Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 5 of 335
Found at i:1410898 original size:16 final size:16
Alignment explanation
Indices: 1410879--1410909 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1410869 ATTATTTTTT
*
1410879 ATTTTTATTAATTTAA
1 ATTTTTAATAATTTAA
1410895 ATTTTTAATAATTTA
1 ATTTTTAATAATTTA
1410910 TTTAATCAAT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTAATAATTTAA
Found at i:1414974 original size:2 final size:2
Alignment explanation
Indices: 1414969--1414999 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1414959 TTACGTCTAT
1414969 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1415000 TAAATGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1415523 original size:2 final size:2
Alignment explanation
Indices: 1415516--1415542 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1415506 TTTCGCTAAC
1415516 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1415543 GTTCTGCTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1415798 original size:17 final size:17
Alignment explanation
Indices: 1415754--1415801 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1415744 AAATAATTTA
*
1415754 AAAATTATAAAAATATTC
1 AAAATT-TAAAAAAATTC
**
1415772 AAAAAATAAAAAAATTC
1 AAAATTTAAAAAAATTC
1415789 AAAATTTAAAAAA
1 AAAATTTAAAAAA
1415802 TTAAAAGTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATTTAAAAAAATTC
Found at i:1415807 original size:7 final size:8
Alignment explanation
Indices: 1415751--1415807 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
1415741 GTCAAATAAT
*
1415751 TTAAAAAT
1 TTAAAAAA
1415759 TATAAAAATA
1 T-TAAAAA-A
1415769 TTCAAAAAA
1 TT-AAAAAA
*
1415778 TAAAAAAA
1 TTAAAAAA
* *
1415786 TTCAAAAT
1 TTAAAAAA
1415794 TTAAAAAA
1 TTAAAAAA
1415802 TTAAAA
1 TTAAAA
1415808 GTCCATAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
8 24 0.62
9 9 0.23
10 6 0.15
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (8 bp):
TTAAAAAA
Found at i:1421016 original size:31 final size:31
Alignment explanation
Indices: 1420981--1421042 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1420971 TACAATTTGA
* *
1420981 TCACTAAATTATTCAAAA-TTTTTCATTTAAG
1 TCACTAAACTATTAAAAAGTTTTT-ATTTAAG
1421012 TCACTAAACTATTAAAAAGTTTTTATTTAAG
1 TCACTAAACTATTAAAAAGTTTTTATTTAAG
1421043 CCATTGGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (31 bp):
TCACTAAACTATTAAAAAGTTTTTATTTAAG
Found at i:1423251 original size:31 final size:31
Alignment explanation
Indices: 1423213--1423361 Score: 210
Period size: 31 Copynumber: 4.8 Consensus size: 31
1423203 ACAAATGACA
* * *
1423213 AGTGAAAAGTGGTAGTTTCAGCTACCTGATT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
1423244 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
1423275 AGTGAAAAGTGATAG-TTCTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-GGCTACCTGATC
* *
1423306 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
1423337 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
1423362 AAGTAACAAG
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
30 3 0.03
31 100 0.95
32 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:1423463 original size:47 final size:45
Alignment explanation
Indices: 1423393--1423516 Score: 140
Period size: 47 Copynumber: 2.7 Consensus size: 45
1423383 AAGTGATTTC
* *
1423393 CGTATAAGACCATATTTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATA-TTGGGATATGGCATCGGTGAGATATATGATA
** * *
1423439 CTGTATAAGACCATATCTGGGATATGGCATAAGTGAGATATGTGATT
1 C-GTATAAGACCATAT-TGGGATATGGCATCGGTGAGATATATGATA
* *
1423486 CGTGTAAGACCATAGTTGGGTTATGGCATCG
1 CGTATAAGACCATA-TTGGGATATGGCATCG
1423517 ATATATGAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
46 26 0.40
47 39 0.60
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.31
Consensus pattern (45 bp):
CGTATAAGACCATATTGGGATATGGCATCGGTGAGATATATGATA
Found at i:1423553 original size:42 final size:43
Alignment explanation
Indices: 1423487--1423601 Score: 153
Period size: 42 Copynumber: 2.7 Consensus size: 43
1423477 TATGTGATTC
* *
1423487 GTGTAAGACCATAGTTGGGTTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGAT
* *
1423529 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGAT
* **
1423571 GTGTAAGACCATAATTGAACTATGGCATCGA
1 GTGTAAGACCATAGTTGGGCTATGGCATCGA
1423602 GAAAACGAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 61 0.97
43 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGAT
Found at i:1424574 original size:24 final size:24
Alignment explanation
Indices: 1424542--1424591 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1424532 TGTTGAGTAG
1424542 AAGAACATACTTTAGGTCCAAGTC
1 AAGAACATACTTTAGGTCCAAGTC
1424566 AAGAACATACTTTAGGTCCAAGTC
1 AAGAACATACTTTAGGTCCAAGTC
1424590 AA
1 AA
1424592 TTTGACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (24 bp):
AAGAACATACTTTAGGTCCAAGTC
Found at i:1434021 original size:27 final size:27
Alignment explanation
Indices: 1433983--1434059 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
1433973 TATATGTAAG
1433983 ATTTATAA-ATAAAATATTAATAATTTT
1 ATTTA-AATATAAAATATTAATAATTTT
*
1434010 ATTTAAATATAATTAA-A-TAATAA-TTA
1 ATTTAAATATAA--AATATTAATAATTTT
1434036 ATTT-AAT-T-AAATATTAA-AATTTT
1 ATTTAAATATAAAATATTAATAATTTT
1434059 A
1 A
1434060 AACTCGATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
21 2 0.05
22 3 0.07
23 7 0.17
24 1 0.02
25 3 0.07
26 8 0.19
27 15 0.36
28 1 0.02
29 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTAAATATAAAATATTAATAATTTT
Found at i:1434021 original size:31 final size:30
Alignment explanation
Indices: 1433990--1434049 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1433980 AAGATTTATA
* *
1433990 AATAAAATATTAA-TAATTTTATTTAAATAT
1 AATAAAATAATAATTAA-TTTAATTAAATAT
*
1434020 AATTAAATAATAATTAATTTAATTAAATAT
1 AATAAAATAATAATTAATTTAATTAAATAT
1434050 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AATAAAATAATAATTAATTTAATTAAATAT
Found at i:1434531 original size:29 final size:29
Alignment explanation
Indices: 1434488--1434556 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1434478 ATTTTAAATT
* *
1434488 AATAATGATAAAATTATACTTT-ATTCTTTTA
1 AATAAT-A-AAAATT-TAATTTAATTCTTTAA
1434519 AATAATAAAAATTTAATTTAATTCTTTAA
1 AATAATAAAAATTTAATTTAATTCTTTAA
*
1434548 AATTATAAA
1 AATAATAAA
1434557 GATATAAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.15
29 22 0.65
30 1 0.03
31 6 0.18
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (29 bp):
AATAATAAAAATTTAATTTAATTCTTTAA
Found at i:1452314 original size:13 final size:13
Alignment explanation
Indices: 1452296--1452320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1452286 AATTAAAGAA
1452296 ATTTTAGATTTAG
1 ATTTTAGATTTAG
1452309 ATTTTAGATTTA
1 ATTTTAGATTTA
1452321 TTTTTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
ATTTTAGATTTAG
Found at i:1452794 original size:16 final size:16
Alignment explanation
Indices: 1452769--1452799 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1452759 TTCATTAAAA
*
1452769 TTTATCTGAATAATTG
1 TTTATATGAATAATTG
1452785 TTTATATGAATAATT
1 TTTATATGAATAATT
1452800 CTAACATCAA
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:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (16 bp):
TTTATATGAATAATTG
Found at i:1455272 original size:17 final size:17
Alignment explanation
Indices: 1455237--1455268 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1455227 TCCCAAGTTT
1455237 TATTTTAATATTTTATA
1 TATTTTAATATTTTATA
1455254 TATTTTAAT-TTTTAT
1 TATTTTAATATTTTAT
1455269 TATACACACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:1469707 original size:21 final size:18
Alignment explanation
Indices: 1469693--1469728 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1469683 CAAAGCTTGG
1469693 ACCCACTTCACCAAATGTT
1 ACCCACTTCACCAAA-GTT
*
1469712 ACCTACTTCACCAAAGT
1 ACCCACTTCACCAAAGT
1469729 ATATTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 2 0.12
19 14 0.88
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.25
Consensus pattern (18 bp):
ACCCACTTCACCAAAGTT
Found at i:1476994 original size:17 final size:17
Alignment explanation
Indices: 1476974--1477006 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1476964 TAAATTTACT
1476974 TATA-ATAACTTTTTATA
1 TATATATAA-TTTTTATA
1476991 TATATATAATTTTTAT
1 TATATATAATTTTTAT
1477007 TGAAATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATATAATTTTTATA
Found at i:1478311 original size:15 final size:15
Alignment explanation
Indices: 1478291--1478321 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1478281 GAAGTCGAAT
*
1478291 AGGTTCCAGCGTTTA
1 AGGTTCCAGAGTTTA
1478306 AGGTTCCAGAGTTTA
1 AGGTTCCAGAGTTTA
1478321 A
1 A
1478322 TTTTCTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (15 bp):
AGGTTCCAGAGTTTA
Found at i:1486700 original size:26 final size:26
Alignment explanation
Indices: 1486671--1486720 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1486661 ATCGATATAG
1486671 AAATTAATT-TTTAAATTTAAATTTAA
1 AAATTAATTATTT-AATTTAAATTTAA
* *
1486697 AAATTTATTATTTATTTTAAATTT
1 AAATTAATTATTTAATTTAAATTT
1486721 GTTTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
AAATTAATTATTTAATTTAAATTTAA
Found at i:1486787 original size:17 final size:16
Alignment explanation
Indices: 1486712--1486787 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
1486702 TATTATTTAT
1486712 TTTAAATTTGTTT-AA
1 TTTAAATTTGTTTAAA
* *
1486727 TTATTAA-TTGTTGAAAA
1 TT-TAAATTTGTT-TAAA
1486744 TTTAAATTTGTTTAAA
1 TTTAAATTTGTTTAAA
*
1486760 TTTAAA---ATTTAAA
1 TTTAAATTTGTTTAAA
1486773 CTTTAAATTTGTTTA
1 -TTTAAATTTGTTTA
1486788 TTTTGAGTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
13 6 0.13
14 6 0.13
15 7 0.15
16 15 0.32
17 13 0.28
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (16 bp):
TTTAAATTTGTTTAAA
Found at i:1495431 original size:16 final size:15
Alignment explanation
Indices: 1495410--1495440 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
1495400 CTCTCTCGTG
1495410 TTCTTTCTTTTTTTTT
1 TTCTTT-TTTTTTTTT
1495426 TTCTTTTTTTTTTTT
1 TTCTTTTTTTTTTTT
1495441 ACTGAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTCTTTTTTTTTTTT
Found at i:1495434 original size:11 final size:12
Alignment explanation
Indices: 1495413--1495439 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1495403 TCTCGTGTTC
1495413 TTTCTTTTTTTT
1 TTTCTTTTTTTT
1495425 TTTCTTTTTTTT
1 TTTCTTTTTTTT
1495437 TTT
1 TTT
1495440 TACTGAAATC
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:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:1496925 original size:6 final size:5
Alignment explanation
Indices: 1496874--1496924 Score: 77
Period size: 5 Copynumber: 10.0 Consensus size: 5
1496864 ATAATACCAC
1496874 CTTTT CTTTT CTTTT CTTTT CTTTT CTTCTT CTTCTT CTTTT -TTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CTT-TT CTTTT CTTTT CTTTT
1496925 TACATCATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 11 0.25
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:1506260 original size:21 final size:21
Alignment explanation
Indices: 1506234--1506277 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1506224 GATCACAAAA
1506234 CATAACCCCCAAATATTCTCC
1 CATAACCCCCAAATATTCTCC
1506255 CATAACCCCCAAATATTCTCC
1 CATAACCCCCAAATATTCTCC
1506276 CA
1 CA
1506278 CGCTTGACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.23
Consensus pattern (21 bp):
CATAACCCCCAAATATTCTCC
Found at i:1507361 original size:12 final size:12
Alignment explanation
Indices: 1507344--1507376 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1507334 CAGTCTACCC
1507344 ATATTAATTTTT
1 ATATTAATTTTT
1507356 ATATT-ATTTTT
1 ATATTAATTTTT
1507367 ATA-TAATTTT
1 ATATTAATTTT
1507377 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:1507531 original size:30 final size:30
Alignment explanation
Indices: 1507497--1507556 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1507487 ACTTAACAAG
1507497 TAAATGTCTCTAAAATAATAACAAAATTAA
1 TAAATGTCTCTAAAATAATAACAAAATTAA
*
1507527 TAAATGTCTTTAAAATAATAACAAAATTAA
1 TAAATGTCTCTAAAATAATAACAAAATTAA
1507557 CAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (30 bp):
TAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:1509208 original size:3 final size:3
Alignment explanation
Indices: 1509200--1509226 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1509190 TTTCCCTTAG
1509200 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1509227 AGCATCCCAA
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:1510392 original size:17 final size:17
Alignment explanation
Indices: 1510370--1510406 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1510360 ATATTTTGTA
* *
1510370 TTTTATATTTTTTATAT
1 TTTTATATTATTAATAT
1510387 TTTTATATTATTAATAT
1 TTTTATATTATTAATAT
1510404 TTT
1 TTT
1510407 AATAATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATATTATTAATAT
Found at i:1510446 original size:22 final size:24
Alignment explanation
Indices: 1510392--1510448 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 24
1510382 TATATTTTTA
*
1510392 TATTATTA-ATATTTTAATAATTC
1 TATTAATATATATTTTAATAATTC
*
1510415 GA-TAAT-TATATTTT-AT-ATTC
1 TATTAATATATATTTTAATAATTC
1510435 TATTAATATATATT
1 TATTAATATATATT
1510449 ATGTAGGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 5 0.18
21 6 0.21
22 16 0.57
23 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (24 bp):
TATTAATATATATTTTAATAATTC
Found at i:1516545 original size:18 final size:18
Alignment explanation
Indices: 1516522--1516561 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1516512 GATGAAATTA
* * *
1516522 GATTTTATTATTTCAATC
1 GATTTTAATATATAAATC
1516540 GATTTTAATATATAAATC
1 GATTTTAATATATAAATC
1516558 GATT
1 GATT
1516562 CACGAGTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (18 bp):
GATTTTAATATATAAATC
Found at i:1528405 original size:20 final size:20
Alignment explanation
Indices: 1528369--1528406 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1528359 GTGAAATTTG
*
1528369 TATAAAAATATAGAATTAAT
1 TATAAAAATATAAAATTAAT
1528389 TATAAAGAATA-AAAATTA
1 TATAAA-AATATAAAATTA
1528407 GTCTCGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TATAAAAATATAAAATTAAT
Found at i:1531027 original size:52 final size:51
Alignment explanation
Indices: 1530949--1531080 Score: 201
Period size: 52 Copynumber: 2.5 Consensus size: 51
1530939 ACCAATGCCA
* *
1530949 ATGGTCTTATACGGAAGTACATATCACAATGCACCGATGCCATAGCCCAGCT
1 ATGGTCTTATACGGCA-CACATATCACAATGCACCGATGCCATAGCCCAGCT
*
1531001 ATGGTCTTATACGGGCACACATATCACAATGCACCGATGTCATAGCCCAGCT
1 ATGGTCTTATAC-GGCACACATATCACAATGCACCGATGCCATAGCCCAGCT
*
1531053 ATGGTCTTATACAGGCGCACATATCACA
1 ATGGTCTTATAC-GGCACACATATCACA
1531081 TCTATTCTGT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
52 71 0.96
53 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (51 bp):
ATGGTCTTATACGGCACACATATCACAATGCACCGATGCCATAGCCCAGCT
Found at i:1531239 original size:22 final size:22
Alignment explanation
Indices: 1531214--1531257 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1531204 TAAGATAACT
1531214 TAGTAATCATAATATTTTCATA
1 TAGTAATCATAATATTTTCATA
1531236 TAGTAATCATAATATTTTCATA
1 TAGTAATCATAATATTTTCATA
1531258 AAAAAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (22 bp):
TAGTAATCATAATATTTTCATA
Found at i:1536608 original size:13 final size:14
Alignment explanation
Indices: 1536585--1536621 Score: 60
Period size: 12 Copynumber: 2.8 Consensus size: 14
1536575 AATCCTTAGT
1536585 TTTCTCTTTTTTTC
1 TTTCTCTTTTTTTC
1536599 TTTC-C-TTTTTTC
1 TTTCTCTTTTTTTC
1536611 TTTCTCTTTTT
1 TTTCTCTTTTT
1536622 CTCCCCTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 11 0.52
13 2 0.10
14 8 0.38
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCTCTTTTTTTC
Found at i:1536725 original size:16 final size:16
Alignment explanation
Indices: 1536704--1536734 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1536694 TTTATTATTT
1536704 TATTAACATAATATAA
1 TATTAACATAATATAA
*
1536720 TATTAATATAATATA
1 TATTAACATAATATA
1536735 TTAAAATATA
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:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:1538705 original size:15 final size:16
Alignment explanation
Indices: 1538696--1538733 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1538686 TAAAGTAAAT
1538696 GAAAT-AAAAGAAAAA
1 GAAATGAAAAGAAAAA
1538711 GAAATGAAAAGAAGGAAA
1 GAAATGAAAAGAA--AAA
1538729 GAAAT
1 GAAAT
1538734 ATAATAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
18 8 0.40
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (16 bp):
GAAATGAAAAGAAAAA
Found at i:1539969 original size:44 final size:44
Alignment explanation
Indices: 1539920--1540011 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
1539910 TGTTTAGGGA
* *
1539920 TACTTCGACCTTGAGTTGATGAGGCA-CTATAAGTGTCGTACTAT
1 TACTTCGACCTTAAGTCGATGAGGCACCT-TAAGTGTCGTACTAT
* * *
1539964 TACTTCGACTTTAAGTCGATGAGGCACCTTATGTGTCGTACTGT
1 TACTTCGACCTTAAGTCGATGAGGCACCTTAAGTGTCGTACTAT
1540008 TACT
1 TACT
1540012 ATTACTTCGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (44 bp):
TACTTCGACCTTAAGTCGATGAGGCACCTTAAGTGTCGTACTAT
Found at i:1540276 original size:18 final size:18
Alignment explanation
Indices: 1540212--1540277 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
1540202 AATTGATCGT
*
1540212 TACTGAATAACTAATTGC
1 TACTGAATAATTAATTGC
** * * *
1540230 TACTGAGCAAATGATTGT
1 TACTGAATAATTAATTGC
1540248 TACTGAATAATTAATTGC
1 TACTGAATAATTAATTGC
1540266 TACTGAATAATT
1 TACTGAATAATT
1540278 GAATGTTACT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
TACTGAATAATTAATTGC
Found at i:1540285 original size:36 final size:36
Alignment explanation
Indices: 1540176--1540287 Score: 118
Period size: 36 Copynumber: 3.1 Consensus size: 36
1540166 TAAATAAAAG
* * * * *
1540176 TACTGAATGACTGACTGTTACTAAATAATTG-ATCGT
1 TACTGAATAACTAATTGCTACTGAATAATTGAAT-GT
** * *
1540212 TACTGAATAACTAATTGCTACTGAGCAAATGATTGT
1 TACTGAATAACTAATTGCTACTGAATAATTGAATGT
*
1540248 TACTGAATAATTAATTGCTACTGAATAATTGAATGT
1 TACTGAATAACTAATTGCTACTGAATAATTGAATGT
1540284 TACT
1 TACT
1540288 AAATGAAATT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
36 60 0.98
37 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (36 bp):
TACTGAATAACTAATTGCTACTGAATAATTGAATGT
Found at i:1540287 original size:18 final size:18
Alignment explanation
Indices: 1540176--1540287 Score: 77
Period size: 18 Copynumber: 6.2 Consensus size: 18
1540166 TAAATAAAAG
* * *
1540176 TACTGAATGACTGACTGT
1 TACTGAATAATTGAATGT
*
1540194 TACTAAATAATTG-ATCGT
1 TACTGAATAATTGAAT-GT
* *
1540212 TACTGAATAACT-AATTGC
1 TACTGAATAATTGAA-TGT
** * *
1540230 TACTGAGCAAATGATTGT
1 TACTGAATAATTGAATGT
*
1540248 TACTGAATAATT-AATTGC
1 TACTGAATAATTGAA-TGT
1540266 TACTGAATAATTGAATGT
1 TACTGAATAATTGAATGT
1540284 TACT
1 TACT
1540288 AAATGAAATT
Statistics
Matches: 70, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
17 2 0.03
18 64 0.91
19 4 0.06
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
TACTGAATAATTGAATGT
Found at i:1541556 original size:61 final size:61
Alignment explanation
Indices: 1541461--1541584 Score: 212
Period size: 61 Copynumber: 2.0 Consensus size: 61
1541451 GTGTGCCCTC
* *
1541461 TGCACGTAAAAATTTCAAGTCAGTATGCATGATAGTAAACACACGGGCAGAGATACGGTCG
1 TGCACGTAAAAATTTCAAGTCAGTATGCATGATAGTAAACACACGAGCAGAGACACGGTCG
* *
1541522 TGCACGTAAAAGTTTCAAGTCAGTATGCATGATAGTAAACACATGAGCAGAGACACGGTCG
1 TGCACGTAAAAATTTCAAGTCAGTATGCATGATAGTAAACACACGAGCAGAGACACGGTCG
1541583 TG
1 TG
1541585 TGTCTCAGCT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (61 bp):
TGCACGTAAAAATTTCAAGTCAGTATGCATGATAGTAAACACACGAGCAGAGACACGGTCG
Found at i:1541706 original size:12 final size:13
Alignment explanation
Indices: 1541689--1541717 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1541679 ATGTTTTTAC
1541689 ACACGGGCTA-GG
1 ACACGGGCTAGGG
1541701 ACACGGGCTAGGG
1 ACACGGGCTAGGG
1541714 ACAC
1 ACAC
1541718 AGGCGTGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.28, G:0.38, T:0.07
Consensus pattern (13 bp):
ACACGGGCTAGGG
Found at i:1549335 original size:2 final size:2
Alignment explanation
Indices: 1549328--1549362 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1549318 ATAAAACAAA
1549328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1549363 TATTGGAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1558659 original size:17 final size:17
Alignment explanation
Indices: 1558639--1558672 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1558629 AGGTTTAGGT
1558639 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
1558656 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
1558673 AAATCTATTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:1571262 original size:22 final size:22
Alignment explanation
Indices: 1571212--1571262 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
1571202 TTTGTTGCAT
* * *
1571212 TATAAATAAAAATTTTAAACTC
1 TATAAATAAAAATTATAAAATA
1571234 TATAAATAAAAAATTATAAAATA
1 TATAAAT-AAAAATTATAAAATA
1571257 TA-AAAT
1 TATAAAT
1571263 GAGTATAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
TATAAATAAAAATTATAAAATA
Found at i:1580841 original size:96 final size:98
Alignment explanation
Indices: 1580724--1580899 Score: 250
Period size: 96 Copynumber: 1.8 Consensus size: 98
1580714 AATTTTAGGG
* * ** *
1580724 TTTTAAGGAAAAAAATTAAATAAATTAAGGTTTAGTGTTTGTTAATTAAATTAATTACT-AATTT
1 TTTTAAGGAAAAAAATAAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTA-TAAATTT
*
1580788 -TAAAAAATTAGATTATGATTTAGTGTTTATGGT
65 AAAAAAAATTAGATTATGATTTAGTGTTTATGGT
* *
1580821 TTTTAAGG-AAAAAATAAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTA
1 TTTTAAGGAAAAAAATAAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTA
1580885 AAAAAAATTAGATTA
66 AAAAAAATTAGATTA
1580900 GGGTTTTAGG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
95 1 0.01
96 46 0.67
97 22 0.32
ACGTcount: A:0.45, C:0.01, G:0.14, T:0.40
Consensus pattern (98 bp):
TTTTAAGGAAAAAAATAAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTA
AAAAAAATTAGATTATGATTTAGTGTTTATGGT
Found at i:1580916 original size:7 final size:8
Alignment explanation
Indices: 1580897--1580931 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
1580887 AAAAATTAGA
1580897 TTAGGGTT
1 TTAGGGTT
1580905 TTAGGG-T
1 TTAGGGTT
1580912 TTAGGGTT
1 TTAGGGTT
1580920 TTAGGGTAT
1 TTAGGGT-T
1580929 TTA
1 TTA
1580932 AGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.28
8 14 0.56
9 4 0.16
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (8 bp):
TTAGGGTT
Found at i:1580917 original size:15 final size:15
Alignment explanation
Indices: 1580897--1580926 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1580887 AAAAATTAGA
1580897 TTAGGGTTTTAGGGT
1 TTAGGGTTTTAGGGT
1580912 TTAGGGTTTTAGGGT
1 TTAGGGTTTTAGGGT
1580927 ATTTAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.40, T:0.47
Consensus pattern (15 bp):
TTAGGGTTTTAGGGT
Found at i:1581548 original size:126 final size:126
Alignment explanation
Indices: 1581010--1581537 Score: 770
Period size: 126 Copynumber: 4.2 Consensus size: 126
1581000 AAAAGCTTCT
* * *
1581010 ACGTGGACGCTCTTTTGCTACAGTAGTCTTTGAAAAAATAAATTTGAGAAGACTTGTCTGCACAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * *
1581075 ACAGTGTCAAAAACACTTCAAGCAGGATGTATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * **
1581136 ACGTAGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * * * * *
1581201 AAAGTGTAAAAAACGCTTCAAGCAGTATGCATTGTCAGTAAAAGTACAGAAAGAAGCTTCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * *
1581262 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGGAAAAATAATTTTGAGAAGACGTGTCTACGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * *
1581327 ATAGTGGT-AAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAATTACTGGAAGAAGCTCCC
66 ATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * * * *
1581388 ACGTGGATGCTCTTTTGCTACGGTGGTCTCTGAAAAAATAATTTTAAGAAGACGTGTCTGCATAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
*
1581453 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* *
1581514 ACATGGACGCTTTTTTGCTACAGT
1 ACGTGGACGCTCTTTTGCTACAGT
1581538 GGTTTTTGAA
Statistics
Matches: 358, Mismatches: 42, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
125 2 0.01
126 354 0.99
127 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (126 bp):
ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
Found at i:1583065 original size:2 final size:2
Alignment explanation
Indices: 1583058--1583085 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1583048 AAATGTACAG
1583058 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
1583086 TAAAATAATT
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:1587009 original size:116 final size:115
Alignment explanation
Indices: 1586783--1587048 Score: 460
Period size: 116 Copynumber: 2.3 Consensus size: 115
1586773 TTTATATTTT
* *
1586783 ATTACATGAAATAATATAAAAAAATTTAAAATGTTGCATTATTTAAAATAATTTTATTTTATTAA
1 ATTACATGAAATAATATAAAAAAATTCAAAATGTTGCACTATTTAAAATAATTTTATTTTATTAA
* *
1586848 AAATATAAAAGTAAATTATAATTACTTTATTTAAAATAACCTTTTATCTA
66 AAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACATTTTATCTA
* *
1586898 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTTCATTTTATTA
1 ATTACATGAAATAATATAAAAAAATTCAAAATGTTGCACTATTTAAAATAATTTT-ATTTTATTA
1586963 AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACATTTTATCTA
65 AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACATTTTATCTA
*
1587014 ATTACATGAAATAATATAAAAAGATTCAAAATGTT
1 ATTACATGAAATAATATAAAAAAATTCAAAATGTT
1587049 TGTACAAATA
Statistics
Matches: 143, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
115 51 0.36
116 92 0.64
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (115 bp):
ATTACATGAAATAATATAAAAAAATTCAAAATGTTGCACTATTTAAAATAATTTTATTTTATTAA
AAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACATTTTATCTA
Found at i:1587435 original size:18 final size:18
Alignment explanation
Indices: 1587409--1587450 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1587399 GACTAGAAAA
* * *
1587409 AGGAAACATATAATGGCT
1 AGGATACATAAAAGGGCT
1587427 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
1587445 AGGATA
1 AGGATA
1587451 TGTACCTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:1589261 original size:22 final size:22
Alignment explanation
Indices: 1589249--1589298 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
1589239 TAACGAGAGT
1589249 TTTGAGAGGAATTTAAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
* *
1589271 TTTGAGA-G-ATTTGAGAGGAA
1 TTTGAGAGGAATTTAAGAGAAA
1589291 TTTGAGAG
1 TTTGAGAG
1589299 AATATTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.68
21 1 0.04
22 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (22 bp):
TTTGAGAGGAATTTAAGAGAAA
Found at i:1589306 original size:11 final size:10
Alignment explanation
Indices: 1589249--1589306 Score: 64
Period size: 11 Copynumber: 5.5 Consensus size: 10
1589239 TAACGAGAGT
1589249 TTTGAGAGGAA
1 TTTGAGA-GAA
*
1589260 TTTAAGAGAAA
1 TTTGAGAG-AA
1589271 TTTGAGAG-A
1 TTTGAGAGAA
1589280 TTTGAGAGGAA
1 TTTGAGA-GAA
1589291 TTTGAGAGAA
1 TTTGAGAGAA
1589301 TATTGA
1 T-TTGA
1589307 AAGATTGAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 8 0.20
10 6 0.15
11 27 0.66
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:1589312 original size:31 final size:31
Alignment explanation
Indices: 1589249--1589312 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1589239 TAACGAGAGT
*
1589249 TTTGAGAGGAATTTAAGAGAAATTTGAGAGA
1 TTTGAGAGGAATTTAAGAGAAATTTGAAAGA
*
1589280 TTTGAGAGGAATTTGAGAG-AATATTGAAAGA
1 TTTGAGAGGAATTTAAGAGAAAT-TTGAAAGA
1589311 TT
1 TT
1589313 GAAGATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 3 0.10
31 27 0.90
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (31 bp):
TTTGAGAGGAATTTAAGAGAAATTTGAAAGA
Found at i:1597167 original size:3 final size:3
Alignment explanation
Indices: 1597156--1597235 Score: 53
Period size: 3 Copynumber: 26.3 Consensus size: 3
1597146 TTTTATTTTT
* *
1597156 TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TT- TCTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-T-A
1597201 TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA T
1 T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T
1597236 ATATACCCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
2 7 0.11
3 46 0.74
4 7 0.11
5 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1597195 original size:18 final size:18
Alignment explanation
Indices: 1597160--1597239 Score: 67
Period size: 18 Copynumber: 4.4 Consensus size: 18
1597150 ATTTTTTTAT
* *
1597160 TTTATTATTTTTACTATTA
1 TTTA-TATTATTATTATTA
1597179 TTTATATTATTATTATT-
1 TTTATATTATTATTATTA
* *
1597196 TCTCAT-GTATATATTATTA
1 T-TTATATTAT-TATTATTA
1597215 TTTATATTATTATTA-TA
1 TTTATATTATTATTATTA
1597232 TTATATAT
1 TT-TATAT
1597240 ACCCTCTCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
17 8 0.16
18 34 0.68
19 8 0.16
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTATATTATTATTATTA
Found at i:1597222 original size:12 final size:12
Alignment explanation
Indices: 1597155--1597235 Score: 78
Period size: 12 Copynumber: 6.8 Consensus size: 12
1597145 GTTTTATTTT
*
1597155 TTTATTTTATTA
1 TTTATATTATTA
* *
1597167 TTTTTACTATTA
1 TTTATATTATTA
1597179 TTTATATTATTA
1 TTTATATTATTA
* *
1597191 -TTAT-TTCTCA
1 TTTATATTATTA
1597201 TGTATATATTATTA
1 T-T-TATATTATTA
1597215 TTTATATTATTA
1 TTTATATTATTA
1597227 -TTATATTAT
1 TTTATATTAT
1597236 ATATACCCTC
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
10 4 0.07
11 13 0.23
12 30 0.54
13 4 0.07
14 5 0.09
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:1597480 original size:16 final size:17
Alignment explanation
Indices: 1597454--1597495 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1597444 ATATATTAGT
* *
1597454 GTATATTTTTATGTATA
1 GTATATATTTATATATA
1597471 -TATATATTTATATATA
1 GTATATATTTATATATA
1597487 GTAT-TATTT
1 GTATATATTT
1597496 TTTATTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (17 bp):
GTATATATTTATATATA
Found at i:1600235 original size:83 final size:83
Alignment explanation
Indices: 1600130--1600290 Score: 277
Period size: 83 Copynumber: 1.9 Consensus size: 83
1600120 TATTACAATA
* *
1600130 GTAACGATATCAACTAAACTTAATTGATGAAATTTAAAAAACAGAAAGGTCAAATTCTTATAAAT
1 GTAACGATACCAACTAAACTTAATTGATGAAATTTAAAAAACAGAAAGATCAAATTCTTATAAAT
1600195 AAAAATAAAAATATAATT
66 AAAAATAAAAATATAATT
* * *
1600213 GTAACGGTACCAACTAAACTTAATTGATGAAATTTAAAAAATAGAGAGATCAAATTCTTATAAAT
1 GTAACGATACCAACTAAACTTAATTGATGAAATTTAAAAAACAGAAAGATCAAATTCTTATAAAT
1600278 AAAAATAAAAATA
66 AAAAATAAAAATA
1600291 AAAATATAGA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (83 bp):
GTAACGATACCAACTAAACTTAATTGATGAAATTTAAAAAACAGAAAGATCAAATTCTTATAAAT
AAAAATAAAAATATAATT
Found at i:1603982 original size:23 final size:23
Alignment explanation
Indices: 1603954--1604026 Score: 137
Period size: 23 Copynumber: 3.2 Consensus size: 23
1603944 CTTGAATAAA
1603954 AAATTAGGTAATTTTTTAAAAAT
1 AAATTAGGTAATTTTTTAAAAAT
*
1603977 AAATTAGGTAGTTTTTTAAAAAT
1 AAATTAGGTAATTTTTTAAAAAT
1604000 AAATTAGGTAATTTTTTAAAAAT
1 AAATTAGGTAATTTTTTAAAAAT
1604023 AAAT
1 AAAT
1604027 AGTTCTTGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (23 bp):
AAATTAGGTAATTTTTTAAAAAT
Found at i:1604979 original size:40 final size:40
Alignment explanation
Indices: 1604913--1604989 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
1604903 TTTAGTTAAC
*
1604913 TTTTTAAAATTTTAAAATTTCAAAAAACTATATAAATTTTA
1 TTTTTAAAATATTAAAATTTCAAAAAACTATA-AAATTTTA
* *
1604954 TTTTTAAAA-ATTAAAATTAT-TAAAAAGTATAAAATT
1 TTTTTAAAATATTAAAATT-TCAAAAAACTATAAAATT
1604990 ATAAAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.16
40 17 0.53
41 10 0.31
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (40 bp):
TTTTTAAAATATTAAAATTTCAAAAAACTATAAAATTTTA
Found at i:1604988 original size:18 final size:16
Alignment explanation
Indices: 1604957--1605000 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
1604947 AATTTTATTT
1604957 TTAAAAATTAAAATTA
1 TTAAAAATTAAAATTA
1604973 TTAAAAAGTATAAAATTA
1 TTAAAAA-T-TAAAATTA
*
1604991 TAAAAAATTA
1 TTAAAAATTA
1605001 TTTTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 9 0.36
17 2 0.08
18 14 0.56
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
TTAAAAATTAAAATTA
Found at i:1611569 original size:55 final size:54
Alignment explanation
Indices: 1611508--1611688 Score: 281
Period size: 55 Copynumber: 3.3 Consensus size: 54
1611498 TTATCCATTT
* *
1611508 TCAATAAAATAAAATATGAATGTTCTTAAACCATAGATTTATCACTTACCCTATC
1 TCAATAAAATAAAATATGAATATT-TTAAACCATAGATTTATCACTTATCCTATC
* * *
1611563 TCAATAAAATAAAATATGAATATTTTTAAAGCATAGACTTATCACATATCCTATC
1 TCAATAAAATAAAATATGAATA-TTTTAAACCATAGATTTATCACTTATCCTATC
*
1611618 TCAATAAAATAAAATATGAATATTTGTAAACCATAGATTTATCACTTATTCTATC
1 TCAATAAAATAAAATATGAATATTT-TAAACCATAGATTTATCACTTATCCTATC
1611673 TCAATAAAATAAAATA
1 TCAATAAAATAAAATA
1611689 AAATAAAATA
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
54 3 0.03
55 110 0.96
56 2 0.02
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (54 bp):
TCAATAAAATAAAATATGAATATTTTAAACCATAGATTTATCACTTATCCTATC
Found at i:1611703 original size:4 final size:5
Alignment explanation
Indices: 1611675--1611700 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1611665 ATTCTATCTC
1611675 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
1611701 TAATGATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:1615431 original size:16 final size:17
Alignment explanation
Indices: 1615400--1615432 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1615390 TTCATAAGTA
1615400 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
1615417 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
1615433 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:1615778 original size:46 final size:47
Alignment explanation
Indices: 1615713--1616029 Score: 421
Period size: 46 Copynumber: 6.9 Consensus size: 47
1615703 TTATCTTTGA
* * * * * *
1615713 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
* *** *
1615759 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
* **
1615805 TACATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTT-ATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
*
1615851 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
* *
1615897 CATGTTGCCATGGTCTCTTTCAACCATGGTCGTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
*
1615943 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTT-ATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
*
1615989 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1616030 CATTTCAGAA
Statistics
Matches: 241, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
45 7 0.03
46 228 0.95
47 6 0.02
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (47 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
Found at i:1615966 original size:138 final size:138
Alignment explanation
Indices: 1615713--1616037 Score: 465
Period size: 138 Copynumber: 2.4 Consensus size: 138
1615703 TTATCTTTGA
* * * * *
1615713 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCAGGTTGCCATGGTATCT
1 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATCT
* *** *
1615777 TTCAACCATGGTCTTGTTCATTTCATGTTACATTGCCATGGTATCTTTCAACCATGGTCTTACAC
65 TTCAACCATGGTCGTACACATTTCATGATACATTGCCATGGTATCTTTCAACCATGGTCTTACAC
1615842 ATTTTATAT
130 ATTTTATAT
* * * *
1615851 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTCTCTT
1 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
* *
1615916 TCAACCATGGTCGTACACATTTCAT-ATCCTGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
66 TCAACCATGGTCGTACACATTTCATGATAC-ATTGCCATGGTATCTTTCAACCATGGTCTTACAC
1615980 ATTTTATAT
130 ATTTTATAT
*
1615989 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAG
1616038 AAAGCACACT
Statistics
Matches: 165, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
137 6 0.04
138 159 0.96
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (138 bp):
CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
TCAACCATGGTCGTACACATTTCATGATACATTGCCATGGTATCTTTCAACCATGGTCTTACACA
TTTTATAT
Found at i:1621562 original size:23 final size:23
Alignment explanation
Indices: 1621531--1621576 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1621521 GACTTCAGCA
1621531 TTATGTA-TTACTTAAAATATATT
1 TTATGTATTTACTTAAAAT-TATT
* *
1621554 TTATTTATTTATTTAAAATTATT
1 TTATGTATTTACTTAAAATTATT
1621577 ATAAAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTATGTATTTACTTAAAATTATT
Found at i:1632715 original size:12 final size:12
Alignment explanation
Indices: 1632700--1632726 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1632690 ATTCCGTAAA
1632700 AAAAATGTATAC
1 AAAAATGTATAC
1632712 AAAAATGTATAC
1 AAAAATGTATAC
1632724 AAA
1 AAA
1632727 TCAATACATA
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:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (12 bp):
AAAAATGTATAC
Found at i:1632998 original size:2 final size:2
Alignment explanation
Indices: 1632991--1633016 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1632981 TGTGTTGTGA
1632991 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
1633017 TGCCTTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1636175 original size:21 final size:22
Alignment explanation
Indices: 1636164--1636206 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
1636154 TCTTTAATTA
1636164 TAAATT-ATTATTTTATACATT
1 TAAATTAATTATTTTATACATT
1636185 TAAATTAATTATATTTAATACA
1 TAAATTAATTAT-TTT-ATACA
1636207 AATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 3 0.16
24 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAATTAATTATTTTATACATT
Found at i:1636218 original size:24 final size:25
Alignment explanation
Indices: 1636162--1636219 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
1636152 ATTCTTTAAT
* **
1636162 TATAAATTATTATTTTATACATTTA
1 TATAAATTATTATTTAATACAAATA
* *
1636187 AATTAATTA-TATTTAATACAAATA
1 TATAAATTATTATTTAATACAAATA
1636211 TATAAATTA
1 TATAAATTA
1636220 AATGAATAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (25 bp):
TATAAATTATTATTTAATACAAATA
Found at i:1636370 original size:21 final size:21
Alignment explanation
Indices: 1636346--1636393 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1636336 TGAAATATGA
1636346 TTTCTTTAATTTAACTAAATC
1 TTTCTTTAATTTAACTAAATC
1636367 TTTCTTTAATTTAACTAAATC
1 TTTCTTTAATTTAACTAAATC
1636388 -TTCTTT
1 TTTCTTT
1636394 TTTCAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTCTTTAATTTAACTAAATC
Found at i:1647628 original size:24 final size:24
Alignment explanation
Indices: 1647585--1647643 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
1647575 CGTTACAGCA
1647585 ATTA-ATTG-TCT-CTTTTTTCAG
1 ATTATATTGTTCTACTTTTTTCAG
1647606 ATTATATTGTTCTACTTTTTTCAG
1 ATTATATTGTTCTACTTTTTTCAG
1647630 ATTATATTGTTCTA
1 ATTATATTGTTCTA
1647644 ACAATTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.11
22 4 0.11
23 3 0.09
24 24 0.69
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (24 bp):
ATTATATTGTTCTACTTTTTTCAG
Found at i:1648519 original size:33 final size:33
Alignment explanation
Indices: 1648462--1648548 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
1648452 ACAGTACTTT
* * *
1648462 GCTCCTTCCAGCTCCTATCTACCACCATACTCC
1 GCTCCTTCTAGCTCGTATCCACCACCATACTCC
* *
1648495 GCTTCTTCTAGCTCGTATCCACCACCGTACTCC
1 GCTCCTTCTAGCTCGTATCCACCACCATACTCC
*
1648528 GCTCCTTCTGGCTCGTATCCA
1 GCTCCTTCTAGCTCGTATCCA
1648549 TCGACATTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.15, C:0.44, G:0.11, T:0.30
Consensus pattern (33 bp):
GCTCCTTCTAGCTCGTATCCACCACCATACTCC
Found at i:1648585 original size:99 final size:99
Alignment explanation
Indices: 1648414--1648592 Score: 225
Period size: 99 Copynumber: 1.8 Consensus size: 99
1648404 TATCTTCAGC
* * * * * *
1648414 CCACCATCGTACTCCGTTCCTTCCGGCTCGTATCCATTACAGTACTTTGCTCCTTCCAGCTCCTA
1 CCACCACCGTACTCCGCTCCTTCCGGCTCGTATCCATGACAGTACTCTACTCCTCCCAGCTCCTA
*
1648479 TCTACCACCATACTCCGCTTCTTCTAGCTCGTAT
66 TCCACCACCATACTCCGCTTCTTCTAGCTCGTAT
* * * * **
1648513 CCACCACCGTACTCCGCTCCTTCTGGCTCGTATCCATCGACA-TTCTCTACTCGTCCCGGCTTGT
1 CCACCACCGTACTCCGCTCCTTCCGGCTCGTATCCAT-GACAGTACTCTACTCCTCCCAGCTCCT
1648577 ATCCACCACCATACTC
65 ATCCACCACCATACTC
1648593 TACTCCTCCA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
99 63 0.95
100 3 0.05
ACGTcount: A:0.16, C:0.41, G:0.12, T:0.31
Consensus pattern (99 bp):
CCACCACCGTACTCCGCTCCTTCCGGCTCGTATCCATGACAGTACTCTACTCCTCCCAGCTCCTA
TCCACCACCATACTCCGCTTCTTCTAGCTCGTAT
Found at i:1654075 original size:46 final size:45
Alignment explanation
Indices: 1654008--1654180 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
1653998 TGTAACCCGC
*
1654008 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACGTT-GCAT
* * *
1654054 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGC-T-CA-GAC--GTTGCAT
* * * *
1654104 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC-GAACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAG-AC-GTTGCAT
1654147 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC
1654181 GGATGCCCAA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
43 7 0.07
44 2 0.02
45 2 0.02
46 58 0.55
47 24 0.23
48 3 0.03
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACGTTGCAT
Found at i:1654128 original size:93 final size:93
Alignment explanation
Indices: 1654016--1654187 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
1654006 GCCCATAAGT
* *
1654016 GAACTCGGACTCAACTCAACGAGCTC-AGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGA-ACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
1654080 ACGAGCTTGGATGCCTAGTTACATCTCAC
65 ACGAGCTCGGATGCCTAGTTACATCTCAC
* *
1654109 GAACTCGGACTCAACTCAACGAGTTCGAACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1654174 CGAGCTCGGATGCC
66 CGAGCTCGGATGCC
1654188 CAAATATTCC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 72 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:1659090 original size:53 final size:53
Alignment explanation
Indices: 1658949--1659099 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
1658939 ATAAGTGCGC
* **
1658949 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
1659002 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
1659055 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
1659100 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:1661327 original size:10 final size:10
Alignment explanation
Indices: 1661312--1661337 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1661302 TAAATGCAGC
1661312 TCGTATTTTA
1 TCGTATTTTA
1661322 TCGTATTTTA
1 TCGTATTTTA
1661332 TCGTAT
1 TCGTAT
1661338 CTCCCAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.58
Consensus pattern (10 bp):
TCGTATTTTA
Found at i:1662362 original size:22 final size:22
Alignment explanation
Indices: 1662337--1662386 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1662327 ATTATATGTG
1662337 TTAAATAAA-ACATTT-TTTATTT
1 TTAAATAAATA-ATTTATTTA-TT
1662359 TTAAATAAATAATTTATTTATT
1 TTAAATAAATAATTTATTTATT
1662381 TTAAAT
1 TTAAAT
1662387 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAATAAATAATTTATTTATT
Found at i:1680162 original size:17 final size:17
Alignment explanation
Indices: 1680140--1680173 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1680130 TTGTAGACTA
1680140 AAGGCAAAACTAGCCTC
1 AAGGCAAAACTAGCCTC
1680157 AAGGCAAAACTAGCCTC
1 AAGGCAAAACTAGCCTC
1680174 TTTCAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.12
Consensus pattern (17 bp):
AAGGCAAAACTAGCCTC
Found at i:1680641 original size:6 final size:7
Alignment explanation
Indices: 1680624--1680648 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1680614 AGATCATTTC
1680624 AAAAAAT
1 AAAAAAT
1680631 AAAAAAT
1 AAAAAAT
1680638 AAAAAAT
1 AAAAAAT
1680645 AAAA
1 AAAA
1680649 TATTATAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1681325 original size:26 final size:28
Alignment explanation
Indices: 1681268--1681346 Score: 92
Period size: 26 Copynumber: 2.9 Consensus size: 28
1681258 GATGTTCATG
*
1681268 TTATTAAT-TTTTACATTTTTTTATAAA
1 TTATTAATATTTTATATTTTTTTATAAA
*
1681295 TTATTAATATTTTTTATTTTTTTA-AAA
1 TTATTAATATTTTATATTTTTTTATAAA
* *
1681322 -TATTAAAATTATATATTTTTATTAT
1 TTATTAATATTTTATATTTTT-TTAT
1681347 TTTTTAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
26 17 0.39
27 14 0.32
28 13 0.30
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (28 bp):
TTATTAATATTTTATATTTTTTTATAAA
Found at i:1681566 original size:23 final size:24
Alignment explanation
Indices: 1681515--1681572 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
1681505 AAGATAAAAA
*
1681515 TATAATATTTAATTTAAAATTGAG
1 TATAATATTAAATTTAAAATTGAG
**
1681539 T-TAATATTAAATTTAAAATT-TT
1 TATAATATTAAATTTAAAATTGAG
1681561 TATAATATTAAA
1 TATAATATTAAA
1681573 AAATACTACG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 28 0.93
24 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (24 bp):
TATAATATTAAATTTAAAATTGAG
Found at i:1682317 original size:21 final size:21
Alignment explanation
Indices: 1682291--1682333 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1682281 TATATATGTG
* *
1682291 TATATATATACAAATTTTATA
1 TATATACATACAAAATTTATA
1682312 TATATACATACAAAATTTATA
1 TATATACATACAAAATTTATA
1682333 T
1 T
1682334 TGCATGAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
TATATACATACAAAATTTATA
Found at i:1691460 original size:14 final size:16
Alignment explanation
Indices: 1691441--1691473 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1691431 CCATGTTTCG
1691441 TATTCTTT-A-CTTAT
1 TATTCTTTAAGCTTAT
1691455 TATTCTTTAAGCTTAT
1 TATTCTTTAAGCTTAT
1691471 TAT
1 TAT
1691474 GTGATTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.61
Consensus pattern (16 bp):
TATTCTTTAAGCTTAT
Found at i:1699851 original size:1 final size:1
Alignment explanation
Indices: 1699845--1699875 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1699835 GCTTGCTTGT
1699845 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1699876 CAAATTCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1701050 original size:4 final size:4
Alignment explanation
Indices: 1701041--1701067 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1701031 CACCTTTGGT
1701041 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
1701068 ATGTTATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:1704198 original size:24 final size:25
Alignment explanation
Indices: 1704151--1704200 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1704141 TTTTAGTTGA
1704151 TGACTGCAAATGCTCTGGTAATATT
1 TGACTGCAAATGCTCTGGTAATATT
*
1704176 TGACTGCTAAAT-CT-TTGTAATATT
1 TGACTGC-AAATGCTCTGGTAATATT
1704200 T
1 T
1704201 CTTTCGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
25 9 0.39
26 4 0.17
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (25 bp):
TGACTGCAAATGCTCTGGTAATATT
Found at i:1712269 original size:41 final size:41
Alignment explanation
Indices: 1712212--1712302 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
1712202 AAATGGGGTA
1712212 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
1712253 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
*
1712294 TGGGGGTGG
1 TGGGAGTGG
1712303 AGAGTTTGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.22, C:0.13, G:0.41, T:0.24
Consensus pattern (41 bp):
TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
Found at i:1717118 original size:3 final size:3
Alignment explanation
Indices: 1717110--1717134 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1717100 GCTTACAATA
1717110 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1717135 TTTTAAAAAA
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1722482 original size:19 final size:20
Alignment explanation
Indices: 1722447--1722487 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1722437 CGATTTAATA
* *
1722447 AAATTTGTTTTATTATTTTT
1 AAATTTGTTTAATTATTATT
1722467 AAATTT-TTTAATTATTATT
1 AAATTTGTTTAATTATTATT
1722486 AA
1 AA
1722488 TTTAGTAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
AAATTTGTTTAATTATTATT
Found at i:1723197 original size:12 final size:12
Alignment explanation
Indices: 1723180--1723206 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1723170 CTTGTTGTCA
1723180 CATCCCCATTCC
1 CATCCCCATTCC
1723192 CATCCCCATTCC
1 CATCCCCATTCC
1723204 CAT
1 CAT
1723207 TATCATCAAT
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:0.19, C:0.56, G:0.00, T:0.26
Consensus pattern (12 bp):
CATCCCCATTCC
Found at i:1723386 original size:23 final size:23
Alignment explanation
Indices: 1723360--1723406 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1723350 GAATTGGTAT
1723360 ATATAGATTAAATTAAGTTAAAC
1 ATATAGATTAAATTAAGTTAAAC
*
1723383 ATATTGATTAAATTAAGTTAAAC
1 ATATAGATTAAATTAAGTTAAAC
1723406 A
1 A
1723407 ATTGGTCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (23 bp):
ATATAGATTAAATTAAGTTAAAC
Found at i:1725316 original size:72 final size:72
Alignment explanation
Indices: 1725217--1725368 Score: 223
Period size: 72 Copynumber: 2.1 Consensus size: 72
1725207 GGATCTAGTT
* * **
1725217 AATCATTTATGATCCGTCACTCGCATACTTCACACCACTCGCTATAAGGTACTTATTATGGATTG
1 AATCA-TTAAGATCCGTCACTCACATACTTCACACCACTCGCTATAAAATACTTATTATGGATTG
1725282 TCCATGAA
65 TCCATGAA
* * *
1725290 AATCATTAAGATCCGTCACTCACATACTTCATACCACTCGCTATAAAATACTTGTTGTGGATTGT
1 AATCATTAAGATCCGTCACTCACATACTTCACACCACTCGCTATAAAATACTTATTATGGATTGT
*
1725355 CCATGAG
66 CCATGAA
1725362 AATCATT
1 AATCATT
1725369 TAGACATAAC
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 66 0.93
73 5 0.07
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (72 bp):
AATCATTAAGATCCGTCACTCACATACTTCACACCACTCGCTATAAAATACTTATTATGGATTGT
CCATGAA
Found at i:1729843 original size:15 final size:16
Alignment explanation
Indices: 1729823--1729855 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1729813 ATATATTTTT
1729823 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
1729838 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
1729855 T
1 T
1729856 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:1729941 original size:22 final size:22
Alignment explanation
Indices: 1729902--1729960 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
1729892 GTTTTAAGAA
*
1729902 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
1729923 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
1729945 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
1729961 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:1729977 original size:26 final size:24
Alignment explanation
Indices: 1729931--1729979 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
1729921 ATTTGTTTTA
*
1729931 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
1729955 ATATTTGATTTATTATATTTTTAAA
1 ATATTT-ATTT-TTATATTTTTAAA
1729980 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:1729991 original size:26 final size:26
Alignment explanation
Indices: 1729934--1729992 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1729924 TGTTTTAATA
*
1729934 TTTATTT-TTATGTTTTTAAATATAT
1 TTTATTTATTATATTTTTAAATATAT
* *
1729959 TTGATTTATTATATTTTTAAA-ATTTT
1 TTTATTTATTATATTTTTAAATA-TAT
1729985 TTTATTTA
1 TTTATTTA
1729993 ATGAAATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (26 bp):
TTTATTTATTATATTTTTAAATATAT
Found at i:1733339 original size:13 final size:12
Alignment explanation
Indices: 1733299--1733340 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1733289 ATTTCTTTTA
*
1733299 TTTTCTTGAATT
1 TTTTATTGAATT
1733311 TTTTATAT-AATT
1 TTTTAT-TGAATT
1733323 TTTTATTGAATT
1 TTTTATTGAATT
1733335 CTTTTA
1 -TTTTA
1733341 AAAATACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 1 0.04
12 19 0.73
13 6 0.23
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (12 bp):
TTTTATTGAATT
Found at i:1739588 original size:2 final size:2
Alignment explanation
Indices: 1739581--1739615 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1739571 TGATTGGTAT
1739581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1739616 GTTCTATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1741890 original size:42 final size:43
Alignment explanation
Indices: 1741830--1741935 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 43
1741820 CCTGATCAGT
*
1741830 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG-
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
* * *
1741872 ATACGACACACGAGGTGCCTAATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTG-A
*
1741916 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
1741936 GATCGATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 38 0.69
44 17 0.31
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (43 bp):
ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
Found at i:1741937 original size:23 final size:23
Alignment explanation
Indices: 1741830--1741925 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 23
1741820 CCTGATCAGT
** *
1741830 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACGAGGTGCCTGAA
1741852 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACGAGGTGCCTGAA
1741872 ATACGACACACGAGGTGCCT--A
1 ATACGACACACGAGGTGCCTGAA
1741893 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTGAA
1741916 ATACGACACA
1 ATACGACACA
1741926 TAAAGTGCCT
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
20 1 0.02
21 53 0.80
22 1 0.02
23 11 0.17
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.14
Consensus pattern (23 bp):
ATACGACACACGAGGTGCCTGAA
Found at i:1743475 original size:29 final size:28
Alignment explanation
Indices: 1743443--1743497 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
1743433 GCTCGAATGC
1743443 TTTCTGTTCTCTT-TTCTCTATTCTTTTTG
1 TTTCTGTTCT-TTATTCTCT-TTCTTTTTG
* *
1743472 TTTCTTTTCTTTATTCTGTTTCTTTT
1 TTTCTGTTCTTTATTCTCTTTCTTTT
1743498 ATTCACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.73
Consensus pattern (28 bp):
TTTCTGTTCTTTATTCTCTTTCTTTTTG
Found at i:1743480 original size:22 final size:23
Alignment explanation
Indices: 1743442--1743488 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1743432 TGCTCGAATG
1743442 CTTTCTGTTCTCTTTTCTCTATT
1 CTTTCTGTTCTCTTTTCTCTATT
* *
1743465 CTTTTTGTT-TCTTTTCTTTATT
1 CTTTCTGTTCTCTTTTCTCTATT
1743487 CT
1 CT
1743489 GTTTCTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.04, C:0.21, G:0.04, T:0.70
Consensus pattern (23 bp):
CTTTCTGTTCTCTTTTCTCTATT
Found at i:1743500 original size:14 final size:12
Alignment explanation
Indices: 1743452--1743501 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1743442 CTTTCTGTTC
*
1743452 TCTTTTCTCTAT
1 TCTTTTCTTTAT
*
1743464 TCTTTT-TGT-T
1 TCTTTTCTTTAT
1743474 TCTTTTCTTTAT
1 TCTTTTCTTTAT
1743486 TCTGTTTCTTTTAT
1 TCT-TTTC-TTTAT
1743500 TC
1 TC
1743502 ACTTTAGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 7 0.22
11 4 0.12
12 10 0.31
13 4 0.12
14 7 0.22
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (12 bp):
TCTTTTCTTTAT
Found at i:1750145 original size:14 final size:14
Alignment explanation
Indices: 1750126--1750155 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1750116 TTATATCGAG
1750126 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
1750140 ACCAATCCAATTCA
1 ACCAATCCAAATCA
1750154 AC
1 AC
1750156 ATATTTTCAA
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:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:1752010 original size:484 final size:484
Alignment explanation
Indices: 1751166--1752138 Score: 1894
Period size: 484 Copynumber: 2.0 Consensus size: 484
1751156 CAATCTCAAG
*
1751166 CATTTAAGAATGTAATTCAAGTTACACGAACTTACCTTGATACTTGTTTGTAAACAGTAAAAATC
1 CATTTAAGAATATAATTCAAGTTACACGAACTTACCTTGATACTTGTTTGTAAACAGTAAAAATC
1751231 TACTAATCCCGAACTTTTTCCTTTCCTCGATCTAGCTTCGTATTTGAATCTTCTGGATTTGGTGT
66 TACTAATCCCGAACTTTTTCCTTTCCTCGATCTAGCTTCGTATTTGAATCTTCTGGATTTGGTGT
*
1751296 AAAAATTATGAAATACCAGCTTAGAGAACCCTCCTATGGCGTTTTTAGCTGCTGGAATTGAAGGG
131 AAAAATTATGAAATACCAGCTTAGAGAACCCTCCTATGGCGTTTTTAGCTGCTGGAATTGAAGAG
1751361 AAATGAAGAGAAATCTAGATATTTCCTATTTAGTCCTAGCTTTATTTAGTTAATTTTGCAATATT
196 AAATGAAGAGAAATCTAGATATTTCCTATTTAGTCCTAGCTTTATTTAGTTAATTTTGCAATATT
1751426 CCAATTTTACCCTTAATTATCAATTTTTCTGCTGATTTCATACCCTTGCCGTCCAGCCCAAATAA
261 CCAATTTTACCCTTAATTATCAATTTTTCTGCTGATTTCATACCCTTGCCGTCCAGCCCAAATAA
1751491 ATTTTGGGTCTAATTGCCTTTTAAATCCTTTCTCATTAGACTCTTAAGCTATTTAATCATTCTAG
326 ATTTTGGGTCTAATTGCCTTTTAAATCCTTTCTCATTAGACTCTTAAGCTATTTAATCATTCTAG
1751556 CAACTTTTACACCTATTACAATTTAGTCCTTTTCATTTAATTAACTACCCAAACATTAAAATTTC
391 CAACTTTTACACCTATTACAATTTAGTCCTTTTCATTTAATTAACTACCCAAACATTAAAATTTC
1751621 CTAACGAAATTTTAATACCACACTAATAA
456 CTAACGAAATTTTAATACCACACTAATAA
1751650 CATTTAAGAATATAATTCAAGTTACACGAACTTACCTTGATACTTGTTTGTAAACAGTAAAAATC
1 CATTTAAGAATATAATTCAAGTTACACGAACTTACCTTGATACTTGTTTGTAAACAGTAAAAATC
1751715 TACTAATCCCGAACTTTTTCCTTTCCTCGATCTAGCTTCGTATTTGAATCTTCTGGATTTGGTGT
66 TACTAATCCCGAACTTTTTCCTTTCCTCGATCTAGCTTCGTATTTGAATCTTCTGGATTTGGTGT
*
1751780 AAAAATTATGAAATACCAGCTTAGAGAACCCTCCTATGGCGTTTTTAGCTGTTGGAATTGAAGAG
131 AAAAATTATGAAATACCAGCTTAGAGAACCCTCCTATGGCGTTTTTAGCTGCTGGAATTGAAGAG
1751845 AAATGAAGAGAAATCTAGATATTTCCTATTTAGTCCTAGCTTTATTTAGTTAATTTTGCAATATT
196 AAATGAAGAGAAATCTAGATATTTCCTATTTAGTCCTAGCTTTATTTAGTTAATTTTGCAATATT
1751910 -CAATTTTACCCTTAATTTATCAATTTTTCTGCTGATTTCATACCCTTGCCGTCCAGCCCAAATA
261 CCAATTTTACCCTTAA-TTATCAATTTTTCTGCTGATTTCATACCCTTGCCGTCCAGCCCAAATA
1751974 AATTTTGGGTCTAATTGCCTTTTAAATCCTTTCTCATTAGACTCTTAAGCTATTTAATCATTCTA
325 AATTTTGGGTCTAATTGCCTTTTAAATCCTTTCTCATTAGACTCTTAAGCTATTTAATCATTCTA
*
1752039 GCAACTTTTACACCTATTACAATTTAGTCCTTTTCATTTAATTGACTACCCAAACATTAAAATTT
390 GCAACTTTTACACCTATTACAATTTAGTCCTTTTCATTTAATTAACTACCCAAACATTAAAATTT
1752104 CCTAACGAAATTTTAATACCACACTAATAA
455 CCTAACGAAATTTTAATACCACACTAATAA
1752134 CATTT
1 CATTT
1752139 CATAAATATT
Statistics
Matches: 484, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
483 15 0.03
484 469 0.97
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (484 bp):
CATTTAAGAATATAATTCAAGTTACACGAACTTACCTTGATACTTGTTTGTAAACAGTAAAAATC
TACTAATCCCGAACTTTTTCCTTTCCTCGATCTAGCTTCGTATTTGAATCTTCTGGATTTGGTGT
AAAAATTATGAAATACCAGCTTAGAGAACCCTCCTATGGCGTTTTTAGCTGCTGGAATTGAAGAG
AAATGAAGAGAAATCTAGATATTTCCTATTTAGTCCTAGCTTTATTTAGTTAATTTTGCAATATT
CCAATTTTACCCTTAATTATCAATTTTTCTGCTGATTTCATACCCTTGCCGTCCAGCCCAAATAA
ATTTTGGGTCTAATTGCCTTTTAAATCCTTTCTCATTAGACTCTTAAGCTATTTAATCATTCTAG
CAACTTTTACACCTATTACAATTTAGTCCTTTTCATTTAATTAACTACCCAAACATTAAAATTTC
CTAACGAAATTTTAATACCACACTAATAA
Found at i:1757324 original size:14 final size:14
Alignment explanation
Indices: 1757305--1757334 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1757295 TTATATCGAG
1757305 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
1757319 ACCAATCCAATTCA
1 ACCAATCCAAATCA
1757333 AC
1 AC
1757335 ATATTTTCAA
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:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:1762568 original size:23 final size:24
Alignment explanation
Indices: 1762533--1762578 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
1762523 AGTCAGAAGA
1762533 AAAACAGCGTGTCAAAAGACAGAG
1 AAAACAGCGTGTCAAAAGACAGAG
1762557 AAAA-AGCGTGTCAAAAGACAGA
1 AAAACAGCGTGTCAAAAGACAGA
1762579 CTACACAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (24 bp):
AAAACAGCGTGTCAAAAGACAGAG
Found at i:1781837 original size:23 final size:23
Alignment explanation
Indices: 1781752--1781835 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
1781742 CTTAATGCCG
*
1781752 TTCTGGTGTGTCTGGGTGGATTA
1 TTCTGGTGTGTTTGGGTGGATTA
*
1781775 TTCTGGTGTGTTTGGGTGGATCA
1 TTCTGGTGTGTTTGGGTGGATTA
* * *
1781798 TTCTAGTGTGTTCGGTTGGATTA
1 TTCTGGTGTGTTTGGGTGGATTA
*
1781821 TTATGGTGTGTTTGG
1 TTCTGGTGTGTTTGG
1781836 TTAGATCCGT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.10, C:0.07, G:0.37, T:0.46
Consensus pattern (23 bp):
TTCTGGTGTGTTTGGGTGGATTA
Found at i:1785512 original size:46 final size:46
Alignment explanation
Indices: 1785448--1785597 Score: 167
Period size: 46 Copynumber: 3.1 Consensus size: 46
1785438 CACACACGTA
*
1785448 GCCATAGCCCAGCCATGGTCTTACACGAATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATTGAT
* * * * *
1785494 GCCATATCCCAGATATGGTCTTATACGGAAGCACGTAATCACATATCTCTGAT
1 GCCATAGCCCAGCTATGGTCTTACAC-GAATCACAT-ATCAC--A--T-TGAT
1785547 GCCATAGCCCAGCTATGGTCTTACAC-AGATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGA-ATCACATATCACATTGAT
1785593 GCCAT
1 GCCAT
1785598 GGTCCAACCA
Statistics
Matches: 85, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
46 31 0.36
47 8 0.09
48 5 0.06
49 1 0.01
50 1 0.01
51 6 0.07
52 6 0.07
53 27 0.32
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (46 bp):
GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATTGAT
Found at i:1786717 original size:21 final size:21
Alignment explanation
Indices: 1786691--1786743 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1786681 CGACACATAA
1786691 GTGCCTGAAATGACACACGAG
1 GTGCCTGAAATGACACACGAG
*
1786712 GTGCCTGAAACGACACACGAG
1 GTGCCTGAAATGACACACGAG
1786733 GTGCCTGAAAT
1 GTGCCTGAAAT
1786744 ACGACACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.28, T:0.15
Consensus pattern (21 bp):
GTGCCTGAAATGACACACGAG
Found at i:1786759 original size:23 final size:23
Alignment explanation
Indices: 1786677--1786763 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 23
1786667 ACCTGATCAG
*
1786677 AATACGACACA-TAAGTGCCTGA
1 AATACGACACACGAAGTGCCTGA
*
1786699 AAT--GACACACGAGGTGCCTG-
1 AATACGACACACGAAGTGCCTGA
*
1786719 AA-ACGACACACGAGGTGCCTGA
1 AATACGACACACGAAGTGCCTGA
**
1786741 AATACGACACATAAAGTGCCTGA
1 AATACGACACACGAAGTGCCTGA
1786764 TCAGTATAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
20 8 0.15
21 25 0.45
22 5 0.09
23 17 0.31
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (23 bp):
AATACGACACACGAAGTGCCTGA
Found at i:1787022 original size:23 final size:23
Alignment explanation
Indices: 1786953--1787050 Score: 70
Period size: 28 Copynumber: 3.8 Consensus size: 23
1786943 AAATGTCCAA
* *
1786953 CCAAAACACACTAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
1786976 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
1787004 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----A-ATAATCC-T
1787033 CCAAAACACACCAGAATA
1 CCAAAACACACCAGAATA
1787051 GTACAAAGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
23 13 0.21
24 3 0.05
25 1 0.02
28 32 0.51
29 14 0.22
ACGTcount: A:0.47, C:0.32, G:0.04, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:1787049 original size:29 final size:28
Alignment explanation
Indices: 1786967--1787050 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
1786957 AACACACTAG
* *
1786967 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
1786995 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
1787023 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
1787051 GTACAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:1815203 original size:2 final size:2
Alignment explanation
Indices: 1815198--1815228 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1815188 ATAATCTTAA
1815198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1815229 CATTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.