Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 138 of 185
Found at i:42735076 original size:19 final size:19
Alignment explanation
Indices: 42735007--42735077 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
42734997 TAAAAATGAA
* *
42735007 AAAAATACAAATAATTATA
1 AAAAATACAAAAAATTATT
*
42735026 AAAAATACAAAATA-T-TT
1 AAAAATACAAAAAATTATT
*
42735043 AAAATTTACAAAAAATTATT
1 AAAA-ATACAAAAAATTATT
*
42735063 AAAAATAGAAAAAAT
1 AAAAATACAAAAAAT
42735078 ACTAACATCT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 5 0.12
18 9 0.21
19 22 0.52
20 6 0.14
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (19 bp):
AAAAATACAAAAAATTATT
Found at i:42736058 original size:88 final size:91
Alignment explanation
Indices: 42735939--42736168 Score: 258
Period size: 88 Copynumber: 2.6 Consensus size: 91
42735929 AGTTCTTATT
* * * * ** * * * **
42735939 TTTTTTTTACATTCAATTGGGTATTTGAACTTTCAAAATATATCAAAAAGGCCCTCAAACTT-TT
1 TTTTTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAGACCCTAAAAATTACA
** *
42736003 TCAAA-AA-AAGCAATTAAGCCTCTA
66 AAAAAGAAGAAGCAATTAAGCCCCTA
42736027 TTTTTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAGACCCTAAAAATTACA
1 TTTTTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAGACCCTAAAAATTACA
42736092 AAAAAGAAGAAGCAATTAAGCCCCTA
66 AAAAAGAAGAAGCAATTAAGCCCCTA
* * *
42736118 ---TTTTTGCACTCGATTGGGTACTTAAAATGTCAAAATGCATCAAAAA-ACCCT
1 TTTTTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAGACCCT
42736169 TTAACCGTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
87 5 0.04
88 96 0.79
89 3 0.02
90 2 0.02
91 16 0.13
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (91 bp):
TTTTTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAGACCCTAAAAATTACA
AAAAAGAAGAAGCAATTAAGCCCCTA
Found at i:42736315 original size:28 final size:28
Alignment explanation
Indices: 42736268--42736344 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
42736258 ACATGTTACA
42736268 AAAAAATGATAAAAA-A-TAAAAATCAAT
1 AAAAAAT-ATAAAAATATTAAAAATCAAT
* * * ** *
42736295 AAAAATTATTAAATTATTAAATTTTAAT
1 AAAAAATATAAAAATATTAAAAATCAAT
42736323 AAAAAATATAAAAATATTAAAA
1 AAAAAATATAAAAATATTAAAA
42736345 TATTAAAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
26 5 0.13
27 7 0.18
28 26 0.68
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (28 bp):
AAAAAATATAAAAATATTAAAAATCAAT
Found at i:42736335 original size:8 final size:8
Alignment explanation
Indices: 42736320--42736431 Score: 52
Period size: 8 Copynumber: 13.2 Consensus size: 8
42736310 ATTAAATTTT
42736320 AATA-AAA
1 AATATAAA
42736327 AATATAAA
1 AATATAAA
*
42736335 AATATTAA
1 AATATAAA
*
42736343 AATATTAA
1 AATATAAA
*
42736351 AAT-TAGA
1 AATATAAA
42736358 AA-A-AAA
1 AATATAAA
*
42736364 ATTATAAA
1 AATATAAA
*
42736372 AATCGTAAAAA
1 AA---TATAAA
42736383 AACTATAAAA
1 AA-TAT-AAA
42736393 AATTATAAA
1 AA-TATAAA
42736402 AATCATAAAA
1 AAT-AT-AAA
42736412 AAGTATAAA
1 AA-TATAAA
*
42736421 ATGTATAAA
1 A-ATATAAA
42736430 AA
1 AA
42736432 AAACCTTTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
6 3 0.04
7 9 0.11
8 26 0.32
9 20 0.25
10 15 0.19
11 8 0.10
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.25
Consensus pattern (8 bp):
AATATAAA
Found at i:42736335 original size:9 final size:9
Alignment explanation
Indices: 42736321--42736432 Score: 59
Period size: 9 Copynumber: 11.9 Consensus size: 9
42736311 TTAAATTTTA
42736321 ATAAAAAAT
1 ATAAAAAAT
42736330 AT-AAAAAT
1 ATAAAAAAT
*
42736338 AT-TAAAAT
1 ATAAAAAAT
* *
42736346 ATTAAAATT
1 ATAAAAAAT
* *
42736355 AGAAAAAAA
1 ATAAAAAAT
42736364 ATTATAAAAAT
1 A-TA-AAAAAT
*
42736375 CGTAAAAAAACT
1 -AT-AAAAAA-T
42736387 ATAAAAAAT
1 ATAAAAAAT
42736396 -TATAAAAAT
1 ATA-AAAAAT
42736405 CATAAAAAAGT
1 -ATAAAAAA-T
**
42736416 ATAAAATGT
1 ATAAAAAAT
42736425 ATAAAAAA
1 ATAAAAAA
42736433 AACCTTTTAA
Statistics
Matches: 78, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
8 17 0.22
9 26 0.33
10 18 0.23
11 15 0.19
12 2 0.03
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.25
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:42736337 original size:37 final size:38
Alignment explanation
Indices: 42736293--42736374 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 38
42736283 ATAAAAATCA
* * *
42736293 ATAAAAATTATTAAATTATTAAATTTTA-ATAAAAAA-T
1 ATAAAAATTATTAAAATATTAAA-ATTAGAAAAAAAATT
42736330 ATAAAAA-TATTAAAATATTAAAATTAGAAAAAAAATT
1 ATAAAAATTATTAAAATATTAAAATTAGAAAAAAAATT
42736367 ATAAAAAT
1 ATAAAAAT
42736375 CGTAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
35 3 0.08
36 21 0.54
37 15 0.38
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (38 bp):
ATAAAAATTATTAAAATATTAAAATTAGAAAAAAAATT
Found at i:42736371 original size:20 final size:20
Alignment explanation
Indices: 42736348--42736393 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
42736338 ATTAAAATAT
* *
42736348 TAAAATTAGAAAAAAAATTA
1 TAAAAATAGAAAAAAAACTA
* *
42736368 TAAAAATCGTAAAAAAACTA
1 TAAAAATAGAAAAAAAACTA
42736388 TAAAAA
1 TAAAAA
42736394 ATTATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (20 bp):
TAAAAATAGAAAAAAAACTA
Found at i:42736372 original size:10 final size:10
Alignment explanation
Indices: 42736359--42736421 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
42736349 AAAATTAGAA
42736359 AAAAAATTAT
1 AAAAAATTAT
42736369 -AAAAATCGTA-
1 AAAAAAT--TAT
*
42736379 AAAAAACTAT
1 AAAAAATTAT
42736389 AAAAAATTAT
1 AAAAAATTAT
*
42736399 -AAAAATCAT
1 AAAAAATTAT
*
42736408 AAAAAAGTAT
1 AAAAAATTAT
42736418 AAAA
1 AAAA
42736422 TGTATAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
9 16 0.37
10 20 0.47
11 7 0.16
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:42736395 original size:30 final size:29
Alignment explanation
Indices: 42736359--42736421 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
42736349 AAAATTAGAA
*
42736359 AAAAAATTATAAAAATCGTAAAAAAACTAT
1 AAAAAATTATAAAAATCAT-AAAAAACTAT
*
42736389 AAAAAATTATAAAAATCATAAAAAAGTAT
1 AAAAAATTATAAAAATCATAAAAAACTAT
42736418 AAAA
1 AAAA
42736422 TGTATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (29 bp):
AAAAAATTATAAAAATCATAAAAAACTAT
Found at i:42736432 original size:19 final size:19
Alignment explanation
Indices: 42736360--42736432 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
42736350 AAATTAGAAA
* *
42736360 AAAAATTATAAAAATCGTAA
1 AAAAATTATAAAAA-AGTAT
* *
42736380 AAAAACTATAAAAAATTAT
1 AAAAATTATAAAAAAGTAT
*
42736399 AAAAATCATAAAAAAGTAT
1 AAAAATTATAAAAAAGTAT
42736418 -AAAATGTATAAAAAA
1 AAAAAT-TATAAAAAA
42736433 AACCTTTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
18 5 0.11
19 26 0.59
20 13 0.30
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (19 bp):
AAAAATTATAAAAAAGTAT
Found at i:42738389 original size:19 final size:19
Alignment explanation
Indices: 42738365--42738436 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
42738355 TTCTATATAG
42738365 TTTATAATTTTTTACGATT
1 TTTATAATTTTTTACGATT
** *
42738384 TTTATAAAATTTTACAATTTTT
1 TTTATAATTTTTTACGA---TT
* *
42738406 TTTATAATTTTTTATGAGT
1 TTTATAATTTTTTACGATT
42738425 TTTAT-ATTTTTT
1 TTTATAATTTTTT
42738437 TTCTAATTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
18 7 0.17
19 20 0.48
22 15 0.36
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTATAATTTTTTACGATT
Found at i:42738397 original size:29 final size:28
Alignment explanation
Indices: 42738306--42738406 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
42738296 TCTTTACATT
**
42738306 TTTTATAATTTTCTTACAACTTTATAAAA
1 TTTTATAATTTT-TTACATTTTTATAAAA
* * *
42738335 TTTTATAATTTTTGCTATATTTCTAT-ATA
1 TTTTATAATTTTT--TACATTTTTATAAAA
*
42738364 GTTTATAATTTTTTACGATTTTTATAAAA
1 TTTTATAATTTTTTAC-ATTTTTATAAAA
*
42738393 TTTTACAATTTTTT
1 TTTTATAATTTTTT
42738407 TTATAATTTT
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
27 2 0.04
28 8 0.14
29 40 0.70
30 7 0.12
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTTATAATTTTTTACATTTTTATAAAA
Found at i:42738496 original size:9 final size:9
Alignment explanation
Indices: 42738482--42738520 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
42738472 TTAAAATTTA
42738482 ATAATTTTT
1 ATAATTTTT
42738491 ATAATTTTT
1 ATAATTTTT
*
42738500 ATAACTTTT
1 ATAATTTTT
*
42738509 ATTTATTTTT
1 A-TAATTTTT
42738519 AT
1 AT
42738521 TTTTATCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (9 bp):
ATAATTTTT
Found at i:42738508 original size:18 final size:19
Alignment explanation
Indices: 42738467--42738520 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
42738457 TAAATATATA
* * *
42738467 TTTTATTAAAATTTAATAAT
1 TTTTATT-AATTTTTATAAC
42738487 TTTTA-TAATTTTTATAAC
1 TTTTATTAATTTTTATAAC
*
42738505 TTTTATTTATTTTTAT
1 TTTTATTAATTTTTAT
42738521 TTTTATCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 14 0.48
19 10 0.34
20 5 0.17
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATTAATTTTTATAAC
Found at i:42741386 original size:39 final size:39
Alignment explanation
Indices: 42741318--42741392 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
42741308 GAGGTATATT
** *
42741318 AGAATTAGTGGCGCTTATGAAAACACGCCGCTAAATCAC
1 AGAATTAGCAGCGCTTATGAAAACACGCCGCAAAATCAC
42741357 AGAATTAGCAGCGCATTAT-AAAA-AGCGCCGCAAAAT
1 AGAATTAGCAGCGC-TTATGAAAACA-CGCCGCAAAAT
42741393 ATCTTAACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
38 1 0.03
39 26 0.84
40 4 0.13
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (39 bp):
AGAATTAGCAGCGCTTATGAAAACACGCCGCAAAATCAC
Found at i:42741395 original size:114 final size:113
Alignment explanation
Indices: 42741265--42741683 Score: 651
Period size: 114 Copynumber: 3.7 Consensus size: 113
42741255 GTTTATTTGT
* *
42741265 AAGCGCCGCAAAATATCTTAACCAAAACGCAACATTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
*
42741330 GCTTATGAAAACACGCCGCTAAATCACAGAATTAGCAGCGCATTATAAA
66 GCTTATGAAAA-ACGCCGCTAAAGCACAGAATTAGCAGCGCATTATAAA
42741379 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
42741444 GCTTATGGAAAAACGCCGCTAAAGCACAGAATTAGCAGCGCATTATAAA
66 GCTTAT-GAAAAACGCCGCTAAAGCACAGAATTAGCAGCGCATTATAAA
* * * *
42741493 AAGCGCCGCAAAATATCTTAACTAAAATGCAGCGTATGGTCTTGAGGTATATTAGAATTAGTGGT
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * * * * *
42741558 GCTTATGAAAAAACGCCGCTAAAGCACAGCATTAACGGTGCAATAGAAA
66 GCTTATG-AAAAACGCCGCTAAAGCACAGAATTAGCAGCGCATTATAAA
* * *
42741607 AAGCGCCACAAAATATCTTAACCAAAATGCAGCGTTTGGTCTTGAGGTATATTAGAACTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
42741672 GCATTAT-AAAAA
66 GC-TTATGAAAAA
42741684 GCGCTGCAAA
Statistics
Matches: 284, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
113 6 0.02
114 269 0.95
115 9 0.03
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (113 bp):
AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
GCTTATGAAAAACGCCGCTAAAGCACAGAATTAGCAGCGCATTATAAA
Found at i:42742444 original size:7 final size:7
Alignment explanation
Indices: 42742432--42742484 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
42742422 GGTGGTTGTT
42742432 GTTTATG
1 GTTTATG
42742439 GTTTATGG
1 GTTTAT-G
42742447 GTTTAAT-
1 GTTT-ATG
42742454 GTTTATG
1 GTTTATG
*
42742461 GTTTAGG
1 GTTTATG
*
42742468 GTTTAAG
1 GTTTATG
*
42742475 ATTTATG
1 GTTTATG
42742482 GTT
1 GTT
42742485 AATGTTTACG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
6 2 0.05
7 29 0.76
8 5 0.13
9 2 0.05
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (7 bp):
GTTTATG
Found at i:42742471 original size:21 final size:20
Alignment explanation
Indices: 42742398--42742484 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 20
42742388 TTTGGCTAGT
*
42742398 TTTAGGGTTTAGAGTTTATGA
1 TTTAGGGTTTA-AGTTTATGG
* *
42742419 TTTGGTGGTTGT-TGTTTATGG
1 TTTAG-GGTT-TAAGTTTATGG
42742440 TTTATGGGTTTAATGTTTATGG
1 TTTA-GGGTTTAA-GTTTATGG
42742462 TTTAGGGTTTAAGATTTATGG
1 TTTAGGGTTTAAG-TTTATGG
42742483 TT
1 TT
42742485 AATGTTTACG
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
20 2 0.04
21 35 0.64
22 17 0.31
23 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (20 bp):
TTTAGGGTTTAAGTTTATGG
Found at i:42742598 original size:21 final size:21
Alignment explanation
Indices: 42742574--42742613 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42742564 ATAGTTTGGG
* *
42742574 GTTTGGGGTTTAAGGTTTATA
1 GTTTAGGGTTTAAGATTTATA
42742595 GTTTAGGGTTTAAGATTTA
1 GTTTAGGGTTTAAGATTTA
42742614 CGGTTAAGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
GTTTAGGGTTTAAGATTTATA
Found at i:42742613 original size:14 final size:14
Alignment explanation
Indices: 42742555--42742606 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
42742545 AATTGACATG
42742555 TTAGGGTTTATAGT
1 TTAGGGTTTATAGT
* ***
42742569 TTGGGGTTTGGGGT
1 TTAGGGTTTATAGT
*
42742583 TTAAGGTTTATAGT
1 TTAGGGTTTATAGT
42742597 TTAGGGTTTA
1 TTAGGGTTTA
42742607 AGATTTACGG
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (14 bp):
TTAGGGTTTATAGT
Found at i:42743023 original size:21 final size:20
Alignment explanation
Indices: 42742983--42743020 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42742973 AATATATTGA
*
42742983 TGTATTTATTTTTTAAAATG
1 TGTAATTATTTTTTAAAATG
42743003 TGTAATTATTTTTTAAAA
1 TGTAATTATTTTTTAAAA
42743021 ATGCATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TGTAATTATTTTTTAAAATG
Found at i:42743677 original size:17 final size:15
Alignment explanation
Indices: 42743643--42743671 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42743633 AAATTTGAAT
42743643 ATTGATAGTATTTAA
1 ATTGATAGTATTTAA
42743658 ATTGATAGTATTTA
1 ATTGATAGTATTTA
42743672 TAAATTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (15 bp):
ATTGATAGTATTTAA
Found at i:42743687 original size:16 final size:16
Alignment explanation
Indices: 42743625--42743694 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 16
42743615 CGCCGCAAAC
42743625 ATATTTATAAATTTGA
1 ATATTTATAAATTTGA
*
42743641 ATATTGATAGTATTTAAATTGA
1 ATATT--TA-TA---AATTTGA
42743663 TAGTATTTATAAATTTGA
1 -A-TATTTATAAATTTGA
*
42743681 ATATTTAGAAATTT
1 ATATTTATAAATTT
42743695 ATTAAATTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
16 17 0.40
17 1 0.02
18 8 0.19
19 2 0.05
21 2 0.05
22 8 0.19
23 1 0.02
24 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (16 bp):
ATATTTATAAATTTGA
Found at i:42743717 original size:25 final size:24
Alignment explanation
Indices: 42743667--42743717 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
42743657 AATTGATAGT
* *
42743667 ATTTATAAATTTGAATATTTAGAA
1 ATTTATAAATTTGAATAATTAAAA
*
42743691 ATTTATTAAATTTGTATAATTAAAA
1 ATTTA-TAAATTTGAATAATTAAAA
42743716 AT
1 AT
42743718 AATATCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (24 bp):
ATTTATAAATTTGAATAATTAAAA
Found at i:42745537 original size:9 final size:9
Alignment explanation
Indices: 42745523--42746216 Score: 199
Period size: 9 Copynumber: 79.4 Consensus size: 9
42745513 TTTTGTTATA
42745523 AACTTACAT
1 AACTTACAT
*
42745532 AACTTATATAAT
1 AAC-T-TA-CAT
42745544 AACTTACAT
1 AACTTACAT
**
42745553 AACTTATTT
1 AACTTACAT
42745562 AAACTTACAT
1 -AACTTACAT
*
42745572 AA--TACAA
1 AACTTACAT
42745579 AACTTA-AT
1 AACTTACAT
** **
42745587 TCCAGA-AT
1 AACTTACAT
42745595 AACTTACAT
1 AACTTACAT
*
42745604 AACTTATAT
1 AACTTACAT
*
42745613 AGAAACTTATATAT
1 ---AAC-T-TACAT
*
42745627 AAACTTGCAT
1 -AACTTACAT
42745637 AACTTACATAGT
1 AACTTAC--A-T
*
42745649 AACATA-AT
1 AACTTACAT
*
42745657 AAATTACAT
1 AACTTACAT
42745666 AA--TACAT
1 AACTTACAT
*
42745673 AA-TAACAT
1 AACTTACAT
42745681 AA--TACAT
1 AACTTACAT
*
42745688 AACTTATATAT
1 AAC-T-TACAT
*
42745699 AAGCTTGCAT
1 AA-CTTACAT
42745709 AACTTACATAAT
1 AACTTAC---AT
*
42745721 AACTCACAT
1 AACTTACAT
42745730 AACTTACAT
1 AACTTACAT
*
42745739 AA--TACAC
1 AACTTACAT
*
42745746 CACTTACAT
1 AACTTACAT
42745755 AACTTACAT
1 AACTTACAT
*
42745764 AGCTTACAT
1 AACTTACAT
* *
42745773 -TC-TACAC
1 AACTTACAT
42745780 AACTTACAT
1 AACTTACAT
*
42745789 AACATACAT
1 AACTTACAT
*
42745798 AA--TACAG
1 AACTTACAT
42745805 AACTTACAT
1 AACTTACAT
**
42745814 AAAATA-A-
1 AACTTACAT
42745821 AACTTACAT
1 AACTTACAT
*
42745830 ATCTTACAT
1 AACTTACAT
42745839 AA--TACAT
1 AACTTACAT
42745846 AACTTACAT
1 AACTTACAT
*
42745855 AA--TACAG
1 AACTTACAT
* * *
42745862 CACTTGCAC
1 AACTTACAT
*
42745871 AACTTAAAT
1 AACTTACAT
*
42745880 AACTTGCAT
1 AACTTACAT
42745889 AA--TACAT
1 AACTTACAT
* *
42745896 AGCCTACAT
1 AACTTACAT
*
42745905 AACTTATAT
1 AACTTACAT
* *
42745914 AGCTTTCAT
1 AACTTACAT
**
42745923 AAAATAC--
1 AACTTACAT
42745930 AACTTACAT
1 AACTTACAT
**
42745939 ATTTTACAT
1 AACTTACAT
*
42745948 AAAACTTATAT
1 --AACTTACAT
42745959 AA--TACAT
1 AACTTACAT
42745966 AACTTACAT
1 AACTTACAT
42745975 AAC--ACA-
1 AACTTACAT
* *
42745981 ACACTTGCAC
1 A-ACTTACAT
*
42745991 AACTTAAAT
1 AACTTACAT
*
42746000 AACTTGCAT
1 AACTTACAT
42746009 AA--TACAT
1 AACTTACAT
* *
42746016 AGCCTACAT
1 AACTTACAT
*
42746025 AACTTATAT
1 AACTTACAT
42746034 AACTTTTACA-
1 AAC--TTACAT
*
42746044 AA-ATAC--
1 AACTTACAT
42746050 AACTTACAT
1 AACTTACAT
*
42746059 ATCTTACAT
1 AACTTACAT
*
42746068 AAAACTTATAT
1 --AACTTACAT
42746079 AA--TACAT
1 AACTTACAT
42746086 AACTTACAT
1 AACTTACAT
42746095 AA--TACA-
1 AACTTACAT
*
42746101 ACACTTACAC
1 A-ACTTACAT
*
42746111 AACTTAAAT
1 AACTTACAT
*
42746120 AACTTGCAT
1 AACTTACAT
42746129 AA--TACAT
1 AACTTACAT
* *
42746136 AGCCTACAT
1 AACTTACAT
*
42746145 AACTTATAT
1 AACTTACAT
*
42746154 -A-GTACAT
1 AACTTACAT
42746161 AACTTACAT
1 AACTTACAT
* *
42746170 AATTTACTT
1 AACTTACAT
42746179 AA--TACAT
1 AACTTACAT
* *
42746186 AA-ATATAT
1 AACTTACAT
* *
42746194 ATCATATCAT
1 AACTTA-CAT
42746204 AACTTACAT
1 AACTTACAT
42746213 AACT
1 AACT
42746217 CATTTAATTT
Statistics
Matches: 497, Mismatches: 117, Indels: 142
0.66 0.15 0.19
Matches are distributed among these distances:
6 4 0.01
7 108 0.22
8 29 0.06
9 266 0.54
10 28 0.06
11 29 0.06
12 27 0.05
13 1 0.00
14 5 0.01
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:42745548 original size:21 final size:19
Alignment explanation
Indices: 42745522--42745573 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 19
42745512 TTTTTGTTAT
42745522 AAACTTACATAACTTATATA
1 AAACTTACATAACTTAT-TA
*
42745542 ATAACTTACATAACTTATTT
1 A-AACTTACATAACTTATTA
42745562 AAACTTACATAA
1 AAACTTACATAA
42745574 TACAAAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 11 0.37
20 3 0.10
21 16 0.53
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (19 bp):
AAACTTACATAACTTATTA
Found at i:42745663 original size:20 final size:19
Alignment explanation
Indices: 42745635--42745677 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
42745625 ATAAACTTGC
* *
42745635 ATAACTTACATAGTAACATA
1 ATAAATTACATAAT-ACATA
42745655 ATAAATTACATAATACATA
1 ATAAATTACATAATACATA
42745674 ATAA
1 ATAA
42745678 CATAATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAATTACATAATACATA
Found at i:42745682 original size:15 final size:15
Alignment explanation
Indices: 42745641--42745689 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
42745631 TTGCATAACT
*
42745641 TACATAGTAACATAA
1 TACATAATAACATAA
*
42745656 T--A-AATTACATAA
1 TACATAATAACATAA
42745668 TACATAATAACATAA
1 TACATAATAACATAA
42745683 TACATAA
1 TACATAA
42745690 CTTATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 9 0.32
13 1 0.04
14 1 0.04
15 17 0.61
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (15 bp):
TACATAATAACATAA
Found at i:42745730 original size:21 final size:21
Alignment explanation
Indices: 42745635--42745764 Score: 106
Period size: 21 Copynumber: 6.0 Consensus size: 21
42745625 ATAAACTTGC
* *
42745635 ATAACTTACAT-AGTAACATA
1 ATAACTTACATAACTTACATA
*
42745655 ATAAATTACATAA--TACATA
1 ATAACTTACATAACTTACATA
*
42745674 ATAACATAATACATAACTTATAT-
1 ATAAC-T--TACATAACTTACATA
*
42745697 ATAAGCTTGCATAACTTACATA
1 ATAA-CTTACATAACTTACATA
*
42745719 ATAACTCACATAACTTACATA
1 ATAACTTACATAACTTACATA
42745740 ATACACCACTTACATAACTTACATA
1 AT--A--ACTTACATAACTTACATA
42745765 GCTTACATTC
Statistics
Matches: 89, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
19 9 0.10
20 11 0.12
21 30 0.34
22 11 0.12
23 6 0.07
24 5 0.06
25 17 0.19
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.31
Consensus pattern (21 bp):
ATAACTTACATAACTTACATA
Found at i:42745764 original size:34 final size:34
Alignment explanation
Indices: 42745719--42746096 Score: 129
Period size: 34 Copynumber: 11.1 Consensus size: 34
42745709 AACTTACATA
* *
42745719 ATAACTCACATAACTTACATAATACACCACTTAC
1 ATAACTTACATAACTTACATAATACACAACTTAC
* **
42745753 ATAACTTACATAGCTTACATTCTACACAACTTAC
1 ATAACTTACATAACTTACATAATACACAACTTAC
* * * **
42745787 ATAACATACATAA--TACAGAACTTACATAAAATA-
1 ATAACTTACATAACTTACATAA--TACACAACTTAC
* *
42745820 A-AACTTACATATCTTACATAATACATAACTTAC
1 ATAACTTACATAACTTACATAATACACAACTTAC
** * * * * *
42745853 ATAA--TACAGCACTTGCACAACTTAAATAACTTGC
1 ATAACTTACATAACTTACATAA--TACACAACTTAC
* * * * * *
42745887 ATAA--TACATAGCCTACATAACTTATATAGCTTTC
1 ATAACTTACATAACTTACATAA--TACACAACTTAC
** * * *
42745921 ATAAAATAC--AACTTACATATTTTACATAAAACTTAT
1 ATAACTTACATAACTTACATA--ATAC--ACAACTTAC
* *
42745957 ATAA--TACATAACTTACATAACACA-ACACTTGC
1 ATAACTTACATAACTTACATAATACACA-ACTTAC
* * * * * *
42745989 ACAACTTAAATAACTTGCATAATACATAGCCTAC
1 ATAACTTACATAACTTACATAATACACAACTTAC
* *
42746023 ATAACTTATATAACTTTTACA-AA-ATACAACTTAC
1 ATAACTTACATAAC--TTACATAATACACAACTTAC
* * *
42746057 ATATCTTACATAAAACTTATATAATACATAACTTAC
1 ATAACTTACAT--AACTTACATAATACACAACTTAC
42746093 ATAA
1 ATAA
42746097 TACAACACTT
Statistics
Matches: 252, Mismatches: 66, Indels: 50
0.68 0.18 0.14
Matches are distributed among these distances:
31 1 0.00
32 41 0.16
33 2 0.01
34 162 0.64
35 5 0.02
36 41 0.16
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.31
Consensus pattern (34 bp):
ATAACTTACATAACTTACATAATACACAACTTAC
Found at i:42745778 original size:25 final size:25
Alignment explanation
Indices: 42745750--42745815 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
42745740 ATACACCACT
* * * **
42745750 TACATAACTTACATAGCTTACATTC
1 TACACAACTTACATAACATACATAA
42745775 TACACAACTTACATAACATACATAA
1 TACACAACTTACATAACATACATAA
*
42745800 TACAGAACTTACATAA
1 TACACAACTTACATAA
42745816 AATAAAACTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.29
Consensus pattern (25 bp):
TACACAACTTACATAACATACATAA
Found at i:42745803 original size:16 final size:16
Alignment explanation
Indices: 42745655--42746214 Score: 152
Period size: 16 Copynumber: 32.8 Consensus size: 16
42745645 TAGTAACATA
*
42745655 ATAAATTACATAATAC
1 ATAACTTACATAATAC
*
42745671 ATAA-TAACATAATAC
1 ATAACTTACATAATAC
* *
42745686 ATAACTTATATATAAGCTTGC
1 ATAAC-T-TACATAA---TAC
42745707 ATAACTTACATAATAACTCAC
1 ATAACTTAC---ATAA-T-AC
42745728 ATAACTTACATAATAC
1 ATAACTTACATAATAC
**
42745744 ACCACTTACATAACTTAC
1 ATAACTTACATAA--TAC
* **
42745762 ATAGCTTACATTCTAC
1 ATAACTTACATAATAC
*
42745778 ACAACTTACATAACATAC
1 ATAACTTACAT-A-ATAC
*
42745796 ATAA--TACAGAACTTAC
1 ATAACTTACATAA--TAC
**
42745812 ATAAAATA-A-AACTTAC
1 ATAACTTACATAA--TAC
*
42745828 ATATCTTACATAATAC
1 ATAACTTACATAATAC
42745844 ATAACTTACATAATAC
1 ATAACTTACATAATAC
** * * *
42745860 AGCACTTGCACAACTTAA
1 ATAACTTACATAA--TAC
*
42745878 ATAACTTGCATAATAC
1 ATAACTTACATAATAC
* * *
42745894 ATAGCCTACATAACTTAT
1 ATAACTTACATAA--TAC
* * * *
42745912 ATAGCTTTCATAAAAT
1 ATAACTTACATAATAC
* *
42745928 ACAACTTACATATTTTAC
1 ATAACTTACATA--ATAC
*
42745946 ATAAAACTTATATAATAC
1 AT--AACTTACATAATAC
*
42745964 ATAACTTACATAACAC
1 ATAACTTACATAATAC
* * *
42745980 A-ACACTTGCACAACTTAA
1 ATA-ACTTACATAA--TAC
*
42745998 ATAACTTGCATAATAC
1 ATAACTTACATAATAC
* * *
42746014 ATAGCCTACATAACTTAT
1 ATAACTTACATAA--TAC
*
42746032 ATAACTTTTACAAAATAC
1 ATAAC--TTACATAATAC
*
42746050 --AACTTACATATCTTAC
1 ATAACTTACATA--ATAC
*
42746066 ATAAAACTTATATAATAC
1 AT--AACTTACATAATAC
42746084 ATAACTTACATAATAC
1 ATAACTTACATAATAC
* *
42746100 A-ACACTTACACAACTTAA
1 ATA-ACTTACATAA--TAC
*
42746118 ATAACTTGCATAATAC
1 ATAACTTACATAATAC
* * *
42746134 ATAGCCTACATAACT-T
1 ATAACTTACATAA-TAC
*
42746150 ATATA-GTACATAACTTAC
1 ATA-ACTTACATAA--TAC
* *
42746168 ATAATTTACTTAATAC
1 ATAACTTACATAATAC
* * *
42746184 ATAAATATATATCATATC
1 ATAACT-TACATAATA-C
42746202 ATAACTTACATAA
1 ATAACTTACATAA
42746215 CTCATTTAAT
Statistics
Matches: 399, Mismatches: 92, Indels: 105
0.67 0.15 0.18
Matches are distributed among these distances:
14 7 0.02
15 17 0.04
16 194 0.49
17 18 0.05
18 112 0.28
19 4 0.01
20 26 0.07
21 17 0.04
22 4 0.01
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (16 bp):
ATAACTTACATAATAC
Found at i:42745835 original size:25 final size:25
Alignment explanation
Indices: 42745807--42745855 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
42745797 TAATACAGAA
*
42745807 CTTACATAAAATAAAACTTACATAT
1 CTTACATAAAACAAAACTTACATAT
* *
42745832 CTTACATAATACATAACTTACATA
1 CTTACATAAAACAAAACTTACATA
42745856 ATACAGCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (25 bp):
CTTACATAAAACAAAACTTACATAT
Found at i:42745999 original size:120 final size:120
Alignment explanation
Indices: 42745832--42746155 Score: 576
Period size: 120 Copynumber: 2.7 Consensus size: 120
42745822 ACTTACATAT
* *
42745832 CTTACATAATACATAACTTACATAATACAGCACTTGCACAACTTAAATAACTTGCATAATACATA
1 CTTATATAATACATAACTTACATAATACAACACTTGCACAACTTAAATAACTTGCATAATACATA
* *
42745897 GCCTACATAACTTATATAGCTTTCATAAAATACAACTTACATATTTTACATAAAA
66 GCCTACATAACTTATATAGCTTTCACAAAATACAACTTACATATCTTACATAAAA
*
42745952 CTTATATAATACATAACTTACATAACACAACACTTGCACAACTTAAATAACTTGCATAATACATA
1 CTTATATAATACATAACTTACATAATACAACACTTGCACAACTTAAATAACTTGCATAATACATA
* *
42746017 GCCTACATAACTTATATAACTTTTACAAAATACAACTTACATATCTTACATAAAA
66 GCCTACATAACTTATATAGCTTTCACAAAATACAACTTACATATCTTACATAAAA
*
42746072 CTTATATAATACATAACTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATA
1 CTTATATAATACATAACTTACATAATACAACACTTGCACAACTTAAATAACTTGCATAATACATA
42746137 GCCTACATAACTTATATAG
66 GCCTACATAACTTATATAG
42746156 TACATAACTT
Statistics
Matches: 194, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 194 1.00
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.31
Consensus pattern (120 bp):
CTTATATAATACATAACTTACATAATACAACACTTGCACAACTTAAATAACTTGCATAATACATA
GCCTACATAACTTATATAGCTTTCACAAAATACAACTTACATATCTTACATAAAA
Found at i:42746146 original size:25 final size:25
Alignment explanation
Indices: 42746070--42746187 Score: 80
Period size: 25 Copynumber: 4.7 Consensus size: 25
42746060 TCTTACATAA
* *
42746070 AACTTATATAATACATAACTTACAT
1 AACTTACATAATACATAACCTACAT
* * *
42746095 AA--TACA-ACACTTACACAACTTAAAT
1 AACTTACATA-A--TACATAACCTACAT
* *
42746120 AACTTGCATAATACATAGCCTACAT
1 AACTTACATAATACATAACCTACAT
* * *
42746145 AACTTATATAGTACATAACTTACAT
1 AACTTACATAATACATAACCTACAT
* *
42746170 AATTTACTTAATACATAA
1 AACTTACATAATACATAA
42746188 ATATATATCA
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
22 1 0.01
23 4 0.06
25 60 0.86
27 4 0.06
28 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.32
Consensus pattern (25 bp):
AACTTACATAATACATAACCTACAT
Found at i:42752177 original size:44 final size:43
Alignment explanation
Indices: 42752081--42752223 Score: 166
Period size: 43 Copynumber: 3.3 Consensus size: 43
42752071 AATCCCAAAA
* * *
42752081 TTAGCGGCGTTTGTGG--AAAATTGCTGCTAAAGAGCATGACCT
1 TTAGCGGCGTTTGTGGAAAAAAATGCCGCTAAAGAACATGA-CT
* * *
42752123 TTATCAGCGTTTGTGGAAAAAAATGCCGCTAAAGAACATTACTT
1 TTAGCGGCGTTTGTGGAAAAAAATGCCGCTAAAGAACATGAC-T
* *
42752167 TTAGCGGCGTTTGT-GAATAAAGTGCCGCTAAAGAACATGAGCT
1 TTAGCGGCGTTTGTGGAAAAAAATGCCGCTAAAGAACATGA-CT
42752210 TTAGCGGCGTTTGT
1 TTAGCGGCGTTTGT
42752224 TGGTAGGCGC
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
42 14 0.16
43 39 0.45
44 33 0.38
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGAAAAAAATGCCGCTAAAGAACATGACT
Found at i:42752296 original size:42 final size:41
Alignment explanation
Indices: 42752147--42752388 Score: 126
Period size: 42 Copynumber: 5.8 Consensus size: 41
42752137 GGAAAAAAAT
* * ** *
42752147 GCCGCTAAAGAACATTACTTTTAGCGGCGTTTGTGAATAAAGT
1 GCCGCTAAAGAACATGACCTTTAGCGGCG-TT-TGAAGGAAGA
* ** * *
42752190 GCCGCTAAAGAACATGAGCTTTAGCGGCGTTTGTTGGTAGGC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGTTTGAAGG-AAGA
* ** ** *
42752232 GCCGCTATAGGTCATGTTCTTTAGCGGTGTTTCCG-AGGAAGA
1 GCCGCTAAAGAACATGACCTTTAGCGGCGTTT--GAAGGAAGA
** **** *
42752274 GCCGCTAAAGAACATGACCTTTATTGGCGTTTTTTTTGAAGC
1 GCCGCTAAAGAACATGACCTTTAGCGGCG-TTTGAAGGAAGA
* * ***** *
42752316 GTCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTAAGC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGTTTGAAGGAAGA
* *
42752357 GCTGCTAAAGAACATGACCTTTAGCTGCGTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGTTT
42752389 ATTTCTTTAA
Statistics
Matches: 155, Mismatches: 39, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
41 41 0.26
42 82 0.53
43 31 0.20
44 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (41 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGTTTGAAGGAAGA
Found at i:42752322 original size:84 final size:84
Alignment explanation
Indices: 42752147--42752388 Score: 202
Period size: 84 Copynumber: 2.9 Consensus size: 84
42752137 GGAAAAAAAT
* ** ** * *
42752147 GCCGCTAAAGAACATTA-CTTTTAGCGGCGTTTGTGAATAAAGTGCCGCTAAAGAACATGAGCTT
1 GCCGCTAAAGAACATGATC-TTTAGCGGCGTTTCCG-AGGAAGAGCCGCTAAAGAACATGACCTT
*
42752211 TAGCGGCGTTTGTTGGTAGGC
64 TAGCGGCGTTTGTTGGTAAGC
* ** * *
42752232 GCCGCTATAGGTCATGTTCTTTAGCGGTGTTTCCGAGGAAGAGCCGCTAAAGAACATGACCTTTA
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTCCGAGGAAGAGCCGCTAAAGAACATGACCTTTA
** **
42752297 TTGGCGTTT-TTTTTGAAGC
66 GCGGCGTTTGTTGGT-AAGC
* ***** * *
42752316 GTCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTTTAAGCGCTGCTAAAGAACATGACCTTTA
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTCCGAGGAAGAGCCGCTAAAGAACATGACCTTTA
*
42752380 GCTGCGTTT
66 GCGGCGTTT
42752389 ATTTCTTTAA
Statistics
Matches: 122, Mismatches: 33, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
83 34 0.28
84 62 0.51
85 25 0.20
86 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (84 bp):
GCCGCTAAAGAACATGATCTTTAGCGGCGTTTCCGAGGAAGAGCCGCTAAAGAACATGACCTTTA
GCGGCGTTTGTTGGTAAGC
Found at i:42752364 original size:41 final size:42
Alignment explanation
Indices: 42752276--42752388 Score: 167
Period size: 41 Copynumber: 2.7 Consensus size: 42
42752266 GAGGAAGAGC
**
42752276 CGCTAAAGAACATGACCTTTATTGGCGTTTTTTTTGAAGCGT
1 CGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTGAAGCGT
*
42752318 CGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT-AAGCG-
1 CGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTGAAGCGT
*
42752358 CTGCTAAAGAACATGACCTTTAGCTGCGTTT
1 C-GCTAAAGAACATGACCTTTAGCGGCGTTT
42752389 ATTTCTTTAA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
40 1 0.02
41 32 0.49
42 32 0.49
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (42 bp):
CGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTGAAGCGT
Found at i:42754375 original size:20 final size:21
Alignment explanation
Indices: 42754334--42754371 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
42754324 ATATTCTATC
42754334 TAGTTGAAAAAAATCTTTACT
1 TAGTTGAAAAAAATCTTTACT
*
42754355 TAGTT-AAAATAAT-TTTA
1 TAGTTGAAAAAAATCTTTA
42754372 ACTTGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 7 0.44
21 5 0.31
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (21 bp):
TAGTTGAAAAAAATCTTTACT
Found at i:42754749 original size:10 final size:10
Alignment explanation
Indices: 42754734--42754763 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
42754724 AATATCAATC
42754734 AATTTACCTT
1 AATTTACCTT
*
42754744 AATTTACCTC
1 AATTTACCTT
42754754 AATTTACCTT
1 AATTTACCTT
42754764 TTCTTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (10 bp):
AATTTACCTT
Found at i:42756194 original size:19 final size:19
Alignment explanation
Indices: 42756138--42756205 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
42756128 AAGTCCTGAG
* **
42756138 GTATTGATATTTTTTACTA
1 GTATCGATATTTTTTAAAA
*
42756157 GTATCGACATTTTTATAAAA
1 GTATCGATATTTTT-TAAAA
*
42756177 GTATCGATATTTTTTAAAT
1 GTATCGATATTTTTTAAAA
42756196 GATATCGATA
1 G-TATCGATA
42756206 CCAAATTGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 17 0.41
20 24 0.59
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (19 bp):
GTATCGATATTTTTTAAAA
Found at i:42761879 original size:21 final size:21
Alignment explanation
Indices: 42761850--42761896 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
42761840 CTGAAATATA
*
42761850 GATACTAGGAAAATTTTTATC
1 GATACTAGGAAAAATTTTATC
*
42761871 GATATTAGGAAAAATTTTATC
1 GATACTAGGAAAAATTTTATC
42761892 GATAC
1 GATAC
42761897 CGGATCGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (21 bp):
GATACTAGGAAAAATTTTATC
Found at i:42763102 original size:9 final size:9
Alignment explanation
Indices: 42763090--42763128 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
42763080 CTTCAATTAC
42763090 ATAAATTGA
1 ATAAATTGA
*
42763099 AT-AATTGC
1 ATAAATTGA
42763107 ATAAATTGA
1 ATAAATTGA
*
42763116 ATAAATTTA
1 ATAAATTGA
42763125 ATAA
1 ATAA
42763129 TTGCTAGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (9 bp):
ATAAATTGA
Found at i:42763109 original size:17 final size:17
Alignment explanation
Indices: 42763084--42763119 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
42763074 AACCAACTTC
42763084 AATTACATAAATTGAAT
1 AATTACATAAATTGAAT
*
42763101 AATTGCATAAATTGAAT
1 AATTACATAAATTGAAT
42763118 AA
1 AA
42763120 ATTTAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (17 bp):
AATTACATAAATTGAAT
Found at i:42768810 original size:46 final size:46
Alignment explanation
Indices: 42768711--42768871 Score: 189
Period size: 46 Copynumber: 3.5 Consensus size: 46
42768701 GAGGGTGTCG
* * * *
42768711 TAGTGTCTTTTAACCATAGTCTTATTTATTCT-CGACTTGATGCCA
1 TAGTGTCTTTCAACCATGGTCTTATTTATTCTCCGTCTTGTTGCCA
* * *
42768756 TAGTGTCTTTCAACCATGGTCTTATTCATTTTCCGTCATGTTGCCA
1 TAGTGTCTTTCAACCATGGTCTTATTTATTCTCCGTCTTGTTGCCA
* * *
42768802 TAGTGTCTTTCAACTATGGTCTTATTTATTCTCCGTCTTGTTTCCG
1 TAGTGTCTTTCAACCATGGTCTTATTTATTCTCCGTCTTGTTGCCA
** * *
42768848 TAACGTCTTTCAGCTATGGTCTTA
1 TAGTGTCTTTCAACCATGGTCTTA
42768872 ATCGATAGAA
Statistics
Matches: 99, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
45 28 0.28
46 71 0.72
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (46 bp):
TAGTGTCTTTCAACCATGGTCTTATTTATTCTCCGTCTTGTTGCCA
Found at i:42768910 original size:45 final size:45
Alignment explanation
Indices: 42768848--42769010 Score: 238
Period size: 45 Copynumber: 3.6 Consensus size: 45
42768838 CTTGTTTCCG
*
42768848 TAACGTCTTTCAGCTATGGTCTTAATCGATAGAATCATGATGCCA
1 TAACGTCTTTCAGCTATGGTCTTACTCGATAGAATCATGATGCCA
* **
42768893 TAACGCCTTTCCA-CTATGGTCTTACTCGATAGAATTTTGATGCCA
1 TAACGTCTTT-CAGCTATGGTCTTACTCGATAGAATCATGATGCCA
* * *
42768938 TAACATCTTTCAGCTATGGTCTTACTTGATAGAATCGTGATGCCA
1 TAACGTCTTTCAGCTATGGTCTTACTCGATAGAATCATGATGCCA
*
42768983 TAACGTCTTTTAGCTATGGTCTTACTCG
1 TAACGTCTTTCAGCTATGGTCTTACTCG
42769011 TTTTTAGTAT
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
44 2 0.02
45 100 0.96
46 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Consensus pattern (45 bp):
TAACGTCTTTCAGCTATGGTCTTACTCGATAGAATCATGATGCCA
Found at i:42769027 original size:90 final size:90
Alignment explanation
Indices: 42768848--42769047 Score: 240
Period size: 90 Copynumber: 2.2 Consensus size: 90
42768838 CTTGTTTCCG
42768848 TAACGTCTTTCAGCTATGGTCTTAATCGATAGAATCATGATGCCATAACGCCTTTCCACTATGGT
1 TAACGTCTTTCAGCTATGGTCTTAATCGATAGAATCATGATGCCATAACGCCTTTCCACTATGGT
* *
42768913 CTTACTCGATAGAATTTTGATGCCA
66 CTTACTCGATAGAAGTATGATGCCA
* * * * * *
42768938 TAACATCTTTCAGCTATGGTCTTACTTGATAGAATCGTGATGCCATAACGTCTTT-TAGCTATGG
1 TAACGTCTTTCAGCTATGGTCTTAATCGATAGAATCATGATGCCATAACGCCTTTCCA-CTATGG
* *** *
42769002 TCTTACTCGTTTTTAGTATGGTGCCA
65 TCTTACTCGATAGAAGTATGATGCCA
** *
42769028 TAGTGTCTTTCAACTATGGT
1 TAACGTCTTTCAGCTATGGT
42769048 ATTATCTATT
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 1 0.01
90 91 0.99
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (90 bp):
TAACGTCTTTCAGCTATGGTCTTAATCGATAGAATCATGATGCCATAACGCCTTTCCACTATGGT
CTTACTCGATAGAAGTATGATGCCA
Found at i:42769705 original size:21 final size:20
Alignment explanation
Indices: 42769681--42769720 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42769671 CAAAAACATT
* *
42769681 GGAAACATTTGAAAAGTTTGA
1 GGAAAAATTAGAAAA-TTTGA
42769702 GGAAAAATTAGAAAATTTG
1 GGAAAAATTAGAAAATTTG
42769721 GACTATAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.28
Consensus pattern (20 bp):
GGAAAAATTAGAAAATTTGA
Found at i:42775302 original size:22 final size:21
Alignment explanation
Indices: 42775274--42775315 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42775264 CTTGAGATAT
42775274 CTTTAGGGGTATGTCGTGACAA
1 CTTTA-GGGTATGTCGTGACAA
* *
42775296 CTTTAGGTTATTTCGTGACA
1 CTTTAGGGTATGTCGTGACA
42775316 TCGAAGGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.38
Consensus pattern (21 bp):
CTTTAGGGTATGTCGTGACAA
Found at i:42775678 original size:25 final size:26
Alignment explanation
Indices: 42775650--42775808 Score: 136
Period size: 25 Copynumber: 6.3 Consensus size: 26
42775640 AATATGTCAT
42775650 AAAGGCTTTTCACAAGATTA-GCCAC
1 AAAGGCTTTTCACAAGATTACGCCAC
42775675 AAAGGC-TTTC-C-AGATAATACGCCAC
1 AAAGGCTTTTCACAAGAT--TACGCCAC
* * *
42775700 AAATGTTTTTCACAAGATCA-GCCAC
1 AAAGGCTTTTCACAAGATTACGCCAC
* * *
42775725 AAAGGCTTTTCA-AATAATACACCAC
1 AAAGGCTTTTCACAAGATTACGCCAC
* * *
42775750 AAAGGCTTTTCA-AATAATACACCAC
1 AAAGGCTTTTCACAAGATTACGCCAC
* * *
42775775 AAAGGCTTTTCAAAATATTA-GTCAC
1 AAAGGCTTTTCACAAGATTACGCCAC
42775800 AAAGGCTTT
1 AAAGGCTTT
42775809 CCAAGTAAAC
Statistics
Matches: 114, Mismatches: 12, Indels: 16
0.80 0.08 0.11
Matches are distributed among these distances:
22 4 0.04
23 1 0.01
24 10 0.09
25 83 0.73
26 11 0.10
27 1 0.01
28 4 0.04
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (26 bp):
AAAGGCTTTTCACAAGATTACGCCAC
Found at i:42775710 original size:50 final size:50
Alignment explanation
Indices: 42775572--42775788 Score: 222
Period size: 50 Copynumber: 4.3 Consensus size: 50
42775562 CAAATCATGG
* * * *
42775572 CACAAAGGCTTTACAAATAATACACCACCAAGGCTTTTCAAAATG-TTAGG
1 CACAAAGGCTTTCCAAATAATACACCACAAAGGCTTTTCACAA-GATTAGC
* * *** *
42775622 GACAAAGGCTTTCCATATAATATGTCATAAAGGCTTTTCACAAGATTAGC
1 CACAAAGGCTTTCCAAATAATACACCACAAAGGCTTTTCACAAGATTAGC
* * * * *
42775672 CACAAAGGCTTTCCAGATAATACGCCACAAATGTTTTTCACAAGATCAGC
1 CACAAAGGCTTTCCAAATAATACACCACAAAGGCTTTTCACAAGATTAGC
* * * *
42775722 CACAAAGGCTTTTCAAATAATACACCACAAAGGCTTTTCA-AATAATACAC
1 CACAAAGGCTTTCCAAATAATACACCACAAAGGCTTTTCACAAGATTA-GC
*
42775772 CACAAAGGCTTTTCAAA
1 CACAAAGGCTTTCCAAA
42775789 ATATTAGTCA
Statistics
Matches: 138, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
49 5 0.04
50 133 0.96
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (50 bp):
CACAAAGGCTTTCCAAATAATACACCACAAAGGCTTTTCACAAGATTAGC
Found at i:42775729 original size:75 final size:75
Alignment explanation
Indices: 42775650--42775808 Score: 194
Period size: 75 Copynumber: 2.1 Consensus size: 75
42775640 AATATGTCAT
* * * * * * *
42775650 AAAGGCTTTTCACAAGATTA-GCCACAAAGGCTTTCCAGATAATACGCCACAAATGTTTTTCACA
1 AAAGGCTTTTCA-AAGAATACACCACAAAGGCTTTCCAAATAATACACCACAAAGGCTTTTCAAA
42775714 AGATCAGCCAC
65 AGATCAGCCAC
* *
42775725 AAAGGCTTTTCAAATAATACACCACAAAGGCTTTTCAAATAATACACCACAAAGGCTTTTCAAAA
1 AAAGGCTTTTCAAAGAATACACCACAAAGGCTTTCCAAATAATACACCACAAAGGCTTTTCAAAA
* * *
42775790 TATTAGTCAC
66 GATCAGCCAC
42775800 AAAGGCTTT
1 AAAGGCTTT
42775809 CCAAGTAAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
74 5 0.07
75 66 0.93
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (75 bp):
AAAGGCTTTTCAAAGAATACACCACAAAGGCTTTCCAAATAATACACCACAAAGGCTTTTCAAAA
GATCAGCCAC
Found at i:42789631 original size:122 final size:122
Alignment explanation
Indices: 42789414--42789659 Score: 492
Period size: 122 Copynumber: 2.0 Consensus size: 122
42789404 CATAAGTGGG
42789414 TAGGGAACCAAGTAGGACCTTCAAATCAATGAAACCAAAATGCTAACCCTCTAAAGCCCAATGCA
1 TAGGGAACCAAGTAGGACCTTCAAATCAATGAAACCAAAATGCTAACCCTCTAAAGCCCAATGCA
42789479 CCATTCCAATATCCATTACCTTTTAGAGCACCCCAAGACCCAAAGAGGAAGCCAACC
66 CCATTCCAATATCCATTACCTTTTAGAGCACCCCAAGACCCAAAGAGGAAGCCAACC
42789536 TAGGGAACCAAGTAGGACCTTCAAATCAATGAAACCAAAATGCTAACCCTCTAAAGCCCAATGCA
1 TAGGGAACCAAGTAGGACCTTCAAATCAATGAAACCAAAATGCTAACCCTCTAAAGCCCAATGCA
42789601 CCATTCCAATATCCATTACCTTTTAGAGCACCCCAAGACCCAAAGAGGAAGCCAACC
66 CCATTCCAATATCCATTACCTTTTAGAGCACCCCAAGACCCAAAGAGGAAGCCAACC
42789658 TA
1 TA
42789660 TAGTAGTGAC
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.39, C:0.30, G:0.14, T:0.17
Consensus pattern (122 bp):
TAGGGAACCAAGTAGGACCTTCAAATCAATGAAACCAAAATGCTAACCCTCTAAAGCCCAATGCA
CCATTCCAATATCCATTACCTTTTAGAGCACCCCAAGACCCAAAGAGGAAGCCAACC
Found at i:42793502 original size:25 final size:25
Alignment explanation
Indices: 42793456--42793503 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
42793446 TGCACATAAG
*
42793456 TTTTTATGTGTATTTAATTTTTTTA
1 TTTTTATGTGTATTTAAGTTTTTTA
* * *
42793481 TTTTTGTGTTTATTTTAGTTTTT
1 TTTTTATGTGTATTTAAGTTTTT
42793504 ATGCATTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.75
Consensus pattern (25 bp):
TTTTTATGTGTATTTAAGTTTTTTA
Found at i:42797703 original size:16 final size:16
Alignment explanation
Indices: 42797682--42797712 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42797672 AAGGCGCCTC
42797682 CACAATATCGTTTCAG
1 CACAATATCGTTTCAG
42797698 CACAATATCGTTTCA
1 CACAATATCGTTTCA
42797713 ATCTTTGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (16 bp):
CACAATATCGTTTCAG
Found at i:42821688 original size:50 final size:50
Alignment explanation
Indices: 42821506--42821695 Score: 229
Period size: 50 Copynumber: 3.8 Consensus size: 50
42821496 TCTTGTACTA
* * * * * ** *
42821506 CCAATTCCATATCCCAGATATGGTCCTACATGAGAGTTCTCATATAGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTG
* * *
42821556 CCCATGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTTGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATCTAGGTG
* *
42821606 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTG
* *
42821656 CCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
42821696 TTACCCAAAT
Statistics
Matches: 120, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
49 1 0.01
50 118 0.98
51 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTG
Found at i:42830554 original size:24 final size:25
Alignment explanation
Indices: 42830506--42830564 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
42830496 ATGTATGCCA
* * *
42830506 ATACGAGCTCTGAATCGGTATGCTC
1 ATACGAGCTGTGAAACGGTAAGCTC
*
42830531 TTACGAGCTGT-AAACGGTAAGCTC
1 ATACGAGCTGTGAAACGGTAAGCTC
*
42830555 ATACAAGCTG
1 ATACGAGCTG
42830565 AATATTGGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (25 bp):
ATACGAGCTGTGAAACGGTAAGCTC
Found at i:42830578 original size:25 final size:25
Alignment explanation
Indices: 42830545--42830629 Score: 125
Period size: 25 Copynumber: 3.4 Consensus size: 25
42830535 GAGCTGTAAA
*
42830545 CGGTAAGCTCATACAAGCTGAATAT
1 CGGTAAGCTCATGCAAGCTGAATAT
*
42830570 TGGTAAGCTCATGCAAGCTGAATAT
1 CGGTAAGCTCATGCAAGCTGAATAT
* **
42830595 CGGTAAGCTCATGCGATTTGAATAT
1 CGGTAAGCTCATGCAAGCTGAATAT
42830620 CGGTAAGCTC
1 CGGTAAGCTC
42830630 TCTCGATCTA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (25 bp):
CGGTAAGCTCATGCAAGCTGAATAT
Found at i:42833319 original size:56 final size:55
Alignment explanation
Indices: 42833258--42833369 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 55
42833248 AATTGTACTT
42833258 AAATTATTAACATATTGAATTTTAATTAATTTTATAAGAAATTTTCATAAATTTTG
1 AAATTATTAACATATTGAATTTTAATTAATTTTATAAGAAA-TTTCATAAATTTTG
* *
42833314 AAATTATTAACATATTTAATTTTAATTAATTTTATAATAAATTTCATAAATTTTG
1 AAATTATTAACATATTGAATTTTAATTAATTTTATAAGAAATTTCATAAATTTTG
42833369 A
1 A
42833370 TTTATTTTCG
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
55 15 0.28
56 39 0.72
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (55 bp):
AAATTATTAACATATTGAATTTTAATTAATTTTATAAGAAATTTCATAAATTTTG
Found at i:42833827 original size:43 final size:43
Alignment explanation
Indices: 42833683--42833933 Score: 335
Period size: 43 Copynumber: 5.9 Consensus size: 43
42833673 TTTTAGAAAT
*** * *
42833683 AAACGCCGCTATAGATCAGGACCTTTAGCGGTAATTTT-ACAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCGC
* * *
42833725 AAACGCCGCTATAGATCAGGACCTTTAGCGGCTCTTTT-ACAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCGC
* *
42833767 AAACGCCGCTATAGATCAGGACCTTTACCTGCGCTTTTCCCGC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCGC
*
42833810 AAACGCTGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCGC
* *
42833853 AAACGCTGCTATAGATCAGGACCTTTAGTGGCGCTTTTCCCGC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCGC
* * * *
42833896 AAACGCCGCTATAGATCATGACTTTTAGCAGCGTTTTT
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTT
42833934 TTAATAAATA
Statistics
Matches: 190, Mismatches: 18, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
42 74 0.39
43 116 0.61
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCGC
Found at i:42834417 original size:45 final size:46
Alignment explanation
Indices: 42834366--42834452 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 46
42834356 AATATATATT
*
42834366 ATGTAAGTTGTGTATAATA-TGATCAAGTTACGTAAGTTGTGTATA
1 ATGTAAGTTGTGTATAATATTAATCAAGTTACGTAAGTTGTGTATA
* *
42834411 ATGTAAGTTGTGTATAATATTAATTAAGTTATGTAAGTTGTG
1 ATGTAAGTTGTGTATAATATTAATCAAGTTACGTAAGTTGTG
42834453 AGTAATAGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 19 0.50
46 19 0.50
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (46 bp):
ATGTAAGTTGTGTATAATATTAATCAAGTTACGTAAGTTGTGTATA
Found at i:42834418 original size:16 final size:16
Alignment explanation
Indices: 42834397--42834428 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42834387 ATCAAGTTAC
42834397 GTAAGTTGTGTATAAT
1 GTAAGTTGTGTATAAT
42834413 GTAAGTTGTGTATAAT
1 GTAAGTTGTGTATAAT
42834429 ATTAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (16 bp):
GTAAGTTGTGTATAAT
Found at i:42835521 original size:17 final size:17
Alignment explanation
Indices: 42835496--42835540 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
42835486 CATCGTTATC
*
42835496 ATTAGTATTATATTAGT
1 ATTATTATTATATTAGT
42835513 ATTATTATTATATTAGT
1 ATTATTATTATATTAGT
42835530 -TTATATATTAT
1 ATTAT-TATTAT
42835541 TTACATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (17 bp):
ATTATTATTATATTAGT
Found at i:42835900 original size:11 final size:11
Alignment explanation
Indices: 42835872--42835920 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
42835862 AATTGATATG
42835872 TATTTAATTTAA
1 TATTT-ATTTAA
* *
42835884 TTTTTATATAA
1 TATTTATTTAA
42835895 TATTTACTTTAA
1 TATTTA-TTTAA
42835907 T-TTTATTTAA
1 TATTTATTTAA
42835917 TATT
1 TATT
42835921 ACTATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 6 0.19
11 16 0.52
12 9 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:42835911 original size:22 final size:23
Alignment explanation
Indices: 42835872--42835920 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
42835862 AATTGATATG
42835872 TATTTAATTTAATTTTTATATAA
1 TATTTAATTTAATTTTTATATAA
* *
42835895 TATTTACTTTAA-TTTTATTTAA
1 TATTTAATTTAATTTTTATATAA
42835917 TATT
1 TATT
42835921 ACTATATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTAATTTAATTTTTATATAA
Found at i:42837348 original size:21 final size:22
Alignment explanation
Indices: 42837293--42837341 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
42837283 TATGAAATTT
42837293 ATTAATATAAATTAAAAACATA
1 ATTAATATAAATTAAAAACATA
* *
42837315 TTTAAATATAAATTAAAAATATA
1 ATT-AATATAAATTAAAAACATA
42837338 ATTA
1 ATTA
42837342 TCTAAATCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTAATATAAATTAAAAACATA
Found at i:42837400 original size:22 final size:22
Alignment explanation
Indices: 42837375--42837417 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42837365 ACCCATGATC
42837375 CTTAAACCCTAAACCCCTAACT
1 CTTAAACCCTAAACCCCTAACT
**
42837397 CTTAGCCCCTAAACCCCTAAC
1 CTTAAACCCTAAACCCCTAAC
42837418 CACTAACCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (22 bp):
CTTAAACCCTAAACCCCTAACT
Found at i:42837430 original size:22 final size:21
Alignment explanation
Indices: 42837379--42837433 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
42837369 ATGATCCTTA
*
42837379 AACCCTAAACCCCTAACTCTT
1 AACCCTAAACCCCTAACTCCT
*
42837400 AGCCCCTAAACCCCTAAC-CACT
1 A-ACCCTAAACCCCTAACTC-CT
42837422 AACCACTAAACC
1 AACC-CTAAACC
42837434 TTATATCCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.36, C:0.45, G:0.02, T:0.16
Consensus pattern (21 bp):
AACCCTAAACCCCTAACTCCT
Found at i:42837454 original size:21 final size:21
Alignment explanation
Indices: 42837428--42837473 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
42837418 CACTAACCAC
*
42837428 TAAACCTTATATCCC-AAACCT
1 TAAACCATA-ATCCCTAAACCT
42837449 TAAACCATAATCCCTAAACCT
1 TAAACCATAATCCCTAAACCT
42837470 TAAA
1 TAAA
42837474 ATGTAACTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACCATAATCCCTAAACCT
Found at i:42837899 original size:39 final size:40
Alignment explanation
Indices: 42837818--42837901 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
42837808 CGACGCTTTT
* *
42837818 TTAGCGGCACTTTCCTGAAACGCCGCTAAAGCCTCAAGCA
1 TTAGCGGCACATTCCTGAAACGCCGCTAAAGCCCCAAGCA
**
42837858 TTAGCGGCACATT-CTAGAAACGCCGC-AAAGCCCCCCGCA
1 TTAGCGGCACATTCCT-GAAACGCCGCTAAAGCCCCAAGCA
42837897 TTAGC
1 TTAGC
42837902 AGCGCTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
39 17 0.44
40 22 0.56
ACGTcount: A:0.27, C:0.35, G:0.20, T:0.18
Consensus pattern (40 bp):
TTAGCGGCACATTCCTGAAACGCCGCTAAAGCCCCAAGCA
Found at i:42837981 original size:41 final size:40
Alignment explanation
Indices: 42837835--42838013 Score: 135
Period size: 41 Copynumber: 4.5 Consensus size: 40
42837825 CACTTTCCTG
* * * * * * * *
42837835 AAACGCCGCTAAAGCCTCAAGCATTAGCGGCACATTCTAG
1 AAACGCTGCTAAATCCCCCAGCATTAGCGGCGCTTTTTAA
* * * *
42837875 AAACGCCGC-AAAGCCCCCCGCATTAGCAGCGCTTTTTCAA
1 AAACGCTGCTAAATCCCCCAGCATTAGCGGCGCTTTTT-AA
* * * *
42837915 AAACGCTGCGATATCCCCCATCATTAGCGGTGCTTTTTAAA
1 AAACGCTGCTAAATCCCCCAGCATTAGCGGCGCTTTTT-AA
* ** *
42837956 AAACGCTGCTAAATCTCTGAGCATTAGCGGCGCTTTTTGA
1 AAACGCTGCTAAATCCCCCAGCATTAGCGGCGCTTTTTAA
* *
42837996 AAACGCCGCTAAAACCCC
1 AAACGCTGCTAAATCCCC
42838014 GAAAGGTAAG
Statistics
Matches: 109, Mismatches: 28, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
39 21 0.19
40 33 0.30
41 55 0.50
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (40 bp):
AAACGCTGCTAAATCCCCCAGCATTAGCGGCGCTTTTTAA
Found at i:42852591 original size:52 final size:53
Alignment explanation
Indices: 42852534--42853003 Score: 201
Period size: 52 Copynumber: 8.6 Consensus size: 53
42852524 AAAAAAGAAA
* *
42852534 TTTTTTTGGGTACTGGCCTGTCAATGACCGACACCACCTTTACGAGAAATT-T
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTACGAGAAATTAT
* * * * * *
42852586 TTTTTTCGAGTGCTGGCCTGTCAATGGCCGTCACCA-GTATACGAAAAAAATTAAAAAT
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTACG--AGAAATT----AT
* * *
42852644 TTTTTTT-GGTGGTGACCTGTCAATGGTCGACACCACCTTTACGAGAAATTAT
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTACGAGAAATTAT
* * * * * * * * *
42852696 TTTTTTTGGGTGTTGGCCTATCAATAGCAAGGCACCA-GTATACGAAAAAATTAAAAAAAAA
1 TTTTTTTGGGTGCTGGCCTGTCAATGGC-CGACACCACCTTTACG-AGAAATT-------AT
** * * * *
42852757 TTTGCTT-GGTGGTGGCTTGTCAATGGCCGGCACCACCTTTACG-GAAAATTCT
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTACGAG-AAATTAT
* * * * * *
42852809 TTTTTTCGGGTGCTGACCTGTCAATGGCC-AGTACCA-GTATACGAAAAAATTTAAAAAAAAAAT
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGA-CACCACCTTTACG-AGAAA-TT---------AT
* ** * *
42852872 TTTTTTT-GGTGGTGGATTGTCAATGGCCGGCACCACCTTTACG-GGAATT-T
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTACGAGAAATTAT
* * * *
42852922 TTTTTTCGGGTGTTGGCCTATCAATGGCC-AGCACCACCTTTACGGGAAATT-T
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCGA-CACCACCTTTACGAGAAATTAT
* *
42852974 TTTTTTCGGGTGCTGGCTTGTCAATGGCCG
1 TTTTTTTGGGTGCTGGCCTGTCAATGGCCG
42853004 GCATAGTATA
Statistics
Matches: 305, Mismatches: 73, Indels: 79
0.67 0.16 0.17
Matches are distributed among these distances:
50 7 0.02
51 35 0.11
52 81 0.27
53 51 0.17
54 14 0.05
56 6 0.02
57 23 0.08
58 12 0.04
59 12 0.04
60 23 0.08
61 8 0.03
62 21 0.07
63 12 0.04
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (53 bp):
TTTTTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTACGAGAAATTAT
Found at i:42852924 original size:112 final size:113
Alignment explanation
Indices: 42852524--42852957 Score: 496
Period size: 113 Copynumber: 3.9 Consensus size: 113
42852514 AGAAAACCCC
* ** * *
42852524 AAAAAAGAAATTTTTTTGGGTACTGGCCTGTCAATGACCGACACCACCTTTACGAGAAATT-TTT
1 AAAAAA-AAATTTTTTTTGGTGGTGGACTGTCAATGGCCGACACCACCTTTACGAGAAATTATTT
* *
42852588 TTTTCGAGTGCTGGCCTGTCAATGGCC-GTCACCAGTATACGAAAAAAATT
65 TTTTCGGGTGCTGGCCTATCAATGGCCAG-CACCAGTATACG-AAAAAATT
*
42852638 ----AAAAATTTTTTTTGGTGGT-GACCTGTCAATGGTCGACACCACCTTTACGAGAAATTATTT
1 AAAAAAAAATTTTTTTTGGTGGTGGA-CTGTCAATGGCCGACACCACCTTTACGAGAAATTATTT
* * * *
42852698 TTTTTGGGTGTTGGCCTATCAATAGCAAGGCACCAGTATACGAAAAAATT
65 TTTTCGGGTGCTGGCCTATCAATGGCCA-GCACCAGTATACGAAAAAATT
** * *
42852748 AAAAAAAAA-TTTGCTTGGTGGTGG-CTTGTCAATGGCCGGCACCACCTTTACG-GAAAATTCTT
1 AAAAAAAAATTTTTTTTGGTGGTGGAC-TGTCAATGGCCGACACCACCTTTACGAG-AAATTATT
* * *
42852810 TTTTTCGGGTGCTGACCTGTCAATGGCCAGTACCAGTATACGAAAAAATTT
64 TTTTTCGGGTGCTGGCCTATCAATGGCCAGCACCAGTATACGAAAAAA-TT
* * *
42852861 AAAAAAAAAATTTTTTTTGGTGGTGGATTGTCAATGGCCGGCACCACCTTTACG-GGAATT-TTT
1 -AAAAAAAAATTTTTTTTGGTGGTGGACTGTCAATGGCCGACACCACCTTTACGAGAAATTATTT
*
42852924 TTTTCGGGTGTTGGCCTATCAATGGCCAGCACCA
65 TTTTCGGGTGCTGGCCTATCAATGGCCAGCACCA
42852958 CCTTTACGGG
Statistics
Matches: 273, Mismatches: 32, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
108 1 0.00
109 46 0.17
110 34 0.12
111 12 0.04
112 21 0.08
113 100 0.37
114 19 0.07
115 40 0.15
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (113 bp):
AAAAAAAAATTTTTTTTGGTGGTGGACTGTCAATGGCCGACACCACCTTTACGAGAAATTATTTT
TTTCGGGTGCTGGCCTATCAATGGCCAGCACCAGTATACGAAAAAATT
Found at i:42853338 original size:115 final size:115
Alignment explanation
Indices: 42853048--42853341 Score: 348
Period size: 116 Copynumber: 2.5 Consensus size: 115
42853038 GAGACACATA
*
42853048 CATTGACAGGCCAGCACCCGAAAATTTTTTTTCCCGTAAAGGTGGTGCCGGCCATTAACAGGCCA
1 CATTGACAGGCCAGCACCCGAAAATTTTTTTTCCCGTAAAGGTGGTGCCGGCCATTGACAGGCCA
*** * * *
42853113 ACACCAAAAATTTTTTTTTGTTTTTCAATTTTTTTCGTATACTGGTGCCGGC
66 ACACCAAAAA--TAAATATGTTTTTCAATTTTTTTCATATACTGGTGCCGAC
** *
42853165 CATTGACAGGCCAATACCCG-AAATTTTTTTTCCCGTAAAGGTGTTGCCGGCCATTGACAGGCCA
1 CATTGACAGGCCAGCACCCGAAAATTTTTTTTCCCGTAAAGGTGGTGCCGGCCATTGACAGGCCA
* *
42853229 CCA-CAAAAA-AAATAT-TTTTT-AA-TTTTTTCATATATTGGTGCCGAC
66 ACACCAAAAATAAATATGTTTTTCAATTTTTTTCATATACTGGTGCCGAC
* * *
42853274 CATTAACAGGCCAGCACCCGAAAAATTTGTTTTTTTTCTCGTAAAGGTGGTGCTGGCCATTGACA
1 CATTGACAGGCCAGCACCCG-AAAA----TTTTTTTTCCCGTAAAGGTGGTGCCGGCCATTGACA
42853339 GGC
61 GGC
42853342 TAGCACCCAA
Statistics
Matches: 153, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
109 37 0.24
110 2 0.01
111 8 0.05
112 2 0.01
115 42 0.27
116 44 0.29
117 18 0.12
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (115 bp):
CATTGACAGGCCAGCACCCGAAAATTTTTTTTCCCGTAAAGGTGGTGCCGGCCATTGACAGGCCA
ACACCAAAAATAAATATGTTTTTCAATTTTTTTCATATACTGGTGCCGAC
Found at i:42853340 original size:57 final size:55
Alignment explanation
Indices: 42853155--42853363 Score: 176
Period size: 57 Copynumber: 3.8 Consensus size: 55
42853145 TTTCGTATAC
** * *
42853155 TGGTGCCGGCCATTGACAGGCCAATACCC-GAAA---TTTTTTTTCCCGTAAAGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTTTTTCTCGTAAAGG
* * ** * * * *
42853206 TGTTGCCGGCCATTGACAGGCCACCACAAAAAAAATATTTTTTAATTTTTTCATATA-T
1 TGGTGCCGGCCATTGACAGGCCAGCAC-CCAAAAAT-TTTTTT--TTTTCTCGTAAAGG
* *
42853264 TGGTGCCGACCATTAACAGGCCAGCACCCGAAAAATTTGTTTTTTTTCTCGTAAAGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCC-AAAAATTT-TTTTTTTTCTCGTAAAGG
* *
42853321 TGGTGCTGGCCATTGACAGGCTAGCACCCAAACAATTTTTTTT
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAA-AATTTTTTTT
42853364 CTTTTTTTTT
Statistics
Matches: 121, Mismatches: 25, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
51 24 0.20
53 3 0.02
56 17 0.14
57 36 0.30
58 33 0.27
59 8 0.07
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (55 bp):
TGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTTTTTCTCGTAAAGG
Found at i:42853362 original size:115 final size:111
Alignment explanation
Indices: 42853048--42853373 Score: 336
Period size: 115 Copynumber: 2.8 Consensus size: 111
42853038 GAGACACATA
*
42853048 CATTGACAGGCCAGCACCCGAAAATTTTTTTTCCCGTAAAGGTGGTGCCGGCCATTAACAGGCCA
1 CATTGACAGGCCAGCACCCGAAAATTTTTTTTCCCGTAAAGGTGGTGCCGGCCATTGACAGGCCA
* *
42853113 ACA-CCAAAAATTTTTTTTTGTTTTTCAATTTTTTTCGTATACTGGTGCCGGC
66 ACACCCAAAAA------TTT-TTTTTCAATTTTTTTCATATACTGGTGCCGAC
** *
42853165 CATTGACAGGCCAATACCCG-AAATTTTTTTTCCCGTAAAGGTGTTGCCGGCCATTGACAGGCCA
1 CATTGACAGGCCAGCACCCGAAAATTTTTTTTCCCGTAAAGGTGGTGCCGGCCATTGACAGGCCA
* ** * *
42853229 CCACAAAAAAAATATTTTTT-AA-TTTTTTCATATATTGGTGCCGAC
66 ACAC-CCAAAAATTTTTTTTCAATTTTTTTCATATACTGGTGCCGAC
* * *
42853274 CATTAACAGGCCAGCACCCGAAAAATTTGTTTTTTTTCTCGTAAAGGTGGTGCTGGCCATTGACA
1 CATTGACAGGCCAGCACCCG-AAAA----TTTTTTTTCCCGTAAAGGTGGTGCCGGCCATTGACA
* * **
42853339 GGCTAGCACCCAAACAATTTTTTTTCTTTTTTTTT
61 GGCCAACACCCAAA-AATTTTTTTTCAATTTTTTT
42853374 TGGTTTTCTG
Statistics
Matches: 174, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
109 37 0.21
110 2 0.01
111 8 0.05
112 2 0.01
114 3 0.02
115 49 0.28
116 44 0.25
117 24 0.14
118 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (111 bp):
CATTGACAGGCCAGCACCCGAAAATTTTTTTTCCCGTAAAGGTGGTGCCGGCCATTGACAGGCCA
ACACCCAAAAATTTTTTTTCAATTTTTTTCATATACTGGTGCCGAC
Found at i:42858208 original size:41 final size:40
Alignment explanation
Indices: 42858069--42858250 Score: 148
Period size: 41 Copynumber: 4.5 Consensus size: 40
42858059 CTTACCTTTC
* * *
42858069 GGGGTTTTAGCGGCGTTTTCAAAAAAGCGCCGCTAATGCTC
1 GGGGATTTAGCGGCGTTTT-TAAAAAGCGCCGCTAATGCTG
* * * * *
42858110 AGAGATTTAGCAGCGTTTTTTAAAAAGCACCGCTAATGATG
1 GGGGATTTAGCGGCG-TTTTTAAAAAGCGCCGCTAATGCTG
* * * * *
42858151 GGGGATATCGCAGCGTTTTTGAAAAAGCGCTGCTAATGCGG
1 GGGGATTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATGCTG
* * * * *
42858192 GGGGCTTTAGCGGCGTTTCTAGAAATGTGCCGCTAATGCTT
1 GGGGATTTAGCGGCGTTTTTA-AAAAGCGCCGCTAATGCTG
* *
42858233 GAGGCTTTAGCGGCGTTT
1 GGGGATTTAGCGGCGTTT
42858251 CAGGAAAAGT
Statistics
Matches: 111, Mismatches: 27, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
40 6 0.05
41 101 0.91
42 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (40 bp):
GGGGATTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTG
Found at i:42858646 original size:21 final size:21
Alignment explanation
Indices: 42858622--42858667 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
42858612 GGAGTTACAT
*
42858622 TTTAAGGTTTAGGGAT-TATGG
1 TTTAAGGTTT-GGGATATAAGG
42858643 TTTAAGGTTTGGGATATAAGG
1 TTTAAGGTTTGGGATATAAGG
42858664 TTTA
1 TTTA
42858668 GTGGTTAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.43
Consensus pattern (21 bp):
TTTAAGGTTTGGGATATAAGG
Found at i:42858687 original size:22 final size:20
Alignment explanation
Indices: 42858662--42858716 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
42858652 TGGGATATAA
*
42858662 GGTTTAGTGGTTAGTGGTTAGG
1 GGTTTAG-GGTTAG-AGTTAGG
*
42858684 GGTTTAGGGGCTAAGAGTTAGG
1 GGTTTA-GGG-TTAGAGTTAGG
42858706 GGTTTAGGGTT
1 GGTTTAGGGTT
42858717 TAAGGATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.04
21 3 0.11
22 20 0.71
23 4 0.14
ACGTcount: A:0.16, C:0.02, G:0.45, T:0.36
Consensus pattern (20 bp):
GGTTTAGGGTTAGAGTTAGG
Found at i:42858777 original size:13 final size:12
Alignment explanation
Indices: 42858755--42858801 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
42858745 TGGATTTAGA
42858755 TTAATTATATTT
1 TTAATTATATTT
42858767 TTAATT-TATATT
1 TTAATTATAT-TT
* *
42858779 TTAAATATGTTT
1 TTAATTATATTT
42858791 TTAATTTATAT
1 TTAA-TTATAT
42858802 ATTAAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 3 0.11
12 19 0.68
13 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (12 bp):
TTAATTATATTT
Found at i:42858791 original size:24 final size:24
Alignment explanation
Indices: 42858754--42858813 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
42858744 TTGGATTTAG
*
42858754 ATTAATTATATTTTTAATTTATAT
1 ATTAAATATATTTTTAATTTATAT
* *
42858778 TTTAAATATGTTTTTAATTTATAT
1 ATTAAATATATTTTTAATTTATAT
42858802 ATTAAATA-ATTT
1 ATTAAATATATTT
42858814 CATATATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTAAATATATTTTTAATTTATAT
Found at i:42859124 original size:9 final size:9
Alignment explanation
Indices: 42859107--42859163 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
42859097 TTTTTTTTAA
*
42859107 TACACAACT
1 TACATAACT
42859116 TACATAACT
1 TACATAACT
*
42859125 TAAATAACT
1 TACATAACT
42859134 TACATAA--
1 TACATAACT
42859141 TACATAACT
1 TACATAACT
*
42859150 TTCATAACT
1 TACATAACT
42859159 TACAT
1 TACAT
42859164 TATACACAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
7 7 0.17
9 34 0.83
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (9 bp):
TACATAACT
Found at i:42859144 original size:25 final size:25
Alignment explanation
Indices: 42859116--42859169 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
42859106 ATACACAACT
42859116 TACATAACTTAAATAACTTACATAA
1 TACATAACTTAAATAACTTACATAA
** *
42859141 TACATAACTTTCATAACTTACATTA
1 TACATAACTTAAATAACTTACATAA
42859166 TACA
1 TACA
42859170 CAATGTCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (25 bp):
TACATAACTTAAATAACTTACATAA
Found at i:42860269 original size:24 final size:24
Alignment explanation
Indices: 42860218--42860266 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
42860208 ATAATATAGT
*
42860218 AATATCTAAATAAAATTTAAAGTA
1 AATATCTAAATAAAAATTAAAGTA
* *
42860242 AATAT-TATATAAAAATTAAATTA
1 AATATCTAAATAAAAATTAAAGTA
42860265 AA
1 AA
42860267 ATACATATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
AATATCTAAATAAAAATTAAAGTA
Found at i:42860635 original size:12 final size:12
Alignment explanation
Indices: 42860627--42860658 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
42860617 AACTAATATA
42860627 AATAATAATACT
1 AATAATAATACT
42860639 AATAATAATACT
1 AATAATAATACT
*
42860651 AATGATAA
1 AATAATAA
42860659 CGATGATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (12 bp):
AATAATAATACT
Found at i:42860648 original size:18 final size:18
Alignment explanation
Indices: 42860606--42860642 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42860596 AAATATGTAA
42860606 ATAAATATATAA-ACTAAT
1 ATAAATA-ATAATACTAAT
42860624 ATAAATAATAATACTAAT
1 ATAAATAATAATACTAAT
42860642 A
1 A
42860643 ATAATACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAATAATACTAAT
Found at i:42861608 original size:15 final size:16
Alignment explanation
Indices: 42861588--42861624 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
42861578 ATTTGTGGTC
42861588 TTGGGCTAGGG-GTAT
1 TTGGGCTAGGGTGTAT
42861603 TTGGGCTAGGGTTGTAT
1 TTGGGCTAGGG-TGTAT
42861620 TTGGG
1 TTGGG
42861625 TCAATGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.11, C:0.05, G:0.46, T:0.38
Consensus pattern (16 bp):
TTGGGCTAGGGTGTAT
Found at i:42861746 original size:16 final size:16
Alignment explanation
Indices: 42861725--42861756 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42861715 CTTAATTAAT
42861725 ATTATACACAACTTAC
1 ATTATACACAACTTAC
42861741 ATTATACACAACTTAC
1 ATTATACACAACTTAC
42861757 GTAACTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTATACACAACTTAC
Found at i:42861783 original size:45 final size:46
Alignment explanation
Indices: 42861701--42861787 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 46
42861691 GCCTATTACT
42861701 CACAACTTACATAACTTAATTAATATTATACACAACTTACATTATA
1 CACAACTTACATAACTTAATTAATATTATACACAACTTACATTATA
* * *
42861747 CACAACTTACGTAACTTGA-TCATATTATACACAACTTACAT
1 CACAACTTACATAACTTAATTAATATTATACACAACTTACAT
42861788 AATATATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 21 0.55
46 17 0.45
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (46 bp):
CACAACTTACATAACTTAATTAATATTATACACAACTTACATTATA
Found at i:42862279 original size:43 final size:43
Alignment explanation
Indices: 42862222--42862473 Score: 335
Period size: 43 Copynumber: 5.9 Consensus size: 43
42862212 TATTTATTAA
* * * *
42862222 AAAAACGCTGCTAAAAGTCATGATCTATAGCGGCGTTTGCGGG
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGCGGG
* *
42862265 AAAAGCGCCACTAAAGGTCCTGATCTATAGCAGCGTTTGCGGG
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGCGGG
*
42862308 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCAGCGTTTGCGGG
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGCGGG
* * * **
42862351 AAAAGCGCAGGTAAAGGTCCTGATCTATAGCGGCGTTTGTGTA
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGCGGG
* * *
42862394 AAAAGAGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTG-TGT
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGCGGG
***
42862436 AAAATTACCGCTAAAGGTCCTGATCTATAGCGGCGTTT
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTT
42862474 ATTTCTAAAA
Statistics
Matches: 187, Mismatches: 22, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
42 35 0.19
43 152 0.81
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGCGGG
Found at i:42862871 original size:56 final size:55
Alignment explanation
Indices: 42862788--42862899 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 55
42862778 CGAAAATAAA
42862788 TCAAAATTTATGAAATTTATTATAAAATTAATTAAAATTAAATATGTTAATAATT
1 TCAAAATTTATGAAATTTATTATAAAATTAATTAAAATTAAATATGTTAATAATT
* *
42862843 TCAAAATTTATGAAAATTTCTTATAAAATTAATTAAAATTCAATATGTTAATAATT
1 TCAAAATTTATG-AAATTTATTATAAAATTAATTAAAATTAAATATGTTAATAATT
42862899 T
1 T
42862900 AAGTACAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
55 12 0.22
56 42 0.78
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (55 bp):
TCAAAATTTATGAAATTTATTATAAAATTAATTAAAATTAAATATGTTAATAATT
Found at i:42865597 original size:25 final size:25
Alignment explanation
Indices: 42865530--42865614 Score: 125
Period size: 25 Copynumber: 3.4 Consensus size: 25
42865520 TAGATCGAGA
** *
42865530 GAGCTTACCGATATTCAAATCGCAT
1 GAGCTTACCGATATTCAGCTTGCAT
42865555 GAGCTTACCGATATTCAGCTTGCAT
1 GAGCTTACCGATATTCAGCTTGCAT
* *
42865580 GAGCTTACCAATATTCAGCTTGTAT
1 GAGCTTACCGATATTCAGCTTGCAT
42865605 GAGCTTACCG
1 GAGCTTACCG
42865615 TTTACAGCTC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGATATTCAGCTTGCAT
Found at i:42865632 original size:24 final size:25
Alignment explanation
Indices: 42865595--42865652 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
42865585 TACCAATATT
* * * *
42865595 CAGCTTGTATGAGCTTACCG-TTTA
1 CAGCTCGTAAGAGCATACCGATTCA
42865619 CAGCTCGTAAGAGCATACCGATTCA
1 CAGCTCGTAAGAGCATACCGATTCA
*
42865644 GAGCTCGTA
1 CAGCTCGTA
42865653 TTGGCATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (25 bp):
CAGCTCGTAAGAGCATACCGATTCA
Found at i:42887985 original size:17 final size:17
Alignment explanation
Indices: 42887963--42887996 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42887953 CTTAATTCGG
42887963 TAAGATTATTTTTCATA
1 TAAGATTATTTTTCATA
42887980 TAAGATTATTTTTCATA
1 TAAGATTATTTTTCATA
42887997 CCTTAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
TAAGATTATTTTTCATA
Found at i:42890807 original size:17 final size:18
Alignment explanation
Indices: 42890785--42890889 Score: 81
Period size: 17 Copynumber: 5.8 Consensus size: 18
42890775 AATTCAAGAC
42890785 TTATGTAATG-TTTTAAA
1 TTATGTAATGATTTTAAA
* **
42890802 TTATGTAGTGATTCAAAGA
1 TTATGTAATGATTTTAA-A
*
42890821 CTTATGTAAT-ATTTTTAA
1 -TTATGTAATGATTTTAAA
* *
42890839 TTATGTAGTGATTTAAAGA
1 TTATGTAATGATTTTAA-A
*
42890858 TTTATGTAATGCTTTT-AA
1 -TTATGTAATGATTTTAAA
*
42890876 TTATGTAGTGATTT
1 TTATGTAATGATTT
42890890 AATTCGGGTA
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
17 29 0.43
18 11 0.16
19 7 0.10
20 20 0.30
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (18 bp):
TTATGTAATGATTTTAAA
Found at i:42890889 original size:37 final size:36
Alignment explanation
Indices: 42890780--42890891 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 36
42890770 GTGTTAATTC
*
42890780 AAGACTTATGTAATGTTTTAAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTT-AATTATGTAGTGATTTA
*
42890817 AAGACTTATGTAATATTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAAT-GTTTTAATTATGTAGTGATTTA
*
42890854 AAGATTTATGTAATGCTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATG-TTTTAATTATGTAGTGATTTA
42890891 A
1 A
42890892 TTCGGGTAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
37 65 0.94
38 4 0.06
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (36 bp):
AAGACTTATGTAATGTTTTAATTATGTAGTGATTTA
Found at i:42890903 original size:9 final size:9
Alignment explanation
Indices: 42890889--42890980 Score: 112
Period size: 9 Copynumber: 9.6 Consensus size: 9
42890879 TGTAGTGATT
42890889 TAATTCGGG
1 TAATTCGGG
42890898 TAATTCGGG
1 TAATTCGGG
*
42890907 TAATTTGGG
1 TAATTCGGG
42890916 TAATTTTCGGG
1 TAA--TTCGGG
42890927 TAATTCGGG
1 TAATTCGGG
42890936 TAATTTTCGGG
1 TAA--TTCGGG
*
42890947 TAATTCGAG
1 TAATTCGGG
42890956 TAATTTTCGGG
1 TAA--TTCGGG
42890967 TAATTCGGG
1 TAATTCGGG
42890976 TAATT
1 TAATT
42890981 TTTAACCAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
9 48 0.66
11 25 0.34
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.40
Consensus pattern (9 bp):
TAATTCGGG
Found at i:42890926 original size:20 final size:20
Alignment explanation
Indices: 42890889--42890982 Score: 156
Period size: 20 Copynumber: 4.8 Consensus size: 20
42890879 TGTAGTGATT
42890889 TAATTCGGGTAA--TTCGGG
1 TAATTCGGGTAATTTTCGGG
*
42890907 TAATTTGGGTAATTTTCGGG
1 TAATTCGGGTAATTTTCGGG
42890927 TAATTCGGGTAATTTTCGGG
1 TAATTCGGGTAATTTTCGGG
*
42890947 TAATTCGAGTAATTTTCGGG
1 TAATTCGGGTAATTTTCGGG
42890967 TAATTCGGGTAATTTT
1 TAATTCGGGTAATTTT
42890983 TAACCAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
18 11 0.16
20 59 0.84
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (20 bp):
TAATTCGGGTAATTTTCGGG
Found at i:42903074 original size:39 final size:40
Alignment explanation
Indices: 42902923--42903092 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
42902913 GGACTAAGAT
* * *
42902923 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
42902963 CCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
** *
42903003 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * * *
42903043 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
42903082 CCGAAGGCATT
1 CCGAAGGCATT
42903093 TGAACGAGGA
Statistics
Matches: 112, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 32 0.29
40 80 0.71
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:42903112 original size:79 final size:80
Alignment explanation
Indices: 42902945--42903127 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 80
42902935 GTGCGAGATA
* * * *
42902945 CTAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
42903010 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * * *
42903025 TTAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
42903089 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
42903104 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
42903128 TACGTGAATT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.16
79 47 0.55
80 24 0.28
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:42907140 original size:3 final size:3
Alignment explanation
Indices: 42907132--42907159 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
42907122 TATTGGCACC
42907132 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
42907160 TTGATTTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:42912250 original size:16 final size:16
Alignment explanation
Indices: 42912229--42912260 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42912219 GTTTTGTTGC
*
42912229 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
42912245 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
42912261 CTTTTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:42912546 original size:51 final size:51
Alignment explanation
Indices: 42912486--42912676 Score: 237
Period size: 51 Copynumber: 3.8 Consensus size: 51
42912476 CCGGTTCATA
* *
42912486 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* ***
42912537 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGTA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
* * * *
42912588 TAGTAGCCTGCACATTGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
42912638 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
42912677 TTCACTTTCA
Statistics
Matches: 117, Mismatches: 17, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
49 4 0.03
50 40 0.34
51 70 0.60
52 2 0.02
53 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:42912665 original size:101 final size:102
Alignment explanation
Indices: 42912484--42912668 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
42912474 TACCGGTTCA
*
42912484 TATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 TATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
42912549 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * *
42912586 TATAGTAGCCTGCACATTGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 TATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
42912649 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
42912669 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 40 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (102 bp):
TATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:42933268 original size:4 final size:4
Alignment explanation
Indices: 42933259--42933290 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
42933249 TTAAACTAAG
42933259 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
42933291 AATAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:42936965 original size:29 final size:31
Alignment explanation
Indices: 42936933--42936992 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
42936923 AGATAATTTT
42936933 AAAGAG-TTT-TTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
42936962 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
42936993 TAATTTGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 6 0.21
30 3 0.10
31 20 0.69
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:42944098 original size:75 final size:75
Alignment explanation
Indices: 42944019--42944174 Score: 217
Period size: 75 Copynumber: 2.1 Consensus size: 75
42944009 AAGGCATATG
* *
42944019 ATAGAATACAATACAAAC-AGTTTTTGATTTTTTTCT-TAGATTGAAAATAAGTGTATATTATTG
1 ATAGAATACAATACAAACAAGTTTTTGAATTTCTTCTGTAGATTGAAAATAA--GTATATTATTG
42944082 ATATAAAATACA
64 ATATAAAATACA
* * * * *
42944094 ATAGAGTACAATATAAACAATTTTTTTAATTTCTTCTGTAGATTGTAAATAAGTATATTATTGAT
1 ATAGAATACAATACAAACAAGTTTTTGAATTTCTTCTGTAGATTGAAAATAAGTATATTATTGAT
42944159 ATAAAATACA
66 ATAAAATACA
42944169 ATAGAA
1 ATAGAA
42944175 AAAATTGTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
75 44 0.62
76 14 0.20
77 13 0.18
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (75 bp):
ATAGAATACAATACAAACAAGTTTTTGAATTTCTTCTGTAGATTGAAAATAAGTATATTATTGAT
ATAAAATACA
Found at i:42951511 original size:50 final size:50
Alignment explanation
Indices: 42951436--42951626 Score: 211
Period size: 50 Copynumber: 3.7 Consensus size: 50
42951426 TCTTGCACTA
* * **
42951436 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* ** *
42951486 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* *
42951536 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTG
* * *
42951592 CCAATGTCATGTTCCAAACATGGTCTTACATGGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
42951627 TCTCATCACC
Statistics
Matches: 117, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
50 81 0.69
53 2 0.02
56 34 0.29
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
Found at i:42980040 original size:24 final size:24
Alignment explanation
Indices: 42980012--42980075 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
42980002 TTTCTACAAG
* *
42980012 ATTTAATATTGATTAGTATAATAT
1 ATTTAACATTGATTAGCATAATAT
*
42980036 ATTTAACATTTATTAGCATAATAT
1 ATTTAACATTGATTAGCATAATAT
* *
42980060 ATTTGACATTAATTAG
1 ATTTAACATTGATTAG
42980076 AATTAGGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.47
Consensus pattern (24 bp):
ATTTAACATTGATTAGCATAATAT
Found at i:42982017 original size:3 final size:3
Alignment explanation
Indices: 42982007--42982049 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
42981997 AAGGAATATG
42982007 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
42982050 GTCAAGTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42982102 original size:20 final size:20
Alignment explanation
Indices: 42982077--42982115 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42982067 CAAATAAGAA
42982077 AAATATAATAATATAAAAAG
1 AAATATAATAATATAAAAAG
* *
42982097 AAATATTATATTATAAAAA
1 AAATATAATAATATAAAAA
42982116 TCAAATTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
AAATATAATAATATAAAAAG
Found at i:42992030 original size:25 final size:25
Alignment explanation
Indices: 42991996--42992084 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
42991986 ATAATTCGCT
*
42991996 ACAAAAGCTTTCCAAATGATACGCC
1 ACAAAGGCTTTCCAAATGATACGCC
* * * *
42992021 ATAAAGGCTTTCTAGA-GAATTCGCC
1 ACAAAGGCTTTCCAAATG-ATACGCC
* *
42992046 ACAAAAGCTTTCCAAATGATACACC
1 ACAAAGGCTTTCCAAATGATACGCC
*
42992071 ACAAAGACTTTCCA
1 ACAAAGGCTTTCCA
42992085 GAGAATTTGC
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
24 1 0.02
25 47 0.96
26 1 0.02
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.22
Consensus pattern (25 bp):
ACAAAGGCTTTCCAAATGATACGCC
Found at i:42992036 original size:50 final size:50
Alignment explanation
Indices: 42991977--42992100 Score: 185
Period size: 50 Copynumber: 2.5 Consensus size: 50
42991967 CACTACAACA
* * * *
42991977 ACTTTCTAGATAATTCGCTACAAAAGCTTTCCAAATGATACGCCATAAAG
1 ACTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACCACAAAG
*
42992027 GCTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACCACAAAG
1 ACTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACCACAAAG
* *
42992077 ACTTTCCAGAGAATTTGCCACAAA
1 ACTTTCTAGAGAATTCGCCACAAA
42992101 GGTTTTCTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (50 bp):
ACTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACCACAAAG
Found at i:42992107 original size:25 final size:25
Alignment explanation
Indices: 42992069--42992116 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
42992059 AAATGATACA
*
42992069 CCACAAAGACTTTCCAGAGAATTTG
1 CCACAAAGACTTTCCAAAGAATTTG
** *
42992094 CCACAAAGGTTTTCTAAAGAATT
1 CCACAAAGACTTTCCAAAGAATT
42992117 CTCGAGTTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (25 bp):
CCACAAAGACTTTCCAAAGAATTTG
Found at i:42998027 original size:131 final size:131
Alignment explanation
Indices: 42997776--42998016 Score: 333
Period size: 131 Copynumber: 1.8 Consensus size: 131
42997766 TGAAACATCG
* * * *
42997776 AAAATAAAGAACATACTCATGATCACATCAGCGGCATCTCTTTCCTCTCAGCGTCGAGCAGCATA
1 AAAATAAAGAACATACCCATGATCACATCAGCGGCATCTCTGTCCTCTCAGCATCAAGCAGCATA
* * *
42997841 AACCAGTGCAGGCTACCTCGCCTCAGTTTGATTAGTACCTCTGCCCGGTACTCTCTGTCCTCGGT
66 AACCAGTGCAGGCTACCCCGCCTCAGTCTAATTAGTACCTCTGCCCGGTACTCTCTGTCCTCGGT
42997906 A
131 A
* * * *
42997907 AAAATAAAGAACGTACCCGTGATCACATCAGGGGCATCTCTGTCCTCTC-GACATCAAGCAGTAT
1 AAAATAAAGAACATACCCATGATCACATCAGCGGCATCTCTGTCCTCTCAG-CATCAAGCAGCAT
* *
42997971 AAACCAGTGTAGGCTACCCCGCTTCAGTCTAATTAGCT-CCTCTGCC
65 AAACCAGTGCAGGCTACCCCGCCTCAGTCTAATTAG-TACCTCTGCC
42998017 TGGTGATCTC
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
130 1 0.01
131 93 0.98
132 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (131 bp):
AAAATAAAGAACATACCCATGATCACATCAGCGGCATCTCTGTCCTCTCAGCATCAAGCAGCATA
AACCAGTGCAGGCTACCCCGCCTCAGTCTAATTAGTACCTCTGCCCGGTACTCTCTGTCCTCGGT
A
Found at i:43000693 original size:67 final size:67
Alignment explanation
Indices: 43000585--43000719 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 67
43000575 TTTTCAATTT
*
43000585 AGAGAGCACACTCCTGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCTGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTG
43000650 CA
66 CA
43000652 AGAGAGCACACT-CTCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCT
1 AGAGAGCACACTCCT-GCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCT
43000716 GCA
65 GCA
43000719 A
1 A
43000720 CGACAATTAC
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
66 2 0.03
67 64 0.97
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCTGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:43000877 original size:57 final size:60
Alignment explanation
Indices: 43000789--43000931 Score: 177
Period size: 57 Copynumber: 2.4 Consensus size: 60
43000779 AATTCGGTTT
* * * *
43000789 ACTCGTCCGGACTAAATCCATTTTCCACATATTCTTCGAGAGGGCTATATC-A-A-GATC
1 ACTCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGAGAGGGATATATCGATAGGATC
*
43000846 ACTCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGATATATCAGGATAGGATC
1 ACTCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGAGAGGGATATATC--GATAGGATC
*
43000908 ACCCGTCCGGGCTAGATCCTTTTT
1 ACTCGTCCGGGCTAGATCCTTTTT
43000932 ACTGTCAATT
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
56 6 0.08
57 39 0.53
60 1 0.01
61 1 0.01
62 20 0.27
63 6 0.08
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (60 bp):
ACTCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGAGAGGGATATATCGATAGGATC
Found at i:43003910 original size:12 final size:13
Alignment explanation
Indices: 43003893--43003922 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
43003883 GCCTAGCCTG
43003893 TGTGGCATGTCC-
1 TGTGGCATGTCCA
43003905 TGTGGCATGTCCA
1 TGTGGCATGTCCA
43003918 TGTGG
1 TGTGG
43003923 GCCCACACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.10, C:0.20, G:0.37, T:0.33
Consensus pattern (13 bp):
TGTGGCATGTCCA
Found at i:43013776 original size:14 final size:14
Alignment explanation
Indices: 43013757--43013790 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
43013747 GCTTGTAGGA
43013757 AACTTTGACTATCG
1 AACTTTGACTATCG
43013771 AACTTTGACTATCG
1 AACTTTGACTATCG
43013785 AACTTT
1 AACTTT
43013791 TTGTTACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (14 bp):
AACTTTGACTATCG
Done.