Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold145
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: 2608604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28749 characters in sequence are not A, C, G, or T
File 14 of 15
Found at i:2377167 original size:20 final size:20
Alignment explanation
Indices: 2377129--2377188 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2377119 TTAAAATATT
*
2377129 ATATATTTATATAAATTTTA
1 ATATATTTATATTAATTTTA
* *
2377149 ATATATTTATATTATTTTTT
1 ATATATTTATATTAATTTTA
2377169 AT-TATATTATATTTAATTTT
1 ATATAT-TTATA-TTAATTTT
2377189 TTTAATTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.09
20 24 0.71
21 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATATTTATATTAATTTTA
Found at i:2378328 original size:22 final size:20
Alignment explanation
Indices: 2378281--2378319 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2378271 ATATTTTTAT
2378281 TTAAATTTAATTATAAAATA
1 TTAAATTTAATTATAAAATA
2378301 TATAAATATTAA-TATAAAA
1 T-TAAAT-TTAATTATAAAA
2378320 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.06
21 12 0.71
22 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAATTTAATTATAAAATA
Found at i:2384104 original size:2 final size:2
Alignment explanation
Indices: 2384087--2384125 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2384077 AAGGCGTAAA
*
2384087 AT AT A- AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2384126 TAGATCTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2385364 original size:2 final size:2
Alignment explanation
Indices: 2385357--2385389 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2385347 GCGTGTGCAT
2385357 AG AG AG 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 AG AG AG A
2385390 AACAGTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2391999 original size:21 final size:21
Alignment explanation
Indices: 2391975--2392019 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2391965 GGGCAATAAC
*
2391975 AACTAGTTTTTATATGTTACA
1 AACTAGTATTTATATGTTACA
2391996 AACTAGTATTTATATGTTACA
1 AACTAGTATTTATATGTTACA
2392017 AAC
1 AAC
2392020 AGATTTGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (21 bp):
AACTAGTATTTATATGTTACA
Found at i:2401264 original size:99 final size:102
Alignment explanation
Indices: 2401139--2401343 Score: 274
Period size: 102 Copynumber: 2.0 Consensus size: 102
2401129 ATAAGTTGCA
* * *
2401139 ATTGACCTCTTTAAAGTGACCCAAAGGAAGACAAT-ATT-CA-TATTAATCATAGCCTAACCTTT
1 ATTGACCTCCTTAAAGTGACCCAAAGGAAGACAATGATTACATTAATAATAATAGCCTAACC-TT
*
2401201 GC-AAGTTCCAGCACCAAACTAAGAAAGCTTGTTTCTC
65 GCTAAGCTCCAGCACCAAACTAAGAAAGCTTGTTTCTC
** * *
2401238 ATTGACCTCCTTAAAGTGATTCAAAGGAAGATAATGTTTACATTAATAATAATAGCCTAACCTTG
1 ATTGACCTCCTTAAAGTGACCCAAAGGAAGACAATGATTACATTAATAATAATAGCCTAACCTTG
* * *
2401303 CTAAGCTCCGGCGCCATACTAAGAAAGCTTGTTTCTC
66 CTAAGCTCCAGCACCAAACTAAGAAAGCTTGTTTCTC
2401340 ATTG
1 ATTG
2401344 GCATCTAGCT
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
99 31 0.34
100 2 0.02
101 6 0.07
102 52 0.57
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (102 bp):
ATTGACCTCCTTAAAGTGACCCAAAGGAAGACAATGATTACATTAATAATAATAGCCTAACCTTG
CTAAGCTCCAGCACCAAACTAAGAAAGCTTGTTTCTC
Found at i:2403382 original size:46 final size:46
Alignment explanation
Indices: 2403313--2403410 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 46
2403303 CAATTTGATT
* *
2403313 TTTTTTATTCATTGATTTTACTTATTAAAAAATAAA-ATTGTCTCTA
1 TTTTTTATTAATTGATTTCACTTATTAAAAAATAAAGA-TGTCTCTA
* * * *
2403359 TTTTTTCTTAATTGGTTTCACTTATTAAAGAGTAAAGATGTCTCTA
1 TTTTTTATTAATTGATTTCACTTATTAAAAAATAAAGATGTCTCTA
2403405 TTTTTT
1 TTTTTT
2403411 TTCTCGTTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (46 bp):
TTTTTTATTAATTGATTTCACTTATTAAAAAATAAAGATGTCTCTA
Found at i:2403534 original size:12 final size:12
Alignment explanation
Indices: 2403517--2403580 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
2403507 CTGTATCATC
2403517 ATTTAAAATAAT
1 ATTTAAAATAAT
*
2403529 ATTTAAAA-ATT
1 ATTTAAAATAAT
* *
2403540 AATTTATATTAAT
1 -ATTTAAAATAAT
*
2403553 ATTTATAATTAA-
1 ATTTA-AAATAAT
2403565 ATTTAAAATAAT
1 ATTTAAAATAAT
2403577 -TTTA
1 ATTTA
2403581 TTTTTATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
11 11 0.26
12 24 0.57
13 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAAAATAAT
Found at i:2403576 original size:24 final size:23
Alignment explanation
Indices: 2403517--2403581 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
2403507 CTGTATCATC
*
2403517 ATTTAAAATAATATTTAAAAATTA
1 ATTTAAAATAATATTT-ATAATTA
* *
2403541 ATTTATATTAATATTTATAATTAA
1 ATTTAAAATAATATTTATAATT-A
2403565 ATTTAAAATAAT-TTTAT
1 ATTTAAAATAATATTTAT
2403582 TTTTATTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 10 0.29
24 25 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAAAATAATATTTATAATTA
Found at i:2404041 original size:13 final size:13
Alignment explanation
Indices: 2404023--2404049 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2404013 TTACTTGTAC
2404023 TTAAATATAAATA
1 TTAAATATAAATA
2404036 TTAAATATAAATA
1 TTAAATATAAATA
2404049 T
1 T
2404050 ATTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:2405409 original size:10 final size:10
Alignment explanation
Indices: 2405391--2405427 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2405381 ACTCTCTCGC
*
2405391 CTCTCTATCT
1 CTCTATATCT
2405401 CTCTATATCT
1 CTCTATATCT
2405411 CTCTAT-TC-
1 CTCTATATCT
2405419 CTCTATATC
1 CTCTATATC
2405428 CTTCTATGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
8 6 0.24
9 4 0.16
10 15 0.60
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.49
Consensus pattern (10 bp):
CTCTATATCT
Found at i:2405414 original size:18 final size:18
Alignment explanation
Indices: 2405391--2405427 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2405381 ACTCTCTCGC
2405391 CTCTCTA-TCTCTCTATAT
1 CTCTCTATTC-CTCTATAT
2405409 CTCTCTATTCCTCTATAT
1 CTCTCTATTCCTCTATAT
2405427 C
1 C
2405428 CTTCTATGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.49
Consensus pattern (18 bp):
CTCTCTATTCCTCTATAT
Found at i:2405433 original size:18 final size:18
Alignment explanation
Indices: 2405391--2405439 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
2405381 ACTCTCTCGC
2405391 CTCTCTAT-CTCTCTATAT
1 CTCTCTATGC-CTCTATAT
*
2405409 CTCTCTATTCCTCTATAT
1 CTCTCTATGCCTCTATAT
2405427 C-CTTCTATGCCTC
1 CTC-TCTATGCCTC
2405440 CTTCAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.14, C:0.37, G:0.02, T:0.47
Consensus pattern (18 bp):
CTCTCTATGCCTCTATAT
Found at i:2405688 original size:40 final size:40
Alignment explanation
Indices: 2405644--2405740 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
2405634 CATTCCCCAT
* ** *
2405644 TATTCTAGAATATTCTAGAATCTTTTAGAGCCTTTCACGA
1 TATTCTAGAACATTCTAGAATCTTCCAGAGCCTTCCACGA
2405684 TATTCTAGAACATTCTAGAATCTTCCAGAGCCTTCCACGA
1 TATTCTAGAACATTCTAGAATCTTCCAGAGCCTTCCACGA
*
2405724 TATTCTAAAACATTCTA
1 TATTCTAGAACATTCTA
2405741 AAATGTTCTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (40 bp):
TATTCTAGAACATTCTAGAATCTTCCAGAGCCTTCCACGA
Found at i:2406323 original size:19 final size:19
Alignment explanation
Indices: 2406299--2406337 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2406289 AAAATCAGAG
*
2406299 AGTAAA-AAAGAGAGAAAAA
1 AGTAAAGAAAAAG-GAAAAA
2406318 AGTAAAGAAAAAGGAAAAA
1 AGTAAAGAAAAAGGAAAAA
2406337 A
1 A
2406338 AAGAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (19 bp):
AGTAAAGAAAAAGGAAAAA
Found at i:2406337 original size:21 final size:22
Alignment explanation
Indices: 2406303--2406347 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2406293 TCAGAGAGTA
* *
2406303 AAAAAGAGAGAAAAAAGTAAAG
1 AAAAAGAGAAAAAAAAGAAAAG
2406325 AAAAAG-GAAAAAAAAGAAAAG
1 AAAAAGAGAAAAAAAAGAAAAG
2406346 AA
1 AA
2406348 TAGTGATAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (22 bp):
AAAAAGAGAAAAAAAAGAAAAG
Found at i:2407254 original size:58 final size:58
Alignment explanation
Indices: 2407189--2407578 Score: 352
Period size: 58 Copynumber: 6.8 Consensus size: 58
2407179 GATTTGGTGC
* * * * * *
2407189 AATTTTATGAA-TTTGAATGTCATATAGGTAATTTTTCATAACTTAGGGACTTGGATGT
1 AATTTTATGAATTTTG-ATATCATTTAAGTCATTTTTCATGACTTAGGGACTTTGATGT
** * * *
2407247 AATTTTATGAATTTTTGACGTCATTTAAGTCATTTTTTATGA-TCTAGGGACTTTAATAT
1 AATTTTATGAA-TTTTGATATCATTTAAGTCATTTTTCATGACT-TAGGGACTTTGATGT
* * * * *
2407306 AATTTTATGGATTTTGATATCATTTAAATAATTTTTTATGA-TCTAAGGACTTTGATGT
1 AATTTTATGAATTTTGATATCATTTAAGTCATTTTTCATGACT-TAGGGACTTTGATGT
* * * **
2407364 AATTTTGTGAATTTTGATATCATTTAAGTTA-TTTTCATGACTTAGGGATTTTGATAC
1 AATTTTATGAATTTTGATATCATTTAAGTCATTTTTCATGACTTAGGGACTTTGATGT
* *
2407421 AATTTTATGAATTTT--T-T-ATGTTAGGTCATTTTTCATGACTTACGGACTTTGATGT
1 AATTTTATGAATTTTGATATCAT-TTAAGTCATTTTTCATGACTTAGGGACTTTGATGT
* * * *
2407476 AATTTTATGAATTTTGATATCATTTAAGTCATTTTTCAT-AATGTAAGGATTTTTATGT
1 AATTTTATGAATTTTGATATCATTTAAGTCATTTTTCATGACT-TAGGGACTTTGATGT
* ** *
2407534 AATTTCAT-ATATTTAAAAAAT-ATTTAAGTCATTTTTCATGACTTA
1 AATTTTATGA-ATTT-TGATATCATTTAAGTCATTTTTCATGACTTA
2407579 AGAATTATTA
Statistics
Matches: 275, Mismatches: 43, Indels: 28
0.79 0.12 0.08
Matches are distributed among these distances:
53 2 0.01
54 7 0.03
55 38 0.14
57 37 0.13
58 139 0.51
59 48 0.17
60 4 0.01
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (58 bp):
AATTTTATGAATTTTGATATCATTTAAGTCATTTTTCATGACTTAGGGACTTTGATGT
Found at i:2407536 original size:170 final size:171
Alignment explanation
Indices: 2407221--2407538 Score: 408
Period size: 170 Copynumber: 1.8 Consensus size: 171
2407211 TATAGGTAAT
** *
2407221 TTTTCATAACTTAGGGACTTGGATGTAATTTTATGAATTTTTGACGTCATTTAAGTCATTTTTTA
1 TTTTCATAACTTAGGGACTTGGATACAATTTTATGAATTTTT---GTCATTTAAGTCATTTTTCA
* * * *
2407286 TGATCTAGGGACTTTAATATAATTTTATGGATTTTGATATCATTTAAATAATTTTTTATGATCTA
63 TGATCTACGGACTTTAATATAATTTTATGAATTTTGATATCATTTAAATAATTTTTCATAATCTA
2407351 AGGACTTTGATGTAATTTTGTGAATTTTGATATCATTTAAGTTA
128 AGGACTTTGATGTAATTTTGTGAATTTTGATATCATTTAAGTTA
* * * *
2407395 TTTTCATGACTTAGGGATTTTGATACAATTTTATGAATTTTT-T-ATGTTAGGTCATTTTTCATG
1 TTTTCATAACTTAGGGACTTGGATACAATTTTATGAATTTTTGTCAT-TTAAGTCATTTTTCATG
* * * * *
2407458 A-CTTACGGACTTTGATGTAATTTTATGAATTTTGATATCATTTAAGTCATTTTTCATAATGTAA
65 ATC-TACGGACTTTAATATAATTTTATGAATTTTGATATCATTTAAATAATTTTTCATAATCTAA
* *
2407522 GGATTTTTATGTAATTT
129 GGACTTTGATGTAATTT
2407539 CATATATTTA
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
169 3 0.02
170 84 0.68
174 37 0.30
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (171 bp):
TTTTCATAACTTAGGGACTTGGATACAATTTTATGAATTTTTGTCATTTAAGTCATTTTTCATGA
TCTACGGACTTTAATATAATTTTATGAATTTTGATATCATTTAAATAATTTTTCATAATCTAAGG
ACTTTGATGTAATTTTGTGAATTTTGATATCATTTAAGTTA
Found at i:2407561 original size:170 final size:172
Alignment explanation
Indices: 2407219--2407578 Score: 399
Period size: 170 Copynumber: 2.1 Consensus size: 172
2407209 CATATAGGTA
* **
2407219 ATTTTTCATAACTTAGGGACTTGGATGTAATTTTATGAATTTTTGACGTCATTTAAGTCATTTTT
1 ATTTTTCATGACTTAGGGACTTGGATACAATTTTATGAATTTTT---GTCATTTAAGTCATTTTT
* * * * *
2407284 TATGATCTAGGGACTTTAATATAATTTTATGGATTTTGATATCATTTAAATAATTTTTTATGATC
63 CATGATCTACGGACTTTAATATAATTTTATGAATTTTGATATCATTTAAATAATTTTTCATAATC
** ** * *
2407349 TAAGGACTTTGATGTAATTTTGTGAATTTTGATATCATTTAAGTT
128 TAAGGACTTTGATGTAATTTCATGAATTTAAAAATCATTTAAGTC
* * *
2407394 A-TTTTCATGACTTAGGGATTTTGATACAATTTTATGAATTTTT-T-ATGTTAGGTCATTTTTCA
1 ATTTTTCATGACTTAGGGACTTGGATACAATTTTATGAATTTTTGTCAT-TTAAGTCATTTTTCA
* * * * *
2407456 TGA-CTTACGGACTTTGATGTAATTTTATGAATTTTGATATCATTTAAGTCATTTTTCATAATGT
65 TGATC-TACGGACTTTAATATAATTTTATGAATTTTGATATCATTTAAATAATTTTTCATAATCT
* *
2407520 AAGGATTTTTATGTAATTTCAT-ATATTTAAAAAAT-ATTTAAGTC
129 AAGGACTTTGATGTAATTTCATGA-ATTT-AAAAATCATTTAAGTC
2407564 ATTTTTCATGACTTA
1 ATTTTTCATGACTTA
2407579 AGAATTATTA
Statistics
Matches: 156, Mismatches: 24, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
169 4 0.03
170 98 0.63
171 16 0.10
174 37 0.24
175 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (172 bp):
ATTTTTCATGACTTAGGGACTTGGATACAATTTTATGAATTTTTGTCATTTAAGTCATTTTTCAT
GATCTACGGACTTTAATATAATTTTATGAATTTTGATATCATTTAAATAATTTTTCATAATCTAA
GGACTTTGATGTAATTTCATGAATTTAAAAATCATTTAAGTC
Found at i:2408036 original size:16 final size:18
Alignment explanation
Indices: 2408004--2408039 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
2407994 TAAGATGAAA
2408004 AAAAATAATATGAATTAT
1 AAAAATAATATGAATTAT
2408022 AAAAATAA-A-GAATTAT
1 AAAAATAATATGAATTAT
2408038 AA
1 AA
2408040 TTAAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (18 bp):
AAAAATAATATGAATTAT
Found at i:2410129 original size:19 final size:19
Alignment explanation
Indices: 2410102--2410177 Score: 63
Period size: 19 Copynumber: 4.1 Consensus size: 19
2410092 TCAATATATC
*
2410102 ATATAATTAAATTATTTTT
1 ATATTATTAAATTATTTTT
*
2410121 ATATTATTAAA-TA-TATT
1 ATATTATTAAATTATTTTT
2410138 ATACTTA-T-AATATATTTTT
1 ATA-TTATTAAAT-TATTTTT
2410157 ATATT-TTAAAACTTATTTTT
1 ATATTATT-AAA-TTATTTTT
2410177 A
1 A
2410178 CATAAAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
16 2 0.04
17 7 0.15
18 10 0.22
19 16 0.35
20 10 0.22
21 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTATTAAATTATTTTT
Found at i:2410134 original size:36 final size:35
Alignment explanation
Indices: 2410086--2410166 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 35
2410076 TAAATATAAC
*
2410086 ATATTTTCAATATATCATATAATTA-AAT-TATTTTT
1 ATATTTTAAATATAT--TATAATTATAATATATTTTT
*
2410121 ATATTATTAAATATATTATACTTATAATATATTTTT
1 ATATT-TTAAATATATTATAATTATAATATATTTTT
2410157 ATATTTTAAA
1 ATATTTTAAA
2410167 ACTTATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 7 0.17
35 13 0.32
36 21 0.51
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (35 bp):
ATATTTTAAATATATTATAATTATAATATATTTTT
Found at i:2416366 original size:13 final size:14
Alignment explanation
Indices: 2416350--2416390 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2416340 TAATATATAT
2416350 AATATATAT-TAAA
1 AATATATATATAAA
*
2416363 AATATTTATATAAA
1 AATATATATATAAA
2416377 AAT-TAATATATAAA
1 AATAT-ATATATAAA
2416391 TTATAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATATATATATAAA
Found at i:2416426 original size:17 final size:17
Alignment explanation
Indices: 2416413--2416451 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
2416403 TTTTTAATAT
2416413 ATAAAATATTTTAAAAA
1 ATAAAATATTTTAAAAA
*
2416430 ATAAAATAATATTTTAAAA
1 ATAAAAT-AT-TTTAAAAA
2416449 ATA
1 ATA
2416452 TTTATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAATATTTTAAAAA
Found at i:2416801 original size:28 final size:28
Alignment explanation
Indices: 2416770--2416828 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
2416760 CATTCTAATA
** *
2416770 AAATTCAATCAAATAA-ATAATTTTATTT
1 AAATTCAAAAAAATAATA-AATTTAATTT
*
2416798 AAATTTAAAAAAATAATAAATTTAATTT
1 AAATTCAAAAAAATAATAAATTTAATTT
2416826 AAA
1 AAA
2416829 ATAATCTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (28 bp):
AAATTCAAAAAAATAATAAATTTAATTT
Found at i:2417154 original size:14 final size:14
Alignment explanation
Indices: 2417123--2417168 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
2417113 AATTTTTTTA
*
2417123 ATTTTTTAAATAA-
1 ATTTTTTAAAAAAT
*
2417136 GTTTTTTAAAAAAT
1 ATTTTTTAAAAAAT
*
2417150 ATTTTTTAAAATAT
1 ATTTTTTAAAAAAT
2417164 ATTTT
1 ATTTT
2417169 GATTACGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTTTTTAAAAAAT
Found at i:2418621 original size:72 final size:72
Alignment explanation
Indices: 2418532--2418863 Score: 348
Period size: 74 Copynumber: 4.6 Consensus size: 72
2418522 TGTATAAAAT
* *
2418532 TTTTTAGGATATTATTTATATTTATTTGTAGAAGTTTAAATTTGTTTTTAGGTATGATTATATGA
1 TTTTTAGGATATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTAGGTATGATTATATGA
*
2418597 GTTGAAA
66 GTTTAAA
* * * * * *
2418604 TTTTTAGGATATAATTTATTTTTATTTGTAAAAGTTTATATATGTTTTTTTGGTATGCTTATATA
1 TTTTTAGGATATAATTTATTTTTATTTGTAGAAGTTTAAATTTG-TTTTTAGGTATGATTATATG
*
2418669 AATTTAAA
65 AGTTTAAA
** *
2418677 TTTTTTATAATATAATTTATTTTTATTTTTAGAAGTTTAAATGTAT-TTTTTAGGTATGATTATA
1 -TTTTTAGGATATAATTTATTTTTATTTGTAGAAGTTTAAAT-T-TGTTTTTAGGTATGATTATA
* *
2418741 CGAGTTTATA
63 TGAGTTTAAA
** * * * * * *
2418751 TTTTTGAACATATAATTTATTTTTATTTGTAGAAATTTAAATATATTTTT---TGTGTTTACATG
1 TTTTT-AGGATATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTAGGTATGATTATATG
2418813 AGTTTAAA
65 AGTTTAAA
* * * *
2418821 TTTTTAGGGTATTATTTATCTTTATTTATAGAAGTTTAAATTT
1 TTTTTAGGATATAATTTATTTTTATTTGTAGAAGTTTAAATTT
2418864 TTATTTAAAG
Statistics
Matches: 214, Mismatches: 40, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
69 30 0.14
70 20 0.09
72 40 0.19
73 33 0.15
74 90 0.42
76 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (72 bp):
TTTTTAGGATATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTAGGTATGATTATATGA
GTTTAAA
Found at i:2418695 original size:146 final size:148
Alignment explanation
Indices: 2418528--2418861 Score: 398
Period size: 146 Copynumber: 2.3 Consensus size: 148
2418518 AATTTGTATA
* *
2418528 AAATTTTTTAGGATATTATTTATATTTATTTGTAGAAGTTTAAAT-T-TGTTTTTAGGTATGATT
1 AAATTTTTTAGAATATAATTTATATTTATTTGTAGAAGTTTAAATGTAT-TTTTTAGGTATGATT
* ** * *
2418591 ATATGAGTTGAAATTTTT-AGGATATAATTTATTTTTATTTGTA-AAAGTTTATATATGTTTTTT
65 ATACGAGTTGAAATTTTTGAACATATAATTTATTTTTATTTGTAGAAA-TTTAAATATATTTTTT
2418654 TGGTATGCTTATATAAATTT
129 TGGTATGCTTATATAAATTT
* * *
2418674 AAATTTTTTATAATATAATTTATTTTTATTTTTAGAAGTTTAAATGTATTTTTTAGGTATGATTA
1 AAATTTTTTAGAATATAATTTATATTTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGATTA
* *
2418739 TACGAGTTTATATTTTTGAACATATAATTTATTTTTATTTGTAGAAATTTAAATATA-TTTTTT-
66 TACGAGTTGAAATTTTTGAACATATAATTTATTTTTATTTGTAGAAATTTAAATATATTTTTTTG
* * * *
2418802 G--TGTTTACATGAGTTT
131 GTATGCTTATATAAATTT
** * * *
2418818 AAA-TTTTTAGGGTATTATTTATCTTTATTTATAGAAGTTTAAAT
1 AAATTTTTTAGAATATAATTTATATTTATTTGTAGAAGTTTAAAT
2418862 TTTTATTTAA
Statistics
Matches: 162, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
143 35 0.22
144 14 0.09
146 41 0.25
147 37 0.23
148 32 0.20
149 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (148 bp):
AAATTTTTTAGAATATAATTTATATTTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGATTA
TACGAGTTGAAATTTTTGAACATATAATTTATTTTTATTTGTAGAAATTTAAATATATTTTTTTG
GTATGCTTATATAAATTT
Found at i:2419870 original size:25 final size:24
Alignment explanation
Indices: 2419833--2419880 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2419823 AACTGTATTG
2419833 TATTATGTTCAAAAGTTAATAATTT
1 TATTATGTTCAAAA-TTAATAATTT
*
2419858 TATTAT-TTACAAAATTGATAATT
1 TATTATGTT-CAAAATTAATAATT
2419881 AATAATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (24 bp):
TATTATGTTCAAAATTAATAATTT
Found at i:2420115 original size:14 final size:16
Alignment explanation
Indices: 2420096--2420127 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2420086 CATGTGCAAG
2420096 AAAAAT-AT-ATATTA
1 AAAAATAATAATATTA
2420110 AAAAATAATAATATTA
1 AAAAATAATAATATTA
2420126 AA
1 AA
2420128 TATAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATAATAATATTA
Found at i:2420135 original size:23 final size:24
Alignment explanation
Indices: 2420104--2420164 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
2420094 AGAAAAATAT
*
2420104 ATATTAAAAAATAATAATAT-TAA
1 ATATAAAAAAATAATAATATCTAA
*
2420127 ATATAAAAAATTAATAATATCGTAA
1 ATATAAAAAAATAATAATATC-TAA
* *
2420152 ATATCAAATAATA
1 ATATAAAAAAATA
2420165 TCAAAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 18 0.58
25 13 0.42
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (24 bp):
ATATAAAAAAATAATAATATCTAA
Found at i:2420603 original size:75 final size:70
Alignment explanation
Indices: 2420511--2420655 Score: 175
Period size: 71 Copynumber: 2.0 Consensus size: 70
2420501 TTACAACAAA
* ** *
2420511 ATTTTATTAAAAATAATAATTAATAGTTTTATTTTTTA-ATATATATTTTTTAAATTTAATTAAA
1 ATTTTATTAAAAATAATAATTAATA-TATTA-AATTTACATA-A-A-ATTTTAAATTTAATTAAA
2420575 ATTTATTTTT
61 ATTTATTTTT
**
2420585 ATTTTATTTAAATTTAATAATTAATATATTAAATTTACATAAAATTTTAAATTTAATTAAAATTT
1 ATTTTA-TTAAAAATAATAATTAATATATTAAATTTACATAAAATTTTAAATTTAATTAAAATTT
2420650 ATTTTT
65 ATTTTT
2420656 TAAATTTTCA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
71 27 0.43
72 1 0.02
73 5 0.08
74 13 0.21
75 17 0.27
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (70 bp):
ATTTTATTAAAAATAATAATTAATATATTAAATTTACATAAAATTTTAAATTTAATTAAAATTTA
TTTTT
Found at i:2420636 original size:18 final size:17
Alignment explanation
Indices: 2420591--2420649 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 17
2420581 TTTTATTTTA
2420591 TTTAAATTTAATAATTAAT
1 TTTAAATTTAATAA--AAT
2420610 ATATTAAATTTACATAAAAT
1 -T-TTAAATTTA-ATAAAAT
2420630 TTTAAATTTAATTAAAAT
1 TTTAAATTTAA-TAAAAT
2420648 TT
1 TT
2420650 ATTTTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.03
18 17 0.47
19 1 0.03
20 4 0.11
21 9 0.25
22 4 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAATTTAATAAAAT
Found at i:2421190 original size:28 final size:30
Alignment explanation
Indices: 2421137--2421204 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 30
2421127 TTTTGAAAAA
*
2421137 TTATAATTAATATATAATATTTTATT-T-T
1 TTATAATTAACATATAATATTTTATTATAT
2421165 TTATAATTAACAT-TAA-ATTTAATATTATAT
1 TTATAATTAACATATAATATTT--TATTATAT
*
2421195 ATATAATTAA
1 TTATAATTAA
2421205 ACAGATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 4 0.12
27 3 0.09
28 16 0.47
29 1 0.03
30 10 0.29
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (30 bp):
TTATAATTAACATATAATATTTTATTATAT
Found at i:2421266 original size:16 final size:16
Alignment explanation
Indices: 2421247--2421280 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2421237 TGTTATAAAA
*
2421247 TATAATATATTATTTT
1 TATAATATATAATTTT
*
2421263 TATATTATATAATTTT
1 TATAATATATAATTTT
2421279 TA
1 TA
2421281 AAATTATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATATATAATTTT
Found at i:2421319 original size:19 final size:19
Alignment explanation
Indices: 2421295--2421352 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
2421285 TATTTAAAAA
*
2421295 TAAAAATAAAAATTTATTT
1 TAAAAATAAAAATTTAATT
* *
2421314 TAAAAATAATATTTTAATT
1 TAAAAATAAAAATTTAATT
*
2421333 TATAAAATAAAAATTAAATT
1 TA-AAAATAAAAATTTAATT
2421353 AAACATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAATAAAAATTTAATT
Found at i:2421350 original size:33 final size:30
Alignment explanation
Indices: 2421313--2421383 Score: 72
Period size: 33 Copynumber: 2.2 Consensus size: 30
2421303 AAAATTTATT
2421313 TTAAAAATA-ATATTTTAATTTATAAAATAAAAA
1 TTAAAAA-ACATA-TTTAA-TTATAAAAT-AAAA
*
2421346 TTAAATTAAACATATTTAATTATCAAATAAAA
1 TTAAA--AAACATATTTAATTATAAAATAAAA
2421378 TTAAAA
1 TTAAAA
2421384 TCAATAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
32 9 0.26
33 13 0.38
34 6 0.18
35 5 0.15
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (30 bp):
TTAAAAAACATATTTAATTATAAAATAAAA
Found at i:2426771 original size:81 final size:82
Alignment explanation
Indices: 2426651--2426812 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 82
2426641 TGCATCTGCA
*
2426651 ACCTGCTTCTCTACTCCTAATGTTGGCCTCCTTTGTAAAATTAAAAAAAATAAATAAATAAAAGA
1 ACCTGCTTCTCTACCCCTAATGTTGGCCTCCTTTGTAAAATTAAAAAAAATAAATAAATAAAAGA
2426716 AAAGGCCATAAACTATC
66 AAAGGCCATAAACTATC
2426733 ACCTGCTT-TCTACCCCTAATGTTGGCCTCCTTTGTAAAATTAAAAAAAATAAATAAATAAAAGA
1 ACCTGCTTCTCTACCCCTAATGTTGGCCTCCTTTGTAAAATTAAAAAAAATAAATAAATAAAAGA
2426797 AAAGGCCATAAACTAT
66 AAAGGCCATAAACTAT
2426813 ATCCTTGAGA
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
81 71 0.90
82 8 0.10
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (82 bp):
ACCTGCTTCTCTACCCCTAATGTTGGCCTCCTTTGTAAAATTAAAAAAAATAAATAAATAAAAGA
AAAGGCCATAAACTATC
Found at i:2430218 original size:26 final size:27
Alignment explanation
Indices: 2430173--2430236 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 27
2430163 ATTTGAGTTG
2430173 AATTTATTAAAATAAAT-AAATT-ATT-T
1 AATTTA-T-AAATAAATAAAATTAATTAT
2430199 AATTTATAAATAAATTTAAAATTAATTAT
1 AATTTATAAATAAA--TAAAATTAATTAT
2430228 AATTATATA
1 AATT-TATA
2430237 TATTTATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
24 7 0.22
25 1 0.03
26 7 0.22
27 5 0.16
28 3 0.09
29 5 0.16
30 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AATTTATAAATAAATAAAATTAATTAT
Found at i:2430329 original size:43 final size:41
Alignment explanation
Indices: 2430257--2430367 Score: 111
Period size: 43 Copynumber: 2.7 Consensus size: 41
2430247 TCAAGTTATT
* *
2430257 TATTTTATTT-AATTATAAATTTTTAATATATTAAAATAATAAA
1 TATTTTATTTAAATT-T-AATTATAAATATATTAAAATAA-AAA
*
2430300 TATTTTATTTAAATTTAATTATAATATATATTAATATAAAAA
1 TATTTTATTTAAATTTAATTATAA-ATATATTAAAATAAAAA
* *
2430342 TA-ATT-TTTAAATTTTTATTATAAATA
1 TATTTTATTTAAA-TTTAATTATAAATA
2430368 ATAAATTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
40 9 0.15
41 12 0.20
42 11 0.18
43 24 0.40
44 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (41 bp):
TATTTTATTTAAATTTAATTATAAATATATTAAAATAAAAA
Found at i:2430752 original size:21 final size:20
Alignment explanation
Indices: 2430728--2430778 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2430718 GAAGTGCTTT
* *
2430728 TTTTAATAAAATTATTAAATA
1 TTTTAATAAAATAAAT-AATA
2430749 TTTTAATTAAAATAAATAATA
1 TTTTAA-TAAAATAAATAATA
2430770 TTTT-ATAAA
1 TTTTAATAAA
2430779 TTAATTACGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 1 0.04
21 14 0.52
22 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTAATAAAATAAATAATA
Found at i:2431153 original size:16 final size:16
Alignment explanation
Indices: 2431135--2431165 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2431125 ATAATTGTTA
2431135 AAAAAATA-TAATATT
1 AAAAAATATTAATATT
2431150 AAAAAATATTAATATT
1 AAAAAATATTAATATT
2431166 TTGATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAAATATTAATATT
Found at i:2431383 original size:19 final size:21
Alignment explanation
Indices: 2431334--2431389 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 21
2431324 AATGGATTGG
*
2431334 TTTTACTTAATTTAAATTATTA
1 TTTTA-TTAATTTAAATTAATA
2431356 TTCTT-TTAA-TTAAA-TAATA
1 TT-TTATTAATTTAAATTAATA
2431375 TTTTATTAAATTTAA
1 TTTTATT-AATTTAA
2431390 TTATAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
18 2 0.07
19 8 0.28
20 7 0.24
21 8 0.28
22 2 0.07
23 2 0.07
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATTAATTTAAATTAATA
Found at i:2431617 original size:20 final size:19
Alignment explanation
Indices: 2431602--2431640 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2431592 TTAAAATAGT
2431602 TTTAATTAATAAAAAATTAA
1 TTTAATTAATAAAAAA-TAA
*
2431622 TTTAATTGATAAAAAATAA
1 TTTAATTAATAAAAAATAA
2431641 AAAAATTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTAATTAATAAAAAATAA
Found at i:2431647 original size:19 final size:19
Alignment explanation
Indices: 2431625--2431678 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
2431615 AAATTAATTT
2431625 AATTGATAAAAAATAAAAA
1 AATTGATAAAAAATAAAAA
* *
2431644 AATTTGTTAAAAATTAAAAA
1 AA-TTGATAAAAAATAAAAA
*
2431664 AA-TCAT-AAAAATAAA
1 AATTGATAAAAAATAAA
2431679 TTTTAAACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 8 0.28
18 2 0.07
19 2 0.07
20 17 0.59
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
AATTGATAAAAAATAAAAA
Found at i:2431763 original size:14 final size:14
Alignment explanation
Indices: 2431740--2431781 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2431730 TTTAACCTCT
2431740 TAAATATATATTAA
1 TAAATATATATTAA
2431754 -AAATTATATACTTAA
1 TAAA-TATATA-TTAA
2431769 TTAAATATATATT
1 -TAAATATATATT
2431782 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.12
14 6 0.25
15 6 0.25
16 6 0.25
17 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATATATATTAA
Found at i:2432144 original size:5 final size:5
Alignment explanation
Indices: 2432114--2432276 Score: 65
Period size: 5 Copynumber: 32.8 Consensus size: 5
2432104 GTTAATTTAG
* * *
2432114 ATATA ATA-A A-ATT ATATA ATATTA ATATA ATATA A-AAA ATTAAA ATATA
1 ATATA ATATA ATATA ATATA ATA-TA ATATA ATATA ATATA A-TATA ATATA
* * * * * * *
2432163 ATATA ATATTA AAAAA ATAAA ATA-A ATA-A ATATT TTAAA AT-TA ATAAA
1 ATATA ATA-TA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * *
2432211 ATATTA ATTATTA ATAT- ATA-A AAATT ATA-A ATATA AAATA ATTTAA
1 ATA-TA A-TA-TA ATATA ATATA ATATA ATATA ATATA ATATA ATAT-A
2432257 ATATA ATTATA ATATA ATAT
1 ATATA A-TATA ATATA ATAT
2432277 GTAAATATAA
Statistics
Matches: 120, Mismatches: 23, Indels: 30
0.69 0.13 0.17
Matches are distributed among these distances:
3 1 0.01
4 25 0.21
5 62 0.52
6 26 0.22
7 6 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:2432202 original size:24 final size:27
Alignment explanation
Indices: 2432121--2432276 Score: 112
Period size: 27 Copynumber: 5.7 Consensus size: 27
2432111 TAGATATAAT
2432121 AAAATTATATAATATTAATATAATA-T-AA
1 AAAATTA-A-AATA-TAATATAATATTAAA
2432149 AAAATTAAAATATAATATAATATTAAA
1 AAAATTAAAATATAATATAATATTAAA
2432176 AAAA-TAAAATA-AATA-AATATTTTAAA
1 AAAATTAAAATATAATATAATA--TTAAA
* *
2432202 ATTAA-TAAAATATTAATTATTAATA-TATA
1 A-AAATTAAAATA-TAA-TA-TAATATTAAA
*
2432231 AAAATTATAAATATAAAATAAT-TTAAA
1 AAAATTA-AAATATAATATAATATTAAA
* *
2432258 TATAATTATAATATAATAT
1 -AAAATTAAAATATAATAT
2432277 GTAAATATAA
Statistics
Matches: 106, Mismatches: 8, Indels: 29
0.74 0.06 0.20
Matches are distributed among these distances:
24 4 0.04
25 14 0.13
26 18 0.17
27 32 0.30
28 16 0.15
29 11 0.10
30 7 0.07
32 4 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAATTAAAATATAATATAATATTAAA
Found at i:2432214 original size:19 final size:18
Alignment explanation
Indices: 2432180--2432215 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2432170 ATTAAAAAAA
2432180 TAAAATAAATAAATATTT
1 TAAAATAAATAAATATTT
*
2432198 TAAAATTAATAAAATATT
1 TAAAATAAAT-AAATATT
2432216 AATTATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATAAATAAATATTT
Found at i:2432236 original size:17 final size:15
Alignment explanation
Indices: 2432216--2432262 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 15
2432206 ATAAAATATT
2432216 AATTATTAATATATAAA
1 AATTA-TAA-ATATAAA
2432233 AATTATAAATATAAAA
1 AATTATAAATAT-AAA
2432249 TAATT-TAAATATAA
1 -AATTATAAATATAA
2432263 TTATAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.21
16 13 0.46
17 9 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTATAAATATAAA
Found at i:2432285 original size:13 final size:12
Alignment explanation
Indices: 2432127--2432296 Score: 65
Period size: 11 Copynumber: 15.4 Consensus size: 12
2432117 TAATAAAATT
*
2432127 ATATAA-TATTA
1 ATATAATTATAA
2432138 ATATAA-TATAA
1 ATATAATTATAA
2432149 A-A-AATTA-AA
1 ATATAATTATAA
2432158 ATATAA-TAT-A
1 ATATAATTATAA
*
2432168 ATATTAA--AAAA
1 ATA-TAATTATAA
* *
2432179 ATAAAATAAATAA
1 ATATAAT-TATAA
*
2432192 ATAT-TTTA-AA
1 ATATAATTATAA
2432202 AT-TAA-TA-AA
1 ATATAATTATAA
*
2432211 ATATTAATTATTA
1 ATA-TAATTATAA
*
2432224 ATAT-A-TAAAA
1 ATATAATTATAA
*
2432234 ATTATAAATATAA
1 A-TATAATTATAA
2432247 A-ATAATT-TAA
1 ATATAATTATAA
2432257 ATATAATTAT-A
1 ATATAATTATAA
*
2432268 ATATAATATGTAA
1 ATATAAT-TATAA
*
2432281 ATATAA-AATAA
1 ATATAATTATAA
2432292 ATATA
1 ATATA
2432297 TAAATTACTT
Statistics
Matches: 122, Mismatches: 16, Indels: 42
0.68 0.09 0.23
Matches are distributed among these distances:
9 12 0.10
10 25 0.20
11 55 0.45
12 8 0.07
13 22 0.18
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (12 bp):
ATATAATTATAA
Found at i:2432291 original size:5 final size:6
Alignment explanation
Indices: 2432236--2432296 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
2432226 ATATAAAAAT
* * *
2432236 TATAAA TATAAA -AT-AA TTTAAA TATAAT TAT-AA TATAATA TGTAAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAA-A TATAAA
2432282 TATAAA -ATAAA TATA
1 TATAAA TATAAA TATA
2432297 TAAATTACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
4 2 0.05
5 12 0.27
6 25 0.57
7 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (6 bp):
TATAAA
Found at i:2440551 original size:37 final size:37
Alignment explanation
Indices: 2440481--2440580 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 37
2440471 ATTTTATTAG
* *
2440481 TTATT-TTTAATATAAATATAATTTTCATAATTTT-TT
1 TTATTATTTAACATAAATATAATTTT-ATAATTTTAAT
*
2440517 TTATTATTTAACATAAATATAATATATT-TTATTTTACAT
1 TTATTATTTAACATAAATATAAT-T-TTATAATTTTA-AT
*
2440556 TTATTATTT-A-ATATATATAATTTTA
1 TTATTATTTAACATAAATATAATTTTA
2440581 ATTATTTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
35 2 0.04
36 6 0.11
37 32 0.59
38 2 0.04
39 12 0.22
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (37 bp):
TTATTATTTAACATAAATATAATTTTATAATTTTAAT
Found at i:2440567 original size:28 final size:27
Alignment explanation
Indices: 2440536--2440623 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
2440526 AACATAAATA
* *
2440536 TAATATATTTTATTTTACATT-TATTATT
1 TAATATATATAATTTTA-ATTAT-TTATT
2440564 TAATATATATAATTTTAATTATTTATT
1 TAATATATATAATTTTAATTATTTATT
*
2440591 T--TATATATACATTTTAATATATTATCTT
1 TAATATATATA-ATTTTAAT-TATT-TATT
2440619 TAATA
1 TAATA
2440624 ATAATTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
25 8 0.16
26 8 0.16
27 13 0.25
28 20 0.39
30 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (27 bp):
TAATATATATAATTTTAATTATTTATT
Found at i:2440584 original size:23 final size:25
Alignment explanation
Indices: 2440551--2440613 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
2440541 TATTTTATTT
2440551 TACA-TTT-ATTATTTA-ATATATA
1 TACATTTTAATTATTTATATATATA
*
2440573 TA-ATTTTAATTATTTATTTTATATA
1 TACATTTTAATTATTTA-TATATATA
2440598 TACATTTTAATATATT
1 TACATTTTAAT-TATT
2440614 ATCTTTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 1 0.03
22 5 0.15
23 8 0.24
25 8 0.24
26 8 0.24
27 4 0.12
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
TACATTTTAATTATTTATATATATA
Found at i:2440597 original size:27 final size:27
Alignment explanation
Indices: 2440538--2440631 Score: 88
Period size: 26 Copynumber: 3.5 Consensus size: 27
2440528 CATAAATATA
* * * *
2440538 ATATATTTTATTTTACATTTATTATTTA
1 ATATATATAATTTTA-ATATATTATTTT
2440566 ATATATATAATTTTAAT-TATTTATTTT
1 ATATATATAATTTTAATATA-TTATTTT
*
2440593 ATATATA-CATTTTAATATATTATCTTT
1 ATATATATAATTTTAATATATTAT-TTT
2440620 A-ATA-ATAATTTT
1 ATATATATAATTTT
2440632 TTATTCTCAT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.02
26 22 0.39
27 21 0.37
28 13 0.23
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (27 bp):
ATATATATAATTTTAATATATTATTTT
Found at i:2440620 original size:14 final size:14
Alignment explanation
Indices: 2440536--2440631 Score: 71
Period size: 13 Copynumber: 7.1 Consensus size: 14
2440526 AACATAAATA
*
2440536 TAATATATTTTATTT
1 TAATATA-TATATTT
*
2440551 TACATTTAT-TA-TT
1 TA-ATATATATATTT
2440564 TAATATATATAATTT
1 TAATATATAT-ATTT
*
2440579 TAAT-TATTTATTT
1 TAATATATATATTT
*
2440592 T-ATATATACATTT
1 TAATATATATATTT
2440605 TAATATAT-TATCTT
1 TAATATATATAT-TT
2440619 TAATA-ATA-ATTT
1 TAATATATATATTT
2440631 T
1 T
2440632 TTATTCTCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
12 10 0.15
13 24 0.36
14 20 0.30
15 9 0.13
16 4 0.06
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATATATATATTT
Found at i:2440691 original size:24 final size:23
Alignment explanation
Indices: 2440656--2440714 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
2440646 TCGATACCAA
*
2440656 TATT-TTAAAATTTAAATACATAT
1 TATTATTATAATTTAAAT-CATAT
* *
2440679 T-TTATTATTAATTTTAATCTTAT
1 TATTATTA-TAATTTAAATCATAT
2440702 TATTATTATAATT
1 TATTATTATAATT
2440715 AATTAAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 2 0.07
23 14 0.47
24 14 0.47
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTATTATAATTTAAATCATAT
Found at i:2441740 original size:15 final size:15
Alignment explanation
Indices: 2441720--2441750 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2441710 ACTTAGGAAA
*
2441720 GACATCAACAGTTTG
1 GACATCAACAATTTG
2441735 GACATCAACAATTTG
1 GACATCAACAATTTG
2441750 G
1 G
2441751 TGCCGTCTGT
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:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (15 bp):
GACATCAACAATTTG
Found at i:2442532 original size:17 final size:17
Alignment explanation
Indices: 2442495--2442538 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2442485 TCGTGTTATA
2442495 TTATATTT-TAATAATT
1 TTATATTTATAATAATT
2442511 TTATATTTATAAT-ATT
1 TTATATTTATAATAATT
*
2442527 TATATAATTATA
1 T-TATATTTATA
2442539 TCTAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATTTATAATAATT
Found at i:2449852 original size:3 final size:3
Alignment explanation
Indices: 2449839--2449869 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2449829 TCTTCCTTTC
*
2449839 CTT CAT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
2449870 CTCGTCTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:2453747 original size:20 final size:22
Alignment explanation
Indices: 2453705--2453747 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
2453695 GAATAATCCA
*
2453705 TTATATTATTATAATTTATTTT
1 TTATATTATTATAATTTAATTT
*
2453727 TTATATT-TT-TATTTTAATTT
1 TTATATTATTATAATTTAATTT
2453747 T
1 T
2453748 CAAAAGGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
TTATATTATTATAATTTAATTT
Found at i:2454611 original size:2 final size:2
Alignment explanation
Indices: 2454604--2454631 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2454594 GCTTTAGTAA
2454604 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
2454632 GTAGGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2455360 original size:26 final size:25
Alignment explanation
Indices: 2455329--2455378 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2455319 TATATTAAAA
2455329 ATAATTAAAATT-TTTAATTTAATTTG
1 ATAATT-AAATTATTTAA-TTAATTTG
*
2455355 ATAATTATATTATTTAATTAATTT
1 ATAATTAAATTATTTAATTAATTT
2455379 CATCTACACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
ATAATTAAATTATTTAATTAATTTG
Found at i:2455549 original size:2 final size:2
Alignment explanation
Indices: 2455536--2455585 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
2455526 AATTATTAAA
* * *
2455536 AT AT AC AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2455578 AT AT AT AT
1 AT AT AT AT
2455586 TTCATAAGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2467336 original size:16 final size:16
Alignment explanation
Indices: 2467291--2467344 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
2467281 GAATATATCA
* *
2467291 AAAT-TTATATAAAAT
1 AAATATTATATATATT
*
2467306 AAATTATTA-ACATATT
1 AAA-TATTATATATATT
2467322 AAATATTATATATATT
1 AAATATTATATATATT
2467338 AAATATT
1 AAATATT
2467345 TTAAATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 8 0.25
16 21 0.66
17 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATTATATATATT
Found at i:2467352 original size:16 final size:16
Alignment explanation
Indices: 2467312--2467352 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2467302 AAATAAATTA
2467312 TTAACATATTAAATATT
1 TTAA-ATATTAAATATT
* *
2467329 ATATATATTAAATATT
1 TTAAATATTAAATATT
2467345 TTAAATAT
1 TTAAATAT
2467353 AAAAATAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATATTAAATATT
Found at i:2468556 original size:124 final size:123
Alignment explanation
Indices: 2468428--2468676 Score: 333
Period size: 124 Copynumber: 2.0 Consensus size: 123
2468418 ATTTTGATAT
* *
2468428 ATTTATTTTTGATATTATCTG-TTAATATTAGTATAAAATGAATAATTTAGTG-TTATAAGTTAA
1 ATTTAATTTTGATATTATCTGCTT-ATATTAGTATAAAATAAATAATTTAG-GATTATAAGTTAA
* * *
2468491 TTA-AGTATTAATTTAATTAATAAAATATATAAAAAATTTAATTAAACTAATAGTAATAGGG
64 TTAGA-TATCAATTTAATTAATAAAATAT-TAAAAAAATTAATTAAACTAATAGTAATAAGG
* * * * *
2468552 ATTTAATTTTGATGTTGTTTGCTTATATTATTATAAAATAAATAATTTAGGATTATGAGTTAATT
1 ATTTAATTTTGATATTATCTGCTTATATTAGTATAAAATAAATAATTTAGGATTATAAGTTAATT
* *
2468617 AGATATCAATTTATTTAATAAAATATTAAAAAAATTCATTAAACTAATAGTAATAAGG
66 AGATATCAATTTAATTAATAAAATATTAAAAAAATTAATTAAACTAATAGTAATAAGG
2468675 AT
1 AT
2468677 GGTTGCATAT
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
123 32 0.29
124 75 0.68
125 3 0.03
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (123 bp):
ATTTAATTTTGATATTATCTGCTTATATTAGTATAAAATAAATAATTTAGGATTATAAGTTAATT
AGATATCAATTTAATTAATAAAATATTAAAAAAATTAATTAAACTAATAGTAATAAGG
Found at i:2469513 original size:15 final size:16
Alignment explanation
Indices: 2469464--2469514 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2469454 TTTTTAGCAG
*
2469464 AAAA-ATTATAATTTAA
1 AAAATATTA-AATTTAT
2469480 AAAATATTAAATTTAT
1 AAAATATTAAATTTAT
*
2469496 AAAATATT-AATTTTT
1 AAAATATTAAATTTAT
2469511 AAAA
1 AAAA
2469515 ATTTTGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 10 0.31
16 18 0.56
17 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTAAATTTAT
Found at i:2470726 original size:17 final size:17
Alignment explanation
Indices: 2470671--2470726 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
2470661 TTTAATATGA
*
2470671 AATATATTTTAAATACAAT
1 AATATA-TTTAATTA-AAT
* *
2470690 AA-ATATTTAATAAAAA
1 AATATATTTAATTAAAT
2470706 AATATATTTAATTAAAT
1 AATATATTTAATTAAAT
2470723 AATA
1 AATA
2470727 CTATCTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 4 0.13
17 22 0.71
18 3 0.10
19 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATATTTAATTAAAT
Found at i:2471086 original size:2 final size:2
Alignment explanation
Indices: 2471079--2471111 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2471069 TTCATTAAAA
2471079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2471112 AAATAGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2472876 original size:13 final size:13
Alignment explanation
Indices: 2472850--2472885 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2472840 AATGCAGACC
2472850 TAATTAAA-TTAA
1 TAATTAAATTTAA
*
2472862 TAATTAGATTTAA
1 TAATTAAATTTAA
2472875 TAATTAAATTT
1 TAATTAAATTT
2472886 CTAACTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
TAATTAAATTTAA
Found at i:2474460 original size:2 final size:2
Alignment explanation
Indices: 2474453--2474494 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2474443 ATGAACTAGC
2474453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2474495 AGATTGAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2476407 original size:22 final size:21
Alignment explanation
Indices: 2476364--2476403 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2476354 TATTTTTATT
*
2476364 TAAATTTAATCATGAAATATA
1 TAAATTTAATCATAAAATATA
2476385 TAAATATTAAT-ATAAAATA
1 TAAAT-TTAATCATAAAATA
2476404 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TAAATTTAATCATAAAATATA
Found at i:2478117 original size:23 final size:23
Alignment explanation
Indices: 2478091--2478135 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2478081 AGCTTTTTGG
2478091 TTCAAGAGAAGATGCTTCATCAA
1 TTCAAGAGAAGATGCTTCATCAA
* * *
2478114 TTCAAGGGAGGATGCTTTATCA
1 TTCAAGAGAAGATGCTTCATCA
2478136 CAATATGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (23 bp):
TTCAAGAGAAGATGCTTCATCAA
Found at i:2478428 original size:46 final size:48
Alignment explanation
Indices: 2478354--2478491 Score: 147
Period size: 46 Copynumber: 2.9 Consensus size: 48
2478344 CATTATAGGA
* *
2478354 GGATAATTTGTAAATTTATCTATTCAAAAGTTATTAGTTGTG-TG-TT
1 GGATAATTTGTAAATTTATCCATACAAAAGTTATTAGTTGTGTTGATT
* * * *
2478400 GGATAATTTATAACTTTATCCATGCAAAAGTTACTAG-TGTGTTGATT
1 GGATAATTTGTAAATTTATCCATACAAAAGTTATTAGTTGTGTTGATT
* *
2478447 GTGATAAGGGTTTGTAATTTTATCCATACAAAAGTTATAAGTTGT
1 G-GATAA---TTTGTAAATTTATCCATACAAAAGTTATTAGTTGT
2478492 TTGTGAAGAG
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
45 4 0.05
46 34 0.45
47 3 0.04
48 5 0.07
51 26 0.35
52 3 0.04
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (48 bp):
GGATAATTTGTAAATTTATCCATACAAAAGTTATTAGTTGTGTTGATT
Found at i:2479163 original size:29 final size:29
Alignment explanation
Indices: 2479088--2479185 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 29
2479078 TTTTTAATGC
* * *
2479088 ATTTAAGTAAGTTTTAAATTTTTAATTTGT
1 ATTTAAATAAATTTT-AATTTTTAATTTAT
**
2479118 AACTAAATAAATTTTTAATTTTTAATTTAT
1 ATTTAAATAAA-TTTTAATTTTTAATTTAT
*
2479148 ATTTAAATAAATTTTAATATTTAATTTAT
1 ATTTAAATAAATTTTAATTTTTAATTTAT
2479177 ATTTAAATA
1 ATTTAAATA
2479186 TTTGTTAATG
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
29 26 0.44
30 29 0.49
31 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (29 bp):
ATTTAAATAAATTTTAATTTTTAATTTAT
Found at i:2479193 original size:29 final size:29
Alignment explanation
Indices: 2479088--2479194 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 29
2479078 TTTTTAATGC
* * * *
2479088 ATTTAAGTAAGTTTTAAATTTTTAATTTGT
1 ATTTAAATAA-TTTTTAATATTTAATTTAT
** *
2479118 AACTAAATAAATTTTTAATTTTTAATTTAT
1 ATTTAAAT-AATTTTTAATATTTAATTTAT
*
2479148 ATTTAAATAAATTTTAATATTTAATTTAT
1 ATTTAAATAATTTTTAATATTTAATTTAT
2479177 ATTTAAAT-ATTTGTTAAT
1 ATTTAAATAATTT-TTAAT
2479195 GTAAATCAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
28 3 0.05
29 32 0.49
30 28 0.43
31 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (29 bp):
ATTTAAATAATTTTTAATATTTAATTTAT
Found at i:2480691 original size:20 final size:20
Alignment explanation
Indices: 2480649--2480692 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2480639 CTTTTATTTT
* *
2480649 TTTTTTATTTTTCACTTTCA
1 TTTTTTATTTTTCACTATAA
**
2480669 TTTTTTATTTTTTTCTATAA
1 TTTTTTATTTTTCACTATAA
2480689 TTTT
1 TTTT
2480693 AAATAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTATTTTTCACTATAA
Found at i:2481488 original size:2 final size:2
Alignment explanation
Indices: 2481481--2481526 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2481471 AATTAAGTGT
2481481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2481523 TA TA
1 TA TA
2481527 AGGTAGTAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2483443 original size:2 final size:2
Alignment explanation
Indices: 2483436--2483481 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
2483426 GCACTACGTA
* * * *
2483436 CT CT CT CT CT CT CT CT CT CC CT CT CC CT CT CT CT CT TT CT TT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2483478 CT CT
1 CT CT
2483482 GGATCGACTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2486523 original size:12 final size:12
Alignment explanation
Indices: 2486506--2486534 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2486496 TCGCCGTTAG
2486506 TCTCTCTCTTTC
1 TCTCTCTCTTTC
2486518 TCTCTCTCTTTC
1 TCTCTCTCTTTC
2486530 TCTCT
1 TCTCT
2486535 ATGTCTCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTCTCTCTTTC
Found at i:2486637 original size:17 final size:17
Alignment explanation
Indices: 2486617--2486651 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2486607 ATATAAGTAT
2486617 ATTTTTA-ATATTTTAAA
1 ATTTTTATATA-TTTAAA
2486634 ATTTTTATATATTTAAA
1 ATTTTTATATATTTAAA
2486651 A
1 A
2486652 GATATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTTATATATTTAAA
Found at i:2488750 original size:14 final size:15
Alignment explanation
Indices: 2488731--2488769 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2488721 ATTATATTTA
2488731 ATATATAAA-CATAT
1 ATATATAAAGCATAT
2488745 ATATATATAAGCATAT
1 ATATATA-AAGCATAT
2488761 ATAT-TAAAG
1 ATATATAAAG
2488770 GGATTTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.43
15 4 0.17
16 9 0.39
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (15 bp):
ATATATAAAGCATAT
Found at i:2488752 original size:16 final size:16
Alignment explanation
Indices: 2488731--2488764 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2488721 ATTATATTTA
2488731 ATATATAAACATATAT
1 ATATATAAACATATAT
*
2488747 ATATATAAGCATATAT
1 ATATATAAACATATAT
2488763 AT
1 AT
2488765 TAAAGGGATT
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:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATATAAACATATAT
Found at i:2491139 original size:2 final size:2
Alignment explanation
Indices: 2491132--2491156 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2491122 CTTATATCTA
2491132 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2491157 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2491850 original size:2 final size:2
Alignment explanation
Indices: 2491843--2491880 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2491833 CAGCATCTGT
2491843 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2491881 AATAAGGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2492845 original size:20 final size:21
Alignment explanation
Indices: 2492811--2492850 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2492801 TTTTATTATA
* *
2492811 TTTTTACAACTCAAAGTTTTC
1 TTTTTACAACCCAAACTTTTC
2492832 TTTTTA-AACCCAAACTTTT
1 TTTTTACAACCCAAACTTTT
2492851 TCAAACTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (21 bp):
TTTTTACAACCCAAACTTTTC
Found at i:2494690 original size:17 final size:17
Alignment explanation
Indices: 2494670--2494742 Score: 57
Period size: 16 Copynumber: 4.5 Consensus size: 17
2494660 ATATTATTAC
*
2494670 ATTAAATATATATTTTT
1 ATTAAATATATATTTAT
* *
2494687 ATTAATTATA-AATTAT
1 ATTAAATATATATTTAT
* *
2494703 ATTTAATATGTATTTAAT
1 ATTAAATATATATTT-AT
2494721 ATTAAA-AT-TATTT-T
1 ATTAAATATATATTTAT
2494735 -TTAAATAT
1 ATTAAATAT
2494743 TAAAAATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
13 5 0.11
14 3 0.07
16 16 0.36
17 14 0.31
18 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (17 bp):
ATTAAATATATATTTAT
Found at i:2494788 original size:13 final size:12
Alignment explanation
Indices: 2494725--2494784 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
2494715 TTTAATATTA
**
2494725 AAATTATTTTTT
1 AAATTATTAATT
2494737 AAA-TATTAA--
1 AAATTATTAATT
2494746 AAATT-TTAATT
1 AAATTATTAATT
2494757 AAATTAATTAATT
1 AAATT-ATTAATT
*
2494770 TAATTATTAATT
1 AAATTATTAATT
2494782 AAA
1 AAA
2494785 ATTACTCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
9 7 0.18
10 1 0.03
11 9 0.23
12 12 0.31
13 10 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATTATTAATT
Found at i:2495551 original size:15 final size:16
Alignment explanation
Indices: 2495531--2495564 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2495521 ATAAAATATT
2495531 TTTTAATTA-ATTTAA
1 TTTTAATTATATTTAA
2495546 TTTTAATTATTATTTAA
1 TTTTAATTA-TATTTAA
2495563 TT
1 TT
2495565 AATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATTATATTTAA
Found at i:2495573 original size:46 final size:49
Alignment explanation
Indices: 2495523--2495631 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 49
2495513 AAATTTAAAT
* **
2495523 AAAATATTTTTTAATT-AATTTAATTTTAAT-TATTATTTA-ATTAATA
1 AAAATATTTTTTAATTAAATTTAATTATAATATATTATAAATATTAATA
* *
2495569 AAAATA-TTTTTATTTAAATTTAATTATAATATTTTATAAATATTAATA
1 AAAATATTTTTTAATTAAATTTAATTATAATATATTATAAATATTAATA
2495617 AAAA-ATTATTTTAAT
1 AAAATATT-TTTTAAT
2495632 ATTTTACAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
45 8 0.15
46 19 0.37
47 7 0.13
48 12 0.23
49 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (49 bp):
AAAATATTTTTTAATTAAATTTAATTATAATATATTATAAATATTAATA
Found at i:2495585 original size:23 final size:22
Alignment explanation
Indices: 2495555--2495629 Score: 60
Period size: 25 Copynumber: 3.1 Consensus size: 22
2495545 ATTTTAATTA
2495555 TTATTTAATTAATAAAAATATTT
1 TTATTTAATTAATAAAAATA-TT
* *
2495578 TTATTTAAATTTAATTATAATATT
1 TTATTT-AA-TTAATAAAAATATT
**
2495602 TTATAAATATTAATAAAAAATTATT
1 TTATTTA-ATTAAT-AAAAA-TATT
2495627 TTA
1 TTA
2495630 ATATTTTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
23 12 0.29
24 12 0.29
25 17 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTTAATTAATAAAAATATT
Found at i:2496418 original size:2 final size:2
Alignment explanation
Indices: 2496411--2496435 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2496401 AGCTCAAAAT
2496411 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 T
2496436 GTATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2497198 original size:17 final size:17
Alignment explanation
Indices: 2497157--2497198 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2497147 TTTTTAATGT
2497157 AAATTTTAAAAATTAAAG
1 AAATTTTAAAAA-TAAAG
2497175 AAA-TTTAAAAA-AAAG
1 AAATTTTAAAAATAAAG
2497190 AAAATTTTA
1 -AAATTTTA
2497199 CAAGGTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.18
16 3 0.14
17 12 0.55
18 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
AAATTTTAAAAATAAAG
Found at i:2498246 original size:6 final size:6
Alignment explanation
Indices: 2498235--2498259 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2498225 ATTAAACATA
2498235 TAATAT TAATAT TAATAT TAATAT T
1 TAATAT TAATAT TAATAT TAATAT T
2498260 TTAATATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Found at i:2500571 original size:3 final size:3
Alignment explanation
Indices: 2500563--2500601 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
2500553 GAATTTCAAT
2500563 GAA GAA GAA GAA GAA GAA GAA G-A GAAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA
2500602 CCCGATTGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2515684 original size:2 final size:2
Alignment explanation
Indices: 2515677--2515703 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2515667 AATACAAGCA
2515677 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
2515704 ATACTGGATA
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:2524350 original size:3 final size:3
Alignment explanation
Indices: 2524342--2524374 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2524332 TTATAACTTA
2524342 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2524375 TGTCCCTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2525070 original size:2 final size:2
Alignment explanation
Indices: 2525063--2525097 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2525053 ATAGTGTGCG
2525063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2525098 AAAATAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2531371 original size:32 final size:32
Alignment explanation
Indices: 2531330--2531390 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
2531320 TAGGCTTACT
2531330 GATAGAATTGATAGAA-TTTAAATTTATTTAAA
1 GATAGAATTGATA-AAGTTTAAATTTATTTAAA
2531362 GATAGAATTGATAAAGTTTAAATTTATTT
1 GATAGAATTGATAAAGTTTAAATTTATTT
2531391 GGAATTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.43
Consensus pattern (32 bp):
GATAGAATTGATAAAGTTTAAATTTATTTAAA
Found at i:2537222 original size:2 final size:2
Alignment explanation
Indices: 2537170--2537210 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2537160 TGTATGTTCT
2537170 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2537211 TGCGCGCTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2539436 original size:22 final size:22
Alignment explanation
Indices: 2539391--2539436 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2539381 CTTCTACCCC
* * *
2539391 TTCTGCTCTTTCTTCTCATTTT
1 TTCTGCTCTTTCCTCACATCTT
*
2539413 TTCTGCTGTTTCCTCACATCTT
1 TTCTGCTCTTTCCTCACATCTT
2539435 TT
1 TT
2539437 GCCAATTACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.28, G:0.07, T:0.59
Consensus pattern (22 bp):
TTCTGCTCTTTCCTCACATCTT
Found at i:2542398 original size:17 final size:17
Alignment explanation
Indices: 2542359--2542402 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2542349 TTCTCTTCTT
* **
2542359 TAATATAATATAAAAGT
1 TAATATAAAATAAAAAA
*
2542376 TTATATAAAATAAAAAA
1 TAATATAAAATAAAAAA
2542393 TAATATAAAA
1 TAATATAAAA
2542403 ATTTATGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
TAATATAAAATAAAAAA
Found at i:2548724 original size:21 final size:21
Alignment explanation
Indices: 2548691--2548733 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
2548681 ATAAAATTTT
2548691 AATATTAATTAAAAATAATAAA
1 AATATTAATTAAAAATAA-AAA
2548713 AATATT-ATTAAAAATAAAAA
1 AATATTAATTAAAAATAAAAA
2548733 A
1 A
2548734 TTTAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AATATTAATTAAAAATAAAAA
Found at i:2549583 original size:31 final size:32
Alignment explanation
Indices: 2549536--2549676 Score: 108
Period size: 36 Copynumber: 4.2 Consensus size: 32
2549526 AATTTTTTAG
2549536 TTTTTATTAAATTATTTTTAATATAAATATAA
1 TTTTTATTAAATTATTTTTAATATAAATATAA
* *
2549568 TTTTTATTATA-TATTTTTGATATAAATATAA
1 TTTTTATTAAATTATTTTTAATATAAATATAA
* * * *
2549599 TTTAATAATTTTTAATAATTATTTAATATTAATATAA
1 TTT--T--TATTAAATTATT-TTTAATATAAATATAA
*
2549636 -TTTTATTTATATTTTTATTATTTAATATAAATAT-A
1 TTTTTA-TTA-A--ATTATT-TTTAATATAAATATAA
2549671 TTTTTA
1 TTTTTA
2549677 AAAAATTTTA
Statistics
Matches: 85, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
31 22 0.26
32 11 0.13
33 3 0.04
34 2 0.02
35 5 0.06
36 28 0.33
37 14 0.16
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
TTTTTATTAAATTATTTTTAATATAAATATAA
Found at i:2549607 original size:39 final size:39
Alignment explanation
Indices: 2549555--2549670 Score: 122
Period size: 37 Copynumber: 3.2 Consensus size: 39
2549545 AATTATTTTT
* *
2549555 AATATAA-ATATAATTTTTATTATATATT-TTTGATATA
1 AATATAATTTATAATTTTTATTATATATTATTTAATATA
*
2549592 AATATAATTTAATAATTTTTA--ATA-ATTATTTAATATT
1 AATATAATTT-ATAATTTTTATTATATATTATTTAATATA
* *
2549629 AATATAATTT-T-ATTTATATT-TTTATTATTTAATATA
1 AATATAATTTATAATTTTTATTATATATTATTTAATATA
2549665 AATATA
1 AATATA
2549671 TTTTTAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
34 6 0.09
35 2 0.03
36 21 0.31
37 27 0.40
38 1 0.01
39 10 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (39 bp):
AATATAATTTATAATTTTTATTATATATTATTTAATATA
Found at i:2549612 original size:10 final size:11
Alignment explanation
Indices: 2549598--2549626 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2549588 TATAAATATA
2549598 ATTTAATAATT
1 ATTTAATAATT
2549609 -TTTAATAATT
1 ATTTAATAATT
2549619 ATTTAATA
1 ATTTAATA
2549627 TTAATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTAATAATT
Found at i:2549685 original size:35 final size:36
Alignment explanation
Indices: 2549552--2549694 Score: 104
Period size: 36 Copynumber: 4.1 Consensus size: 36
2549542 TTAAATTATT
*
2549552 TTTAATATAAATATAATTTT-T----ATTATATATT-
1 TTTAATATAAATATAATTTTATAAAAATTTTA-ATTA
* * **
2549583 TTTGATATAAATATAATTTAAT-AATTTTTAATAATTA
1 TTTAATATAAATATAATTTTATAAAAATTT--TAATTA
* ** * *
2549620 TTTAATATTAATATAATTTTATTTATATTTTTATTA
1 TTTAATATAAATATAATTTTATAAAAATTTTAATTA
*
2549656 TTTAATATAAATATATTTTTA-AAAAATTTTAATTA
1 TTTAATATAAATATAATTTTATAAAAATTTTAATTA
2549691 TTTA
1 TTTA
2549695 TAATATATAT
Statistics
Matches: 88, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
31 18 0.20
32 1 0.01
35 16 0.18
36 27 0.31
37 21 0.24
38 5 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.57
Consensus pattern (36 bp):
TTTAATATAAATATAATTTTATAAAAATTTTAATTA
Found at i:2550081 original size:15 final size:17
Alignment explanation
Indices: 2550041--2550082 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
2550031 ATAAATTATT
2550041 TTTTATATATTTTAATAA
1 TTTTA-ATATTTTAATAA
2550059 TATTTAATA-TTTAA-AA
1 T-TTTAATATTTTAATAA
2550075 TTTTAATA
1 TTTTAATA
2550083 AATATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.30
16 3 0.13
17 5 0.22
18 4 0.17
19 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAATATTTTAATAA
Found at i:2550091 original size:22 final size:23
Alignment explanation
Indices: 2550025--2550094 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 23
2550015 ATGTAAAAAT
* * *
2550025 ATTTTTATAAATTATTTTTTATAT
1 ATTTTAATAAATTATTATTTA-AA
*
2550049 ATTTTAATAATATTTAATATTTAAA
1 ATTTTAATAA-A-TTATTATTTAAA
2550074 ATTTTAATAAA-TATTATTTAA
1 ATTTTAATAAATTATTATTTAA
2550095 TATAAATGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 9 0.23
24 10 0.26
25 12 0.31
26 8 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTTAATAAATTATTATTTAAA
Found at i:2550731 original size:11 final size:11
Alignment explanation
Indices: 2550683--2550773 Score: 76
Period size: 12 Copynumber: 7.8 Consensus size: 11
2550673 AATTACAAGT
2550683 TATTAAAATTA
1 TATTAAAATTA
* *
2550694 TATTCATATTA
1 TATTAAAATTA
* *
2550705 AATAAAAATATA
1 TATTAAAAT-TA
2550717 TATTAAAATTA
1 TATTAAAATTA
*
2550728 TATTTACTAAATAA
1 TA-TTA--AAATTA
2550742 TAATTAAAATTA
1 T-ATTAAAATTA
2550754 TATTAAAAATTA
1 TATT-AAAATTA
2550766 -ATTAAAAT
1 TATTAAAAT
2550774 AAAAAAAGTA
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
10 5 0.08
11 24 0.38
12 25 0.39
14 9 0.14
15 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:2550761 original size:71 final size:70
Alignment explanation
Indices: 2550576--2550754 Score: 186
Period size: 71 Copynumber: 2.5 Consensus size: 70
2550566 AAAAAAATTT
* *
2550576 AATTAAAATT-TTTATATATAATAAATAATTTAAAATTATTAAAATTATATTTATATTAAATAAT
1 AATTAAAATTATATATATA-AAT-AATAA-TTAAAATTATTAAAATTATATTCATATTAAATAAT
2550640 AAAATATA
63 AAAATATA
* *** * *
2550648 AATTAAAATGATGGCTAT-GATAAATAATTACAAGTTATTAAAATTATATTCATATTAAAT-A-A
1 AATTAAAATTATATATATAAAT-AATAATTA-AAATTATTAAAATTATATTCATATTAAATAATA
2550710 AAATATA
64 AAATATA
* *
2550717 TATTAAAATTATATTTACTAAATAATAATTAAAATTAT
1 AATTAAAATTATATATA-TAAATAATAATTAAAATTAT
2550755 ATTAAAAATT
Statistics
Matches: 89, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
69 26 0.29
70 13 0.15
71 37 0.42
72 9 0.10
73 4 0.04
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (70 bp):
AATTAAAATTATATATATAAATAATAATTAAAATTATTAAAATTATATTCATATTAAATAATAAA
ATATA
Found at i:2550767 original size:22 final size:23
Alignment explanation
Indices: 2550707--2550773 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 23
2550697 TCATATTAAA
2550707 TAAAAATATATATTAAAATTATATT
1 TAAAAAT-TA-ATTAAAATTATATT
*
2550732 TACTAAATAATAATTAAAATTATA-T
1 TA--AAA-ATTAATTAAAATTATATT
2550757 TAAAAATTAATTAAAAT
1 TAAAAATTAATTAAAAT
2550774 AAAAAAAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 11 0.30
23 3 0.08
25 5 0.14
26 12 0.32
27 5 0.14
28 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAAAATTAATTAAAATTATATT
Found at i:2553433 original size:7 final size:7
Alignment explanation
Indices: 2553421--2553450 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2553411 TTTCTCTATT
2553421 TATAAAA
1 TATAAAA
2553428 TATAAAA
1 TATAAAA
2553435 TATAAAA
1 TATAAAA
2553442 TATAAAA
1 TATAAAA
2553449 TA
1 TA
2553451 ACAAATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TATAAAA
Found at i:2557124 original size:8 final size:8
Alignment explanation
Indices: 2557113--2557152 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
2557103 TGTAAATTAT
2557113 TAAAAAAA
1 TAAAAAAA
2557121 TAAAAAAA
1 TAAAAAAA
*
2557129 TAAAGATAA
1 TAAA-AAAA
2557138 TAAAAAAA
1 TAAAAAAA
2557146 TATAAAA
1 TA-AAAA
2557153 TATCAAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 17 0.61
9 11 0.39
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (8 bp):
TAAAAAAA
Found at i:2557160 original size:27 final size:25
Alignment explanation
Indices: 2557113--2557162 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
2557103 TGTAAATTAT
2557113 TAAAAAAATAAAAAAATAAAGATAA
1 TAAAAAAATAAAAAAATAAAGATAA
*
2557138 TAAAAAAATATAAAATATCAAAGAT
1 TAAAAAAATA-AAAAAAT-AAAGAT
2557163 TTAACGAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (25 bp):
TAAAAAAATAAAAAAATAAAGATAA
Found at i:2557835 original size:17 final size:17
Alignment explanation
Indices: 2557813--2557856 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2557803 AAATTCGAGT
2557813 ATATATATTAAATATAA
1 ATATATATTAAATATAA
* *
2557830 ATATATATTTAATATGA
1 ATATATATTAAATATAA
2557847 ATATAT-TTAA
1 ATATATATTAA
2557857 TTTTTCTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATATATTAAATATAA
Found at i:2560090 original size:15 final size:15
Alignment explanation
Indices: 2560072--2560101 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2560062 TAAAATATAT
*
2560072 AAAAATAATTAAACA
1 AAAAATAAATAAACA
2560087 AAAAATAAATAAACA
1 AAAAATAAATAAACA
2560102 TCATTTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAATAAACA
Found at i:2560091 original size:25 final size:26
Alignment explanation
Indices: 2560050--2560099 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
2560040 ATCACATATT
*
2560050 ATAATATAAAAATAAAATATATAAAA
1 ATAATATAAAAATAAAATAAATAAAA
2560076 ATAAT-TAAACAA-AAAATAAATAAA
1 ATAATATAAA-AATAAAATAAATAAA
2560100 CATCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (26 bp):
ATAATATAAAAATAAAATAAATAAAA
Done.