Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 6 of 410
Found at i:1565376 original size:13 final size:13
Alignment explanation
Indices: 1565360--1565385 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1565350 TATTTAATTA
1565360 ATTTATCATCTTT
1 ATTTATCATCTTT
1565373 ATTTATCATCTTT
1 ATTTATCATCTTT
1565386 CCAATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTATCATCTTT
Found at i:1570588 original size:15 final size:16
Alignment explanation
Indices: 1570557--1570589 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1570547 TAAGAATTTT
*
1570557 TTTATTTTAATGTAAA
1 TTTATTGTAATGTAAA
1570573 TTTATTGTAA-GTAAA
1 TTTATTGTAATGTAAA
1570588 TT
1 TT
1570590 GTTCTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (16 bp):
TTTATTGTAATGTAAA
Found at i:1579309 original size:23 final size:23
Alignment explanation
Indices: 1579283--1579350 Score: 127
Period size: 23 Copynumber: 3.0 Consensus size: 23
1579273 CTCGAAGGAT
*
1579283 TGTTCTTGGTTTATAAGGCTAAG
1 TGTTTTTGGTTTATAAGGCTAAG
1579306 TGTTTTTGGTTTATAAGGCTAAG
1 TGTTTTTGGTTTATAAGGCTAAG
1579329 TGTTTTTGGTTTATAAGGCTAA
1 TGTTTTTGGTTTATAAGGCTAA
1579351 TACTTTCGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.22, C:0.06, G:0.25, T:0.47
Consensus pattern (23 bp):
TGTTTTTGGTTTATAAGGCTAAG
Found at i:1585330 original size:19 final size:17
Alignment explanation
Indices: 1585293--1585340 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
1585283 CTCCTTCTCC
1585293 TTCTTCTTCTTCTCTTCT
1 TTCTT-TTCTTCTCTTCT
1585311 TTCTTTTCTTCTCTCCTCT
1 TTCTTTTCTTCTCT--TCT
*
1585330 TTCATTTCTTC
1 TTCTTTTCTTC
1585341 ATCCCGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.33
18 5 0.19
19 13 0.48
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTTTTCTTCTCTTCT
Found at i:1585443 original size:27 final size:27
Alignment explanation
Indices: 1585413--1585471 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1585403 GTGCATGAGG
* * *
1585413 CCAGTGCCGCCTGTGGCAGGCACACCA
1 CCAGTGCCACCTATGGAAGGCACACCA
1585440 CCAGTGCCACCTATGGAAGGCACACCA
1 CCAGTGCCACCTATGGAAGGCACACCA
1585467 CCAGT
1 CCAGT
1585472 TCCAACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.24, C:0.39, G:0.25, T:0.12
Consensus pattern (27 bp):
CCAGTGCCACCTATGGAAGGCACACCA
Found at i:1585506 original size:22 final size:21
Alignment explanation
Indices: 1585474--1585528 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1585464 CCACCAGTTC
1585474 CAACTTTTTTTTTTTCAAATT
1 CAACTTTTTTTTTTTCAAATT
1585495 CAACTTTTTTTTTTTCAAATT
1 CAACTTTTTTTTTTTCAAATT
* *
1585516 CAGCCTTTTTTTT
1 CAACTTTTTTTTT
1585529 CAGTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.62
Consensus pattern (21 bp):
CAACTTTTTTTTTTTCAAATT
Found at i:1588312 original size:27 final size:27
Alignment explanation
Indices: 1588279--1589157 Score: 1078
Period size: 27 Copynumber: 32.6 Consensus size: 27
1588269 AAAGTACTCC
*
1588279 CGATTTACAGAATTACCTTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
1588306 C-AGTTTATAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
** *
1588333 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
1588360 CGATTTACAGAATTACCGTTTTATCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
1588387 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
1588414 CGATTTACAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
***
1588441 C-AGTTTACAGAATTATTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
1588468 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
1588495 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
1588522 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
1588549 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
1588576 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
1588603 CGATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * ** *
1588629 CTAATTTACATAATTACTATTTTACCCC
1 C-GATTTACAGAATTACCGTTTTACCCT
* * *
1588657 CGATTTACATAATTATCGTTTTATCCT
1 CGATTTACAGAATTACCGTTTTACCCT
1588684 CGATTTACAGAATTACCGTTTTA-CCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
1588710 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
1588737 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
1588764 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
1588791 C-AGTTTATAGAATTATTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
1588818 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
1588845 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
1588872 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
1588899 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
1588926 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
1588953 CGATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
1588979 CTAATTTACATAATTACCATTTTACTCC-
1 C-GATTTACAGAATTACCGTTTTAC-CCT
* *
1589007 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
1589034 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
1589061 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
1589088 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
1589115 TGATTGACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
1589142 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
1589158 TAAAATACCC
Statistics
Matches: 743, Mismatches: 89, Indels: 40
0.85 0.10 0.05
Matches are distributed among these distances:
26 36 0.05
27 696 0.94
28 11 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:1590496 original size:9 final size:9
Alignment explanation
Indices: 1590484--1590540 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
1590474 TTTGATAAAC
1590484 ATGATATGT
1 ATGATATGT
*
1590493 ATGATATGCAC
1 ATGATATG--T
*
1590504 ATGACATGT
1 ATGATATGT
*
1590513 ATGATATGCAC
1 ATGATATG--T
1590524 ATGATATGT
1 ATGATATGT
1590533 ATGATATG
1 ATGATATG
1590541 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:1590507 original size:20 final size:20
Alignment explanation
Indices: 1590482--1590544 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
1590472 ATTTTGATAA
1590482 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
1590502 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
1590522 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
1590542 ACA
1 ACA
1590545 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:1590632 original size:24 final size:24
Alignment explanation
Indices: 1590600--1590742 Score: 227
Period size: 24 Copynumber: 6.0 Consensus size: 24
1590590 AGGAAGTGCA
1590600 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
1590624 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
1590648 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
1590672 -AAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATT
*
1590695 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
1590719 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
1590743 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 22 0.20
24 78 0.70
25 11 0.10
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:1590699 original size:47 final size:48
Alignment explanation
Indices: 1590599--1590743 Score: 231
Period size: 47 Copynumber: 3.0 Consensus size: 48
1590589 GAGGAAGTGC
1590599 AAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTAT
*
1590647 TAAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTAT
* *
1590694 AAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATTAAAAG-GGCTTATGCC-CCAGTTAT
1590743 A
1 A
1590744 TGATAAAGCA
Statistics
Matches: 90, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 45 0.50
48 33 0.37
49 12 0.13
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (48 bp):
AAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTAT
Found at i:1590717 original size:71 final size:72
Alignment explanation
Indices: 1590601--1590742 Score: 234
Period size: 71 Copynumber: 2.0 Consensus size: 72
1590591 GGAAGTGCAA
* *
1590601 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTAAAAG-GGCTTATGCC-C
1 AAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTC
1590664 CAGTTATT
65 CAGTTATT
*
1590672 AAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTCC
1 AAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCC
1590737 AGTTAT
66 AGTTAT
1590743 ATGATAAAGC
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
71 55 0.83
72 11 0.17
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (72 bp):
AAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCC
AGTTATT
Found at i:1590998 original size:31 final size:31
Alignment explanation
Indices: 1590935--1590998 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1590925 CGTTTACAGT
* * *
1590935 AAAGGCTTCGGCCCAGTAATATTAAATTTGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
**
1590966 AAAGGCTTCAGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
1590997 AA
1 AA
1590999 TATGAAAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTAATATGAAATATGA
Found at i:1599377 original size:40 final size:40
Alignment explanation
Indices: 1599329--1599463 Score: 173
Period size: 40 Copynumber: 3.4 Consensus size: 40
1599319 ATTGATTATT
** * *
1599329 TATGGCACTTAGTGTGCGATACGACACAGCTTCGATTATA
1 TATGGCACTTAGTGTGCGATTTGACATAGCTTCGACTATA
*
1599369 TATGGCAC-TAGTGTGCGATTTGACATAGCTTCGGCTATA
1 TATGGCACTTAGTGTGCGATTTGACATAGCTTCGACTATA
* * * *
1599408 TATAGCACTTAGTGTGCGATTTGAGATAGCTTCGGCTATG
1 TATGGCACTTAGTGTGCGATTTGACATAGCTTCGACTATA
*
1599448 TATGGAACTTAGTGTG
1 TATGGCACTTAGTGTG
1599464 TGAGATATCG
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 33 0.39
40 51 0.61
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.33
Consensus pattern (40 bp):
TATGGCACTTAGTGTGCGATTTGACATAGCTTCGACTATA
Found at i:1599505 original size:28 final size:28
Alignment explanation
Indices: 1599447--1599506 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1599437 CTTCGGCTAT
* *
1599447 GTATGGAACTTAGTGTGTGAGATATCGA
1 GTATGGAACTTAGTGTGTGAGACATCAA
* *
1599475 GTATGGCACTTAGTGTGCT-AGACATTAA
1 GTATGGAACTTAGTGTG-TGAGACATCAA
1599503 GTAT
1 GTAT
1599507 TCAACGACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.33
Consensus pattern (28 bp):
GTATGGAACTTAGTGTGTGAGACATCAA
Found at i:1601477 original size:42 final size:43
Alignment explanation
Indices: 1601411--1601576 Score: 176
Period size: 42 Copynumber: 3.8 Consensus size: 43
1601401 TACTTCATTT
* ** *
1601411 TATCGACGCCATAGTTCAACTATGGTCTTACACAT-TTTCACA
1 TATCGATGCCATAGCCCAGCTATGGTCTTACACATATTTCACA
* *
1601453 TAAT-GAAGCCATAGCCCAGCTATGGTCTTACACATATTT-ATA
1 T-ATCGATGCCATAGCCCAGCTATGGTCTTACACATATTTCACA
* *
1601495 TATCGATGTCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACA
1 TATCGATGCCATAGCCCAGCTATGGTCTTACAC---AT---ATTTCACA
1601544 TATCGATGCCATAGCCCAGCTATGGTCTTACAC
1 TATCGATGCCATAGCCCAGCTATGGTCTTACAC
1601577 GAATCACATA
Statistics
Matches: 104, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
41 2 0.02
42 58 0.56
43 5 0.05
45 2 0.02
48 3 0.03
49 34 0.33
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (43 bp):
TATCGATGCCATAGCCCAGCTATGGTCTTACACATATTTCACA
Found at i:1601557 original size:49 final size:48
Alignment explanation
Indices: 1601494--1601618 Score: 173
Period size: 49 Copynumber: 2.6 Consensus size: 48
1601484 ACATATTTAT
*
1601494 ATATCGATGTCATAGCCCAGCTATGGTCTTACACGTAATCACATATCAC
1 ATATCGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATATCAC
*
1601543 ATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTC
1 ATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCAC
* * * *
1601591 A-CT-GATGCCATATCCTAGATATGGTCTT
1 ATATCGATGCCATAGCCCAGCTATGGTCTT
1601619 GTACGGAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
46 22 0.31
47 1 0.01
48 13 0.19
49 34 0.49
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (48 bp):
ATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCAC
Found at i:1601676 original size:31 final size:31
Alignment explanation
Indices: 1601641--1601758 Score: 184
Period size: 31 Copynumber: 3.8 Consensus size: 31
1601631 CTTGTCACTT
* *
1601641 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1601672 GTAGCCGGTA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
*
1601703 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1601734 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
1601759 TGTCATTTGT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
30 2 0.03
31 77 0.96
32 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:1601846 original size:50 final size:50
Alignment explanation
Indices: 1601734--1601910 Score: 275
Period size: 50 Copynumber: 3.5 Consensus size: 50
1601724 CACTGATCAG
* * *
1601734 GTAGCCGAAGCTACCACTTTTCACTTGTCA-TTTGTCATTGATTAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCATTGATCAGATAAGT
* *
1601785 GTAGCCAAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTTTCATTGATCAGATAAGT
*
1601835 GTAGCCGAAGCTATCACTTATCACTTTCACTTTTCTTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTTTCATTGATCAGATAAGT
1601885 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
1601911 GTTGCCATGG
Statistics
Matches: 118, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
50 92 0.78
51 26 0.22
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCACTTTTCATTGATCAGATAAGT
Found at i:1604265 original size:39 final size:39
Alignment explanation
Indices: 1604210--1604340 Score: 156
Period size: 39 Copynumber: 3.3 Consensus size: 39
1604200 GTATGAGATT
* * *
1604210 GAAAATATATCTGGACATGAAGTTCGCAGGTTATATGCTG
1 GAAAA-ATATCCGGACATGAAGTCCGCAGGCTATATGCTG
*
1604250 GAAAAATATCCGGACATG-AGATCCGCAGGCTATATGCTA
1 GAAAAATATCCGGACATGAAG-TCCGCAGGCTATATGCTG
* * * **
1604289 GAAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTG
1 GAAAAATATCCGGACATGAAGTCCGCAGGCTATATGCTG
1604328 GAAAAATATCCGG
1 GAAAAATATCCGG
1604341 GTTAAAAACC
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
38 2 0.03
39 70 0.90
40 6 0.08
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (39 bp):
GAAAAATATCCGGACATGAAGTCCGCAGGCTATATGCTG
Found at i:1604554 original size:2 final size:2
Alignment explanation
Indices: 1604547--1604578 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1604537 TCAAAGCACG
1604547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1604579 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1604583 original size:2 final size:2
Alignment explanation
Indices: 1604578--1604649 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1604568 TATATATATA
1604578 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1604620 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1604650 AATGAATTCG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1606285 original size:3 final size:3
Alignment explanation
Indices: 1606277--1606318 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1606267 TCAATACTAG
1606277 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1606319 ATAAATAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1611451 original size:9 final size:9
Alignment explanation
Indices: 1611437--1611462 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1611427 CTCATCAACT
1611437 TGTAATTTA
1 TGTAATTTA
1611446 TGTAATTTA
1 TGTAATTTA
1611455 TGTAATTT
1 TGTAATTT
1611463 TATTCAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (9 bp):
TGTAATTTA
Found at i:1615221 original size:29 final size:30
Alignment explanation
Indices: 1615179--1615237 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1615169 TATAGTTTAA
*
1615179 TGTGTAATTGTATACAT-AAATTTTGATTT
1 TGTGTAATTGTATACATGAAATCTTGATTT
*
1615208 TGTGTAATTTTATACATGAAATCTTGATTT
1 TGTGTAATTGTATACATGAAATCTTGATTT
1615238 GATTCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
TGTGTAATTGTATACATGAAATCTTGATTT
Found at i:1615755 original size:42 final size:43
Alignment explanation
Indices: 1615677--1615758 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
1615667 AAATTATTTT
* * *
1615677 ATATATTTAATGAATTTTTAAATTCGAACAAGTTAATATCCCA
1 ATATATTTAATGAATATTTAAATTCAAACAAATTAATATCCCA
*
1615720 ATATATTTAATGAA-ATTTAAATTTAAACAAATTAATATC
1 ATATATTTAATGAATATTTAAATTCAAACAAATTAATATC
1615759 AATCTAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 21 0.60
43 14 0.40
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (43 bp):
ATATATTTAATGAATATTTAAATTCAAACAAATTAATATCCCA
Found at i:1616452 original size:54 final size:54
Alignment explanation
Indices: 1616362--1616468 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
1616352 ATGATGTGTC
** *
1616362 ACGTGTACATCATGTTTACATACAAAAATTAATTTTTAATTGTATAAATAGATG
1 ACGTGTACATCATGTTTACATACAAAAACCAATTTTTAATTGTACAAATAGATG
* *
1616416 ACGTGTACATCATGTTTACATACAAGAACCAGTTTTTAATTGTACAAATAGAT
1 ACGTGTACATCATGTTTACATACAAAAACCAATTTTTAATTGTACAAATAGAT
1616469 AAGAATTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (54 bp):
ACGTGTACATCATGTTTACATACAAAAACCAATTTTTAATTGTACAAATAGATG
Found at i:1619653 original size:25 final size:23
Alignment explanation
Indices: 1619617--1619663 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1619607 GACGATAGTA
1619617 CTATATATACACACATATGGTTT
1 CTATATATACACACATATGGTTT
1619640 CTATATATACACACATATGGTTT
1 CTATATATACACACATATGGTTT
1619663 C
1 C
1619664 CATGAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (23 bp):
CTATATATACACACATATGGTTT
Found at i:1626295 original size:31 final size:34
Alignment explanation
Indices: 1626251--1626314 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 34
1626241 ATAATATTAT
1626251 AAATATTAAATTTATTATTATAT-TTT-TTTAAA
1 AAATATTAAATTTATTATTATATATTTCTTTAAA
* *
1626283 AAATATT-TATTTATTTTTATATATTTCTTTAA
1 AAATATTAAATTTATTATTATATATTTCTTTAA
1626315 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 13 0.46
32 10 0.36
33 5 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (34 bp):
AAATATTAAATTTATTATTATATATTTCTTTAAA
Found at i:1626534 original size:120 final size:120
Alignment explanation
Indices: 1626399--1626636 Score: 458
Period size: 120 Copynumber: 2.0 Consensus size: 120
1626389 AATTAATATA
1626399 TTAAATTTTATATATATTTATAAAATGTTTACTTGTTTAATCTAAATCAATCTTTAGGACATGTA
1 TTAAATTTTATATATATTTATAAAATGTTTACTTGTTTAATCTAAATCAATCTTTAGGACATGTA
* *
1626464 TTGAATCCGTATACGACTATACTTATTCTATTAGACATTGGTTATAAAAAAAGGG
66 CTGAATCCGTAAACGACTATACTTATTCTATTAGACATTGGTTATAAAAAAAGGG
1626519 TTAAATTTTATATATATTTATAAAATGTTTACTTGTTTAATCTAAATCAATCTTTAGGACATGTA
1 TTAAATTTTATATATATTTATAAAATGTTTACTTGTTTAATCTAAATCAATCTTTAGGACATGTA
1626584 CTGAATCCGTAAACGACTATACTTATTCTATTAGACATTGGTTATAAAAAAAG
66 CTGAATCCGTAAACGACTATACTTATTCTATTAGACATTGGTTATAAAAAAAG
1626637 AGTTGTTTAA
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (120 bp):
TTAAATTTTATATATATTTATAAAATGTTTACTTGTTTAATCTAAATCAATCTTTAGGACATGTA
CTGAATCCGTAAACGACTATACTTATTCTATTAGACATTGGTTATAAAAAAAGGG
Found at i:1630126 original size:2 final size:2
Alignment explanation
Indices: 1630119--1630146 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1630109 GAAGTTTTTG
1630119 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1630147 TTTGAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1639445 original size:30 final size:30
Alignment explanation
Indices: 1639411--1639472 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
1639401 TATTCCTTAA
* *
1639411 GTATTTTACATTACTTAGGTATTTTACTTG
1 GTATTTAACATTACTTAAGTATTTTACTTG
*
1639441 GTATTTAACGTTACTTAAGTATTTTACTTG
1 GTATTTAACATTACTTAAGTATTTTACTTG
1639471 GT
1 GT
1639473 CTCCGGTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.52
Consensus pattern (30 bp):
GTATTTAACATTACTTAAGTATTTTACTTG
Found at i:1642362 original size:3 final size:3
Alignment explanation
Indices: 1642356--1642384 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1642346 CAATAATAAT
1642356 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1642385 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1642449 original size:16 final size:16
Alignment explanation
Indices: 1642430--1642463 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1642420 TAGGTATATA
1642430 TATAGATAACCTCATC
1 TATAGATAACCTCATC
1642446 TATAGATAACCTCATC
1 TATAGATAACCTCATC
1642462 TA
1 TA
1642464 ATTAGGACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (16 bp):
TATAGATAACCTCATC
Found at i:1642980 original size:30 final size:30
Alignment explanation
Indices: 1642931--1642993 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1642921 ACTTAACAAG
*
1642931 CAAATGCTTCTAAAATAATAACAAAATTAA
1 CAAATGCTTCTAAAATAATAAAAAAATTAA
*
1642961 CAAATGTCTT-TAAAGTAATAAAAAAATTAA
1 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1642991 CAA
1 CAA
1642994 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGCTTCTAAAATAATAAAAAAATTAA
Found at i:1643049 original size:22 final size:22
Alignment explanation
Indices: 1643024--1643066 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1643014 ATTCAAACAA
1643024 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
1643046 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
1643067 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:1643070 original size:11 final size:11
Alignment explanation
Indices: 1643031--1643071 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1643021 CAAATAACAA
1643031 CAAAATAGTAG
1 CAAAATAGTAG
* *
1643042 CAACATAATAG
1 CAAAATAGTAG
*
1643053 TAAAATAGTAG
1 CAAAATAGTAG
1643064 CAAAATAG
1 CAAAATAG
1643072 GGAGAAAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:1643504 original size:15 final size:15
Alignment explanation
Indices: 1643463--1643504 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1643453 CATACAAGTG
1643463 CATCTAGGGTTCGCA
1 CATCTAGGGTTCGCA
* * *
1643478 CATTTTGAGTTCGCA
1 CATCTAGGGTTCGCA
1643493 CATCTAGGGTTC
1 CATCTAGGGTTC
1643505 ACATATATAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (15 bp):
CATCTAGGGTTCGCA
Found at i:1643635 original size:23 final size:23
Alignment explanation
Indices: 1643608--1643664 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
1643598 AAATAACATA
1643608 TAGGGTTCGCATATTAGTGCATG
1 TAGGGTTCGCATATTAGTGCATG
1643631 TAGGGTTCGCATATTAGTGCATG
1 TAGGGTTCGCATATTAGTGCATG
*
1643654 TAGGATTCGCA
1 TAGGGTTCGCA
1643665 AGTTATACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (23 bp):
TAGGGTTCGCATATTAGTGCATG
Found at i:1643643 original size:45 final size:46
Alignment explanation
Indices: 1643535--1643643 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 46
1643525 AATTAGGGTT
* * *
1643535 TGCATATAGAGTTCGCA-AAATAAACAAATAGGGTTTGCATATTCC
1 TGCATGTAGAGTTCGCATAAATAAACAAATAGGGTTCGCATATTAC
* * * * *
1643580 TACAAGTAGAGTTTGCATAAAT-AACATATAGGGTTCGCATATTAG
1 TGCATGTAGAGTTCGCATAAATAAACAAATAGGGTTCGCATATTAC
*
1643625 TGCATGTAGGGTTCGCATA
1 TGCATGTAGAGTTCGCATA
1643644 TTAGTGCATG
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
45 47 0.92
46 4 0.08
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (46 bp):
TGCATGTAGAGTTCGCATAAATAAACAAATAGGGTTCGCATATTAC
Found at i:1643839 original size:29 final size:29
Alignment explanation
Indices: 1643805--1643892 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
1643795 TAGGAGGTCA
*
1643805 CCTATAGGGATTCACATACATGAGGCTCG
1 CCTATAGGGATTCACATACATGGGGCTCG
* *
1643834 CCTATAGGTG-TTCACATACAGGGGGTTCG
1 CCTATAGG-GATTCACATACATGGGGCTCG
* *
1643863 CCTATAAGGATTCGCATACATGGGGCTCG
1 CCTATAGGGATTCACATACATGGGGCTCG
1643892 C
1 C
1643893 ATACAGGGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.02
29 48 0.96
30 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (29 bp):
CCTATAGGGATTCACATACATGGGGCTCG
Found at i:1646575 original size:3 final size:3
Alignment explanation
Indices: 1646567--1646606 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1646557 CTTATAATGC
1646567 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1646607 GTGGAACACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1647433 original size:45 final size:46
Alignment explanation
Indices: 1647329--1647436 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 46
1647319 AATCAAGGTT
* ** * *
1647329 TGCATATAGAGTTCACA-AAATAAACAAATAGGGTTCGCATATTCC
1 TGCATGTAGAGTTTGCATAAATAAACAAATAAGGTTCGCATATTAC
* *
1647374 TGCATGTAGAGTTTGCATAAAT-AACATATAAGGTTCGCATATTAG
1 TGCATGTAGAGTTTGCATAAATAAACAAATAAGGTTCGCATATTAC
*
1647419 TGCATGTAGGGTTTGCAT
1 TGCATGTAGAGTTTGCAT
1647437 GTTATACAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 50 0.93
46 4 0.07
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (46 bp):
TGCATGTAGAGTTTGCATAAATAAACAAATAAGGTTCGCATATTAC
Found at i:1647436 original size:23 final size:23
Alignment explanation
Indices: 1647357--1647436 Score: 56
Period size: 23 Copynumber: 3.5 Consensus size: 23
1647347 AATAAACAAA
**
1647357 TAGGGTTCGCATATTCCTGCATG
1 TAGGGTTCGCATATTAATGCATG
* * * *
1647380 TAGAGTTTGCATA--AATAACATA
1 TAGGGTTCGCATATTAAT-GCATG
* *
1647402 TAAGGTTCGCATATTAGTGCATG
1 TAGGGTTCGCATATTAATGCATG
*
1647425 TAGGGTTTGCAT
1 TAGGGTTCGCAT
1647437 GTTATACAGA
Statistics
Matches: 40, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
21 1 0.03
22 13 0.32
23 24 0.60
24 2 0.05
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (23 bp):
TAGGGTTCGCATATTAATGCATG
Found at i:1647455 original size:45 final size:45
Alignment explanation
Indices: 1647329--1647458 Score: 113
Period size: 45 Copynumber: 2.9 Consensus size: 45
1647319 AATCAAGGTT
* ** * * *
1647329 TGCATATAGAGTTCACA-AAATAAACAAATAGGGTTCGCATATTCC
1 TGCATGTAGAGTTTGCATAAAT-AACAGATAGAGTTCGCATATTAC
* *
1647374 TGCATGTAGAGTTTGCATAAATAACATATA-AGGTTCGCATATTAG
1 TGCATGTAGAGTTTGCATAAATAACAGATAGA-GTTCGCATATTAC
* **
1647419 TGCATGTAGGGTTTGCAT-GTTATACAGATAGAGTTCGCAT
1 TGCATGTAGAGTTTGCATAAATA-ACAGATAGAGTTCGCAT
1647459 GGCATAACAG
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
44 2 0.03
45 63 0.90
46 5 0.07
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (45 bp):
TGCATGTAGAGTTTGCATAAATAACAGATAGAGTTCGCATATTAC
Found at i:1647481 original size:23 final size:21
Alignment explanation
Indices: 1647428--1647482 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
1647418 GTGCATGTAG
**
1647428 GGTTTGCATGTTATACAGATA
1 GGTTTGCATGGCATACAGATA
*
1647449 GAGTTCGCATGGCATAACAGATA
1 G-GTTTGCATGGCAT-ACAGATA
1647472 TGGTTTGCATG
1 -GGTTTGCATG
1647483 TATATCCCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 1 0.04
22 10 0.37
23 15 0.56
24 1 0.04
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (21 bp):
GGTTTGCATGGCATACAGATA
Found at i:1647685 original size:30 final size:30
Alignment explanation
Indices: 1647644--1647710 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
1647634 CCTATAAGGT
* *
1647644 TTCGCATACATAGGGCTT-GCATACCGGGGG
1 TTCGTATACATAAGG-TTCGCATACCGGGGG
*
1647674 TTCGTATACATAAGGTTCGCATACGGGGGG
1 TTCGTATACATAAGGTTCGCATACCGGGGG
1647704 TTCGTAT
1 TTCGTAT
1647711 GTACAGATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (30 bp):
TTCGTATACATAAGGTTCGCATACCGGGGG
Found at i:1650766 original size:18 final size:19
Alignment explanation
Indices: 1650730--1650766 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
1650720 AAAAATAAAA
1650730 TTTATATTTATATTATTTT
1 TTTATATTTATATTATTTT
1650749 TTTA-ATTTAGTATT-TTTT
1 TTTATATTTA-TATTATTTT
1650767 AATTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTATATTTATATTATTTT
Found at i:1652678 original size:19 final size:19
Alignment explanation
Indices: 1652629--1652680 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1652619 TAGCCCGTTG
1652629 TTTT-TAATATTAAACAATA
1 TTTTATAATA-TAAACAATA
*
1652648 TTTTATATTATAAACAATA
1 TTTTATAATATAAACAATA
1652667 TTTGTA-AATATAAA
1 TTT-TATAATATAAA
1652681 GTAAATTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTTATAATATAAACAATA
Found at i:1657804 original size:22 final size:22
Alignment explanation
Indices: 1657774--1657818 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1657764 TATTTTTATA
*
1657774 TTATCAAATTACATTATT-GCCC
1 TTAT-AAAATACATTATTAGCCC
*
1657796 TTATAAAATATATTATTAGCCC
1 TTATAAAATACATTATTAGCCC
1657818 T
1 T
1657819 AAGCTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (22 bp):
TTATAAAATACATTATTAGCCC
Found at i:1664830 original size:30 final size:30
Alignment explanation
Indices: 1664761--1664823 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
1664751 AGCTACCACA
1664761 AAAGTATTCATTTACTTTGATTGAAGACAT
1 AAAGTATTCATTTACTTTGATTGAAGACAT
1664791 AAAGTATTCATTTACTTTGATTGAAGACAT
1 AAAGTATTCATTTACTTTGATTGAAGACAT
1664821 AAA
1 AAA
1664824 TGATTCAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (30 bp):
AAAGTATTCATTTACTTTGATTGAAGACAT
Found at i:1672376 original size:30 final size:27
Alignment explanation
Indices: 1672320--1672385 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 27
1672310 TAAACTTTTT
*
1672320 TTTGTTATAAGTGATGCCTAAATTATA
1 TTTGTTATAAGTGATACCTAAATTATA
* *
1672347 CTTTGTTACCTAAGTGATACTTAACTTATA
1 -TTTGTTA--TAAGTGATACCTAAATTATA
1672377 TTATGTTAT
1 TT-TGTTAT
1672386 CCAAATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
28 8 0.25
29 2 0.06
30 22 0.69
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (27 bp):
TTTGTTATAAGTGATACCTAAATTATA
Found at i:1672497 original size:13 final size:15
Alignment explanation
Indices: 1672468--1672514 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1672458 GTTTGAAAAA
1672468 ATTAAATATTATTTT
1 ATTAAATATTATTTT
1672483 ATTAAAT-TT-TTTT
1 ATTAAATATTATTTT
* *
1672496 ATAAACATATTAATTT
1 ATTAA-ATATTATTTT
1672512 ATT
1 ATT
1672515 TTGTTCTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 8 0.31
14 4 0.15
15 9 0.35
16 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAAATATTATTTT
Found at i:1673400 original size:14 final size:15
Alignment explanation
Indices: 1673381--1673415 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1673371 GTTTAGTGAC
*
1673381 TTAAATAA-AAATTA
1 TTAAATAATAAATAA
1673395 TTAAATAATAAATAA
1 TTAAATAATAAATAA
1673410 TTAAAT
1 TTAAAT
1673416 TATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAATAATAAATAA
Found at i:1679159 original size:31 final size:31
Alignment explanation
Indices: 1679121--1679185 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1679111 ACTTACTAAT
1679121 GACTAATTTGAATCATTCCCTATAATAAAAG
1 GACTAATTTGAATCATTCCCTATAATAAAAG
1679152 GACTAATTTGAATCATTCCCTATAATAAAAG
1 GACTAATTTGAATCATTCCCTATAATAAAAG
1679183 GAC
1 GAC
1679186 CTGACAGGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (31 bp):
GACTAATTTGAATCATTCCCTATAATAAAAG
Found at i:1689220 original size:39 final size:39
Alignment explanation
Indices: 1689166--1689244 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1689156 GTACATAGTT
1689166 TCCACGCGCATAGTGTGATAAAATTTCTTATATTATTTA
1 TCCACGCGCATAGTGTGATAAAATTTCTTATATTATTTA
1689205 TCCACGCGCATAGTGTGATAAAATTTCTTATATTATTTA
1 TCCACGCGCATAGTGTGATAAAATTTCTTATATTATTTA
1689244 T
1 T
1689245 TAAATGTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (39 bp):
TCCACGCGCATAGTGTGATAAAATTTCTTATATTATTTA
Found at i:1703427 original size:60 final size:58
Alignment explanation
Indices: 1703268--1703435 Score: 160
Period size: 62 Copynumber: 2.8 Consensus size: 58
1703258 ACTGCAGTAT
* *
1703268 TAGTCACTCAACTGTT-ATTAAATTTCTTTTTTGGTTATCCAACTATGAAAAGTTACAAAA
1 TAGTCACTCAACTGTTAATT---TTTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAA
* * * * *
1703328 AATGATCACTCGACTATTAGTGAATTTC-TTTTTGAGTCACCCAACTATGAAAAGTTACAAAA
1 TA-G-TCACTCAACTGTTAAT--TTTTCTTTTTTG-GTCACCCAACTATGAAAAGTTACAAAA
*
1703390 TAGTCACTCAACTGTTCAATTTTATCTTTTTTGGTCACCCGACTAT
1 TAGTCACTCAACTGTT-AATTTT-TCTTTTTTGGTCACCCAACTAT
1703436 CTTAGATTTT
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
59 2 0.02
60 26 0.30
61 16 0.19
62 41 0.48
63 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.38
Consensus pattern (58 bp):
TAGTCACTCAACTGTTAATTTTTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAA
Found at i:1714340 original size:2 final size:2
Alignment explanation
Indices: 1714333--1714371 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1714323 AGTCAAAGAA
*
1714333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1714372 ACCTAAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1714829 original size:176 final size:174
Alignment explanation
Indices: 1714370--1714838 Score: 439
Period size: 176 Copynumber: 2.7 Consensus size: 174
1714360 TATATATGTA
* * * *
1714370 TAACCTAAATCTCAACAATCAATTAAAT-AAAGGATTAAATC-ACAACTTGATGCAAATTGAGAG
1 TAACCTAGATCTCAACAATCAATTAAATCAAA-GATCAAATCGA-AACTTGAT-CTAATTAAGAG
* ** * *
1714433 ATCCAATAATAAAATTTC-CATTTTAAAAAGACACGGGATTGTCTCCTAATATCTTAGAGTTTAG
63 ATCCAATAATAAAA-TTCACACTTTAAAAAGACACGTAATTGTCTCC-AACATCTTAGAGTATAG
*** * * * *
1714497 CTTGTCTAACACATTAAGATTCATGTTAGATTCGACATTCAAGACAACC
126 CTCACCTAACACATTAACATTCATGTCAGACTCGACACTCAAGACAACC
* * * * * *
1714546 TAACCTAGATCTTAACAATCAATTAAATCAATGATCAAATTGGAGA-TTAATCTGACTTAAGAGA
1 TAACCTAGATCTCAACAATCAATTAAATCAAAGATCAAA-TCGAAACTTGATCT-AATTAAGAGA
* * * **
1714610 CCCATTAATAAAATTCA-ATTCTTT-AAAAGACACATTGTTGTCTCTCAACATCTTAGAGCTAT-
64 TCCAATAATAAAATTCACA--CTTTAAAAAGACACGTAATTGTCTC-CAACATCTTAGAG-TATA
* ** * * *
1714672 GCTCACCTAGCATGTTAACATTCGTGTCATACTCGACACTCAAGGCAACC
125 GCTCACCTAACACATTAACATTCATGTCAGACTCGACACTCAAGACAACC
* * *
1714722 TAATCTAGATCTCAACAATCAATTAAATCAAAAATCAAATCGAAACTCGATCTAATTAAAGAGAT
1 TAACCTAGATCTCAACAATCAATTAAATCAAAGATCAAATCGAAACTTGATCTAATT-AAGAGAT
*
1714787 CCAATAATAAAATTCACACTTTAAAAAAACACGTAATTGTCTCCCAACATCT
65 CCAATAATAAAATTCACACTTTAAAAAGACACGTAATTGTCT-CCAACATCT
1714839 CGAAACTGAG
Statistics
Matches: 232, Mismatches: 47, Indels: 28
0.76 0.15 0.09
Matches are distributed among these distances:
175 16 0.07
176 203 0.88
177 12 0.05
178 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (174 bp):
TAACCTAGATCTCAACAATCAATTAAATCAAAGATCAAATCGAAACTTGATCTAATTAAGAGATC
CAATAATAAAATTCACACTTTAAAAAGACACGTAATTGTCTCCAACATCTTAGAGTATAGCTCAC
CTAACACATTAACATTCATGTCAGACTCGACACTCAAGACAACC
Found at i:1718564 original size:30 final size:30
Alignment explanation
Indices: 1718528--1718585 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1718518 ATCTAGTGAC
*
1718528 TTAAATAAA-ACCTTTCGAATAGTTTAATGA
1 TTAAATAAACA-CTTTCGAATAATTTAATGA
*
1718558 TTAAATAAACATTTTCGAATAATTTAAT
1 TTAAATAAACACTTTCGAATAATTTAAT
1718586 AATCATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.40
Consensus pattern (30 bp):
TTAAATAAACACTTTCGAATAATTTAATGA
Found at i:1723933 original size:17 final size:16
Alignment explanation
Indices: 1723898--1723936 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1723888 TATATAAATT
* *
1723898 TTAAAAATATAATAAA
1 TTAAATATATAAAAAA
1723914 TTAAATATATTAAAAAA
1 TTAAATATA-TAAAAAA
1723931 TTAAAT
1 TTAAAT
1723937 TAAATATTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TTAAATATATAAAAAA
Found at i:1727579 original size:8 final size:8
Alignment explanation
Indices: 1727557--1727688 Score: 68
Period size: 8 Copynumber: 17.0 Consensus size: 8
1727547 TATTTTTGAA
1727557 AAATATAT
1 AAATATAT
1727565 AAAATATAT
1 -AAATATAT
1727574 AAATATAT
1 AAATATAT
1727582 AAATATAT
1 AAATATAT
1727590 --ATA-A-
1 AAATATAT
1727594 AAATATAT
1 AAATATAT
1727602 AAA-ACGTAT
1 AAATA--TAT
* *
1727611 AATTTTAT
1 AAATATAT
1727619 AAA-AGTAT
1 AAATA-TAT
**
1727627 GTAT-TAT
1 AAATATAT
*
1727634 AAAAAT-T
1 AAATATAT
1727641 ATAATATAT
1 A-AATATAT
*
1727650 AAATTTAT
1 AAATATAT
1727658 AAA-ATAT
1 AAATATAT
*
1727665 ATAT-TAT
1 AAATATAT
*
1727672 AAATTTAT
1 AAATATAT
1727680 GAAATATAT
1 -AAATATAT
1727689 TATTTTAATA
Statistics
Matches: 93, Mismatches: 15, Indels: 30
0.67 0.11 0.22
Matches are distributed among these distances:
5 1 0.01
6 6 0.06
7 19 0.20
8 45 0.48
9 22 0.24
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (8 bp):
AAATATAT
Found at i:1727581 original size:10 final size:9
Alignment explanation
Indices: 1727556--1727605 Score: 75
Period size: 9 Copynumber: 5.4 Consensus size: 9
1727546 TTATTTTTGA
1727556 AAAATATAT
1 AAAATATAT
1727565 AAAATATAT
1 AAAATATAT
1727574 -AAATATAT
1 AAAATATAT
1727582 AAATATATAT
1 AAA-ATATAT
1727592 AAAAATATAT
1 -AAAATATAT
1727602 AAAA
1 AAAA
1727606 CGTATAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.21
9 15 0.39
10 12 0.32
11 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATATAT
Found at i:1727599 original size:37 final size:38
Alignment explanation
Indices: 1727555--1727688 Score: 132
Period size: 37 Copynumber: 3.5 Consensus size: 38
1727545 ATTATTTTTG
*
1727555 AAAAATATATAAAATATATAAATATAT-AAATATATAT
1 AAAAATATATAAAATATATAAATTTATAAAATATATAT
** *
1727592 AAAAATATATAAAACGTATAATTTTATAAAAGTATGTATTAT
1 AAAAATATATAAAATATATAAATTTATAAAA-TA--TA-TAT
1727634 AAAAAT-TAT--AATATATAAATTTATAAAATATATATT
1 AAAAATATATAAAATATATAAATTTATAAAATATATA-T
* * *
1727670 ATAAATTTATGAAATATAT
1 AAAAATATATAAAATATAT
1727689 TATTTTAATA
Statistics
Matches: 80, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
35 2 0.03
36 8 0.10
37 26 0.32
38 5 0.06
39 25 0.31
41 5 0.06
42 9 0.11
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (38 bp):
AAAAATATATAAAATATATAAATTTATAAAATATATAT
Found at i:1727672 original size:22 final size:24
Alignment explanation
Indices: 1727630--1727688 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 24
1727620 AAAGTATGTA
1727630 TTATAAAA-ATTATAATATATAAAT
1 TTATAAAATA-TATAATATATAAAT
1727654 TTATAAAATATAT-AT-TATAAAT
1 TTATAAAATATATAATATATAAAT
*
1727676 TTATGAAATATAT
1 TTATAAAATATAT
1727689 TATTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 19 0.58
23 2 0.06
24 11 0.33
25 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TTATAAAATATATAATATATAAAT
Found at i:1727686 original size:39 final size:39
Alignment explanation
Indices: 1727557--1727688 Score: 144
Period size: 39 Copynumber: 3.4 Consensus size: 39
1727547 TATTTTTGAA
* *
1727557 AAATATATAAAATATATAAATATAT-AAATATATA-TAA
1 AAATATATAAAATATATAAATTTATAAAATATATATTAT
** * *
1727594 AAATATATAAAACGTATAATTTTATAAAAGTATGTATTAT
1 AAATATATAAAATATATAAATTTATAAAA-TATATATTAT
* *
1727634 AAAAAT-TATAATATATAAATTTATAAAATATATATTAT
1 AAATATATAAAATATATAAATTTATAAAATATATATTAT
* *
1727672 AAATTTATGAAATATAT
1 AAATATATAAAATATAT
1727689 TATTTTAATA
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
37 21 0.28
38 16 0.21
39 31 0.41
40 7 0.09
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (39 bp):
AAATATATAAAATATATAAATTTATAAAATATATATTAT
Found at i:1732700 original size:29 final size:29
Alignment explanation
Indices: 1732645--1732703 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1732635 AAATTGAATC
*
1732645 AAATCAAAATGTTATGTATAAAATTACACA
1 AAATCAAAATCTTATG-ATAAAATTACACA
*
1732675 AAATCAAAATTCTTATG-TAACATTACACA
1 AAATCAAAA-TCTTATGATAAAATTACACA
1732704 TTAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 9 0.35
31 6 0.23
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (29 bp):
AAATCAAAATCTTATGATAAAATTACACA
Found at i:1735967 original size:5 final size:5
Alignment explanation
Indices: 1735957--1735983 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1735947 GACCCACCAT
1735957 TTCTC TTCTC TTCTC TTCTC TTCTC TT
1 TTCTC TTCTC TTCTC TTCTC TTCTC TT
1735984 TGGACACCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
TTCTC
Found at i:1736379 original size:16 final size:16
Alignment explanation
Indices: 1736358--1736388 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1736348 AATATATTTT
1736358 TTATAAATGTTATATA
1 TTATAAATGTTATATA
*
1736374 TTATAAATTTTATAT
1 TTATAAATGTTATAT
1736389 TTTTTTTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTATAAATGTTATATA
Found at i:1737332 original size:21 final size:20
Alignment explanation
Indices: 1737308--1737352 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1737298 TATTATATGA
*
1737308 TAATAAAAAAGTAATATTAAT
1 TAATAAAAAAGT-ACATTAAT
* *
1737329 TAATATAATAGTACATTAAT
1 TAATAAAAAAGTACATTAAT
1737349 TAAT
1 TAAT
1737353 GTGAAACTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
TAATAAAAAAGTACATTAAT
Found at i:1738914 original size:53 final size:53
Alignment explanation
Indices: 1738842--1738950 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
1738832 TATCACATAA
1738842 TTATACTTCGAACACATATTAAATTACACTTATTATTCTAGACTAATTATCAC
1 TTATACTTCGAACACATATTAAATTACACTTATTATTCTAGACTAATTATCAC
* *
1738895 TTATACTTCGAACACATATTAAATTATACTTATTATTCTAGACTAATTGTCAC
1 TTATACTTCGAACACATATTAAATTACACTTATTATTCTAGACTAATTATCAC
1738948 TTA
1 TTA
1738951 ATTAGTGTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (53 bp):
TTATACTTCGAACACATATTAAATTACACTTATTATTCTAGACTAATTATCAC
Found at i:1744278 original size:15 final size:14
Alignment explanation
Indices: 1744261--1744305 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1744251 TCAAAATTTA
1744261 AAAATATATAAATT
1 AAAATATATAAATT
*
1744275 AAAATTTATCAAATT
1 AAAATATAT-AAATT
*
1744290 AAAATA-ATAAACT
1 AAAATATATAAATT
1744303 AAA
1 AAA
1744306 TCCGTAACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 7 0.26
14 10 0.37
15 10 0.37
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATATATAAATT
Found at i:1755731 original size:30 final size:29
Alignment explanation
Indices: 1755697--1755781 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 29
1755687 TTTTAGGGTG
* *
1755697 AATTATACTAATAATCATCTAACTATGAAA
1 AATTATA-AAATAATCATCTAACTATAAAA
* *
1755727 AATTATAAAATGATCA-CTAAATTATAAAA
1 AATTATAAAATAATCATCT-AACTATAAAA
*
1755756 AATTTATAAAATAGTCATCTAACTAT
1 AA-TTATAAAATAATCATCTAACTAT
1755782 TTAGTTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.04
29 17 0.38
30 24 0.53
31 2 0.04
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.34
Consensus pattern (29 bp):
AATTATAAAATAATCATCTAACTATAAAA
Found at i:1759082 original size:39 final size:39
Alignment explanation
Indices: 1759029--1759140 Score: 110
Period size: 39 Copynumber: 3.0 Consensus size: 39
1759019 TTTAATTAAT
* *
1759029 TTTTTAGAATTTAAAATTTTTAAAATATTATAAAAAATA
1 TTTTTAAAAATTAAAATTTTTAAAATATTATAAAAAATA
* *
1759068 TTTTTAAAAATTAAAATTATTAAAGA-A--ATATAAAA-A
1 TTTTTAAAAATTAAAATTTTTAAA-ATATTATAAAAAATA
* *
1759104 TTATAAAAAATTAAATATTTTTAAAAT-TT-TAAAAAAT
1 TTTTTAAAAATTAAA-ATTTTTAAAATATTATAAAAAAT
1759141 TAATTAAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
36 15 0.25
37 21 0.36
39 22 0.37
40 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (39 bp):
TTTTTAAAAATTAAAATTTTTAAAATATTATAAAAAATA
Found at i:1759129 original size:17 final size:17
Alignment explanation
Indices: 1759063--1759129 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
1759053 ATATTATAAA
*
1759063 AAATATTTTTAAAAATT
1 AAATATTTTAAAAAATT
1759080 AAA-ATTATTAAAGAAATAT
1 AAATATT-TTAAA-AAAT-T
* *
1759099 AAAAATTATAAAAAATT
1 AAATATTTTAAAAAATT
1759116 AAATATTTTTAAAA
1 AAATA-TTTTAAAA
1759130 TTTTAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.07
17 12 0.29
18 15 0.37
19 8 0.20
20 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (17 bp):
AAATATTTTAAAAAATT
Found at i:1767090 original size:55 final size:55
Alignment explanation
Indices: 1767006--1767119 Score: 228
Period size: 55 Copynumber: 2.1 Consensus size: 55
1766996 CACTCTAAAG
1767006 AAAAAGAAAGTGAAGTAGTAAAAAACAGGTTTACTTGCTTAGATAAGAGTAGATC
1 AAAAAGAAAGTGAAGTAGTAAAAAACAGGTTTACTTGCTTAGATAAGAGTAGATC
1767061 AAAAAGAAAGTGAAGTAGTAAAAAACAGGTTTACTTGCTTAGATAAGAGTAGATC
1 AAAAAGAAAGTGAAGTAGTAAAAAACAGGTTTACTTGCTTAGATAAGAGTAGATC
1767116 AAAA
1 AAAA
1767120 TTGCAATAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (55 bp):
AAAAAGAAAGTGAAGTAGTAAAAAACAGGTTTACTTGCTTAGATAAGAGTAGATC
Found at i:1768236 original size:11 final size:10
Alignment explanation
Indices: 1768219--1768257 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1768209 TTTATACACA
1768219 TTATTTATAT
1 TTATTTATAT
1768229 TGTATTTATAT
1 T-TATTTATAT
*
1768240 TTTTTTATAT
1 TTATTTATAT
1768250 TT-TTTATA
1 TTATTTATA
1768258 CTCTACTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 6 0.22
10 11 0.41
11 10 0.37
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (10 bp):
TTATTTATAT
Found at i:1769103 original size:25 final size:25
Alignment explanation
Indices: 1769071--1769122 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
1769061 AAATGTTTGG
1769071 TTTTTATATGACCATTTTGAAATGT
1 TTTTTATATGACCATTTTGAAATGT
*
1769096 TTTTTATATGACTATTTTGAAATGT
1 TTTTTATATGACCATTTTGAAATGT
1769121 TT
1 TT
1769123 AACCTCTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.56
Consensus pattern (25 bp):
TTTTTATATGACCATTTTGAAATGT
Found at i:1778216 original size:18 final size:18
Alignment explanation
Indices: 1778193--1778230 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1778183 AAATATATAT
1778193 ATATATATATTCACACAC
1 ATATATATATTCACACAC
1778211 ATATATATATTCACACAC
1 ATATATATATTCACACAC
1778229 AT
1 AT
1778231 TTACTGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATATATATTCACACAC
Found at i:1780221 original size:26 final size:28
Alignment explanation
Indices: 1780177--1780257 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 28
1780167 TAAAAAATGT
*
1780177 TTAAAATGACTATATATAAAATTTTAATAAA
1 TTAAAAT-AATATA-ATAAAATTTTAA-AAA
1780208 -TAAAA-AAT-TAATAAAATTATTAAAAA
1 TTAAAATAATATAATAAAATT-TTAAAAA
1780234 TTAAAATAATATAA-AAATATTTTA
1 TTAAAATAATATAATAAA-ATTTTA
1780258 TTTTTTAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
26 11 0.25
27 11 0.25
28 11 0.25
29 6 0.14
30 5 0.11
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (28 bp):
TTAAAATAATATAATAAAATTTTAAAAA
Found at i:1781865 original size:11 final size:11
Alignment explanation
Indices: 1781845--1781874 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1781835 GGGCTTTCAA
1781845 TTTTTGTATTAC
1 TTTTT-TATTAC
1781857 TTTTTTATTAC
1 TTTTTTATTAC
1781868 TTTTTTA
1 TTTTTTA
1781875 GAGAGACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (11 bp):
TTTTTTATTAC
Found at i:1783083 original size:14 final size:14
Alignment explanation
Indices: 1783060--1783089 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1783050 TAGTATCTAC
*
1783060 ATTATGTTGGCATG
1 ATTATATTGGCATG
1783074 ATTATATTGGCATG
1 ATTATATTGGCATG
1783088 AT
1 AT
1783090 GGTTAAGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (14 bp):
ATTATATTGGCATG
Found at i:1785858 original size:44 final size:45
Alignment explanation
Indices: 1785768--1785896 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
1785758 GACAGAACGA
*
1785768 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
1785814 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
1785858 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1785897 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:1792765 original size:44 final size:45
Alignment explanation
Indices: 1792675--1792803 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
1792665 GACAGAACGA
*
1792675 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
1792721 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
1792765 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1792804 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:1795572 original size:22 final size:22
Alignment explanation
Indices: 1795544--1795601 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1795534 TTTTACTCTA
*
1795544 TAATTCAACACGAACAAATAAT
1 TAATTCAACACAAACAAATAAT
1795566 TAATTCAACACAAACAAATAAT
1 TAATTCAACACAAACAAATAAT
* *
1795588 TAATTGATCACAAA
1 TAATTCAACACAAA
1795602 TCATAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.24
Consensus pattern (22 bp):
TAATTCAACACAAACAAATAAT
Found at i:1805380 original size:21 final size:21
Alignment explanation
Indices: 1805356--1805400 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1805346 TGGCTTGAAC
1805356 AAAAAGTAAGGCTCGTTTAGG
1 AAAAAGTAAGGCTCGTTTAGG
1805377 AAAAAGTAAGGCTCGTTTAGG
1 AAAAAGTAAGGCTCGTTTAGG
1805398 AAA
1 AAA
1805401 CAGGTCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.22
Consensus pattern (21 bp):
AAAAAGTAAGGCTCGTTTAGG
Found at i:1805519 original size:22 final size:22
Alignment explanation
Indices: 1805494--1805541 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1805484 TTGTTTTTAC
1805494 TGTTTTGCT-ACTATTTTCTTGT
1 TGTTTT-CTCACTATTTTCTTGT
* *
1805516 TGTTTTCTCATTATTTTGTTGT
1 TGTTTTCTCACTATTTTCTTGT
1805538 TGTT
1 TGTT
1805542 ATTTGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.08, C:0.10, G:0.15, T:0.67
Consensus pattern (22 bp):
TGTTTTCTCACTATTTTCTTGT
Found at i:1807547 original size:29 final size:29
Alignment explanation
Indices: 1807514--1807577 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1807504 TTAATACATA
1807514 AAACTTG-ATT-TAGTATAATTATATATATG
1 AAACTTGAATTATAGT-TAATT-TATATATG
* *
1807543 AAACTTGAATTATGGTTCATTTATATATG
1 AAACTTGAATTATAGTTAATTTATATATG
1807572 AAACTT
1 AAACTT
1807578 TCATTATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 21 0.68
30 7 0.23
31 3 0.10
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (29 bp):
AAACTTGAATTATAGTTAATTTATATATG
Found at i:1807583 original size:29 final size:29
Alignment explanation
Indices: 1807535--1807590 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1807525 AGTATAATTA
*
1807535 TATATATGAAACTTGAATTATGGTTCATT
1 TATATATGAAACTTGAATTATGATTCATT
**
1807564 TATATATGAAACTTTCATTATGATTCA
1 TATATATGAAACTTGAATTATGATTCA
1807591 ACTATACACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.45
Consensus pattern (29 bp):
TATATATGAAACTTGAATTATGATTCATT
Found at i:1810631 original size:13 final size:13
Alignment explanation
Indices: 1810613--1810638 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1810603 GCATCGTCCC
1810613 ATTTCCTACATTT
1 ATTTCCTACATTT
1810626 ATTTCCTACATTT
1 ATTTCCTACATTT
1810639 TTTTTTTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTCCTACATTT
Found at i:1811353 original size:3 final size:3
Alignment explanation
Indices: 1811347--1811375 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1811337 TATTTTTACT
1811347 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1811376 GTTGTTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1814491 original size:23 final size:23
Alignment explanation
Indices: 1814465--1814509 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1814455 ATCTAATTTT
1814465 TTTTAAAAATTTAAAAAATTATA
1 TTTTAAAAATTTAAAAAATTATA
* *
1814488 TTTTAAAATTTTCAAAAATTAT
1 TTTTAAAAATTTAAAAAATTAT
1814510 GTAAATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTAAAAATTTAAAAAATTATA
Found at i:1825984 original size:185 final size:184
Alignment explanation
Indices: 1825665--1826034 Score: 650
Period size: 185 Copynumber: 2.0 Consensus size: 184
1825655 CTTATTAAAT
*
1825665 AATGAAAAACAAATAAAAAAACATATAAAACTTAAGATAATACTAGTCCAAACCGACTCATGAAA
1 AATGAAAAACAAATAAAAAAACATATAAAACTTAAGATAATACGAGTCCAAACCGACTCATGAAA
*
1825730 TTATTTATTATTCTGAAATTCTCAAAACAGAAACAGATTAATAAGTCAACGAAGAGCTACCCACT
66 TTATTTATTATTCTGAAATTCTCAAAACAGAAACAGATTAAGAAGTCAACGAAGAGCTACCCACT
* * * *
1825795 TTTTAAAAGAAATTGTCAGTGGTCGGTGGTGTTTCAATGATGATAGGCACTGTC
131 TTTTAAAAGAAACTGTCAGTGGCCGGTGGTGTTTCAACGATGATAGACACTGTC
1825849 AATGAAAAAACAAATAAAAAAACATATAAAACTTAAGATAATACGAGTCCAAACCGACTCATGAA
1 AATG-AAAAACAAATAAAAAAACATATAAAACTTAAGATAATACGAGTCCAAACCGACTCATGAA
* *
1825914 ATTATTTATTATTCTGAAATTCTCAAAACAGGAACAGATTAAGAAGTCAACGAAGAGCTACCCGC
65 ATTATTTATTATTCTGAAATTCTCAAAACAGAAACAGATTAAGAAGTCAACGAAGAGCTACCCAC
*
1825979 TTTTTAAAAGAAACTGTCGGTGGCCGGTGGTGTTTCAACGATGATAGACACTGTC
130 TTTTTAAAAGAAACTGTCAGTGGCCGGTGGTGTTTCAACGATGATAGACACTGTC
1826034 A
1 A
1826035 TTTGTCTAAC
Statistics
Matches: 176, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
184 4 0.02
185 172 0.98
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (184 bp):
AATGAAAAACAAATAAAAAAACATATAAAACTTAAGATAATACGAGTCCAAACCGACTCATGAAA
TTATTTATTATTCTGAAATTCTCAAAACAGAAACAGATTAAGAAGTCAACGAAGAGCTACCCACT
TTTTAAAAGAAACTGTCAGTGGCCGGTGGTGTTTCAACGATGATAGACACTGTC
Found at i:1831236 original size:28 final size:28
Alignment explanation
Indices: 1831195--1831268 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
1831185 ATTAGGAAAG
* *
1831195 GTACATAAAAAATATATACATAA-AAAAT
1 GTACA-AAATAATATATAAATAATAAAAT
* *
1831223 TTACAACAATAATATA-AAATAATAATAT
1 GTACAA-AATAATATATAAATAATAAAAT
1831251 GTACAAAATATATATATA
1 GTACAAAATA-ATATATA
1831269 TATACATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 10 0.27
28 26 0.70
29 1 0.03
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (28 bp):
GTACAAAATAATATATAAATAATAAAAT
Found at i:1831260 original size:17 final size:19
Alignment explanation
Indices: 1831238--1831274 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1831228 ACAATAATAT
*
1831238 AAAATA-ATA-ATATGTAC
1 AAAATATATATATATATAC
1831255 AAAATATATATATATATAC
1 AAAATATATATATATATAC
1831274 A
1 A
1831275 TATGTACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAATATATATATATATAC
Found at i:1831260 original size:27 final size:29
Alignment explanation
Indices: 1831224--1831291 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 29
1831214 ATAAAAAATT
1831224 TACAACAATAATATAAAATA-ATA-ATATG
1 TACAA-AATAATATAAAATATATACATATG
*
1831252 TACAAAAT-ATAT-ATATATATACATATG
1 TACAAAATAATATAAAATATATACATATG
*
1831279 TACATAA-AATATA
1 TACAAAATAATATA
1831292 CACTAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
25 4 0.12
26 7 0.21
27 18 0.53
28 5 0.15
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.32
Consensus pattern (29 bp):
TACAAAATAATATAAAATATATACATATG
Found at i:1831300 original size:29 final size:27
Alignment explanation
Indices: 1831247--1831301 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
1831237 TAAAATAATA
*
1831247 ATATGTACAAAATATATATATATATAC
1 ATATGTACAAAATATACATATATATAC
1831274 ATATGTACATAAAATATACACTA-ATATA
1 ATATGTAC--AAAATATACA-TATATATA
1831302 ATAATAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
29 14 0.58
30 2 0.08
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (27 bp):
ATATGTACAAAATATACATATATATAC
Found at i:1831396 original size:14 final size:14
Alignment explanation
Indices: 1831374--1831414 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
1831364 GTATTTTAAA
*
1831374 ATATATATATATAT
1 ATATGTATATATAT
1831388 ATATGTATATATAT
1 ATATGTATATATAT
1831402 ATATGTATATATA
1 ATATGTATATATA
1831415 ATAGTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:1831433 original size:2 final size:2
Alignment explanation
Indices: 1831374--1831414 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1831364 GTATTTTAAA
* *
1831374 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1831415 ATAGTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1832167 original size:13 final size:13
Alignment explanation
Indices: 1832148--1832199 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 13
1832138 AAAGGTAAAT
1832148 TTTTTTTTA-ATA
1 TTTTTTTTATATA
1832160 TTTGTTTTGTATATA
1 TTT-TTTT-TATATA
*
1832175 TATATTTTTATTATA
1 T-TTTTTTTA-TATA
1832190 TTTTTTTTAT
1 TTTTTTTTAT
1832200 TATGATGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
14 11 0.33
15 13 0.39
16 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTTTTTATATA
Found at i:1832198 original size:14 final size:14
Alignment explanation
Indices: 1832146--1832202 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
1832136 AAAAAGGTAA
*
1832146 ATTTTTTTT-TAAT
1 ATTTTTTTTATTAT
1832159 ATTTGTTTTGTA-TAT
1 ATTT-TTTT-TATTAT
*
1832174 ATATATTTTTATTAT
1 AT-TTTTTTTATTAT
1832189 ATTTTTTTTATTAT
1 ATTTTTTTTATTAT
1832203 GATGTATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.11
14 17 0.47
15 14 0.39
16 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (14 bp):
ATTTTTTTTATTAT
Found at i:1832273 original size:17 final size:17
Alignment explanation
Indices: 1832253--1832290 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1832243 AAATAAAATA
*
1832253 AAAATAA-AAATAAGAGT
1 AAAATAATAAAGAAGA-T
1832270 AAAATAATAAAGAAGAT
1 AAAATAATAAAGAAGAT
1832287 AAAA
1 AAAA
1832291 CACCTTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (17 bp):
AAAATAATAAAGAAGAT
Found at i:1836653 original size:16 final size:16
Alignment explanation
Indices: 1836624--1836661 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1836614 ATTTATTTTT
1836624 AAAA-AATAAATATAG
1 AAAATAATAAATATAG
*
1836639 AAAATAATAAGTATAG
1 AAAATAATAAATATAG
1836655 AAAATAA
1 AAAATAA
1836662 AATATTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (16 bp):
AAAATAATAAATATAG
Found at i:1840561 original size:24 final size:24
Alignment explanation
Indices: 1840490--1840564 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 24
1840480 GCAAAATGTG
*
1840490 TAAATGTTTGCAAGTTAAATTTGT
1 TAAATGTTTGCAGGTTAAATTTGT
* *
1840514 TAAA---TT--AGGATCAAA-ATGT
1 TAAATGTTTGCAGG-TTAAATTTGT
1840533 GTAAATGTTTGCAGGTTAAATTTGT
1 -TAAATGTTTGCAGGTTAAATTTGT
1840558 TAAATGT
1 TAAATGT
1840565 GTAAATGTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 16
0.64 0.08 0.27
Matches are distributed among these distances:
19 5 0.13
20 8 0.21
21 2 0.05
23 2 0.05
24 15 0.39
25 6 0.16
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (24 bp):
TAAATGTTTGCAGGTTAAATTTGT
Found at i:1841514 original size:23 final size:24
Alignment explanation
Indices: 1841470--1841516 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1841460 TAATATATAT
*
1841470 AATATTTTCTATATTAATTTTTCA
1 AATATTTTCTATATTAAATTTTCA
*
1841494 AATATTTT-TATTTTAAATTTTCA
1 AATATTTTCTATATTAAATTTTCA
1841517 TATCAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (24 bp):
AATATTTTCTATATTAAATTTTCA
Found at i:1853629 original size:28 final size:28
Alignment explanation
Indices: 1853598--1853655 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
1853588 GAGGTGATTA
*
1853598 TTCGAAAATTTGAAAATTGACTTTCGAT
1 TTCGAAAATTTGAAAATCGACTTTCGAT
1853626 TTCGAAAATTTGAAAATCGACTTTCGAT
1 TTCGAAAATTTGAAAATCGACTTTCGAT
1853654 TT
1 TT
1853656 TATTAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (28 bp):
TTCGAAAATTTGAAAATCGACTTTCGAT
Found at i:1854759 original size:17 final size:19
Alignment explanation
Indices: 1854727--1854763 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1854717 ATAAATATAC
1854727 ACATATATATATATTAAAA
1 ACATATATATATATTAAAA
1854746 ACATA-ATA-ATATTAAAA
1 ACATATATATATATTAAAA
1854763 A
1 A
1854764 TACGTACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 3 0.17
19 5 0.28
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
ACATATATATATATTAAAA
Found at i:1854838 original size:27 final size:28
Alignment explanation
Indices: 1854778--1854864 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 28
1854768 TACATAGTAT
1854778 ATATACACATATAATATAGTTATTAAGA
1 ATATACACATATAATATAGTTATTAAGA
* *
1854806 AAATACATATA-ATATATAG-TATTAAGA
1 ATATACACATATA-ATATAGTTATTAAGA
* *
1854833 ATATACACA-ATACATAT-GGTATTAAAA
1 ATATACACATATA-ATATAGTTATTAAGA
1854860 ATATA
1 ATATA
1854865 TAGTATTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
26 2 0.04
27 33 0.66
28 15 0.30
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (28 bp):
ATATACACATATAATATAGTTATTAAGA
Found at i:1854870 original size:16 final size:16
Alignment explanation
Indices: 1854846--1854876 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1854836 TACACAATAC
*
1854846 ATATGGTATTAAAAAT
1 ATATAGTATTAAAAAT
1854862 ATATAGTATTAAAAA
1 ATATAGTATTAAAAA
1854877 CATAATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATATAGTATTAAAAAT
Found at i:1855278 original size:20 final size:19
Alignment explanation
Indices: 1855255--1855316 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
1855245 ATATACATAT
1855255 ATATATACCTATATAATAA-A
1 ATATATA-CTA-ATAATAATA
1855275 ATATATACTAATAATAATA
1 ATATATACTAATAATAATA
* **
1855294 ATA-ATAATAATAAGGATA
1 ATATATACTAATAATAATA
1855312 ATATA
1 ATATA
1855317 AAAACATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 22 0.59
19 8 0.22
20 7 0.19
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATACTAATAATAATA
Found at i:1855289 original size:3 final size:3
Alignment explanation
Indices: 1855267--1855306 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1855257 ATATACCTAT
*
1855267 ATA ATA A-A ATA TATA CTA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1855307 GGATAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1861356 original size:14 final size:15
Alignment explanation
Indices: 1861337--1861371 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1861327 ATAAAATAGG
1861337 ATTTAAGA-TTTAAA
1 ATTTAAGATTTTAAA
1861351 ATTTAAGATTTTTAAA
1 ATTTAAGA-TTTTAAA
1861367 ATTTA
1 ATTTA
1861372 TATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
16 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (15 bp):
ATTTAAGATTTTAAA
Found at i:1863300 original size:19 final size:19
Alignment explanation
Indices: 1863256--1863294 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1863246 TGAAAGAAAT
*
1863256 AAAA-ATTTAAAAATTATG
1 AAAATATTTAAAAAATATG
1863274 AAAATATTTAAAAAATA-G
1 AAAATATTTAAAAAATATG
1863292 AAA
1 AAA
1863295 TTTATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAATATTTAAAAAATATG
Found at i:1863813 original size:30 final size:28
Alignment explanation
Indices: 1863762--1863822 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
1863752 TTTTTGAACT
*
1863762 TTTATATATTTTTTAATATTTTTTA-CA
1 TTTATATATTTTTTAATATTTTCTATCA
*
1863789 TTTATTATACTTTTTTTATGATTTTCTATCA
1 TTTA-TATA-TTTTTTAAT-ATTTTCTATCA
1863820 TTT
1 TTT
1863823 CTATCGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.14
28 4 0.14
29 8 0.29
30 7 0.25
31 5 0.18
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.67
Consensus pattern (28 bp):
TTTATATATTTTTTAATATTTTCTATCA
Found at i:1865339 original size:19 final size:19
Alignment explanation
Indices: 1865315--1865352 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1865305 TCTATGAGTA
1865315 AGGTCTC-AGATTTAAGTTT
1 AGGTCTCGA-ATTTAAGTTT
1865334 AGGTCTCGAATTTAAGTTT
1 AGGTCTCGAATTTAAGTTT
1865353 TGTAGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (19 bp):
AGGTCTCGAATTTAAGTTT
Found at i:1874037 original size:19 final size:19
Alignment explanation
Indices: 1874013--1874053 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1874003 GCCATTCAAG
1874013 GAAGTAACCAAACCACATT
1 GAAGTAACCAAACCACATT
1874032 GAAGTAACCAAACCACATT
1 GAAGTAACCAAACCACATT
1874051 GAA
1 GAA
1874054 CTCTACTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.24, G:0.12, T:0.15
Consensus pattern (19 bp):
GAAGTAACCAAACCACATT
Found at i:1879815 original size:17 final size:18
Alignment explanation
Indices: 1879785--1879826 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1879775 TTTTATAATT
*
1879785 TTGATAATAAAATTTTAA
1 TTGATAATAAAATTATAA
*
1879803 TTGA-AATATAATTATAA
1 TTGATAATAAAATTATAA
1879820 TT-ATAAT
1 TTGATAAT
1879827 CATATTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.76
18 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
TTGATAATAAAATTATAA
Found at i:1881344 original size:2 final size:2
Alignment explanation
Indices: 1881333--1881366 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1881323 TCAACACCAA
1881333 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1881367 ATTTTGTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1884294 original size:82 final size:80
Alignment explanation
Indices: 1884132--1884299 Score: 273
Period size: 82 Copynumber: 2.1 Consensus size: 80
1884122 TACTGTGTTG
* * * *
1884132 TAGTGATCACATCATGCATGCATTCGTAACTACCAGCATAGACAAACACTATGGTAAGGCATTAA
1 TAGTGATCACATCATGCATGCATACATAACTACCAGCATAGAAAAACACCATGGTAAGGCATTAA
1884197 ACAAAATGGTAAACT
66 ACAAAATGGTAAACT
*
1884212 TAGTGATCACATCATGCATGCATACATGACTACCAGCATAGAAAAAAACACCATGGTAAGGCATT
1 TAGTGATCACATCATGCATGCATACATAACTACCAGCATAG--AAAAACACCATGGTAAGGCATT
1884277 AAACAAAATGGTAAACT
64 AAACAAAATGGTAAACT
1884294 TAGTGA
1 TAGTGA
1884300 CCTTTTTTTC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 38 0.47
82 43 0.53
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (80 bp):
TAGTGATCACATCATGCATGCATACATAACTACCAGCATAGAAAAACACCATGGTAAGGCATTAA
ACAAAATGGTAAACT
Found at i:1891686 original size:16 final size:15
Alignment explanation
Indices: 1891667--1891706 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
1891657 AAATTACAAT
1891667 AAATAATAAATTTATA
1 AAATAATAAATTT-TA
*
1891683 AAATTATTAAATTTTA
1 AAA-TAATAAATTTTA
1891699 AAATAATA
1 AAATAATA
1891707 TAATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 4 0.19
16 8 0.38
17 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATAATAAATTTTA
Done.