Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 5 of 318
Found at i:1448235 original size:31 final size:31
Alignment explanation
Indices: 1448197--1448314 Score: 175
Period size: 31 Copynumber: 3.8 Consensus size: 31
1448187 ACAAATGACA
*
1448197 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1448228 AGTGAAAAGTGGTAG-TTCTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-GGCTACCTGATC
* *
1448259 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
1448290 AATGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
1448315 AAGTAACAAG
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
30 3 0.04
31 73 0.94
32 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:1448409 original size:47 final size:46
Alignment explanation
Indices: 1448340--1448503 Score: 142
Period size: 47 Copynumber: 3.6 Consensus size: 46
1448330 AGTGATTTCC
* *
1448340 GTATAAGACCATATTTGGGATATGGCATCGGTGTGATATATG-CTA
1 GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGACTA
** * *
1448385 CTGTATAAGACCATATCTGGGATATGGCATAAGTGAGATATGTGATTA
1 --GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGACTA
* * * *
1448433 GTGTAAGACCATAGCTGGGTTATGGCATC-----GATATATGAATA
1 GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGACTA
* * *
1448474 TGTGTAAGACCATAGCTGGGCTATGGCATC
1 -GTATAAGACCATATCTGGGATATGGCATC
1448504 ATTATGTGAA
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
41 10 0.10
42 28 0.27
46 25 0.25
47 37 0.36
48 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (46 bp):
GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGACTA
Found at i:1448457 original size:46 final size:44
Alignment explanation
Indices: 1448390--1448530 Score: 132
Period size: 42 Copynumber: 3.2 Consensus size: 44
1448380 TGCTACTGTA
* * *
1448390 TAAGACCATATCTGGGATATGGCATAAGTGAGATATGTGATTA-GTG
1 TAAGACCATAGCTGGGATATGGCAT-A-T-AGATATATGAATATGTG
* *
1448436 TAAGACCATAGCTGGGTTATGGC--ATCGATATATGAATATGTG
1 TAAGACCATAGCTGGGATATGGCATATAGATATATGAATATGTG
* * *
1448478 TAAGACCATAGCTGGGCTATGGCATCAT---TATGTGAAGATGTG
1 TAAGACCATAGCTGGGATATGGCAT-ATAGATATATGAATATGTG
1448520 TAAGACCATAG
1 TAAGACCATAG
1448531 TTGAACTATG
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
41 10 0.12
42 49 0.59
43 1 0.01
45 2 0.02
46 21 0.25
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (44 bp):
TAAGACCATAGCTGGGATATGGCATATAGATATATGAATATGTG
Found at i:1448491 original size:42 final size:42
Alignment explanation
Indices: 1448433--1448545 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
1448423 TATGTGATTA
* *
1448433 GTGTAAGACCATAGCTGGGTTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATATGAAGAT
*
1448475 GTGTAAGACCATAGCTGGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCATTATATGAAGAT
* **
1448517 GTGTAAGACCATAGTTGAACTATGGCATC
1 GTGTAAGACCATAGCTGGGCTATGGCATC
1448546 GAGAAAACGA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.02
42 63 0.98
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCATTATATGAAGAT
Found at i:1449521 original size:24 final size:24
Alignment explanation
Indices: 1449489--1449538 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1449479 TGTTGAGTAG
1449489 AAGAACATACTTTAGGTCCAAGTC
1 AAGAACATACTTTAGGTCCAAGTC
1449513 AAGAACATACTTTAGGTCCAAGTC
1 AAGAACATACTTTAGGTCCAAGTC
1449537 AA
1 AA
1449539 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:1458926 original size:31 final size:30
Alignment explanation
Indices: 1458895--1458954 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1458885 AAGATTTATA
* *
1458895 AATAAAATATTAA-TAATTTTATTTAAATAT
1 AATAAAATAATAATTAA-TTTAATTAAATAT
*
1458925 AATTAAATAATAATTAATTTAATTAAATAT
1 AATAAAATAATAATTAATTTAATTAAATAT
1458955 TAAAATCTTA
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:1459434 original size:29 final size:29
Alignment explanation
Indices: 1459391--1459459 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1459381 ATTTTAAATT
* *
1459391 AATAATGATAAAATTGTACTTT-ATTCTTTTA
1 AATAAT-A-AAAATT-TAATTTAATTCTTTAA
1459422 AATAATAAAAATTTAATTTAATTCTTTAA
1 AATAATAAAAATTTAATTTAATTCTTTAA
*
1459451 AATTATAAA
1 AATAATAAA
1459460 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:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (29 bp):
AATAATAAAAATTTAATTTAATTCTTTAA
Found at i:1477160 original size:13 final size:13
Alignment explanation
Indices: 1477142--1477166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1477132 AATTAAAGAA
1477142 ATTTTAGATTTAG
1 ATTTTAGATTTAG
1477155 ATTTTAGATTTA
1 ATTTTAGATTTA
1477167 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:1477640 original size:16 final size:16
Alignment explanation
Indices: 1477615--1477645 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1477605 TTCATTAAAA
*
1477615 TTTATCTGAATAATTG
1 TTTATATGAATAATTG
1477631 TTTATATGAATAATT
1 TTTATATGAATAATT
1477646 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:1480116 original size:17 final size:17
Alignment explanation
Indices: 1480081--1480112 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1480071 TCCCAAGTTT
1480081 TATTTTAATATTTTATA
1 TATTTTAATATTTTATA
1480098 TATTTTAAT-TTTTAT
1 TATTTTAATATTTTAT
1480113 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:1489805 original size:18 final size:18
Alignment explanation
Indices: 1489782--1489817 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1489772 ATTGAAGACC
1489782 AAGAAGGTTAAAATATGT
1 AAGAAGGTTAAAATATGT
1489800 AAGAAGGTTAAAATATGT
1 AAGAAGGTTAAAATATGT
1489818 GATAAGTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (18 bp):
AAGAAGGTTAAAATATGT
Found at i:1494612 original size:21 final size:18
Alignment explanation
Indices: 1494598--1494633 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1494588 CAAAGCTTGG
1494598 ACCCACTTCACCAAATGTT
1 ACCCACTTCACCAAA-GTT
*
1494617 ACCTACTTCACCAAAGT
1 ACCCACTTCACCAAAGT
1494634 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:1497303 original size:16 final size:16
Alignment explanation
Indices: 1497282--1497314 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1497272 TATATTTTAA
1497282 TATTTAAAATATATTT
1 TATTTAAAATATATTT
*
1497298 TATTTAAATTATATTT
1 TATTTAAAATATATTT
1497314 T
1 T
1497315 TTAATAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTAAAATATATTT
Found at i:1497471 original size:20 final size:20
Alignment explanation
Indices: 1497434--1497472 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1497424 TCTTAAACAC
* *
1497434 TTAAATCTTAAATCAACCTT
1 TTAAAACTTAAATAAACCTT
*
1497454 TTAAAACTTAAGTAAACCT
1 TTAAAACTTAAATAAACCT
1497473 GAGCCATCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (20 bp):
TTAAAACTTAAATAAACCTT
Found at i:1503196 original size:15 final size:15
Alignment explanation
Indices: 1503176--1503206 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1503166 GAAGTCGAAT
*
1503176 AGGTTCCAGCGTTTA
1 AGGTTCCAGAGTTTA
1503191 AGGTTCCAGAGTTTA
1 AGGTTCCAGAGTTTA
1503206 A
1 A
1503207 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:1511628 original size:17 final size:16
Alignment explanation
Indices: 1511553--1511628 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
1511543 TATTATTTAT
1511553 TTTAAATTTGTTT-AA
1 TTTAAATTTGTTTAAA
* *
1511568 TTATTAA-TTGTTGAAAA
1 TT-TAAATTTGTT-TAAA
1511585 TTTAAATTTGTTTAAA
1 TTTAAATTTGTTTAAA
*
1511601 TTTAAA---ATTTAAA
1 TTTAAATTTGTTTAAA
1511614 CTTTAAATTTGTTTA
1 -TTTAAATTTGTTTA
1511629 TTTTAAGTTG
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:1519634 original size:10 final size:11
Alignment explanation
Indices: 1519614--1519638 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1519604 TCTCGTGTTC
1519614 TTTCTTTTTTT
1 TTTCTTTTTTT
1519625 TTTCTTTTTTT
1 TTTCTTTTTTT
1519636 TTT
1 TTT
1519639 TACTGAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:1521123 original size:6 final size:5
Alignment explanation
Indices: 1521072--1521122 Score: 77
Period size: 5 Copynumber: 10.0 Consensus size: 5
1521062 ATAATACCAC
1521072 CTTTT CTTTT CTTTT CTTTT CTTTT CTTCTT CTTCTT CTTTT -TTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CTT-TT CTTTT CTTTT CTTTT
1521123 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:1531520 original size:12 final size:12
Alignment explanation
Indices: 1531503--1531535 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1531493 CAGTCTACCC
1531503 ATATTAATTTTT
1 ATATTAATTTTT
1531515 ATATT-ATTTTT
1 ATATTAATTTTT
1531526 ATA-TAATTTT
1 ATATTAATTTT
1531536 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:1531702 original size:30 final size:30
Alignment explanation
Indices: 1531657--1531718 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1531647 CTTAACAAGT
*
1531657 AAATGTCTCTAAAATAATAACAAAATTAAC
1 AAATATCTCTAAAATAATAACAAAATTAAC
*
1531687 AAATATCTTTAAAATAATAACAAAATTAAC
1 AAATATCTCTAAAATAATAACAAAATTAAC
1531717 AA
1 AA
1531719 TAAAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (30 bp):
AAATATCTCTAAAATAATAACAAAATTAAC
Found at i:1534549 original size:17 final size:17
Alignment explanation
Indices: 1534524--1534577 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
1534514 GTTATTAATA
*
1534524 TTTTGTATTTTATATTT
1 TTTTATATTTTATATTT
1534541 TTTTATATTTT-TATATT
1 TTTTATATTTTATAT-TT
1534558 TTTTATATTATTAATATTT
1 TTTTATATT-TT-ATATTT
1534577 T
1 T
1534578 AATAATTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 3 0.09
17 21 0.66
18 2 0.06
19 3 0.09
20 3 0.09
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTATATTTTATATTT
Found at i:1534551 original size:8 final size:8
Alignment explanation
Indices: 1534524--1534577 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
1534514 GTTATTAATA
*
1534524 TTTTGTAT
1 TTTTATAT
*
1534532 TTTATATTT
1 TTT-TATAT
1534541 TTTTATAT
1 TTTTATAT
1534549 TTTTATATT
1 TTTTATA-T
1534558 TTTTATAT
1 TTTTATAT
*
1534566 TATTAATAT
1 T-TTTATAT
1534575 TTT
1 TTT
1534578 AATAATTCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 18 0.46
9 21 0.54
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (8 bp):
TTTTATAT
Found at i:1534551 original size:9 final size:9
Alignment explanation
Indices: 1534531--1534577 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
1534521 ATATTTTGTA
1534531 TTTTATATT
1 TTTTATATT
1534540 TTTT-TATAT
1 TTTTATAT-T
1534549 TTTTATATT
1 TTTTATATT
1534558 TTTTATATT
1 TTTTATATT
* *
1534567 ATTAATATT
1 TTTTATATT
1534576 TT
1 TT
1534578 AATAATTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 3 0.09
9 27 0.82
10 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATATT
Found at i:1534552 original size:18 final size:18
Alignment explanation
Indices: 1534531--1534577 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
1534521 ATATTTTGTA
1534531 TTTTATATTTTTTTATAT
1 TTTTATATTTTTTTATAT
1534549 TTTTATA-TTTTTTATAT
1 TTTTATATTTTTTTATAT
*
1534566 TATTAATATTTT
1 T-TTTATATTTT
1534578 AATAATTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 11 0.42
18 12 0.46
19 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATATTTTTTTATAT
Found at i:1534578 original size:25 final size:24
Alignment explanation
Indices: 1534515--1534578 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
1534505 TTGGGTTGTG
*
1534515 TTATTAATATTTTGTATTTTATAT
1 TTATTAATATTTTATATTTTATAT
* * *
1534539 TTTTTTATATTTTTATATTTTTTAT
1 TTATTAATA-TTTTATATTTTATAT
1534564 ATTATTAATATTTTA
1 -TTATTAATATTTTA
1534579 ATAATTCGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 7 0.22
25 18 0.56
26 7 0.22
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TTATTAATATTTTATATTTTATAT
Found at i:1534617 original size:22 final size:24
Alignment explanation
Indices: 1534563--1534619 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 24
1534553 ATATTTTTTA
*
1534563 TATTATTA-ATATTTTAATAATTC
1 TATTAATATATATTTTAATAATTC
*
1534586 GA-TAAT-TATATTTT-AT-ATTC
1 TATTAATATATATTTTAATAATTC
1534606 TATTAATATATATT
1 TATTAATATATATT
1534620 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:1539140 original size:53 final size:53
Alignment explanation
Indices: 1539060--1539166 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
1539050 TATTGAGAGG
1539060 CGCCAATAGGTTATGTTTTTCGACCATGATGCAGGAGCCGCAAAAAAACCACT
1 CGCCAATAGGTTATGTTTTTCGACCATGATGCAGGAGCCGCAAAAAAACCACT
1539113 CGCCAATAGGTTATGTTTTTCGACCATGATGCAGGAGCCGCAAAAAAACCACT
1 CGCCAATAGGTTATGTTTTTCGACCATGATGCAGGAGCCGCAAAAAAACCACT
1539166 C
1 C
1539167 TTTCACGACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (53 bp):
CGCCAATAGGTTATGTTTTTCGACCATGATGCAGGAGCCGCAAAAAAACCACT
Found at i:1552625 original size:20 final size:20
Alignment explanation
Indices: 1552589--1552626 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1552579 GTGAAATTTG
*
1552589 TATAAAAATATAGAATTAAT
1 TATAAAAATATAAAATTAAT
1552609 TATAAAGAATA-AAAATTA
1 TATAAA-AATATAAAATTA
1552627 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:1555941 original size:52 final size:52
Alignment explanation
Indices: 1555863--1555994 Score: 219
Period size: 52 Copynumber: 2.5 Consensus size: 52
1555853 ACCAATGCCA
* * *
1555863 ATGGTCTTATACGGGAGTACATATCACAATGCACCGATGCCATTGCCCAGCT
1 ATGGTCTTATACGGGCGCACATATCACAATGCACCGATGCCATAGCCCAGCT
*
1555915 ATGGTCTTATACGGGCGCACATATCACAATGCACCGATGTCATAGCCCAGCT
1 ATGGTCTTATACGGGCGCACATATCACAATGCACCGATGCCATAGCCCAGCT
*
1555967 ATGGTCTTATACAGGCGCACATATCACA
1 ATGGTCTTATACGGGCGCACATATCACA
1555995 TCTATTCTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (52 bp):
ATGGTCTTATACGGGCGCACATATCACAATGCACCGATGCCATAGCCCAGCT
Found at i:1556153 original size:22 final size:22
Alignment explanation
Indices: 1556128--1556171 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1556118 TAAGATAACT
1556128 TAGTAATCATAATATTTTCATA
1 TAGTAATCATAATATTTTCATA
1556150 TAGTAATCATAATATTTTCATA
1 TAGTAATCATAATATTTTCATA
1556172 ATAAAACATT
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:1559394 original size:46 final size:44
Alignment explanation
Indices: 1559311--1559425 Score: 126
Period size: 46 Copynumber: 2.5 Consensus size: 44
1559301 GACGAGTACT
*
1559311 AGTGTAAGACATGTCTGGGACATGCTTCGGCCTCGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCTTCAGCCTCGAGACGT--GCC
* * *
1559357 AGTGTAAGACATGTTTGGGACATGCATT-AG-CTACGAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGC-TTCAGCCT-CGAGACGTGCC
*
1559401 AGTGTAAGACCATGTCTAGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
1559426 ATGTAACACC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
44 11 0.18
45 15 0.25
46 32 0.53
47 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCTTCAGCCTCGAGACGTGCC
Found at i:1561519 original size:13 final size:13
Alignment explanation
Indices: 1561503--1561531 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1561493 TTCTCTTTTA
1561503 TTTTTCTTTC-CT
1 TTTTTCTTTCTCT
1561515 TTTTTCTTTCTCT
1 TTTTTCTTTCTCT
1561528 TTTT
1 TTTT
1561532 CTCCCTTACT
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:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTCTCT
Found at i:1563565 original size:15 final size:16
Alignment explanation
Indices: 1563556--1563593 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1563546 TAAAGTAAAT
1563556 GAAAT-AAAAGAAAAA
1 GAAATGAAAAGAAAAA
1563571 GAAATGAAAAGAAGGAAA
1 GAAATGAAAAGAA--AAA
1563589 GAAAT
1 GAAAT
1563594 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:1564829 original size:44 final size:44
Alignment explanation
Indices: 1564780--1564871 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
1564770 TGTTTAGGGA
* *
1564780 TACTTCGACCTTGAGTTGATGAGGCA-CTATAAGTGTCGTACTAT
1 TACTTCGACCTTAAGTCGATGAGGCACCT-TAAGTGTCGTACTAT
* * *
1564824 TACTTCGACTTTAAGTCGATGAGGCACCTTATGTGTCGTACTGT
1 TACTTCGACCTTAAGTCGATGAGGCACCTTAAGTGTCGTACTAT
1564868 TACT
1 TACT
1564872 ATTACTTCAG
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:1565068 original size:18 final size:18
Alignment explanation
Indices: 1565036--1565147 Score: 107
Period size: 18 Copynumber: 6.2 Consensus size: 18
1565026 TAAATAAAAG
* *
1565036 TACTGAATGACTGATTGT
1 TACTGAATAATTGATTGT
* *
1565054 TACTAAATAATTGATCGT
1 TACTGAATAATTGATTGT
* * *
1565072 TACTGAATAACTAATTGC
1 TACTGAATAATTGATTGT
** *
1565090 TACTGAGCAAATGATTGT
1 TACTGAATAATTGATTGT
* *
1565108 TACTGAATAATTAATTGC
1 TACTGAATAATTGATTGT
*
1565126 TACTGAATAATTGAATGT
1 TACTGAATAATTGATTGT
1565144 TACT
1 TACT
1565148 AAATGAAATT
Statistics
Matches: 72, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 72 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (18 bp):
TACTGAATAATTGATTGT
Found at i:1565076 original size:36 final size:35
Alignment explanation
Indices: 1565036--1565147 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 35
1565026 TAAATAAAAG
* * * *
1565036 TACTGAATGACTGATTGTTACTAAATAATTGATCGT
1 TACTGAATAACTAATTGCTACTGAATAATTGAT-GT
** *
1565072 TACTGAATAACTAATTGCTACTGAGCAAATGATTGT
1 TACTGAATAACTAATTGCTACTGAATAATTGA-TGT
*
1565108 TACTGAATAATTAATTGCTACTGAATAATTGAATGT
1 TACTGAATAACTAATTGCTACTGAATAATTG-ATGT
1565144 TACT
1 TACT
1565148 AAATGAAATT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
36 61 0.97
37 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (35 bp):
TACTGAATAACTAATTGCTACTGAATAATTGATGT
Found at i:1566416 original size:61 final size:61
Alignment explanation
Indices: 1566321--1566444 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
1566311 GTGTGCCCTC
* *
1566321 TGCACGTAAAAATTTCAAGTCAGTATGCATGATAGTAAACACACGGGCAGAGATACGGTCG
1 TGCACGTAAAAATTTCAAGTCAGTATGCATGATAGTAAACACACGAGCAGAGACACGGTCG
* * *
1566382 TGCACGTAAAAGTTTCAAGTCAGTATGCATGATAGTAAACACATGAGTAGAGACACGGTCG
1 TGCACGTAAAAATTTCAAGTCAGTATGCATGATAGTAAACACACGAGCAGAGACACGGTCG
1566443 TG
1 TG
1566445 TGTCTCAGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (61 bp):
TGCACGTAAAAATTTCAAGTCAGTATGCATGATAGTAAACACACGAGCAGAGACACGGTCG
Found at i:1573616 original size:6 final size:6
Alignment explanation
Indices: 1573605--1573635 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1573595 ACAGTGACCA
1573605 TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
1573636 CCCGGGCGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTCTT
Found at i:1583379 original size:13 final size:13
Alignment explanation
Indices: 1583376--1583400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1583366 AAAATTTTAA
1583376 TTAATTAAAAATT
1 TTAATTAAAAATT
1583389 TTAATTAAAAAT
1 TTAATTAAAAAT
1583401 CTATTTTCAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAATTAAAAATT
Found at i:1583383 original size:17 final size:17
Alignment explanation
Indices: 1583363--1583396 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1583353 AGGTTTAGGT
1583363 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
1583380 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
1583397 AAATCTATTT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:1592796 original size:37 final size:37
Alignment explanation
Indices: 1592759--1592828 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
1592749 ATATTTTTTA
1592759 AATATTTTACATATTT-ATAT-TTTAAAAAATAAATTT
1 AATATTTT-CATATTTAATATCTTTAAAAAATAAATTT
* **
1592795 AATATTTTCATCTTTAATATCTTTTTAAAATAAA
1 AATATTTTCATATTTAATATCTTTAAAAAATAAA
1592829 AAATAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 6 0.21
36 12 0.41
37 11 0.38
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (37 bp):
AATATTTTCATATTTAATATCTTTAAAAAATAAATTT
Found at i:1595233 original size:46 final size:46
Alignment explanation
Indices: 1595215--1595371 Score: 149
Period size: 46 Copynumber: 3.3 Consensus size: 46
1595205 TGACAAGTGG
* * *
1595215 AAAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
*
1595261 AAAGTGATAAGTGATAGCT-TCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* * *
1595307 AAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
1595359 AAAGTGATAAGTG
1 AAAGTGATAAGTG
1595372 GCTACACTTA
Statistics
Matches: 101, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
46 57 0.56
52 44 0.44
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
Found at i:1595234 original size:52 final size:51
Alignment explanation
Indices: 1595163--1595371 Score: 284
Period size: 52 Copynumber: 4.1 Consensus size: 51
1595153 ATCAAGTGAC
* **
1595163 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
1595215 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1595261 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
1595312 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAGTG
1595365 ATAAGTG
1 A-AAGTG
1595372 GCTACACTTA
Statistics
Matches: 140, Mismatches: 9, Indels: 15
0.85 0.05 0.09
Matches are distributed among these distances:
46 44 0.31
52 86 0.61
53 10 0.07
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:1595269 original size:98 final size:98
Alignment explanation
Indices: 1595149--1595372 Score: 394
Period size: 98 Copynumber: 2.3 Consensus size: 98
1595139 TTTGAGTACT
*
1595149 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
1595214 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
1595247 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
1595312 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
1595345 TCTGATCAAGAGACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
1595373 CTACACTTAT
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 119 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:1595381 original size:37 final size:37
Alignment explanation
Indices: 1595334--1595480 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
1595324 TGATAGCTTC
* *
1595334 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1595371 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
1595408 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
**
1595445 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1595480 G
1 G
1595481 ATCATACGTA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Found at i:1610189 original size:12 final size:12
Alignment explanation
Indices: 1610174--1610198 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1610164 CAATATTTTA
1610174 TATACATATTAT
1 TATACATATTAT
1610186 TATACATATTAT
1 TATACATATTAT
1610198 T
1 T
1610199 CTTGTAACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TATACATATTAT
Found at i:1610613 original size:5 final size:5
Alignment explanation
Indices: 1610603--1610673 Score: 62
Period size: 5 Copynumber: 14.6 Consensus size: 5
1610593 AAAGAAATAT
* *
1610603 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
1610649 -A-TA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT
1610674 ACATAAAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
3 4 0.07
4 8 0.15
5 31 0.56
6 11 0.20
7 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:1610655 original size:19 final size:19
Alignment explanation
Indices: 1610631--1610673 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1610621 ATTATGTTTT
1610631 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
1610650 TATATTATATTATATTATA
1 TATATTATATTATATTATA
1610669 TATAT
1 TATAT
1610674 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:1610704 original size:16 final size:16
Alignment explanation
Indices: 1610683--1610715 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1610673 TACATAAAAC
*
1610683 AAAAGAAAGAATAGAA
1 AAAAGAAAGAAAAGAA
1610699 AAAAGAAAGAAAAGAA
1 AAAAGAAAGAAAAGAA
1610715 A
1 A
1610716 CAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAGAAAGAAAAGAA
Found at i:1611735 original size:46 final size:44
Alignment explanation
Indices: 1611676--1611790 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
1611666 ACAGGACAGA
* *
1611676 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
1611722 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
1611766 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
1611791 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:1611771 original size:44 final size:45
Alignment explanation
Indices: 1611676--1611809 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
1611666 ACAGGACAGA
* *
1611676 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
1611722 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
1611766 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1611810 CAGGGTATTG
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:1614205 original size:13 final size:13
Alignment explanation
Indices: 1614189--1614216 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1614179 CGATTTCTTC
1614189 TGGGTATTCTATA
1 TGGGTATTCTATA
1614202 TGGGTATTCTATA
1 TGGGTATTCTATA
1614215 TG
1 TG
1614217 CTCTTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:1614535 original size:12 final size:12
Alignment explanation
Indices: 1614520--1614583 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
1614510 TTCTTCTTGT
1614520 GGATTTTCTCTG
1 GGATTTTCTCTG
* * *
1614532 GGATATTCTTTT
1 GGATTTTCTCTG
*
1614544 GGACTTTCTCTG
1 GGATTTTCTCTG
* * *
1614556 GGATATTCTTTT
1 GGATTTTCTCTG
1614568 GGATTTTCTCTG
1 GGATTTTCTCTG
1614580 GGAT
1 GGAT
1614584 ATCATCGATC
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.12, C:0.14, G:0.23, T:0.50
Consensus pattern (12 bp):
GGATTTTCTCTG
Found at i:1614546 original size:24 final size:24
Alignment explanation
Indices: 1614513--1614585 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
1614503 AGTGATATTC
*
1614513 TTCTTGTGGATTTTCTCTGGGATA
1 TTCTTTTGGATTTTCTCTGGGATA
*
1614537 TTCTTTTGGACTTTCTCTGGGATA
1 TTCTTTTGGATTTTCTCTGGGATA
1614561 TTCTTTTGGATTTTCTCTGGGATA
1 TTCTTTTGGATTTTCTCTGGGATA
1614585 T
1 T
1614586 CATCGATCTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.12, C:0.14, G:0.22, T:0.52
Consensus pattern (24 bp):
TTCTTTTGGATTTTCTCTGGGATA
Found at i:1616165 original size:5 final size:5
Alignment explanation
Indices: 1616155--1616225 Score: 62
Period size: 5 Copynumber: 14.6 Consensus size: 5
1616145 AAAGAAATAT
* *
1616155 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
1616201 -A-TA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT
1616226 ACATAAAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
3 4 0.07
4 8 0.15
5 31 0.56
6 11 0.20
7 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:1616207 original size:19 final size:19
Alignment explanation
Indices: 1616183--1616225 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1616173 ATTATGTTTT
1616183 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
1616202 TATATTATATTATATTATA
1 TATATTATATTATATTATA
1616221 TATAT
1 TATAT
1616226 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:1616256 original size:16 final size:16
Alignment explanation
Indices: 1616235--1616267 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1616225 TACATAAAAC
*
1616235 AAAAGAAAGAATAGAA
1 AAAAGAAAGAAAAGAA
1616251 AAAAGAAAGAAAAGAA
1 AAAAGAAAGAAAAGAA
1616267 A
1 A
1616268 CAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAGAAAGAAAAGAA
Found at i:1616334 original size:4 final size:4
Alignment explanation
Indices: 1616327--1616360 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1616317 GAGAAGGAAG
1616327 GAAA GAAA GAAA GAAA GAAA GAAA -AAA -AAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1616361 AAGGGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:1617291 original size:46 final size:44
Alignment explanation
Indices: 1617232--1617346 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
1617222 ACAGGACAGA
* *
1617232 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
1617278 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
1617322 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
1617347 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:1617327 original size:44 final size:45
Alignment explanation
Indices: 1617232--1617365 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
1617222 ACAGGACAGA
* *
1617232 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
1617278 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
1617322 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1617366 CAGGGTATTG
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:1626861 original size:132 final size:132
Alignment explanation
Indices: 1626622--1627437 Score: 1409
Period size: 132 Copynumber: 6.2 Consensus size: 132
1626612 GGATGGATTG
*
1626622 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
* * *
1626687 ATCTTCCTATATTGGTAGGAAGTGGATCGACGACGCAAATCTTGTCTTCCCATACTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
1626752 GT
131 GT
*
1626754 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1626819 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
1626884 GT
131 GT
* *
1626886 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
* *
1626951 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGACGCAGATCTTGTCTTCCCATACTGGTGACGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
1627016 GT
131 GT
*
1627018 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
* *
1627083 ATCTTCCTATATTGGTAGGAAGTGGATCGAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
1627148 GT
131 GT
* * * *
1627150 AGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
*
1627215 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
1627280 GT
131 GT
*
1627282 AGATCACAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
* * *
1627347 ATCTTCCTATATTGATAGGAAGTGGATTC-AAGATACAGATCTTGTCTTCCCATACTGGTGGTGA
66 ATCTTCCTATATTGGTAGGAAGTGGA-TCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGA
1627411 AGT
130 AGT
* *
1627414 AGATCGAAGAAAGCAGATATTGTC
1 AGATCGCAGAAAGCAGATCTTGTC
1627438 CCTGTATTTG
Statistics
Matches: 652, Mismatches: 31, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
132 650 1.00
133 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (132 bp):
AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
GT
Found at i:1627663 original size:40 final size:42
Alignment explanation
Indices: 1627566--1627731 Score: 187
Period size: 42 Copynumber: 4.0 Consensus size: 42
1627556 CCGATAACTC
1627566 ATCTCCCTAAGCAGTAGTGGAGCAGACAAAACCACAGATCTT
1 ATCTCCCTAAGCAGTAGTGGAGCAGACAAAACCACAGATCTT
* ** *
1627608 ATCTCCCTAAACAGTAGTGGAGCAGATC-GCATCA-AG-TCTT
1 ATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAACCACAGATCTT
* *
1627648 ATCTCCTTAAGCAGTAGCGGAGCAGA-AGAAACCACAGATCTT
1 ATCTCCCTAAGCAGTAGTGGAGCAGACA-AAACCACAGATCTT
** * *
1627690 ATCTCCCTAAATAGTAGTGGAGCAGACTAAAAACACAAATCT
1 ATCTCCCTAAGCAGTAGTGGAGCAGAC-AAAACCACAGATCT
1627732 CATCCCCATG
Statistics
Matches: 101, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
40 30 0.30
41 4 0.04
42 54 0.53
43 12 0.12
44 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
ATCTCCCTAAGCAGTAGTGGAGCAGACAAAACCACAGATCTT
Found at i:1629466 original size:12 final size:12
Alignment explanation
Indices: 1629451--1629475 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1629441 AATATTTTTA
1629451 TATACATATTAT
1 TATACATATTAT
1629463 TATACATATTAT
1 TATACATATTAT
1629475 T
1 T
1629476 CTCATTGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TATACATATTAT
Found at i:1632717 original size:16 final size:17
Alignment explanation
Indices: 1632693--1632737 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1632683 GCAATTAGGG
1632693 TTAGAGTTTTAAGAATT
1 TTAGAGTTTTAAGAATT
*
1632710 TT-GAGTTTTTA-AATT
1 TTAGAGTTTTAAGAATT
*
1632725 TTAGGGTTTTAAG
1 TTAGAGTTTTAAG
1632738 GAAAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 6 0.26
16 15 0.65
17 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (17 bp):
TTAGAGTTTTAAGAATT
Found at i:1632848 original size:96 final size:96
Alignment explanation
Indices: 1632724--1632926 Score: 250
Period size: 96 Copynumber: 2.1 Consensus size: 96
1632714 GTTTTTAAAT
* ** *
1632724 TTTAGGG-TTTTAAGGAAAAAAATTAAATAAATTAAGGTTTAGTGTTTGTTAATTAAATTAATTA
1 TTTAGGGTTTTTAAGG-AAAAAATTAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTA
* * * * *
1632788 CTAATTTTAAAAAATTAGATTATGA-TTTAGTG
65 -TAAGTTAAAAAAAATAGATTAGGATTTTAGGG
* * *
1632820 TTTATGGTTTTTAAGG-AAAAATTAAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTA
1 TTTAGGGTTTTTAAGGAAAAAATT-AAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTA
1632884 TAAGTTAAAAAAAATAGATTAGGATTTTAGGG
65 TAAGTTAAAAAAAATAGATTAGGATTTTAGGG
1632916 TTTAGGGTTTT
1 TTTAGGGTTTT
1632927 AGGGCATTTA
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
95 27 0.30
96 56 0.62
97 8 0.09
ACGTcount: A:0.40, C:0.01, G:0.18, T:0.41
Consensus pattern (96 bp):
TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTAT
AAGTTAAAAAAAATAGATTAGGATTTTAGGG
Found at i:1633412 original size:125 final size:126
Alignment explanation
Indices: 1633014--1633550 Score: 767
Period size: 126 Copynumber: 4.3 Consensus size: 126
1633004 AAAAGCTTCT
* *
1633014 ACGTGGACGCTCTTTTGCTACAGTAGTCTTTGAAAAAATACA-TTTGAGAAGACGTGTCTGCGCA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATA-ATTTTGAGAAGACGTGTCTGCACA
* *
1633078 AATAGTGTCAAAAACACTTTAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
65 AATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * * **
1633140 ACGTAGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAAATTTGAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * * *
1633205 AAAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTTCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * *
1633266 ATGTGGATGCTCTTTTGCTACAGTAGTCTCTGGAAAAATAATTTTGAGAAGACGTGTCTGCACAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * * *
1633331 ATAGTGGT-AAAAACGCTTCAAG-AAGATGCATTTTCAGCAAAATTACTGGAAGAAGCTCCC
66 ATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * * * *
1633391 ACGTGGATGCTCTTTTGCTACAGTGGTCTCTG-AAAAATAATTTTAAGAAGACATGTCTGCATAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* *
1633455 ATAGTGTCAAAAATGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* *
1633516 ACGTGGACGCTCTTTTGCTACAGTGGTTTCTGAAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
1633551 TAACTTGGGC
Statistics
Matches: 370, Mismatches: 36, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
123 2 0.01
124 47 0.13
125 128 0.35
126 191 0.52
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:1633530 original size:250 final size:251
Alignment explanation
Indices: 1633014--1633550 Score: 769
Period size: 250 Copynumber: 2.1 Consensus size: 251
1633004 AAAAGCTTCT
* *
1633014 ACGTGGACGCTCTTTTGCTACAGTAGTCTTTGAAAAAATACATTTGAGAAGACGTGTCTGCGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATACATTTGAGAAGACGTGTCTGCACAA
* *
1633079 ATAGTGTCAAAAACACTTTAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGT
66 ATAGTGTCAAAAACACTTCAAGCAAGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGT
* *
1633144 AGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAAATTTGAGAAGACGTGTCTGTGCAAAAAG
131 AGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAAATTTAAGAAGACATGTC-GTGCAAAAAG
*
1633209 TGTAAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTTCC
195 TGTAAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTCCC
* * *
1633266 ATGTGGATGCTCTTTTGCTACAGTAGTCTCTGGAAAAATA-ATTTTGAGAAGACGTGTCTGCACA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATACA-TTTGAGAAGACGTGTCTGCACA
* * * *
1633330 AATAGTGGT-AAAAACGCTTCAAG-AAGATGCATTTTCAGCAAAATTACTGGAAGAAGCTCCCAC
65 AATAGT-GTCAAAAACACTTCAAGCAAGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCCAC
* * * * *
1633393 GTGGATGCTCTTTTGCTACAGTGGTCTCTG-AAAAATAATTTTAAGAAGACATGTC-TGCATAAA
129 GTAGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAAATTTAAGAAGACATGTCGTGCA-AAA
* * * *
1633456 TAGTGTCAAAAATGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
193 -AGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTCCC
* *
1633516 ACGTGGACGCTCTTTTGCTACAGTGGTTTCTGAAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
1633551 TAACTTGGGC
Statistics
Matches: 253, Mismatches: 28, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
248 4 0.02
249 3 0.01
250 106 0.42
251 63 0.25
252 75 0.30
253 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (251 bp):
ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATACATTTGAGAAGACGTGTCTGCACAA
ATAGTGTCAAAAACACTTCAAGCAAGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGT
AGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAAATTTAAGAAGACATGTCGTGCAAAAAGT
GTAAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTCCC
Found at i:1640707 original size:55 final size:55
Alignment explanation
Indices: 1640645--1640824 Score: 195
Period size: 55 Copynumber: 3.2 Consensus size: 55
1640635 TACATGAAAT
1640645 AATATAAAAATATTTAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTAAA
1 AATATAAAAATATTTAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTAAA
* * * * *
1640700 AATATAAAAATAAATTATAA--TTACTTTATTTAAAACAACCTTTT-ATCTAATTACATGAAA
1 AATATAAAAAT-ATTTAAAATGTTGCTTTATTTAAAATAA--TTTTCAT-T--TT--ATTAAA
* *
1640760 TAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTTCATTTTATTAAA
1 -AATATAAAAATATTTAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTAAA
1640816 AATATAAAA
1 AATATAAAA
1640825 GTAAATTACA
Statistics
Matches: 101, Mismatches: 12, Indels: 24
0.74 0.09 0.18
Matches are distributed among these distances:
54 16 0.16
55 22 0.22
56 16 0.16
58 4 0.04
60 15 0.15
61 13 0.13
62 15 0.15
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (55 bp):
AATATAAAAATATTTAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTAAA
Found at i:1640766 original size:61 final size:60
Alignment explanation
Indices: 1640633--1640886 Score: 209
Period size: 54 Copynumber: 4.4 Consensus size: 60
1640623 TTTATATTTT
* * *
1640633 ATTACATGAAATAATATAAAAAT-ATTTAAAATGTTGCTTTATTTAAAATAA-TTTTCAT-T-
1 ATTACATGAAATAATATAAAAATAAATTAAAA--TTACTTTATTTAAAACAACTTTT-ATCTA
* *
1640692 -TT--ATTAAA-AATATAAAAATAAATTATAATTACTTTATTTAAAACAACCTTTTATCTA
1 ATTACATGAAATAATATAAAAATAAATTAAAATTACTTTATTTAAAACAA-CTTTTATCTA
* * *
1640749 ATTACATGAAATAATATAAAAAT--ATTCAAAATGTTGCCTTATTTAAAATAA-TTTTCAT-T-
1 ATTACATGAAATAATATAAAAATAAATT-AAAA--TTACTTTATTTAAAACAACTTTT-ATCTA
* * *
1640808 -TT--ATTAAA-AATATAAAAGTAAATTACAATTACTTTATTTAAAACAACATTTTATCTA
1 ATTACATGAAATAATATAAAAATAAATTAAAATTACTTTATTTAAAACAAC-TTTTATCTA
1640865 ATTACATGAAATAATATAAAAA
1 ATTACATGAAATAATATAAAAA
1640887 GATTCAAAAT
Statistics
Matches: 154, Mismatches: 18, Indels: 44
0.71 0.08 0.20
Matches are distributed among these distances:
54 31 0.20
55 25 0.16
56 29 0.19
57 3 0.02
58 8 0.05
59 3 0.02
60 18 0.12
61 22 0.14
62 15 0.10
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (60 bp):
ATTACATGAAATAATATAAAAATAAATTAAAATTACTTTATTTAAAACAACTTTTATCTA
Found at i:1640805 original size:116 final size:116
Alignment explanation
Indices: 1640633--1640897 Score: 476
Period size: 116 Copynumber: 2.3 Consensus size: 116
1640623 TTTATATTTT
* *
1640633 ATTACATGAAATAATATAAAAATATTTAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTTCATTTTATTA
* *
1640698 AAAATATAAAAATAAATTATAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAATAAATTACAATTACTTTATTTAAAACAACATTTTATCTA
1640749 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTTCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTTCATTTTATTA
*
1640814 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACATTTTATCTA
66 AAAATATAAAAATAAATTACAATTACTTTATTTAAAACAACATTTTATCTA
*
1640865 ATTACATGAAATAATATAAAAAGATTCAAAATG
1 ATTACATGAAATAATATAAAAATATTCAAAATG
1640898 CTTGTACAAA
Statistics
Matches: 143, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 143 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (116 bp):
ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTTCATTTTATTA
AAAATATAAAAATAAATTACAATTACTTTATTTAAAACAACATTTTATCTA
Found at i:1641311 original size:18 final size:18
Alignment explanation
Indices: 1641285--1641327 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1641275 GACTAAAAAA
* *
1641285 AGGAAACATATAAGGGCT
1 AGGATACATAAAAGGGCT
1641303 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
1641321 AGGATAC
1 AGGATAC
1641328 GTACCTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.12, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:1641428 original size:30 final size:29
Alignment explanation
Indices: 1641381--1641446 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
1641371 GTTGAACTGT
* *
1641381 TGGGCTCGGTGACTGTGTAGGTC-CTGTTGC
1 TGGGC-CGGTGACTGTGT-GGGCACTGTTGA
*
1641411 TGGGCCGAGTGATTGTGTGGGCACTGTTGA
1 TGGGCCG-GTGACTGTGTGGGCACTGTTGA
1641441 TGGGCC
1 TGGGCC
1641447 TGCGTCGTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.09, C:0.18, G:0.42, T:0.30
Consensus pattern (29 bp):
TGGGCCGGTGACTGTGTGGGCACTGTTGA
Found at i:1643058 original size:46 final size:46
Alignment explanation
Indices: 1642991--1643083 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
1642981 TTGCATTTGT
1642991 TCAACGGATATATGTTTATCATTGAAGCGAATTAGTTCTCCGACCA
1 TCAACGGATATATGTTTATCATTGAAGCGAATTAGTTCTCCGACCA
1643037 TCAACGGATATATGTTTATCATTGAAGCGAATTAGTTCTCCGACCA
1 TCAACGGATATATGTTTATCATTGAAGCGAATTAGTTCTCCGACCA
1643083 T
1 T
1643084 TGCTAACATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (46 bp):
TCAACGGATATATGTTTATCATTGAAGCGAATTAGTTCTCCGACCA
Found at i:1643182 original size:22 final size:22
Alignment explanation
Indices: 1643170--1643219 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
1643160 TAACGAGAGT
1643170 TTTGAGAGGAATTTAAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
* *
1643192 TTTGAGA-G-ATTTGAGAGGAA
1 TTTGAGAGGAATTTAAGAGAAA
1643212 TTTGAGAG
1 TTTGAGAG
1643220 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:1643227 original size:11 final size:10
Alignment explanation
Indices: 1643170--1643227 Score: 64
Period size: 11 Copynumber: 5.5 Consensus size: 10
1643160 TAACGAGAGT
1643170 TTTGAGAGGAA
1 TTTGAGA-GAA
*
1643181 TTTAAGAGAAA
1 TTTGAGAG-AA
1643192 TTTGAGAG-A
1 TTTGAGAGAA
1643201 TTTGAGAGGAA
1 TTTGAGA-GAA
1643212 TTTGAGAGAA
1 TTTGAGAGAA
1643222 TATTGA
1 T-TTGA
1643228 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:1643233 original size:31 final size:31
Alignment explanation
Indices: 1643170--1643233 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1643160 TAACGAGAGT
*
1643170 TTTGAGAGGAATTTAAGAGAAATTTGAGAGA
1 TTTGAGAGGAATTTAAGAGAAATTTGAAAGA
*
1643201 TTTGAGAGGAATTTGAGAG-AATATTGAAAGA
1 TTTGAGAGGAATTTAAGAGAAAT-TTGAAAGA
1643232 TT
1 TT
1643234 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:1649859 original size:23 final size:22
Alignment explanation
Indices: 1649807--1649860 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
1649797 AATTGTTTTT
* * *
1649807 TTATTTAATTTGTAATTTAATA
1 TTATTTTATTTGTAAGTGAATA
*
1649829 TAATTTTTATTTGTACAGTGAATA
1 TTA-TTTTATTTGTA-AGTGAATA
1649853 TTATTTTA
1 TTATTTTA
1649861 AAGGTTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.08
23 15 0.60
24 8 0.32
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (22 bp):
TTATTTTATTTGTAAGTGAATA
Found at i:1657664 original size:23 final size:23
Alignment explanation
Indices: 1657636--1657685 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1657626 CTTGAATAAA
1657636 AAATTAGGTAATTATTTAAAAAT
1 AAATTAGGTAATTATTTAAAAAT
*
1657659 AAATTAGGTAATTTTTTAAAAAT
1 AAATTAGGTAATTATTTAAAAAT
1657682 AAAT
1 AAAT
1657686 AGTTCTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (23 bp):
AAATTAGGTAATTATTTAAAAAT
Found at i:1658646 original size:18 final size:16
Alignment explanation
Indices: 1658615--1658656 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
1658605 AATTTTATTT
1658615 TTAAAAATTAAAATTA
1 TTAAAAATTAAAATTA
1658631 TTAAAAAGTATAAAATTA
1 TTAAAAA-T-TAAAATTA
*
1658649 TAAAAAAT
1 TTAAAAAT
1658657 CATTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 2 0.09
18 14 0.61
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
TTAAAAATTAAAATTA
Found at i:1658647 original size:39 final size:40
Alignment explanation
Indices: 1658572--1658647 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
1658562 TTTAGTTAAC
*
1658572 TTTTTAAAATTTTAAAATTTCAAAAACTATATAAATTTTA
1 TTTTTAAAATATTAAAATTTCAAAAACTATATAAATTTTA
* *
1658612 TTTTTAAAA-ATTAAAATTATTAAAAAGTATA-AAATT
1 TTTTTAAAATATTAAAATT-TCAAAAACTATATAAATT
1658648 ATAAAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 13 0.41
40 19 0.59
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (40 bp):
TTTTTAAAATATTAAAATTTCAAAAACTATATAAATTTTA
Found at i:1658897 original size:50 final size:51
Alignment explanation
Indices: 1658820--1658916 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 51
1658810 GCACCAGAAA
* * *
1658820 ATACTAGTGTCGCTCATCTCTCTCCCTCCACCCTTAAAAAA-TATTTTTTT
1 ATACTAGTATCGCCCATCTCTCCCCCTCCACCCTTAAAAAACTATTTTTTT
* *
1658870 ATACTGGTATCGCCCATCTCTCCCCCTCCACCTTTAAAAAACTATTT
1 ATACTAGTATCGCCCATCTCTCCCCCTCCACCCTTAAAAAACTATTT
1658917 AAAAAAAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 36 0.88
51 5 0.12
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.36
Consensus pattern (51 bp):
ATACTAGTATCGCCCATCTCTCCCCCTCCACCCTTAAAAAACTATTTTTTT
Found at i:1659861 original size:15 final size:15
Alignment explanation
Indices: 1659843--1659888 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1659833 TAATTATTTA
1659843 ATTTTAAATTAAAAT
1 ATTTTAAATTAAAAT
*
1659858 ATTTTAAAATAAAA-
1 ATTTTAAATTAAAAT
* *
1659872 AATTT-AATAAAAAT
1 ATTTTAAATTAAAAT
1659886 ATT
1 ATT
1659889 ATTTTCATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATTAAAAT
Found at i:1660381 original size:12 final size:12
Alignment explanation
Indices: 1660364--1660411 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
1660354 TAAATTGTTA
*
1660364 TTAAAAAGTATT
1 TTAAAAAATATT
1660376 TTAAAAAATATT
1 TTAAAAAATATT
**
1660388 TTAAAATTTA-T
1 TTAAAAAATATT
*
1660399 TAAAAAAATATT
1 TTAAAAAATATT
1660411 T
1 T
1660412 GATGCATCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:1663242 original size:13 final size:13
Alignment explanation
Indices: 1663224--1663250 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1663214 AAAGTGAAAC
1663224 CAACAGTTTATAT
1 CAACAGTTTATAT
1663237 CAACAGTTTATAT
1 CAACAGTTTATAT
1663250 C
1 C
1663251 GAATTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (13 bp):
CAACAGTTTATAT
Found at i:1665173 original size:55 final size:54
Alignment explanation
Indices: 1665112--1665292 Score: 281
Period size: 55 Copynumber: 3.3 Consensus size: 54
1665102 TTATCCATTT
* *
1665112 TCAATAAAATAAAATATGAATGTTCTTAAACCATAGATTTATCACTTACCCTATC
1 TCAATAAAATAAAATATGAATATT-TTAAACCATAGATTTATCACTTATCCTATC
* * *
1665167 TCAATAAAATAAAATATGAATATTTTTAAAGCATAGACTTATCACATATCCTATC
1 TCAATAAAATAAAATATGAATA-TTTTAAACCATAGATTTATCACTTATCCTATC
*
1665222 TCAATAAAATAAAATATGAATATTTGTAAACCATAGATTTATCACTTATTCTATC
1 TCAATAAAATAAAATATGAATATTT-TAAACCATAGATTTATCACTTATCCTATC
1665277 TCAATAAAATAAAATA
1 TCAATAAAATAAAATA
1665293 AAATAAATAA
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:1669042 original size:16 final size:17
Alignment explanation
Indices: 1669011--1669043 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1669001 TTCATAAGTA
1669011 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
1669028 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
1669044 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:1669389 original size:46 final size:45
Alignment explanation
Indices: 1669329--1669599 Score: 344
Period size: 46 Copynumber: 5.9 Consensus size: 45
1669319 TTTGACATGA
* * *** *
1669329 TGCCATAGTGTCTTTCAACCATGGTCTTGTTCATTTCATGTTACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT-TTACGT
* * *
1669375 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCCTGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTAC-GT
* *
1669421 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT-TTACGT
* *
1669467 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCCTGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTAC-GT
* * *
1669513 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT-TTACGT
*
1669559 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATTT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTT
1669600 CAGAAAGCAC
Statistics
Matches: 195, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
45 3 0.02
46 192 0.98
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTACGT
Found at i:1669486 original size:92 final size:92
Alignment explanation
Indices: 1669329--1669597 Score: 430
Period size: 92 Copynumber: 2.9 Consensus size: 92
1669319 TTTGACATGA
* * *** * * **
1669329 TGCCATAGTGTCTTTCAACCATGGTCTTGTTCATTTCATGTTACATTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
*
1669394 CATGGTCTTACACATTTTATATCCTGT
66 CATGGTCTTACACATTTCATATCCTGT
1669421 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
1669486 CATGGTCTTACACATTTCATATCCTGT
66 CATGGTCTTACACATTTCATATCCTGT
* *
1669513 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCATGTTGCCATGGTGTCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
1669578 CATGGTCTTACACATTTCAT
66 CATGGTCTTACACATTTCAT
1669598 TTCAGAAAGC
Statistics
Matches: 165, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 165 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCCTGT
Found at i:1669577 original size:138 final size:138
Alignment explanation
Indices: 1669324--1669597 Score: 433
Period size: 138 Copynumber: 2.0 Consensus size: 138
1669314 TTATCTTTGA
* *** *
1669324 CATGATGCCATAGTGTCTTTCAACCATGGTCTTGTTCATTTCATGTTACATTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATGATACATTGCCATGGTATCTT
*
1669389 TCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
66 TCAACCATGGTCTTACACATTTTATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1669454 TTTCATAT
131 TTTCATAT
* * * *
1669462 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT-ATCCTGTTGCCATGGTATCT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATGATAC-ATTGCCATGGTATCT
*
1669526 TTCAACCATGGTCTTACACATTTTATATCATGTTGCCATGGTGTCTTTCAACCATGGTCTTACAC
65 TTCAACCATGGTCTTACACATTTTATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1669591 ATTTCAT
130 ATTTCAT
1669598 TTCAGAAAGC
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
137 2 0.02
138 122 0.98
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (138 bp):
CATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATGATACATTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTTATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
TTTCATAT
Found at i:1669620 original size:35 final size:35
Alignment explanation
Indices: 1669574--1669645 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1669564 TGGTGTCTTT
1669574 CAACCATGGTCTTACACATTTCATTTCAGAAAGCA
1 CAACCATGGTCTTACACATTTCATTTCAGAAAGCA
1669609 CAACCATGGTCTTACACATTTCATTTCAGAAAGCA
1 CAACCATGGTCTTACACATTTCATTTCAGAAAGCA
1669644 CA
1 CA
1669646 CTCCCGCGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (35 bp):
CAACCATGGTCTTACACATTTCATTTCAGAAAGCA
Found at i:1671813 original size:11 final size:13
Alignment explanation
Indices: 1671793--1671824 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1671783 AATAAAATAA
1671793 TAAAATATC-ATT
1 TAAAATATCAATT
1671805 TAAAA-ATCAATT
1 TAAAATATCAATT
1671817 TAAAATAT
1 TAAAATAT
1671825 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 13 0.72
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCAATT
Found at i:1674276 original size:17 final size:18
Alignment explanation
Indices: 1674251--1674284 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1674241 ATATAAACAT
1674251 TATTAAAAAAAT-AATTG
1 TATTAAAAAAATCAATTG
*
1674268 TATTCAAAAAATCAATT
1 TATTAAAAAAATCAATT
1674285 TAAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
TATTAAAAAAATCAATTG
Found at i:1675162 original size:23 final size:23
Alignment explanation
Indices: 1675131--1675176 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1675121 GACTTCAGCA
1675131 TTATGTA-TTACTTAAAATATATT
1 TTATGTATTTACTTAAAAT-TATT
* *
1675154 TTATTTATTTATTTAAAATTATT
1 TTATGTATTTACTTAAAATTATT
1675177 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:1686310 original size:13 final size:13
Alignment explanation
Indices: 1686294--1686322 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1686284 TATTCCGTAA
1686294 AAAAAATGTATAC
1 AAAAAATGTATAC
1686307 AAAAAATGTATAC
1 AAAAAATGTATAC
1686320 AAA
1 AAA
1686323 TCAATACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAAAATGTATAC
Found at i:1686488 original size:29 final size:31
Alignment explanation
Indices: 1686446--1686507 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
1686436 TAATAAAAGT
*
1686446 AAAATTGTACTTTAACCCCTTA-AAATTATA
1 AAAATTGTAATTTAACCCCTTATAAATTATA
* *
1686476 AAAATT-TAATTTAATCCTTTATAAATTATA
1 AAAATTGTAATTTAACCCCTTATAAATTATA
1686506 AA
1 AA
1686508 GATATAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (31 bp):
AAAATTGTAATTTAACCCCTTATAAATTATA
Found at i:1689788 original size:21 final size:22
Alignment explanation
Indices: 1689777--1689819 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
1689767 TCTTTAATTA
1689777 TAAATT-ATTATTTTATACATT
1 TAAATTAATTATTTTATACATT
1689798 TAAATTAATTATATTTAATACA
1 TAAATTAATTAT-TTT-ATACA
1689820 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:1689831 original size:24 final size:25
Alignment explanation
Indices: 1689775--1689832 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
1689765 ATTCTTTAAT
* **
1689775 TATAAATTATTATTTTATACATTTA
1 TATAAATTATTATTTAATACAAATA
* *
1689800 AATTAATTA-TATTTAATACAAATA
1 TATAAATTATTATTTAATACAAATA
1689824 TATAAATTA
1 TATAAATTA
1689833 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:1699486 original size:29 final size:29
Alignment explanation
Indices: 1699446--1699523 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
1699436 TGTTATAAAT
*
1699446 AATCTATTTTCGTAAATAATGTATCTGGC
1 AATCTATTTTCGTAAATAATGTATCTGAC
*
1699475 AATCTATTTTCGTAAATAATGTATCTGAT
1 AATCTATTTTCGTAAATAATGTATCTGAC
* *
1699504 AATCTATTTTCATATATAAT
1 AATCTATTTTCGTAAATAAT
1699524 AATTTTTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.45
Consensus pattern (29 bp):
AATCTATTTTCGTAAATAATGTATCTGAC
Found at i:1701191 original size:24 final size:24
Alignment explanation
Indices: 1701148--1701206 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
1701138 CGTTACAGCA
1701148 ATTA-ATTG-TCT-CTTTTTTCAG
1 ATTATATTGTTCTACTTTTTTCAG
1701169 ATTATATTGTTCTACTTTTTTCAG
1 ATTATATTGTTCTACTTTTTTCAG
*
1701193 ATTATGTTGTTCTA
1 ATTATATTGTTCTA
1701207 ACAATTTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 3 0.09
24 23 0.68
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (24 bp):
ATTATATTGTTCTACTTTTTTCAG
Found at i:1702076 original size:33 final size:33
Alignment explanation
Indices: 1702024--1702110 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
1702014 ACAGTACTTT
* **
1702024 GCTCCTTCCAGCTCCTATCCACCACCATACTCC
1 GCTCCTTCTAGCTAGTATCCACCACCATACTCC
* *
1702057 GCTTCTTCTAGCTAGTATCCACCACCGTACTCC
1 GCTCCTTCTAGCTAGTATCCACCACCATACTCC
* *
1702090 GCTCCTTCTGGCTCGTATCCA
1 GCTCCTTCTAGCTAGTATCCA
1702111 TCGACATTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.16, C:0.44, G:0.11, T:0.29
Consensus pattern (33 bp):
GCTCCTTCTAGCTAGTATCCACCACCATACTCC
Found at i:1702147 original size:99 final size:99
Alignment explanation
Indices: 1701976--1702154 Score: 234
Period size: 99 Copynumber: 1.8 Consensus size: 99
1701966 TATCTTCAGC
* * * * * *
1701976 CCACCATCGTACTCCGTTCCTTCCGGCTCGTATCCATTACAGTACTTTGCTCCTTCCAGCTCCTA
1 CCACCACCGTACTCCGCTCCTTCCGGCTCGTATCCATGACAGTACTCTACTCCTCCCAGCTCCTA
1702041 TCCACCACCATACTCCGCTTCTTCTAGCTAGTAT
66 TCCACCACCATACTCCGCTTCTTCTAGCTAGTAT
* * * * **
1702075 CCACCACCGTACTCCGCTCCTTCTGGCTCGTATCCATCGACA-TTCTCTACTCGTCCCGGCTTGT
1 CCACCACCGTACTCCGCTCCTTCCGGCTCGTATCCAT-GACAGTACTCTACTCCTCCCAGCTCCT
1702139 ATCCACCACCATACTC
65 ATCCACCACCATACTC
1702155 TACTCCTCCA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
99 64 0.96
100 3 0.04
ACGTcount: A:0.17, C:0.41, G:0.12, T:0.30
Consensus pattern (99 bp):
CCACCACCGTACTCCGCTCCTTCCGGCTCGTATCCATGACAGTACTCTACTCCTCCCAGCTCCTA
TCCACCACCATACTCCGCTTCTTCTAGCTAGTAT
Found at i:1711301 original size:22 final size:23
Alignment explanation
Indices: 1711275--1711319 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1711265 ACCTGATCAG
1711275 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
*
1711297 AATACGACACATAAAGTGTCTGA
1 AATACGACACATAAAGTGCCTGA
1711320 TCAGTAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:1711579 original size:23 final size:23
Alignment explanation
Indices: 1711490--1711580 Score: 76
Period size: 23 Copynumber: 3.7 Consensus size: 23
1711480 GATTCCATCC
* *
1711490 AAACACACCAAAAT-GTCCAACCA
1 AAACACACCAAAATAATCC-TCCA
**
1711513 AAACACACCAGTATAATCCTCCA
1 AAACACACCAAAATAATCCTCCA
*
1711536 AAACACACCAGTATCATATAATCCTCCC
1 AAACACACCA--A--A-ATAATCCTCCA
1711564 AAACACACCAAAATAAT
1 AAACACACCAAAATAAT
1711581 ATAATCCATC
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
23 30 0.55
24 4 0.07
26 1 0.02
28 20 0.36
ACGTcount: A:0.48, C:0.33, G:0.03, T:0.15
Consensus pattern (23 bp):
AAACACACCAAAATAATCCTCCA
Found at i:1711607 original size:29 final size:28
Alignment explanation
Indices: 1711524--1711607 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
1711514 AACACACCAG
* *
1711524 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
* *
1711552 TATAATCCTCCCAAACACACCAAAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
1711580 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
1711608 GCACAAAGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 32 0.65
29 17 0.35
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:1714205 original size:17 final size:17
Alignment explanation
Indices: 1714185--1714237 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1714175 ATCATTTCCC
1714185 ACAATTTTGCATTTGAT
1 ACAATTTTGCATTTGAT
***
1714202 ACAATTTAAT-CATTTCCC
1 ACAATTT--TGCATTTGAT
1714220 ACAATTTTGCATTTGAT
1 ACAATTTTGCATTTGAT
1714237 A
1 A
1714238 AAATATTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
16 1 0.04
17 13 0.48
18 12 0.44
19 1 0.04
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (17 bp):
ACAATTTTGCATTTGAT
Found at i:1714209 original size:35 final size:35
Alignment explanation
Indices: 1714170--1714237 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
1714160 ATACTAACTT
1714170 ATTTAATCATTTCCCACAATTTTGCATTTGATACA
1 ATTTAATCATTTCCCACAATTTTGCATTTGATACA
1714205 ATTTAATCATTTCCCACAATTTTGCATTTGATA
1 ATTTAATCATTTCCCACAATTTTGCATTTGATA
1714238 AAATATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (35 bp):
ATTTAATCATTTCCCACAATTTTGCATTTGATACA
Found at i:1714223 original size:18 final size:18
Alignment explanation
Indices: 1714170--1714226 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
1714160 ATACTAACTT
1714170 ATTTAATCATTTCCCACA
1 ATTTAATCATTTCCCACA
***
1714188 ATTT--TGCATTTGATACA
1 ATTTAAT-CATTTCCCACA
1714205 ATTTAATCATTTCCCACA
1 ATTTAATCATTTCCCACA
1714223 ATTT
1 ATTT
1714227 TGCATTTGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 1 0.03
17 12 0.40
18 16 0.53
19 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.44
Consensus pattern (18 bp):
ATTTAATCATTTCCCACA
Found at i:1715690 original size:46 final size:46
Alignment explanation
Indices: 1715623--1715798 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
1715613 TGTAACCAGC
*
1715623 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * *
1715669 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGC-TCG--GAC--GTTCGCAT
* * * * * *
1715719 -C-TCA-CGAACTCGGACTCAACTCAATGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
1715762 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1715799 TGCCCAAATA
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 60 0.58
47 24 0.23
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:1715801 original size:93 final size:93
Alignment explanation
Indices: 1715631--1715802 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
1715621 GCCCATAAGT
** *
1715631 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
1715696 CGAGCTTAGATGCCTAGTTACATCTCAC
66 CGAGCTCAGATGCCTAGTTACATCTCAC
* *
1715724 GAACTCGGACTCAACTCAATGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
1715789 CGAGCTCGGATGCC
66 CGAGCTCAGATGCC
1715803 CAAATATTCC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCAGATGCCTAGTTACATCTCAC
Found at i:1721581 original size:27 final size:27
Alignment explanation
Indices: 1721528--1721581 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1721518 CCTGACAGGT
* *
1721528 GCGACATGTTGAGCCTGTCAGGTAGGC
1 GCGACATGTCGAGCCTCTCAGGTAGGC
*
1721555 GCGACATGTCGTGCCTACTCAGG-AGGC
1 GCGACATGTCGAGCCT-CTCAGGTAGGC
1721582 TCAACCCGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.20
Consensus pattern (27 bp):
GCGACATGTCGAGCCTCTCAGGTAGGC
Found at i:1721824 original size:28 final size:28
Alignment explanation
Indices: 1721770--1721829 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
1721760 CATTACTAAA
*
1721770 AAATAAATTTATTGCACAACCATTTTAG
1 AAATAAATTTATTGCACAACCATTTTAC
1721798 AAATAAATTTTATTGCACCAA-CA-TTTAC
1 AAATAAA-TTTATTGCA-CAACCATTTTAC
1721826 AAAT
1 AAAT
1721830 TTTATTGCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 15 0.52
29 11 0.38
30 3 0.10
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (28 bp):
AAATAAATTTATTGCACAACCATTTTAC
Found at i:1722576 original size:22 final size:22
Alignment explanation
Indices: 1722551--1722600 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1722541 ATTATATGTG
1722551 TTAAATAAA-ACATTT-TTTATTT
1 TTAAATAAATA-ATTTATTTA-TT
1722573 TTAAATAAATAATTTATTTATT
1 TTAAATAAATAATTTATTTATT
1722595 TTAAAT
1 TTAAAT
1722601 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:1740379 original size:17 final size:17
Alignment explanation
Indices: 1740357--1740390 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1740347 TTGTAGACTA
1740357 AAGGCAAAACTAGCCTC
1 AAGGCAAAACTAGCCTC
1740374 AAGGCAAAACTAGCCTC
1 AAGGCAAAACTAGCCTC
1740391 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:1740858 original size:6 final size:7
Alignment explanation
Indices: 1740841--1740865 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1740831 AGATCATTTC
1740841 AAAAAAT
1 AAAAAAT
1740848 AAAAAAT
1 AAAAAAT
1740855 AAAAAAT
1 AAAAAAT
1740862 AAAA
1 AAAA
1740866 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:1741520 original size:35 final size:34
Alignment explanation
Indices: 1741493--1741573 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 34
1741483 TTTTACATTT
* * *
1741493 TTTATAAATTATTAATATTTTTTATTTTT-TATTT
1 TTTATAAATT-TTAAAATTATATATTTTTATATTT
1741527 TTT-TAAAATTTTAAAATTATATATTTTTATTATTT
1 TTTAT-AAATTTTAAAATTATATATTTTTA-TATTT
1741562 TTTAATAAATTT
1 TTT-ATAAATTT
1741574 ATAAGTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
33 16 0.41
34 8 0.21
35 8 0.21
36 6 0.15
37 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (34 bp):
TTTATAAATTTTAAAATTATATATTTTTATATTT
Found at i:1741588 original size:34 final size:32
Alignment explanation
Indices: 1741515--1741590 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 32
1741505 TAATATTTTT
*
1741515 TATTTTTTA-TTTTTTTAAAATTTTAAAATTA
1 TATTTTTTATTTTTTTTAAAAATTTAAAATTA
*
1741546 TATATTTTTATTATTTTTTAATAAATTTATAAGTTA
1 TAT-TTTTTATT-TTTTTTAA-AAATTTA-AAATTA
1741582 T-TTTTTTAT
1 TATTTTTTAT
1741591 AAATTTGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 3 0.08
32 6 0.16
33 1 0.03
34 15 0.39
35 7 0.18
36 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (32 bp):
TATTTTTTATTTTTTTTAAAAATTTAAAATTA
Found at i:1741649 original size:24 final size:25
Alignment explanation
Indices: 1741622--1741670 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1741612 GAATTTAGAC
* *
1741622 AAATAATTATCTATT-TTTTTTTAT
1 AAATAATAATCTATTAATTTTTTAT
*
1741646 AAATAATAATTTATTAATTTTTTAT
1 AAATAATAATCTATTAATTTTTTAT
1741671 TTAACATGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
AAATAATAATCTATTAATTTTTTAT
Found at i:1741780 original size:23 final size:24
Alignment explanation
Indices: 1741729--1741786 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
1741719 AAGATAAAAA
*
1741729 TATAATATTTAATTTAAAATTGAG
1 TATAATATTAAATTTAAAATTGAG
**
1741753 T-TAATATTAAATTTAAAATT-TT
1 TATAATATTAAATTTAAAATTGAG
1741775 TATAATATTAAA
1 TATAATATTAAA
1741787 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:1742297 original size:36 final size:36
Alignment explanation
Indices: 1742247--1742325 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
1742237 ACTTCACAAC
* *
1742247 TTAGCCGTTCCTTCTATTTCTTCTTTCTGTTTCAGT
1 TTAGCTGTTCCTTCTATTTCTTCCTTCTGTTTCAGT
* *
1742283 TTAGCTGTTTCTTCTGTTTCTTCCTTCTGTTTCAGT
1 TTAGCTGTTCCTTCTATTTCTTCCTTCTGTTTCAGT
1742319 TTAGCTG
1 TTAGCTG
1742326 CTTCACAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.08, C:0.23, G:0.14, T:0.56
Consensus pattern (36 bp):
TTAGCTGTTCCTTCTATTTCTTCCTTCTGTTTCAGT
Found at i:1748377 original size:120 final size:120
Alignment explanation
Indices: 1748180--1749759 Score: 3040
Period size: 120 Copynumber: 13.2 Consensus size: 120
1748170 TTTTCAAGTT
1748180 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1748245 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1748300 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1748365 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATT-AA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1748419 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
1748484 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1748539 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1748604 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1748659 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1748724 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1748779 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1748844 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1748899 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
1748964 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1749019 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1749084 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1749139 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
1749204 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1749259 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1749324 TAATATAAGAATATTAATTATTAAGAA-TTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
*
1749378 ATATATTTAATAATAATTATGTT-ATTTATATTTTACAGTATGATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
1749442 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1749497 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
1749562 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1749617 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
1749682 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
1749737 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
1749760 TAAATATGAT
Statistics
Matches: 1440, Mismatches: 17, Indels: 6
0.98 0.01 0.00
Matches are distributed among these distances:
118 67 0.05
119 213 0.15
120 1160 0.81
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
Done.