Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 195 of 196
Found at i:58382221 original size:11 final size:11
Alignment explanation
Indices: 58382168--58382301 Score: 83
Period size: 11 Copynumber: 12.7 Consensus size: 11
58382158 TTTTTTAATG
58382168 TTAAAATATTT
1 TTAAAATATTT
* *
58382179 TTTACATACTTT
1 TTAAAATA-TTT
58382191 TT-AAAT-TTT
1 TTAAAATATTT
**
58382200 TTTTAA-A-TT
1 TTAAAATATTT
58382209 TTAAAATATTT
1 TTAAAATATTT
58382220 TTAAAATACTTTTT
1 TTAAAATA---TTT
**
58382234 TTTTAAT-TTT
1 TTAAAATATTT
*
58382244 TTTAAA-A--T
1 TTAAAATATTT
58382252 TTAAAATATTT
1 TTAAAATATTT
58382263 TTAAAATACTTT
1 TTAAAATA-TTT
58382275 TTAAAAT-TTT
1 TTAAAATATTT
58382285 TT-AAA-ATTT
1 TTAAAATATTT
58382294 TTAAAATA
1 TTAAAATA
58382302 AAAATGGGCC
Statistics
Matches: 97, Mismatches: 10, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
8 6 0.06
9 20 0.21
10 19 0.20
11 29 0.30
12 15 0.15
14 8 0.08
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTAAAATATTT
Found at i:58382276 original size:31 final size:30
Alignment explanation
Indices: 58382242--58382301 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
58382232 TTTTTTAATT
58382242 TTTTTAAAA-TTTAAAATATTTTTAAAATAC
1 TTTTTAAAATTTTAAAA-ATTTTTAAAATAC
*
58382272 TTTTTAAAATTTTTTAAAATTTTTAAAATA
1 TTTTTAAAA-TTTTAAAAATTTTTAAAATA
58382302 AAAATGGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 9 0.33
31 12 0.44
32 6 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTTTAAAATTTTAAAAATTTTTAAAATAC
Found at i:58387579 original size:23 final size:23
Alignment explanation
Indices: 58387534--58387579 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
58387524 TTCTTAATTA
*
58387534 TATTTTTATTTATTAATTGTTTT
1 TATTTTTATCTATTAATTGTTTT
*
58387557 TATTTTTATACTATTTATT-TTTT
1 TATTTTTAT-CTATTAATTGTTTT
58387580 AGAATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (23 bp):
TATTTTTATCTATTAATTGTTTT
Found at i:58388611 original size:8 final size:8
Alignment explanation
Indices: 58388598--58388631 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
58388588 AAACTTATAG
58388598 GAAAAAAA
1 GAAAAAAA
58388606 GAAAAAAA
1 GAAAAAAA
58388614 GAAAAAAA
1 GAAAAAAA
58388622 -AAAGAAAA
1 GAAA-AAAA
58388630 GA
1 GA
58388632 GAGGCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 3 0.12
8 20 0.83
9 1 0.04
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:58399233 original size:15 final size:15
Alignment explanation
Indices: 58399215--58399261 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
58399205 AAATTTGGAA
*
58399215 TTTAGTTTTTGTATT
1 TTTAGTTTTTTTATT
**
58399230 TTTA-TTTTTTTAAAA
1 TTTAGTTTTTTT-ATT
58399245 TTTAGTTTTTTTATT
1 TTTAGTTTTTTTATT
58399260 TT
1 TT
58399262 AGATTTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 6 0.24
15 12 0.48
16 7 0.28
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTAGTTTTTTTATT
Found at i:58399234 original size:30 final size:30
Alignment explanation
Indices: 58399192--58399261 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
58399182 CTTTAAGTAG
**
58399192 TTGTATTTTTTATAAATTTGGAATTTAGTTT
1 TTGTA-TTTTTATAAATTTAAAATTTAGTTT
***
58399223 TTGTATTTTTATTTTTTTAAAATTTAGTTT
1 TTGTATTTTTATAAATTTAAAATTTAGTTT
*
58399253 TTTTATTTT
1 TTGTATTTT
58399262 AGATTTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (30 bp):
TTGTATTTTTATAAATTTAAAATTTAGTTT
Found at i:58404385 original size:13 final size:13
Alignment explanation
Indices: 58404364--58404435 Score: 59
Period size: 13 Copynumber: 5.9 Consensus size: 13
58404354 AAAGGCCTCA
*
58404364 AATAGAATAACAT
1 AATATAATAACAT
58404377 AATATAATAACA-
1 AATATAATAACAT
58404389 AAT-TAACTTAACAT
1 AATATAA--TAACAT
*
58404403 CATATAATAAC--
1 AATATAATAACAT
58404414 AA-AT--TAACAT
1 AATATAATAACAT
58404424 AATATAATAACA
1 AATATAATAACA
58404436 AATTATATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 18
0.69 0.04 0.26
Matches are distributed among these distances:
8 4 0.09
10 4 0.09
11 6 0.13
12 3 0.06
13 25 0.53
14 2 0.04
15 3 0.06
ACGTcount: A:0.60, C:0.11, G:0.01, T:0.28
Consensus pattern (13 bp):
AATATAATAACAT
Found at i:58404395 original size:21 final size:21
Alignment explanation
Indices: 58404371--58404440 Score: 86
Period size: 21 Copynumber: 3.1 Consensus size: 21
58404361 TCAAATAGAA
58404371 TAACATAATATAATAACAAATTAACT
1 TAACATAATATAATAAC--A--AA-T
*
58404397 TAACATCATATAATAACAAAT
1 TAACATAATATAATAACAAAT
58404418 TAACATAATATAATAACAAAT
1 TAACATAATATAATAACAAAT
58404439 TA
1 TA
58404441 TATTATGGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 23 0.55
22 2 0.05
24 1 0.02
26 16 0.38
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (21 bp):
TAACATAATATAATAACAAAT
Found at i:58404401 original size:26 final size:26
Alignment explanation
Indices: 58404370--58404432 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
58404360 CTCAAATAGA
58404370 ATAACATAATATAATAACAAATTAAC
1 ATAACATAATATAATAACAAATTAAC
* *
58404396 TTAACATCATATAATAACAAATTAAC
1 ATAACATAATATAATAACAAATTAAC
*
58404422 ATAATATAATA
1 ATAACATAATA
58404433 ACAAATTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (26 bp):
ATAACATAATATAATAACAAATTAAC
Found at i:58404445 original size:26 final size:25
Alignment explanation
Indices: 58404371--58404445 Score: 95
Period size: 26 Copynumber: 3.1 Consensus size: 25
58404361 TCAAATAGAA
58404371 TAACATAATATAATAACAAATTAACT
1 TAACATAATATAATAACAAATTAA-T
*
58404397 TAACATCATATAATAAC--A--AAT
1 TAACATAATATAATAACAAATTAAT
58404418 TAACATAATATAATAACAAATTATAT
1 TAACATAATATAATAACAAATTA-AT
58404444 TA
1 TA
58404446 TGGCATAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
21 17 0.40
22 2 0.05
23 1 0.02
24 1 0.02
25 1 0.02
26 20 0.48
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (25 bp):
TAACATAATATAATAACAAATTAAT
Found at i:58410548 original size:242 final size:242
Alignment explanation
Indices: 58410123--58410612 Score: 980
Period size: 242 Copynumber: 2.0 Consensus size: 242
58410113 TAAAGATCAA
58410123 GGTTTAACATATCTAATAGTGGAAAATGAAATACATATACACGCATTGTGCAAATTCCTAATTAC
1 GGTTTAACATATCTAATAGTGGAAAATGAAATACATATACACGCATTGTGCAAATTCCTAATTAC
58410188 TAGTTGAAACCATAAATGTTTTGCTAATATATATAGGTAACAAGCATCGTTCTGCATCGGTAAAA
66 TAGTTGAAACCATAAATGTTTTGCTAATATATATAGGTAACAAGCATCGTTCTGCATCGGTAAAA
58410253 AATTGGTTCCAATGAAAATCTAGAAGCTATAGAACATTGGGAATGGTTATCTAGGAAAAGATGCA
131 AATTGGTTCCAATGAAAATCTAGAAGCTATAGAACATTGGGAATGGTTATCTAGGAAAAGATGCA
58410318 GCTTCAGAATCTAAGCACAGAATGTTCTCCTATATGATCCGAGTGTT
196 GCTTCAGAATCTAAGCACAGAATGTTCTCCTATATGATCCGAGTGTT
58410365 GGTTTAACATATCTAATAGTGGAAAATGAAATACATATACACGCATTGTGCAAATTCCTAATTAC
1 GGTTTAACATATCTAATAGTGGAAAATGAAATACATATACACGCATTGTGCAAATTCCTAATTAC
58410430 TAGTTGAAACCATAAATGTTTTGCTAATATATATAGGTAACAAGCATCGTTCTGCATCGGTAAAA
66 TAGTTGAAACCATAAATGTTTTGCTAATATATATAGGTAACAAGCATCGTTCTGCATCGGTAAAA
58410495 AATTGGTTCCAATGAAAATCTAGAAGCTATAGAACATTGGGAATGGTTATCTAGGAAAAGATGCA
131 AATTGGTTCCAATGAAAATCTAGAAGCTATAGAACATTGGGAATGGTTATCTAGGAAAAGATGCA
58410560 GCTTCAGAATCTAAGCACAGAATGTTCTCCTATATGATCCGAGTGTT
196 GCTTCAGAATCTAAGCACAGAATGTTCTCCTATATGATCCGAGTGTT
58410607 GGTTTA
1 GGTTTA
58410613 TCAAACCAGA
Statistics
Matches: 248, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
242 248 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (242 bp):
GGTTTAACATATCTAATAGTGGAAAATGAAATACATATACACGCATTGTGCAAATTCCTAATTAC
TAGTTGAAACCATAAATGTTTTGCTAATATATATAGGTAACAAGCATCGTTCTGCATCGGTAAAA
AATTGGTTCCAATGAAAATCTAGAAGCTATAGAACATTGGGAATGGTTATCTAGGAAAAGATGCA
GCTTCAGAATCTAAGCACAGAATGTTCTCCTATATGATCCGAGTGTT
Found at i:58419564 original size:31 final size:29
Alignment explanation
Indices: 58419487--58419567 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
58419477 GAATTAGAAC
* *
58419487 AAATCAAAATTTAATGTATAAAATTGCACA
1 AAATC-AAAGTTAATGTATAAAATTACACA
*
58419517 AAATCAAAGTTAATGTATACAATTACACA
1 AAATCAAAGTTAATGTATAAAATTACACA
*
58419546 TTAAATCATAA-TTCATGTATAA
1 --AAATCA-AAGTTAATGTATAA
58419568 TTTTAGGATG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 21 0.49
30 5 0.12
31 15 0.35
32 2 0.05
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (29 bp):
AAATCAAAGTTAATGTATAAAATTACACA
Found at i:58433296 original size:31 final size:31
Alignment explanation
Indices: 58433261--58433334 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
58433251 GTTACAAAAT
*
58433261 AGTCATTGAACT-ATTCAAAAGTTTTCATTTA
1 AGTCACTGAACTAATTCAAAA-TTTTCATTTA
* * * *
58433292 AGTCACTAAACTAATTGAATATTTTTATTTA
1 AGTCACTGAACTAATTCAAAATTTTCATTTA
58433323 AGTCACTGAACT
1 AGTCACTGAACT
58433335 GTTAAGTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 30 0.83
32 6 0.17
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (31 bp):
AGTCACTGAACTAATTCAAAATTTTCATTTA
Found at i:58437528 original size:24 final size:25
Alignment explanation
Indices: 58437501--58437556 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
58437491 AGTTAAGGAT
*
58437501 TTAACAAA-TATATTATA-AAATGAA
1 TTAACAAATTA-ATTATATAAATAAA
*
58437525 TTAAAAAATTAATTATATAAATAAA
1 TTAACAAATTAATTATATAAATAAA
58437550 TGTAACA
1 T-TAACA
58437557 CTTGCTATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 13 0.50
25 9 0.35
26 4 0.15
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.34
Consensus pattern (25 bp):
TTAACAAATTAATTATATAAATAAA
Found at i:58449443 original size:13 final size:13
Alignment explanation
Indices: 58449427--58449451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58449417 AAAATAAAAA
58449427 ATAATCATTTAAT
1 ATAATCATTTAAT
58449440 ATAATCATTTAA
1 ATAATCATTTAA
58449452 AAGTAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATCATTTAAT
Found at i:58450530 original size:24 final size:24
Alignment explanation
Indices: 58450498--58450547 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
58450488 TTTGCACACT
* *
58450498 CCTCAAAGGTATCTCTATGGAGCC
1 CCTCAAAGGTATCCCTAAGGAGCC
58450522 CCTCAAAGGTATCCCTAAGGAGCC
1 CCTCAAAGGTATCCCTAAGGAGCC
58450546 CC
1 CC
58450548 CTTGCCTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (24 bp):
CCTCAAAGGTATCCCTAAGGAGCC
Found at i:58456978 original size:20 final size:22
Alignment explanation
Indices: 58456948--58456991 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
58456938 AGAAAAAGAG
58456948 AAATACAAAAA-AGAATAG-ATC
1 AAATACAAAAAGA-AATAGAATC
58456969 AAAT-CAAAAAGAAATAGAATC
1 AAATACAAAAAGAAATAGAATC
58456990 AA
1 AA
58456992 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.14
Consensus pattern (22 bp):
AAATACAAAAAGAAATAGAATC
Found at i:58459845 original size:32 final size:32
Alignment explanation
Indices: 58459802--58460045 Score: 308
Period size: 32 Copynumber: 7.3 Consensus size: 32
58459792 AAATAATACA
* *
58459802 TGAACATGAGAGATTCTCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
58459834 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
* * *
58459866 TGAACAGTAGAGATTCCCTGCAACAAAATAATCCG
1 TGAACAGGAGAGATTCCCTGCAA-GAAATGAT--G
58459901 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
* * * *
58459933 TGAACAGGAAAGATTCCCTACAACAAAATAATGTG
1 TGAACAGGAGAGATTCCCTGCAA-GAAATGA--TG
* *
58459968 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAA-GAAATGAT--G
58460003 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
58460035 TGAACAGGAGA
1 TGAACAGGAGA
58460046 TACGATTTCA
Statistics
Matches: 188, Mismatches: 16, Indels: 16
0.85 0.07 0.07
Matches are distributed among these distances:
32 86 0.46
33 12 0.06
34 12 0.06
35 78 0.41
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (32 bp):
TGAACAGGAGAGATTCCCTGCAAGAAATGATG
Found at i:58459919 original size:67 final size:65
Alignment explanation
Indices: 58459802--58460045 Score: 312
Period size: 67 Copynumber: 3.7 Consensus size: 65
58459792 AAATAATACA
* * * *
58459802 TGAACATGAGAGATTCTCTGCAA-GAAATGATGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
*
58459866 TGAACAGTAGAGATTCCCTGCAACAAAATAATCCGTGAACAGGAGAGATTCCCTGCAAGAAATGA
1 TGAACAGGAGAGATTCCCTGCAACAAAATAAT--GTGAACAGGAGAGATTCCCTGCAAGAAATGA
58459931 TG
64 TG
* * * *
58459933 TGAACAGGAAAGATTCCCTACAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
1 TGAACAGGAGAGATTCCCTGCAACAAAATAA--TGTGAACAGGAGAGATTCCCTGCAA-GAAATG
58459998 ATGCG
63 AT--G
* *
58460003 TGAACAGGAGAGATTCCCTGCAA-GAAATGATGTGAACAGGAGA
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTGAACAGGAGA
58460046 TACGATTTCA
Statistics
Matches: 158, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
64 20 0.13
65 6 0.04
67 98 0.62
68 6 0.04
69 6 0.04
70 22 0.14
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (65 bp):
TGAACAGGAGAGATTCCCTGCAACAAAATAATGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
Found at i:58460979 original size:24 final size:24
Alignment explanation
Indices: 58460943--58460991 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
58460933 ACCGTCGTGG
58460943 ACACCGGCGACAACTCCTAGTGTA
1 ACACCGGCGACAACTCCTAGTGTA
* *
58460967 ACACCGGCTACAACTCTTAGTGTA
1 ACACCGGCGACAACTCCTAGTGTA
58460991 A
1 A
58460992 GAAGTTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (24 bp):
ACACCGGCGACAACTCCTAGTGTA
Found at i:58463828 original size:45 final size:45
Alignment explanation
Indices: 58463764--58463969 Score: 337
Period size: 45 Copynumber: 4.6 Consensus size: 45
58463754 TTTGAGTACT
*
58463764 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
58463809 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-TCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCT-TAGCTACACTTA
*
58463854 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACATTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
58463900 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
58463945 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
58463970 ATCATACGTA
Statistics
Matches: 153, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
43 12 0.08
44 6 0.04
45 91 0.59
46 43 0.28
47 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:58463920 original size:91 final size:90
Alignment explanation
Indices: 58463764--58463969 Score: 353
Period size: 91 Copynumber: 2.3 Consensus size: 90
58463754 TTTGAGTACT
*
58463764 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTG
*
58463829 ATAAGTGGTAGTCTAGCTACACTTA
66 ATAAGTGGTAGCCTAGCTACACTTA
*
58463854 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACATTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGACAAAGT
58463919 GATAAGTGGTAGCCTAGCTACACTTA
65 GATAAGTGGTAGCCTAGCTACACTTA
*
58463945 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
58463970 ATCATACGTA
Statistics
Matches: 111, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
89 12 0.11
90 36 0.32
91 63 0.57
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (90 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTG
ATAAGTGGTAGCCTAGCTACACTTA
Found at i:58466561 original size:24 final size:25
Alignment explanation
Indices: 58466515--58466564 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
58466505 ATTTATATAG
***
58466515 TGCTTCCTCTTCTCTTTTGTTCCTT
1 TGCTTCCTCTTCTCTTCCATTCCTT
58466540 TGCTTCC-CTTCTCTTCCATTCCTT
1 TGCTTCCTCTTCTCTTCCATTCCTT
58466564 T
1 T
58466565 TTTTTTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.02, C:0.36, G:0.06, T:0.56
Consensus pattern (25 bp):
TGCTTCCTCTTCTCTTCCATTCCTT
Found at i:58481953 original size:17 final size:17
Alignment explanation
Indices: 58481918--58481965 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
58481908 TAAATATTTG
* *
58481918 TTAAATTTA-AATTTAA
1 TTAAATATATAATATAA
58481934 TTAAATATATAATATAA
1 TTAAATATATAATATAA
*
58481951 TTAAAAATATAATAT
1 TTAAATATATAATAT
58481966 TTAATACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATATATAATATAA
Found at i:58482152 original size:35 final size:35
Alignment explanation
Indices: 58482096--58482164 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
58482086 ACCATTAACC
58482096 TTTTTGTTAACTTCACATTCGCCACGTGGCATGCT
1 TTTTTGTTAACTTCACATTCGCCACGTGGCATGCT
* * *
58482131 TTTTTGTTAATTTTACCTTCGCCACGTGGCATGC
1 TTTTTGTTAACTTCACATTCGCCACGTGGCATGC
58482165 CAAAGTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (35 bp):
TTTTTGTTAACTTCACATTCGCCACGTGGCATGCT
Found at i:58489790 original size:27 final size:26
Alignment explanation
Indices: 58489721--58489790 Score: 61
Period size: 26 Copynumber: 2.6 Consensus size: 26
58489711 ATTTAAATAC
**
58489721 TTTTTTAGAATTTTACAAAATAAATTT
1 TTTTTTA-AATTTTTTAAAATAAATTT
* * *
58489748 ATTTTTAAACTCTTTAAAA-AATATTT
1 TTTTTTAAATTTTTTAAAATAA-ATTT
58489774 TTTTTTACAATTTTTTA
1 TTTTTTA-AATTTTTTA
58489791 TAATTTCTAC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
25 2 0.06
26 18 0.55
27 13 0.39
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (26 bp):
TTTTTTAAATTTTTTAAAATAAATTT
Found at i:58499897 original size:21 final size:22
Alignment explanation
Indices: 58499861--58499901 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58499851 AGTGTATTAA
*
58499861 AATCAAATTTTCATGTATACCG
1 AATCAAAATTTCATGTATACCG
58499883 AATCAAAATTT-ATGTATAC
1 AATCAAAATTTCATGTATAC
58499902 AGATCATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (22 bp):
AATCAAAATTTCATGTATACCG
Found at i:58500253 original size:31 final size:30
Alignment explanation
Indices: 58500217--58500285 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
58500207 GATTAAATCA
*
58500217 AAATTAAAATTTCAAGTGTACATTTGAACC
1 AAATTAAAATTTCAAGTGTACAATTGAACC
* * * * *
58500247 ATAATTAGAGTTTCATGTGTATAATTGCACC
1 A-AATTAAAATTTCAAGTGTACAATTGAACC
58500278 AAATTAAA
1 AAATTAAA
58500286 GTTGATGTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (30 bp):
AAATTAAAATTTCAAGTGTACAATTGAACC
Found at i:58514184 original size:16 final size:16
Alignment explanation
Indices: 58514163--58514201 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
58514153 TTTTTAGTTG
* *
58514163 TATTTAACTATTATTA
1 TATTTAAATATTATCA
*
58514179 TATTTAAATTTTATCA
1 TATTTAAATATTATCA
58514195 TATTTAA
1 TATTTAA
58514202 TGTCGATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAAATATTATCA
Found at i:58519502 original size:29 final size:28
Alignment explanation
Indices: 58519461--58519519 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
58519451 TTTAATTTGA
* *
58519461 TACTTGAATTTATTTTTGGTCTCAATTAAG
1 TACTTGAAGTTATTTTT--TCCCAATTAAG
58519491 TACTTG-AGTTATTTTTTCCCAATTAAG
1 TACTTGAAGTTATTTTTTCCCAATTAAG
58519518 TA
1 TA
58519520 TCTTTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 12 0.44
29 9 0.33
30 6 0.22
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (28 bp):
TACTTGAAGTTATTTTTTCCCAATTAAG
Found at i:58528057 original size:3 final size:3
Alignment explanation
Indices: 58528049--58528078 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
58528039 CACATGAAAC
58528049 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
58528079 CAAGAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:58530215 original size:2 final size:2
Alignment explanation
Indices: 58530208--58530235 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58530198 GAATTGCTTT
58530208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58530236 ATTTAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58560423 original size:21 final size:23
Alignment explanation
Indices: 58560371--58560426 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
58560361 GGATGATCCT
*
58560371 AATTATATTTTTGAATTTTTTTAC
1 AATTA-ATTTTTGAATTTTTATAC
* *
58560395 TATCAATTTTT-AATTTTTATA-
1 AATTAATTTTTGAATTTTTATAC
58560416 AATTAATTTTT
1 AATTAATTTTT
58560427 TCTAACATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 9 0.33
22 9 0.33
23 6 0.22
24 3 0.11
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (23 bp):
AATTAATTTTTGAATTTTTATAC
Found at i:58566894 original size:18 final size:20
Alignment explanation
Indices: 58566863--58566902 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
58566853 TTAATTTTAA
*
58566863 TTTTTCAATATTATTTAATT
1 TTTTTCAATATTATGTAATT
58566883 TTTTTC-AT-TTATGTAATT
1 TTTTTCAATATTATGTAATT
58566901 TT
1 TT
58566903 AATTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 2 0.11
20 6 0.32
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTTCAATATTATGTAATT
Found at i:58568436 original size:18 final size:18
Alignment explanation
Indices: 58568413--58568455 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
58568403 TGCCAGGTAC
58568413 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
58568431 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
58568449 GTTTCCT
1 GTATCCT
58568456 TTTCCCAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:58568706 original size:21 final size:22
Alignment explanation
Indices: 58568671--58568714 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
58568661 CCAAACATCC
* *
58568671 ACAACTATAAACCCCCGTTGGA
1 ACAACCATAAACCCCCGCTGGA
58568693 ACAACCAT-AACCCCCGCTGGA
1 ACAACCATAAACCCCCGCTGGA
58568714 A
1 A
58568715 GTTAAACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (22 bp):
ACAACCATAAACCCCCGCTGGA
Found at i:58568885 original size:46 final size:46
Alignment explanation
Indices: 58568834--58568937 Score: 127
Period size: 46 Copynumber: 2.3 Consensus size: 46
58568824 TATTATTTCG
** * ***
58568834 TTTAATAAAATAAAAGTTGTTTTTAATATTTTAATAGTATTATATT
1 TTTAATAAAATAAAAGTTCCTTTGAATAAGGTAATAGTATTATATT
* * *
58568880 TTTAATAAAATAGAAGTTCCTTTGAATAAGGTAATATTTTTATATT
1 TTTAATAAAATAAAAGTTCCTTTGAATAAGGTAATAGTATTATATT
58568926 TTTAATAAAATA
1 TTTAATAAAATA
58568938 GAAATAATGC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (46 bp):
TTTAATAAAATAAAAGTTCCTTTGAATAAGGTAATAGTATTATATT
Found at i:58572209 original size:34 final size:34
Alignment explanation
Indices: 58572161--58572248 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 34
58572151 TTAAAAAATT
* *
58572161 AAACATAATTTAATTAATTT-TCTTAAAAACCC-T
1 AAACCTAATTTAATTAATTTAT-TTAAAAACCCAA
*
58572194 AAACCTTAATTTAATTAATTTATTTAAAACCCCAA
1 AAACC-TAATTTAATTAATTTATTTAAAAACCCAA
58572229 AAACCTAATTTAATT-ATTTA
1 AAACCTAATTTAATTAATTTA
58572249 AAAAAAACCC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
33 9 0.18
34 34 0.69
35 6 0.12
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (34 bp):
AAACCTAATTTAATTAATTTATTTAAAAACCCAA
Found at i:58573450 original size:17 final size:17
Alignment explanation
Indices: 58573428--58573461 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
58573418 AAAAAGTATT
*
58573428 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTTAAAA
58573445 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
58573462 AGTATTTTAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:58573462 original size:40 final size:41
Alignment explanation
Indices: 58573409--58573524 Score: 164
Period size: 40 Copynumber: 2.9 Consensus size: 41
58573399 AATTTATTTT
58573409 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATT-AA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTGAA
** *
58573449 AAAAATTTTAAAAAGTATTTTAAAAATATTTTTAAATTGAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTGAA
* *
58573490 AAATAA-TAAAAAAAGCATTTTAAAAATATTCTAAA
1 AAA-AATTAAAAAAAGTATTTTAAAAATATTTTAAA
58573525 CGGGCCTCGT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 35 0.53
41 29 0.44
42 2 0.03
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.35
Consensus pattern (41 bp):
AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTGAA
Found at i:58573484 original size:12 final size:11
Alignment explanation
Indices: 58573418--58573480 Score: 64
Period size: 11 Copynumber: 6.0 Consensus size: 11
58573408 TAAAAATTAA
58573418 AAAAAGTATTTT
1 AAAAA-TATTTT
58573430 AAAAATATTTT
1 AAAAATATTTT
58573441 --AAA-A--TT
1 AAAAATATTTT
*
58573447 AAAAAAATTTT
1 AAAAATATTTT
58573458 AAAAAGTATTTT
1 AAAAA-TATTTT
58573470 AAAAATATTTT
1 AAAAATATTTT
58573481 TAAATTGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
6 2 0.05
8 4 0.09
9 4 0.09
11 19 0.43
12 15 0.34
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:58575169 original size:55 final size:55
Alignment explanation
Indices: 58575069--58575172 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
58575059 TATGTAACAG
* ** * *
58575069 TCGATTTAAACATAAAAACAATTGATTCAAAAGAAGTAGTGTTCCAACATGACAA
1 TCGATTTAAAAATAAAAACAATTGATTCAAAAGAAACAATATTCCAACATGACAA
58575124 TCGATTTAAAAATATAAAA-AATAT-ATTCAAAAGAAACAATATTCCAACA
1 TCGATTTAAAAATA-AAAACAAT-TGATTCAAAAGAAACAATATTCCAACA
58575173 ATTAAGACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
55 37 0.88
56 5 0.12
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (55 bp):
TCGATTTAAAAATAAAAACAATTGATTCAAAAGAAACAATATTCCAACATGACAA
Found at i:58576313 original size:16 final size:17
Alignment explanation
Indices: 58576277--58576313 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
58576267 AATTTTATTT
*
58576277 TAATAGTAAATTTTAAA
1 TAATAATAAATTTTAAA
58576294 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
58576309 TAATA
1 TAATA
58576314 TTATTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:58577293 original size:19 final size:21
Alignment explanation
Indices: 58577265--58577309 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
58577255 TTTAAGCATT
*
58577265 TAAA-AAGTAAA-AGA-ATAA
1 TAAATAAGTAAATAGATAAAA
58577283 TAAATAAGTAAATAGATAAAA
1 TAAATAAGTAAATAGATAAAA
58577304 TAAATA
1 TAAATA
58577310 TACATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 3 0.13
21 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (21 bp):
TAAATAAGTAAATAGATAAAA
Found at i:58577317 original size:69 final size:68
Alignment explanation
Indices: 58577177--58577560 Score: 342
Period size: 69 Copynumber: 5.6 Consensus size: 68
58577167 AACAAATGAC
* * * * *
58577177 ATTAAATTGAAGTATTTAAAAAAAGTAAAATAATAAATAAGTGAATAAATAGATAAAACAAACAT
1 ATTAAATTTAAGTATTT--AAAAAGTAAAAGAAT-AATAAAT-AATAAATAGATAAAATAAATAT
58577242 AAATAAT
62 AAATAAT
* *
58577249 ATTAAATTTAAGCATTTAAAAAGTAAAAGAATAATAAATAAGTAAATAGATAAAATAAATATACA
1 ATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAA-TAAATAGATAAAATAAATATAAA
58577314 TAAT
65 TAAT
* * * *
58577318 ATTAAATTTAAATATTTTAAAAGTAAAAGAATAATAAATAAATGAATAAATTGATAAAATATATA
1 ATTAAATTTAAGTATTTAAAAAGTAAAAG---AAT-AATAAAT-AATAAATAGATAAAATAAATA
58577383 TAAA-AAT
61 TAAATAAT
* * * *
58577390 ATTAAATTTAA--ACTTTTAAAAGATAAAAGAATAATAAACAAATAAATA-ATTATAATAGATAT
1 ATTAAATTTAAGTA-TTTAAAAAG-TAAAAGAATAATAAA-TAATAAATAGA-TAAAATAAATAT
58577452 AAATAAT
62 AAATAAT
* * * **
58577459 ATTAAATTTAGGTATTT----A--AAAA-AATAATGAATAATAAATATATAAAACGAATATAAAT
1 ATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAATAAATAGATAAAATAAATATAAAT
58577517 AAT
66 AAT
* * *
58577520 ATTAACTTTTAGGTATTTAAAAAGT-GAAGAATAATAAATAA
1 ATTAA-ATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAA
58577561 ATTAATATAT
Statistics
Matches: 263, Mismatches: 27, Indels: 48
0.78 0.08 0.14
Matches are distributed among these distances:
61 28 0.11
62 20 0.08
63 4 0.02
66 2 0.01
67 3 0.01
68 39 0.15
69 72 0.27
70 18 0.07
71 10 0.04
72 38 0.14
73 27 0.10
74 2 0.01
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (68 bp):
ATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAATAAATAGATAAAATAAATATAAAT
AAT
Found at i:58577418 original size:141 final size:142
Alignment explanation
Indices: 58577177--58577498 Score: 397
Period size: 141 Copynumber: 2.3 Consensus size: 142
58577167 AACAAATGAC
* * *
58577177 ATTAAATTGAAGTATTTAAAAAAAGTAA--AATAATAAATAAGTGAATAAATAGATAAAACAAAC
1 ATTAAATTTAAATATTTAAAAAAA-TAATGAATAATAAATAAATGAATAAATAGATAAAACAAAC
* * *
58577240 ATAAATAATATTAAATTTAAGCATTTAAAAAGTAAAAGAATAATAAATAAGTAAATAGA-TAAAA
65 ATAAATAATATTAAATTTAAACATTTAAAAAGTAAAAGAATAATAAACAAATAAATA-ATTAAAA
*
58577304 TAAATATACATAAT
129 TAAATATAAATAAT
* * * *
58577318 ATTAAATTTAAATATTTTAAAAGTAA-AA-GAATAATAAATAAATGAATAAATTGATAAAATATA
1 ATTAAATTTAAATA-TTTAAAA-AAATAATGAATAATAAATAAATGAATAAATAGATAAAACAAA
* * *
58577381 TATAAA-AATATTAAATTTAAAC-TTTTAAAAGATAAAAGAATAATAAACAAATAAATAATTATA
64 CATAAATAATATTAAATTTAAACATTTAAAAAG-TAAAAGAATAATAAACAAATAAATAATTAAA
*
58577444 ATAGATATAAATAAT
128 ATAAATATAAATAAT
**
58577459 ATTAAATTTAGGTATTTAAAAAAATAATGAATAATAAATA
1 ATTAAATTTAAATATTTAAAAAAATAATGAATAATAAATA
58577499 TATAAAACGA
Statistics
Matches: 156, Mismatches: 18, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
139 2 0.01
140 18 0.12
141 92 0.59
142 42 0.27
143 2 0.01
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (142 bp):
ATTAAATTTAAATATTTAAAAAAATAATGAATAATAAATAAATGAATAAATAGATAAAACAAACA
TAAATAATATTAAATTTAAACATTTAAAAAGTAAAAGAATAATAAACAAATAAATAATTAAAATA
AATATAAATAAT
Found at i:58577585 original size:61 final size:61
Alignment explanation
Indices: 58577430--58577562 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
58577420 ATAATAAACA
* * * *
58577430 AATAAATAATTATAATAGATATAAATAATATTAA-ATTTAGGTATTTAAAAAAATAATGAAT
1 AATAAATAAATAAAACA-ATATAAATAATATTAACTTTTAGGTATTTAAAAAAATAATGAAT
* *
58577491 AATAAATATATAAAACGAATATAAATAATATTAACTTTTAGGTATTT-AAAAAGTGAA-GAAT
1 AATAAATAAATAAAAC-AATATAAATAATATTAACTTTTAGGTATTTAAAAAAAT-AATGAAT
58577552 AATAAATAAAT
1 AATAAATAAAT
58577563 TAATATATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
61 48 0.77
62 14 0.23
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.34
Consensus pattern (61 bp):
AATAAATAAATAAAACAATATAAATAATATTAACTTTTAGGTATTTAAAAAAATAATGAAT
Found at i:58580140 original size:37 final size:37
Alignment explanation
Indices: 58580095--58580171 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
58580085 TTCATATGAC
58580095 ATAATTCATTCACATATCCATTATATTTAAACACATA
1 ATAATTCATTCACATATCCATTATATTTAAACACATA
* *
58580132 ATAATTCATTCGCATATCCATTATATTTAAACACGTA
1 ATAATTCATTCACATATCCATTATATTTAAACACATA
58580169 ATA
1 ATA
58580172 TAAACAGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.38
Consensus pattern (37 bp):
ATAATTCATTCACATATCCATTATATTTAAACACATA
Found at i:58580282 original size:41 final size:41
Alignment explanation
Indices: 58580237--58580394 Score: 156
Period size: 41 Copynumber: 3.9 Consensus size: 41
58580227 GGCTTTTGGC
* *
58580237 CTGCTAGACTTAAAGTCTGAAATATTTCACCGGCATCAAGA
1 CTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCCAGA
* * *
58580278 CTGCTAGACATAAAGTCT-AAATTGTTTCACTGGCATCCAGC
1 CTGCTAGACATAAAGTCTGAAA-TATTTCACCGGCATCCAGA
* * * * * *
58580319 CTGGTAGACATAGAGTCTGAATTGTTTCACCGGTATCCAGT
1 CTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCCAGA
* * * * *
58580360 CTGCTAGAAATAGAGTCTGAATTATCTCACTGGCA
1 CTGCTAGACATAAAGTCTGAAATATTTCACCGGCA
58580395 ATAAGCCTTC
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
40 3 0.03
41 93 0.95
42 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (41 bp):
CTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCCAGA
Found at i:58580336 original size:82 final size:82
Alignment explanation
Indices: 58580235--58580394 Score: 203
Period size: 82 Copynumber: 2.0 Consensus size: 82
58580225 CCGGCTTTTG
* *
58580235 GCCTGCTAGACTTAAAGTCTGAAATATTTCACCGGCATCAAGACTGCTAGACATAAAGTCTAAAT
1 GCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCAAGACTGCTAGAAATAAAGTCTAAAT
* *
58580300 TGTTTCACTGGCATCCA
66 TATCTCACTGGCATCCA
* * * * * * * * *
58580317 GCCTGGTAGACATAGAGTCTGAATTGTTTCACCGGTATCCAGTCTGCTAGAAATAGAGTCTGAAT
1 GCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCAAGACTGCTAGAAATAAAGTCTAAAT
58580382 TATCTCACTGGCA
66 TATCTCACTGGCA
58580395 ATAAGCCTTC
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (82 bp):
GCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCAAGACTGCTAGAAATAAAGTCTAAAT
TATCTCACTGGCATCCA
Found at i:58592205 original size:27 final size:28
Alignment explanation
Indices: 58592156--58592209 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
58592146 TAAGGTCTGC
* *
58592156 AAATAACTTTTATATATTATTATTTTCG
1 AAATAACTATAATATATTATTATTTTCG
58592184 AAATAACTATAATA-ATTATTATTTTC
1 AAATAACTATAATATATTATTATTTTC
58592210 ATTTACATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (28 bp):
AAATAACTATAATATATTATTATTTTCG
Found at i:58599983 original size:4 final size:4
Alignment explanation
Indices: 58599974--58600018 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
58599964 ATTTAAGGGA
58599974 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
58600019 CGATGTTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:58604255 original size:18 final size:19
Alignment explanation
Indices: 58604214--58604260 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
58604204 CATTACAACC
58604214 CAAAAAGAAAAAGGAGATA
1 CAAAAAGAAAAAGGAGATA
* * *
58604233 GAAAAAGAAAAGGGGGAT-
1 CAAAAAGAAAAAGGAGATA
58604251 CAAAAAGAAA
1 CAAAAAGAAA
58604261 GAACATATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.66, C:0.04, G:0.26, T:0.04
Consensus pattern (19 bp):
CAAAAAGAAAAAGGAGATA
Found at i:58611752 original size:16 final size:16
Alignment explanation
Indices: 58611731--58611770 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
58611721 CCTACTCCCT
58611731 CCCAATTTAAAACCAG
1 CCCAATTTAAAACCAG
*
58611747 CCCAATTTAAATCCAG
1 CCCAATTTAAAACCAG
58611763 CCCAATTT
1 CCCAATTT
58611771 TCTCTTAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.25
Consensus pattern (16 bp):
CCCAATTTAAAACCAG
Found at i:58612693 original size:16 final size:16
Alignment explanation
Indices: 58612672--58612705 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
58612662 AATTATTGAA
*
58612672 TATATTGTAATTAATG
1 TATATTATAATTAATG
58612688 TATATTATAATTAATG
1 TATATTATAATTAATG
58612704 TA
1 TA
58612706 AGAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
TATATTATAATTAATG
Found at i:58615827 original size:24 final size:24
Alignment explanation
Indices: 58615770--58615828 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
58615760 GGTTTAATGC
* *
58615770 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
*
58615794 AAATGAATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
58615818 AAATGGATATA
1 AAATGGATATA
58615829 AATGGAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:58615923 original size:37 final size:37
Alignment explanation
Indices: 58615869--58615981 Score: 183
Period size: 37 Copynumber: 3.1 Consensus size: 37
58615859 TTATGTTTTA
*
58615869 ATTC-AAGACTTGTGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
*
58615905 ATTCAAAGACTTATGTAATATTTTTAATTATTTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* *
58615942 ATTCAAAGATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
58615979 ATT
1 ATT
58615982 TAATTCGGGT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
36 4 0.06
37 67 0.94
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:58615996 original size:9 final size:9
Alignment explanation
Indices: 58615982--58616107 Score: 189
Period size: 9 Copynumber: 13.6 Consensus size: 9
58615972 TGTAGTGATT
58615982 TAATTCGGG
1 TAATTCGGG
58615991 TAATTCGGG
1 TAATTCGGG
58616000 TAATTTTCGGG
1 TAA--TTCGGG
58616011 TAATTCGGG
1 TAATTCGGG
*
58616020 TAATTTGGG
1 TAATTCGGG
58616029 TAATTTTCGGG
1 TAA--TTCGGG
58616040 TAATTCGGG
1 TAATTCGGG
58616049 TAATTCGGG
1 TAATTCGGG
*
58616058 TAAGTCGGG
1 TAATTCGGG
58616067 TAATTCGGG
1 TAATTCGGG
*
58616076 TAAGTCGGG
1 TAATTCGGG
58616085 TAATTCGGG
1 TAATTCGGG
58616094 TAATTCGGG
1 TAATTCGGG
58616103 TAATT
1 TAATT
58616108 TTTAACCAAA
Statistics
Matches: 107, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
9 90 0.84
11 17 0.16
ACGTcount: A:0.22, C:0.10, G:0.33, T:0.36
Consensus pattern (9 bp):
TAATTCGGG
Found at i:58616024 original size:29 final size:27
Alignment explanation
Indices: 58615982--58616107 Score: 189
Period size: 29 Copynumber: 4.5 Consensus size: 27
58615972 TGTAGTGATT
58615982 TAATTCGGGTAATTCGGGTAATTTTCGGG
1 TAATTCGGGTAATTCGGGTAA--TTCGGG
*
58616011 TAATTCGGGTAATTTGGGTAATTTTCGGG
1 TAATTCGGGTAATTCGGGTAA--TTCGGG
*
58616040 TAATTCGGGTAATTCGGGTAAGTCGGG
1 TAATTCGGGTAATTCGGGTAATTCGGG
*
58616067 TAATTCGGGTAAGTCGGGTAATTCGGG
1 TAATTCGGGTAATTCGGGTAATTCGGG
58616094 TAATTCGGGTAATT
1 TAATTCGGGTAATT
58616108 TTTAACCAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
27 43 0.47
29 48 0.53
ACGTcount: A:0.22, C:0.10, G:0.33, T:0.36
Consensus pattern (27 bp):
TAATTCGGGTAATTCGGGTAATTCGGG
Found at i:58616917 original size:13 final size:13
Alignment explanation
Indices: 58616899--58616923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58616889 GATAGGTAAA
58616899 TTTTAATAATTTT
1 TTTTAATAATTTT
58616912 TTTTAATAATTT
1 TTTTAATAATTT
58616924 CATTATAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTAATAATTTT
Found at i:58622250 original size:21 final size:22
Alignment explanation
Indices: 58622210--58622259 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
58622200 ATAATTTAAA
*
58622210 ATTTTCAAAAAATATGAAAACT
1 ATTTTCAAAAAATATAAAAACT
* *
58622232 ATTTT-AAAAATTATAAAAAAT
1 ATTTTCAAAAAATATAAAAACT
58622253 ATATTTC
1 AT-TTTC
58622260 TTTTTGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTTTCAAAAAATATAAAAACT
Found at i:58624541 original size:36 final size:35
Alignment explanation
Indices: 58624497--58624569 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 35
58624487 AAGTTTAAAA
*
58624497 ATTATA-TTTAATACAATAAAATATTTATTATATTT
1 ATTATATTTTAATACAAT-AAACATTTATTATATTT
* *
58624532 ATTAGTATTTTAATATAATAAACATTTGTTATATTT
1 ATTA-TATTTTAATACAATAAACATTTATTATATTT
58624568 AT
1 AT
58624570 GATAGTGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 4 0.12
36 19 0.58
37 10 0.30
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (35 bp):
ATTATATTTTAATACAATAAACATTTATTATATTT
Found at i:58630691 original size:12 final size:12
Alignment explanation
Indices: 58630667--58630699 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58630657 TCCTAGCTGT
58630667 AAATTCATTTCA
1 AAATTCATTTCA
58630679 AAATT-ATTGTCA
1 AAATTCATT-TCA
58630691 AAATTCATT
1 AAATTCATT
58630700 AAAATTCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 13 0.68
13 3 0.16
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (12 bp):
AAATTCATTTCA
Found at i:58633159 original size:2 final size:2
Alignment explanation
Indices: 58633152--58633181 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
58633142 AACCCATCAA
58633152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58633182 TCCATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58640865 original size:12 final size:12
Alignment explanation
Indices: 58640848--58640884 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
58640838 AATAATGTTT
58640848 TGTTTTGATTTA
1 TGTTTTGATTTA
*
58640860 TGTTTTGATTCA
1 TGTTTTGATTTA
*
58640872 TGTTTTGGTTTA
1 TGTTTTGATTTA
58640884 T
1 T
58640885 TTATGTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.14, C:0.03, G:0.19, T:0.65
Consensus pattern (12 bp):
TGTTTTGATTTA
Found at i:58642749 original size:12 final size:12
Alignment explanation
Indices: 58642732--58642764 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
58642722 AACTGAATTG
58642732 TTTTTTTCCTTT
1 TTTTTTTCCTTT
*
58642744 TTTTTTTCTTTT
1 TTTTTTTCCTTT
58642756 TTTTTTTCC
1 TTTTTTTCC
58642765 AATAGGCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTCCTTT
Found at i:58642761 original size:11 final size:11
Alignment explanation
Indices: 58642732--58642761 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
58642722 AACTGAATTG
*
58642732 TTTTTTTCCTT
1 TTTTTTTTCTT
58642743 TTTTTTTTCTT
1 TTTTTTTTCTT
58642754 TTTTTTTT
1 TTTTTTTT
58642762 TCCAATAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:58658323 original size:26 final size:26
Alignment explanation
Indices: 58658283--58658332 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
58658273 TGCGAGTTCA
*
58658283 ATACGCGAGCCCAATGTACAAGCTTG
1 ATACACGAGCCCAATGTACAAGCTTG
* *
58658309 ATACACGAGCTCAATGTGCAAGCT
1 ATACACGAGCCCAATGTACAAGCT
58658333 CAATGCATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (26 bp):
ATACACGAGCCCAATGTACAAGCTTG
Found at i:58668618 original size:3 final size:3
Alignment explanation
Indices: 58668605--58668644 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
58668595 CCAACTGTAT
*
58668605 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
58668645 AATTTTGAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:58677689 original size:18 final size:17
Alignment explanation
Indices: 58677655--58677703 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
58677645 TAACATTTTA
* *
58677655 AATATAAATTTTTATTTT
1 AATATAAA-TTTAAATTT
*
58677673 TATATAAATTTAAATTT
1 AATATAAATTTAAATTT
58677690 AATTATAAATTTAA
1 AA-TATAAATTTAA
58677704 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATAAATTTAAATTT
Found at i:58680154 original size:43 final size:38
Alignment explanation
Indices: 58680072--58680156 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 38
58680062 AATTATAATT
* *
58680072 ATAAACTATTCTCATCAAATTTAGTAATTTTTTATTTA
1 ATAAACTATTCTCATCAAATTAAGTAATTATTTATTTA
*
58680110 ATAAATTATTCTCATCAAATTAACGTAAAATATATTTACTTTA
1 ATAAACTATTCTCATCAAATTAA-GT--AAT-TATTTA-TTTA
58680153 ATAA
1 ATAA
58680157 TAAAATAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
38 21 0.54
39 2 0.05
41 3 0.08
42 5 0.13
43 8 0.21
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (38 bp):
ATAAACTATTCTCATCAAATTAAGTAATTATTTATTTA
Found at i:58689378 original size:19 final size:17
Alignment explanation
Indices: 58689356--58689418 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 17
58689346 ATTATCTTCT
58689356 TCATTATTTTAATGTATTA
1 TCATTATTTT-AT-TATTA
58689375 TCATTTATTATTATTATTA
1 TCA-TTATT-TTATTATTA
*
58689394 TTATTATTTCTATTATTA
1 TCATTATTT-TATTATTA
*
58689412 TTATTAT
1 TCATTAT
58689419 GCACATTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 1 0.03
18 20 0.50
19 10 0.25
20 7 0.17
21 2 0.05
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
TCATTATTTTATTATTA
Found at i:58689387 original size:3 final size:3
Alignment explanation
Indices: 58689379--58689418 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
58689369 GTATTATCAT
58689379 TTA TTA TTA TTA TTA TTA TTA TT- TCTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
58689419 GCACATTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:58702042 original size:86 final size:86
Alignment explanation
Indices: 58701846--58702057 Score: 234
Period size: 86 Copynumber: 2.5 Consensus size: 86
58701836 GAAGACAAAG
* * *
58701846 GATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCCATCGATCGC
1 GATCTTACCTCCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCATCCATCGATCGC
58701910 AGTGGAGCTAGTTAAAGAAGTA
65 AGTGGAGCTAGTTAAAGAAGTA
* * * * *
58701932 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
1 GATCTTACCTCCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCATCCATCGATCGCA
* * *
58701997 TTGGAGC-AGATTGAAGCCAG-A
66 GTGGAGCTAG-TTAAAG-AAGTA
* * *
58702018 GATCTTATCTCCCTGAGATT-ACAGCGGAGCAGATCAAAGA
1 GATCTTACCTCCCTG-CATTAACAGCGAAGCAGATCAAAGA
58702058 TAGTAATCCT
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
85 5 0.05
86 100 0.91
87 5 0.05
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (86 bp):
GATCTTACCTCCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCATCCATCGATCGCA
GTGGAGCTAGTTAAAGAAGTA
Found at i:58702303 original size:174 final size:170
Alignment explanation
Indices: 58702017--58702390 Score: 554
Period size: 174 Copynumber: 2.2 Consensus size: 170
58702007 TTGAAGCCAG
* *
58702017 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCCTGAGATT
58702082 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
58702147 TATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
131 TATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
* *
58702187 AGATCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATA-TAATCCTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCCTGAGA-T
* * *
58702250 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATC
65 TACAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATC
* * **
58702315 AGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGC
125 AGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
* * *
58702361 AGATCCTATCTCCCTGAAGTTACAGTGGAG
1 AGATCTTATCTCCCTGAGGTTACAGCGGAG
58702391 TGGGTTAAAA
Statistics
Matches: 183, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
168 1 0.01
169 30 0.16
170 41 0.22
174 111 0.61
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (170 bp):
AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCCTGAGATT
ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
TATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
Found at i:58702371 original size:46 final size:44
Alignment explanation
Indices: 58702138--58702570 Score: 255
Period size: 46 Copynumber: 9.9 Consensus size: 44
58702128 AGAAGATCAC
* * **
58702138 ATCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGA
1 ATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* * * *
58702182 ATTGCAGATCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGA
1 A-T-CAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* * ** **
58702228 TAT-A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-A
1 -ATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* * * * * *
58702269 ATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GC
1 AT-CA-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* *
58702312 ATCAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGA
1 ATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* * ****
58702356 ATTGCAGATCCTATCTCCCTGAAGTTACAGTGGAGT-GGGTTAA-A
1 A-T-CAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* * * * * *
58702400 ATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GC
1 AT-CA-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* * *
58702443 ATCAGGTCTTATTTCTCTGAGGTTACAGTGGAGTAGACCGAAGA
1 ATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* * **
58702487 ATTGCAGATCTTATCCCCCTGAGGTTACAGTGGAGCAGATTGAAG-
1 A-T-CAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* **
58702532 -CCAGAGGTCTTATCTCCCTGATATTACAGTGGAGTAGAC
1 ATCAGA--TCTTATCTCCCTGAGGTTACAGTGGAGTAGAC
58702571 TTAAACCTAA
Statistics
Matches: 302, Mismatches: 63, Indels: 48
0.73 0.15 0.12
Matches are distributed among these distances:
40 2 0.01
41 62 0.21
42 9 0.03
43 33 0.11
44 89 0.29
45 7 0.02
46 99 0.33
47 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
ATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
Found at i:58702371 original size:87 final size:87
Alignment explanation
Indices: 58702101--58702391 Score: 293
Period size: 87 Copynumber: 3.3 Consensus size: 87
58702091 CGGATTAAAG
* * * *
58702101 GATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAG
*
58702166 TGGAACAGACCGAAGAATTGCA
66 TGGAGCAGACCGAAGAATTGCA
* * ** * * ** * *
58702188 GATCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAT-ATAATCCTATCTCCCTGAAGTTA
1 GATCTTATCTCCCTGAAGTTACAGTAGAGTAGATCG--CATCA-GGTCTTATCTCCCTGAGGTTA
* ** **
58702252 CAGTGGAGCGGA-TTAA-AA-TAAA
63 CAGTGGAGCAGACCGAAGAATTGCA
* *
58702274 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCTCTGAGGTTACA
1 -GATCTTATCTCCCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACA
*
58702339 GTGGAGTAGACCGAAGAATTGCA
65 GTGGAGCAGACCGAAGAATTGCA
* *
58702362 GATCCTATCTCCCTGAAGTTACAGTGGAGT
1 GATCTTATCTCCCTGAAGTTACAGTAGAGT
58702392 GGGTTAAAAT
Statistics
Matches: 156, Mismatches: 40, Indels: 16
0.74 0.19 0.08
Matches are distributed among these distances:
85 28 0.18
86 5 0.03
87 90 0.58
88 5 0.03
89 28 0.18
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (87 bp):
GATCTTATCTCCCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAG
TGGAGCAGACCGAAGAATTGCA
Found at i:58702477 original size:41 final size:42
Alignment explanation
Indices: 58702103--58702569 Score: 228
Period size: 44 Copynumber: 10.7 Consensus size: 42
58702093 GATTAAAGGA
* *
58702103 TCTTATCTCTCTGAAGTTACAGTAGAGAAGATC-ACAT-CAGG
1 TCTTATCTCTCTGAAGTTACAGTGGAGTAGATCGA-ATACAGG
* ** * * *
58702144 TCTTATCTCCCTG-AGATTACAGTGGAACAGACCGAAGAATTGCAGA
1 TCTTATCTCTCTGAAG-TTACAGTGGAGTAGATC---GAA-TACAGG
* * * * * * *
58702190 TCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATA-A
1 TCTTATCTCTCTGAAGTTACAGTGGAGTAGATCG-A-ATACAGG
* * ** ** *
58702233 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGG
1 TCTTATCTCTCTGAAGTTACAGTGGAGTAGA-TCGAATACAGG
* *
58702276 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT-CAGG
1 -TCTTATCTCTCTGAAGTTACAGTGGAGTAGATCGAATACAGG
* * * *
58702318 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCAGA
1 TCTTATCTCTCTGAAGTTACAGTGGAGTAGATC---GAA-TACAGG
* * * * ** *
58702364 TCCTATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAGG
1 TCTTATCTCTCTGAAGTTACAGTGGAGT-AGATCGAATACAGG
* *
58702407 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT-CAGG
1 -TCTTATCTCTCTGAAGTTACAGTGGAGTAGATCGAATACAGG
* * * * *
58702449 TCTTATTTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCAGA
1 TCTTATCTCTCTGAAGTTACAGTGGAGTAGATC---GAA-TACAGG
* * * * * * *
58702495 TCTTATCCCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGG
1 TCTTATCTCTCTGAAGTTACAGTGGAGTAGATCGAA--TACAGG
*
58702539 TCTTATCTCCCTGATA-TTACAGTGGAGTAGA
1 TCTTATCTCTCTGA-AGTTACAGTGGAGTAGA
58702570 CTTAAACCTA
Statistics
Matches: 323, Mismatches: 76, Indels: 51
0.72 0.17 0.11
Matches are distributed among these distances:
40 2 0.01
41 84 0.26
42 10 0.03
43 42 0.13
44 91 0.28
45 5 0.02
46 87 0.27
47 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (42 bp):
TCTTATCTCTCTGAAGTTACAGTGGAGTAGATCGAATACAGG
Found at i:58702569 original size:131 final size:131
Alignment explanation
Indices: 58702190--58702527 Score: 531
Period size: 131 Copynumber: 2.6 Consensus size: 131
58702180 GAATTGCAGA
* * * * *
58702190 TCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAG-ATAT--A-ATCCTATCTCCCTGAAGTT
1 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAAT-TGCAGATCCTATCTCCCTGAAGTT
58702251 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
65 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
58702316 GG
130 GG
58702318 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCAGATCCTATCTCCCTGAAGTTA
1 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCAGATCCTATCTCCCTGAAGTTA
* *
58702383 CAGTGGAGTGGGTTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
58702448 G
131 G
* * * *
58702449 TCTTATTTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCAGATCTTATCCCCCTGAGGTTA
1 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCAGATCCTATCTCCCTGAAGTTA
*
58702514 CAGTGGAGCAGATT
66 CAGTGGAGCGGATT
58702528 GAAGCCAGAG
Statistics
Matches: 192, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
128 33 0.17
129 2 0.01
130 1 0.01
131 156 0.81
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (131 bp):
TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCAGATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
G
Found at i:58703910 original size:19 final size:17
Alignment explanation
Indices: 58703888--58703950 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 17
58703878 ATTATCTTCT
58703888 TCATTATTTTAATGTATTA
1 TCATTATTTT-AT-TATTA
58703907 TCATTTATTATTATTATTA
1 TCA-TTATT-TTATTATTA
*
58703926 TTATTATTTCTATTATTA
1 TCATTATTT-TATTATTA
*
58703944 TTATTAT
1 TCATTAT
58703951 GCACATTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 1 0.03
18 20 0.50
19 10 0.25
20 7 0.17
21 2 0.05
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
TCATTATTTTATTATTA
Found at i:58703919 original size:3 final size:3
Alignment explanation
Indices: 58703911--58703950 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
58703901 GTATTATCAT
58703911 TTA TTA TTA TTA TTA TTA TTA TT- TCTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
58703951 GCACATTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:58711008 original size:20 final size:20
Alignment explanation
Indices: 58710983--58711022 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
58710973 CGTAAAATGA
*
58710983 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
58711003 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
58711023 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:58711012 original size:34 final size:35
Alignment explanation
Indices: 58710968--58711034 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
58710958 CAGTAAAATA
*
58710968 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
58711002 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
58711035 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:58711603 original size:9 final size:10
Alignment explanation
Indices: 58711583--58711607 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
58711573 CCTTTTATTT
58711583 AAAAAGGAAA
1 AAAAAGGAAA
58711593 AAAAAGGAAA
1 AAAAAGGAAA
58711603 AAAAA
1 AAAAA
58711608 TTCAGGCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGGAAA
Found at i:58714065 original size:57 final size:57
Alignment explanation
Indices: 58713949--58714116 Score: 193
Period size: 57 Copynumber: 3.0 Consensus size: 57
58713939 GAGTCCCAAG
* *
58713949 GAAGTAGTCAAATCAGATATTCTATCACCAG--G-TCGTCGGTCCACTCGGCTTAA-A
1 GAAGTAGCCAAATCAGATATT-TATCACCAGTTGTTCGTCGGTCCCCTCGGCTTAAGA
* * *
58714003 GAAGTAGCCAAATCAGAAATCTTATCACCAGTTGTTCATCGGTCCCCCCGGCTTAAGA
1 GAAGTAGCCAAATCAGATAT-TTATCACCAGTTGTTCGTCGGTCCCCTCGGCTTAAGA
* * * *
58714061 -AAGTAGCAAAACCAGATCTTTTATCACCAGTTGTTCGTCAGTCCCCTCGGCTTAAG
1 GAAGTAGCCAAATCAGAT-ATTTATCACCAGTTGTTCGTCGGTCCCCTCGGCTTAAG
58714117 GTATTATATC
Statistics
Matches: 96, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
54 27 0.28
55 1 0.01
56 1 0.01
57 65 0.68
58 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (57 bp):
GAAGTAGCCAAATCAGATATTTATCACCAGTTGTTCGTCGGTCCCCTCGGCTTAAGA
Found at i:58716099 original size:17 final size:17
Alignment explanation
Indices: 58716077--58716137 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
58716067 AATCTTAGAG
58716077 TTCTAATTGTGTACAAC
1 TTCTAATTGTGTACAAC
*
58716094 TTCTAATTGTGTA-AGAG
1 TTCTAATTGTGTACA-AC
* *
58716111 TTCTAATTGTATACAGC
1 TTCTAATTGTGTACAAC
*
58716128 TTTTAATTGT
1 TTCTAATTGT
58716138 AGCCATTGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 1 0.03
17 35 0.95
18 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (17 bp):
TTCTAATTGTGTACAAC
Found at i:58716116 original size:34 final size:34
Alignment explanation
Indices: 58716073--58716137 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
58716063 ATGTAATCTT
*
58716073 AGAGTTCTAATTGTGTACAACTTCTAATTGTGTA
1 AGAGTTCTAATTGTATACAACTTCTAATTGTGTA
* *
58716107 AGAGTTCTAATTGTATACAGCTTTTAATTGT
1 AGAGTTCTAATTGTATACAACTTCTAATTGT
58716138 AGCCATTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (34 bp):
AGAGTTCTAATTGTATACAACTTCTAATTGTGTA
Found at i:58720997 original size:17 final size:17
Alignment explanation
Indices: 58720975--58721036 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
58720965 AATCTTAGAG
58720975 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
58720992 TTCTAATTGTGTA-AGAG
1 TTCTAATTGTATACAG-C
*
58721009 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAGC
*
58721026 TTTTAATTGTA
1 TTCTAATTGTA
58721037 GCCATTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
16 2 0.05
17 34 0.92
18 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:58721014 original size:34 final size:34
Alignment explanation
Indices: 58720971--58721035 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
58720961 ATGTAATCTT
*
58720971 AGAGTTCTAATTGTATACAGCTTCTAATTGTGTA
1 AGAGTTCTAATTGTATACAACTTCTAATTGTGTA
*
58721005 AGAGTTCTAATTGTATACAACTTTTAATTGT
1 AGAGTTCTAATTGTATACAACTTCTAATTGT
58721036 AGCCATTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (34 bp):
AGAGTTCTAATTGTATACAACTTCTAATTGTGTA
Found at i:58731613 original size:25 final size:25
Alignment explanation
Indices: 58731584--58731634 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
58731574 CAAATAATTT
58731584 AAAAT-TCATAAAA-TATAAAAATATA
1 AAAATATCATAAAAGT-T-AAAATATA
*
58731609 AAAATATTATAAAAGTTAAAATATA
1 AAAATATCATAAAAGTTAAAATATA
58731634 A
1 A
58731635 CATTATGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 14 0.61
26 8 0.35
27 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAATATCATAAAAGTTAAAATATA
Found at i:58738862 original size:17 final size:17
Alignment explanation
Indices: 58738817--58738863 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
58738807 TGGATGTTAC
58738817 ATAATAAAATTATTAAA
1 ATAATAAAATTATTAAA
** *
58738834 ATTTTAATATTATT-AA
1 ATAATAAAATTATTAAA
58738850 ATAAATAAAATTAT
1 AT-AATAAAATTAT
58738864 ATAGTTAAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATAAAATTATTAAA
Found at i:58740600 original size:24 final size:23
Alignment explanation
Indices: 58740580--58740622 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
58740570 TACTTGTCAT
58740580 AACAT-TAATCTTTTAAATTGTC
1 AACATATAATCTTTTAAATTGTC
58740602 AACATATAATCTTTTAAATTG
1 AACATATAATCTTTTAAATTG
58740623 ATCCGATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (23 bp):
AACATATAATCTTTTAAATTGTC
Found at i:58741545 original size:9 final size:9
Alignment explanation
Indices: 58741534--58741585 Score: 68
Period size: 9 Copynumber: 5.8 Consensus size: 9
58741524 TTTGGTTAAA
*
58741534 AATTAACCA
1 AATTAACCG
58741543 AATTAACCG
1 AATTAACCG
*
58741552 AATTAACTG
1 AATTAACCG
*
58741561 AATTACCCG
1 AATTAACCG
*
58741570 AATTACCCG
1 AATTAACCG
58741579 AATTAAC
1 AATTAAC
58741586 AAAATTGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:58741573 original size:27 final size:27
Alignment explanation
Indices: 58741534--58741585 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
58741524 TTTGGTTAAA
58741534 AATTAACCAAATTAACCGAATTAACTG
1 AATTAACCAAATTAACCGAATTAACTG
* * *
58741561 AATTACCCGAATTACCCGAATTAAC
1 AATTAACCAAATTAACCGAATTAAC
58741586 AAAATTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (27 bp):
AATTAACCAAATTAACCGAATTAACTG
Found at i:58741591 original size:27 final size:27
Alignment explanation
Indices: 58741532--58741591 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
58741522 TTTTTGGTTA
58741532 AAAATTAACCAAATTAACCGAATTAAC
1 AAAATTAACCAAATTAACCGAATTAAC
** * * *
58741559 TGAATTACCCGAATTACCCGAATTAAC
1 AAAATTAACCAAATTAACCGAATTAAC
58741586 AAAATT
1 AAAATT
58741592 GAATCACTAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.25
Consensus pattern (27 bp):
AAAATTAACCAAATTAACCGAATTAAC
Found at i:58743148 original size:27 final size:28
Alignment explanation
Indices: 58743114--58743176 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
58743104 AAAAATAACC
58743114 AAAATATTAT-AACTTTTTTATTTACCA
1 AAAATATTATAAACTTTTTTATTTACCA
* *
58743141 AAAATATTATAAATTTTTTTATTTACTA
1 AAAATATTATAAACTTTTTTATTTACCA
58743169 AAATATAT
1 AAA-ATAT
58743177 CAAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 10 0.31
28 18 0.56
29 4 0.12
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.49
Consensus pattern (28 bp):
AAAATATTATAAACTTTTTTATTTACCA
Found at i:58743536 original size:18 final size:18
Alignment explanation
Indices: 58743500--58743537 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
58743490 ATTTTATTAG
*
58743500 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
58743518 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
58743536 AG
1 AG
58743538 AGTTATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:58744158 original size:17 final size:18
Alignment explanation
Indices: 58744136--58744169 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
58744126 GGTGCCGCCA
58744136 CAGGTTTTT-TTTTTTTG
1 CAGGTTTTTGTTTTTTTG
58744153 CAGGTTTTTGTTTTTTT
1 CAGGTTTTTGTTTTTTT
58744170 TGATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.06, C:0.06, G:0.18, T:0.71
Consensus pattern (18 bp):
CAGGTTTTTGTTTTTTTG
Found at i:58744218 original size:15 final size:15
Alignment explanation
Indices: 58744176--58744218 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
58744166 TTTTTGATAT
58744176 ATTTTGGTAAATAAA
1 ATTTTGGTAAATAAA
*
58744191 ATTTT--T-TATAAA
1 ATTTTGGTAAATAAA
58744203 ATTTTGGTAAATAAA
1 ATTTTGGTAAATAAA
58744218 A
1 A
58744219 AAATTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 10 0.43
13 1 0.04
14 1 0.04
15 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (15 bp):
ATTTTGGTAAATAAA
Found at i:58744232 original size:26 final size:27
Alignment explanation
Indices: 58744174--58744236 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
58744164 TTTTTTTGAT
***
58744174 ATATTTTGGTAAATAAAATTTTTTATA
1 ATATTTTGGTAAATAAAATAAATTATA
*
58744201 AAATTTTGGTAAATAAAA-AAATTATA
1 ATATTTTGGTAAATAAAATAAATTATA
58744227 ATATTTTGGT
1 ATATTTTGGT
58744237 TAGTTTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
26 14 0.45
27 17 0.55
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAATAAATTATA
Found at i:58745786 original size:12 final size:12
Alignment explanation
Indices: 58745769--58745794 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58745759 TCTTATATCC
58745769 TAAATAAAAAAT
1 TAAATAAAAAAT
58745781 TAAATAAAAAAT
1 TAAATAAAAAAT
58745793 TA
1 TA
58745795 GAGTAGTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAATAAAAAAT
Found at i:58763174 original size:12 final size:13
Alignment explanation
Indices: 58763155--58763191 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
58763145 ATTTTTTAAA
58763155 TATTATTTAATTT
1 TATTATTTAATTT
58763168 T-TTATTTAATTT
1 TATTATTTAATTT
*
58763180 TATAATTTAATT
1 TATTATTTAATT
58763192 AATATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTTAATTT
Found at i:58763180 original size:31 final size:29
Alignment explanation
Indices: 58763145--58763211 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
58763135 GGTTAATTCC
* *
58763145 ATTTTTTAAATATTATTTAAT-TTTTTATTTA
1 ATTTTTT-AAT-TTAATTAATATTTTT-TATA
*
58763176 ATTTTATAATTTAATTAATATTTTTTATA
1 ATTTTTTAATTTAATTAATATTTTTTATA
58763205 ATTTTTT
1 ATTTTTT
58763212 TTATAATAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 17 0.55
30 8 0.26
31 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
ATTTTTTAATTTAATTAATATTTTTTATA
Found at i:58763280 original size:29 final size:29
Alignment explanation
Indices: 58763237--58763307 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
58763227 ATAACCCGGC
* *
58763237 AAATAATTTTTTCAGCACACATCACATCA
1 AAATTATTTTTTCAGAACACATCACATCA
* * ***
58763266 AATTTATTTTTTCAGAACCCATCTTGTCA
1 AAATTATTTTTTCAGAACACATCACATCA
58763295 AAATTATTTTTTC
1 AAATTATTTTTTC
58763308 CGGAACAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (29 bp):
AAATTATTTTTTCAGAACACATCACATCA
Found at i:58763578 original size:86 final size:86
Alignment explanation
Indices: 58763412--58763578 Score: 253
Period size: 86 Copynumber: 1.9 Consensus size: 86
58763402 AACCCAAAAA
58763412 CCCTAAATAGCAAATAACCCACTCGAGATTACACGGCCAAAAACGCTTCCACGTCAGAGCGATTT
1 CCCTAAATAGCAAATAACCCACTCGAGATTACACGGCCAAAAACGCTTCCACGTCAGAGCGATTT
**
58763477 TGCCTGACATGAGGAAGAATG
66 TGCCTGACACAAGGAAGAATG
* * * ** *
58763498 CCCTAATTAGCAAATAACCCACTGGGGATTACACGGCCAAAAGTGCTTCCACGTCAGAGCGCTTT
1 CCCTAAATAGCAAATAACCCACTCGAGATTACACGGCCAAAAACGCTTCCACGTCAGAGCGATTT
*
58763563 TGCCTGGCACAAGGAA
66 TGCCTGACACAAGGAA
58763579 AAAAGTGTTG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 72 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (86 bp):
CCCTAAATAGCAAATAACCCACTCGAGATTACACGGCCAAAAACGCTTCCACGTCAGAGCGATTT
TGCCTGACACAAGGAAGAATG
Found at i:58770568 original size:6 final size:6
Alignment explanation
Indices: 58770557--58770587 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
58770547 CCACCATGAT
*
58770557 CATCAC CATCAC CATCAC CATCAC CACCAC C
1 CATCAC CATCAC CATCAC CATCAC CATCAC C
58770588 GTCATCTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.55, G:0.00, T:0.13
Consensus pattern (6 bp):
CATCAC
Found at i:58770569 original size:18 final size:18
Alignment explanation
Indices: 58770545--58770587 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
58770535 TCATCATGAT
* *
58770545 CACCACCATGATCATCAC
1 CACCACCATCACCATCAC
*
58770563 CATCACCATCACCATCAC
1 CACCACCATCACCATCAC
58770581 CACCACC
1 CACCACC
58770588 GTCATCTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.51, G:0.02, T:0.14
Consensus pattern (18 bp):
CACCACCATCACCATCAC
Found at i:58771127 original size:21 final size:22
Alignment explanation
Indices: 58771103--58771144 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
58771093 ATTTTAGTCC
* *
58771103 TTCTA-TTTTTATTTTAAAATT
1 TTCTACTTTTCATTTAAAAATT
58771124 TTCTACTTTTCATTTAAAAAT
1 TTCTACTTTTCATTTAAAAAT
58771145 GCATGTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (22 bp):
TTCTACTTTTCATTTAAAAATT
Found at i:58771777 original size:15 final size:15
Alignment explanation
Indices: 58771757--58771807 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
58771747 AATTTCTGTA
58771757 AATTTTTAAATATTT
1 AATTTTTAAATATTT
58771772 AA-TTTT-AATATTTT
1 AATTTTTAAATA-TTT
* *
58771786 TATTTTTAAAAATTT
1 AATTTTTAAATATTT
58771801 AATTTTT
1 AATTTTT
58771808 TCTACTTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.13
14 8 0.27
15 15 0.50
16 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTTTAAATATTT
Found at i:58771779 original size:14 final size:14
Alignment explanation
Indices: 58771760--58771806 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
58771750 TTCTGTAAAT
58771760 TTTTAAATATTTAA
1 TTTTAAATATTTAA
* *
58771774 TTTTAATATTTTTAT
1 TTTTAA-ATATTTAA
*
58771789 TTTTAAAAATTTAA
1 TTTTAAATATTTAA
58771803 TTTT
1 TTTT
58771807 TTCTACTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAATATTTAA
Found at i:58772287 original size:28 final size:23
Alignment explanation
Indices: 58772231--58772275 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
58772221 GGAAATTCAT
58772231 AAAAATATTATTTTATAAATTAA
1 AAAAATATTATTTTATAAATTAA
58772254 AAAAATATTATTTTATAAATTA
1 AAAAATATTATTTTATAAATTA
58772276 CAACAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAAATATTATTTTATAAATTAA
Found at i:58799947 original size:50 final size:50
Alignment explanation
Indices: 58799872--58799972 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
58799862 TAAAAATTAG
58799872 TGTGACTGATAGAATAACTAAACAATTACACGTGACGTGCCACATGTACC
1 TGTGACTGATAGAATAACTAAACAATTACACGTGACGTGCCACATGTACC
58799922 TGTGACTGATAGAATAACTAAACAATTACACGTGACGTGCCACATGTACC
1 TGTGACTGATAGAATAACTAAACAATTACACGTGACGTGCCACATGTACC
58799972 T
1 T
58799973 ACTTATGATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (50 bp):
TGTGACTGATAGAATAACTAAACAATTACACGTGACGTGCCACATGTACC
Found at i:58822680 original size:97 final size:95
Alignment explanation
Indices: 58822430--58822752 Score: 215
Period size: 97 Copynumber: 3.3 Consensus size: 95
58822420 TCTAATGGAT
* * * * * *
58822430 AAGGATCAAATCCACACAACCTCAAATATATAAAAACAAA-TTGAGCTAACAATCATGTTATCTG
1 AAGGACCAAA-CCCCACAATCTC-AA-ATATCAAAACAAAGTTGAGCCAACAATCATGTCATCTG
*
58822494 TCGGTAGATAGCTTGAATCATAGTTTAACAGCC
63 TCGGTAGATAGCTTGAATCATAGTCTAACAGCC
* * * * * ** *** *
58822527 AAGCATCAAAACCCAAAAATCTCAAATATCAAAAACCAAGTCAAGCCAATGGTCATGTCGTCTGT
1 AAGGA-CCAAACCCCACAATCTCAAATATC-AAAACAAAGTTGAGCCAACAATCATGTCATCTGT
* * * **
58822592 TGGTAGATTGCTT-AACTCATAGCTCTGATGGCC
64 CGGTAGATAGCTTGAA-TCATAG-TCTAACAGCC
* *
58822625 AAGGACCAAACCCTCACAATCTCAAATATCAAAACAAAGTTGAGCCAACAATCATGTAATTTG-C
1 AAGGACCAAACCC-CACAATCTCAAATATCAAAACAAAGTTGAGCCAACAATCATGTCATCTGTC
* * * *
58822689 TAGTAGAGT-GTTTGAGTCATAGTTCTAATAGCC
65 -GGTAGA-TAGCTTGAATCATAG-TCTAACAGCC
* * *
58822722 AAGGATCAAACTCTACAA-CTTCAAATATCAA
1 AAGGACCAAACCCCACAATC-TCAAATATCAA
58822753 CAAACAAGTT
Statistics
Matches: 170, Mismatches: 46, Indels: 21
0.72 0.19 0.09
Matches are distributed among these distances:
95 5 0.03
96 26 0.15
97 110 0.65
98 29 0.17
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (95 bp):
AAGGACCAAACCCCACAATCTCAAATATCAAAACAAAGTTGAGCCAACAATCATGTCATCTGTCG
GTAGATAGCTTGAATCATAGTCTAACAGCC
Found at i:58830034 original size:30 final size:31
Alignment explanation
Indices: 58829995--58830054 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
58829985 GGAGGTGAGA
*
58829995 TGGGAAGGGAATAAAAGTTTT-AGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTGA-GGGAAAAG
*
58830026 TGGG-AGGGAGTAAAAATTTTGAGGGAAAA
1 TGGGAAGGGAATAAAAATTTTGAGGGAAAA
58830055 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGAGGGAAAAG
Found at i:58830283 original size:9 final size:9
Alignment explanation
Indices: 58830269--58830305 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
58830259 TATAGTTTGA
58830269 TATTCGAAT
1 TATTCGAAT
58830278 TATTCGAAT
1 TATTCGAAT
*
58830287 TATTCGAGT
1 TATTCGAAT
58830296 TATTCGAAT
1 TATTCGAAT
58830305 T
1 T
58830306 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:58832054 original size:44 final size:44
Alignment explanation
Indices: 58832003--58832097 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 44
58831993 TACAAAGTAG
** * *
58832003 TATCTAAATATTAAATT-GGTAAAAATAAAGTTTAATAATTACAA
1 TATCTAAATATT-AATTAGACAAAAATAAACTTAAATAATTACAA
*
58832047 TATCTAAATATTAATTAGACAAAAATAAACTTAAATAATTATAA
1 TATCTAAATATTAATTAGACAAAAATAAACTTAAATAATTACAA
58832091 TATCTAA
1 TATCTAA
58832098 GACAAATTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
43 4 0.09
44 41 0.91
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (44 bp):
TATCTAAATATTAATTAGACAAAAATAAACTTAAATAATTACAA
Found at i:58834735 original size:30 final size:31
Alignment explanation
Indices: 58834696--58834755 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
58834686 GGAGGTGGGA
*
58834696 TGGGAAGGGAATAAAAGTTTTAAGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAAGGGAAAAG
* **
58834727 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAAGGGAAAA
58834756 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAAGGGAAAAG
Found at i:58834979 original size:9 final size:9
Alignment explanation
Indices: 58834965--58835001 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
58834955 TATAGTTTGA
58834965 TATTCGAAT
1 TATTCGAAT
58834974 TATTCGAAT
1 TATTCGAAT
*
58834983 TATTCGAGT
1 TATTCGAAT
58834992 TATTCGAAT
1 TATTCGAAT
58835001 T
1 T
58835002 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:58835276 original size:6 final size:6
Alignment explanation
Indices: 58835265--58835290 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
58835255 AGTTTGGTTT
58835265 ATTTTA ATTTTA ATTTTA ATTTTA AT
1 ATTTTA ATTTTA ATTTTA ATTTTA AT
58835291 ATGAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:58838284 original size:40 final size:41
Alignment explanation
Indices: 58838221--58838308 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 41
58838211 AATTATGGAA
* * *
58838221 TACTGAATATTGTTTTTGAGTACTGAATTGAATTGTGAAGG
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAG
* * *
58838262 TACTGAATATTG-TTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAG
58838302 TACTGAA
1 TACTGAA
58838309 GTAATGAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 29 0.71
41 12 0.29
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.40
Consensus pattern (41 bp):
TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAG
Done.