Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008275.1 Hibiscus syriacus cultivar Beakdansim tig00110933_pilon, whole genome shotgun sequence
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: 1991061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1526418 original size:19 final size:19
Alignment explanation
Indices: 1526354--1526419 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
1526344 AACTTGGACT
1526354 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGG-A-AA
* **
1526375 ATCGCAACGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGAAA
1526396 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
1526415 ATCGC
1 ATCGC
1526420 GTTGCGATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 14 0.38
21 14 0.38
22 1 0.03
23 8 0.22
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:1532530 original size:21 final size:22
Alignment explanation
Indices: 1532486--1532534 Score: 57
Period size: 25 Copynumber: 2.2 Consensus size: 22
1532476 AAATGAAATA
1532486 AAAAAAATAACTTTAGATATGATTT
1 AAAAAAATAAC-TTAGA-ATGA-TT
1532511 AAAAAAATAA-TTAG-ATGATT
1 AAAAAAATAACTTAGAATGATT
1532531 AAAA
1 AAAA
1532535 TTGAACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.25
21 4 0.17
23 4 0.17
25 10 0.42
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (22 bp):
AAAAAAATAACTTAGAATGATT
Found at i:1533326 original size:2 final size:2
Alignment explanation
Indices: 1533310--1533349 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1533300 CGACCAAAGC
*
1533310 TA TA TG TA T- 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 TA TA TA T
1533350 TATTTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1534315 original size:11 final size:11
Alignment explanation
Indices: 1534301--1534325 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1534291 TGTACGTTTT
1534301 TATTTATTTAA
1 TATTTATTTAA
1534312 TATTTATTTAA
1 TATTTATTTAA
1534323 TAT
1 TAT
1534326 ATTTTTTTCT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:1538133 original size:106 final size:106
Alignment explanation
Indices: 1537947--1539361 Score: 2479
Period size: 106 Copynumber: 13.3 Consensus size: 106
1537937 TACAGCCTTT
*
1537947 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
1538012 CGAAGGGACCGCTGGTTGTCAATAAACAAATTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* *
1538053 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACATCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
1538118 CGAAGGGACCACTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
1538159 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1538224 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
1538265 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
1538330 CGAAGGGACCGCTGGTTGTCAATAAACTATTTCCCGATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
1538371 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1538436 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
1538477 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1538542 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
1538583 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1538648 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
1538689 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
1538754 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
1538795 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1538860 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
1538901 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
1538966 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* *
1539007 AGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * * *
1539072 CAAAGGGACCGTTGGTTGTCAACAAATAACTTCTCAATTTT
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* *
1539113 AGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACGACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
1539178 CGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCGATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
1539219 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
1539284 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAGTTCC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
** *
1539325 AGAGCCAATTTCAACTTCACGGCGGAGGATATTGGAC
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
1539362 CTGGAACAAT
Statistics
Matches: 1254, Mismatches: 55, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 1254 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
Found at i:1540347 original size:2 final size:2
Alignment explanation
Indices: 1540331--1540368 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1540321 CGACCAAAGC
*
1540331 TA TA TG TA T- 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 TA TA T
1540369 TATTTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1541334 original size:11 final size:11
Alignment explanation
Indices: 1541320--1541344 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1541310 TGTACGTTTT
1541320 TATTTATTTAA
1 TATTTATTTAA
1541331 TATTTATTTAA
1 TATTTATTTAA
1541342 TAT
1 TAT
1541345 ATTTTTTTCT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:1541389 original size:23 final size:24
Alignment explanation
Indices: 1541344--1541389 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1541334 TTATTTAATA
* *
1541344 TATTTTTTTCTAACATTTTCAATT
1 TATTTTTTTCTAACAATTCCAATT
*
1541368 TATTTTTTT-TAAGAATTCCAAT
1 TATTTTTTTCTAACAATTCCAAT
1541390 CAATCAAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.59
Consensus pattern (24 bp):
TATTTTTTTCTAACAATTCCAATT
Found at i:1541856 original size:9 final size:9
Alignment explanation
Indices: 1541842--1541866 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1541832 TTCAGGGTTG
1541842 GATTAGATT
1 GATTAGATT
1541851 GATTAGATT
1 GATTAGATT
1541860 GATTAGA
1 GATTAGA
1541867 GTTAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (9 bp):
GATTAGATT
Found at i:1547573 original size:11 final size:13
Alignment explanation
Indices: 1547547--1547587 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1547537 AAATTCTCCA
1547547 TTTTCTCTCTTGT
1 TTTTCTCTCTTGT
1547560 TTTTCTCTCTT-T
1 TTTTCTCTCTTGT
1547572 TTAATTCTCT-TTGT
1 TT--TTCTCTCTTGT
1547586 TT
1 TT
1547588 GTTATAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.12
13 13 0.52
14 9 0.36
ACGTcount: A:0.05, C:0.20, G:0.05, T:0.71
Consensus pattern (13 bp):
TTTTCTCTCTTGT
Found at i:1559073 original size:23 final size:23
Alignment explanation
Indices: 1559055--1559113 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
1559045 CTCGTATAAA
1559055 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
1559078 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
1559100 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
1559114 ATATAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:1559889 original size:67 final size:67
Alignment explanation
Indices: 1559717--1559867 Score: 207
Period size: 66 Copynumber: 2.3 Consensus size: 67
1559707 TTCTTCTCAT
* * * * *
1559717 GGGGGAATCGGTTCCCCCCCCT-GGGGTATCGGTTCCCCTATAGCATTCTGGAATTTGATATCCG
1 GGGGGTATCGGTT--CCCCCATGGGGGTATCGATTCCCCTATAGCATTCTGGAATATCATATCCG
1559781 TTGA
64 TTGA
* *
1559785 GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTATAGCATTCTGGAATATCATATCCGTT
1559849 GA
66 GA
1559851 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1559868 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 34 0.45
67 29 0.39
68 12 0.16
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTATAGCATTCTGGAATATCATATCCGTT
GA
Found at i:1565941 original size:23 final size:23
Alignment explanation
Indices: 1565915--1565981 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 23
1565905 CACCACAGCT
*
1565915 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
*
1565938 CGTAGAATTGCACCGAAGTG-CC
1 CGTAGAAATGCACCGAAGTGCCC
* * *
1565960 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1565982 ATATAATGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 20 0.51
23 19 0.49
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1565964 original size:22 final size:22
Alignment explanation
Indices: 1565923--1565981 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
1565913 CTCGTATAAA
1565923 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1565946 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
* *
1565968 TACACCGTAGTGCC
1 TGCACCGAAGTGCC
1565982 ATATAATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 22 0.65
23 12 0.35
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1566757 original size:67 final size:67
Alignment explanation
Indices: 1566585--1566735 Score: 198
Period size: 66 Copynumber: 2.3 Consensus size: 67
1566575 TTCTTCTCAT
* * * * * *
1566585 GGGGGAATCGGTTCCCCCCCCT-GGGGTATCGGTTCCCCTATAGCATTCTGGAATTTGATATCCG
1 GGGGGTATCGGTT--CCCCCATGGGGGTATCGATTCCCCTATAGCATTATGGAATATCATATCCG
1566649 TTGA
64 TTGA
* *
1566653 GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTCTAGCATTATGGAA-ATCATATTCGTT
1 GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTATAGCATTATGGAATATCATATCCGTT
1566717 GA
66 GA
1566719 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1566736 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 34 0.46
67 28 0.38
68 12 0.16
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTATAGCATTATGGAATATCATATCCGTT
GA
Found at i:1572808 original size:23 final size:23
Alignment explanation
Indices: 1572782--1572848 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 23
1572772 CACCACAGCT
*
1572782 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
*
1572805 CGTAGAATTGCACCGAAGTG-CC
1 CGTAGAAATGCACCGAAGTGCCC
* * *
1572827 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1572849 ATATAATGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 20 0.51
23 19 0.49
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1572831 original size:22 final size:22
Alignment explanation
Indices: 1572790--1572848 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
1572780 CTCGTATAAA
1572790 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1572813 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
* *
1572835 TACACCGTAGTGCC
1 TGCACCGAAGTGCC
1572849 ATATAATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 22 0.65
23 12 0.35
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1573621 original size:67 final size:67
Alignment explanation
Indices: 1573449--1573599 Score: 198
Period size: 66 Copynumber: 2.3 Consensus size: 67
1573439 TTCTTCTCAT
* * * * * *
1573449 GGGGGAATCGGTTCCCCCCCCT-GGGGTATCGGTTCCCCTATAGCATTCTGGAATTTGATATCCG
1 GGGGGTATCGGTT--CCCCCATGGGGGTATCGATTCCCCTATAGCATTATGGAATATCATATCCG
1573513 TTGA
64 TTGA
* *
1573517 GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTCTAGCATTATGGAA-ATCATATTCGTT
1 GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTATAGCATTATGGAATATCATATCCGTT
1573581 GA
66 GA
1573583 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1573600 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 34 0.46
67 28 0.38
68 12 0.16
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTATAGCATTATGGAATATCATATCCGTT
GA
Found at i:1577751 original size:2 final size:2
Alignment explanation
Indices: 1577744--1577778 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1577734 ACAATAACAA
1577744 AT AT 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 AT AT A
1577779 CAATTGGTGG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1578387 original size:20 final size:21
Alignment explanation
Indices: 1578342--1578379 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1578332 TTAAAAGTTT
1578342 AAAATTATCATATATTTTAAA
1 AAAATTATCATATATTTTAAA
1578363 AAAATTAT-ATAT-TTTTA
1 AAAATTATCATATATTTTA
1578380 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATTATCATATATTTTAAA
Found at i:1582004 original size:15 final size:16
Alignment explanation
Indices: 1581979--1582016 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1581969 ATATTTACTT
1581979 TATTTTAAAAT-ATAA
1 TATTTTAAAATCATAA
1581994 -ATTTATAAAATCATAA
1 TATTT-TAAAATCATAA
1582010 TATTTTA
1 TATTTTA
1582017 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.20
15 6 0.30
16 6 0.30
17 4 0.20
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTTAAAATCATAA
Found at i:1587614 original size:2 final size:2
Alignment explanation
Indices: 1587607--1587642 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1587597 ATACTAAATA
1587607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1587643 TAAAAATCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1590710 original size:60 final size:60
Alignment explanation
Indices: 1590608--1590764 Score: 172
Period size: 60 Copynumber: 2.6 Consensus size: 60
1590598 CCATGATTCT
* * * * * * * *
1590608 TATTCTATATTGGTCCCTAAACTTTTGGATATTCTAATTTCATCCAT-AAATTATAACTAA
1 TATTCTAAATTGGTCCCCAAACTTTTGAACATTCCAAATTCAT-CATCAAACTATAACCAA
* * **
1590668 TATTCTAAATTGGTCCCCAAACTATTGAACATTCCAAATTCATCATCAAACTATGACCCT
1 TATTCTAAATTGGTCCCCAAACTTTTGAACATTCCAAATTCATCATCAAACTATAACCAA
* *
1590728 TATTCTAAATTAGTCCCCAAACTTTTGAGCATTCCAA
1 TATTCTAAATTGGTCCCCAAACTTTTGAACATTCCAA
1590765 TAATATCCCC
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 3 0.04
60 78 0.96
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (60 bp):
TATTCTAAATTGGTCCCCAAACTTTTGAACATTCCAAATTCATCATCAAACTATAACCAA
Found at i:1590749 original size:31 final size:30
Alignment explanation
Indices: 1590668--1590755 Score: 74
Period size: 29 Copynumber: 2.9 Consensus size: 30
1590658 TTATAACTAA
*
1590668 TATTCTAAATTGGTCCCCAAACTATTGAAC
1 TATTCTAAATTAGTCCCCAAACTATTGAAC
* ** *
1590698 -ATTCCAAATTCA-TCATCAAACTA-TGACCC
1 TATTCTAAATT-AGTCCCCAAACTATTGA-AC
*
1590727 TTATTCTAAATTAGTCCCCAAACTTTTGA
1 -TATTCTAAATTAGTCCCCAAACTATTGA
1590756 GCATTCCAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
28 3 0.07
29 19 0.44
30 1 0.02
31 17 0.40
32 3 0.07
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (30 bp):
TATTCTAAATTAGTCCCCAAACTATTGAAC
Found at i:1591771 original size:20 final size:23
Alignment explanation
Indices: 1591732--1591774 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 23
1591722 AATTACTAAC
1591732 TGATAAGAACAAGATAAATTTTA
1 TGATAAGAACAAGATAAATTTTA
1591755 TGATAA-AA-AAG-TAAATTTTA
1 TGATAAGAACAAGATAAATTTTA
1591775 AACCAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 2 0.10
23 6 0.30
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (23 bp):
TGATAAGAACAAGATAAATTTTA
Found at i:1592765 original size:2 final size:2
Alignment explanation
Indices: 1592758--1592792 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1592748 CGATCCATCT
1592758 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1592793 ATATATATAT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1592797 original size:2 final size:2
Alignment explanation
Indices: 1592792--1592862 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
1592782 TCTCTCTCTC
1592792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1592833 TA T- 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
1592863 CTGCATAATC
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 65 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1595554 original size:43 final size:43
Alignment explanation
Indices: 1595493--1595581 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
1595483 GAAGCAGGAA
1595493 GGTTCCTATAAAGCTGATTTTAAAGGACAGTCACACTTCTTTG
1 GGTTCCTATAAAGCTGATTTTAAAGGACAGTCACACTTCTTTG
1595536 GGTTCCTATAAAGCTGATTTTAAAGGACAGTCACACTTCTTTG
1 GGTTCCTATAAAGCTGATTTTAAAGGACAGTCACACTTCTTTG
1595579 GGT
1 GGT
1595582 ACTAATCACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (43 bp):
GGTTCCTATAAAGCTGATTTTAAAGGACAGTCACACTTCTTTG
Found at i:1604710 original size:2 final size:2
Alignment explanation
Indices: 1604705--1604734 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1604695 TAATTAGAAC
1604705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1604735 TATTATACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1605993 original size:2 final size:2
Alignment explanation
Indices: 1605986--1606029 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1605976 TTATGAAATA
1605986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1606028 AT
1 AT
1606030 TGAACCAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1606573 original size:36 final size:37
Alignment explanation
Indices: 1606506--1606575 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
1606496 GAAAATATTT
**
1606506 ATATATTTTCTTTAAAAAATTTAAATTTATAAAATTC
1 ATATATTTTCTTTAAAAAATTTAAAAATATAAAATTC
* *
1606543 ATATATTTTGTTTACAAAA-TTAAAAATATAAAA
1 ATATATTTTCTTTAAAAAATTTAAAAATATAAAA
1606576 AAGTTTAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 12 0.41
37 17 0.59
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
ATATATTTTCTTTAAAAAATTTAAAAATATAAAATTC
Found at i:1608348 original size:20 final size:20
Alignment explanation
Indices: 1608311--1608348 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1608301 ATTTTGGGTA
1608311 AACTACACATTTAGTTTTCT
1 AACTACACATTTAGTTTTCT
*
1608331 AACTATCACTTTTA-TTTT
1 AACTA-CACATTTAGTTTT
1608349 ATTTTAGTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.29, C:0.18, G:0.03, T:0.50
Consensus pattern (20 bp):
AACTACACATTTAGTTTTCT
Found at i:1611925 original size:15 final size:15
Alignment explanation
Indices: 1611905--1611956 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
1611895 ATTAAAATAG
1611905 TTATTTTAGTTTATA
1 TTATTTTAGTTTATA
*
1611920 TTATTTT--TTT-GA
1 TTATTTTAGTTTATA
*
1611932 GTATTTTAGTTTATA
1 TTATTTTAGTTTATA
*
1611947 TTTTTTTAGT
1 TTATTTTAGT
1611957 ATTTTAGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
14 3 0.10
15 16 0.55
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (15 bp):
TTATTTTAGTTTATA
Found at i:1611936 original size:27 final size:25
Alignment explanation
Indices: 1611906--1611967 Score: 92
Period size: 24 Copynumber: 2.5 Consensus size: 25
1611896 TTAAAATAGT
1611906 TATTTTAGTTTATATTATTTTTTTGAG
1 TATTTTAGTTTATA-TATTTTTTT-AG
1611933 TATTTTAG-TT-TATATTTTTTTAG
1 TATTTTAGTTTATATATTTTTTTAG
1611956 TATTTTAGTTTA
1 TATTTTAGTTTA
1611968 CAACGTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 10 0.30
24 11 0.33
25 2 0.06
26 2 0.06
27 8 0.24
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (25 bp):
TATTTTAGTTTATATATTTTTTTAG
Found at i:1611957 original size:23 final size:25
Alignment explanation
Indices: 1611906--1611967 Score: 92
Period size: 23 Copynumber: 2.5 Consensus size: 25
1611896 TTAAAATAGT
1611906 TATTTTAGTTTATATTATTTTTTTGAG
1 TATTTTAG-TT-TATTATTTTTTTGAG
1611933 TATTTTAGTTTA-TATTTTTTT-AG
1 TATTTTAGTTTATTATTTTTTTGAG
1611956 TATTTTAGTTTA
1 TATTTTAGTTTA
1611968 CAACGTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
23 14 0.40
24 9 0.26
25 2 0.06
26 2 0.06
27 8 0.23
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (25 bp):
TATTTTAGTTTATTATTTTTTTGAG
Found at i:1611976 original size:23 final size:24
Alignment explanation
Indices: 1611926--1611977 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1611916 TATATTATTT
* **
1611926 TTTTGAGTATTTTAGTTTA-TATT
1 TTTTGAGTATTTTAGTTTACAACG
*
1611949 TTTTTAGTATTTTAGTTTACAACG
1 TTTTGAGTATTTTAGTTTACAACG
1611973 TTTTG
1 TTTTG
1611978 TTTTGGGATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.21, C:0.04, G:0.13, T:0.62
Consensus pattern (24 bp):
TTTTGAGTATTTTAGTTTACAACG
Found at i:1612540 original size:2 final size:2
Alignment explanation
Indices: 1612533--1612575 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1612523 AATAAAACAT
1612533 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1612575 T
1 T
1612576 TGTCAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1621311 original size:184 final size:183
Alignment explanation
Indices: 1620994--1621380 Score: 607
Period size: 184 Copynumber: 2.1 Consensus size: 183
1620984 AATAAATTTT
* *
1620994 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
*
1621059 TTTAAGATCCAATAATTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
* * *
1621124 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAA
131 TTATTTTATAATTAGATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAA
* *
1621178 AAATATTAAATATATTATATATAACATTTGGGCTAAGCCCAAACAATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
** * *
1621243 TTTAAGATCCAATAACTTTTAAATTTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-TT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
1621307 TTTATTTTATAATTAGATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
130 TTTATTTTATAATTAGATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
* * *
1621361 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1621381 AATTAGAAAA
Statistics
Matches: 187, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
182 8 0.04
183 21 0.11
184 155 0.83
185 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
TTATTTTATAATTAGATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
Found at i:1627304 original size:26 final size:26
Alignment explanation
Indices: 1627251--1627305 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
1627241 TAACCATGTA
* *
1627251 AATGTGATCCAAGAGGGTCTTGTTTC
1 AATGTGATCCAAAAGGGTATTGTTTC
1627277 AATGTGATCCAAAAGGGTATT-TTATC
1 AATGTGATCCAAAAGGGTATTGTT-TC
1627303 AAT
1 AAT
1627306 TTAGGACCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.35
Consensus pattern (26 bp):
AATGTGATCCAAAAGGGTATTGTTTC
Found at i:1632151 original size:18 final size:17
Alignment explanation
Indices: 1632103--1632142 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
1632093 TAGTCTCTTC
1632103 GATTTTATACATTTTCT
1 GATTTTATACATTTTCT
1632120 GATTTTATACATTTTCT
1 GATTTTATACATTTTCT
1632137 GATTTT
1 GATTTT
1632143 GTTACATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (17 bp):
GATTTTATACATTTTCT
Found at i:1635638 original size:18 final size:18
Alignment explanation
Indices: 1635611--1635645 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1635601 TGAGGAGGCT
1635611 GGGGAATGTGTGGGAATC
1 GGGGAATGTGTGGGAATC
* *
1635629 GGGGAGTGTGTTGGAAT
1 GGGGAATGTGTGGGAAT
1635646 TGAGCAAGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.51, T:0.26
Consensus pattern (18 bp):
GGGGAATGTGTGGGAATC
Found at i:1641116 original size:2 final size:2
Alignment explanation
Indices: 1641109--1641155 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1641099 ATGTAAAAAT
1641109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1641151 TA TA T
1 TA TA T
1641156 CGTATATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1641884 original size:3 final size:3
Alignment explanation
Indices: 1641876--1641918 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1641866 GAATACTCAC
1641876 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1641919 GTTTGTGTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1645359 original size:10 final size:10
Alignment explanation
Indices: 1645331--1645384 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
1645321 AATTAATTAA
**
1645331 AATATTTAAA
1 AATATTTATT
1645341 AATATTTATT
1 AATATTTATT
1645351 AATATTTA-T
1 AATATTTATT
*
1645360 AATATAATATT
1 AATAT-TTATT
1645371 -ATATTT-TT
1 AATATTTATT
1645379 AATATT
1 AATATT
1645385 ATATAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
8 2 0.05
9 12 0.32
10 22 0.59
11 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
AATATTTATT
Found at i:1645374 original size:19 final size:20
Alignment explanation
Indices: 1645347--1645388 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1645337 TAAAAATATT
1645347 TATTAATATTTATAATATAA
1 TATTAATATTTATAATATAA
* *
1645367 TATT-ATATTTTTAATATTA
1 TATTAATATTTATAATATAA
1645386 TAT
1 TAT
1645389 AAAATAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTAATATTTATAATATAA
Found at i:1645406 original size:31 final size:29
Alignment explanation
Indices: 1645342--1645413 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
1645332 ATATTTAAAA
*
1645342 ATATTTATTAATATTTATAATATAATATT
1 ATATTTATTAATATTTATAAAATAATATT
1645371 ATATTT-TTAATATTATATAAAATAATCAATT
1 ATATTTATTAATATT-TATAAAATAAT--ATT
1645402 ATA-TTA-TAATAT
1 ATATTTATTAATAT
1645414 AAGATATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 8 0.21
29 16 0.42
30 8 0.21
31 6 0.16
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
ATATTTATTAATATTTATAAAATAATATT
Found at i:1645458 original size:49 final size:48
Alignment explanation
Indices: 1645353--1645467 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 48
1645343 TATTTATTAA
*
1645353 TATTTATAATATAATATTATATTTTTAATATTATATAAAATAATCAAT
1 TATTTATAATATAATATTATATTTTTAATATTATATAAAATAATAAAT
*
1645401 TATATTATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAAT
1 TAT-TTATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAAT
*
1645452 T-TTTATATATTTAATA
1 TATTTATA-ATATAATA
1645468 ATGAATAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
48 6 0.10
49 19 0.33
50 11 0.19
51 22 0.38
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (48 bp):
TATTTATAATATAATATTATATTTTTAATATTATATAAAATAATAAAT
Found at i:1645464 original size:29 final size:27
Alignment explanation
Indices: 1645412--1645500 Score: 87
Period size: 29 Copynumber: 3.3 Consensus size: 27
1645402 ATATTATAAT
* *
1645412 ATAAGATATTATA-TTTT-TAT-TTTA
1 ATAATATATAATATTTTTATATATTTA
1645436 ATAATATATAATAAATTTTTATATATTTA
1 ATAATATATAAT--ATTTTTATATATTTA
1645465 ATAATGA-ATAATATTATTTATATATTTCA
1 ATAAT-ATATAATATT-TTTATATATTT-A
1645494 ATAATAT
1 ATAATAT
1645501 TTTAGTAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
24 10 0.19
26 1 0.02
27 7 0.13
28 15 0.28
29 20 0.37
30 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (27 bp):
ATAATATATAATATTTTTATATATTTA
Found at i:1645691 original size:20 final size:20
Alignment explanation
Indices: 1645666--1645735 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
1645656 TTTCCAGATG
1645666 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1645686 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
* *
1645706 TTTTACAGAAATGTAATTTA
1 TTTTCCAGAAATGTAATTCA
1645726 TTTTCCAGAA
1 TTTTCCAGAA
1645736 TTCAAATTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1645752 original size:15 final size:15
Alignment explanation
Indices: 1645734--1645799 Score: 82
Period size: 15 Copynumber: 4.4 Consensus size: 15
1645724 TATTTTCCAG
1645734 AATTCAAATTTCAGT
1 AATTCAAATTTCAGT
*
1645749 AATTC-ATTTTCCAGT
1 AATTCAAATTT-CAGT
1645764 AATTCAAA-TTCTAGT
1 AATTCAAATTTC-AGT
*
1645779 AATTCAAATTCCAGT
1 AATTCAAATTTCAGT
1645794 AATTCA
1 AATTCA
1645800 TTTTCTGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
14 5 0.11
15 36 0.82
16 3 0.07
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (15 bp):
AATTCAAATTTCAGT
Found at i:1645770 original size:30 final size:30
Alignment explanation
Indices: 1645718--1645799 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
1645708 TTACAGAAAT
*
1645718 GTAATTTATTTTCCAG-AATTCAAATT-TCA
1 GTAATTCATTTTCCAGTAATTCAAATTCT-A
1645747 GTAATTCATTTTCCAGTAATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCTA
**
1645777 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
1645800 TTTTCTGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
29 15 0.31
30 32 0.67
31 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCTA
Found at i:1652211 original size:311 final size:306
Alignment explanation
Indices: 1651643--1652260 Score: 1175
Period size: 311 Copynumber: 2.0 Consensus size: 306
1651633 TCAAATGGTT
1651643 GAAAGTTATATTTGAACAGATAATACATTTTACTTACTCAAATTAATGGAAAAAATTATAAAATT
1 GAAAGTTATATTTGAACAGATAATACATTTTACTTACTCAAATTAATGGAAAAAATTATAAAATT
1651708 TAAGATTTAAAATTTAAGTAGATAAAAGTTTACACAATAAATAAATAAAAAGTTACTCACACATT
66 TAAGATTTAAAATTTAAGTAGATAAAAGTTTACACAATAAATAAATAAAAAGTTACTCACACATT
1651773 GAGAAACTATTAAGGAGAAATTGGGTGGTTGATCTGAAGCACATACCAAGAGAGGCCAATCGTGT
131 GAGAAACTATTAAGGAGAAATTGGGTGGTTGATCTGAAGCACATACCAAGAGAGGCCAATCGTGT
1651838 TGCTGACTTTGTTGTCAAACAGATGTGGAAGCATCAGGAAGACACAATATTTATGCAAAATTACC
196 TGCTGACTTTGTTGTCAAACAGATGTGGAAGCATCAGGAAGACACAATATTTATGCAAAATTACC
1651903 CTAAGGAAGCTGAGGAATTGTTATTAGCTGATATAACGGGTAGCTA
261 CTAAGGAAGCTGAGGAATTGTTATTAGCTGATATAACGGGTAGCTA
1651949 GAAAGTTATA-TTGAACAGATAATACATTTTACTTACTCAAATTAATGGAAAAAAAAAATTATAA
1 GAAAGTTATATTTGAACAGATAATACATTTTACTTACTCAAATTAATGG----AAAAAATTATAA
1652013 AATTTAAGATTTAAAATTTAAGTAGATAAAAGTTTACACAATAAATAAATAAAAAGTTACTCACA
62 AATTTAAGATTTAAAATTTAAGTAGATAAAAGTTTACACAATAAATAAATAAAAAGTTACTCACA
1652078 CATTGAGAGAAACTATTAAGGAGAAATTGGGTGGTTGATCTGAAGCACATACCAAGAGAGGCCAA
127 CATT--GAGAAACTATTAAGGAGAAATTGGGTGGTTGATCTGAAGCACATACCAAGAGAGGCCAA
1652143 TCGTGTTGCTGACTTTGTTGTCAAACAGATGTGGAAGCATCAGGAAGACACAATATTTATGCAAA
190 TCGTGTTGCTGACTTTGTTGTCAAACAGATGTGGAAGCATCAGGAAGACACAATATTTATGCAAA
1652208 ATTACCCTAAGGAAGCTGAGGAATTGTTATTAGCTGATATAACGGGTAGCTA
255 ATTACCCTAAGGAAGCTGAGGAATTGTTATTAGCTGATATAACGGGTAGCTA
1652260 G
1 G
1652261 GCGGCCCCTT
Statistics
Matches: 306, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
305 38 0.12
306 10 0.03
309 81 0.26
311 177 0.58
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (306 bp):
GAAAGTTATATTTGAACAGATAATACATTTTACTTACTCAAATTAATGGAAAAAATTATAAAATT
TAAGATTTAAAATTTAAGTAGATAAAAGTTTACACAATAAATAAATAAAAAGTTACTCACACATT
GAGAAACTATTAAGGAGAAATTGGGTGGTTGATCTGAAGCACATACCAAGAGAGGCCAATCGTGT
TGCTGACTTTGTTGTCAAACAGATGTGGAAGCATCAGGAAGACACAATATTTATGCAAAATTACC
CTAAGGAAGCTGAGGAATTGTTATTAGCTGATATAACGGGTAGCTA
Found at i:1654436 original size:29 final size:29
Alignment explanation
Indices: 1654403--1654497 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 29
1654393 TTGAGTCCCC
1654403 GACTATTAAAAGTTATGAAATGGTCCCTT
1 GACTATTAAAAGTTATGAAATGGTCCCTT
* * * *
1654432 GACTATTGGACAATGTTTTG--TTGGGT-CATT
1 GACTATT--A-AAAGTTATGAAAT-GGTCCCTT
1654462 CGACTATTAAAAGTTATGAAATGGTCCCTT
1 -GACTATTAAAAGTTATGAAATGGTCCCTT
1654492 GACTAT
1 GACTAT
1654498 AGGACATTGC
Statistics
Matches: 50, Mismatches: 8, Indels: 16
0.68 0.11 0.22
Matches are distributed among these distances:
28 7 0.14
29 17 0.34
30 8 0.16
31 11 0.22
32 7 0.14
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (29 bp):
GACTATTAAAAGTTATGAAATGGTCCCTT
Found at i:1654472 original size:60 final size:60
Alignment explanation
Indices: 1654361--1654547 Score: 241
Period size: 60 Copynumber: 3.1 Consensus size: 60
1654351 TAAAGTACAC
* * * ** * *
1654361 AAATGGCCCCCTGATTATAGGATTATGCTTTATTGAGTC-CCCGACTATTAAAAGTTATG
1 AAATGGTCCCTTGACTATAGGACAATGCTTTGTTGAGTCATCCGACTATTAAAAGTTATG
* * * *
1654420 AAATGGTCCCTTGACTATTGGACAATGTTTTGTTGGGTCATTCGACTATTAAAAGTTATG
1 AAATGGTCCCTTGACTATAGGACAATGCTTTGTTGAGTCATCCGACTATTAAAAGTTATG
* * *
1654480 AAATGGTCCCTTGACTATAGGACATTGCTTTGTTGAGTCCTCCGACTATTAAAAGTTATA
1 AAATGGTCCCTTGACTATAGGACAATGCTTTGTTGAGTCATCCGACTATTAAAAGTTATG
1654540 AAATGGTC
1 AAATGGTC
1654548 ACCGACTATT
Statistics
Matches: 109, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 30 0.28
60 79 0.72
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (60 bp):
AAATGGTCCCTTGACTATAGGACAATGCTTTGTTGAGTCATCCGACTATTAAAAGTTATG
Found at i:1656081 original size:14 final size:16
Alignment explanation
Indices: 1656062--1656093 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1656052 ACATTTAAAT
1656062 ATTTTTT-AT-TTATA
1 ATTTTTTAATATTATA
1656076 ATTTTTTAATATTATA
1 ATTTTTTAATATTATA
1656092 AT
1 AT
1656094 AATGACCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTTTAATATTATA
Found at i:1656171 original size:17 final size:18
Alignment explanation
Indices: 1656146--1656179 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1656136 CTAATATTTT
1656146 TTATATATTATCATTTAA
1 TTATATATTATCATTTAA
*
1656164 TTAT-TATTATCTTTTA
1 TTATATATTATCATTTA
1656180 GAATTTGTCA
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:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATATTATCATTTAA
Found at i:1657479 original size:2 final size:2
Alignment explanation
Indices: 1657472--1657497 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1657462 GCATACATCA
1657472 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
1657498 TCTGTGTTCT
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:1671653 original size:15 final size:15
Alignment explanation
Indices: 1671629--1671661 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1671619 AGAACCACCA
1671629 CCACCACCACCGCCT
1 CCACCACCACCGCCT
*
1671644 CCACCGCCACCGCCT
1 CCACCACCACCGCCT
1671659 CCA
1 CCA
1671662 ATGCCTGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.67, G:0.09, T:0.06
Consensus pattern (15 bp):
CCACCACCACCGCCT
Found at i:1671757 original size:15 final size:15
Alignment explanation
Indices: 1671734--1671763 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1671724 ACTGCCACCT
1671734 CCACCTCCTCCTCCA
1 CCACCTCCTCCTCCA
*
1671749 CCACTTCCTCCTCCA
1 CCACCTCCTCCTCCA
1671764 GTTCCAACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.63, G:0.00, T:0.23
Consensus pattern (15 bp):
CCACCTCCTCCTCCA
Found at i:1671798 original size:108 final size:102
Alignment explanation
Indices: 1671674--1671907 Score: 306
Period size: 108 Copynumber: 2.2 Consensus size: 102
1671664 GCCTGCTCCT
* * * *
1671674 GCACCAAAACCACTACCATGACCAAACCCTTCCCCAGAACTACCATAACCACTGCCACCTCCACC
1 GCACCATATCCACTACCATGACCAAACCCTTCACCAGAACTACCATAACCACTGCCACCACCACC
* * * * *
1671739 TCCTCCTCCACCACTTCCTCCTCCAGTTCCAACTCCACTACCG
66 ACCACCT----C-C-TCCTCCTCCAATCCCAACTCCAATACCG
* * *
1671782 GCACCATATCCACTACCATGACCAAACCCTTCACCAGAATTACCATAACCATTTCCACCACCACC
1 GCACCATATCCACTACCATGACCAAACCCTTCACCAGAACTACCATAACCACTGCCACCACCACC
1671847 ACCACCTCCTCCTCCTCCAATCCCAACTCCAATACCG
66 ACCACCTCCTCCTCCTCCAATCCCAACTCCAATACCG
1671884 GCACCATATCCACTACCATGACCA
1 GCACCATATCCACTACCATGACCA
1671908 TATCCTCCAT
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
102 49 0.43
103 1 0.01
104 1 0.01
108 63 0.55
ACGTcount: A:0.29, C:0.48, G:0.05, T:0.18
Consensus pattern (102 bp):
GCACCATATCCACTACCATGACCAAACCCTTCACCAGAACTACCATAACCACTGCCACCACCACC
ACCACCTCCTCCTCCTCCAATCCCAACTCCAATACCG
Found at i:1672258 original size:3 final size:3
Alignment explanation
Indices: 1672250--1672289 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
1672240 TACCTGAGGA
* *
1672250 ACC ACC ACC TCC ACC ACC ACC ACC ACC ACC ATC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC A
1672290 AACTTACCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.62, G:0.00, T:0.05
Consensus pattern (3 bp):
ACC
Found at i:1672275 original size:111 final size:105
Alignment explanation
Indices: 1672045--1672280 Score: 310
Period size: 111 Copynumber: 2.2 Consensus size: 105
1672035 GCAGTAGCAT
* * * * *
1672045 CACCTCCACCACCTCCACCTCCTCCTACTCCACCATTTCCATTGCCTCCTCCTGCACCGTACCCT
1 CACCACCACCACCACCACCACCTCCTACTCCACCAATGCCATTGCCTCCTCCTGCACCGTACCCT
*
1672110 TCCCCATGTCCAACACCATTACCTGAGGAACCACCACCAG
66 TCCCCATGTCCAACACCATTACCTGAGGAACCACCACCAC
* * * * *
1672150 CACTAGCACTACCACCTCCACCTCCTACTCCATCAATGCCATTGCCTCCTCCTGCACCAGCACCA
1 CACCACCACCACCACCACCACCTCCTACTCCACCAATGCCATTGCCTCCTCCTGCACC-G-----
*
1672215 TACCCTTCCCCATGTCCAACACCATTACCTGAGGAACCACCACCTC
60 TACCCTTCCCCATGTCCAACACCATTACCTGAGGAACCACCACCAC
1672261 CACCACCACCACCACCACCA
1 CACCACCACCACCACCACCA
1672281 TCACCACCAA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
105 48 0.44
106 1 0.01
111 60 0.55
ACGTcount: A:0.24, C:0.50, G:0.07, T:0.19
Consensus pattern (105 bp):
CACCACCACCACCACCACCACCTCCTACTCCACCAATGCCATTGCCTCCTCCTGCACCGTACCCT
TCCCCATGTCCAACACCATTACCTGAGGAACCACCACCAC
Found at i:1672276 original size:105 final size:99
Alignment explanation
Indices: 1672045--1672276 Score: 293
Period size: 105 Copynumber: 2.2 Consensus size: 99
1672035 GCAGTAGCAT
* * * *
1672045 CACCTCCACCACCTCCACCTCCTCCTACTCCACCATTTCCATTGCCTCCTCCTGCACCGTACCCT
1 CACCTCCACCACCACCACCACCTCCTACTCCACCAATGCCATTGCCTCCTCCTGCACCGTACCCT
1672110 TCCCCATGTCCAACACCATTACCTGAGGAACCAC
66 TCCCCATGTCCAACACCATTACCTGAGGAACCAC
* * *
1672144 CACCAGCACTAGCACTACCACCTCCACCTCCTACTCCATCAATGCCATTGCCTCCTCCTGCACCA
1 CACC-TC-C-A-C-C-ACCACCACCACCTCCTACTCCACCAATGCCATTGCCTCCTCCTGCACC-
1672209 GCACCATACCCTTCCCCATGTCCAACACCATTACCTGAGGAACCAC
59 G-----TACCCTTCCCCATGTCCAACACCATTACCTGAGGAACCAC
1672255 CACCTCCACCACCACCACCACC
1 CACCTCCACCACCACCACCACC
1672277 ACCATCACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
99 4 0.04
100 1 0.01
101 1 0.01
102 1 0.01
103 1 0.01
104 1 0.01
105 53 0.47
106 2 0.02
107 1 0.01
108 1 0.01
109 1 0.01
110 1 0.01
111 44 0.39
ACGTcount: A:0.23, C:0.50, G:0.07, T:0.19
Consensus pattern (99 bp):
CACCTCCACCACCACCACCACCTCCTACTCCACCAATGCCATTGCCTCCTCCTGCACCGTACCCT
TCCCCATGTCCAACACCATTACCTGAGGAACCAC
Found at i:1673509 original size:17 final size:17
Alignment explanation
Indices: 1673483--1673530 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1673473 TAATACTATA
*
1673483 TAATTTCTATTTAATTT
1 TAATTCCTATTTAATTT
1673500 TAATTCCTATTT--TTT
1 TAATTCCTATTTAATTT
*
1673515 TAATTCTTTATTTAAT
1 TAATTC-CTATTTAAT
1673531 CCATCAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 9 0.35
16 5 0.19
17 11 0.42
18 1 0.04
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTCCTATTTAATTT
Found at i:1677410 original size:37 final size:38
Alignment explanation
Indices: 1677341--1677412 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
1677331 ACCCAAACCT
*
1677341 GACCCTAATATCACACTTAAAAAAACCCGACCCGACTC
1 GACCCAAATATCACACTTAAAAAAACCCGACCCGACTC
1677379 GACCCAAATATCACACTT-AAAAAACCCGACCCGA
1 GACCCAAATATCACACTTAAAAAAACCCGACCCGA
1677413 ACAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 16 0.48
38 17 0.52
ACGTcount: A:0.42, C:0.36, G:0.08, T:0.14
Consensus pattern (38 bp):
GACCCAAATATCACACTTAAAAAAACCCGACCCGACTC
Found at i:1677667 original size:37 final size:38
Alignment explanation
Indices: 1677586--1677703 Score: 177
Period size: 38 Copynumber: 3.2 Consensus size: 38
1677576 CTAAACCCTA
*
1677586 ACCCGACCCGACCCAAATATCACACTTAAAAAAACCCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
*
1677624 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCTG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
* * *
1677662 A-CCGACTCGACTCGAACATCACACTT-AAAAAACCCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
1677698 ACCCGA
1 ACCCGA
1677704 ACAAAATAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
36 10 0.14
37 26 0.36
38 37 0.51
ACGTcount: A:0.40, C:0.38, G:0.10, T:0.12
Consensus pattern (38 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:1677706 original size:291 final size:288
Alignment explanation
Indices: 1677341--1677891 Score: 888
Period size: 291 Copynumber: 1.9 Consensus size: 288
1677331 ACCCAAACCT
* *
1677341 GACCCTAATATCACACTTAAAAAAACCCGACCCGACTCGACCCAAATATCACACTTAAAAAACCC
1 GACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCAAACATCACACTTAAAAAACCC
* *
1677406 GACCCGAACAAAATAAAGTTTCATTCGACCCGACCCGAATATATAAATTAGAAATCCGACCCGAC
66 GACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATAAATTAGAAATCCAACCCGAC
* *
1677471 CCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCTGACCC
131 CCGACCCGAAATAATAAAAAA--A--ATTATTTAATAAAAACAGTGACTTAATCCGACCCGACCC
* * * *
1677536 AAATTATATATATTTTCGGGCCGGTCCAGTTTTTTTCACCCTAAACCCTAACCCGACCCGACCCA
192 AAATTATATATATTTTCGGGCCGGTCCAATTTTTTTCACCCTAAACCCGAACCCGAACCGACCAA
1677601 AATATCACACTTAAAAAAACCCGACCCGACCC
257 AATATCACACTTAAAAAAACCCGACCCGACCC
* * *
1677633 GACCCGAATATCACACTTAAAAAAACCTGA-CCGACTCGACTCGAACATCACACTTAAAAAACCC
1 GACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCAAACATCACACTTAAAAAACCC
*
1677697 GACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACCCGAC
66 GACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATAAATTAGAAATCCAACCCGAC
* **
1677762 CCGACCCGAAATAATAAAAAAAATTATTTAATAAAAACAGTGACTTAATCCGACCCGGCCTGAAT
131 CCGACCCGAAATAATAAAAAAAATTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCAAAT
* *
1677827 TATATATATTTTCGGGTCGGTCCAATTTTTTTCACCCTAAATCCGAACCCGAACCGACCAAAATA
196 TATATATATTTTCGGGCCGGTCCAATTTTTTTCACCCTAAACCCGAACCCGAACCGACCAAAATA
1677892 AAGTTTCACC
Statistics
Matches: 240, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
287 97 0.40
289 1 0.00
291 114 0.47
292 28 0.12
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (288 bp):
GACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCAAACATCACACTTAAAAAACCC
GACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATAAATTAGAAATCCAACCCGAC
CCGACCCGAAATAATAAAAAAAATTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCAAAT
TATATATATTTTCGGGCCGGTCCAATTTTTTTCACCCTAAACCCGAACCCGAACCGACCAAAATA
TCACACTTAAAAAAACCCGACCCGACCC
Found at i:1682702 original size:16 final size:16
Alignment explanation
Indices: 1682681--1682711 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1682671 AGTAAACTTG
1682681 TCTGAATTAAGGACAA
1 TCTGAATTAAGGACAA
1682697 TCTGAATTAAGGACA
1 TCTGAATTAAGGACA
1682712 TAAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (16 bp):
TCTGAATTAAGGACAA
Found at i:1686700 original size:18 final size:18
Alignment explanation
Indices: 1686677--1686712 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1686667 CTTCTTGGAT
*
1686677 AAAAGTATAGTTGGGAAG
1 AAAAGTACAGTTGGGAAG
1686695 AAAAGTACAGTTGGGAAG
1 AAAAGTACAGTTGGGAAG
1686713 CTTCCCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.33, T:0.19
Consensus pattern (18 bp):
AAAAGTACAGTTGGGAAG
Found at i:1696098 original size:37 final size:37
Alignment explanation
Indices: 1696033--1696121 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 37
1696023 TGACGATCAA
1696033 TTATATTT-TTAATAATTTACATATACGCATTATCCTT
1 TTATATTTATTAA-AATTTACATATACGCATTATCCTT
*
1696070 TTATATTATATTAAAATTTA-AT-TGACGCATTATCTTT
1 TTATATT-TATTAAAATTTACATAT-ACGCATTATCCTT
1696107 TTATATTTTATTAAA
1 TTATA-TTTATTAAA
1696122 TTTTTTACTT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
36 1 0.02
37 33 0.70
38 9 0.19
39 4 0.09
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (37 bp):
TTATATTTATTAAAATTTACATATACGCATTATCCTT
Found at i:1700188 original size:42 final size:42
Alignment explanation
Indices: 1700129--1700214 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
1700119 TCTAATTTGA
1700129 TGCTCACGGTCCCCCTCACTATATTGGTGATAAGGACATTCG
1 TGCTCACGGTCCCCCTCACTATATTGGTGATAAGGACATTCG
*
1700171 TGCTCATGGTCCCCCTCACTATATTGGTGATAAGGACATTCG
1 TGCTCACGGTCCCCCTCACTATATTGGTGATAAGGACATTCG
1700213 TG
1 TG
1700215 AATGCTTCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (42 bp):
TGCTCACGGTCCCCCTCACTATATTGGTGATAAGGACATTCG
Found at i:1701539 original size:60 final size:59
Alignment explanation
Indices: 1701393--1701583 Score: 181
Period size: 60 Copynumber: 3.2 Consensus size: 59
1701383 TTTAAAGGGC
* * * *
1701393 AAAG-TACACAATGATCACCGATTATAGGACATTATTTTATTGAGTCATTAGACTATTA
1 AAAGTTACAAAATGATCACCGATTATAGGGCGTTGTTTTATTGAGTCATTAGACTATTA
* * * *
1701451 AAAATTACAAAATAATCTACCAATTATAGGGCGTTGTTTTATTGAGTTTATT-GACTATTA
1 AAAGTTACAAAATGATC-ACCGATTATAGGGCGTTGTTTTATTGAG-TCATTAGACTATTA
* * * * * **
1701511 AAAGTTACAAAATGATCCCCTGACTATAGGGTGTTGTTTTGTTAAGTC-CCACGACTATTA
1 AAAGTTACAAAATGATCACC-GATTATAGGGCGTTGTTTTATTGAGTCATTA-GACTATTA
*
1701571 AAAGTTATAAAAT
1 AAAGTTACAAAAT
1701584 AGTCATTCGA
Statistics
Matches: 107, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
58 3 0.03
59 13 0.12
60 87 0.81
61 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (59 bp):
AAAGTTACAAAATGATCACCGATTATAGGGCGTTGTTTTATTGAGTCATTAGACTATTA
Found at i:1712481 original size:5 final size:5
Alignment explanation
Indices: 1712471--1712495 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1712461 TTTAAGTATT
1712471 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
1712496 ACTCACAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:1712783 original size:7 final size:7
Alignment explanation
Indices: 1712761--1712795 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1712751 TTCCGCACTG
*
1712761 CTTTCCT
1 CTTTCTT
*
1712768 CTATCTT
1 CTTTCTT
1712775 CTTTCTT
1 CTTTCTT
1712782 CTTTCTT
1 CTTTCTT
1712789 CTTTCTT
1 CTTTCTT
1712796 AATTCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (7 bp):
CTTTCTT
Found at i:1716250 original size:164 final size:164
Alignment explanation
Indices: 1715972--1716299 Score: 629
Period size: 164 Copynumber: 2.0 Consensus size: 164
1715962 TGCCGGGTCA
1715972 TGTTGGTCGAACATAGGGTTGACAGAATAATTTTTTAATGAAGTTAAAACTCAAACTTATCAAAC
1 TGTTGGTCGAACATAGGGTTGACAGAATAATTTTTTAATGAAGTTAAAACTCAAACTTATCAAAC
* *
1716037 TTTAATTATGGTAGTTGCCTCTCTCTCGCTGAGTAGACATTCTCTCTTTTGCAGGTCTTTACAAT
66 TTTAATTATGGTAGTTGCCTCTCTCTCGCTGAGTAGACACTCACTCTTTTGCAGGTCTTTACAAT
1716102 GAAAATGTTGCAATTTATCTTCTCATCGCTTCTT
131 GAAAATGTTGCAATTTATCTTCTCATCGCTTCTT
1716136 TGTTGGTCGAACATAGGGTTGACAGAATAATTTTTTAATGAAGTTAAAACTCAAACTTATCAAAC
1 TGTTGGTCGAACATAGGGTTGACAGAATAATTTTTTAATGAAGTTAAAACTCAAACTTATCAAAC
*
1716201 TTTAATTATGGTAGTTGCCTTTCTCTCGCTGAGTAGACACTCACTCTTTTGCAGGTCTTTACAAT
66 TTTAATTATGGTAGTTGCCTCTCTCTCGCTGAGTAGACACTCACTCTTTTGCAGGTCTTTACAAT
1716266 GAAAATGTTGCAATTTATCTTCTCATCGCTTCTT
131 GAAAATGTTGCAATTTATCTTCTCATCGCTTCTT
1716300 CGATGACCAT
Statistics
Matches: 161, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 161 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (164 bp):
TGTTGGTCGAACATAGGGTTGACAGAATAATTTTTTAATGAAGTTAAAACTCAAACTTATCAAAC
TTTAATTATGGTAGTTGCCTCTCTCTCGCTGAGTAGACACTCACTCTTTTGCAGGTCTTTACAAT
GAAAATGTTGCAATTTATCTTCTCATCGCTTCTT
Found at i:1721197 original size:102 final size:102
Alignment explanation
Indices: 1721021--1721225 Score: 394
Period size: 102 Copynumber: 2.0 Consensus size: 102
1721011 TCGGATATAC
1721021 TAACAAGTATGAACTTTGTAGAATACAGTATGCTCACTTACCTAAGGTCTCACAGTGATGAAGAA
1 TAACAAGTATGAACTTTGTAGAATACAGTATGCTCACTTACCTAAGGTCTCACAGTGATGAAGAA
1721086 TGCCACTGATGCTTTTCATGCTTTCGTAGTT-TGAAAG
66 TGCCACTGATGCTTTTCATGC-TTCGTAGTTCTGAAAG
1721123 TAACAAGTATGAACTTTGTAGAATACAGTATGCTCACTTACCTAAGGTCTCACAGTGATGAAGAA
1 TAACAAGTATGAACTTTGTAGAATACAGTATGCTCACTTACCTAAGGTCTCACAGTGATGAAGAA
1721188 TGCCACTGATGCTTTTCATGCTTCGTAGTTCTGAAAG
66 TGCCACTGATGCTTTTCATGCTTCGTAGTTCTGAAAG
1721225 T
1 T
1721226 GCTGATAACA
Statistics
Matches: 102, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
101 9 0.09
102 93 0.91
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (102 bp):
TAACAAGTATGAACTTTGTAGAATACAGTATGCTCACTTACCTAAGGTCTCACAGTGATGAAGAA
TGCCACTGATGCTTTTCATGCTTCGTAGTTCTGAAAG
Found at i:1722269 original size:174 final size:173
Alignment explanation
Indices: 1721782--1722348 Score: 795
Period size: 174 Copynumber: 3.3 Consensus size: 173
1721772 TTTTCGCCGC
*
1721782 CGGAAATTACTTTGGATTTTTATTTATTGCTTGCTTCTTCTTCATAAAACTTCTTCTCAACTGCC
1 CGGAAATTACTTTGAATTTTTA-TTATTGCTTGCTTCTTCTTCATAAAACTTCTTCTCAACTGCC
* *
1721847 AAGCACGGAACCGACTCTGGATTTCGGTTGCAGCTAATGTCTGATTTTGAAGAGATCTACAGG-C
65 AAGCACGGAACTGACTCTGAATTT-GGTTGCAGCTAATGTCTGATTTTGAAGAGATCTAC-GGAC
1721911 AAATTCCTTCCTAGCAATCTGAAAGGCCCTATAGCATTTCAGTCGT
128 AAATTCCTTCCTAGCAATCTGAAAGGCCCTATAGCATTTCAGTCGT
*
1721957 CGGAAATTACTTTGGATTTTTATTATTGCTTG---CTTCTTCATAAAACTTCTTCTCAACTGCCA
1 CGGAAATTACTTTGAATTTTTATTATTGCTTGCTTCTTCTTCATAAAACTTCTTCTCAACTGCCA
* *
1722019 AGCACGGAACTGACTCTGAATTTTGGTTGCAGCTAATGTCTGAGTTTGAAGAGATCTAC-AAGCA
66 AGCACGGAACTGACTCTGAA-TTTGGTTGCAGCTAATGTCTGATTTTGAAGAGATCTACGGA-CA
* *
1722083 AATTCTTTCCTAGCAATCTGAAAGGCCTTATAGCATTTCAGTCGT
129 AATTCCTTCCTAGCAATCTGAAAGGCCCTATAGCATTTCAGTCGT
* ** * * *
1722128 C-GAATATTACTTTGAATTTTTATTATTGCTTGTTTCTTCTTTGTATAACTTCTTCTTAACAGCC
1 CGGAA-ATTACTTTGAATTTTTATTATTGCTTGCTTCTTCTTCATAAAACTTCTTCTCAACTGCC
* * * *
1722192 AAGCACGGAACTGAGTCTGAATTCTGGTAGCAGCTAATGTCTGATTTTGAAGGGATTTACGGACA
65 AAGCACGGAACTGACTCTGAATT-TGGTTGCAGCTAATGTCTGATTTTGAAGAGATCTACGGACA
* * ** * *
1722257 AATTCCTTCCTAGAAATCTGAAAGACCCTCCAACATTTCAGTTGT
129 AATTCCTTCCTAGCAATCTGAAAGGCCCTATAGCATTTCAGTCGT
* *
1722302 CGGAAATTACTTTGAATTTTTGTTATTGCTTGCTTCTGCTTCATAAA
1 CGGAAATTACTTTGAATTTTTATTATTGCTTGCTTCTTCTTCATAAA
1722349 CCTCCTCCTT
Statistics
Matches: 350, Mismatches: 32, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
170 3 0.01
171 154 0.44
172 3 0.01
173 2 0.01
174 162 0.46
175 26 0.07
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (173 bp):
CGGAAATTACTTTGAATTTTTATTATTGCTTGCTTCTTCTTCATAAAACTTCTTCTCAACTGCCA
AGCACGGAACTGACTCTGAATTTGGTTGCAGCTAATGTCTGATTTTGAAGAGATCTACGGACAAA
TTCCTTCCTAGCAATCTGAAAGGCCCTATAGCATTTCAGTCGT
Found at i:1731751 original size:15 final size:15
Alignment explanation
Indices: 1731731--1731760 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1731721 GCAAAGTTGG
1731731 GGCCAACTGAAGGGA
1 GGCCAACTGAAGGGA
1731746 GGCCAACTGAAGGGA
1 GGCCAACTGAAGGGA
1731761 AGGAACATTT
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:0.33, C:0.20, G:0.40, T:0.07
Consensus pattern (15 bp):
GGCCAACTGAAGGGA
Found at i:1732194 original size:55 final size:55
Alignment explanation
Indices: 1732123--1732291 Score: 207
Period size: 57 Copynumber: 3.0 Consensus size: 55
1732113 CGAGAGCTGG
* * *
1732123 ACATTGATCGCGGATGTCGTTAA-TGCCTTCGAGTTTCTAGCCAGGCTGAAAGGCA
1 ACATTGATCACGGATGTCG-TAACTGCCATCGAGTTTCTAGCCAGGCCGAAAGGCA
* * *
1732178 ACATTGATCACAGATGTCGTAATTGCCATCGAGTTTCCCCAGCCAGGCCGAAAGGCA
1 ACATTGATCACGGATGTCGTAACTGCCATCGAGTTT--CTAGCCAGGCCGAAAGGCA
* * *
1732235 ACATTGATCGA-GGATGTCGTAACTGCCATCGTGTTTCTAGTCAGGCCAAAAGGCA
1 ACATTGATC-ACGGATGTCGTAACTGCCATCGAGTTTCTAGCCAGGCCGAAAGGCA
1732290 AC
1 AC
1732292 GAAAACATCA
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
54 3 0.03
55 47 0.47
57 48 0.48
58 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (55 bp):
ACATTGATCACGGATGTCGTAACTGCCATCGAGTTTCTAGCCAGGCCGAAAGGCA
Found at i:1739074 original size:148 final size:148
Alignment explanation
Indices: 1738820--1739115 Score: 583
Period size: 148 Copynumber: 2.0 Consensus size: 148
1738810 AAATAATATG
*
1738820 AAGGTTAAGTTCAGACATTCTTAATAAGATAATTAAGCAAGCAGAAGGAAAATACCATCTGAGAA
1 AAGGTTAAGTTCAGACATTCTTAATAAGATAATTAAGCAAGCAGAAGAAAAATACCATCTGAGAA
1738885 ATCATCAAGATAATATGGGGCAGCAGAAGAAGCTCTTATAGCTTGCCATATATGGTGTTTACAAC
66 ATCATCAAGATAATATGGGGCAGCAGAAGAAGCTCTTATAGCTTGCCATATATGGTGTTTACAAC
1738950 TTCCTATAAAAGCACTTC
131 TTCCTATAAAAGCACTTC
1738968 AAGGTTAAGTTCAGACATTCTTAATAAGATAATTAAGCAAGCAGAAGAAAAATACCATCTGAGAA
1 AAGGTTAAGTTCAGACATTCTTAATAAGATAATTAAGCAAGCAGAAGAAAAATACCATCTGAGAA
1739033 ATCATCAAGATAATATGGGGCAGCAGAAGAAGCTCTTATAGCTTGCCATATATGGTGTTTACAAC
66 ATCATCAAGATAATATGGGGCAGCAGAAGAAGCTCTTATAGCTTGCCATATATGGTGTTTACAAC
1739098 TTCCTATAAAAGCACTTC
131 TTCCTATAAAAGCACTTC
1739116 GTTTGTAGCC
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 147 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (148 bp):
AAGGTTAAGTTCAGACATTCTTAATAAGATAATTAAGCAAGCAGAAGAAAAATACCATCTGAGAA
ATCATCAAGATAATATGGGGCAGCAGAAGAAGCTCTTATAGCTTGCCATATATGGTGTTTACAAC
TTCCTATAAAAGCACTTC
Found at i:1741387 original size:99 final size:99
Alignment explanation
Indices: 1741216--1741414 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
1741206 TCAGCTTGTG
1741216 TCTAGATGCACCAAAATAAGAACTATTCTCCATCTGTAATACAACACAAGAAGCAGTTTTAATCA
1 TCTAGATGCACCAAAATAAGAACTATTCTCCATCTGTAATACAACACAAGAAGCAGTTTTAATCA
1741281 TAGATTTATCCATGCTCATGTGAAAGCATGAGCA
66 TAGATTTATCCATGCTCATGTGAAAGCATGAGCA
1741315 TCTAGATGCACCAAAATAAGAACTATTCTCCATCTGTAATACAACACAAGAAGCAGTTTTAATCA
1 TCTAGATGCACCAAAATAAGAACTATTCTCCATCTGTAATACAACACAAGAAGCAGTTTTAATCA
1741380 TAGATTTATCCATGCTCATGTGAAAGCATGAGCA
66 TAGATTTATCCATGCTCATGTGAAAGCATGAGCA
1741414 T
1 T
1741415 ACAAACAGCT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (99 bp):
TCTAGATGCACCAAAATAAGAACTATTCTCCATCTGTAATACAACACAAGAAGCAGTTTTAATCA
TAGATTTATCCATGCTCATGTGAAAGCATGAGCA
Found at i:1744102 original size:14 final size:14
Alignment explanation
Indices: 1744079--1744123 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1744069 AAACAACTTG
* *
1744079 ATAAGACAATTACA
1 ATAAGCCAATCACA
*
1744093 ATAATCCAATCACA
1 ATAAGCCAATCACA
1744107 ATAAGCCAATCATCA
1 ATAAGCCAATCA-CA
1744122 AT
1 AT
1744124 CCGTACACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.22
Consensus pattern (14 bp):
ATAAGCCAATCACA
Found at i:1747115 original size:2 final size:2
Alignment explanation
Indices: 1747108--1747137 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1747098 TTCTCTGTTC
1747108 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1747138 TTGCAGGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1747845 original size:16 final size:16
Alignment explanation
Indices: 1747807--1747853 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1747797 TTACCCGACC
* *
1747807 TGTTTTCAACCTGAGT
1 TGTTTTTAACCTGACT
1747823 TGTTTTTAACCTGACT
1 TGTTTTTAACCTGACT
*
1747839 TGTTTTTAACTTGAC
1 TGTTTTTAACCTGAC
1747854 CTGTAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (16 bp):
TGTTTTTAACCTGACT
Found at i:1748136 original size:14 final size:14
Alignment explanation
Indices: 1748114--1748160 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1748104 GCAAAAGGAA
*
1748114 AATTAATATAGTTT
1 AATTTATATAGTTT
1748128 AATTTATATA----
1 AATTTATATAGTTT
1748138 AA-TTATATAGTTT
1 AATTTATATAGTTT
1748151 AATTTATATA
1 AATTTATATA
1748161 AAGAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:1748147 original size:23 final size:24
Alignment explanation
Indices: 1748113--1748162 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1748103 TGCAAAAGGA
1748113 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1748137 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1748160 AAA
1 AAA
1748163 GAAAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:1749621 original size:14 final size:15
Alignment explanation
Indices: 1749602--1749630 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1749592 TGGCACCAAA
1749602 AGCTGAGAA-AAGCC
1 AGCTGAGAAGAAGCC
1749616 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
1749631 CTATACATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.21, G:0.31, T:0.07
Consensus pattern (15 bp):
AGCTGAGAAGAAGCC
Found at i:1749714 original size:31 final size:30
Alignment explanation
Indices: 1749653--1749765 Score: 88
Period size: 31 Copynumber: 3.5 Consensus size: 30
1749643 TATAATTTGT
*
1749653 AATTAATATTAATATAAA-ATATAATCTATAA
1 AATTAATATTAATATAAACATAT-GT-TATAA
1749684 AATTAATATTAATATAAACGATATGTTAT-A
1 AATTAATATTAATATAAAC-ATATGTTATAA
* *
1749714 AATTATATAGTATAGTTTATAAAC-TATAGTTAATAT
1 AATTA-ATA-T-TA--ATATAAACATAT-GTT-ATAA
1749750 AATTAATATTAATATA
1 AATTAATATTAATATA
1749766 GTATAGTTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
30 6 0.09
31 28 0.41
32 2 0.03
33 11 0.16
34 4 0.06
35 12 0.18
36 5 0.07
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAACATATGTTATAA
Found at i:1749733 original size:14 final size:14
Alignment explanation
Indices: 1749716--1749777 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
1749706 ATGTTATAAA
1749716 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
1749730 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
1749744 TAATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
1749759 TAATATAGTATAGT
1 TTATATAGTATAGT
1749773 TTATA
1 TTATA
1749778 AACTATATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.61
15 9 0.24
16 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:1749766 original size:43 final size:40
Alignment explanation
Indices: 1749718--1749808 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 40
1749708 GTTATAAATT
*
1749718 ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA--TAATAT-ATTAATATAA
*
1749761 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
1749801 ATTATAGT
1 A-TATAGT
1749809 TAAGATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 10 0.22
41 11 0.24
43 24 0.53
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
Found at i:1749771 original size:29 final size:29
Alignment explanation
Indices: 1749738--1749830 Score: 78
Period size: 29 Copynumber: 3.0 Consensus size: 29
1749728 GTTTATAAAC
1749738 TATAGTTAATATAATTAATATTAATATAG
1 TATAGTTAATATAATTAATATTAATATAG
* * *
1749767 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTAATATA--AT-TA--ATATTAATAT--AG
* *
1749803 TATAGTTAAGATAATTAACATTAATATA
1 TATAGTTAATATAATTAATATTAATATA
1749831 AACTATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
29 12 0.24
31 11 0.22
32 2 0.04
33 2 0.04
34 12 0.24
36 11 0.22
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
TATAGTTAATATAATTAATATTAATATAG
Found at i:1749845 original size:22 final size:22
Alignment explanation
Indices: 1749820--1749921 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
1749810 AAGATAATTA
1749820 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
1749842 ACATTAATATAAAC--TATAGT
1 ACATTAATATAAACTATATAGT
** * * *
1749862 TTATAAATTATATACTATA-GGT
1 ACATTAA-TATAAACTATATAGT
* *
1749884 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
1749906 ACACTAATATAAACTA
1 ACATTAATATAAACTA
1749922 CTATTTATAA
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
20 10 0.16
21 22 0.34
22 27 0.42
23 5 0.08
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:1749878 original size:21 final size:21
Alignment explanation
Indices: 1749849--1749901 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1749839 AGTACATTAA
* *
1749849 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
1749870 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
1749891 TATAAACTATA
1 TATAAACTATA
1749902 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:1749995 original size:24 final size:20
Alignment explanation
Indices: 1749944--1750036 Score: 72
Period size: 20 Copynumber: 4.7 Consensus size: 20
1749934 TATAAGTTAC
1749944 ATATATAGTTTATATAACAT
1 ATATATAGTTTATATAACAT
*
1749964 ATAAATAGATTGTATATATACAT
1 ATATATAG-TT-TATATA-ACAT
*
1749987 ATACTATAGGTTATAT---AT
1 ATA-TATAGTTTATATAACAT
1750005 A-A-ATAGTTTATATATAC-T
1 ATATATAGTTTATATA-ACAT
*
1750023 ATACATAGTTTATA
1 ATATATAGTTTATA
1750037 CATACACGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
15 10 0.17
17 1 0.02
18 5 0.08
19 1 0.02
20 17 0.29
21 2 0.03
22 11 0.19
23 8 0.14
24 4 0.07
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (20 bp):
ATATATAGTTTATATAACAT
Found at i:1750078 original size:57 final size:58
Alignment explanation
Indices: 1749932--1750084 Score: 179
Period size: 57 Copynumber: 2.6 Consensus size: 58
1749922 CTATTTATAA
* * *
1749932 ACTATAAGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATAGTTTATATATACATATACATAGATTGTATACATACACAT
* * *
1749989 ACTATAGGTTATATATAAATAGTTTATATATAC-TATACATAG-TT-TATACATACACGT
1 ACTATAAGTTACATAT--ATAGTTTATATATACATATACATAGATTGTATACATACACAT
*
1750046 ACTATAAGTTACATATATAGTTTACATGTATACATATAC
1 ACTATAAGTTACATATATAGTTT--ATATATACATATAC
1750085 TATATGTTAC
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
55 7 0.09
57 45 0.56
58 7 0.09
59 20 0.25
60 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (58 bp):
ACTATAAGTTACATATATAGTTTATATATACATATACATAGATTGTATACATACACAT
Found at i:1750234 original size:15 final size:14
Alignment explanation
Indices: 1750207--1750240 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1750197 TAATTTACTT
1750207 TATAT-GGTTTATA
1 TATATAGGTTTATA
1750220 TATATAGGTTATATA
1 TATATAGGTT-TATA
1750235 TATATA
1 TATATA
1750241 TACTATACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 4 0.21
15 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
TATATAGGTTTATA
Found at i:1750550 original size:2 final size:2
Alignment explanation
Indices: 1750543--1750829 Score: 109
Period size: 2 Copynumber: 145.0 Consensus size: 2
1750533 TATTTCTTTA
*
1750543 AT AT AT AT AT AT AT AT AT AT -T A- AT AT AA AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1750581 AT AA ACT AT AT AT -T TT AT AT ACT TT AT AC AT AT AT AGT TT AT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT
* * *
1750623 AT AC AT AT AT AT AT ACT AT AT -T A- AT AT AA AT A- AT AT -T TT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
1750662 AT AA ACT AT AT ACT TT TT AT AGT TT AT AC AT AT AT AGT TT AT AT
1 AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT
* * * * * * * *
1750706 AC AT AGT TT AT AT AC AT AT TT CAC AT AA AC AT A- AT TT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
* * * *
1750749 AT AT AG CT -T AT A- AT A- AT -T AT AT AGT TT AT A- AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
*
1750787 AT AGT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1750830 TTATTTCAAA
Statistics
Matches: 208, Mismatches: 50, Indels: 54
0.67 0.16 0.17
Matches are distributed among these distances:
1 15 0.07
2 181 0.87
3 12 0.06
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1750607 original size:81 final size:82
Alignment explanation
Indices: 1750513--1750725 Score: 265
Period size: 81 Copynumber: 2.6 Consensus size: 82
1750503 AATTTATTAC
* * * * *
1750513 TTTATAAAGTTTATGCATAGTATTTCTTTA-ATATATATATATATA-TATATTAATATAAATTAT
1 TTTATATAGTTTATACATA-TA-TACTTTATATACATATATATATACTATATTAATATAAATAAT
1750576 AATATATAAACTATATA-T
64 AATATATAAACTATATACT
* * *
1750594 TTTATATACTTTATACATATATAGTTTATATACATATATATATACTATATTAATATAAATAATAT
1 TTTATATAGTTTATACATATATACTTTATATACATATATATATACTATATTAATATAAATAATAA
*
1750659 TTTATAAACTATATACT
66 TATATAAACTATATACT
* *
1750676 TTT-TATAGTTTATACATATATAGTTTATATACATAGTTTATATAC-ATATT
1 TTTATATAGTTTATACATATATACTTTATATACATA-TATATATACTATATT
1750726 TCACATAAAC
Statistics
Matches: 117, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
79 5 0.04
80 16 0.14
81 84 0.72
82 12 0.10
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (82 bp):
TTTATATAGTTTATACATATATACTTTATATACATATATATATACTATATTAATATAAATAATAA
TATATAAACTATATACT
Found at i:1750616 original size:15 final size:17
Alignment explanation
Indices: 1750596--1750633 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1750586 CTATATATTT
1750596 TATATA-CTT-TATACA
1 TATATAGCTTATATACA
*
1750611 TATATAGTTTATATACA
1 TATATAGCTTATATACA
1750628 TATATA
1 TATATA
1750634 TATACTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 2 0.10
17 12 0.60
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (17 bp):
TATATAGCTTATATACA
Found at i:1750699 original size:15 final size:14
Alignment explanation
Indices: 1750679--1750833 Score: 67
Period size: 13 Copynumber: 10.7 Consensus size: 14
1750669 ATATACTTTT
1750679 TATAGTTTATACATA
1 TATAGTTTATA-ATA
1750694 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
1750707 CATAGTTTAT-ATA
1 TATAGTTTATAATA
*
1750720 CATA-TTTCACATAA-A
1 TATAGTTT---ATAATA
* *
1750735 CATAATTTATATATA
1 TATAGTTTATA-ATA
1750750 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
1750768 TATAGTTTATAATATAAA
1 TATAGTTTAT-A-AT--A
1750786 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
1750799 TATA-TATAT-ATA
1 TATAGTTTATAATA
*
1750811 TATA-TATATATATA
1 TATAGTTTATA-ATA
1750825 TATA-TTTAT
1 TATAGTTTAT
1750834 TTCAAATTTT
Statistics
Matches: 118, Mismatches: 5, Indels: 35
0.75 0.03 0.22
Matches are distributed among these distances:
12 19 0.16
13 27 0.23
14 12 0.10
15 25 0.21
16 9 0.08
17 5 0.04
18 21 0.18
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:1750744 original size:81 final size:81
Alignment explanation
Indices: 1750539--1750753 Score: 262
Period size: 81 Copynumber: 2.7 Consensus size: 81
1750529 ATAGTATTTC
* * * *
1750539 TTTA-ATATATATATATATA-TATATTAATATAAATTATAATATATAAACTATATATTTTATATA
1 TTTATATACATATATATATACTATATTAACATAAATAATAATTTATAAACTATATATTTTATATA
1750602 CTTTATACATATATAG
66 CTTTATACATATATAG
* *
1750618 TTTATATACATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTT-TAT
1 TTTATATACATATATATATACTATATTAACATAAATAATAATTTATAAACTATATA-TTTTATAT
*
1750682 AGTTTATACATATATAG
65 ACTTTATACATATATAG
* * * *
1750699 TTTATATACATAGTTTATATAC-ATATTTCACATAAA-CATAATTTATATA-TATATA
1 TTTATATACATA-TATATATACTATA-TTAACATAAATAATAATTTATAAACTATATA
1750754 GCTTATAATA
Statistics
Matches: 120, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
79 4 0.03
80 20 0.17
81 76 0.63
82 20 0.17
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (81 bp):
TTTATATACATATATATATACTATATTAACATAAATAATAATTTATAAACTATATATTTTATATA
CTTTATACATATATAG
Found at i:1751760 original size:14 final size:14
Alignment explanation
Indices: 1751743--1751772 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1751733 ATATATTTCT
*
1751743 TTGAATATTTATTA
1 TTGAATATGTATTA
1751757 TTGAATATGTATTA
1 TTGAATATGTATTA
1751771 TT
1 TT
1751773 TACATCAATT
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:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (14 bp):
TTGAATATGTATTA
Found at i:1757819 original size:2 final size:2
Alignment explanation
Indices: 1757812--1757848 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1757802 AATAGCAATA
1757812 AT AT AT 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 AT AT AT A
1757849 AAACTCTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1759484 original size:4 final size:4
Alignment explanation
Indices: 1759475--1759515 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
1759465 CGGTTAGTGT
1759475 AATA AATA AATAA AATA AA-A AATA AA-A AATA AA-A AATA AAT
1 AATA AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AAT
1759516 GATAAATGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 9 0.27
4 20 0.61
5 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:1759498 original size:7 final size:7
Alignment explanation
Indices: 1759486--1759514 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1759476 ATAAATAAAT
1759486 AAAATAA
1 AAAATAA
1759493 AAAATAA
1 AAAATAA
1759500 AAAATAA
1 AAAATAA
1759507 AAAATAA
1 AAAATAA
1759514 A
1 A
1759515 TGATAAATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:1759521 original size:14 final size:12
Alignment explanation
Indices: 1759475--1759514 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 12
1759465 CGGTTAGTGT
1759475 AATAAATAAATAA
1 AATAAA-AAATAA
1759488 AATAAAAAATAAAA
1 AATAAAAAAT--AA
1759502 AATAAAAAATAA
1 AATAAAAAATAA
1759514 A
1 A
1759515 TGATAAATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 12 0.48
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:1763547 original size:59 final size:60
Alignment explanation
Indices: 1763441--1763553 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 60
1763431 AAATGTCTCG
* * *
1763441 ACTATAGGATTTCATTTTATTGAGTCATCCGACTATTAAAAGTTATAAAATGGTCCTTCA
1 ACTATAGGACTTCACTTTATTGAGTCACCCGACTATTAAAAGTTATAAAATGGTCCTTCA
* * *
1763501 ACTATAGGACTTCGCTTTGTTGAGTC-CCCGCCTATTAAAAGTTATAAAATGGT
1 ACTATAGGACTTCACTTTATTGAGTCACCCGACTATTAAAAGTTATAAAATGGT
1763554 GACCCGACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 25 0.53
60 22 0.47
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (60 bp):
ACTATAGGACTTCACTTTATTGAGTCACCCGACTATTAAAAGTTATAAAATGGTCCTTCA
Found at i:1764522 original size:60 final size:60
Alignment explanation
Indices: 1764400--1764512 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
1764390 GTCTCTTGAT
*** ** *
1764400 TATATGATATTATTTTGTTGAGTCTTTTGACTATTAAAAGTTACAAAATGGTCCTTCAAC
1 TATATGATATTATTTTGTTGAGTCTTCCAACTATTAAAAGTTACAAAACAGTCCTCCAAC
* *
1764460 TATATGATATTGTTTTGTTGAGT-TCTCCAACTATTAGAAGTTACAAAACAGTC
1 TATATGATATTATTTTGTTGAGTCT-TCCAACTATTAAAAGTTACAAAACAGTC
1764513 ACCCGACTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.02
60 44 0.98
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (60 bp):
TATATGATATTATTTTGTTGAGTCTTCCAACTATTAAAAGTTACAAAACAGTCCTCCAAC
Found at i:1766523 original size:21 final size:21
Alignment explanation
Indices: 1766497--1766544 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1766487 TAATTTTCAA
1766497 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1766518 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1766539 ACATTG
1 ACATTG
1766545 CAATATTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1771174 original size:21 final size:21
Alignment explanation
Indices: 1771148--1771195 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1771138 TAATTTTCAA
1771148 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1771169 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1771190 ACATTG
1 ACATTG
1771196 CAATATTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1772630 original size:60 final size:60
Alignment explanation
Indices: 1772544--1772660 Score: 191
Period size: 60 Copynumber: 1.9 Consensus size: 60
1772534 ATTTTTTAGT
* *
1772544 CGAGTTGAGTTGTTCGATTTTCTATTTAAATTTAATTGTAAATATTTATAATATTATTTG
1 CGAGTTAAGTTGTTCGATTTTCTATTTAAATTTAATTGTAAATATTTATAAAATTATTTG
*
1772604 CGAGTTAAGTTGTTTGAGTTTT-TATTTAAATTTAATTGTAAATATTTATAAAATTAT
1 CGAGTTAAGTTGTTCGA-TTTTCTATTTAAATTTAATTGTAAATATTTATAAAATTAT
1772661 GATACTATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
60 49 0.92
61 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.51
Consensus pattern (60 bp):
CGAGTTAAGTTGTTCGATTTTCTATTTAAATTTAATTGTAAATATTTATAAAATTATTTG
Found at i:1776719 original size:60 final size:60
Alignment explanation
Indices: 1776645--1776796 Score: 168
Period size: 60 Copynumber: 2.5 Consensus size: 60
1776635 ATTGGTCCAT
*
1776645 AAACTTTTAAACATTTCAATTTCATCCCTAAACTATGA-CTATCATTCTAGA-TCAGTCATC
1 AAACTTTTAAACATTTCAATTTCATCCCTAAACTATGATCT-TCATTCTA-ATTCAGTCACC
** * * *
1776705 AAACTTTTTCACATTTCAGTTTCATCTCC-AAACTATGATCTTCATTCTAATTTAGTCCCC
1 AAACTTTTAAACATTTCAATTTCATC-CCTAAACTATGATCTTCATTCTAATTCAGTCACC
* *
1776765 AAACTTCTTGAACATTTCAATTTAAT-CCTAAA
1 AAACTT-TTAAACATTTCAATTTCATCCCTAAA
1776797 TTATAAGTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
59 3 0.04
60 55 0.71
61 19 0.25
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
AAACTTTTAAACATTTCAATTTCATCCCTAAACTATGATCTTCATTCTAATTCAGTCACC
Found at i:1777018 original size:60 final size:60
Alignment explanation
Indices: 1776919--1777098 Score: 202
Period size: 60 Copynumber: 3.0 Consensus size: 60
1776909 GGATGATTTT
* * * *
1776919 GGGATGAAATTGGAATATTCAAAAGTTTATGGACCAATTTAGATTGAGAGTCATAGTTTG
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTG
* *
1776979 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGACTCATAGTTTG
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTG
* * * * * * * *
1777039 AGAATTAATTTATAATGTTTAAAAGTTTAAGGA-TCAATTT-GAAATGAGGGTCATAGTTTG
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACT-AATTTAG-AATGAGAGTCATAGTTTG
1777099 AGGACATATG
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.01
60 101 0.99
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (60 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTG
Found at i:1778965 original size:7 final size:7
Alignment explanation
Indices: 1778953--1778979 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1778943 AAGACACTGC
1778953 TTTTTAT
1 TTTTTAT
1778960 TTTTTAT
1 TTTTTAT
1778967 TTTTTAT
1 TTTTTAT
1778974 TTTTTA
1 TTTTTA
1778980 AGTCTCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:1779503 original size:44 final size:44
Alignment explanation
Indices: 1779440--1779528 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1779430 TATAGGGGTT
1779440 TTGGTCGTGGATGGTTGGCTTGTCACATGTCATTGGGTGTTCGA
1 TTGGTCGTGGATGGTTGGCTTGTCACATGTCATTGGGTGTTCGA
1779484 TTGGTCGTGGATGGTTGGCTTGTCACATGTCATTGGGTGTTCGA
1 TTGGTCGTGGATGGTTGGCTTGTCACATGTCATTGGGTGTTCGA
1779528 T
1 T
1779529 CGATTAATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.11, C:0.13, G:0.36, T:0.39
Consensus pattern (44 bp):
TTGGTCGTGGATGGTTGGCTTGTCACATGTCATTGGGTGTTCGA
Found at i:1780483 original size:36 final size:36
Alignment explanation
Indices: 1780412--1780484 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
1780402 GTTGGAAAAT
* *
1780412 ATTTATATATTTTATTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAATTGAAAATCATAAA
1780448 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTATTTA-AAAATTGAAAATCATAAA
1780484 A
1 A
1780485 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTATTTAAAAATTGAAAATCATAAA
Found at i:1782164 original size:28 final size:30
Alignment explanation
Indices: 1782106--1782175 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
1782096 GTCGACTGAT
* *
1782106 GGTCAAATTAATATTTTATCTAAACTTTA-G
1 GGTC-AATTAATATTTTATCTAAAATCTAGG
* *
1782136 GGTCAATTAGTA-TTTGTCTAAAATCTAGG
1 GGTCAATTAATATTTTATCTAAAATCTAGG
1782165 GGTCAAGTTAA
1 GGTCAA-TTAA
1782176 AATTAAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 12 0.36
29 14 0.42
30 7 0.21
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (30 bp):
GGTCAATTAATATTTTATCTAAAATCTAGG
Found at i:1783207 original size:2 final size:2
Alignment explanation
Indices: 1783200--1783238 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1783190 TAACTATAGT
1783200 TA TA 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 TA TA T
1783239 TAAATATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1783928 original size:23 final size:23
Alignment explanation
Indices: 1783845--1783933 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 23
1783835 CTGAACACAC
* * * *
1783845 AAACAAACATTTTAACAAACATT
1 AAACAAACATGTTCACGAACGTT
** *
1783868 AAACGGACATGTTCAGGAACGTT
1 AAACAAACATGTTCACGAACGTT
* * *
1783891 AAACAAATATATTCACGAATGTT
1 AAACAAACATGTTCACGAACGTT
*
1783914 AAACTAACATGTTCACGAAC
1 AAACAAACATGTTCACGAAC
1783934 ACTAAACGAA
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (23 bp):
AAACAAACATGTTCACGAACGTT
Found at i:1784006 original size:19 final size:19
Alignment explanation
Indices: 1783980--1784025 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1783970 ATGAACACTA
1783980 AAAC-AATATTAAAAATT-T
1 AAACAAATA-TAAAAATTAT
* *
1783998 AAACAAATATGAACATTAT
1 AAACAAATATAAAAATTAT
1784017 AAACAAATA
1 AAACAAATA
1784026 AACAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (19 bp):
AAACAAATATAAAAATTAT
Done.