCTTTAATCCCCAAGCAACTTTCGTTGTCTTGC
389 TGCAACACATTCAAAAACAAGTGGACCAAATTCCTTCAATCACCAAGCAACTTCCGTTGTCTTGC
34905313 TTGTTAGTTTAAACTATCAATGCACCTTCTAATGACTGCACCTTCTAATGACAGTGACTT
454 TTGTTAGTTTAAACTATCAATGCACCTTCTAATGACTGCACCTTCTAATGACAGTGACTT
* * *
34905373 TGATCACGCTGTGAACGTCACAGCAAATATGTGCAAGCGTACACT-ATCGATGCAAGTATAGTGG
1 TGATCACGCTATGAACGTCACAACAAATATGTGCAAGCGTACACTGA-CGATGCAAGTATAGTAG
* *
34905437 ACAAAAGTGAATCTATCGGATATCGATCCCAC-GGATGGGCGTCTGTTTTCTA-AAAT-TATCGG
65 ACAAAAGTGAATCTATCGGATATCGATCCCACAGGATGGACGTCTGTTGTCTATAAATGT-T--G
* * * *
34905499 T-GCATTGAATAAGTAAAATGCAAT-AAATTGTGAGAATGGTTGTTGGAGCAATAATGTGAAAAT
127 TCGCAATGAATAAGT-AAATGCAATAAAATTGTGAGAATGATTGTCGAAGCAATAATGTGAAAAT
* * * * * *
34905562 AAAGATTAAATGTAATAA-AGGTAAAAT-GAGATCCACAACGTGAATAATTAGCAGAAAACTAAG
191 AAAGATGAAATGCAATAATA-ATAAAATGGAG-TCCACAACGTGAATAATGAACAGAAAACTAAC
* *
34905625 TGTG-G-CTTACAAGGTTAAAAATAACACGTAATT-T-GTCGGCACAATGAAGTGCAATGAACAT
254 TGTGCGACTCACAAGGTTAAAAATAACACGTAATTATCGTC-GCA-AAT-AAGTACAATGAACAT
* * *
34905686 CTTACCAAACTTGGCTTTTCTATTAGATCTATGAATTTAGTATACT-CA-CTAA-CTACACCTTC
316 CTTACCAAACTTGGCTTCTCTATTAGATCTAAG-ATTTA-AATA-TGCATCTAACCT-CACCTTC
* *
34905748 CAGTGCTAGCAATGCAACACACTT-AAGAACAAGTGGACCAAATTCCTTCAATCACCAAGCAACT
377 CAGTGATAGCAATGCAACACA-TTCAAAAACAAGTGGACCAAATTCCTTCAATCACCAAGCAACT
* *
34905812 TCCGTTGTCTTGCTTGTTAGTTTAAACTGTCACTGCACCTT
441 TCCGTTGTCTTGCTTGTTAGTTTAAACTATCAATGCACCTT
34905853 TCAGTGACTG
Statistics
Matches: 409, Mismatches: 56, Indels: 33
0.82 0.11 0.07
Matches are distributed among these distances:
509 3 0.01
510 4 0.01
511 28 0.07
512 151 0.37
513 120 0.29
514 17 0.04
515 86 0.21
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (513 bp):
TGATCACGCTATGAACGTCACAACAAATATGTGCAAGCGTACACTGACGATGCAAGTATAGTAGA
CAAAAGTGAATCTATCGGATATCGATCCCACAGGATGGACGTCTGTTGTCTATAAATGTTGTCGC
AATGAATAAGTAAATGCAATAAAATTGTGAGAATGATTGTCGAAGCAATAATGTGAAAATAAAGA
TGAAATGCAATAATAATAAAATGGAGTCCACAACGTGAATAATGAACAGAAAACTAACTGTGCGA
CTCACAAGGTTAAAAATAACACGTAATTATCGTCGCAAATAAGTACAATGAACATCTTACCAAAC
TTGGCTTCTCTATTAGATCTAAGATTTAAATATGCATCTAACCTCACCTTCCAGTGATAGCAATG
CAACACATTCAAAAACAAGTGGACCAAATTCCTTCAATCACCAAGCAACTTCCGTTGTCTTGCTT
GTTAGTTTAAACTATCAATGCACCTTCTAATGACTGCACCTTCTAATGACAGTGACTT
Found at i:34909946 original size:16 final size:16
Alignment explanation
Indices: 34909925--34909955 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34909915 AATAATGTGA
34909925 AAATAAAGATAAAATG
1 AAATAAAGATAAAATG
*
34909941 AAATAAAGGTAAAAT
1 AAATAAAGATAAAAT
34909956 AAGATCCATA
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:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (16 bp):
AAATAAAGATAAAATG
Found at i:34910838 original size:37 final size:38
Alignment explanation
Indices: 34910797--34910875 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
34910787 GTATATGTTC
*
34910797 ATGCAACGACA-TTCCTGGGTGCAA-TTGAAGAATACTT
1 ATGCAACGACAGTT-CTGGATGCAATTTGAAGAATACTT
* * *
34910834 ATGCAGCGATAGTTCTGGATGCAATTTGAAGAATATTT
1 ATGCAACGACAGTTCTGGATGCAATTTGAAGAATACTT
34910872 ATGC
1 ATGC
34910876 TCAATAGTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 18 0.50
38 18 0.50
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (38 bp):
ATGCAACGACAGTTCTGGATGCAATTTGAAGAATACTT
Found at i:34910883 original size:37 final size:37
Alignment explanation
Indices: 34910811--34910883 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 37
34910801 AACGACATTC
* *
34910811 CTGGGTGCAATTGAAGAATACTTATGCAGCGATAGTT
1 CTGGATGCAATTGAAGAATACTTATGCAGCAATAGTT
* *
34910848 CTGGATGCAATTTGAAGAATATTTATGC-TCAATAGT
1 CTGGATGCAA-TTGAAGAATACTTATGCAGCAATAGT
34910884 CTTGGGTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 15 0.48
38 16 0.52
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (37 bp):
CTGGATGCAATTGAAGAATACTTATGCAGCAATAGTT
Found at i:34914743 original size:34 final size:34
Alignment explanation
Indices: 34914691--34914774 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 34
34914681 TGGTTAACCG
**
34914691 TCCAACACACCAGTTGCTCGTATGAGCCAATCCA
1 TCCAACACACCAAATGCTCGTATGAGCCAATCCA
* * * *
34914725 TCCAGCACACCAAATGCTCGTATGAGCTAGTTCA
1 TCCAACACACCAAATGCTCGTATGAGCCAATCCA
*
34914759 ACCAACACACCAAATG
1 TCCAACACACCAAATG
34914775 TTGTAACATA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.19
Consensus pattern (34 bp):
TCCAACACACCAAATGCTCGTATGAGCCAATCCA
Found at i:34914938 original size:115 final size:115
Alignment explanation
Indices: 34914735--34915120 Score: 569
Period size: 115 Copynumber: 3.4 Consensus size: 115
34914725 TCCAGCACAC
* * * ** *
34914735 CAAATGCTCGTATGAGCTAGTTCAACCAACACACC-AAATGTTGTAACATATCTCGTTAGTCTGC
1 CAAATGCTCGTAAGAGCTAGTCCATCCAACACACCAAAATACTGTAACATATCTCGTTAGTCCGC
* * * *
34914799 AACAGATGCAGGACCTCAATATATCTAGTGAACATAGAATATATTGTAAT
66 AATAGATGCAGGACCTCAATATATCCAGTGAACATAGAATCTAATGTAAT
* * *
34914849 CGAATGCTCGTAAGCGCTAGTCCATCCAACACACCAAAATACTGTAACATATCTCGTTAGTCCAC
1 CAAATGCTCGTAAGAGCTAGTCCATCCAACACACCAAAATACTGTAACATATCTCGTTAGTCCGC
* * * *
34914914 AATAGATGCAGGACCACAATATATCCAGAGAGCATAGAATCTACTGTAAT
66 AATAGATGCAGGACCTCAATATATCCAGTGAACATAGAATCTAATGTAAT
* *
34914964 CAAATGCTCGTAAGAGCTAGTCTATCCAACACACCAAAATACTGTAACATATCTCATTAGTCCGC
1 CAAATGCTCGTAAGAGCTAGTCCATCCAACACACCAAAATACTGTAACATATCTCGTTAGTCCGC
*
34915029 AATAGATGCAGGACCTCAAT-TATCCAATGAACATAGAATCTAATGTAAT
66 AATAGATGCAGGACCTCAATATATCCAGTGAACATAGAATCTAATGTAAT
*
34915078 CAAATGCTCGTAAGAGCTAGTCTATCCAACACACCAAAATACT
1 CAAATGCTCGTAAGAGCTAGTCCATCCAACACACCAAAATACT
34915121 ATAATCATCT
Statistics
Matches: 245, Mismatches: 26, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
114 98 0.40
115 147 0.60
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (115 bp):
CAAATGCTCGTAAGAGCTAGTCCATCCAACACACCAAAATACTGTAACATATCTCGTTAGTCCGC
AATAGATGCAGGACCTCAATATATCCAGTGAACATAGAATCTAATGTAAT
Found at i:34925241 original size:23 final size:23
Alignment explanation
Indices: 34925215--34925269 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
34925205 TCTGCGTGAG
34925215 TGTACAACTAGAAATAACCAATT
1 TGTACAACTAGAAATAACCAATT
* *
34925238 TGTACAGCTGGAAATAACCAATT
1 TGTACAACTAGAAATAACCAATT
34925261 TGTACAACT
1 TGTACAACT
34925270 GCAAAAGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (23 bp):
TGTACAACTAGAAATAACCAATT
Found at i:34930487 original size:8 final size:8
Alignment explanation
Indices: 34930476--34930521 Score: 56
Period size: 8 Copynumber: 5.2 Consensus size: 8
34930466 AAAAGCAACA
34930476 TTTAAAAT
1 TTTAAAAT
34930484 TTTAAAAT
1 TTTAAAAT
34930492 TTTAAAAAT
1 TTT-AAAAT
34930501 TTATATAAATT
1 TT-TA-AAA-T
34930512 TTTAAAAT
1 TTTAAAAT
34930520 TT
1 TT
34930522 CAAGCAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 14 0.41
9 11 0.32
10 6 0.18
11 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAAAT
Found at i:34930501 original size:9 final size:9
Alignment explanation
Indices: 34930479--34930521 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
34930469 AGCAACATTT
34930479 AAAATTTT-
1 AAAATTTTA
34930487 AAAATTTTA
1 AAAATTTTA
34930496 AAAATTTATA
1 AAAATTT-TA
* *
34930506 TAAATTTTT
1 AAAATTTTA
34930515 AAAATTT
1 AAAATTT
34930522 CAAGCAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 8 0.27
9 14 0.47
10 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AAAATTTTA
Found at i:34930604 original size:2 final size:2
Alignment explanation
Indices: 34930597--34930631 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34930587 AACAAAAACT
34930597 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34930632 GTTTCAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34930818 original size:16 final size:18
Alignment explanation
Indices: 34930799--34930833 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34930789 AATAAGAATT
34930799 ATTTA-AAAA-TAAAAAA
1 ATTTATAAAAGTAAAAAA
34930815 ATTTATAAAAGTAAAAAA
1 ATTTATAAAAGTAAAAAA
34930833 A
1 A
34930834 AAAAATCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 4 0.24
18 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
ATTTATAAAAGTAAAAAA
Found at i:34949752 original size:3 final size:3
Alignment explanation
Indices: 34949744--34949772 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34949734 TAATTTGTTT
34949744 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
34949773 GGATGATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:34950442 original size:26 final size:26
Alignment explanation
Indices: 34950385--34950440 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
34950375 TTCTCTCTCC
*
34950385 TTTTTAAAAAAGATATTATTTTATTA
1 TTTTTAAAAAAGATATTATTCTATTA
* *
34950411 TATTTAAAAAAGATATT-TTCTATTT
1 TTTTTAAAAAAGATATTATTCTATTA
34950436 TTTTT
1 TTTTT
34950441 TACTTTCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTTTAAAAAAGATATTATTCTATTA
Found at i:34950957 original size:20 final size:20
Alignment explanation
Indices: 34950932--34950978 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
34950922 GCTCATTTAT
*
34950932 TTATATAA-AAAAATATGTA
1 TTATATAATAAAAATATATA
*
34950951 GTTATATAATGAAAATATATA
1 -TTATATAATAAAAATATATA
34950972 TTATATA
1 TTATATA
34950979 TATGGTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (20 bp):
TTATATAATAAAAATATATA
Found at i:34950980 original size:24 final size:24
Alignment explanation
Indices: 34950953--34951035 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
34950943 AATATGTAGT
34950953 TATATAATGAAAATATATATTATA
1 TATATAATGAAAATATATATTATA
*
34950977 TATATGGTTATGTTACAAATA-ATATGTAGT-
1 TATA---TAATG--A-AAATATATAT-TA-TA
*
34951007 TATATAATGAAAATGTATATTATA
1 TATATAATGAAAATATATATTATA
34951031 TATAT
1 TATAT
34951036 TGTTATGTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 20
0.67 0.04 0.29
Matches are distributed among these distances:
23 1 0.02
24 15 0.33
25 5 0.11
27 8 0.17
29 5 0.11
30 11 0.24
31 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.10, T:0.43
Consensus pattern (24 bp):
TATATAATGAAAATATATATTATA
Found at i:34951026 original size:54 final size:54
Alignment explanation
Indices: 34950943--34951051 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
34950933 TATATAAAAA
34950943 AATATGTAGTTATATAATGAAAATATATATTATATATATGGTTATGTTACAAAT
1 AATATGTAGTTATATAATGAAAATATATATTATATATATGGTTATGTTACAAAT
* * *
34950997 AATATGTAGTTATATAATGAAAATGTATATTATATATATTGTTATGTTATAAAT
1 AATATGTAGTTATATAATGAAAATATATATTATATATATGGTTATGTTACAAAT
34951051 A
1 A
34951052 TTTTATTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (54 bp):
AATATGTAGTTATATAATGAAAATATATATTATATATATGGTTATGTTACAAAT
Found at i:34951103 original size:15 final size:15
Alignment explanation
Indices: 34951078--34951115 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
34951068 GCATCAATTA
*
34951078 ATTTTTA-TTTATTT
1 ATTTTTATTTTATAT
34951092 ATTTTTATTTTATAT
1 ATTTTTATTTTATAT
34951107 ATATTTTAT
1 AT-TTTTAT
34951116 ATGTCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTATTTTATAT
Found at i:34951355 original size:19 final size:21
Alignment explanation
Indices: 34951306--34951359 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
34951296 ATATGGATTG
34951306 AAAAATAA--ATATTTCACAT
1 AAAAATAATTATATTTCACAT
34951325 ATAAAA-AATTATATTT-AC-T
1 A-AAAATAATTATATTTCACAT
34951344 AAAAATAATTATATTT
1 AAAAATAATTATATTT
34951360 GAAATAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.13
19 15 0.48
20 6 0.19
21 6 0.19
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATAATTATATTTCACAT
Found at i:34951615 original size:41 final size:41
Alignment explanation
Indices: 34951465--34951924 Score: 361
Period size: 41 Copynumber: 11.3 Consensus size: 41
34951455 AGTGGCACTT
* * *
34951465 TTAGCGGCGTTTGGACACAAAGCGCCGCAAAAAGT-GAAG-CA
1 TTAGCGGCGCTTAGACAC-AAGCGCCGCTAAAAGTCG-AGTCA
** * *
34951506 TTAGCGGCGCTT-TTC-CTAATGCGCCGC-AAAAGGT-AAATCA
1 TTAGCGGCGCTTAGACAC-AA-GCGCCGCTAAAA-GTCGAGTCA
* * *
34951546 TTAGC-GCGCTTACACA-AAGCGCCGCTAAAGGTCGACTCA
1 TTAGCGGCGCTTAGACACAAGCGCCGCTAAAAGTCGAGTCA
* * * *
34951585 TTAGCGGCGTTTAGACACAAGCGCCACTAAAAGTTGGGTCA
1 TTAGCGGCGCTTAGACACAAGCGCCGCTAAAAGTCGAGTCA
*
34951626 TTAGCGGCGCTTAGACACAAGCGCCGCTAAAGGTCGAGTCA
1 TTAGCGGCGCTTAGACACAAGCGCCGCTAAAAGTCGAGTCA
* * * * * *
34951667 TTAGCGACGCTT-TACAAAAGTGCCGCTAAAAGTCGGGTTA
1 TTAGCGGCGCTTAGACACAAGCGCCGCTAAAAGTCGAGTCA
* *
34951707 TTAGCGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCA
1 TTAGCGGCGCTTAGACACAAGCGCCGCTAAAAGTCGAGTCA
* **
34951748 TTAGCGGCGCTTAGCCACAAGCGCCGCTAATGGTCG-GATCA
1 TTAGCGGCGCTTAGACACAAGCGCCGCTAAAAGTCGAG-TCA
* * * *
34951789 TTAGCGACGCTTCA-CCGCAAGCGCCGCTAAAAGTGGAGTCA
1 TTAGCGGCGCTT-AGACACAAGCGCCGCTAAAAGTCGAGTCA
** * * * *
34951830 TTAGCGGCGCTTACCCACAAACACCGGT-AAAGATCGTGTCA
1 TTAGCGGCGCTTAGACACAAGCGCCGCTAAAAG-TCGAGTCA
* * * * * *
34951871 TTAGCGGCGCTTATATAAAAAGCGCCGGTAAAGGTC-AGGTTA
1 TTAGCGGCGCTTAGA-CACAAGCGCCGCTAAAAGTCGA-GTCA
34951913 TTAGCGGCGCTT
1 TTAGCGGCGCTT
34951925 TTCTAATAAG
Statistics
Matches: 340, Mismatches: 61, Indels: 35
0.78 0.14 0.08
Matches are distributed among these distances:
38 9 0.03
39 28 0.08
40 66 0.19
41 206 0.61
42 28 0.08
43 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTAGACACAAGCGCCGCTAAAAGTCGAGTCA
Found at i:34951724 original size:122 final size:122
Alignment explanation
Indices: 34951526--34951963 Score: 446
Period size: 122 Copynumber: 3.6 Consensus size: 122
34951516 TTTTCCTAAT
* * * * **
34951526 GCGCCGCAAAAGGT-AAATCATTAGCG-CGC-TTACACAAAGCGCCGCTAAAGGTCGACTCATTA
1 GCGCCGCTAAAGGTCGAGTCATTAGCGACGCTTTACA-AAAGCGCCGCTAAAAGTCGGGTCATTA
* *
34951588 GCGGCGTTTAGACACAAGCGCCACTAAAAGTTGGGTCATTAGCGGCGCTTAGACACAA
65 GCGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCGGCGCTTAGACACAA
* *
34951646 GCGCCGCTAAAGGTCGAGTCATTAGCGACGCTTTACAAAAGTGCCGCTAAAAGTCGGGTTATTAG
1 GCGCCGCTAAAGGTCGAGTCATTAGCGACGCTTTACAAAAGCGCCGCTAAAAGTCGGGTCATTAG
*
34951711 CGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCGGCGCTTAGCCACAA
66 CGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCGGCGCTTAGACACAA
* * **
34951768 GCGCCGCTAATGGTCG-GATCATTAGCGACGCTTCACCGCAAGCGCCGCTAAAAGT-GGAGTCAT
1 GCGCCGCTAAAGGTCGAG-TCATTAGCGACGCTTTA-CAAAAGCGCCGCTAAAAGTCGG-GTCAT
** * * ** * * * *
34951831 TAGCGGCGCTTACCCACAAACACCGGT-AAAGATCGTGTCATTAGCGGCGCTTATATAAAAA
63 TAGCGGCGCTTAGACACAAGCGCCACTAAAAG-TCGGGTCATTAGCGGCGCTTAGA-CACAA
* * * * * *
34951892 GCGCCGGTAAAGGTC-AGGTTATTAGCGGCGCTTTTCTAATAAGCGCCGCT-AAGGT-GTG-CAT
1 GCGCCGCTAAAGGTCGA-GTCATTAGCGACGCTTTAC-AA-AAGCGCCGCTAAAAGTCGGGTCAT
34951953 TAGCGGCGCTT
63 TAGCGGCGCTT
34951964 TTCTATAAGC
Statistics
Matches: 268, Mismatches: 38, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
120 13 0.05
121 11 0.04
122 131 0.49
123 68 0.25
124 34 0.13
125 11 0.04
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (122 bp):
GCGCCGCTAAAGGTCGAGTCATTAGCGACGCTTTACAAAAGCGCCGCTAAAAGTCGGGTCATTAG
CGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCGGCGCTTAGACACAA
Found at i:34951792 original size:163 final size:161
Alignment explanation
Indices: 34951545--34951841 Score: 398
Period size: 163 Copynumber: 1.8 Consensus size: 161
34951535 AAGGTAAATC
* * *
34951545 ATTAGCGCGCTTACACAAAGCGCCGCTAAAGGTCGACTCATTAGCGGCGTTTAGACACAAGCGCC
1 ATTAGCGCGCTTACACAAAGCGCCACTAAAAGTCGACTCATTAGCGGCGCTTAGACACAAGCGCC
* * * *
34951610 ACTAAAAGTTGGGTCATTAGCGGCGCTT-AGACACAAGCGCCGCTAAAGGTCGAGTCATTAGCGA
66 ACTAAAAGTCGGATCATTAGCGACGCTTCA-ACACAAGCGCCGCTAAAAGTCGAGTCATTAGCGA
34951674 CGCTTTACAAAAGTGCCGCTAAAAGTCGGGTT
130 CGCTTTACAAAAGTGCCGCTAAAAGTCGGGTT
* ** *
34951706 ATTAGCGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCGGCGCTTAGCCACAAGCG
1 ATTAGC-GCGCTTACACA-AAGCGCCACTAAAAGTCGACTCATTAGCGGCGCTTAGACACAAGCG
* ** * * *
34951771 CCGCTAATGGTCGGATCATTAGCGACGCTTCACCGCAAGCGCCGCTAAAAGTGGAGTCATTAGCG
64 CCACTAAAAGTCGGATCATTAGCGACGCTTCAACACAAGCGCCGCTAAAAGTCGAGTCATTAGCG
*
34951836 GCGCTT
129 ACGCTT
34951842 ACCCACAAAC
Statistics
Matches: 115, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
161 6 0.05
162 10 0.09
163 98 0.85
164 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (161 bp):
ATTAGCGCGCTTACACAAAGCGCCACTAAAAGTCGACTCATTAGCGGCGCTTAGACACAAGCGCC
ACTAAAAGTCGGATCATTAGCGACGCTTCAACACAAGCGCCGCTAAAAGTCGAGTCATTAGCGAC
GCTTTACAAAAGTGCCGCTAAAAGTCGGGTT
Found at i:34951916 original size:42 final size:42
Alignment explanation
Indices: 34951826--34951963 Score: 124
Period size: 42 Copynumber: 3.4 Consensus size: 42
34951816 TAAAAGTGGA
*** * *
34951826 GTCATTAGCGGCGCTTACCCACAAA-CACCGGTAAAGATCGT
1 GTCATTAGCGGCGCTTATATAAAAAGCGCCGGTAAAGATCGT
*
34951867 GTCATTAGCGGCGCTTATATAAAAAGCGCCGGTAAAGGTCAG-
1 GTCATTAGCGGCGCTTATATAAAAAGCGCCGGTAAAGATC-GT
* * * * * *
34951909 GTTATTAGCGGCGCTTTTCTAATAAGCGCCGCT-AAGGT-GT
1 GTCATTAGCGGCGCTTATATAAAAAGCGCCGGTAAAGATCGT
34951949 G-CATTAGCGGCGCTT
1 GTCATTAGCGGCGCTT
34951964 TTCTATAAGC
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
39 14 0.17
40 1 0.01
41 26 0.32
42 40 0.49
43 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (42 bp):
GTCATTAGCGGCGCTTATATAAAAAGCGCCGGTAAAGATCGT
Found at i:34953073 original size:44 final size:43
Alignment explanation
Indices: 34952994--34953136 Score: 187
Period size: 44 Copynumber: 3.3 Consensus size: 43
34952984 CAGACCGCAG
* * * *
34952994 AACCCTCTTCTGTTTCCCTTACTCCATTGCCTCTTCACCCCCAA
1 AACCCGCTTCTGTTCCCCTCACTCCGTT-CCTCTTCACCCCCAA
*
34953038 AACCCGCTTCTGTTCCCCTCACCCCGTTCCTTCTTCACCCCCAA
1 AACCCGCTTCTGTTCCCCTCACTCCGTTCC-TCTTCACCCCCAA
* * *
34953082 AACCCGCTTCTCTTCCCCTCACTCTGTTCCCTCTTCACCCCCAG
1 AACCCGCTTCTGTTCCCCTCACTCCGTT-CCTCTTCACCCCCAA
34953126 AACCCGCTTCT
1 AACCCGCTTCT
34953137 TGAGCAGATC
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
43 2 0.02
44 84 0.95
45 2 0.02
ACGTcount: A:0.14, C:0.50, G:0.06, T:0.30
Consensus pattern (43 bp):
AACCCGCTTCTGTTCCCCTCACTCCGTTCCTCTTCACCCCCAA
Found at i:34953095 original size:23 final size:23
Alignment explanation
Indices: 34953024--34953096 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
34953014 ACTCCATTGC
34953024 CTCTTCACCCCCAAAACCCGCTT
1 CTCTTCACCCCCAAAACCCGCTT
* * *
34953047 CTGTTC-CCCTC--ACCCCG-TT
1 CTCTTCACCCCCAAAACCCGCTT
34953066 CCTTCTTCACCCCCAAAACCCGCTT
1 -C-TCTTCACCCCCAAAACCCGCTT
34953091 CTCTTC
1 CTCTTC
34953097 CCCTCACTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
19 2 0.05
20 6 0.16
21 4 0.11
22 8 0.21
23 10 0.26
24 6 0.16
25 2 0.05
ACGTcount: A:0.15, C:0.52, G:0.05, T:0.27
Consensus pattern (23 bp):
CTCTTCACCCCCAAAACCCGCTT
Found at i:34955722 original size:36 final size:36
Alignment explanation
Indices: 34955680--34955838 Score: 96
Period size: 36 Copynumber: 4.3 Consensus size: 36
34955670 TAAAATATTT
34955680 AATTATTTAATTATATTAAAGTAAATAATTACATTA
1 AATTATTTAATTATATTAAAGTAAATAATTACATTA
* * ** *
34955716 AATTATTTAATGATGTTTAATTATGTATTTAATT--ATAA
1 AATTATTTAATTAT-ATTAA--A-GTAAATAATTACATTA
* * * * *
34955754 ACACTATCGATTAATTAGATATTTAAGT---TAA-AAGATTT
1 A-ATTAT---TTAATT--ATATTAAAGTAAATAATTACATTA
34955792 AATTATTTAATTATATTAAAGTAAATAATTACATTA
1 AATTATTTAATTATATTAAAGTAAATAATTACATTA
34955828 AATTATTTAAT
1 AATTATTTAAT
34955839 CATGTTTAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
32 9 0.10
34 6 0.07
35 3 0.03
36 28 0.31
37 11 0.12
38 7 0.08
39 5 0.06
40 10 0.11
41 1 0.01
42 5 0.06
43 3 0.03
44 2 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
AATTATTTAATTATATTAAAGTAAATAATTACATTA
Found at i:34955726 original size:18 final size:18
Alignment explanation
Indices: 34955680--34955726 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
34955670 TAAAATATTT
*
34955680 AATTATTTAATTATATTA
1 AATTATTTAATTACATTA
* **
34955698 AAGTAAATAATTACATTA
1 AATTATTTAATTACATTA
34955716 AATTATTTAAT
1 AATTATTTAAT
34955727 GATGTTTAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
AATTATTTAATTACATTA
Found at i:34955748 original size:58 final size:58
Alignment explanation
Indices: 34955683--34955864 Score: 186
Period size: 58 Copynumber: 3.2 Consensus size: 58
34955673 AATATTTAAT
34955683 TATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATGATGTTTAATTATG
1 TATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATGATGTTTAATTATG
* * * **
34955741 TATTTAATTATA--AACACT--ATCGATTA-ATTAGA-TATTTAA-G-T-TAAAAGATTTAAT-
1 TATTTAATTATATTAA-AGTAAAT-AATTACATTAAATTATTTAATGATGT-TTA-A-TT-ATG
*
34955795 TATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTTTAATTATG
1 TATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATGATGTTTAATTATG
34955853 TATTTAATTATA
1 TATTTAATTATA
34955865 AATAATATCA
Statistics
Matches: 97, Mismatches: 11, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
51 1 0.01
52 2 0.02
53 2 0.02
54 21 0.22
55 11 0.11
56 12 0.12
57 11 0.11
58 33 0.34
59 1 0.01
60 2 0.02
61 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (58 bp):
TATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATGATGTTTAATTATG
Found at i:34955818 original size:112 final size:112
Alignment explanation
Indices: 34955621--34956424 Score: 508
Period size: 112 Copynumber: 7.1 Consensus size: 112
34955611 AATAATTAAA
* *
34955621 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAAAATATTTAATTAT
1 TAATTATGTATTTAATTATAAACAATATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
*
34955686 TTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATGATGTT
66 TTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTT
* *
34955733 TAATTATGTATTTAATTATAAACACTATCGATTAATTAGATATTTAAGTTAAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAATATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
34955798 TTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTT
66 TTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTT
* * * *
34955845 TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAA-TTATTTAATTATATTAA
1 TAATTATGTATTTAATTATAAACAATATCGATTAATTAAATATTTAAGTTA---AA--AGATTTA
* ** * * * * ***
34955909 AGTAAATAATTATATTAAATTAAAGATTTA-ATTATTTAATTATATTAAAC-TAAA
61 ATTATTTAATTATATTAAAGTAAATAATTACATTA---AATTAT-TTAATCATGTT
* ** * ** * **
34955963 TAATTA--TATTAAATTAT--TTAATCAT-GTTTAATTATGTATTTAA-TTATGAAGACTATCGA
1 TAATTATGTATTTAATTATAAACAAT-ATCGATTAATTAAATATTTAAGTTA-AAAGA-T-TTAA
* *
34956022 TTAATTAA--ATATTTAAGTTAAA-AGATTTA-ATTATTTAATTATATTAA--A-G-T
62 TTATTTAATTATATTAAAG-TAAATA-A-TTACATTA---AATTAT-TTAATCATGTT
* * ** * *
34956072 AAATAAT-TATATTAAGTTA-AAA-AAT-TTAATTATTTAATTATATTAAAG-TAAATA-A-TTA
1 TAATTATGTAT-TTAA-TTATAAACAATATCGATTAATTAA--ATATTTAAGTTAAA-AGATTTA
* * * * * ** * * ** * *
34956130 TATTAAGTTAA-AAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATT
61 -ATT-ATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTT
* ** * ** ** * * * * *
34956183 AAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAATTTAAAAGATATAAT
1 TAATTATGTATTTAATTA-TAAACAATA-TCGATTAATTAAATAT-TTAAGTTAAAAGATTTAAT
* *
34956248 TATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTT
63 TATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTT
* *
34956298 TAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAAATTTAATTAT
1 TAATTATGTATTTAATTATAAACAATATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
* * *
34956363 TTAATTATATTAAAGTAAATAATTATATTAAAATT-TTTAATTATATT
66 TTAATTATATTAAAGTAAATAATTACATT-AAATTATTTAATCATGTT
**
34956410 TAATTAACTATTTAA
1 TAATTATGTATTTAA
34956425 CTTAAAATGT
Statistics
Matches: 542, Mismatches: 103, Indels: 94
0.73 0.14 0.13
Matches are distributed among these distances:
107 3 0.01
108 4 0.01
109 6 0.01
110 23 0.04
111 39 0.07
112 273 0.50
113 30 0.06
114 37 0.07
115 68 0.13
116 41 0.08
118 13 0.02
119 5 0.01
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (112 bp):
TAATTATGTATTTAATTATAAACAATATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
TTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTT
Found at i:34955905 original size:18 final size:18
Alignment explanation
Indices: 34955788--34956415 Score: 124
Period size: 18 Copynumber: 35.5 Consensus size: 18
34955778 AAGTTAAAAG
34955788 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
* * ** *
34955806 ATTAAAGTAAATAATTAC
1 ATTTAATTATTTAATTAT
* *
34955824 ATTAAATTATTTAATCAT
1 ATTTAATTATTTAATTAT
*
34955842 GTTTAATTATGTATTTAATTAT
1 ATTT-A--AT-TATTTAATTAT
** *
34955864 AAATAATATCAATTAATTAAAT
1 ATTTAAT-T-ATTTAATT--AT
34955886 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
* * **
34955904 ATTAAAGTAAATAATTAT
1 ATTTAATTATTTAATTAT
*
34955922 A-TTAA--A-TTAA--AG
1 ATTTAATTATTTAATTAT
34955934 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
* * **
34955952 ATTAAACTAAATAATTAT
1 ATTTAATTATTTAATTAT
* *
34955970 ATTAAATTATTTAATCAT
1 ATTTAATTATTTAATTAT
* * *
34955988 GTTTAATTATGTATTTA-
1 ATTTAATTATTTAATTAT
* **
34956005 ATTATGAA-GACTATCGATTA-
1 ATT-T-AATTA-T-TTAATTAT
* *
34956025 A-TTAAATATTTAAGTTAAAAG
1 ATTTAATTATTTAA-TT---AT
34956046 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
* * **
34956064 ATTAAAGTAAATAATTAT
1 ATTTAATTATTTAATTAT
*
34956082 A-TTAAGTTA---AA--AA
1 ATTTAA-TTATTTAATTAT
34956095 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
* * **
34956113 ATTAAAGTAAATAATTAT
1 ATTTAATTATTTAATTAT
*
34956131 A-TTAAGTTA---AA--AG
1 ATTTAA-TTATTTAATTAT
34956144 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
* * **
34956162 ATTAAAGTAAATAATTAT
1 ATTTAATTATTTAATTAT
34956180 A-TTAA--A-TTAA--AT
1 ATTTAATTATTTAATTAT
34956192 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
* * **
34956210 ATTAAAGTAAATAATTAT
1 ATTTAATTATTTAATTAT
* *
34956228 A-TT-A--ATTTAA-AAG
1 ATTTAATTATTTAATTAT
*
34956241 ATATAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
* * **
34956259 ATTAAACTAAATAATTAT
1 ATTTAATTATTTAATTAT
* *
34956277 ATTAAATTATTTAATCAT
1 ATTTAATTATTTAATTAT
* * *
34956295 GTTTAATTATGTATTTA-
1 ATTTAATTATTTAATTAT
** **
34956312 ATTATAAACACTATCGATTA-
1 ATT-TAATTA-T-TTAATTAT
* *
34956332 A-TTAAATATTTAAGTTAAAAA
1 ATTTAATTATTTAA-TT---AT
34956353 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
* * **
34956371 ATTAAAGTAAATAATTAT
1 ATTTAATTATTTAATTAT
*
34956389 ATTAAAATT-TTTAATTAT
1 ATT-TAATTATTTAATTAT
34956407 ATTTAATTA
1 ATTTAATTA
34956416 ACTATTTAAC
Statistics
Matches: 429, Mismatches: 121, Indels: 120
0.64 0.18 0.18
Matches are distributed among these distances:
12 5 0.01
13 20 0.05
14 19 0.04
15 9 0.02
16 17 0.04
17 35 0.08
18 236 0.55
19 14 0.03
20 24 0.06
21 10 0.02
22 40 0.09
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (18 bp):
ATTTAATTATTTAATTAT
Found at i:34955930 original size:48 final size:48
Alignment explanation
Indices: 34955798--34955978 Score: 203
Period size: 48 Copynumber: 3.7 Consensus size: 48
34955788 ATTTAATTAT
*
34955798 TTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTTTAATTAT
1 TTAATTATATTAAAGTAAATAATTATATTAAATTA---AAT-A--TTTAATTAT
* *
34955852 GTATTTA-ATT--A-TAAATAA-TATCAATT-AATTAAATATTTAATTAT
1 TTAATTATATTAAAGTAAATAATTAT--ATTAAATTAAATATTTAATTAT
*
34955896 TTAATTATATTAAAGTAAATAATTATATTAAATTAAAGATTTAATTAT
1 TTAATTATATTAAAGTAAATAATTATATTAAATTAAATATTTAATTAT
*
34955944 TTAATTATATTAAACTAAATAATTATATTAAATTA
1 TTAATTATATTAAAGTAAATAATTATATTAAATTA
34955979 TTTAATCATG
Statistics
Matches: 112, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
44 14 0.12
45 3 0.03
46 1 0.01
47 7 0.06
48 58 0.52
49 5 0.04
50 12 0.11
51 4 0.04
53 3 0.03
54 5 0.04
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (48 bp):
TTAATTATATTAAAGTAAATAATTATATTAAATTAAATATTTAATTAT
Found at i:34955945 original size:146 final size:146
Alignment explanation
Indices: 34955784--34956344 Score: 625
Period size: 146 Copynumber: 3.7 Consensus size: 146
34955774 ATTTAAGTTA
* *
34955784 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTTTAAT
1 AAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAAT
34955849 TATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAATTATTTAATTATATTAAAGTAA
66 TATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAATTATTTAATTATATTAAAGTAA
34955914 ATAATTATATTAAATT
131 ATAATTATATTAAATT
34955930 AAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAAT
1 AAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAAT
* * * *
34955995 TATGTATTTAATTATGAAGACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAA
66 TATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAA-TT-----ATTTAATTA--T-A
* * * *
34956060 TTATATTAAAGTAAATA-ATTATATT
122 TTAAAGTAAA-TAATTATATTAAATT
* ** * * * * * *
34956085 -AAG-TTAAAAAATTTAATTATTTAATTATATTAAAGTAAATA-ATTATATTAAGTTAA--AAGA
1 AAAGATTTAATTATTTAATTA--T-ATTAAACTAAA-TAATTATATTAAATT-ATTTAATCATG-
* *
34956145 TTTAATTATTTAATTATATTAAAGTAAATAAT-T-ATATTAAATTAAATATTTAATTATTTAATT
60 TTTAATTATGTATTTA-ATT--A-TAAATAATATCA-ATT-AATTAAATATTTAATTATTTAATT
*
34956208 ATATTAAAGTAAATAATTATATTAATTT
119 ATATTAAAGTAAATAATTATATTAAATT
*
34956236 AAAAGATATAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAA
1 -AAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAA
* * *
34956301 TTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAA
65 TTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAA
34956345 GTTAAAAAAT
Statistics
Matches: 339, Mismatches: 45, Indels: 61
0.76 0.10 0.14
Matches are distributed among these distances:
146 102 0.30
147 22 0.06
148 5 0.01
150 18 0.05
151 45 0.13
152 13 0.04
153 16 0.05
154 25 0.07
155 19 0.06
156 35 0.10
157 13 0.04
159 7 0.02
160 19 0.06
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (146 bp):
AAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAAT
TATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAATTATTTAATTATATTAAAGTAA
ATAATTATATTAAATT
Found at i:34956059 original size:258 final size:257
Alignment explanation
Indices: 34955676--34956232 Score: 874
Period size: 258 Copynumber: 2.2 Consensus size: 257
34955666 AAGTTAAAAT
* *
34955676 ATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATGATGTTTAATTATG
1 ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTTTAATTATG
*
34955741 TATTTAATTATAAACACTATCGATTAATTAGATATTTAAGTTAAAAGATTTAATTATTTAATTAT
66 TATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTAT
** *
34955806 ATTAAAGTAAATAATTACATTAAATTATTTAATCATGTTTAATTATGTATTTA-ATT-A-TAAAT
131 ATTAAAGTAAATAATTACATTAAATTA---AA--AAATTTAATTATGTAATTATATTAAGTAAAT
*
34955868 AA-TATCAATTAA-TT-AAATATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
191 AATTAT--ATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
34955930 AAAG
254 AAAG
*
34955934 ATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATG
1 ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTTTAATTATG
* *
34955999 TATTTAATTATGAAGACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTAT
66 TATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTAT
* * *
34956064 ATTAAAGTAAATAATTATATTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATT
131 ATTAAAGTAAATAATTACATTAAATTAAAAAATTTAATTATGTAATTATATT-AAGTAAATAATT
*
34956129 ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAT
195 ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAG
34956192 ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAA
1 ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAA
34956233 TTTAAAAGAT
Statistics
Matches: 277, Mismatches: 15, Indels: 14
0.91 0.05 0.05
Matches are distributed among these distances:
253 15 0.05
254 3 0.01
255 2 0.01
256 6 0.02
257 9 0.03
258 242 0.87
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (257 bp):
ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTTTAATTATG
TATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTAT
ATTAAAGTAAATAATTACATTAAATTAAAAAATTTAATTATGTAATTATATTAAGTAAATAATTA
TATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAG
Found at i:34956092 original size:49 final size:49
Alignment explanation
Indices: 34956034--34956281 Score: 435
Period size: 49 Copynumber: 5.1 Consensus size: 49
34956024 AATTAAATAT
34956034 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
*
34956083 TTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
34956132 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* *
34956181 TTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * *
34956229 TTAATTTAAAAGATATAATTATTTAATTATATTAAACTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
34956278 TTAA
1 TTAA
34956282 ATTATTTAAT
Statistics
Matches: 190, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
48 46 0.24
49 144 0.76
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (49 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
Found at i:34956254 original size:307 final size:303
Alignment explanation
Indices: 34955776--34956393 Score: 1010
Period size: 307 Copynumber: 2.0 Consensus size: 303
34955766 AATTAGATAT
*
34955776 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCA
1 TTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTA--TAA-CA
*
34955841 TGTTTAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAATTATTTAATTATAT
63 TGTTTAATTATGTAATTAATTATAAATAATAT-AATTAATTAAATATTTAATTATTTAATTATAT
*
34955906 TAAAGTAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATA
127 TAAAGTAAATAATTATATTAAATTAAAGATATAATTATTTAATTATATTAAACTAAATAATTATA
* *
34955971 TTAAATTATTTAATCATGTTTAATTATGTATTTAATTATGAAGACTATCGATTAATTAAATATTT
192 TTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTT
*
34956036 AAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
257 AAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* *
34956083 TTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA-AA-A-GA
1 TTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTATAACATG-
*
34956145 TTTAATTATTTAATTATATTAAAGTAAATAAT-TATATTAAATTAAATATTTAATTATTTAATTA
65 TTTAATTATGTAATTA-ATT--A-TAAATAATATA-ATT-AATTAAATATTTAATTATTTAATTA
*
34956209 TATTAAAGTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTAAATAAT
124 TATTAAAGTAAATAATTATATTAAATT-AAAGATATAATTATTTAATTATATTAAACTAAATAAT
34956274 TATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAAT
188 TATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAAT
34956339 ATTTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTATA
253 ATTTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTATA
34956390 TTAA
1 TTAA
34956394 AATTTTTAAT
Statistics
Matches: 293, Mismatches: 10, Indels: 16
0.92 0.03 0.05
Matches are distributed among these distances:
301 1 0.00
302 15 0.05
303 3 0.01
304 3 0.01
305 5 0.02
306 59 0.20
307 207 0.71
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (303 bp):
TTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTATAACATGT
TTAATTATGTAATTAATTATAAATAATATAATTAATTAAATATTTAATTATTTAATTATATTAAA
GTAAATAATTATATTAAATTAAAGATATAATTATTTAATTATATTAAACTAAATAATTATATTAA
ATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGT
TAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTATA
Found at i:34956311 original size:58 final size:56
Alignment explanation
Indices: 34955939--34956424 Score: 288
Period size: 49 Copynumber: 9.2 Consensus size: 56
34955929 TAAAGATTTA
*
34955939 ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATT
1 ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAAT-ATATTTAATT
* * **
34955996 ATGTATTTAATTATGA--AGACT--ATCGATTA-ATTAAA-TATTTAAGT-TA-AAAGATTT
1 AT-TATTTAATTAT-ATTAAACTAAAT-AATTATATTAAATTATTTAA-TATATTTA-A-TT
* * *
34956050 AATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA---AA-AAATTT-A--
1 -ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATATATTTAATT
* * *
34956100 ATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA---AA-AGATTT-A--
1 ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATATATTTAATT
*
34956149 ATTATTTAATTATATTAAAGTAAATAATTATATT-AA--A-TTAA-ATATTT-A--
1 ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATATATTTAATT
* ** *
34956197 ATTATTTAATTATATTAAAGTAAATAATTATATT--A--ATTTAA-A-AGAT-ATA
1 ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATATATTTAATT
*
34956246 ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATT
1 ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAAT-ATATTTAATT
* ***
34956303 ATGTATTTAATTATA--AACACT--ATCGATTA-ATTAAA-TATTTAAGT-TAAAAAATTT
1 AT-TATTTAATTATATTAA-ACTAAAT-AATTATATTAAATTATTTAA-TATATTTAA-TT
*
34956357 AATTATTTAATTATATTAAAGTAAATAATTATATTAAAATT-TTTAATTATATTTAATT
1 -ATTATTTAATTATATTAAACTAAATAATTATATT-AAATTATTTAA-TATATTTAATT
*
34956415 AACTATTTAA
1 -ATTATTTAA
34956425 CTTAAAATGT
Statistics
Matches: 353, Mismatches: 34, Indels: 83
0.75 0.07 0.18
Matches are distributed among these distances:
46 1 0.00
47 5 0.01
48 48 0.14
49 115 0.33
51 1 0.00
52 1 0.00
53 13 0.04
54 42 0.12
55 30 0.08
56 21 0.06
57 25 0.07
58 45 0.13
59 6 0.02
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (56 bp):
ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATATATTTAATT
Found at i:34956347 original size:258 final size:254
Alignment explanation
Indices: 34955776--34956394 Score: 348
Period size: 258 Copynumber: 2.4 Consensus size: 254
34955766 AATTAGATAT
* * *
34955776 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCA
1 TTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA---AA--A
* * *
34955841 TG-TTTAATTATGTATTTA-ATT--A-TAAATAA-TATCAATT-AATTAAATATTTAATTATTTA
61 -GATTTAATTATTTAATTATATTAAAGTAAATAATTAT--ATTAAATTAAAGATTTAATTATTTA
* * * *
34955899 ATTATATTAAAGTAAATAATTATATTAA-A-TT-A-AAGATTTAATTATTTAATT-A-TATTAA-
123 ATTATATTAAACTAAATAATTATATTAATATTTAACAAG-TATAATTATGTAATTAATTATGAAG
* * * *
34955957 ACTAAAT-AATTATATTAAATTATTTAA-T-CATG-TTTAATTATGTATTTAATTATGAAGACTA
187 ACT--ATCAATTA-ATTAAA-TATTTAAGTAAAAGATTTAATTATGTAATT-A-TAT-AAAACTA
*
34956018 TCGATTAATTAAATA
245 ---AATAATT--ATA
* *
34956033 TTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAAATT
1 -TTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
*
34956098 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATA
65 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT-AAAGATTTAATTATTTAATTATA
* * *
34956163 TTAAAGTAAATAATTATATTAA-A-TTAA-ATA-TTTAATTATTTAATTATATTA--AAG--TA-
129 TTAAACTAAATAATTATATTAATATTTAACA-AGTATAATTATGTAATTA-ATTATGAAGACTAT
* * * *
34956219 -AA-TAATT--ATA-TTAATTTAAAAGATATAATTATTTAATTATATTAAACTAAATAATTATA
192 CAATTAATTAAATATTTAA-GTAAAAGATTTAATTATGTAATTATATAAAACTAAATAATTATA
* ** * * * * *
34956278 TTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTT
1 TTAAGTTA---AA--AAATTTAATTATTTAATT-A-TATTAA-AGTA---AATAATT--ATA-TT
*
34956343 AAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAA
52 AAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAA
34956395 ATTTTTAATT
Statistics
Matches: 305, Mismatches: 24, Indels: 64
0.78 0.06 0.16
Matches are distributed among these distances:
244 7 0.02
245 3 0.01
247 8 0.03
249 18 0.06
250 8 0.03
251 10 0.03
252 6 0.02
253 30 0.10
254 5 0.02
255 10 0.03
256 5 0.02
257 13 0.04
258 174 0.57
259 4 0.01
260 2 0.01
261 2 0.01
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (254 bp):
TTAAGTTAAAAAATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
AATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATT
AAACTAAATAATTATATTAATATTTAACAAGTATAATTATGTAATTAATTATGAAGACTATCAAT
TAATTAAATATTTAAGTAAAAGATTTAATTATGTAATTATATAAAACTAAATAATTATA
Found at i:34956480 original size:8 final size:8
Alignment explanation
Indices: 34956444--34956537 Score: 56
Period size: 8 Copynumber: 11.8 Consensus size: 8
34956434 TGGTCGTAAA
34956444 TAATTATAT
1 TAATTAT-T
34956453 ATAATTATT
1 -TAATTATT
34956462 TAAGCTTATT
1 TAA--TTATT
34956472 TAATTATT
1 TAATTATT
34956480 TAATTGA--
1 TAATT-ATT
**
34956487 -AAAGATT
1 TAATTATT
34956494 TAATTATT
1 TAATTATT
34956502 TAATTATAT
1 TAATTAT-T
34956511 TAA--A-T
1 TAATTATT
* *
34956516 GAAATATT
1 TAATTATT
34956524 TAATTATT
1 TAATTATT
34956532 TAATTA
1 TAATTA
34956538 ATAAAAACAG
Statistics
Matches: 67, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
5 4 0.06
6 2 0.03
7 2 0.03
8 38 0.57
9 6 0.09
10 15 0.22
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (8 bp):
TAATTATT
Found at i:34962155 original size:66 final size:67
Alignment explanation
Indices: 34962049--34962206 Score: 239
Period size: 67 Copynumber: 2.4 Consensus size: 67
34962039 CAAATTGCTC
* *
34962049 AACTTAAAGAGGAGGCTGCAGCT-AGAGAAGCAGAGGCTC-AAAAAAAATATGATGAACTCCATC
1 AACTTAAAGAGGAGGCTGCAG-TGAGAGAAGCAGAGGCTCAAAAAAAAATATGAAGAACTCCACC
34962112 TAA
65 TAA
*
34962115 AACTTAAAGAGGAGGCTGCAGTGAGAGAAGCAGAGTCTCAAAAAAAAATATGAAGAACTCCACCT
1 AACTTAAAGAGGAGGCTGCAGTGAGAGAAGCAGAGGCTCAAAAAAAAATATGAAGAACTCCACCT
*
34962180 AC
66 AA
* *
34962182 AACTTAAAGTGGAGGCAGCAGTGAG
1 AACTTAAAGAGGAGGCTGCAGTGAG
34962207 GCAAGCGGAG
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
65 1 0.01
66 36 0.43
67 47 0.56
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16
Consensus pattern (67 bp):
AACTTAAAGAGGAGGCTGCAGTGAGAGAAGCAGAGGCTCAAAAAAAAATATGAAGAACTCCACCT
AA
Found at i:34962218 original size:21 final size:21
Alignment explanation
Indices: 34962192--34962244 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
34962182 AACTTAAAGT
*
34962192 GGAGGCAGCAGTGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
34962213 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
* *
34962234 GAAGGAAGCAG
1 GGAGGCAGCAG
34962245 AGGCTACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.47, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCAGCGAGGCAAGC
Found at i:34962657 original size:15 final size:15
Alignment explanation
Indices: 34962637--34962670 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
34962627 TTCGCATAAA
34962637 CGGCGTTATCTTTAG
1 CGGCGTTATCTTTAG
34962652 CGGCGTTATCTTTAG
1 CGGCGTTATCTTTAG
34962667 CGGC
1 CGGC
34962671 ATTTTTTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.29, T:0.35
Consensus pattern (15 bp):
CGGCGTTATCTTTAG
Found at i:34963586 original size:19 final size:19
Alignment explanation
Indices: 34963537--34963595 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
34963527 TTATTTATAT
* *
34963537 AAATAAAAGAATTATTAATTA
1 AAATAAAA-AATTA-AAAATA
*
34963558 AAAT-ATAAATTAAAAATA
1 AAATAAAAAATTAAAAATA
*
34963576 AAATAAAAAATTGAAAATA
1 AAATAAAAAATTAAAAATA
34963595 A
1 A
34963596 CACATTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 8 0.25
19 18 0.56
20 2 0.06
21 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
AAATAAAAAATTAAAAATA
Found at i:34964505 original size:21 final size:21
Alignment explanation
Indices: 34964481--34964531 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
34964471 AACAGTTACG
*
34964481 AAACAACAATAAAACAACACC
1 AAACAACAAAAAAACAACACC
34964502 AAACAACACAAAAAACAACACC
1 AAACAACA-AAAAAACAACACC
34964524 -AACAACAA
1 AAACAACAA
34964532 CACCAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 1 0.04
21 15 0.54
22 12 0.43
ACGTcount: A:0.69, C:0.29, G:0.00, T:0.02
Consensus pattern (21 bp):
AAACAACAAAAAAACAACACC
Done.