Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 7 of 345
Found at i:2361602 original size:44 final size:45
Alignment explanation
Indices: 2361547--2361662 Score: 153
Period size: 53 Copynumber: 2.4 Consensus size: 45
2361537 TTTTTTTGTT
2361547 AATTTCATTTGTTAATGTAC-TAGTACTATGTAGCCCTGCTATGA
1 AATTTCATTTGTTAATGTACATAGTACTATGTAGCCCTGCTATGA
2361591 AATTTCATTTGTTAATGTCCATTTGTACATAGTACTATGTAGCCCTGCTATGA
1 AATTTCATTTGTT-A-----A--TGTACATAGTACTATGTAGCCCTGCTATGA
2361644 AATTTCATTTGTTAATGTA
1 AATTTCATTTGTTAATGTA
2361663 GAACGAGGTT
Statistics
Matches: 63, Mismatches: 0, Indels: 17
0.79 0.00 0.21
Matches are distributed among these distances:
44 13 0.21
45 5 0.08
47 1 0.02
50 1 0.02
52 6 0.10
53 37 0.59
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (45 bp):
AATTTCATTTGTTAATGTACATAGTACTATGTAGCCCTGCTATGA
Found at i:2361635 original size:53 final size:52
Alignment explanation
Indices: 2361562--2361661 Score: 191
Period size: 53 Copynumber: 1.9 Consensus size: 52
2361552 CATTTGTTAA
2361562 TGTACTAGTACTATGTAGCCCTGCTATGAAATTTCATTTGTTAATGTCCATT
1 TGTACTAGTACTATGTAGCCCTGCTATGAAATTTCATTTGTTAATGTCCATT
2361614 TGTACATAGTACTATGTAGCCCTGCTATGAAATTTCATTTGTTAATGT
1 TGTAC-TAGTACTATGTAGCCCTGCTATGAAATTTCATTTGTTAATGT
2361662 AGAACGAGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 5 0.11
53 42 0.89
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (52 bp):
TGTACTAGTACTATGTAGCCCTGCTATGAAATTTCATTTGTTAATGTCCATT
Found at i:2367384 original size:47 final size:46
Alignment explanation
Indices: 2367271--2367451 Score: 184
Period size: 47 Copynumber: 3.8 Consensus size: 46
2367261 TGTACATAGT
* ** * *
2367271 CACATATCATACACCGAAGCCATAGCCCAGCCATGGTCTTACACGGAT
1 CACATATC--ACACCGATGCCATAGCCCAGATATGGTCTTACACGAAG
* * *
2367319 CACATATCACACTGATGCCATATCCTAGATATGGTCTTACACAGAAG
1 CACATATCACACCGATGCCATAGCCCAGATATGGTCTTACAC-GAAG
* * * *
2367366 CACATATCACACCGATGCCATATCTCACATATGGTCTTATACGTAAG
1 CACATATCACACCGATGCCATAGCCCAGATATGGTCTTACACG-AAG
* *
2367413 CTCATATCACACCGATACCATAGCCCA-ACTATGGTCTTA
1 CACATATCACACCGATGCCATAGCCCAGA-TATGGTCTTA
2367452 TATGGAAATC
Statistics
Matches: 113, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
46 30 0.27
47 75 0.66
48 8 0.07
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (46 bp):
CACATATCACACCGATGCCATAGCCCAGATATGGTCTTACACGAAG
Found at i:2370349 original size:130 final size:130
Alignment explanation
Indices: 2370101--2370494 Score: 486
Period size: 130 Copynumber: 3.0 Consensus size: 130
2370091 AAATTCTCCA
* * * *
2370101 AAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGAGTTGTAAT
1 AAACAAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
* * * * * *
2370166 TTCGCATTTGCTCAAAATAATCGAATTTCCCTTCGAAATTTCATTCATATCTTTTAAAATCCCTT
66 TTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCGTGTCTTTTAAAATCCCTT
* *
2370231 AAACAAATATGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
1 AAACAAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
* * *
2370296 TTCGCATTTGCTCAAAATAATCGAATATCACTTTAAAATTTCGCTCGTGTCTTTTAAAATCCCTA
66 TTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCGTGTCTTTTAAAATCCCTT
* * * * * * *
2370361 AAACGAAGGCGATATGTGATATTTGGCAATTCGCGGGATCGTGCCCTAACGTGTTGGGTAGCAAT
1 AAACAAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
* * * * * *
2370426 TTCCCGA-TTGTTTAAAATAATCAAATATCGCTTCAAAATTTCACTCG-GCTCTTCTAAAAATCC
66 TTCGC-ATTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCGTG-TCTT-TTAAAATCC
*
2370489 TTT
128 CTT
2370492 AAA
1 AAA
2370495 ACGAAGGCAA
Statistics
Matches: 227, Mismatches: 34, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
129 1 0.00
130 213 0.94
131 13 0.06
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (130 bp):
AAACAAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
TTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCGTGTCTTTTAAAATCCCTT
Found at i:2375951 original size:20 final size:20
Alignment explanation
Indices: 2375928--2375965 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2375918 AACAAAAATC
2375928 TATTTAATTA-TAAAATATTT
1 TATTT-ATTATTAAAATATTT
2375948 TATTTATTATTAAAATAT
1 TATTTATTATTAAAATAT
2375966 AAATTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTATTATTAAAATATTT
Found at i:2376041 original size:21 final size:21
Alignment explanation
Indices: 2376000--2376042 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2375990 TTATATGTGA
**
2376000 AACATAATGTATTTTTCAATT
1 AACATAATGTATTTTAAAATT
2376021 AACATAA-GATATTTTAAAATT
1 AACATAATG-TATTTTAAAATT
2376042 A
1 A
2376043 TAAGTAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
AACATAATGTATTTTAAAATT
Found at i:2376084 original size:14 final size:14
Alignment explanation
Indices: 2376067--2376098 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2376057 TTGCAGAGAA
2376067 TATATCAAAATAAT
1 TATATCAAAATAAT
2376081 TATATCAAAATAAT
1 TATATCAAAATAAT
2376095 TATA
1 TATA
2376099 ATCAGTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
TATATCAAAATAAT
Found at i:2397348 original size:29 final size:27
Alignment explanation
Indices: 2397303--2397362 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
2397293 TATTGTTTTT
2397303 TTTTAAGTTATGAATTTAGTCATTATA
1 TTTTAAGTTATGAATTTAGTCATTATA
* **
2397330 TTTTAATTTGATGAAATTTAGTTTTTATA
1 TTTTAAGTT-ATG-AATTTAGTCATTATA
2397359 TTTT
1 TTTT
2397363 CAAATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.29
28 3 0.11
29 17 0.61
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (27 bp):
TTTTAAGTTATGAATTTAGTCATTATA
Found at i:2399257 original size:11 final size:11
Alignment explanation
Indices: 2399241--2399266 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2399231 TTAGCTTTTG
2399241 AAAAAAAGAAA
1 AAAAAAAGAAA
2399252 AAAAAAAGAAA
1 AAAAAAAGAAA
2399263 AAAA
1 AAAA
2399267 GAGAGACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:2425006 original size:20 final size:19
Alignment explanation
Indices: 2424981--2425051 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 19
2424971 AACTTGTAAA
*
2424981 TAAATATTAATAATTTTATT
1 TAAATATTAATAATTATA-T
2425001 TAAATA-TAATTAA--ATAT
1 TAAATATTAA-TAATTATAT
* *
2425018 T-AATATTAATCATTATAAA
1 TAAATATTAATAATTAT-AT
2425037 TAAATATTAATAATT
1 TAAATATTAATAATT
2425052 TTTTGATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
16 6 0.15
17 5 0.12
18 4 0.10
19 5 0.12
20 21 0.51
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATATTAATAATTATAT
Found at i:2427263 original size:23 final size:24
Alignment explanation
Indices: 2427221--2427265 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2427211 TAAATATTAT
*
2427221 TTTATTAATATTTTTGTTTAGATA
1 TTTATTAATATTTTTATTTAGATA
*
2427245 TTTATTATTA-TTTTATTTAGA
1 TTTATTAATATTTTTATTTAGA
2427266 AAAATGGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (24 bp):
TTTATTAATATTTTTATTTAGATA
Found at i:2428421 original size:2 final size:2
Alignment explanation
Indices: 2428416--2428442 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2428406 AAAAAAAAAA
2428416 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2428443 GTAGATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2429706 original size:23 final size:23
Alignment explanation
Indices: 2429673--2429722 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2429663 AATGGGTAAA
*
2429673 ATAACTTTTAGTTCTCGAATTTG
1 ATAACTCTTAGTTCTCGAATTTG
*
2429696 ATAACTCTTAGTTTTCGAATTTG
1 ATAACTCTTAGTTCTCGAATTTG
2429719 ATAA
1 ATAA
2429723 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (23 bp):
ATAACTCTTAGTTCTCGAATTTG
Found at i:2430423 original size:24 final size:25
Alignment explanation
Indices: 2430386--2430441 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
2430376 AATGATATTA
*
2430386 ATAAAATTACAAATAATTA-TATGTTT
1 ATAAAAATACAAAT-ATTATTAT-TTT
2430412 -TAAAAATA-AAATATTATTATTTT
1 ATAAAAATACAAATATTATTATTTT
2430435 ATAAAAA
1 ATAAAAA
2430442 CAATATCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 7 0.26
24 13 0.48
25 7 0.26
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
ATAAAAATACAAATATTATTATTTT
Found at i:2430440 original size:23 final size:27
Alignment explanation
Indices: 2430386--2430440 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 27
2430376 AATGATATTA
*
2430386 ATAAAATTACAAATAATTATATGTTTT
1 ATAAAATTACAAATAATTATATATTTT
2430413 A-AAAA-TA-AAAT-ATTAT-TATTTT
1 ATAAAATTACAAATAATTATATATTTT
2430435 ATAAAA
1 ATAAAA
2430441 ACAATATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 6 0.23
23 9 0.35
24 4 0.15
25 2 0.08
26 4 0.15
27 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
ATAAAATTACAAATAATTATATATTTT
Found at i:2430721 original size:11 final size:11
Alignment explanation
Indices: 2430707--2430749 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2430697 TTTTTGTCAA
*
2430707 TATTTTGGTAC
1 TATTTTGTTAC
* *
2430718 TATTTCGTTAT
1 TATTTTGTTAC
*
2430729 TATATTGTTAC
1 TATTTTGTTAC
2430740 TATTTTGTTA
1 TATTTTGTTA
2430750 TTTTTATTTG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (11 bp):
TATTTTGTTAC
Found at i:2440415 original size:19 final size:20
Alignment explanation
Indices: 2440377--2440416 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2440367 ATTAGCAATA
* *
2440377 TGGATCATATTTACAATATG
1 TGGATCAAATCTACAATATG
2440397 TGGATCAAATCTA-AATATG
1 TGGATCAAATCTACAATATG
2440416 T
1 T
2440417 ACACACCACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
TGGATCAAATCTACAATATG
Found at i:2441747 original size:50 final size:50
Alignment explanation
Indices: 2441672--2441815 Score: 182
Period size: 50 Copynumber: 2.9 Consensus size: 50
2441662 ATCTATTATG
* * **
2441672 AGGTCACGTGTGCAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* *
2441722 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* * * **
2441772 -GGTCGCATGTGTAGTACTAAGTGCAGGTTACTATGCATACCAGA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
2441816 GATTTGGCTA
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
49 37 0.46
50 44 0.54
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
Found at i:2444957 original size:21 final size:22
Alignment explanation
Indices: 2444914--2444964 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
2444904 AATGACAAAA
* *
2444914 AATTAATTTTGAAAAATTAAAT
1 AATTAAATTTAAAAAATTAAAT
2444936 AATTAAATTTAAAAAATT-AAT
1 AATTAAATTTAAAAAATTAAAT
2444957 AATTAAAT
1 AATTAAAT
2444965 GATTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AATTAAATTTAAAAAATTAAAT
Found at i:2445702 original size:22 final size:22
Alignment explanation
Indices: 2445671--2445713 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2445661 AAACTTCATT
2445671 TTTTGCTGTAATTTCGTTGTTG
1 TTTTGCTGTAATTTCGTTGTTG
*
2445693 TTTTGTTGTAATTTCGTTGTT
1 TTTTGCTGTAATTTCGTTGTT
2445714 ATATTGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.07, G:0.21, T:0.63
Consensus pattern (22 bp):
TTTTGCTGTAATTTCGTTGTTG
Found at i:2445720 original size:22 final size:22
Alignment explanation
Indices: 2445677--2445737 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
2445667 CATTTTTTGC
* *
2445677 TGTAATTTCGTTGTTGTTTTGT
1 TGTAATTTCGTTGTTATATTGT
2445699 TGTAATTTCGTTGTTATATTGT
1 TGTAATTTCGTTGTTATATTGT
* * *
2445721 TATTATTTTGTTGTTAT
1 TGTAATTTCGTTGTTAT
2445738 TATTTGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.15, C:0.03, G:0.18, T:0.64
Consensus pattern (22 bp):
TGTAATTTCGTTGTTATATTGT
Found at i:2445738 original size:11 final size:11
Alignment explanation
Indices: 2445671--2445738 Score: 64
Period size: 11 Copynumber: 6.2 Consensus size: 11
2445661 AAACTTCATT
* *
2445671 TTTTGCTGTAA
1 TTTTGTTGTTA
* *
2445682 TTTCGTTGTTG
1 TTTTGTTGTTA
*
2445693 TTTTGTTGTAA
1 TTTTGTTGTTA
*
2445704 TTTCGTTGTTA
1 TTTTGTTGTTA
* *
2445715 TATTGTTATTA
1 TTTTGTTGTTA
2445726 TTTTGTTGTTA
1 TTTTGTTGTTA
2445737 TT
1 TT
2445739 ATTTGGTTAT
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.13, C:0.04, G:0.18, T:0.65
Consensus pattern (11 bp):
TTTTGTTGTTA
Found at i:2455260 original size:19 final size:18
Alignment explanation
Indices: 2455236--2455274 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2455226 TAAAATCAAC
*
2455236 TAATAAATATGTATTTATA
1 TAATAAATATCTA-TTATA
*
2455255 TAATAATTATCTATTATA
1 TAATAAATATCTATTATA
2455273 TA
1 TA
2455275 TCATTATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
TAATAAATATCTATTATA
Found at i:2455374 original size:13 final size:14
Alignment explanation
Indices: 2455356--2455388 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2455346 TGTATTTTTC
2455356 TTTATATGT-AATA
1 TTTATATGTAAATA
2455369 TTTATATGTCAAATA
1 TTTATATGT-AAATA
2455384 TTTAT
1 TTTAT
2455389 CTTCTCCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTATATGTAAATA
Found at i:2455430 original size:16 final size:17
Alignment explanation
Indices: 2455406--2455444 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
2455396 ACCTATGTCA
2455406 AATTATATTACTT-TAT
1 AATTATATTACTTATAT
*
2455422 AATTTTATTACTTATAT
1 AATTATATTACTTATAT
2455439 ATATTA
1 A-ATTA
2455445 ATATACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 12 0.63
17 4 0.21
18 3 0.16
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTATATTACTTATAT
Found at i:2459023 original size:15 final size:15
Alignment explanation
Indices: 2459003--2459032 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2458993 ATCTGTTGCT
*
2459003 ATTGATTAGATTAAA
1 ATTGATTAAATTAAA
2459018 ATTGATTAAATTAAA
1 ATTGATTAAATTAAA
2459033 TTTTATGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATTGATTAAATTAAA
Found at i:2459962 original size:31 final size:29
Alignment explanation
Indices: 2459895--2459962 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 29
2459885 AGTCTATATA
* * *
2459895 TTTATAATTTTTAAAAGATTAAATTAAAT
1 TTTATTATTTTTAAAAAATTAAAATAAAT
2459924 TTATATTATTTTTAAAGAAATTAAAATACAAT
1 TT-TATTATTTTTAAA-AAATTAAAATA-AAT
2459956 TTTATTA
1 TTTATTA
2459963 ATATTAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 2 0.06
30 12 0.36
31 14 0.42
32 5 0.15
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (29 bp):
TTTATTATTTTTAAAAAATTAAAATAAAT
Found at i:2460814 original size:58 final size:59
Alignment explanation
Indices: 2460700--2460838 Score: 147
Period size: 58 Copynumber: 2.4 Consensus size: 59
2460690 TCTTTTCTTT
* * * * * * *
2460700 TCTTCTTTGGTCACTCAATTATGAAAATTACAAAATGGTCGCTCAACTAGTAAA-TTTC
1 TCTTTTTTAGTCACTCAACTATGAAAATTACAAAATGATCACTCAACAAGTAAATTTTA
* * * * *
2460758 T-TTTTTTATTCACCCAACTATGAAAAATTACAAAATGATTACTCAACAATTTAATTTTA
1 TCTTTTTTAGTCACTCAACTATG-AAAATTACAAAATGATCACTCAACAAGTAAATTTTA
2460817 TCTTTTTTAGTCACTCAACTAT
1 TCTTTTTTAGTCACTCAACTAT
2460839 CTTAAATTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
57 16 0.25
58 26 0.41
59 4 0.06
60 18 0.28
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (59 bp):
TCTTTTTTAGTCACTCAACTATGAAAATTACAAAATGATCACTCAACAAGTAAATTTTA
Found at i:2464029 original size:227 final size:230
Alignment explanation
Indices: 2463630--2464083 Score: 797
Period size: 227 Copynumber: 2.0 Consensus size: 230
2463620 TTTGAAACTT
*
2463630 AATTTTATCGTAATTAATCATAAAAAGTCGACAATTCAAATCTAAATTTTAATTATTTAAAAAAA
1 AATTTTATCGTAATTAATCATAAAAAGTCGACAATTCAAATCCAAATTTTAATTATTTAAAAAAA
*
2463695 CACGATATTCAAATACAAATAAACTAAACCCAAAACATTTAAAACCCATAATAATTCAAAAATTT
66 CACGATATTCAAATAC-AACAAACTAAACCCAAAACATTTAAAACCCATAATAATTCAAAAATTT
2463760 TAAAACTCCGAATTTTCTCAATCCAGAAAACAGCCCAATTAAAAATTGAAACATGTCACATGGGA
130 TAAAACTCCGAATTTTCTCAATCCAGAAAACAGCCCAATTAAAAATTGAAACATGTCACATGGGA
* *
2463825 ATTTGTATGTAACGTGTAGATAGTGTTAAAAACCTA
195 ACTTGTATGAAACGTGTAGATAGTGTTAAAAACCTA
2463861 AATTTTATCGTAATTAATCATAAAAAGTCGACAATTCAAATCCAAATTTTAATTATTTAAAAAAA
1 AATTTTATCGTAATTAATCATAAAAAGTCGACAATTCAAATCCAAATTTTAATTATTTAAAAAAA
* * *
2463926 CACGATATT-TAA-AC-ACAAACTAAACCCAAAACATTTAAAATCCATAATAATTCAAAATTTTT
66 CACGATATTCAAATACAACAAACTAAACCCAAAACATTTAAAACCCATAATAATTCAAAAATTTT
*
2463988 AAAACTCCGAATTTTTTCAATCCAGAAAACAGCCCAATTAAAAATTGAAACATGTCACATGGGAA
131 AAAACTCCGAATTTTCTCAATCCAGAAAACAGCCCAATTAAAAATTGAAACATGTCACATGGGAA
*
2464053 CTTGTATGAAATGTGTAGATAGTGTTAAAAA
196 CTTGTATGAAACGTGTAGATAGTGTTAAAAA
2464084 GAGGCAGATG
Statistics
Matches: 214, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
227 137 0.64
229 2 0.01
230 2 0.01
231 73 0.34
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (230 bp):
AATTTTATCGTAATTAATCATAAAAAGTCGACAATTCAAATCCAAATTTTAATTATTTAAAAAAA
CACGATATTCAAATACAACAAACTAAACCCAAAACATTTAAAACCCATAATAATTCAAAAATTTT
AAAACTCCGAATTTTCTCAATCCAGAAAACAGCCCAATTAAAAATTGAAACATGTCACATGGGAA
CTTGTATGAAACGTGTAGATAGTGTTAAAAACCTA
Found at i:2476763 original size:14 final size:14
Alignment explanation
Indices: 2476744--2476770 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2476734 CTTCCACCTT
2476744 TTTTTTTTCTTTTC
1 TTTTTTTTCTTTTC
2476758 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
2476771 ATATAATCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTTCTTTTC
Found at i:2487555 original size:36 final size:36
Alignment explanation
Indices: 2487508--2487579 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2487498 CATTAGTCAC
*
2487508 GCCAATTTCTTATGATATAAATAGATGAAATTTTTA
1 GCCAATTTCTTATGATATAAATAGATAAAATTTTTA
*
2487544 GCCAATTTCTTATGATATAAATGGATAAAATTTTTA
1 GCCAATTTCTTATGATATAAATAGATAAAATTTTTA
2487580 ACAGAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (36 bp):
GCCAATTTCTTATGATATAAATAGATAAAATTTTTA
Found at i:2487640 original size:30 final size:29
Alignment explanation
Indices: 2487574--2487648 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
2487564 ATGGATAAAA
* *
2487574 TTTTTAACA-GAAAAAACTAATTTGCTCT
1 TTTTTAACATGTAAAAACTAATTTACTCT
*
2487602 TTAATTTAACATGTAAGAACTAATTTACTCAT
1 TT--TTTAACATGTAAAAACTAATTTACTC-T
2487634 TTTTTAA-ATGTAAAA
1 TTTTTAACATGTAAAA
2487649 GACAAAATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 2 0.05
29 7 0.18
30 12 0.31
31 15 0.38
32 3 0.08
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (29 bp):
TTTTTAACATGTAAAAACTAATTTACTCT
Found at i:2495651 original size:117 final size:117
Alignment explanation
Indices: 2495479--2496193 Score: 968
Period size: 117 Copynumber: 6.0 Consensus size: 117
2495469 TGTTTATTCT
2495479 TTGAACCCTTTGGCCGACCACGTTTAGGCTTGGCTTTAAGGGGATCTTCCATTTCAACCTTGCTA
1 TTGAACCCTTTGGCCGACCACGTTTA-----GGC-TTAAGGGGATCTTCCATTTCAACCTTGCTA
* * * *
2495544 TTACTAAACCCTTCAATACTCTGCTCAGCACCAATAGTTTTCTTCTTCTTCTTGTTCA
60 TCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCTTCTTGTTCA
*
2495602 TTGTACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCACTT
1 TTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCACTT
* * **
2495667 AACCCTTCAATACTTTGTTCACCACCAATAGTTTTCTTCTTCTTCTTCTTTG
66 AACCCTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCTTCTTGTTCA
* *
2495719 TTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATTTTCCATTTCAACCCTGCTATCACTT
1 TTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCACTT
* ** *
2495784 AACCCTACAATACAATGTTCACCACCAATAGTTTTCTTCTTCTTCTTCTTCTTCTTCTTCA
66 AACCCTTCAATACTCTGTTCACCACCAATAG--------TT-TTCTTCTTCTTCTTGTTCA
* * *
2495845 TTGTACCCTTTGGCCGACCACGTTTACGCTTAAGGGGATCTTCCATTTCAACCTTGCTACCACTT
1 TTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCACTT
* *
2495910 AACCCTTCAATACTCTGTTCATCACCAATAGTTTTCTTCTTCTTC---TTCG
66 AACCCTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCTTCTTGTTCA
*
2495959 TTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTT
1 TTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCACTT
* * *
2496024 AACACTTCAATGCTCTGTTCACCATCAATAGTTTTCTTCTTCTTCTTCTTGTTCA
66 AACCCTTCAATACTCTGTTCACCACCAATAG--TT-TTCTTCTTCTTCTTGTTCA
* * *
2496079 TTGCACCCTTTGGCCGACCACGTTTAGGCTTAAAGGGATCTTCCATTTCAACCTTGTTATCACTT
1 TTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCACTT
* * * *
2496144 AACCCTTCAATAATCTGTTCACCACCAGTAGTTTTCTTCTTGTTGTTGTT
66 AACCCTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCTTCTTGTT
2496194 GTTTTTCTTC
Statistics
Matches: 530, Mismatches: 47, Indels: 36
0.86 0.08 0.06
Matches are distributed among these distances:
114 91 0.17
116 2 0.00
117 209 0.39
118 7 0.01
120 90 0.17
123 25 0.05
125 2 0.00
126 104 0.20
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.38
Consensus pattern (117 bp):
TTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCACTT
AACCCTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCTTCTTGTTCA
Found at i:2495823 original size:3 final size:3
Alignment explanation
Indices: 2495817--2495843 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2495807 ACCAATAGTT
2495817 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
2495844 ATTGTACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2496032 original size:114 final size:114
Alignment explanation
Indices: 2495829--2496184 Score: 532
Period size: 114 Copynumber: 3.1 Consensus size: 114
2495819 CTTCTTCTTC
* * *
2495829 TTCTTCTTCTTCTTCATTGTACCCTTTGGCCGACCACGTTTACGCTTAAGGGGATCTTCCATTTC
1 TTCTTCTTCTTCTTCGTTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTC
* *
2495894 AACCTTGCTACCACTTAACCCTTCAATACTCTGTTCATCACCAATAGTT
66 AACCTTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTT
2495943 TTCTTCTTCTTCTTCGTTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTC
1 TTCTTCTTCTTCTTCGTTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTC
* * * *
2496008 AACCCTGCTATCACTTAACACTTCAATGCTCTGTTCACCATCAATAGTT
66 AACCTTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTT
* *
2496057 TTCTTCTTCTTCTTCTTGTTCATTGCACCCTTTGGCCGACCACGTTTAGGCTTAAAGGGATCTTC
1 TTCTTCTTCTTCTTC--G----TTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTC
* * *
2496122 CATTTCAACCTTGTTATCACTTAACCCTTCAATAATCTGTTCACCACCAGTAGTT
60 CATTTCAACCTTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTT
2496177 TTCTTCTT
1 TTCTTCTT
2496185 GTTGTTGTTG
Statistics
Matches: 218, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
114 120 0.55
116 1 0.00
120 97 0.44
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (114 bp):
TTCTTCTTCTTCTTCGTTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTC
AACCTTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTT
Found at i:2496178 original size:360 final size:361
Alignment explanation
Indices: 2495483--2496184 Score: 1099
Period size: 360 Copynumber: 1.9 Consensus size: 361
2495473 TATTCTTTGA
**
2495483 ACCCTTTGGCCGACCACGTTTAGGCTTGGCTTTAAGGGGATCTTCCATTTCAACCTTGCTATTAC
1 ACCCTTTGGCCGACCACGTTTA-GC-T-GCTTTAAGGGGATCTTCCATTTCAACCTTGCTACCAC
*
2495548 TAAACCCTTCAATACTCTGCTCAGCACCAATAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTT
63 TAAACCCTTCAATACTCTGCTCAGCACCAATAGTTTTCTTCTTCTTC-T-TTCATTGAACCCTTT
* *
2495613 GGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCACTTAACCCTTCAAT
126 GGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACACTTCAAT
* *
2495678 ACTTTGTTCACCACCAATAGTTTTCTTCTTCTTCTTCTTTGTTGAACCCTTTGGCCGACCACGTT
191 ACTCTGTTCACCACCAATAGTTTTCTTCTTCTTCTTCTTTATTGAACCCTTTGGCCGACCACGTT
* *
2495743 TAGGCTTAAGGGGATTTTCCATTTCAACCCTGCTATCACTTAACCCTACAATACAATGTTCACCA
256 TAGGCTTAAAGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTACAATACAATGTTCACCA
2495808 CCAATAGTTTTCTTCTTCTTCTTCTTCTTCTTCTTCATTGT
321 CCAATAGTTTTCTTCTTCTTCTTCTTCTTCTTCTTCATTGT
*
2495849 ACCCTTTGGCCGACCACGTTTA-C-GC-TTAAGGGGATCTTCCATTTCAACCTTGCTACCACTTA
1 ACCCTTTGGCCGACCACGTTTAGCTGCTTTAAGGGGATCTTCCATTTCAACCTTGCTACCACTAA
* * *
2495911 ACCCTTCAATACTCTGTTCATCACCAATAGTTTTCTTCTTCTTC-TTCGTTGAACCCTTTGGCCG
66 ACCCTTCAATACTCTGCTCAGCACCAATAGTTTTCTTCTTCTTCTTTCATTGAACCCTTTGGCCG
*
2495975 ACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACACTTCAATGCTCT
131 ACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACACTTCAATACTCT
* *
2496040 GTTCACCATCAATAGTTTTCTTCTTCTTCTTCTTGTTCATTGCACCCTTTGGCCGACCACGTTTA
196 GTTCACCACCAATAGTTTTCTTCTTCTTCTTC-T-TT-ATTGAACCCTTTGGCCGACCACGTTTA
* * * *
2496105 GGCTTAAAGGGATCTTCCATTTCAACCTTGTTATCACTTAACCCTTCAATA-ATCTGTTCACCAC
258 GGCTTAAAGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTACAATACA-ATGTTCACCAC
*
2496169 CAGTAGTTTTCTTCTT
322 CAATAGTTTTCTTCTT
2496185 GTTGTTGTTG
Statistics
Matches: 311, Mismatches: 21, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
357 110 0.35
358 1 0.00
359 3 0.01
360 172 0.55
361 2 0.01
364 1 0.00
366 22 0.07
ACGTcount: A:0.20, C:0.29, G:0.13, T:0.38
Consensus pattern (361 bp):
ACCCTTTGGCCGACCACGTTTAGCTGCTTTAAGGGGATCTTCCATTTCAACCTTGCTACCACTAA
ACCCTTCAATACTCTGCTCAGCACCAATAGTTTTCTTCTTCTTCTTTCATTGAACCCTTTGGCCG
ACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACACTTCAATACTCT
GTTCACCACCAATAGTTTTCTTCTTCTTCTTCTTTATTGAACCCTTTGGCCGACCACGTTTAGGC
TTAAAGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTACAATACAATGTTCACCACCAAT
AGTTTTCTTCTTCTTCTTCTTCTTCTTCTTCATTGT
Found at i:2499627 original size:6 final size:6
Alignment explanation
Indices: 2499612--2499651 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
2499602 AATTATATGT
2499612 TTTTTA -TTTTA TTTTTA TTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTT--A TTTTTA TTTTTA TTT
2499652 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
8 6 0.19
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:2499641 original size:14 final size:14
Alignment explanation
Indices: 2499622--2499648 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2499612 TTTTTATTTT
2499622 ATTTTTATTTTTAG
1 ATTTTTATTTTTAG
2499636 ATTTTTATTTTTA
1 ATTTTTATTTTTA
2499649 TTTATTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (14 bp):
ATTTTTATTTTTAG
Found at i:2506222 original size:31 final size:32
Alignment explanation
Indices: 2506163--2506226 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
2506153 TAATATTTTT
*
2506163 ATTTAGTACTTGAGTTTTGGCTTCAATATTCA
1 ATTTAGTACTTGAATTTTGGCTTCAATATTCA
*
2506195 ATTTAGTACTTGAATTTT-GTTTCAATATTCA
1 ATTTAGTACTTGAATTTTGGCTTCAATATTCA
2506226 A
1 A
2506227 ATCTATACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.48
Consensus pattern (32 bp):
ATTTAGTACTTGAATTTTGGCTTCAATATTCA
Found at i:2512287 original size:26 final size:26
Alignment explanation
Indices: 2512246--2512305 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
2512236 TTGGTTGCAC
*
2512246 AAAAATAAAAATATT-AACTTATGAAA
1 AAAAATAAAAATATTAAAATT-TGAAA
*
2512272 AAAAAT-AAAATAATTAAAATTTGTAA
1 AAAAATAAAAAT-ATTAAAATTTGAAA
2512298 AAAAATAA
1 AAAAATAA
2512306 GTTGATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 5 0.17
26 19 0.66
27 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (26 bp):
AAAAATAAAAATATTAAAATTTGAAA
Found at i:2518002 original size:13 final size:14
Alignment explanation
Indices: 2517972--2518010 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
2517962 AAATAATAAT
2517972 TTATAAAATTTATTA
1 TTAT-AAATTTATTA
2517987 TTATAAATTT-TTA
1 TTATAAATTTATTA
*
2518000 TTAAAAATTTA
1 TTATAAATTTA
2518011 ATTAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.55
14 6 0.27
15 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATAAATTTATTA
Found at i:2518815 original size:14 final size:14
Alignment explanation
Indices: 2518796--2518823 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2518786 AACCGAAATC
2518796 GAACTAAACTATAA
1 GAACTAAACTATAA
2518810 GAACTAAACTATAA
1 GAACTAAACTATAA
2518824 AAAGAACCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
GAACTAAACTATAA
Found at i:2519361 original size:12 final size:12
Alignment explanation
Indices: 2519344--2519370 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2519334 ACACTGATTC
2519344 AATTTAATCCGG
1 AATTTAATCCGG
2519356 AATTTAATCCGG
1 AATTTAATCCGG
2519368 AAT
1 AAT
2519371 GAAGATACGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (12 bp):
AATTTAATCCGG
Found at i:2523215 original size:26 final size:26
Alignment explanation
Indices: 2523180--2523229 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2523170 GTTTGTTTTG
* * *
2523180 AAAATTTCTCTTGAAAGAGTCAGTTA
1 AAAACTTCTCTTAAAAGAGCCAGTTA
2523206 AAAACTTCTCTTAAAAGAGCCAGT
1 AAAACTTCTCTTAAAAGAGCCAGT
2523230 CCATCTCAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (26 bp):
AAAACTTCTCTTAAAAGAGCCAGTTA
Found at i:2525113 original size:16 final size:17
Alignment explanation
Indices: 2525092--2525126 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2525082 CATTAACCAA
2525092 TTCTTTAGATAT-ATAT
1 TTCTTTAGATATAATAT
*
2525108 TTCTTTATATATAATAT
1 TTCTTTAGATATAATAT
2525125 TT
1 TT
2525127 ATATGTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (17 bp):
TTCTTTAGATATAATAT
Found at i:2532003 original size:16 final size:17
Alignment explanation
Indices: 2531972--2532005 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2531962 TTATTCGTCC
2531972 ATTTAATAATAATTAAA
1 ATTTAATAATAATTAAA
*
2531989 ATTTTATAA-AATTAAA
1 ATTTAATAATAATTAAA
2532005 A
1 A
2532006 AAATTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAATAATAATTAAA
Found at i:2535966 original size:1 final size:1
Alignment explanation
Indices: 2535960--2535988 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
2535950 TCTTGTATCC
2535960 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2535989 GCTTGTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2536675 original size:2 final size:2
Alignment explanation
Indices: 2536668--2536700 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2536658 GAAACGGTTG
*
2536668 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 A
2536701 ATTAAACCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2536829 original size:2 final size:2
Alignment explanation
Indices: 2536822--2536846 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2536812 GTGTGATTCC
2536822 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2536847 AACAATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2540051 original size:6 final size:6
Alignment explanation
Indices: 2540042--2540080 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
2540032 TATTCATACA
* *
2540042 TATATT TATATT TATATT TATAAT TGTA-T TATATT TATA
1 TATATT TATATT TATATT TATATT TATATT TATATT TATA
2540081 CTTGTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:2540075 original size:17 final size:17
Alignment explanation
Indices: 2540053--2540086 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2540043 ATATTTATAT
2540053 TTATATTTATAATTGTA
1 TTATATTTATAATTGTA
*
2540070 TTATATTTATACTTGTA
1 TTATATTTATAATTGTA
2540087 AATTCCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (17 bp):
TTATATTTATAATTGTA
Found at i:2548747 original size:19 final size:20
Alignment explanation
Indices: 2548709--2548747 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2548699 GGAAAGGGGG
*
2548709 GAATCGATTGTATTTTAGAGA
1 GAATAGATTGTA-TTTAGAGA
2548730 GAATAGATTGTA-TTAGAG
1 GAATAGATTGTATTTAGAG
2548748 GGGGTTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (20 bp):
GAATAGATTGTATTTAGAGA
Found at i:2549416 original size:39 final size:38
Alignment explanation
Indices: 2549369--2549506 Score: 172
Period size: 39 Copynumber: 3.6 Consensus size: 38
2549359 ATAAAGTATG
* *
2549369 GTTTTAATTAATAATAAAACAAAATAGTACGAGGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGTATG-GGAAGTA
*
2549408 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAATA
1 GTTTTAATTAACAATAAAACAAAATAGTAT-GGGAAGTA
* *
2549447 ATTTTAATTAACAATAAAACAAAATAGCATGGG-AGT-
1 GTTTTAATTAACAATAAAACAAAATAGTATGGGAAGTA
* *
2549483 GTTTTTGATTAATAATAAAACAAA
1 G-TTTTAATTAACAATAAAACAAA
2549507 GTAACATGGG
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
37 22 0.25
38 3 0.03
39 62 0.70
40 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.30
Consensus pattern (38 bp):
GTTTTAATTAACAATAAAACAAAATAGTATGGGAAGTA
Found at i:2549520 original size:78 final size:78
Alignment explanation
Indices: 2549370--2549517 Score: 194
Period size: 76 Copynumber: 1.9 Consensus size: 78
2549360 TAAAGTATGG
* * *
2549370 TTTTAATTAATAATAAAACAAAATAGTACGAGGAAGTAGTTTTAATTAACAATAAAACAAAATAG
1 TTTTAATTAACAATAAAACAAAATAGCACGAGGAAGTAGTTTTAATTAACAATAAAACAAAATAA
*
2549435 TATGGGGAAATAA
66 CATGGGGAAATAA
* * * *
2549448 TTTTAATTAACAATAAAACAAAATAGCATG-GG-AGT-GTTTTTGATTAATAATAAAACAAAGTA
1 TTTTAATTAACAATAAAACAAAATAGCACGAGGAAGTAG-TTTTAATTAACAATAAAACAAAATA
2549510 ACATGGGG
65 ACATGGGG
2549518 GGAGTGGGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
75 1 0.02
76 31 0.51
77 2 0.03
78 27 0.44
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (78 bp):
TTTTAATTAACAATAAAACAAAATAGCACGAGGAAGTAGTTTTAATTAACAATAAAACAAAATAA
CATGGGGAAATAA
Found at i:2551676 original size:47 final size:47
Alignment explanation
Indices: 2551567--2551677 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
2551557 CCGGGATAAG
*
2551567 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
2551614 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
2551661 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
2551678 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:2552448 original size:4 final size:4
Alignment explanation
Indices: 2552434--2552467 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
2552424 AAATTTCCCT
*
2552434 TTTC TTTTC TTTC TTTC TTTC CTTC TTTC TTTC T
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
2552468 CACGTTTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:2558931 original size:47 final size:47
Alignment explanation
Indices: 2558822--2558932 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
2558812 CCGGGATAAG
*
2558822 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
2558869 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
2558916 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
2558933 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:2563125 original size:19 final size:18
Alignment explanation
Indices: 2563103--2563149 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
2563093 ATTTAAGTTG
2563103 TTTTATATAATTTTAATA
1 TTTTATATAATTTTAATA
2563121 TTTTTATATAA--TTAATA
1 -TTTTATATAATTTTAATA
2563138 TTTTA-ATAATTT
1 TTTTATATAATTT
2563150 AATCTTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 7 0.27
19 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATATAATTTTAATA
Found at i:2563129 original size:8 final size:8
Alignment explanation
Indices: 2563112--2563179 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
2563102 GTTTTATATA
2563112 ATTTTAAT
1 ATTTTAAT
*
2563120 ATTTTTAT
1 ATTTTAAT
*
2563128 ATAATTAAT
1 AT-TTTAAT
2563137 ATTTTAAT
1 ATTTTAAT
*
2563145 AATTTAAT
1 ATTTTAAT
*
2563153 -CTTTAACT
1 ATTTTAA-T
2563161 -TTATTAAT
1 ATT-TTAAT
*
2563169 ATTTTAGT
1 ATTTTAAT
2563177 ATT
1 ATT
2563180 AATCATGAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
7 5 0.10
8 31 0.65
9 12 0.25
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (8 bp):
ATTTTAAT
Found at i:2563135 original size:17 final size:18
Alignment explanation
Indices: 2563103--2563152 Score: 70
Period size: 16 Copynumber: 2.9 Consensus size: 18
2563093 ATTTAAGTTG
2563103 TTTTATATAATTTTAATAT
1 TTTTATATAA-TTTAATAT
2563122 TTTTATATAA-TTAATA-
1 TTTTATATAATTTAATAT
2563138 TTTTA-ATAATTTAAT
1 TTTTATATAATTTAAT
2563153 CTTTAACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 6 0.20
19 10 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATATAATTTAATAT
Found at i:2563229 original size:22 final size:22
Alignment explanation
Indices: 2563202--2563254 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2563192 AAATTTTTTA
* *
2563202 ATTAATATAATATCTCTAT-TAT
1 ATTAATATAAAATAT-TATATAT
*
2563224 ATTAATTTAAAATATTATATAT
1 ATTAATATAAAATATTATATAT
2563246 ATTAATATA
1 ATTAATATA
2563255 TATTTAACGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAATATAAAATATTATATAT
Found at i:2577939 original size:31 final size:31
Alignment explanation
Indices: 2577881--2577944 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
2577871 CTTAACAGCC
*
2577881 CAGTGACTTAAATAAAAAAGTTTGAATAATT
1 CAGTGACTTAAATAAAAAACTTTGAATAATT
* *
2577912 CAGTGACTTAAAT-GAAAACTTTCGAATAGTT
1 CAGTGACTTAAATAAAAAACTTT-GAATAATT
2577943 CA
1 CA
2577945 AAAACAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAAACTTTGAATAATT
Found at i:2582358 original size:30 final size:30
Alignment explanation
Indices: 2582313--2582375 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2582303 CATATTAAGT
* *
2582313 TTGAACTGGTTTTATGATATTTGTCTAATG
1 TTGAAATGGTCTTATGATATTTGTCTAATG
2582343 TTGAAATGGTCTTATGATATTTGTCTAATG
1 TTGAAATGGTCTTATGATATTTGTCTAATG
2582373 TTG
1 TTG
2582376 TTTATCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.49
Consensus pattern (30 bp):
TTGAAATGGTCTTATGATATTTGTCTAATG
Found at i:2589204 original size:35 final size:35
Alignment explanation
Indices: 2589158--2589227 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2589148 AAATATATCT
2589158 TTGGTTGACATTTCACTTTTGTGCAGTCAAAAATA
1 TTGGTTGACATTTCACTTTTGTGCAGTCAAAAATA
2589193 TTGGTTGACATTTCACTTTTGTGCAGTCAAAAATA
1 TTGGTTGACATTTCACTTTTGTGCAGTCAAAAATA
2589228 AAAAGTCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (35 bp):
TTGGTTGACATTTCACTTTTGTGCAGTCAAAAATA
Found at i:2596566 original size:32 final size:32
Alignment explanation
Indices: 2596525--2596589 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
2596515 AACAACAATA
2596525 TAGTATATATAGCTATACATTTATATATACAT
1 TAGTATATATAGCTATACATTTATATATACAT
*
2596557 TAGTATATATAGCTATACATTTATATTTACAT
1 TAGTATATATAGCTATACATTTATATATACAT
2596589 T
1 T
2596590 CTCAACACCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.46
Consensus pattern (32 bp):
TAGTATATATAGCTATACATTTATATATACAT
Found at i:2612646 original size:20 final size:21
Alignment explanation
Indices: 2612618--2612659 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2612608 AATATTTGAT
* *
2612618 ATTAGAAT-AAATTTTATAAA
1 ATTAAAATAAAATATTATAAA
2612638 ATTAAAATAAAATATTATAAA
1 ATTAAAATAAAATATTATAAA
2612659 A
1 A
2612660 AATATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
ATTAAAATAAAATATTATAAA
Found at i:2612655 original size:21 final size:20
Alignment explanation
Indices: 2612588--2612659 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
2612578 ACAAAATTAT
* *
2612588 AATATAATAATATTAAACAT-
1 AATATTATAAAATTAAA-ATA
* * *
2612608 AATATT-TGATATTAGAATA
1 AATATTATAAAATTAAAATA
*
2612627 AATTTTATAAAATTAAAATAA
1 AATATTATAAAATTAAAAT-A
2612648 AATATTATAAAA
1 AATATTATAAAA
2612660 AATATTTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
18 2 0.05
19 13 0.32
20 14 0.34
21 12 0.29
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (20 bp):
AATATTATAAAATTAAAATA
Found at i:2613645 original size:2 final size:2
Alignment explanation
Indices: 2613638--2613675 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
2613628 TAGGTTATTG
2613638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
2613676 GATGAGATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2616397 original size:31 final size:32
Alignment explanation
Indices: 2616343--2616412 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
2616333 TATGAAATGA
* * * *
2616343 TAATTAAACTGTTTGAAAGTTTTTA-TTTAAG
1 TAATTGAACTATTAGAAAATTTTTATTTTAAG
2616374 TAATTGAACTATTAGAAAATTTTTATTTTAAG
1 TAATTGAACTATTAGAAAATTTTTATTTTAAG
2616406 TAATTGA
1 TAATTGA
2616413 GTTATTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.62
32 13 0.38
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (32 bp):
TAATTGAACTATTAGAAAATTTTTATTTTAAG
Found at i:2620661 original size:22 final size:23
Alignment explanation
Indices: 2620614--2620663 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
2620604 AACAAGAAAC
* *
2620614 ACAAAACACAAAGAACAAGTTTA
1 ACAAAACACAAAGAACAAATTAA
2620637 ACAAAA-ACAAAG-ACTAAATTAA
1 ACAAAACACAAAGAAC-AAATTAA
2620659 ACAAA
1 ACAAA
2620664 CAAAACAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.67
23 6 0.25
ACGTcount: A:0.66, C:0.16, G:0.06, T:0.12
Consensus pattern (23 bp):
ACAAAACACAAAGAACAAATTAA
Found at i:2621742 original size:17 final size:16
Alignment explanation
Indices: 2621700--2621743 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
2621690 GAAACGCATT
2621700 TCAATTA-TTTTTAAA
1 TCAATTATTTTTTAAA
2621715 TCAAATATATTTTCTTAAA
1 TC-AAT-TATTTT-TTAAA
2621734 TCAATTATTT
1 TCAATTATTT
2621744 CAATAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.08
16 3 0.12
17 7 0.28
18 6 0.24
19 7 0.28
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (16 bp):
TCAATTATTTTTTAAA
Found at i:2622714 original size:27 final size:27
Alignment explanation
Indices: 2622633--2622722 Score: 81
Period size: 33 Copynumber: 3.1 Consensus size: 27
2622623 CATTGAGTCC
*
2622633 ATTATAATTTTATTTTATATATTTTAT
1 ATTATAATTTAATTTTATATATTTTAT
* *
2622660 ATCATAATATTAATTATTTAATAAATATTTTTT
1 ATTATAAT-TTAA-T-TTT-AT--ATATTTTAT
*
2622693 ATTATAATGTAATTTTATATATTTTCAT
1 ATTATAATTTAATTTTATATATTTT-AT
2622721 AT
1 AT
2622723 ACTATACTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
27 14 0.28
28 6 0.12
29 3 0.06
30 6 0.12
31 3 0.06
32 3 0.06
33 15 0.30
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (27 bp):
ATTATAATTTAATTTTATATATTTTAT
Found at i:2622845 original size:15 final size:15
Alignment explanation
Indices: 2622817--2622846 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2622807 CTACTTTTCC
*
2622817 AAAAACACTTTTTTT
1 AAAAACAATTTTTTT
2622832 AAAAACAATTTTTTT
1 AAAAACAATTTTTTT
2622847 TAATGAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAAACAATTTTTTT
Found at i:2623605 original size:4 final size:4
Alignment explanation
Indices: 2623598--2623623 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2623588 ATATATATAT
2623598 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
2623624 GTAATATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2628919 original size:31 final size:31
Alignment explanation
Indices: 2628870--2628937 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
2628860 TATTTCTTTC
* *
2628870 AATATGTATAATTGAATCAAAATCAAAAT-TT
1 AATATATATAATTAAATCAAAATC-AAATCTT
* *
2628901 AATATATATATTTAAATCACAATCAAATCTT
1 AATATATATAATTAAATCAAAATCAAATCTT
2628932 AATATA
1 AATATA
2628938 CATACTTGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (31 bp):
AATATATATAATTAAATCAAAATCAAATCTT
Found at i:2631521 original size:21 final size:21
Alignment explanation
Indices: 2631495--2631536 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2631485 TTTTCTCTTT
2631495 AATCTAATGTATAGAAACTAA
1 AATCTAATGTATAGAAACTAA
*
2631516 AATCTAATGTATAGAGACTAA
1 AATCTAATGTATAGAAACTAA
2631537 CTCCTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (21 bp):
AATCTAATGTATAGAAACTAA
Found at i:2631946 original size:16 final size:17
Alignment explanation
Indices: 2631892--2631946 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
2631882 ATCTGCTGTA
*
2631892 AATTTAATATATGCAATTT
1 AATTGAATATATG--ATTT
2631911 -ATTGAATATATGAGTTT
1 AATTGAATATATGA-TTT
*
2631928 AATTGGATA-ATGATTT
1 AATTGAATATATGATTT
2631944 AAT
1 AAT
2631947 AATTGGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 7 0.22
17 7 0.22
18 18 0.56
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (17 bp):
AATTGAATATATGATTT
Found at i:2633288 original size:3 final size:3
Alignment explanation
Indices: 2633282--2633306 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2633272 TATTATTATT
2633282 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
2633307 AGTACTCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:2634455 original size:3 final size:3
Alignment explanation
Indices: 2634447--2634473 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2634437 AACTGTGCGG
2634447 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2634474 CTCCACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2643609 original size:20 final size:20
Alignment explanation
Indices: 2643584--2643622 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2643574 TAGGGATCGA
*
2643584 ATTAAATTAATTATTTTATT
1 ATTAAATTAATTAATTTATT
2643604 ATTAAATTAATTAATTTAT
1 ATTAAATTAATTAATTTAT
2643623 CCCATAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTAAATTAATTAATTTATT
Found at i:2644020 original size:29 final size:27
Alignment explanation
Indices: 2643987--2644040 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
2643977 TATGTGATTG
2643987 AATTTTATCACTAAACTTTTAATTTTACT
1 AATTTTATCA-TAAA-TTTTAATTTTACT
* *
2644016 AATTTTTTCATTAATTTTAATTTTA
1 AATTTTATCATAAATTTTAATTTTA
2644041 ATTAGCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 3 0.13
29 9 0.39
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.57
Consensus pattern (27 bp):
AATTTTATCATAAATTTTAATTTTACT
Found at i:2644303 original size:25 final size:25
Alignment explanation
Indices: 2644242--2644303 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
2644232 TAAATATTTT
* * *
2644242 TTATTAATTTTCAGTATTATATTAAT
1 TTATT-ATTTTAAGTATTAAATTAAA
* *
2644268 TTAATAATTTAAGTATTAAATTAAA
1 TTATTATTTTAAGTATTAAATTAAA
2644293 TTATTATTTTA
1 TTATTATTTTA
2644304 TTAAATTTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (25 bp):
TTATTATTTTAAGTATTAAATTAAA
Found at i:2644424 original size:25 final size:25
Alignment explanation
Indices: 2644390--2644452 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
2644380 ATTCAATAAA
*
2644390 AAAAATTAAAACGACAAAAATCAAT
1 AAAAATTAAAACGACAAAAATCAAG
* *
2644415 AAAAATTAAAACTACAAAATTCAAG
1 AAAAATTAAAACGACAAAAATCAAG
*
2644440 ATAAAGTTAAAAC
1 A-AAAATTAAAAC
2644453 ATAGTGGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 23 0.70
26 10 0.30
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.19
Consensus pattern (25 bp):
AAAAATTAAAACGACAAAAATCAAG
Found at i:2645007 original size:29 final size:31
Alignment explanation
Indices: 2644964--2645021 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
2644954 ATAAATTTAA
* * *
2644964 AATTTAGTTTCTTTA-TTTTTAT-TTTTAGT
1 AATTTAGTCTATTTACTTTTCATATTTTAGT
2644993 AATTTAGTCTATTTACTTTTCATATTTTA
1 AATTTAGTCTATTTACTTTTCATATTTTA
2645022 AAAATCAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.54
30 6 0.25
31 5 0.21
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (31 bp):
AATTTAGTCTATTTACTTTTCATATTTTAGT
Found at i:2647791 original size:23 final size:22
Alignment explanation
Indices: 2647745--2647799 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
2647735 TCTCTTACTT
*
2647745 AGATTAATTTTTTTAATAGTAA
1 AGATTAATTTTTTTAATAGAAA
2647767 AGATTAATAATTTTTTAATA-AAA
1 AGATTAAT--TTTTTTAATAGAAA
2647790 AGATTAATTT
1 AGATTAATTT
2647800 ATTATTTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.07
22 8 0.27
23 10 0.33
24 10 0.33
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (22 bp):
AGATTAATTTTTTTAATAGAAA
Found at i:2647958 original size:19 final size:19
Alignment explanation
Indices: 2647934--2647975 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 19
2647924 AATTAATATA
*
2647934 ATAATATTATATTCACATG
1 ATAATATTATATCCACATG
2647953 AT-A-A-TATATCCACATG
1 ATAATATTATATCCACATG
2647969 ATAATAT
1 ATAATAT
2647976 GGCACGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 6
0.73 0.04 0.23
Matches are distributed among these distances:
16 13 0.68
17 2 0.11
18 2 0.11
19 2 0.11
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (19 bp):
ATAATATTATATCCACATG
Found at i:2647966 original size:16 final size:16
Alignment explanation
Indices: 2647941--2647975 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2647931 ATAATAATAT
*
2647941 TATATTCACATGATAA
1 TATATCCACATGATAA
2647957 TATATCCACATGATAA
1 TATATCCACATGATAA
2647973 TAT
1 TAT
2647976 GGCACGGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (16 bp):
TATATCCACATGATAA
Found at i:2673071 original size:22 final size:23
Alignment explanation
Indices: 2673046--2673089 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2673036 TAAAAAATTA
*
2673046 TAAAATGATTA-TTAAATTATTT
1 TAAAAAGATTATTTAAATTATTT
*
2673068 TAAAAAGTTTATTTAAATTATT
1 TAAAAAGATTATTTAAATTATT
2673090 AAACTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
TAAAAAGATTATTTAAATTATTT
Found at i:2673088 original size:31 final size:31
Alignment explanation
Indices: 2673053--2673114 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2673043 TTATAAAATG
* * **
2673053 ATTATTAAATTATTTTAAAAAGTTTATTTAA
1 ATTATTAAACTATTTAAAAAAAATTATTTAA
2673084 ATTATTAAACTATTTAAAAAAAATTATTTAA
1 ATTATTAAACTATTTAAAAAAAATTATTTAA
2673115 TATACTAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (31 bp):
ATTATTAAACTATTTAAAAAAAATTATTTAA
Found at i:2674274 original size:14 final size:13
Alignment explanation
Indices: 2674248--2674273 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2674238 TTATCGATAT
2674248 CATTTTTTTAAAA
1 CATTTTTTTAAAA
2674261 CATTTTTTTAAAA
1 CATTTTTTTAAAA
2674274 ATACTTCTCA
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
CATTTTTTTAAAA
Found at i:2678623 original size:16 final size:16
Alignment explanation
Indices: 2678602--2678633 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2678592 ACTAAAATGT
2678602 TAGTTTTTTATTTTAC
1 TAGTTTTTTATTTTAC
2678618 TAGTTTTTTATTTTAC
1 TAGTTTTTTATTTTAC
2678634 CTAAAGTAAG
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:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (16 bp):
TAGTTTTTTATTTTAC
Found at i:2680913 original size:102 final size:102
Alignment explanation
Indices: 2680737--2680941 Score: 401
Period size: 102 Copynumber: 2.0 Consensus size: 102
2680727 ACAAAACTTC
*
2680737 CCGGACCCCGAAACGGCTCTAGTCCCAGTCGAGAAAGTGAGGGTCTTCTGAGTAAGGGGCGGCGA
1 CCGGACCCCGAAACGGCTCTAGTCCCAGTCGAGAAAGTGAGGGTCTTCTGAGTAAGGGGCGACGA
2680802 GAATAATGAAGGATGGAAAGGAAGACCAGGGGATTTT
66 GAATAATGAAGGATGGAAAGGAAGACCAGGGGATTTT
2680839 CCGGACCCCGAAACGGCTCTAGTCCCAGTCGAGAAAGTGAGGGTCTTCTGAGTAAGGGGCGACGA
1 CCGGACCCCGAAACGGCTCTAGTCCCAGTCGAGAAAGTGAGGGTCTTCTGAGTAAGGGGCGACGA
2680904 GAATAATGAAGGATGGAAAGGAAGACCAGGGGATTTT
66 GAATAATGAAGGATGGAAAGGAAGACCAGGGGATTTT
2680941 C
1 C
2680942 GTAACGACGG
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.30, C:0.19, G:0.35, T:0.17
Consensus pattern (102 bp):
CCGGACCCCGAAACGGCTCTAGTCCCAGTCGAGAAAGTGAGGGTCTTCTGAGTAAGGGGCGACGA
GAATAATGAAGGATGGAAAGGAAGACCAGGGGATTTT
Found at i:2685371 original size:46 final size:44
Alignment explanation
Indices: 2685312--2685426 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
2685302 ACAGGACAGA
* *
2685312 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
2685358 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
2685402 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2685427 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:2685407 original size:44 final size:45
Alignment explanation
Indices: 2685312--2685445 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
2685302 ACAGGACAGA
* *
2685312 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2685358 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
2685402 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2685446 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2690962 original size:183 final size:185
Alignment explanation
Indices: 2690619--2690979 Score: 645
Period size: 183 Copynumber: 2.0 Consensus size: 185
2690609 ATAAGTAAGA
*
2690619 TTGGACTCTAATTCCTGGTCTTTTGCATTACACCAAAAAGCCTCAAGCCCGTTAAGAAGTTGGAT
1 TTGGACTCTAATTCCTGCTCTTTTGCATTACACCAAAAAGCCTCAAGCCCGTTAAGAAGTTGGAT
*
2690684 TTTAAGCCCACTAAAATTAATAATTAAAAACTGACAGCTGTGGGATTTGAACCCACGCCCTTTCG
66 TTTAAGCCCAATAAAATTAATAATTAAAAACTGACAGCTGTGGGATTTGAACCCACGCCCTTTCG
2690749 GACCAGAGCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCACTGCAGGG
131 GACCAGAGCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCACTGCAGGG
* * * * *
2690804 TTGGACTCTAATTCC-GCTGTTTTGTATTATACTAAAAAGCCTCAAGCCCGTTAATAAGTTGGA-
1 TTGGACTCTAATTCCTGCTCTTTTGCATTACACCAAAAAGCCTCAAGCCCGTTAAGAAGTTGGAT
2690867 TTTAAGCCCAATAAAATTAATAATTAAAAACTGACAGCTGTGGGATTTGAACCCACGCCCTTTCG
66 TTTAAGCCCAATAAAATTAATAATTAAAAACTGACAGCTGTGGGATTTGAACCCACGCCCTTTCG
2690932 GACCAGAGCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCAC
131 GACCAGAGCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCAC
2690980 CGCTTGTCTA
Statistics
Matches: 169, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
183 112 0.66
184 42 0.25
185 15 0.09
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (185 bp):
TTGGACTCTAATTCCTGCTCTTTTGCATTACACCAAAAAGCCTCAAGCCCGTTAAGAAGTTGGAT
TTTAAGCCCAATAAAATTAATAATTAAAAACTGACAGCTGTGGGATTTGAACCCACGCCCTTTCG
GACCAGAGCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCACTGCAGGG
Found at i:2693313 original size:17 final size:17
Alignment explanation
Indices: 2693293--2693326 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2693283 TTTATTATTA
2693293 AATTTTTAATTTAATTT
1 AATTTTTAATTTAATTT
* *
2693310 AATTTTTTATTTCATTT
1 AATTTTTAATTTAATTT
2693327 TATAATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
AATTTTTAATTTAATTT
Found at i:2694318 original size:21 final size:22
Alignment explanation
Indices: 2694280--2694320 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2694270 TTTTAAAATT
*
2694280 GAAATAAAGTTATAAAATTTGA
1 GAAAAAAAGTTATAAAATTTGA
2694302 GAAAAAAAGTT-TAAAATTT
1 GAAAAAAAGTTATAAAATTT
2694321 TATTAGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (22 bp):
GAAAAAAAGTTATAAAATTTGA
Found at i:2695098 original size:125 final size:125
Alignment explanation
Indices: 2694962--2695274 Score: 448
Period size: 125 Copynumber: 2.5 Consensus size: 125
2694952 GCCAAACGGT
* *
2694962 AAATCGAAACCCAGCACGATTTGGCACGATTTATCAAACTTCCAAATACGAAATATTGTCTCATT
1 AAATCGAAACCCAGCACGATTTGGCACGATTTATCAAACTTCCAAATACGAAATATTGCCTCACT
*
2695027 TTAATTTAAGAAAACATGGATGAAATTCCAAAAGAATATTCCGTATTTTAGTCAAATGAA
66 TTAATTTAAGAAAACATAGATGAAATTCCAAAAGAATATTCCGTATTTTAGTCAAATGAA
* * * *
2695087 AAATCGAAACCCAACACGATTGGGCACGATTTATCGAACTTTCAAATACGAAATATTGCCTCACT
1 AAATCGAAACCCAGCACGATTTGGCACGATTTATCAAACTTCCAAATACGAAATATTGCCTCACT
* * * * * *
2695152 TTAATTTAAGAGAACATAGATGAAATTTCAAAAGGATATTCTGTATTTTTGTCGAATGAA
66 TTAATTTAAGAAAACATAGATGAAATTCCAAAAGAATATTCCGTATTTTAGTCAAATGAA
* * * * *
2695212 AAATCGAAACCCAGCACGA-TTGTGCACGATCTCTCAAACTTCCAAACACGAAAGATTTCCTCA
1 AAATCGAAACCCAGCACGATTTG-GCACGATTTATCAAACTTCCAAATACGAAATATTGCCTCA
2695275 TGTTGGGGGG
Statistics
Matches: 165, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
124 2 0.01
125 163 0.99
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (125 bp):
AAATCGAAACCCAGCACGATTTGGCACGATTTATCAAACTTCCAAATACGAAATATTGCCTCACT
TTAATTTAAGAAAACATAGATGAAATTCCAAAAGAATATTCCGTATTTTAGTCAAATGAA
Found at i:2696017 original size:28 final size:27
Alignment explanation
Indices: 2695971--2696026 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
2695961 ATAATATCAT
2695971 AAAAAAATTTTAAACAAT-ATTATATA
1 AAAAAAATTTTAAACAATAATTATATA
* *
2695997 AAAAGAAATTTTAAAATAATAATTTTATA
1 AAAA-AAATTTT-AAACAATAATTATATA
2696026 A
1 A
2696027 CTTAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
27 7 0.28
28 6 0.24
29 8 0.32
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
AAAAAAATTTTAAACAATAATTATATA
Found at i:2696126 original size:21 final size:22
Alignment explanation
Indices: 2696101--2696162 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 22
2696091 AATGAATGCC
*
2696101 AAATGAATTTAAAGAA-ATAAT
1 AAATGAATTTAAAGAATATAAA
*
2696122 GAATGAATTATAAAGAATATAAA
1 AAATGAATT-TAAAGAATATAAA
2696145 AACATGAATTTTAAAGAA
1 AA-ATGAA-TTTAAAGAA
2696163 CTCAATGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 8 0.24
22 7 0.21
23 5 0.15
24 12 0.35
25 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.27
Consensus pattern (22 bp):
AAATGAATTTAAAGAATATAAA
Found at i:2696527 original size:13 final size:13
Alignment explanation
Indices: 2696509--2696534 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2696499 GGTAATGGAG
2696509 TTAGTGGGGTGAT
1 TTAGTGGGGTGAT
2696522 TTAGTGGGGTGAT
1 TTAGTGGGGTGAT
2696535 GGAGTTACTG
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:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
TTAGTGGGGTGAT
Found at i:2700019 original size:6 final size:6
Alignment explanation
Indices: 2700008--2700067 Score: 68
Period size: 6 Copynumber: 9.3 Consensus size: 6
2699998 TTTCATACCT
2700008 TTTTTA TTTTTA TTTTTA TTTTTA TTATTT- TTTATTA TTATTTA TTTATTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTT-TTA TT-TTTA -TT-TTTA
2700060 TTTTTA TT
1 TTTTTA TT
2700068 GTTACATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
5 1 0.02
6 30 0.61
7 10 0.20
8 8 0.16
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:2700059 original size:28 final size:28
Alignment explanation
Indices: 2700007--2700061 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2699997 ATTTCATACC
* *
2700007 TTTTTTATTTTTATTTTTATTTTTATTA
1 TTTTTTATTATTATTTTTATATTTATTA
2700035 TTTTTTATTATTATTTATT-TATTTATT
1 TTTTTTATTATTATTT-TTATATTTATT
2700062 TTTATTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTTTATTATTATTTTTATATTTATTA
Found at i:2700060 original size:25 final size:23
Alignment explanation
Indices: 2700010--2700064 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
2700000 TCATACCTTT
*
2700010 TTTA-TTTTTATTTTTATTTTTA
1 TTTATTTTTTATTATTATTTTTA
2700032 -TTATTTTTTATTATTATTTATTTA
1 TTTATTTTTTATTATTA-TT-TTTA
2700056 TTTATTTTT
1 TTTATTTTT
2700065 ATTGTTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 11 0.39
23 2 0.07
24 4 0.14
25 8 0.29
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTATTTTTTATTATTATTTTTA
Found at i:2700630 original size:2 final size:2
Alignment explanation
Indices: 2700623--2700651 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2700613 AAATTATAAA
2700623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2700652 ACGAATGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2705463 original size:31 final size:30
Alignment explanation
Indices: 2705428--2705515 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 30
2705418 GAATTTATCA
2705428 TTTATATTTTAATTTGATTAATTTTAATTTT
1 TTTATATTTTAATTTG-TTAATTTTAATTTT
* *
2705459 TTTATCTTTTAAATTTGTTATTTTTAATTTT
1 TTTATATTTT-AATTTGTTAATTTTAATTTT
* *
2705490 TATATTTTTTAAATTT-TTAAATTTTA
1 TTTATATTTT-AATTTGTT-AATTTTA
2705516 TAATATATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
30 2 0.04
31 42 0.84
32 6 0.12
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.68
Consensus pattern (30 bp):
TTTATATTTTAATTTGTTAATTTTAATTTT
Found at i:2705470 original size:16 final size:15
Alignment explanation
Indices: 2705428--2705498 Score: 70
Period size: 15 Copynumber: 4.6 Consensus size: 15
2705418 GAATTTATCA
*
2705428 TTTATATTTTAATTTG
1 TTTAT-TTTTAATTTT
* *
2705444 ATTAATTTTAATTTT
1 TTTATTTTTAATTTT
*
2705459 TTTATCTTTTAAATTT
1 TTTAT-TTTTAATTTT
*
2705475 GTTATTTTTAATTTT
1 TTTATTTTTAATTTT
*
2705490 TATATTTTT
1 TTTATTTTT
2705499 TAAATTTTTA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
15 28 0.64
16 16 0.36
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTATTTTTAATTTT
Found at i:2705496 original size:8 final size:8
Alignment explanation
Indices: 2705465--2705514 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
2705455 TTTTTTTATC
2705465 TTTTAAAT
1 TTTTAAAT
2705473 TTGTT--AT
1 TT-TTAAAT
2705480 TTTT-AAT
1 TTTTAAAT
*
2705487 TTTTATATT
1 TTTTA-AAT
2705496 TTTTAAAT
1 TTTTAAAT
2705504 TTTTAAAT
1 TTTTAAAT
2705512 TTT
1 TTT
2705515 ATAATATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
6 2 0.06
7 10 0.28
8 15 0.42
9 9 0.25
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
TTTTAAAT
Found at i:2705498 original size:15 final size:15
Alignment explanation
Indices: 2705428--2705519 Score: 66
Period size: 16 Copynumber: 5.9 Consensus size: 15
2705418 GAATTTATCA
2705428 TTTATA-TTTTAATT
1 TTTATATTTTTAATT
2705442 TGATTA-A-TTTTAATT
1 T--TTATATTTTTAATT
*
2705457 TTTTTATCTTTTAAATT
1 TTTATAT-TTTT-AATT
*
2705474 TGT-TATTTTTAATT
1 TTTATATTTTTAATT
2705488 TTTATATTTTTTAAATT
1 TTTATA-TTTTT-AATT
*
2705505 TTTAAATTTTATAAT
1 TTTATATTTT-TAAT
2705520 ATATTTATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
13 2 0.03
14 8 0.12
15 16 0.25
16 22 0.34
17 16 0.25
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTATATTTTTAATT
Found at i:2705500 original size:16 final size:16
Alignment explanation
Indices: 2705449--2705519 Score: 65
Period size: 17 Copynumber: 4.4 Consensus size: 16
2705439 ATTTGATTAA
*
2705449 TTTTAATTTTTTTATCT
1 TTTTAATTTTTATAT-T
* *
2705466 TTTAAATTTGT-TA-T
1 TTTTAATTTTTATATT
2705480 TTTTAATTTTTATATT
1 TTTTAATTTTTATATT
*
2705496 TTTTAAATTTTTAAATT
1 TTTT-AATTTTTATATT
*
2705513 TTATAAT
1 TTTTAAT
2705520 ATATTTATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.22
15 2 0.04
16 10 0.22
17 23 0.51
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (16 bp):
TTTTAATTTTTATATT
Found at i:2709958 original size:3 final size:3
Alignment explanation
Indices: 2709950--2710049 Score: 191
Period size: 3 Copynumber: 33.0 Consensus size: 3
2709940 CTTTGGCGTC
2709950 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2709998 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AATG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G
2710047 AAG
1 AAG
2710050 CCACTTTACC
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 93 0.97
4 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:2710199 original size:29 final size:31
Alignment explanation
Indices: 2710136--2710200 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
2710126 ACTGTTAATC
* *
2710136 AGTGACTATTTTGTCACTTTTTTATAACGTT
1 AGTGACTATTTTGTCACATTTTTATAAAGTT
*
2710167 AGTGGCTATTTTGT-A-ATTTTTA-AAAGTT
1 AGTGACTATTTTGTCACATTTTTATAAAGTT
2710195 GAGTGA
1 -AGTGA
2710201 TTGAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 5 0.17
29 10 0.34
30 1 0.03
31 13 0.45
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (31 bp):
AGTGACTATTTTGTCACATTTTTATAAAGTT
Found at i:2714359 original size:21 final size:22
Alignment explanation
Indices: 2714333--2714373 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2714323 CAATGCATTA
*
2714333 TTAGTTGTG-TCAAAGTTTTCT
1 TTAGTTATGTTCAAAGTTTTCT
*
2714354 TTAGTTATGTTCAATGTTTT
1 TTAGTTATGTTCAAAGTTTT
2714374 TTCATCTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.56
Consensus pattern (22 bp):
TTAGTTATGTTCAAAGTTTTCT
Found at i:2717255 original size:18 final size:17
Alignment explanation
Indices: 2717218--2717263 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
2717208 ATTTTTGTTG
2717218 AATTATTTAAATTATAA
1 AATTATTTAAATTATAA
2717235 AATTATTTAAAATT-TATA
1 AATTATTT-AAATTATA-A
2717253 AATTA-TTAAAT
1 AATTATTTAAAT
2717264 CTCGTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.15
17 12 0.44
18 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTATTTAAATTATAA
Found at i:2724148 original size:23 final size:23
Alignment explanation
Indices: 2724118--2724188 Score: 142
Period size: 23 Copynumber: 3.1 Consensus size: 23
2724108 ACAAAATAGG
2724118 ATGAACGGCACAATTGGATAACT
1 ATGAACGGCACAATTGGATAACT
2724141 ATGAACGGCACAATTGGATAACT
1 ATGAACGGCACAATTGGATAACT
2724164 ATGAACGGCACAATTGGATAACT
1 ATGAACGGCACAATTGGATAACT
2724187 AT
1 AT
2724189 TTTTATTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (23 bp):
ATGAACGGCACAATTGGATAACT
Found at i:2725370 original size:25 final size:27
Alignment explanation
Indices: 2725333--2725383 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
2725323 TCAAACATGC
2725333 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
2725359 ATTTCGGT-AATTTATCTCCTAGGGG
1 ATTTAGGTCAATTTAACTCCTAGGGG
2725384 GTAAAACTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:2726903 original size:26 final size:26
Alignment explanation
Indices: 2726872--2726979 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
2726862 TGAAATGCCC
*
2726872 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
2726898 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
2726924 ATCATGGAATATTTACTTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
2726950 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2726976 ATCA
1 ATCA
2726980 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2728120 original size:15 final size:15
Alignment explanation
Indices: 2728108--2728140 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2728098 TTTAATAATA
2728108 AATACAAATATAAAT
1 AATACAAATATAAAT
*
2728123 AATACAAATTTAAAT
1 AATACAAATATAAAT
2728138 AAT
1 AAT
2728141 GATGTGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (15 bp):
AATACAAATATAAAT
Found at i:2733965 original size:13 final size:14
Alignment explanation
Indices: 2733941--2733969 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2733931 ACATCATTAC
2733941 AAAATAAATTTTTT
1 AAAATAAATTTTTT
2733955 AAAAT-AATTTTTT
1 AAAATAAATTTTTT
2733968 AA
1 AA
2733970 TAGTGGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATAAATTTTTT
Found at i:2750759 original size:50 final size:50
Alignment explanation
Indices: 2750677--2750853 Score: 282
Period size: 50 Copynumber: 3.5 Consensus size: 50
2750667 CCATGGCAAC
*
2750677 AAGTGATAAGTGATAGCTTCGGCTACAGTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
2750727 AAGTGATAAGTAATAGCTTTGGCAACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
2750777 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
2750827 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
2750854 CTGATCAGTG
Statistics
Matches: 115, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
50 91 0.79
51 24 0.21
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Done.