Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 113 of 132
Found at i:34289044 original size:31 final size:31
Alignment explanation
Indices: 34288985--34289126 Score: 232
Period size: 31 Copynumber: 4.5 Consensus size: 31
34288975 TAAGTTTAAG
*
34288985 TTAATTTTAAATTTTATTTAGATTTAAATTTA-T
1 TTAAATTTAAA-TTTATTT--ATTTAAATTTACT
34289018 CTTAAATTTAAATTTATTTATTTAAATTTACT
1 -TTAAATTTAAATTTATTTATTTAAATTTACT
34289050 TTAAATTTAAATTTATTTATTTAAATTTACT
1 TTAAATTTAAATTTATTTATTTAAATTTACT
34289081 TTAAATTTAAATTTATTTATTTAAATTTACT
1 TTAAATTTAAATTTATTTATTTAAATTTACT
34289112 TTAAATTTAAATTTA
1 TTAAATTTAAATTTA
34289127 ATTAAATTTA
Statistics
Matches: 106, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
31 88 0.83
32 1 0.01
33 7 0.07
34 10 0.09
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.58
Consensus pattern (31 bp):
TTAAATTTAAATTTATTTATTTAAATTTACT
Found at i:34291192 original size:30 final size:30
Alignment explanation
Indices: 34291155--34291615 Score: 490
Period size: 30 Copynumber: 15.4 Consensus size: 30
34291145 TTTGACCCTA
34291155 AACCCTAAAACTTTTCCAAAATTACATTTT
1 AACCCTAAAACTTTTCCAAAATTACATTTT
* **
34291185 GACCCTAAAACTTTTCTGGAAATTACATTTT
1 AACCCTAAAACTTTTC-CAAAATTACATTTT
* * * *
34291216 GATCCTAAAAC-TTTCTAGAAATTACATTTC
1 AACCCTAAAACTTTTCCA-AAATTACATTTT
*
34291246 GACCCTAAAACTTTTCCAAAATTACATTTT
1 AACCCTAAAACTTTTCCAAAATTACATTTT
**
34291276 AACCC-AAAACTTTTCCAAAATTTTATTTT
1 AACCCTAAAACTTTTCCAAAATTACATTTT
34291305 AACCCTAAAAC-TTTCCAAAATTACATTTT
1 AACCCTAAAACTTTTCCAAAATTACATTTT
* *
34291334 GACCCTAAAACTTTTCCAAAATTATATTTT
1 AACCCTAAAACTTTTCCAAAATTACATTTT
* * ***
34291364 GACCCCAAAACTTTTTGGAAATTACATTTT
1 AACCCTAAAACTTTTCCAAAATTACATTTT
* * **
34291394 AACCCTAAAAC-TTTCTAAAAATTACGTTAC
1 AACCCTAAAACTTTTC-CAAAATTACATTTT
* *
34291424 AACCCCATAACTTTTCCAAAATTACATTTT
1 AACCCTAAAACTTTTCCAAAATTACATTTT
*
34291454 AACCCTAAAACTTTTCCAAAATTATATTTT
1 AACCCTAAAACTTTTCCAAAATTACATTTT
34291484 AACCCTAAAACTTTTCCAAAATTACATTTT
1 AACCCTAAAACTTTTCCAAAATTACATTTT
* *
34291514 AA-CCTCAAAACTTTTCCAAAATCATATTTT
1 AACCCT-AAAACTTTTCCAAAATTACATTTT
* *
34291544 AACCCCAAAA--TTTCAAAAAAATTACATTTT
1 AACCCTAAAACTTTTC--CAAAATTACATTTT
* ** *
34291574 TACCCCGAAAC-TTTCAAAAATTACCA-TTT
1 AACCCTAAAACTTTTCCAAAATTA-CATTTT
* *
34291603 CACCCTCAAACTT
1 AACCCTAAAACTT
34291616 CCCTAAATTC
Statistics
Matches: 366, Mismatches: 51, Indels: 28
0.82 0.11 0.06
Matches are distributed among these distances:
28 4 0.01
29 78 0.21
30 247 0.67
31 37 0.10
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AACCCTAAAACTTTTCCAAAATTACATTTT
Found at i:34295403 original size:337 final size:342
Alignment explanation
Indices: 34294612--34295425 Score: 1242
Period size: 337 Copynumber: 2.4 Consensus size: 342
34294602 GGTGAGAATG
* * *
34294612 GTTGAGAAGGTAGACAAGAGAACCAAAA-GAGAGAT-TTTTGGTGTTTAGATGATCTGCCCTTCA
1 GTTGAGAAGGTGGACAAGAGAA-CAAAAGGAGAGATATTTTGGTGTTTGGATGATCTACCCTTCA
* * * *
34294675 TTAGTGAAGTGAGAAGGTTTATATACATGGGATAC-A-AG-ATATCATATGTCAGGATCTCATTA
65 TTAGTGAAGTGAGAAGGCTTATATACATGGGAT-CGAGGGTGTGTCATATGTCAGGATCTCATTA
34294737 GCAAAAAAAGTCACATCTTGTCTAATGGGTGTTTAGGTTTTGGGCTTGATGGGCTTGTGGGTGTT
129 GCAAAAAAAGTCACATCTTGTCTAATGGGTGTTTAGGTTTTGGGCTTGATGGGCTTGTGGGTGTT
* *
34294802 TGGGTTTAGGTAATTGTTGGGTTTGGATTGGGTTTGTAAATGAGTTGTAAAGGGACATTTAAATT
194 TGGGTTTAAGTAATTGTTAGGTTTGGATTGGGTTTGTAAATGAGTTGTAAAGGGACATTTAAATT
*
34294867 AAAATTGATTTTAATTTTAATTTATTTTTTTATTATTTTTGGATTTGAGTTTTGAGTTGAACCCG
259 AAAATGGATTTTAATTTTAATTTATTTTTTTATTATTTTTGGATTTGAGTTTTGAGTTGAACCCG
34294932 AAAAAATTGGATTTCAACA
324 AAAAAATTGGATTTCAACA
* * * *
34294951 ATTGAGAAGGTGGATAAGAGAACCAAAGGAGAGATATTTTGGTGTTTGGATGATCTATCCTTCAT
1 GTTGAGAAGGTGGACAAGAGAACAAAAGGAGAGATATTTTGGTGTTTGGATGATCTACCCTTCAT
* * *
34295016 TAATGAAGTGAGAAGGCTTATATACATGGGATAGAGGGTGTGTCATATGTCAAGATCTCATTAGC
66 TAGTGAAGTGAGAAGGCTTATATACATGGGATCGAGGGTGTGTCATATGTCAGGATCTCATTAGC
34295081 AAAAAAAGTCACATCTTGTCTAATGGGTGTTTAGGTTTTGGGCTTGATGGGCTTGTGGGTTGTTT
131 AAAAAAAGTCACATCTTGTCTAATGGGTGTTTAGGTTTTGGGCTTGATGGGCTTGTGGG-TGTTT
* *
34295146 GGGTTTAAGT--CTGTTTAGGTAATT-G-TTGGGTTTGTAAATGGGTTGTAAAGGGACATTTAAA
195 GGGTTTAAGTAATTG-TTAGGT--TTGGATTGGGTTTGTAAATGAGTTGTAAAGGGACATTTAAA
*
34295207 TTAAAATGGATTTTAA-TTTAA-TT-TTTTTTT-TT-TTTTTGGATTTGAGTTTTGAGTTGAGCC
257 TTAAAATGGATTTTAATTTTAATTTATTTTTTTATTATTTTTGGATTTGAGTTTTGAGTTGAACC
* * *
34295267 CGAATAAATTGGGTTTCAATA
322 CGAAAAAATTGGATTTCAACA
* *
34295288 GTTGAGAAAGTGGACAAGAGAACAAAAGGAGAGATATTTTGCTGTTTGGATGATCTACCCTTCAT
1 GTTGAGAAGGTGGACAAGAGAACAAAAGGAGAGATATTTTGGTGTTTGGATGATCTACCCTTCAT
*
34295353 TAGTGAAGTGAGCAGGCTTATATACATGGGATCGAGGGTGTGTCATATGTCAGGATCTCATTAGC
66 TAGTGAAGTGAGAAGGCTTATATACATGGGATCGAGGGTGTGTCATATGTCAGGATCTCATTAGC
34295418 AAAAAAAG
131 AAAAAAAG
34295426 ACACCTATTG
Statistics
Matches: 433, Mismatches: 33, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
337 173 0.40
338 6 0.01
339 33 0.08
340 59 0.14
341 8 0.02
342 137 0.32
343 15 0.03
344 2 0.00
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.36
Consensus pattern (342 bp):
GTTGAGAAGGTGGACAAGAGAACAAAAGGAGAGATATTTTGGTGTTTGGATGATCTACCCTTCAT
TAGTGAAGTGAGAAGGCTTATATACATGGGATCGAGGGTGTGTCATATGTCAGGATCTCATTAGC
AAAAAAAGTCACATCTTGTCTAATGGGTGTTTAGGTTTTGGGCTTGATGGGCTTGTGGGTGTTTG
GGTTTAAGTAATTGTTAGGTTTGGATTGGGTTTGTAAATGAGTTGTAAAGGGACATTTAAATTAA
AATGGATTTTAATTTTAATTTATTTTTTTATTATTTTTGGATTTGAGTTTTGAGTTGAACCCGAA
AAAATTGGATTTCAACA
Found at i:34299882 original size:30 final size:30
Alignment explanation
Indices: 34299842--34299916 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
34299832 AAAGATAAAT
*
34299842 TAATTGATTTTTTATTATTTTATGAGGGTG
1 TAATTGATTTTTAATTATTTTATGAGGGTG
* * *
34299872 TAATTTATTTTTAATTATTTTATGTGGGTT
1 TAATTGATTTTTAATTATTTTATGAGGGTG
*
34299902 TAATTGTTTCTTTAA
1 TAATTGATT-TTTAA
34299917 ATCAAAATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
30 33 0.87
31 5 0.13
ACGTcount: A:0.24, C:0.01, G:0.15, T:0.60
Consensus pattern (30 bp):
TAATTGATTTTTAATTATTTTATGAGGGTG
Found at i:34300009 original size:19 final size:17
Alignment explanation
Indices: 34299987--34300045 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 17
34299977 TATAAAAGTA
34299987 TATAAAAACTTATTAAAAT
1 TATAAAAA-TT-TTAAAAT
34300006 TATAAAAATTTTAAAA-
1 TATAAAAATTTTAAAAT
* *
34300022 GA-AAAAA-TATAAAA-
1 TATAAAAATTTTAAAAT
34300036 TATAAAAATT
1 TATAAAAATT
34300046 ATTACTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 7 0.20
15 10 0.29
16 2 0.06
17 6 0.17
18 2 0.06
19 8 0.23
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
TATAAAAATTTTAAAAT
Found at i:34300013 original size:9 final size:9
Alignment explanation
Indices: 34299941--34300047 Score: 50
Period size: 9 Copynumber: 12.4 Consensus size: 9
34299931 AATGATTTTT
34299941 TTATAGAAAA
1 TTATA-AAAA
*
34299951 -TATAAATA
1 TTATAAAAA
*
34299959 TT-TATAAA
1 TTATAAAAA
* **
34299967 TAATAAATG
1 TTATAAAAA
*
34299976 TTATAAAAG
1 TTATAAAAA
34299985 TATATAAAAA
1 T-TATAAAAA
*
34299995 CTTATTAAAA
1 -TTATAAAAA
34300005 TTATAAAAA
1 TTATAAAAA
*
34300014 TT-TTAAAA
1 TTATAAAAA
*
34300022 -GA-AAAAA
1 TTATAAAAA
34300029 -TAT-AAAA
1 TTATAAAAA
34300036 -TATAAAAA
1 TTATAAAAA
34300044 TTAT
1 TTAT
34300048 TACTTTTTTT
Statistics
Matches: 73, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
7 12 0.16
8 17 0.23
9 29 0.40
10 14 0.19
11 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:34306864 original size:143 final size:143
Alignment explanation
Indices: 34306606--34306892 Score: 511
Period size: 143 Copynumber: 2.0 Consensus size: 143
34306596 AAAATAATGG
* * **
34306606 AAGAAATTGACTGTTTATATAAGGATAAAACTTGTAATCATACTATGCGTATAGATTTTAAAAAC
1 AAGAAACTGACTATTTATATAAGGATAAAACTTGTAATCATACTATGCAAATAGATTTTAAAAAC
*
34306671 GAAAATAATATTTCATCTATTAGTAAAGGTTTTAACAGTCTAATAGATATAACTTCTATCTATTT
66 GAAAATAATATTTCATCTATTAGTAAAGGTTTTAACAGTCTAATAAATATAACTTCTATCTATTT
34306736 TAATAAGTTATAT
131 TAATAAGTTATAT
34306749 AAGAAACTGACTATTTATATAAGGATAAAACTTGTAATCATACTATGCAAATAGATTTTAAAAAC
1 AAGAAACTGACTATTTATATAAGGATAAAACTTGTAATCATACTATGCAAATAGATTTTAAAAAC
* *
34306814 GAAAATAATATTTCATTTATTAGTAAAGGTTTTAATAGTCTAATAAATATAACTTCTATCTATTT
66 GAAAATAATATTTCATCTATTAGTAAAGGTTTTAACAGTCTAATAAATATAACTTCTATCTATTT
34306879 TAATAAGTTATAT
131 TAATAAGTTATAT
34306892 A
1 A
34306893 GTAAAGTTAA
Statistics
Matches: 137, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
143 137 1.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (143 bp):
AAGAAACTGACTATTTATATAAGGATAAAACTTGTAATCATACTATGCAAATAGATTTTAAAAAC
GAAAATAATATTTCATCTATTAGTAAAGGTTTTAACAGTCTAATAAATATAACTTCTATCTATTT
TAATAAGTTATAT
Found at i:34307397 original size:15 final size:17
Alignment explanation
Indices: 34307366--34307397 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
34307356 TTCTGAAAAT
34307366 TCTAGTAATAGTATAAA
1 TCTAGTAATAGTATAAA
34307383 TCTAG-AATA-TATAAA
1 TCTAGTAATAGTATAAA
34307398 AGTAACAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (17 bp):
TCTAGTAATAGTATAAA
Found at i:34310768 original size:59 final size:58
Alignment explanation
Indices: 34310675--34310924 Score: 301
Period size: 58 Copynumber: 4.3 Consensus size: 58
34310665 ACCCGAGGGC
* * *
34310675 AAAATGGTAA-TTTTGGTGAAATCGGGGTTGAAAATGGAATTTTAAAAGGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAA-GTTCAGGGGT
* * * * *
34310733 AAAATGGTATTTTTTGATGAAATCGAGGTTAAAAATAGAATTTGAAACA-TTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAA-AGTTCAGGGGT
* * *
34310791 AAAATGGTAATTTTTGGTAAAATCGAGGTT-AAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-AAAAGTTCAGGGGT
* * *
34310849 AAAACGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTC-GAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTA-AAAGTTCAG-GGGT
34310908 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
34310925 AAGTTTCGGG
Statistics
Matches: 164, Mismatches: 21, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
57 12 0.07
58 82 0.50
59 69 0.42
60 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGTTCAGGGGT
Found at i:34310876 original size:29 final size:29
Alignment explanation
Indices: 34310786--34310924 Score: 92
Period size: 30 Copynumber: 4.8 Consensus size: 29
34310776 GAAACATTTA
*
34310786 GGGGTAAAATGGTAATTTTTGGTAAAATC
1 GGGGTAAAATGGTAATTTTTGGTGAAATC
* *
34310815 GAGGTTAAAATGG-AA-TTTT-G-GAAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGGTGAAA---TC
*
34310844 GGGGTAAAACGGTAATTTTTGGTGAAATC
1 GGGGTAAAATGGTAATTTTTGGTGAAATC
* ** **
34310873 GGGGTTAAAAATGG-AATTTTAGAAG-GTTC
1 GGGG-T-AAAATGGTAATTTTTGGTGAAATC
34310902 GAGGGTAAAATGGTAATTTTTGG
1 G-GGGTAAAATGGTAATTTTTGG
34310925 AAGTTTCGGG
Statistics
Matches: 84, Mismatches: 14, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
26 3 0.04
27 1 0.01
28 20 0.24
29 23 0.27
30 26 0.31
31 7 0.08
32 4 0.05
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATC
Found at i:34311286 original size:161 final size:162
Alignment explanation
Indices: 34311075--34311385 Score: 525
Period size: 161 Copynumber: 1.9 Consensus size: 162
34311065 AATTGTAAAT
* **
34311075 CTTGAAAAATTCTTGGGCCAATTTTGTAATTAAGTAAAAGTTGATTTAGGGATTAAATTAAAACA
1 CTTGAAAAATGCTTGGGCCAATTTTGTAATTAAACAAAAGTTGATTTAGGGATTAAATTAAAACA
*
34311140 AATTAAAAATGTCAGGGACTAAATGCATAAATAAGCCAAAAA-TGACACGTGGCAGCCTCTGGTG
66 AATTAAAAATGTCAGGGACTAAATGCATAAATAAGCCAAAAAGTGACACATGGCAGCCTCTGGTG
*
34311204 CAATCAAACAGTCAAAGGACGAATTTATGAAC
131 CAATCAAACAATCAAAGGACGAATTTATGAAC
*
34311236 CTTGAAAAATGCTTGGGCCAATTTTGTAATTAAACAAAAGTTGATTTAGGGATTAAATTAAAATA
1 CTTGAAAAATGCTTGGGCCAATTTTGTAATTAAACAAAAGTTGATTTAGGGATTAAATTAAAACA
* * *
34311301 AATTAAAAATGTCAGGGACTAAATGCATAAATGAGCCAAAAAGTGACACATGGCAGTCTTTGGTG
66 AATTAAAAATGTCAGGGACTAAATGCATAAATAAGCCAAAAAGTGACACATGGCAGCCTCTGGTG
*
34311366 CAGTCAAACAATCAAAGGAC
131 CAATCAAACAATCAAAGGAC
34311386 TAAATCAAAA
Statistics
Matches: 139, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
161 102 0.73
162 37 0.27
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (162 bp):
CTTGAAAAATGCTTGGGCCAATTTTGTAATTAAACAAAAGTTGATTTAGGGATTAAATTAAAACA
AATTAAAAATGTCAGGGACTAAATGCATAAATAAGCCAAAAAGTGACACATGGCAGCCTCTGGTG
CAATCAAACAATCAAAGGACGAATTTATGAAC
Found at i:34311861 original size:12 final size:12
Alignment explanation
Indices: 34311844--34311912 Score: 81
Period size: 12 Copynumber: 6.0 Consensus size: 12
34311834 GTAAGCCGTC
*
34311844 CTTCTTTCTTCT
1 CTTCTTTCTTTT
*
34311856 CTTCTTT-TCTT
1 CTTCTTTCTTTT
34311867 CTTCTTT-TTTT
1 CTTCTTTCTTTT
34311878 CTTC-TTCTTTT
1 CTTCTTTCTTTT
*
34311889 ATTCTTTCTTTT
1 CTTCTTTCTTTT
*
34311901 ATTCTTTCTTTT
1 CTTCTTTCTTTT
34311913 TTCATTAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
10 2 0.04
11 23 0.45
12 26 0.51
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (12 bp):
CTTCTTTCTTTT
Found at i:34312167 original size:3 final size:3
Alignment explanation
Indices: 34312153--34312226 Score: 98
Period size: 3 Copynumber: 24.7 Consensus size: 3
34312143 CGTTTTTCTC
*
34312153 TTA TTT TTA TTA TTAA TGT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
34312199 TTA TTA TTA TTA TT- TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
34312227 TAATATTTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.05
3 57 0.90
4 2 0.03
5 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:34313117 original size:6 final size:6
Alignment explanation
Indices: 34313104--34313175 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
34313094 TTTAAATTGT
* ** *
34313104 TTTATAA TTTTAA TTTAAA TTTAAA TTT-AA GGTAAT TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
34313154 TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
34313176 ATCAATTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
4 4 0.08
5 3 0.06
6 36 0.69
7 3 0.06
8 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:34313132 original size:17 final size:16
Alignment explanation
Indices: 34313112--34313175 Score: 69
Period size: 17 Copynumber: 4.0 Consensus size: 16
34313102 GTTTTATAAT
34313112 TTTAATTTAAATTTAAA
1 TTTAA-TTAAATTTAAA
* *
34313129 TTTAAGGTAATTTTAAA
1 TTTAA-TTAAATTTAAA
34313146 --TAATTAAATTTAAA
1 TTTAATTAAATTTAAA
*
34313160 TTTAAATAAATTTAAA
1 TTTAATTAAATTTAAA
34313176 ATCAATTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 9 0.23
15 3 0.08
16 13 0.33
17 14 0.36
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTTAATTAAATTTAAA
Found at i:34313172 original size:31 final size:32
Alignment explanation
Indices: 34313118--34313182 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
34313108 TAATTTTAAT
* *
34313118 TTAAATTTAAATTTAAGGTAATTTTAAAT-AA
1 TTAAATTTAAATTTAAGATAATTTAAAATCAA
34313149 TTAAATTTAAATTTAA-ATAAATTTAAAATCAA
1 TTAAATTTAAATTTAAGAT-AATTTAAAATCAA
34313181 TT
1 TT
34313183 TAACCTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 1 0.03
31 25 0.83
32 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (32 bp):
TTAAATTTAAATTTAAGATAATTTAAAATCAA
Found at i:34313564 original size:76 final size:76
Alignment explanation
Indices: 34313474--34314114 Score: 906
Period size: 76 Copynumber: 8.7 Consensus size: 76
34313464 TGCTCTTCAG
* * *
34313474 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAGACGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
34313539 ACTTCAATTTC
66 ACTTCAATTTC
*
34313550 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTACTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
34313615 ACTTCAATTTC
66 ACTTCAATTTC
* *
34313626 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGTGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
34313691 ACTTCAATTTC
66 ACTTCAATTTC
** * * *
34313702 --AG----AGACTTGACATCCAGCTTTACTTCGATTTCAAGAGGATGGGAAACGATCTTG---TT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
*
34313758 -CTT--ACTTC
66 ACTTCAATTTC
* *
34313766 ------AAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGTGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
34313825 ACTTCAATTTC
66 ACTTCAATTTC
* *
34313836 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGTGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
34313901 ACTTCAATTTC
66 ACTTCAATTTC
** * * *
34313912 AGAGATAAAGACTTGACATCCAGCTTTACTTTAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
34313977 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
34313988 AGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
34314052 ACTTCAATTTC
66 ACTTCAATTTC
* *
34314063 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAA
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAA
34314115 TGATGTTGGT
Statistics
Matches: 510, Mismatches: 40, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
64 49 0.10
66 3 0.01
67 4 0.01
68 3 0.01
70 49 0.10
74 2 0.00
75 68 0.13
76 332 0.65
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
ACTTCAATTTC
Found at i:34314093 original size:151 final size:152
Alignment explanation
Indices: 34313766--34314114 Score: 567
Period size: 151 Copynumber: 2.3 Consensus size: 152
34313756 TTCTTACTTC
* *
34313766 AAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGTGAAATGATCTTGCTCTTACTTCA
1 AAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTTACTTCA
* *
34313831 ATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGTGAAATGATCTTG
66 ATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGTGAAAAGATCTTG
34313896 CTCTTACTTCAATTTCAGAGAT
131 CTCTTACTTCAATTTCAGAGAT
** * * *
34313918 AAAGACTTGACATCCAGCTTTACTTTAATTTCAAGAGGATGGGAAACGATCTTGCTCTTACTTCA
1 AAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTTACTTCA
*
34313983 ATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGATAG-GAAAAGATCTT
66 ATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT-GTGAAAAGATCTT
34314046 GCTCTTACTTCAATTTCAGAGAT
130 GCTCTTACTTCAATTTCAGAGAT
* *
34314069 AAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAA
1 AAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAA
34314115 TGATGTTGGT
Statistics
Matches: 179, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
151 95 0.53
152 84 0.47
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (152 bp):
AAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTTACTTCA
ATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGTGAAAAGATCTTG
CTCTTACTTCAATTTCAGAGAT
Found at i:34326300 original size:59 final size:59
Alignment explanation
Indices: 34326200--34326456 Score: 342
Period size: 58 Copynumber: 4.4 Consensus size: 59
34326190 TTTGGATACC
* * *
34326200 CGGGGGCAAAATGGTAA-TTTTGGTAAAATCAGGGTTGAAAATGGAATTTTAGAAGGTT
1 CGGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGGTT
* * * *
34326258 CGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAA-TTTGGAATGTT
1 CGGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGGTT
* * *
34326316 TGGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGGT-AAAATGGAATTTTAGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGGTT
* * * * *
34326374 -TGGGATAAAAACGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTT
1 CGGGGGT-AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGGTT
34326433 CGGGGGTAAAATGGTAATTTTTGG
1 CGGGGGTAAAATGGTAATTTTTGG
34326457 AAGTTTTGGG
Statistics
Matches: 171, Mismatches: 23, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
57 13 0.08
58 93 0.54
59 61 0.36
60 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.32
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGGTT
Found at i:34326467 original size:29 final size:29
Alignment explanation
Indices: 34326237--34326510 Score: 124
Period size: 30 Copynumber: 9.4 Consensus size: 29
34326227 ATCAGGGTTG
* *
34326237 AAAATGG-AA-TTTTAGAAGGTTCGGGGGT
1 AAAATGGTAATTTTTGGAA-GTTTGGGGGT
* * *
34326265 AAAATGGTAATTTTTGATGAA-ATCGGGGTT
1 AAAATGGTAATTTTTG--GAAGTTTGGGGGT
34326295 AAAAATGG-AA--TTTGGAATGTTTGGGGGT
1 -AAAATGGTAATTTTTGGAA-GTTTGGGGGT
** *
34326323 AAAATGGTAATTTTTGGTAAAATCGGGGGT
1 AAAATGGTAATTTTTGG-AAGTTTGGGGGT
* * *
34326353 AAAATGG-AATTTTAGAAAGTTT-GGGAT
1 AAAATGGTAATTTTTGGAAGTTTGGGGGT
* * * * *
34326380 AAAAACGGTAATTTTTGGTGAA-ATCGAGGTT
1 -AAAATGGTAATTTTT-G-GAAGTTTGGGGGT
* *
34326411 AAAAATGG-AA-TTTTAGAAGGTTCGGGGGT
1 -AAAATGGTAATTTTTGGAA-GTTTGGGGGT
*
34326440 AAAATGGTAATTTTTGGAAGTTTTGGGGT
1 AAAATGGTAATTTTTGGAAGTTTGGGGGT
* * * **
34326469 CAGAAT-GTAATTTTCTGTAATTTTGGGGCC
1 -AAAATGGTAATTTT-TGGAAGTTTGGGGGT
34326499 AAAAT-GTAATTT
1 AAAATGGTAATTT
34326511 CTAGACTGTT
Statistics
Matches: 187, Mismatches: 37, Indels: 43
0.70 0.14 0.16
Matches are distributed among these distances:
26 3 0.02
27 14 0.07
28 35 0.19
29 54 0.29
30 57 0.30
31 21 0.11
32 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTTGGGGGT
Found at i:34326955 original size:163 final size:162
Alignment explanation
Indices: 34326584--34327080 Score: 780
Period size: 163 Copynumber: 3.1 Consensus size: 162
34326574 AGGCATCCAG
** * * * * * *
34326584 CAGTCAAAGGATTAAATTATAAATCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAGTAAAAGT
1 CAGTCAAAGGAAGAATTTATGAACCTTGAAAAATGCTTGGGCCAATTTTGTAATTAAATAAAAGT
*
34326649 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGTATAAATAAGCC-AAA
66 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGCATAAATAAGCCAAAA
*
34326713 AATGACACGTGGCAGCCTCTGGTGCAGTCAAA
131 AATGACACATGGCAGCCTCTGGTGCAGTCAAA
* * * *
34326745 TAGTCAAAGGACGAATTTATGAACCTTAAAAAATGCTTGGGCCAATTTTGTAATTAAACAAAAGT
1 CAGTCAAAGGAAGAATTTATGAACCTTGAAAAATGCTTGGGCCAATTTTGTAATTAAATAAAAGT
*
34326810 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGCAGAAATAAGCCTAAA
66 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGCATAAATAAGCC-AAA
* *
34326875 AAATGACACTTGGCAGCCTCTGGTGCTGTCAAA
130 AAATGACACATGGCAGCCTCTGGTGCAGTCAAA
34326908 CAGTCAAAGGAAGAATTTATGAACCTTGAAAAATGCTTGGGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAAGGAAGAATTTATGAACCTTGAAAAATGCTTGGGCCAATTTTGTAATTAAATAAAAGT
* *
34326973 TGATTTAGGGATTAAATTAAAATAAATTAAAAATGTCAGGGACTAAATGCATAAATGAGCCAAAA
66 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGCATAAATAAGCCAAAA
* * *
34327038 AGTGACACATGGAAGTCTCTGGTGCAGTCAAA
131 AATGACACATGGCAGCCTCTGGTGCAGTCAAA
34327070 CAGTCAAAGGA
1 CAGTCAAAGGA
34327081 CTAAATCGAA
Statistics
Matches: 307, Mismatches: 27, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
161 113 0.37
162 42 0.14
163 152 0.50
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (162 bp):
CAGTCAAAGGAAGAATTTATGAACCTTGAAAAATGCTTGGGCCAATTTTGTAATTAAATAAAAGT
TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGCATAAATAAGCCAAAA
AATGACACATGGCAGCCTCTGGTGCAGTCAAA
Found at i:34327571 original size:14 final size:14
Alignment explanation
Indices: 34327542--34327608 Score: 81
Period size: 14 Copynumber: 5.1 Consensus size: 14
34327532 GCTGTCCTTC
*
34327542 TTTCTTC-TCTTCT
1 TTTCTTCTTCTTTT
34327555 TTTCTTCTTCTTTT
1 TTTCTTCTTCTTTT
34327569 TTTCTTCTTCTTTT
1 TTTCTTCTTCTTTT
34327583 TTTC-T-TTCTTTT
1 TTTCTTCTTCTTTT
*
34327595 ATTC-T-TTCTTTT
1 TTTCTTCTTCTTTT
34327607 TT
1 TT
34327609 CATTAATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
12 19 0.38
13 8 0.16
14 23 0.46
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCTTCTTCTTTT
Found at i:34327860 original size:3 final size:3
Alignment explanation
Indices: 34327846--34327903 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
34327836 CGTTTTTCTC
* * * *
34327846 TTA TTT TTA TTA TTA ATA TTA TTA TTA ATA TTA TTA TTA ATA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
34327893 TTA ATA TTA TT
1 TTA TTA TTA TT
34327904 TAATATTTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:34327865 original size:6 final size:6
Alignment explanation
Indices: 34327856--34327910 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
34327846 TTATTTTTAT
* * *
34327856 TATTAA TATTAT TATTAA TATTAT TATTAA TATT-T TATTAA TATT-A
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
34327902 T-TTAA TATT
1 TATTAA TATT
34327911 TCAACAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
4 2 0.05
5 8 0.20
6 30 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
TATTAA
Found at i:34327867 original size:12 final size:12
Alignment explanation
Indices: 34327852--34327903 Score: 97
Period size: 12 Copynumber: 4.4 Consensus size: 12
34327842 TCTCTTATTT
34327852 TTATTATTAATA
1 TTATTATTAATA
34327864 TTATTATTAATA
1 TTATTATTAATA
34327876 TTATTATTAATA
1 TTATTATTAATA
34327888 TT-TTATTAATA
1 TTATTATTAATA
34327899 TTATT
1 TTATT
34327904 TAATATTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.28
12 28 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:34328797 original size:6 final size:6
Alignment explanation
Indices: 34328782--34328889 Score: 75
Period size: 6 Copynumber: 18.2 Consensus size: 6
34328772 TTAAATTTGT
* **
34328782 TTTATAA TTTTAA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TTTAAGA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* *
34328831 --TAAA TTTAAA TTTTTAAA TTTAAA --TAAA TTTAAA ATT-AA TTTAACC
1 TTTAAA TTTAAA --TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
*
34328877 TTTAAA TTAAAA T
1 TTTAAA TTTAAA T
34328890 AAAAAGTCCA
Statistics
Matches: 80, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
4 5 0.06
5 10 0.12
6 50 0.62
7 9 0.11
8 6 0.08
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:34328802 original size:12 final size:12
Alignment explanation
Indices: 34328782--34328889 Score: 75
Period size: 11 Copynumber: 9.1 Consensus size: 12
34328772 TTAAATTTGT
*
34328782 TTTATAATTTTAA
1 TTTA-AATTTAAA
34328795 TTTAAATTTAAA
1 TTTAAATTTAAA
**
34328807 TTT-AAGGTAAA
1 TTTAAATTTAAA
34328818 TTTAAATTTAAGA
1 TTTAAATTTAA-A
34328831 --TAAATTTAAA
1 TTTAAATTTAAA
34328841 TTTTTAAATTTAAA
1 --TTTAAATTTAAA
34328855 --TAAATTTAAA
1 TTTAAATTTAAA
* *
34328865 ATT-AATTTAACC
1 TTTAAATTTAA-A
*
34328877 TTTAAATTAAAA
1 TTTAAATTTAAA
34328889 T
1 T
34328890 AAAAAGTCCA
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
10 11 0.14
11 25 0.33
12 19 0.25
13 11 0.14
14 10 0.13
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:34328817 original size:17 final size:17
Alignment explanation
Indices: 34328797--34328843 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
34328787 AATTTTAATT
*
34328797 TAAATTTAAATTTAAGG
1 TAAATTTAAATTTAAGA
34328814 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAGA
34328831 TAAATTTAAATTT
1 TAAATTTAAATTT
34328844 TTAAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTAAGA
Found at i:34328859 original size:35 final size:34
Alignment explanation
Indices: 34328820--34328892 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
34328810 AAGGTAAATT
* ** *
34328820 TAAATTTAAGATAAATTTAAATTTTTAAATTTAAA
1 TAAATTTAAAATAAATTT-AACCTTTAAATTAAAA
*
34328855 TAAATTTAAAATTAATTTAACCTTTAAATTAAAA
1 TAAATTTAAAATAAATTTAACCTTTAAATTAAAA
34328889 TAAA
1 TAAA
34328893 AAGTCCAAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (34 bp):
TAAATTTAAAATAAATTTAACCTTTAAATTAAAA
Found at i:34328862 original size:24 final size:25
Alignment explanation
Indices: 34328818--34328864 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
34328808 TTAAGGTAAA
34328818 TTTAAATTTAAGATAAATTTAAATT
1 TTTAAATTTAAGATAAATTTAAATT
34328843 TTTAAATTTAA-ATAAATTTAAA
1 TTTAAATTTAAGATAAATTTAAA
34328865 ATTAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTAAATTTAAGATAAATTTAAATT
Found at i:34328884 original size:42 final size:42
Alignment explanation
Indices: 34328793--34328869 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
34328783 TTATAATTTT
* *
34328793 AATTTAAA--TTTAAATTTAAGGTAAATTTAAATTTAAGATA
1 AATTTAAATTTTTAAATTTAAGATAAATTTAAAATTAAGATA
34328833 AATTTAAATTTTTAAATTTAA-ATAAATTTAAAATTAA
1 AATTTAAATTTTTAAATTTAAGATAAATTTAAAATTAA
34328870 TTTAACCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 8 0.24
41 14 0.42
42 11 0.33
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (42 bp):
AATTTAAATTTTTAAATTTAAGATAAATTTAAAATTAAGATA
Found at i:34330822 original size:31 final size:31
Alignment explanation
Indices: 34330754--34330834 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
34330744 GCATTAACTC
* * * * *
34330754 CAAGAAGGAAATTAGGCAAAGGCATTGATAT
1 CAAGAAAGATATTTGGCAAAGGCATTAATAG
34330785 CAAGAAAGATATTTGGCAAAGGCATTAATAG
1 CAAGAAAGATATTTGGCAAAGGCATTAATAG
* *
34330816 CCAGAAAGATATTTAGCAA
1 CAAGAAAGATATTTGGCAA
34330835 TAAGGATGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21
Consensus pattern (31 bp):
CAAGAAAGATATTTGGCAAAGGCATTAATAG
Found at i:34332447 original size:31 final size:31
Alignment explanation
Indices: 34332412--34332472 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
34332402 GAAATTAGAC
* *
34332412 AAAGGCATTGATATCAAGAAAGATATTTGGA
1 AAAGGCATTAATAGCAAGAAAGATATTTGGA
*
34332443 AAAGGCATTAATAGCTAGAAAGATATTTGG
1 AAAGGCATTAATAGCAAGAAAGATATTTGG
34332473 CAATAAGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (31 bp):
AAAGGCATTAATAGCAAGAAAGATATTTGGA
Found at i:34334073 original size:31 final size:31
Alignment explanation
Indices: 34334024--34334114 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
34334014 AGAAATAGAA
** * * *
34334024 GCATTAATTCCAAAAAAGAAATTAGGCAAAG
1 GCATTAATAGCAAGAAAGATATTTGGCAAAG
* *
34334055 GCATTGATATCAAGAAAGATATTTGGCAAAG
1 GCATTAATAGCAAGAAAGATATTTGGCAAAG
*
34334086 GCATTAATAGCCAGAAAGATATTTGGCAA
1 GCATTAATAGCAAGAAAGATATTTGGCAA
34334115 TAAGGATGGG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (31 bp):
GCATTAATAGCAAGAAAGATATTTGGCAAAG
Found at i:34341156 original size:31 final size:31
Alignment explanation
Indices: 34341079--34341168 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 31
34341069 GAAAAAGAAG
** * * *
34341079 CATTAATTCCAAGAAGGAAATTAGGCAAAGA
1 CATTAATAGCAAGAAAGATATTTGGCAAAGA
* * *
34341110 CATTGATATCAAGAAAGATATTTGGCAAAGG
1 CATTAATAGCAAGAAAGATATTTGGCAAAGA
*
34341141 CATTAATAGCCAGAAAGATATTTGGCAA
1 CATTAATAGCAAGAAAGATATTTGGCAA
34341169 TAAGGATGAG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.23
Consensus pattern (31 bp):
CATTAATAGCAAGAAAGATATTTGGCAAAGA
Found at i:34341555 original size:19 final size:19
Alignment explanation
Indices: 34341515--34341565 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
34341505 ATTAATTTTT
34341515 AAATTTTAAAAATTCATAA
1 AAATTTTAAAAATTCATAA
34341534 AAATTATTAAAAA-T-ATAA
1 AAATT-TTAAAAATTCATAA
* *
34341552 AAAATTTAATAATT
1 AAATTTTAAAAATT
34341566 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
19 6 0.21
20 7 0.25
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTTTAAAAATTCATAA
Found at i:34342184 original size:29 final size:30
Alignment explanation
Indices: 34342134--34342208 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
34342124 CCTCGTGTTT
* * **
34342134 TTATTTTGGTCACCCATTTTAAA-AATTTG
1 TTATTTTAGTCACTCATTTTAAATAAGCTG
34342163 TTATTTTAGTCACTC-TTATTAAATAAGCTG
1 TTATTTTAGTCACTCATT-TTAAATAAGCTG
34342193 TTAATTTTAGTCACTC
1 TT-ATTTTAGTCACTC
34342209 CCATTAGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.05
29 18 0.46
30 6 0.15
31 13 0.33
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (30 bp):
TTATTTTAGTCACTCATTTTAAATAAGCTG
Found at i:34342252 original size:31 final size:31
Alignment explanation
Indices: 34342160--34342255 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 31
34342150 TTTTAAAAAT
** *
34342160 TTGTT-ATTTTAGTCACTCTTATTAAATAAG
1 TTGTTAATTTTAGTCACTCCAATTAGATAAG
* *
34342190 CTGTTAATTTTAGTCACTCCCATTAGATAAG
1 TTGTTAATTTTAGTCACTCCAATTAGATAAG
*
34342221 TTGTTAATTTTAGCCACTCCAATTAGATAAG
1 TTGTTAATTTTAGTCACTCCAATTAGATAAG
34342252 TTGT
1 TTGT
34342256 CATTTTATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 4 0.07
31 54 0.93
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (31 bp):
TTGTTAATTTTAGTCACTCCAATTAGATAAG
Found at i:34343468 original size:28 final size:27
Alignment explanation
Indices: 34343428--34343483 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
34343418 AGAGGAACCA
* *
34343428 ACTTGGAAAAAAAGTAGTTTAGATACC
1 ACTTGGAAAAAAAGAAGTATAGATACC
* *
34343455 ACTTGTAATAAAAAGAAGTATAGGTACC
1 ACTTGGAA-AAAAAGAAGTATAGATACC
34343483 A
1 A
34343484 AAATAAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (27 bp):
ACTTGGAAAAAAAGAAGTATAGATACC
Found at i:34343844 original size:9 final size:9
Alignment explanation
Indices: 34343804--34343853 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
34343794 TTGAAATTAG
34343804 AAATATATA
1 AAATATATA
34343813 AAAGT-TATTA
1 AAA-TATA-TA
*
34343823 AAATTTA-A
1 AAATATATA
34343831 AAATATATA
1 AAATATATA
*
34343840 AAATAAATA
1 AAATATATA
34343849 AAATA
1 AAATA
34343854 ATTTATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 7 0.20
9 20 0.57
10 8 0.23
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (9 bp):
AAATATATA
Found at i:34346222 original size:32 final size:30
Alignment explanation
Indices: 34346151--34346223 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
34346141 TTTAAAATCC
* *
34346151 TATATTTTTATAATTTTTAAAGAATTAAAT
1 TATAATTTTATAATTTTTAAAGAATCAAAT
* *
34346181 TA-AATTTTTATTATTTTTAAAGGGAGTCAAAT
1 TATAA-TTTTATAATTTTTAAA--GAATCAAAT
34346213 TATAATTTTAT
1 TATAATTTTAT
34346224 CTTTAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 1 0.03
30 17 0.49
32 15 0.43
33 2 0.06
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (30 bp):
TATAATTTTATAATTTTTAAAGAATCAAAT
Found at i:34346494 original size:24 final size:24
Alignment explanation
Indices: 34346466--34346512 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
34346456 AAATTTAACT
*
34346466 TTTAATGTTTATTTTTTTGGTTAA
1 TTTAATGTTTATTTTTTTAGTTAA
*
34346490 TTTAATTTTTATTTTTTTAGTTA
1 TTTAATGTTTATTTTTTTAGTTA
34346513 CACCTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (24 bp):
TTTAATGTTTATTTTTTTAGTTAA
Found at i:34347353 original size:3 final size:3
Alignment explanation
Indices: 34347345--34347382 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
34347335 ATTAACATTC
34347345 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
34347383 TGTGAAACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:34348887 original size:15 final size:15
Alignment explanation
Indices: 34348867--34348897 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34348857 GATCTAAGGA
34348867 AAAATTAAAAAAAAT
1 AAAATTAAAAAAAAT
*
34348882 AAAATTAAAAGAAAT
1 AAAATTAAAAAAAAT
34348897 A
1 A
34348898 GAAAATAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAATTAAAAAAAAT
Found at i:34353157 original size:27 final size:25
Alignment explanation
Indices: 34353119--34353187 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 25
34353109 AATTGGACTC
* **
34353119 ATATAATATAAAATATTTTATTTCAAA
1 ATATAATTTAAAATAAATTATTT--AA
*
34353146 ATATAATTTAAAATAAATTATTTTA
1 ATATAATTTAAAATAAATTATTTAA
*
34353171 ATATAATTTAATATAAA
1 ATATAATTTAAAATAAA
34353188 AATAATTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 17 0.46
27 20 0.54
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATAATTTAAAATAAATTATTTAA
Found at i:34353228 original size:62 final size:62
Alignment explanation
Indices: 34353162--34353307 Score: 177
Period size: 62 Copynumber: 2.3 Consensus size: 62
34353152 TTTAAAATAA
* * *
34353162 ATTATTTTAATATAATTTA-ATATAAAAATAATTATATTAAGAATGTTACTAAATTATATATT
1 ATTATTTTAAT-TAAATTATATATAAAAATAATTATATTAAAAATATTACTAAATTATATATT
* * * * *
34353224 ATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATATTATTAAATTATTTATT
1 ATTATTTTAATTAAATTATATATAAAAATAATTATATTAAAAATATTACTAAATTATATATT
* *
34353286 ATCTTTTTTTATTAAATTATAT
1 AT-TATTTTAATTAAATTATAT
34353308 TCAATAACAA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
61 6 0.08
62 49 0.67
63 18 0.25
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (62 bp):
ATTATTTTAATTAAATTATATATAAAAATAATTATATTAAAAATATTACTAAATTATATATT
Found at i:34353325 original size:63 final size:62
Alignment explanation
Indices: 34353195--34353325 Score: 172
Period size: 63 Copynumber: 2.1 Consensus size: 62
34353185 AAAAATAATT
* * * * *
34353195 ATATTAAGAATGTTACTAAATTATATATTATTATTTTTATTAAATTATATTTAATAATAATT
1 ATATTAAAAATATTACTAAATTATATATTATTATTTTTATTAAATTATATTCAATAACAATC
* * *
34353257 ATATTAAAAATATTATTAAATTATTTATTATCTTTTTTTATTAAATTATATTCAATAACAATC
1 ATATTAAAAATATTACTAAATTATATATTAT-TATTTTTATTAAATTATATTCAATAACAATC
*
34353320 CTATTA
1 ATATTA
34353326 TATTTAATAG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
62 27 0.46
63 32 0.54
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (62 bp):
ATATTAAAAATATTACTAAATTATATATTATTATTTTTATTAAATTATATTCAATAACAATC
Found at i:34354817 original size:6 final size:6
Alignment explanation
Indices: 34354806--34354839 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
34354796 ATACTCACCG
34354806 GAACCA GAACCA GAACCA GAACCA GAACCA GAAC
1 GAACCA GAACCA GAACCA GAACCA GAACCA GAAC
34354840 TTCCCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.32, G:0.18, T:0.00
Consensus pattern (6 bp):
GAACCA
Found at i:34379415 original size:13 final size:13
Alignment explanation
Indices: 34379397--34379422 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34379387 AAGTAAAAAT
34379397 TATTCTGAATTGG
1 TATTCTGAATTGG
34379410 TATTCTGAATTGG
1 TATTCTGAATTGG
34379423 AGAGAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TATTCTGAATTGG
Found at i:34381208 original size:2 final size:2
Alignment explanation
Indices: 34381203--34381229 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34381193 ATATATATAT
34381203 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
34381230 ATGTATCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34390038 original size:16 final size:16
Alignment explanation
Indices: 34390014--34390044 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34390004 CAGTTTAATT
*
34390014 ATTCTTTTTAAATAAC
1 ATTCATTTTAAATAAC
34390030 ATTCATTTTAAATAA
1 ATTCATTTTAAATAA
34390045 AAATAAAGGA
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:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTCATTTTAAATAAC
Found at i:34393625 original size:14 final size:15
Alignment explanation
Indices: 34393606--34393638 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
34393596 GATTGTATTT
34393606 TATTAAA-TTTAAAA
1 TATTAAACTTTAAAA
34393620 TATTAAACTTTAAAA
1 TATTAAACTTTAAAA
34393635 -ATTA
1 TATTA
34393639 GTTTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TATTAAACTTTAAAA
Found at i:34401973 original size:139 final size:138
Alignment explanation
Indices: 34401693--34402113 Score: 734
Period size: 139 Copynumber: 3.0 Consensus size: 138
34401683 GTCATCATCC
*
34401693 ATTGCCATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
* * *
34401758 TGTTGTACAAATATTATGTTGCTTCCGATTTTGCATAACCATGTTTGCAGAAACTGTGTTTTGAG
66 TGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGAG
34401823 ACCCAAAT
131 ACCCAAAT
*
34401831 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGGGGTTCAATGTGTTGC
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
* *
34401896 TGATTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAAAAACTGTATTTTGA
66 TG-TTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
*
34401961 GACCTAAAT
130 GACCCAAAT
* *
34401970 ATTGACATTCTGTTAGTATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGT
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
34402035 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
66 T-GTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
34402100 GACCCAAAT
130 GACCCAAAT
34402109 ATTGA
1 ATTGA
34402114 GTGTTGCTTA
Statistics
Matches: 267, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
138 65 0.24
139 201 0.75
140 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.43
Consensus pattern (138 bp):
ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
TGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGAG
ACCCAAAT
Found at i:34402971 original size:25 final size:25
Alignment explanation
Indices: 34402937--34402985 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
34402927 AAAGTATATT
34402937 AGTTTAGGATTAAGAAATAAGACTC
1 AGTTTAGGATTAAGAAATAAGACTC
34402962 AGTTTAGGATTAAGAAATAAGACT
1 AGTTTAGGATTAAGAAATAAGACT
34402986 ACAAGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (25 bp):
AGTTTAGGATTAAGAAATAAGACTC
Found at i:34406715 original size:32 final size:29
Alignment explanation
Indices: 34406670--34406808 Score: 103
Period size: 26 Copynumber: 4.8 Consensus size: 29
34406660 CATATTTTAA
*
34406670 TAATA-ATTATATTAAAAATATAATTAAAT
1 TAATATATTTTATT-AAAATATAATTAAAT
* *
34406699 TATATATTATTTTATTAAATTAT-ATTTAA-
1 TA-ATA-TATTTTATTAAAATATAATTAAAT
*
34406728 TAATA-ATTATATTAAAATATAATTAAAT
1 TAATATATTTTATTAAAATATAATTAAAT
* *
34406756 TAATTAATATTTTTATTAAATTAT-ATTTAA-
1 TAA-T-ATA-TTTTATTAAAATATAATTAAAT
* *
34406786 TAATA-ATCTTATTAAAATTTAAT
1 TAATATATTTTATTAAAATATAAT
34406809 AAGAATAATC
Statistics
Matches: 88, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
26 24 0.27
27 8 0.09
28 7 0.08
29 6 0.07
30 12 0.14
31 12 0.14
32 19 0.22
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (29 bp):
TAATATATTTTATTAAAATATAATTAAAT
Found at i:34406803 original size:58 final size:58
Alignment explanation
Indices: 34406638--34406808 Score: 224
Period size: 58 Copynumber: 2.9 Consensus size: 58
34406628 TCTAATATTA
* *
34406638 TATATTATAATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATAATTAAAT
1 TATATAAT-ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAAT
*
34406699 TATATATTA-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
1 TATATAATATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
*
34406756 TA-ATTAATATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TATA-TAATATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
34406809 AAGAATAATC
Statistics
Matches: 101, Mismatches: 5, Indels: 11
0.86 0.04 0.09
Matches are distributed among these distances:
56 1 0.01
57 21 0.21
58 58 0.57
59 10 0.10
60 5 0.05
61 6 0.06
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (58 bp):
TATATAATATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
Found at i:34406933 original size:39 final size:44
Alignment explanation
Indices: 34406878--34406982 Score: 114
Period size: 46 Copynumber: 2.5 Consensus size: 44
34406868 TTTCTTATGC
*
34406878 TATTACAGCATC-ATTCCATT-CAACCAA-ACACAA-GAA-TA-T
1 TATTACAGC-TCTATTCCATTCCAACCAACAAACAATGAATTACT
*
34406917 TATTACAGCTCTATTCCATTCCAATCAACCAAACAATTGAATTACT
1 TATTACAGCTCTATTCCATTCCAACCAA-CAAACAA-TGAATTACT
*
34406963 GATTACAGCTCTATTCCATT
1 TATTACAGCTCTATTCCATT
34406983 ACAGCTCTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 2 0.04
39 17 0.31
40 6 0.11
42 5 0.09
44 3 0.05
45 2 0.04
46 20 0.36
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (44 bp):
TATTACAGCTCTATTCCATTCCAACCAACAAACAATGAATTACT
Found at i:34406981 original size:46 final size:44
Alignment explanation
Indices: 34406889--34406982 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
34406879 ATTACAGCAT
* *
34406889 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
34406933 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
34406979 CATT
1 CATT
34406983 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:34406985 original size:16 final size:16
Alignment explanation
Indices: 34406964--34407018 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
34406954 TGAATTACTG
34406964 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
34406980 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTCC
* *
34406996 ATTACACCTCTATTCT
1 ATTACAGCTCTATTCC
34407012 ATTACAG
1 ATTACAG
34407019 TGAACCAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:34410857 original size:22 final size:21
Alignment explanation
Indices: 34410827--34410870 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
34410817 ATGAAATTAT
*
34410827 TAAAAAAATATTTTTTTACAAA
1 TAAAAAAATATTATTTTA-AAA
*
34410849 TAAACAAATATTATTTTAAAA
1 TAAAAAAATATTATTTTAAAA
34410870 T
1 T
34410871 TATTTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAAAATATTATTTTAAAA
Found at i:34411533 original size:24 final size:22
Alignment explanation
Indices: 34411506--34411551 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
34411496 TGTTCCTTTA
34411506 AATTAATTATTAATCAAAATAATT
1 AATTAATT-TTAAT-AAAATAATT
*
34411530 AATTAATTTTAATTAAATAATT
1 AATTAATTTTAATAAAATAATT
34411552 TACATAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 5 0.24
24 8 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTAATTTTAATAAAATAATT
Found at i:34413526 original size:7 final size:7
Alignment explanation
Indices: 34413514--34413541 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
34413504 AAACCTTTGG
34413514 CTATTTA
1 CTATTTA
34413521 CTATTTA
1 CTATTTA
34413528 CTATTTA
1 CTATTTA
34413535 CTATTTA
1 CTATTTA
34413542 AGTCCTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (7 bp):
CTATTTA
Found at i:34420465 original size:15 final size:16
Alignment explanation
Indices: 34420436--34420467 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
34420426 TATTTCATTC
34420436 TTAATTTTAGTTCACA
1 TTAATTTTAGTTCACA
34420452 TTAATTTT-GTTCACA
1 TTAATTTTAGTTCACA
34420467 T
1 T
34420468 CTTCGTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAATTTTAGTTCACA
Found at i:34426136 original size:20 final size:20
Alignment explanation
Indices: 34426113--34426150 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34426103 TAATACAAAA
* *
34426113 ATTAAATTAATTCATTTATT
1 ATTAAATGAATTAATTTATT
34426133 ATTAAATGAATTAATTTA
1 ATTAAATGAATTAATTTA
34426151 ATTAAATCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTAAATGAATTAATTTATT
Found at i:34429371 original size:16 final size:16
Alignment explanation
Indices: 34429302--34429363 Score: 97
Period size: 16 Copynumber: 3.9 Consensus size: 16
34429292 CATTTGGTTC
34429302 GCTGTAATGGAATAAA
1 GCTGTAATGGAATAAA
*
34429318 GCTGTAATAGAATAAA
1 GCTGTAATGGAATAAA
* *
34429334 GCTGTAATGTAATAGA
1 GCTGTAATGGAATAAA
34429350 GCTGTAATGGAATA
1 GCTGTAATGGAATA
34429364 TGACTGTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (16 bp):
GCTGTAATGGAATAAA
Found at i:34429613 original size:57 final size:58
Alignment explanation
Indices: 34429543--34429694 Score: 191
Period size: 57 Copynumber: 2.6 Consensus size: 58
34429533 TTGTTAAATT
* * * *
34429543 TTAATAAAATTATTATTAAATATAATTTAATAAAAAAATAAACATTTTAATCATATT-
1 TTAATATAATTATTATTAAATATAATTTAATAAAAAAATAAACAATTTAATAACATTC
* * * *
34429600 TTAACT-TGATTATTATTAAATATAATTTAATAAAACAATATATAATTTAATAACATTC
1 TTAA-TATAATTATTATTAAATATAATTTAATAAAAAAATAAACAATTTAATAACATTC
*
34429658 TTAATATAATTATTATTAAAATATAAATTAATAAAAA
1 TTAATATAATTATTATT-AAATATAATTTAATAAAAA
34429695 TCATAATATA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
57 48 0.60
58 15 0.19
59 17 0.21
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (58 bp):
TTAATATAATTATTATTAAATATAATTTAATAAAAAAATAAACAATTTAATAACATTC
Found at i:34439574 original size:2 final size:2
Alignment explanation
Indices: 34439567--34439597 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34439557 GCAGGCCATT
34439567 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
34439598 TTATTTTTTC
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:34449743 original size:6 final size:6
Alignment explanation
Indices: 34449732--34449770 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
34449722 TGATCAAAAT
* * *
34449732 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
34449771 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:34451331 original size:17 final size:17
Alignment explanation
Indices: 34451309--34451345 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
34451299 GATTGAGTTT
34451309 GTGGCAAGATGTTTGAC
1 GTGGCAAGATGTTTGAC
*
34451326 GTGGCATGATGTTTGAC
1 GTGGCAAGATGTTTGAC
34451343 GTG
1 GTG
34451346 CCAACAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.11, G:0.38, T:0.32
Consensus pattern (17 bp):
GTGGCAAGATGTTTGAC
Found at i:34455925 original size:16 final size:16
Alignment explanation
Indices: 34455882--34455928 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
34455872 CACTAAAATT
34455882 GAATAAGGTTGTAATG
1 GAATAAGGTTGTAATG
*
34455898 GAAT-TGGATTGTAATG
1 GAATAAGG-TTGTAATG
*
34455914 GAATAAAGTTGTAAT
1 GAATAAGGTTGTAAT
34455929 CAGTAATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.08
16 23 0.88
17 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (16 bp):
GAATAAGGTTGTAATG
Found at i:34455974 original size:16 final size:16
Alignment explanation
Indices: 34455890--34455974 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
34455880 TTGAATAAGG
*
34455890 TTGTAATGGAATTGGA
1 TTGTAATGGAATTGAA
*
34455906 TTGTAATGGAA-TAAA
1 TTGTAATGGAATTGAA
* *
34455921 GTTGTAATCAGTAATTCAA
1 -TTGTAAT--GGAATTGAA
*
34455940 TTGT-TTGG--TTGAA
1 TTGTAATGGAATTGAA
*
34455953 -TGTAATGGAATAGAA
1 TTGTAATGGAATTGAA
34455968 TTGTAAT
1 TTGTAAT
34455975 AGTATTATTG
Statistics
Matches: 52, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
12 3 0.06
13 7 0.13
15 7 0.13
16 24 0.46
17 1 0.02
18 7 0.13
19 3 0.06
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (16 bp):
TTGTAATGGAATTGAA
Found at i:34455974 original size:46 final size:44
Alignment explanation
Indices: 34455907--34456000 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 44
34455897 GGAATTGGAT
*
34455907 TGTAATGGAATAAAGTTGTAATCAGTAATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAAAGTTGTAAT-AGT-ATT-AATGTGTTTGATTGAA
*
34455953 TGTAATGGAATAGAA-TTGTAATAGTATTATTGTGTTTGATTGAA
1 TGTAATGGAATA-AAGTTGTAATAGTATTAATGTGTTTGATTGAA
34455997 TGTA
1 TGTA
34456001 GAGGTGTTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
43 2 0.05
44 18 0.41
45 3 0.07
46 19 0.43
47 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.41
Consensus pattern (44 bp):
TGTAATGGAATAAAGTTGTAATAGTATTAATGTGTTTGATTGAA
Found at i:34456724 original size:61 final size:61
Alignment explanation
Indices: 34456659--34456794 Score: 182
Period size: 61 Copynumber: 2.2 Consensus size: 61
34456649 TATTTAAATA
* * * *
34456659 TAATAGGATTATTATTGAATATAATTTAATAAAAATGATAGTAAATAATTTAATCATATTT
1 TAATAGAATTATTATTAAATATAATTTAATAAAAATAATAATAAATAATTTAATCATATTT
* * * *
34456720 TAATATAATTATTATTAAATATAATTTAATAAAAATAATAATATATAATTTAATAACATTCT
1 TAATAGAATTATTATTAAATATAATTTAATAAAAATAATAATAAATAATTTAATCATATT-T
*
34456782 TAATATAATTATT
1 TAATAGAATTATT
34456795 TTTATATTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
61 52 0.79
62 14 0.21
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (61 bp):
TAATAGAATTATTATTAAATATAATTTAATAAAAATAATAATAAATAATTTAATCATATTT
Found at i:34456751 original size:24 final size:23
Alignment explanation
Indices: 34456730--34456791 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
34456720 TAATATAATT
34456730 ATTATTAAATATAATTTAATAAA
1 ATTATTAAATATAATTTAATAAA
* * *
34456753 AATAATAATATATAATTTAATAAC
1 ATTATTAA-ATATAATTTAATAAA
*
34456777 ATTCTT-AATATAATT
1 ATTATTAAATATAATT
34456792 ATTTTTATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 8 0.25
23 7 0.22
24 17 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTATTAAATATAATTTAATAAA
Found at i:34456884 original size:30 final size:30
Alignment explanation
Indices: 34456790--34456889 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
34456780 CTTAATATAA
*
34456790 TTATTTTTATATTAAATTATATTGAAATATT
1 TTATTTTTATATTAAAATAT-TTGAAATATT
* * **
34456821 TTA-TTTTAAATT-ATAT-TTTGAAATAAA
1 TTATTTTTATATTAAAATATTTGAAATATT
* *
34456848 AT-TTTTTATATTAAAATATTTCAAATATT
1 TTATTTTTATATTAAAATATTTGAAATATT
34456877 TTATTTTTATATT
1 TTATTTTTATATT
34456890 TTTTAATAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
27 17 0.32
28 4 0.08
29 11 0.21
30 18 0.34
31 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (30 bp):
TTATTTTTATATTAAAATATTTGAAATATT
Found at i:34457704 original size:25 final size:25
Alignment explanation
Indices: 34457670--34457721 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
34457660 CGAGTGAAAG
34457670 TAAAATTCTTACGTACATATAGCCA
1 TAAAATTCTTACGTACATATAGCCA
34457695 TAAAATTCTTACGTACATATAGCCA
1 TAAAATTCTTACGTACATATAGCCA
34457720 TA
1 TA
34457722 CACACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (25 bp):
TAAAATTCTTACGTACATATAGCCA
Found at i:34466079 original size:15 final size:16
Alignment explanation
Indices: 34466059--34466091 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
34466049 TGATACTTTT
*
34466059 AATAAAAT-TTAGTTA
1 AATAAAATATTAATTA
34466074 AATAAAATATTAATTA
1 AATAAAATATTAATTA
34466090 AA
1 AA
34466092 CCGAGTAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATAAAATATTAATTA
Found at i:34467255 original size:40 final size:41
Alignment explanation
Indices: 34467170--34467277 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 41
34467160 CGCAGCGCCA
* * * * **
34467170 CTAAAGATCAGAGTATTAGTGGCACTTATAGAAAAGCGTCG
1 CTAAAGGTCAGAGTATTAGCGACGCTTATAGAAAAGCACCG
*
34467211 CTAAAGGTCAGAGCATTAGCGACGCTTAT-GAAAAGCACCG
1 CTAAAGGTCAGAGTATTAGCGACGCTTATAGAAAAGCACCG
* *
34467251 CTAAAGGTTAGAGTATCAGCGACGCTT
1 CTAAAGGTCAGAGTATTAGCGACGCTT
34467278 TCTCATAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 33 0.58
41 24 0.42
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (41 bp):
CTAAAGGTCAGAGTATTAGCGACGCTTATAGAAAAGCACCG
Found at i:34469581 original size:20 final size:20
Alignment explanation
Indices: 34469528--34469581 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
34469518 CTCCAGTGAG
* * *
34469528 ACTTCTATCGCTAAAACTCA
1 ACTTCTACCGATACAACTCA
*
34469548 ACTTCTACCGATACAACTCT
1 ACTTCTACCGATACAACTCA
34469568 ACTTCTACCGATAC
1 ACTTCTACCGATAC
34469582 CTTGAAGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.30
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCA
Found at i:34472529 original size:43 final size:43
Alignment explanation
Indices: 34472476--34472709 Score: 202
Period size: 42 Copynumber: 5.3 Consensus size: 43
34472466 CTTGTTAATG
* ** *
34472476 TTAGTGGCGTTTGTGGAAAAAATGCCGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTCT
* * * *
34472519 TTAGCGGCGTTTGT-GAGAAAGTGTCGTTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTCT
* * * * *
34472561 TTAGCGACATTTGTGGGAAAAGCGCCGCTAAAGAACATGGTCT
1 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTCT
* *
34472604 TTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTG-GAAAA-AG-CGC------CGCTAAAGACCATGTTCT
* * *
34472656 TTAGCGGCATTTGTGG-AGAAGCGCCGCTAAAGACTATGTTCT
1 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTCT
*
34472698 ATAGCGGCGTTT
1 TTAGCGGCGTTT
34472710 TTTCTCATAA
Statistics
Matches: 152, Mismatches: 29, Indels: 21
0.75 0.14 0.10
Matches are distributed among these distances:
42 62 0.41
43 46 0.30
44 4 0.03
45 1 0.01
46 3 0.02
48 3 0.02
49 1 0.01
50 2 0.01
51 1 0.01
52 29 0.19
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:34472669 original size:52 final size:51
Alignment explanation
Indices: 34472586--34472687 Score: 150
Period size: 52 Copynumber: 2.0 Consensus size: 51
34472576 GGAAAAGCGC
*
34472586 CGCTAAAGAACATGGTCTTTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAGT
1 CGCTAAAGAACATGGTCTTTAGCAGCATTTGTG-GAAAAGCGCCGCTAAAGT
* * * *
34472638 CGCTAAAGACCATGTTCTTTAGCGGCATTTGTGGAGAAGCGCCGCTAAAG
1 CGCTAAAGAACATGGTCTTTAGCAGCATTTGTGGAAAAGCGCCGCTAAAG
34472688 ACTATGTTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 16 0.36
52 29 0.64
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (51 bp):
CGCTAAAGAACATGGTCTTTAGCAGCATTTGTGGAAAAGCGCCGCTAAAGT
Found at i:34478325 original size:6 final size:6
Alignment explanation
Indices: 34478314--34478342 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
34478304 GTGTAAAATT
34478314 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
34478343 TTAATGAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:34502879 original size:21 final size:22
Alignment explanation
Indices: 34502839--34502880 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
34502829 AAATGTGCCT
*
34502839 TAATAATTATAACACCAATAAA
1 TAATAATTATAACAACAATAAA
*
34502861 TAAT-ATTATAACAATAATAA
1 TAATAATTATAACAACAATAA
34502881 TGCCTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (22 bp):
TAATAATTATAACAACAATAAA
Found at i:34507820 original size:19 final size:19
Alignment explanation
Indices: 34507776--34507812 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
34507766 ATTTTATTTT
34507776 ATTTTTAATATTTATTTAA
1 ATTTTTAATATTTATTTAA
*
34507795 ATTTTTAGTATTTATTTA
1 ATTTTTAATATTTATTTA
34507813 TTTATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTTAATATTTATTTAA
Found at i:34517785 original size:31 final size:30
Alignment explanation
Indices: 34517725--34517782 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
34517715 GCATGTGACA
34517725 AAGATTTAAGCCAAACAGACAAAAAAAATT
1 AAGATTTAAGCCAAACAGACAAAAAAAATT
34517755 AAGATTTAAGCCAAACAGACAAAAAAAA
1 AAGATTTAAGCCAAACAGACAAAAAAAA
34517783 ATTTAATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.62, C:0.14, G:0.10, T:0.14
Consensus pattern (30 bp):
AAGATTTAAGCCAAACAGACAAAAAAAATT
Found at i:34520595 original size:25 final size:26
Alignment explanation
Indices: 34520536--34520595 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
34520526 CATTCATTAG
34520536 TTTCCTTCACTTATTAAAGCGAACCA
1 TTTCCTTCACTTATTAAAGCGAACCA
*** * *
34520562 TTGATTTCACTTATTCAAGC-AATCA
1 TTTCCTTCACTTATTAAAGCGAACCA
34520587 TTTCCTTCA
1 TTTCCTTCA
34520596 TTGAAGTTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (26 bp):
TTTCCTTCACTTATTAAAGCGAACCA
Found at i:34526917 original size:34 final size:34
Alignment explanation
Indices: 34526874--34526943 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
34526864 TAAAGACACA
*
34526874 CATTTTACAATTTATTTAATTTAGTTCCTAAACC
1 CATTTTACAATTTATTTAATTTAGTCCCTAAACC
34526908 CATTTTACAATTTATTTAATTTAGTCCCTAAACC
1 CATTTTACAATTTATTTAATTTAGTCCCTAAACC
34526942 CA
1 CA
34526944 GGACAAACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.44
Consensus pattern (34 bp):
CATTTTACAATTTATTTAATTTAGTCCCTAAACC
Found at i:34531912 original size:24 final size:24
Alignment explanation
Indices: 34531884--34531932 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
34531874 ATTTTGTTGA
34531884 AGATGGTAATTGAATCGATGAGTG
1 AGATGGTAATTGAATCGATGAGTG
34531908 AGATGGTAATTGAATCGATGAGTG
1 AGATGGTAATTGAATCGATGAGTG
34531932 A
1 A
34531933 CTAAGTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.33, T:0.29
Consensus pattern (24 bp):
AGATGGTAATTGAATCGATGAGTG
Found at i:34534990 original size:57 final size:57
Alignment explanation
Indices: 34534897--34535045 Score: 187
Period size: 57 Copynumber: 2.6 Consensus size: 57
34534887 TAACCAATTT
* * * *
34534897 ATACC-ATTTTCACAT-ATCTCATCTCAATGTCATATTCTATCATTAATCCATAAGATC
1 ATACCAATTTT-ACATAAT-TCATTTCAAAGTCATATTCCATCATCAATCCATAAGATC
* *
34534954 ATACCAATTTTACATAATTCATTTCAAAGTCCTATTCCATTATCAATCCATAAGATC
1 ATACCAATTTTACATAATTCATTTCAAAGTCATATTCCATCATCAATCCATAAGATC
*
34535011 ATACCAATTTCACATAATTCATTTCAATA-TCATAT
1 ATACCAATTTTACATAATTCATTTCAA-AGTCATAT
34535046 CAAATTGGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
57 73 0.90
58 8 0.10
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (57 bp):
ATACCAATTTTACATAATTCATTTCAAAGTCATATTCCATCATCAATCCATAAGATC
Found at i:34550175 original size:21 final size:21
Alignment explanation
Indices: 34550149--34550199 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
34550139 ACTGAATTTG
**
34550149 AAACTTTAAATTTTAAATCCT
1 AAACTTTAAACATTAAATCCT
* *
34550170 AAACTTTATACATTAAATCTT
1 AAACTTTAAACATTAAATCCT
34550191 AAACTTTAA
1 AAACTTTAA
34550200 GATTCAAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
AAACTTTAAACATTAAATCCT
Found at i:34554015 original size:241 final size:242
Alignment explanation
Indices: 34553509--34554218 Score: 772
Period size: 241 Copynumber: 2.9 Consensus size: 242
34553499 CATAAATGTG
*
34553509 TGCTTAAAATAACATACAATAAATAATGAAATGTATAGCTTGAAACTAATTAATAATAACACATA
1 TGCTTAAAATAACATATAATAAATAATGAAATG--TA---TGAAACTAATTAATAATAACACATA
* ** * *
34553574 AAATATGTACAATATT-AAATTTTAAAAAATTAGATTAAATCATTTATCATTTTGTTGTCATCAG
61 AAATATGTACGATATTAAAATTTT-AAAAATTAGATTAAATTGTTTATCATTGTGTTGTCATCAA
* * * *
34553638 TTTTGAGTCGATGTTGAGTTAACTTGTGACACCAGCTCAATCAAATACATTATTA-ATACTAGAA
125 TCTTGAGTCGGTGTTGAGTTAACTTGTGACACCAACTCAATCAAATACATTAATATATACTAGAA
* * ** * * ** *
34553702 ATCCTATCATACGTGTATGCATTTGGAAACCACAAATTTAAAATACAAATGTG
190 ATACTATCACACGCATATGCATGTGGAAACAACAAATTTAAAATACAAAAATA
*
34553755 TGCTTAAAATAACATATAATAAATAATGAAATGTATGAAACTAATTAATAATAACACATGAAATA
1 TGCTTAAAATAACATATAATAAATAATGAAATGTATGAAACTAATTAATAATAACACATAAAATA
* *
34553820 TGTACGATATTAAAATTTTAAAAATTAGATTAAATTGTTTATGAATGTGTTGTCATCAATCTTGA
66 TGTACGATATTAAAATTTTAAAAATTAGATTAAATTGTTTATCATTGTGTTGTCATCAATCTTGA
* * *
34553885 GTCGGTGTCGAGTTAACTTGTGACACCAACTCAATCAAATAAATTAATATATACTAGAAATATTA
131 GTCGGTGTTGAGTTAACTTGTGACACCAACTCAATCAAATACATTAATATATACTAGAAATACTA
* *
34553950 TCACACGCATATG-AGTGTGGGAACAACAAATTTAGAATACAAAAATA
196 TCACACGCATATGCA-TGTGGAAACAACAAATTTAAAATACAAAAATA
* ** * ** **
34553997 TGTTTAAAA-ATA-ATATAATAAATGGTGTAACATATGGTTTGAAACTGGTTAATAATAACATGT
1 TGCTTAAAATA-ACATATAATAAATAATG--A-A-AT-GTATGAAACTAATTAATAATAACACAT
** * * ** * *
34554060 TCAATATGCATGATATTAAAATTAAAAAAACATAGATTAAATTGTTTATCATTGTGTTGTTATCA
60 AAAATATGTACGATATTAAAATTTTAAAAA-TTAGATTAAATTGTTTATCATTGTGTTGTCATCA
* * *
34554125 ATCTTGAGTCGGTGTTGAGTTAATTTTTTTGACACAAACTCAATCAAATACATTAATAT-TCACT
124 ATCTTGAGTCGGTGTTGAGTTAA--CTTGTGACACCAACTCAATCAAATACATTAATATAT-ACT
* *
34554189 AGAAAT-CT-T-TCACGCGTATGCATGTGGAAA
186 AGAAATACTATCACACGCATATGCATGTGGAAA
34554219 TCATGGACTT
Statistics
Matches: 396, Mismatches: 54, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
241 137 0.35
242 64 0.16
243 1 0.00
244 3 0.01
245 2 0.01
246 94 0.24
247 54 0.14
248 2 0.01
249 39 0.10
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (242 bp):
TGCTTAAAATAACATATAATAAATAATGAAATGTATGAAACTAATTAATAATAACACATAAAATA
TGTACGATATTAAAATTTTAAAAATTAGATTAAATTGTTTATCATTGTGTTGTCATCAATCTTGA
GTCGGTGTTGAGTTAACTTGTGACACCAACTCAATCAAATACATTAATATATACTAGAAATACTA
TCACACGCATATGCATGTGGAAACAACAAATTTAAAATACAAAAATA
Found at i:34560527 original size:18 final size:19
Alignment explanation
Indices: 34560506--34560551 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
34560496 TAATATCGTA
34560506 TATATTATTAATTAAT-TT
1 TATATTATTAATTAATATT
* *
34560524 TATATAATT-TTTAATATT
1 TATATTATTAATTAATATT
34560542 TATATT-TTAA
1 TATATTATTAA
34560552 ATTTATGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTATTAATTAATATT
Found at i:34566686 original size:21 final size:21
Alignment explanation
Indices: 34566665--34566706 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34566655 ATTATTGATT
34566665 AATTAATTTAAATAATTAATTA
1 AATT-ATTTAAATAATTAATTA
*
34566687 AATTATTTACATAATTAATT
1 AATTATTTAAATAATTAATT
34566707 TCTAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTATTTAAATAATTAATTA
Found at i:34571756 original size:41 final size:41
Alignment explanation
Indices: 34571602--34571755 Score: 139
Period size: 41 Copynumber: 3.8 Consensus size: 41
34571592 CTATCTTTCG
* * ** * * *
34571602 CCATGTTGGTGTTGCAGAGTTCAGAGTTGATCCTCCCCTCG
1 CCATGTTGGTATTACAGAGTTTGGAATTGATCCTCCCTTCA
* **
34571643 CCATGTTGGTATTACAGAGTTCGGAATTGGCCCTCCCTT-A
1 CCATGTTGGTATTACAGAGTTTGGAATTGATCCTCCCTTCA
* * ** * *
34571683 CCGTGTTGGTGTTGTAGAGTTTGGAATTGATCTTCCCTTCT
1 CCATGTTGGTATTACAGAGTTTGGAATTGATCCTCCCTTCA
* *
34571724 CCATGTTGGTATTACAAAGTTTGGAAGTGATC
1 CCATGTTGGTATTACAGAGTTTGGAATTGATC
34571756 TATCTCTCGT
Statistics
Matches: 89, Mismatches: 23, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 31 0.35
41 58 0.65
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (41 bp):
CCATGTTGGTATTACAGAGTTTGGAATTGATCCTCCCTTCA
Found at i:34572609 original size:19 final size:20
Alignment explanation
Indices: 34572585--34572624 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
34572575 AATAAAAAGG
*
34572585 AAAAAAATA-AAACTTTTGA
1 AAAAAAATATAAAATTTTGA
34572604 AAAAAAATATAAAATTTTGA
1 AAAAAAATATAAAATTTTGA
34572624 A
1 A
34572625 CTAACATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAAAATATAAAATTTTGA
Found at i:34573973 original size:25 final size:23
Alignment explanation
Indices: 34573945--34573990 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
34573935 GTTGGATCCA
34573945 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
34573970 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
34573991 CCCTAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:34589981 original size:30 final size:29
Alignment explanation
Indices: 34589915--34589981 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
34589905 AAATTTTAAA
*
34589915 TTAATAAA-GATAAAATTTCACTTTAACCC
1 TTAA-AAATGATAAAATTTCAATTTAACCC
* * *
34589944 CTAAAAATGATAAAATTTTAATTTAATCCT
1 TTAAAAATGATAAAATTTCAATTTAA-CCC
34589974 TTAAAAAT
1 TTAAAAAT
34589982 TATACTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 3 0.10
29 19 0.61
30 9 0.29
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (29 bp):
TTAAAAATGATAAAATTTCAATTTAACCC
Found at i:34590203 original size:25 final size:26
Alignment explanation
Indices: 34590175--34590225 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
34590165 AGTTGTTTTG
* *
34590175 TTTTTATAATT-TTAATTTTTTAATA
1 TTTTTATAATTATAAATTTTTGAATA
34590200 TTTTTATAATTATAAATTTTTGAATA
1 TTTTTATAATTATAAATTTTTGAATA
34590226 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTTATAATTATAAATTTTTGAATA
Found at i:34590876 original size:5 final size:5
Alignment explanation
Indices: 34590866--34590891 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34590856 CACATCGCCC
34590866 TCTCA TCTCA TCTCA TCTCA TCTCA T
1 TCTCA TCTCA TCTCA TCTCA TCTCA T
34590892 GTTCTTAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.42
Consensus pattern (5 bp):
TCTCA
Found at i:34597781 original size:20 final size:20
Alignment explanation
Indices: 34597758--34597806 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
34597748 TAATTTTTTA
34597758 AAATAATTATTAAAAATCAT
1 AAATAATTATTAAAAATCAT
**
34597778 AAATAATTATTAAAAATTGT
1 AAATAATTATTAAAAATCAT
34597798 AAATAATTA
1 AAATAATTA
34597807 ACAAATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATAATTATTAAAAATCAT
Found at i:34598094 original size:41 final size:40
Alignment explanation
Indices: 34598025--34598157 Score: 143
Period size: 41 Copynumber: 3.3 Consensus size: 40
34598015 CCACTGGTCC
*
34598025 ATAAT-TTTTAAATAA-ATTTACATTTTTTAATAA-TTATTT
1 ATAATATTTTAAATAATATTT-TATTTTTTAATAACTT-TTT
34598064 ATAATATTTTAAATAATATTTTATTCTTTTAATAACTTTTT
1 ATAATATTTTAAATAATATTTTATT-TTTTAATAACTTTTT
* *
34598105 ACAA-ATTTTAAATAATGTTTTATAATTTTTAATAACTTTTT
1 ATAATATTTTAAATAATATTTTAT--TTTTTAATAACTTTTT
34598146 -TACA-ATTTTAAA
1 ATA-ATATTTTAAA
34598158 ACATTTTGGC
Statistics
Matches: 83, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
39 5 0.06
40 32 0.39
41 43 0.52
42 3 0.04
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.55
Consensus pattern (40 bp):
ATAATATTTTAAATAATATTTTATTTTTTAATAACTTTTT
Found at i:34598146 original size:21 final size:20
Alignment explanation
Indices: 34598048--34598154 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 20
34598038 AAATTTACAT
*
34598048 TTTTTAATAATTATTTATAA
1 TTTTTAATAATTTTTTATAA
*
34598068 TATTTTAAATAATATTTTAT--
1 T-TTTT-AATAATTTTTTATAA
* *
34598088 TCTTTTAATAACTTTTTACAAA
1 T-TTTTAATAATTTTTTA-TAA
* *
34598110 TTTTAAATAATGTTTTATAA
1 TTTTTAATAATTTTTTATAA
*
34598130 TTTTTAATAACTTTTTTACAA
1 TTTTTAATAA-TTTTTTATAA
34598151 TTTT
1 TTTT
34598155 AAAACATTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
19 10 0.15
20 17 0.25
21 29 0.43
22 12 0.18
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (20 bp):
TTTTTAATAATTTTTTATAA
Found at i:34598154 original size:10 final size:10
Alignment explanation
Indices: 34598046--34598154 Score: 51
Period size: 10 Copynumber: 10.5 Consensus size: 10
34598036 ATAAATTTAC
34598046 ATTTTTTAATA
1 ATTTTTT-ATA
*
34598057 ATTATTTATA
1 ATTTTTTATA
*
34598067 ATATTTTAAATA
1 AT-TTTT-TATA
*
34598079 ATATTTTAT-
1 ATTTTTTATA
*
34598088 -TCTTTTAATA
1 AT-TTTTTATA
* *
34598098 ACTTTTTACAA
1 ATTTTTTA-TA
**
34598109 ATTTTAAATA
1 ATTTTTTATA
*
34598119 ATGTTTTATA
1 ATTTTTTATA
*
34598129 ATTTTTAATA
1 ATTTTTTATA
*
34598139 ACTTTTTTACA
1 A-TTTTTTATA
34598150 ATTTT
1 ATTTT
34598155 AAAACATTTT
Statistics
Matches: 70, Mismatches: 21, Indels: 15
0.66 0.20 0.14
Matches are distributed among these distances:
8 1 0.01
9 5 0.07
10 33 0.47
11 26 0.37
12 5 0.07
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.58
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:34598164 original size:20 final size:20
Alignment explanation
Indices: 34598100--34598164 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
34598090 TTTTAATAAC
34598100 TTTTTACAAATTTTAAATA-AT
1 TTTTTAC-AATTTTAAA-ACAT
* *
34598121 GTTTTATAATTTTTAATAAC-T
1 TTTTTACAA-TTTTAA-AACAT
34598142 TTTTTACAATTTTAAAACAT
1 TTTTTACAATTTTAAAACAT
34598162 TTT
1 TTT
34598165 GGCAATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
19 3 0.08
20 12 0.33
21 20 0.56
22 1 0.03
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTTACAATTTTAAAACAT
Found at i:34600193 original size:15 final size:16
Alignment explanation
Indices: 34600173--34600202 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34600163 CTTGTCTATT
34600173 GATTTTTT-TATTTTG
1 GATTTTTTATATTTTG
34600188 GATTTTTTATATTTT
1 GATTTTTTATATTTT
34600203 AATAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (16 bp):
GATTTTTTATATTTTG
Found at i:34610497 original size:21 final size:21
Alignment explanation
Indices: 34610473--34610528 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
34610463 GTTATATGCT
*
34610473 TTGTATAGGTAGAATCCATAC
1 TTGTATCGGTAGAATCCATAC
34610494 TTGTATCGGTAGAATCCATAC
1 TTGTATCGGTAGAATCCATAC
34610515 TTGTATCGGTAGAA
1 TTGTATCGGTAGAA
34610529 CTATCACAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (21 bp):
TTGTATCGGTAGAATCCATAC
Found at i:34612280 original size:22 final size:21
Alignment explanation
Indices: 34612236--34612282 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
34612226 TATTTAAATT
* * *
34612236 TAATAATATTATTTATTATAA
1 TAATAATAATATATATTACAA
34612257 TAATAATAAATATATATTACAA
1 TAATAAT-AATATATATTACAA
34612279 TAAT
1 TAAT
34612283 TGTTTTATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATAATAATATATATTACAA
Found at i:34612763 original size:45 final size:48
Alignment explanation
Indices: 34612713--34612809 Score: 130
Period size: 45 Copynumber: 2.1 Consensus size: 48
34612703 ATTTCTCAAC
* *
34612713 AAATTAAAAATAAATTAATAA-T-TA-AATACTTTTAA-AATAATAACA
1 AAATTAAAAATAAAATAATAATTATACAATA-TTTAAATAATAATAACA
*
34612758 AAATTAACAATAAAATAATAATTATACAATATTTAAATAATAATAACA
1 AAATTAAAAATAAAATAATAATTATACAATATTTAAATAATAATAACA
34612806 AAAT
1 AAAT
34612810 AGTAACATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
45 19 0.42
46 1 0.02
47 7 0.16
48 18 0.40
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (48 bp):
AAATTAAAAATAAAATAATAATTATACAATATTTAAATAATAATAACA
Found at i:34614857 original size:138 final size:138
Alignment explanation
Indices: 34614688--34614962 Score: 469
Period size: 138 Copynumber: 2.0 Consensus size: 138
34614678 AGGCTGCTTG
*
34614688 GGAATCATGCTCTTTCACAAAATCTTCATCATCATTAAAAGCTGCCTGGAAATCATGCTTGTCAA
1 GGAATCATGCTCTTTCACAAAATCTTCATCATCATTAAAAGCTACCTGGAAATCATGCTTGTCAA
* * *
34614753 ACAGGGAATCCAGACATCGATCATCTGAAACCACTAATGACCTCGCTTTCTCTGTCAAAGTGGTT
66 ACAGGGAATCCAGACATCGATCATCTGAAACCACTAATGACCTCACTTCCTCTGCCAAAGTGGTT
34614818 TTGACACA
131 TTGACACA
* *
34614826 GGAATCATGCTCTTTCACACAATCTTCATCATCATTAAAGGCTACCTGGAAATCATGCTTGTCAA
1 GGAATCATGCTCTTTCACAAAATCTTCATCATCATTAAAAGCTACCTGGAAATCATGCTTGTCAA
* * *
34614891 ACAGGGAATCCGGACATCGCTCATCTGAAACCATTAATGACCTCACTTCCTCTGCCAAAGTGGTT
66 ACAGGGAATCCAGACATCGATCATCTGAAACCACTAATGACCTCACTTCCTCTGCCAAAGTGGTT
34614956 TTGACAC
131 TTGACAC
34614963 TCTCTTTATC
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
138 128 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (138 bp):
GGAATCATGCTCTTTCACAAAATCTTCATCATCATTAAAAGCTACCTGGAAATCATGCTTGTCAA
ACAGGGAATCCAGACATCGATCATCTGAAACCACTAATGACCTCACTTCCTCTGCCAAAGTGGTT
TTGACACA
Found at i:34616138 original size:21 final size:21
Alignment explanation
Indices: 34616112--34616153 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34616102 GCCGCTTGAA
* *
34616112 TTTTGATGGATCCATATTGCC
1 TTTTGAAGGATCCACATTGCC
*
34616133 TTTTGAAGGATTCACATTGCC
1 TTTTGAAGGATCCACATTGCC
34616154 ATCAAATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (21 bp):
TTTTGAAGGATCCACATTGCC
Found at i:34618075 original size:46 final size:47
Alignment explanation
Indices: 34617982--34618096 Score: 125
Period size: 46 Copynumber: 2.6 Consensus size: 47
34617972 ATAATCACGG
** *
34617982 TTAGGATATTATTATGCGATATTATTCTTTAGTAATTTAATTTTTAA
1 TTAGGATATTATTATGCGATATTATTCTTTAACAATTTAATTCTTAA
* * *
34618029 -TAGGATATTATTATGTGATATTA-TCTCTTAACAGTTTGATTCTTAA
1 TTAGGATATTATTATGCGATATTATTCT-TTAACAATTTAATTCTTAA
34618075 TTA-GATATTA-TA-G-GATATTATT
1 TTAGGATATTATTATGCGATATTATT
34618097 ATGGGATATT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
43 7 0.12
44 2 0.03
45 5 0.08
46 43 0.73
47 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.50
Consensus pattern (47 bp):
TTAGGATATTATTATGCGATATTATTCTTTAACAATTTAATTCTTAA
Found at i:34618098 original size:13 final size:13
Alignment explanation
Indices: 34618080--34618109 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34618070 CTTAATTAGA
34618080 TATTATAGGATAT
1 TATTATAGGATAT
*
34618093 TATTATGGGATAT
1 TATTATAGGATAT
34618106 TATT
1 TATT
34618110 TTTTAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (13 bp):
TATTATAGGATAT
Found at i:34627948 original size:35 final size:35
Alignment explanation
Indices: 34627902--34627972 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
34627892 ACCTTGCTCT
* *
34627902 CGCACTATTCCTCTTGTCGCCTTGAAACCGACTTC
1 CGCACCATTCCTCTAGTCGCCTTGAAACCGACTTC
34627937 CGCACCATTCCTCTAGTCGCCTTGAAACCGACTTC
1 CGCACCATTCCTCTAGTCGCCTTGAAACCGACTTC
34627972 C
1 C
34627973 TTCAAGACGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.18, C:0.39, G:0.14, T:0.28
Consensus pattern (35 bp):
CGCACCATTCCTCTAGTCGCCTTGAAACCGACTTC
Found at i:34648754 original size:20 final size:20
Alignment explanation
Indices: 34648717--34648754 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34648707 CTCGAATTAG
*
34648717 AATCTCTAAAAATCAGCTGT
1 AATCTCTAAAAATAAGCTGT
*
34648737 AATCTCTAAAGATAAGCT
1 AATCTCTAAAAATAAGCT
34648755 ATTCAATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (20 bp):
AATCTCTAAAAATAAGCTGT
Found at i:34651070 original size:237 final size:237
Alignment explanation
Indices: 34650645--34651117 Score: 865
Period size: 237 Copynumber: 2.0 Consensus size: 237
34650635 ACAGAAGAGG
* * *
34650645 GTGTTATCTCTTCATTTTTAATAATCTCCCCCTGAAGAGATGGTTGTGATGAATAAAAGTAGGGC
1 GTGTCATCTCTTCATTTTTAATAATCTCCCCCTCAAGAGATGGTTGTGATGAAGAAAAGTAGGGC
34650710 TTATACTCACGAAATGTTACATCCATACTTACATAATACTTTCTAGATGGTGGATGATAACATTT
66 TTATACTCACGAAATGTTACATCCATACTTACATAATACTTTCTAGATGGTGGATGATAACATTT
* *
34650775 GTAACCCTTCTGTGTGGGAGAGTATCCAATGAAAACACATTTGTCTGCTCGAGGATCCAGTTTGC
131 GTAACCCTTCTGTGTGGGAGAGTATCCAATGAAAACACATTTCTCTGCTCGAGGATCCAATTTGC
34650840 TCCCATGTCGAAGATGGACGAAGCAAACACAACCAAAAACCA
196 TCCCATGTCGAAGATGGACGAAGCAAACACAACCAAAAACCA
*
34650882 GTGTCATCTTTTCATTTTTAATAATCTCCCCCTCAAGAGATGGTTGTGATGAAGAAAAGTAGGGC
1 GTGTCATCTCTTCATTTTTAATAATCTCCCCCTCAAGAGATGGTTGTGATGAAGAAAAGTAGGGC
* *
34650947 TTATACTTACGAAATGTTACATCCATACTTACATAATACTTTTTAGATGGTGGATGATAACATTT
66 TTATACTCACGAAATGTTACATCCATACTTACATAATACTTTCTAGATGGTGGATGATAACATTT
*
34651012 GTAACCCTTTTGTGTGGGAGAGTATCCAATGAAAACACATTTCTCTGCTCGAGGATCCAATTTGC
131 GTAACCCTTCTGTGTGGGAGAGTATCCAATGAAAACACATTTCTCTGCTCGAGGATCCAATTTGC
34651077 TCCCATGTCGAAGATGGACGAAGCAAACACAACCAAAAACC
196 TCCCATGTCGAAGATGGACGAAGCAAACACAACCAAAAACC
34651118 TTCAATGAAA
Statistics
Matches: 227, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
237 227 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (237 bp):
GTGTCATCTCTTCATTTTTAATAATCTCCCCCTCAAGAGATGGTTGTGATGAAGAAAAGTAGGGC
TTATACTCACGAAATGTTACATCCATACTTACATAATACTTTCTAGATGGTGGATGATAACATTT
GTAACCCTTCTGTGTGGGAGAGTATCCAATGAAAACACATTTCTCTGCTCGAGGATCCAATTTGC
TCCCATGTCGAAGATGGACGAAGCAAACACAACCAAAAACCA
Found at i:34664937 original size:236 final size:236
Alignment explanation
Indices: 34664518--34665214 Score: 1227
Period size: 236 Copynumber: 3.0 Consensus size: 236
34664508 TTATTTTTTA
* * * *
34664518 ACACCGACAAAAATCGAGTCGTTATAAGGGTCTTGACTTCTTGAAGTCTTTGGTAATAATAAGCA
1 ACACCAACAAAAATCGAGTCGTTACAAGGGTTTTGACATCTTGAAGTCTTTGGTAATAATAAGCA
* * *
34664583 AAAAGGAAAAAAAAAATAAAAACTAGCAATAATAGGGAGAAACCCTGAAAGAGGAAATAAGAGAT
66 AAATGGAAAAAAAAAATAAAAACTAGCAATAACAGGGAGAAACCCTGAAAGAGGAAATAAGAAAT
* *
34664648 TGGACAGGAATTTTTTAGTAAGCAGCATTGCGTTGAATTTGTCATTTGTTAAAAATATTCTGGGA
131 TGGACAGGAATTTCTTAGAAAGCAGCATTGCGTTGAATTTGTCATTTGTTAAAAATATTCTGGGA
*
34664713 AGATTGAAAATCCTGCTAGCAATCAACAAGCCGTATTTTCG
196 AGACTGAAAATCCTGCTAGCAATCAACAAGCCGTATTTTCG
34664754 ACACCAACAAAAATCGAGTCGTTACAAGGGTTTTGACATCTTGAAGTCTTTGGTAATAATAAGCA
1 ACACCAACAAAAATCGAGTCGTTACAAGGGTTTTGACATCTTGAAGTCTTTGGTAATAATAAGCA
*
34664819 AAATGGAAAAAAAAAATAAAAACTAGCAATAACAGGGAGAAACCTTGAAAGAGGAAATAAGAAAT
66 AAATGGAAAAAAAAAATAAAAACTAGCAATAACAGGGAGAAACCCTGAAAGAGGAAATAAGAAAT
* *
34664884 TGGACAGAAATTTCTTAGAAAGTAGCATTGCGTTGAATTTGTCATTTGTTAAAAATATTCTGGGA
131 TGGACAGGAATTTCTTAGAAAGCAGCATTGCGTTGAATTTGTCATTTGTTAAAAATATTCTGGGA
34664949 AGACTGAAAATCCTGCTAGCAATCAACAAGCCGTATTTTCG
196 AGACTGAAAATCCTGCTAGCAATCAACAAGCCGTATTTTCG
* *
34664990 ACACCAACAAAAGTCGAGTCGTTACAAGGGTTTTAACATCTTGAAGTCTTTGGTAATAATAAGCA
1 ACACCAACAAAAATCGAGTCGTTACAAGGGTTTTGACATCTTGAAGTCTTTGGTAATAATAAGCA
34665055 AAATGGAAAAAAAAAATAAAAACTAGCAATAACAGGGAGAAACCCTGAAAGAGGAAATAAGAAAT
66 AAATGGAAAAAAAAAATAAAAACTAGCAATAACAGGGAGAAACCCTGAAAGAGGAAATAAGAAAT
* *
34665120 TTGACGGGAATTTCTTAGAAAGCAGCATTGCGTT-AATTTGTCATTTGTTAAAAATATTCTGGGA
131 TGGACAGGAATTTCTTAGAAAGCAGCATTGCGTTGAATTTGTCATTTGTTAAAAATATTCTGGGA
34665184 AGACTGAAAATCCTG-TAGCAATCAACAAGCC
196 AGACTGAAAATCCTGCTAGCAATCAACAAGCC
34665215 TAGTACGTGG
Statistics
Matches: 441, Mismatches: 20, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
234 16 0.04
235 45 0.10
236 380 0.86
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (236 bp):
ACACCAACAAAAATCGAGTCGTTACAAGGGTTTTGACATCTTGAAGTCTTTGGTAATAATAAGCA
AAATGGAAAAAAAAAATAAAAACTAGCAATAACAGGGAGAAACCCTGAAAGAGGAAATAAGAAAT
TGGACAGGAATTTCTTAGAAAGCAGCATTGCGTTGAATTTGTCATTTGTTAAAAATATTCTGGGA
AGACTGAAAATCCTGCTAGCAATCAACAAGCCGTATTTTCG
Found at i:34665397 original size:17 final size:17
Alignment explanation
Indices: 34665375--34665408 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34665365 ATGTTCCACA
34665375 GTTGATTTTCATCTGTT
1 GTTGATTTTCATCTGTT
*
34665392 GTTGATTTTCATTTGTT
1 GTTGATTTTCATCTGTT
34665409 TTATGAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.18, T:0.62
Consensus pattern (17 bp):
GTTGATTTTCATCTGTT
Found at i:34670166 original size:4 final size:4
Alignment explanation
Indices: 34670157--34670181 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34670147 GAGAGCAAAG
34670157 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
34670182 TGAGAGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:34675414 original size:12 final size:12
Alignment explanation
Indices: 34675399--34675429 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34675389 ATATTTATAA
*
34675399 TTAATATTATTT
1 TTAATAATATTT
34675411 TTAATAATATTT
1 TTAATAATATTT
34675423 TTAATAA
1 TTAATAA
34675430 AAATAAAAAG
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTAATAATATTT
Found at i:34681476 original size:30 final size:31
Alignment explanation
Indices: 34681441--34681523 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 31
34681431 CCCCGATTTC
34681441 ACCAAAAATTACCATTTTACACC-CAAACTTT
1 ACCAAAAATTACCATTTTACACCTC-AACTTT
* ** *
34681472 -CC-AAAATT-TCATTTTTTACCTCAATTTT
1 ACCAAAAATTACCATTTTACACCTCAACTTT
34681500 ACCAAAAATTACCATTTTAC-CCTC
1 ACCAAAAATTACCATTTTACACCTC
34681524 GGATGTCCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
28 14 0.34
29 9 0.22
30 12 0.29
31 6 0.15
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (31 bp):
ACCAAAAATTACCATTTTACACCTCAACTTT
Done.