Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009574.1 Hibiscus syriacus cultivar Beakdansim tig00116939_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: 2686660
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1196443 original size:30 final size:31
Alignment explanation
Indices: 1196384--1196443 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
1196374 CAACCATTCA
* *
1196384 CAACTGTTCTAAAATTACCAAATTGGTCCCC
1 CAACTGTTCAAAAATTACCAAAATGGTCCCC
* *
1196415 CAACTTTTCAAAAATTA-TAAAATGGTCCC
1 CAACTGTTCAAAAATTACCAAAATGGTCCC
1196444 TAAATTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (31 bp):
CAACTGTTCAAAAATTACCAAAATGGTCCCC
Found at i:1197234 original size:30 final size:31
Alignment explanation
Indices: 1197200--1197264 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
1197190 TTTGGTCCCT
* *
1197200 AAACTTTTCAAAGT-TTATACTTTAGTCACC
1 AAACTTTTCAAAATATTATAATTTAGTCACC
* *
1197230 AAAC-TTTCAAAATATTATAATTTGGTCACT
1 AAACTTTTCAAAATATTATAATTTAGTCACC
1197260 AAACT
1 AAACT
1197265 AAATCCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (31 bp):
AAACTTTTCAAAATATTATAATTTAGTCACC
Found at i:1199542 original size:41 final size:41
Alignment explanation
Indices: 1199447--1199552 Score: 126
Period size: 39 Copynumber: 2.6 Consensus size: 41
1199437 TATTTGGTTT
* *
1199447 TTCGAAACTGAAAAAAAGTTTTTTCTTTTTTTTTGTTGTTA
1 TTCGAAACTGAAAAAAAGTTTTTTATCTTTTTTTGTTGTTA
* * * * *
1199488 CTCAAAACT--AAAAAGGGTTTTTATCTTTTTTTGTTGTTG
1 TTCGAAACTGAAAAAAAGTTTTTTATCTTTTTTTGTTGTTA
*
1199527 TTCGAAATTGAAAAAAAGTTTTTTAT
1 TTCGAAACTGAAAAAAAGTTTTTTAT
1199553 TCGAAACTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
39 31 0.61
41 20 0.39
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (41 bp):
TTCGAAACTGAAAAAAAGTTTTTTATCTTTTTTTGTTGTTA
Found at i:1199548 original size:40 final size:39
Alignment explanation
Indices: 1199446--1199550 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 39
1199436 TTATTTGGTT
1199446 TTTCGAAACTGAAAAAAAGTTTTTTCTTTTTTTTTGTTG
1 TTTCGAAACTGAAAAAAAGTTTTTTCTTTTTTTTTGTTG
* **
1199485 TTACTCAAAACT-AAAAAGGGTTTTTATCTTTTTTTGTTGTTG
1 TT--TCGAAACTGAAAAAAAGTTTTT-TCTTTTTTT-TTGTTG
*
1199527 -TTCGAAATTGAAAAAAAGTTTTTT
1 TTTCGAAACTGAAAAAAAGTTTTTT
1199551 ATTCGAAACT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
39 9 0.17
40 22 0.41
41 17 0.31
42 6 0.11
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.50
Consensus pattern (39 bp):
TTTCGAAACTGAAAAAAAGTTTTTTCTTTTTTTTTGTTG
Found at i:1199948 original size:25 final size:24
Alignment explanation
Indices: 1199910--1199993 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
1199900 CCTAGTTCCG
* * *
1199910 GTTTGGTTTAGGGCCTGGGTTT-GG
1 GTTTGATTTGGGGCCT-GGTTTAGA
1199934 GTTTTGATTTGGGGCCTGGTTTAGA
1 G-TTTGATTTGGGGCCTGGTTTAGA
* **
1199959 GTTTGATCTGGGGCCTATTTTAG-
1 GTTTGATTTGGGGCCTGGTTTAGA
*
1199982 GTTTTATTTGGG
1 GTTTGATTTGGG
1199994 TATGGTTTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
23 10 0.20
24 25 0.50
25 15 0.30
ACGTcount: A:0.10, C:0.08, G:0.37, T:0.45
Consensus pattern (24 bp):
GTTTGATTTGGGGCCTGGTTTAGA
Found at i:1199954 original size:24 final size:25
Alignment explanation
Indices: 1199911--1200031 Score: 94
Period size: 23 Copynumber: 5.1 Consensus size: 25
1199901 CTAGTTCCGG
* *
1199911 TTTGGTTTAGGGCCTGGGTTT-GGGT
1 TTTGATTTGGGGCCT-GGTTTAGGGT
*
1199936 TTTGATTTGGGGCCTGGTTTAGAG-
1 TTTGATTTGGGGCCTGGTTTAGGGT
* **
1199960 TTTGATCTGGGGCCTATTTTA-GGT
1 TTTGATTTGGGGCCTGGTTTAGGGT
**
1199984 TTT-ATTT-GGGTATGGTTTAGGGT
1 TTTGATTTGGGGCCTGGTTTAGGGT
* *
1200007 TTTG-TTT-GGGCTTAGTTTAGGGT
1 TTTGATTTGGGGCCTGGTTTAGGGT
1200030 TT
1 TT
1200032 GGGGCTTAGT
Statistics
Matches: 77, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
22 8 0.10
23 28 0.36
24 26 0.34
25 15 0.19
ACGTcount: A:0.10, C:0.07, G:0.36, T:0.48
Consensus pattern (25 bp):
TTTGATTTGGGGCCTGGTTTAGGGT
Found at i:1200031 original size:18 final size:17
Alignment explanation
Indices: 1200010--1200051 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
1200000 TTAGGGTTTT
*
1200010 GTTTGGGCTTAGTTTAGG
1 GTTTGGGCTTAGTTCA-G
1200028 GTTTGGGGCTTAGTTCAG
1 GTTT-GGGCTTAGTTCAG
1200046 GTTTGG
1 GTTTGG
1200052 TTTAGGCCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 9 0.41
19 11 0.50
ACGTcount: A:0.10, C:0.07, G:0.40, T:0.43
Consensus pattern (17 bp):
GTTTGGGCTTAGTTCAG
Found at i:1200038 original size:19 final size:18
Alignment explanation
Indices: 1200010--1200051 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1200000 TTAGGGTTTT
*
1200010 GTTT-GGGCTTAGTTTAGG
1 GTTTGGGGCTTAGTTCA-G
1200028 GTTTGGGGCTTAGTTCAG
1 GTTTGGGGCTTAGTTCAG
1200046 GTTTGG
1 GTTTGG
1200052 TTTAGGCCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.10, C:0.07, G:0.40, T:0.43
Consensus pattern (18 bp):
GTTTGGGGCTTAGTTCAG
Found at i:1200100 original size:22 final size:22
Alignment explanation
Indices: 1200040--1200101 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 22
1200030 TTGGGGCTTA
*
1200040 GTTCAGGTTTGGTTTAGGCCTG
1 GTTCAGGTTTGGTTTGGGCCTG
* * *
1200062 CTTC-GATTTTGTTTGGGCCTG
1 GTTCAGGTTTGGTTTGGGCCTG
1200083 GTTCAGGTTTGGTTTGGGC
1 GTTCAGGTTTGGTTTGGGC
1200102 TCAGTTTGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.06, C:0.15, G:0.35, T:0.44
Consensus pattern (22 bp):
GTTCAGGTTTGGTTTGGGCCTG
Found at i:1200671 original size:139 final size:139
Alignment explanation
Indices: 1200418--1201622 Score: 1667
Period size: 139 Copynumber: 8.7 Consensus size: 139
1200408 TGATGAAAAT
* * * * *
1200418 GAGCTAAGATTGAACAAGTTCTTCTCATTATAAACTTTTTCTCCCTCATCGGATAAGTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
* * * **
1200483 ATTATGAACTATCCACTAGAAATGTTGATCCCTCGAGTGAGGTGCCGCTGATTCAACTTTATATG
66 ATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCCATATG
* *
1200548 CGATAAATA
131 CGATGAATC
* *
1200557 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
* * *
1200622 ACTATGAACTCTCCACTGGAAATATTGATTCCTCGAGTGAGGTGTCGCTGATTTC-ACTCCATAT
66 ATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGA-TTCAACTCCATAT
1200686 GCGATGAATC
130 GCGATGAATC
* * * * * *
1200696 GAGCTAAGTTTGAATAAGTTCTTCTCATTATGAAATTCTTCCCCCTTATCGAATGAGTTCTTCTT
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
* * *
1200761 ATTATGAACTCTCTACTGGAAATATTGATCCCTCGAGTGAAGTGTCGCTGATTCAACTCCATATG
66 ATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCCATATG
*
1200826 CAATGAATC
131 CGATGAATC
* * *
1200835 GAGCTAAGGTTGAACAAGTACTTCTCATTATGAACTTATTCTCCCTTATTGGATGAGTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
* * * * *
1200900 ATTATGAGCACTCTACTAGAAATGTTGATCCCTCGAGTGAGGTGTCGATGATTCAACTCCATATG
66 ATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCCATATG
*
1200965 AGATGAATC
131 CGATGAATC
* * * * *
1200974 CAGCTAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTGCCTCATTGGATGAGTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
* * * * * *
1201039 ACTATGAACTCTCCACTGGAAATATTAATCCATCGGGTGAGGTGTCGCTGATTTAACTCCATATG
66 ATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCCATATG
1201104 CGATGAATC
131 CGATGAATC
* * * * *
1201113 AAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTATCCTTTGTCGGATGAGTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
* * * * * * * *
1201178 ATTATGAACTCTCTAATTGAAATATTAATCCCTCGAGTGACGTGTC-ATTATTCAACTCCATATG
66 ATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCCATATG
1201242 CGATGAATC
131 CGATGAATC
1201251 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
* * * * * *
1201316 ATTATAAACTCTCCACTAGAAATGTTAATCCCTCGAGTGAGGTGCCGCTGATTCAACTTCATATA
66 ATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCCATATG
*
1201381 TGATGAATC
131 CGATGAATC
* *
1201390 GAGCTAAGGTTGAACAACTTCTTCTCAATATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
* * *
1201455 ATTATGAACTCTCCACTGGAAATGTTTATCCCTCGAGTGAGGTGTCACTGATGCAACTCCATATG
66 ATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCCATATG
*
1201520 CAATGAATC
131 CGATGAATC
* * * * *
1201529 GAGCTAAGGTTGAAAAAGTTCTTATTATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
* *
1201594 GTTATGAGCTCTCCACTGGAAATGTTGAT
66 ATTATGAACTCTCCACTGGAAATGTTGAT
1201623 TGGTTTATCC
Statistics
Matches: 944, Mismatches: 119, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
138 126 0.13
139 815 0.86
140 3 0.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35
Consensus pattern (139 bp):
GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
ATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCCATATG
CGATGAATC
Found at i:1202686 original size:5 final size:5
Alignment explanation
Indices: 1202669--1202729 Score: 61
Period size: 5 Copynumber: 11.8 Consensus size: 5
1202659 ATTTCTCTTG
* * *
1202669 TTTTC TTTCC TTTTC TTTTTC TTTTC TTTTCC TCTTG TTTT- TTTCTC
1 TTTTC TTTTC TTTTC -TTTTC TTTTC TTTT-C TTTTC TTTTC TTT-TC
1202716 TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTT
1202730 TCTCTTGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
4 3 0.06
5 32 0.68
6 12 0.26
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:1202694 original size:11 final size:11
Alignment explanation
Indices: 1202669--1202732 Score: 62
Period size: 11 Copynumber: 6.1 Consensus size: 11
1202659 ATTTCTCTTG
*
1202669 TTTTC-TTTCC
1 TTTTCTTTTTC
1202679 TTTTCTTTTTC
1 TTTTCTTTTTC
*
1202690 TTTTCTTTTCC
1 TTTTCTTTTTC
* *
1202701 TCTTGTTTTT-
1 TTTTCTTTTTC
*
1202711 TTCTC-TTTTC
1 TTTTCTTTTTC
1202721 TTTTCTTTTTC
1 TTTTCTTTTTC
1202732 T
1 T
1202733 CTTGTATTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
9 4 0.10
10 11 0.26
11 27 0.64
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:1202698 original size:26 final size:24
Alignment explanation
Indices: 1202660--1202728 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 24
1202650 ATCTTGAACA
* *
1202660 TTTCTCTTGTTTTCTTTCCTTTTCTT
1 TTTCTTTTCTTTTCTTT-CTTTT-TT
*
1202686 TTTCTTTTCTTTTCCTCTTGTTTTTT
1 TTTCTTTTCTTTT-CT-TTCTTTTTT
*
1202712 TCTCTTTTCTTTTCTTT
1 TTTCTTTTCTTTTCTTT
1202729 TTCTCTTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
24 2 0.05
25 2 0.05
26 25 0.68
27 6 0.16
28 2 0.05
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (24 bp):
TTTCTTTTCTTTTCTTTCTTTTTT
Found at i:1202720 original size:31 final size:31
Alignment explanation
Indices: 1202679--1202747 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
1202669 TTTTCTTTCC
1202679 TTTTCTTTTTCTTTTCTTTTCCTCTTGT-TT
1 TTTTCTTTTTCTTTTCTTTTCCTCTTGTATT
*
1202709 TTTTCTCTTTTCTTTTCTTTTTCTCTTGTATT
1 TTTTCT-TTTTCTTTTCTTTTCCTCTTGTATT
1202741 TTTTCTT
1 TTTTCTT
1202748 AGGCATAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 6 0.17
31 22 0.61
32 8 0.22
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.77
Consensus pattern (31 bp):
TTTTCTTTTTCTTTTCTTTTCCTCTTGTATT
Found at i:1202742 original size:18 final size:18
Alignment explanation
Indices: 1202708--1202742 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1202698 TCCTCTTGTT
* *
1202708 TTTTTCTCTTTTCTTTTC
1 TTTTTCTCTTGTATTTTC
1202726 TTTTTCTCTTGTATTTT
1 TTTTTCTCTTGTATTTT
1202743 TTCTTAGGCA
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:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTCTCTTGTATTTTC
Found at i:1202747 original size:20 final size:18
Alignment explanation
Indices: 1202674--1202735 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
1202664 TCTTGTTTTC
1202674 TTTC-CTTTTCTTTT-TCT
1 TTTCTCTTTTCTTTTCT-T
1202691 TTTCT-TTTCCTCTTGTT-TT
1 TTTCTCTTT--TCTT-TTCTT
1202710 TTTCTCTTTTCTTTTCTT
1 TTTCTCTTTTCTTTTCTT
1202728 TTTCTCTT
1 TTTCTCTT
1202736 GTATTTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
17 9 0.23
18 14 0.36
19 10 0.26
20 6 0.15
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTCTCTTTTCTTTTCTT
Found at i:1215603 original size:23 final size:22
Alignment explanation
Indices: 1215507--1215597 Score: 101
Period size: 24 Copynumber: 4.0 Consensus size: 22
1215497 GGCCCAAGTC
* *
1215507 GGGTTTGGTTTGGGCCTAGTTG
1 GGGTTTTGTTTGGGCCTAGTTT
*
1215529 GGGTTTTAATTTGGGGCCTAGTTT
1 GGGTTTT-GTTT-GGGCCTAGTTT
* *
1215553 GGGTTTTGATTTGGGGTCTGGTTT
1 GGGTTTTG-TTT-GGGCCTAGTTT
1215577 GGGTTTTGTTTGGGCCTAGTT
1 GGGTTTTGTTTGGGCCTAGTT
1215598 CAGGGTCTAG
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
22 14 0.24
23 6 0.10
24 38 0.66
ACGTcount: A:0.07, C:0.08, G:0.40, T:0.46
Consensus pattern (22 bp):
GGGTTTTGTTTGGGCCTAGTTT
Found at i:1215611 original size:34 final size:34
Alignment explanation
Indices: 1215566--1215635 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
1215556 TTTTGATTTG
* *
1215566 GGGTCTGGTTTGGGTTTTGTTTGGGCCTAGTTCA
1 GGGTCTAGTTTGGGTTTTATTTGGGCCTAGTTCA
*
1215600 GGGTCTAGTTTGGGTTTTATTTGGGCCTCGTTCA
1 GGGTCTAGTTTGGGTTTTATTTGGGCCTAGTTCA
1215634 GG
1 GG
1215636 TTTGTTTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.07, C:0.13, G:0.37, T:0.43
Consensus pattern (34 bp):
GGGTCTAGTTTGGGTTTTATTTGGGCCTAGTTCA
Found at i:1215958 original size:14 final size:14
Alignment explanation
Indices: 1215939--1215967 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1215929 TATATATATA
1215939 TGTGTGTGTCTGTG
1 TGTGTGTGTCTGTG
1215953 TGTGTGTGTCTGTG
1 TGTGTGTGTCTGTG
1215967 T
1 T
1215968 ATGAGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.41, T:0.52
Consensus pattern (14 bp):
TGTGTGTGTCTGTG
Found at i:1218889 original size:3 final size:3
Alignment explanation
Indices: 1218883--1218994 Score: 107
Period size: 3 Copynumber: 35.0 Consensus size: 3
1218873 ATAATACTAA
* *
1218883 TAT TAT TAT TAAT TAT TAT TAG TAT TAAT TAT TAT TAT TAAG TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT T-AT TAT TAT
* * *
1218931 TAT TACT TAT TGT TAAT TAT TGT TAT TAT TAT TAAT TGT TAT TAT TGAT
1 TAT TA-T TAT TAT T-AT TAT TAT TAT TAT TAT T-AT TAT TAT TAT T-AT
*
1218980 TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
1218995 AATCATAAGT
Statistics
Matches: 90, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
3 71 0.79
4 19 0.21
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1218901 original size:13 final size:13
Alignment explanation
Indices: 1218884--1218994 Score: 100
Period size: 13 Copynumber: 8.4 Consensus size: 13
1218874 TAATACTAAT
1218884 ATTATTATTAATT-
1 ATTATTATT-ATTA
*
1218897 ATTATTAGTATTA
1 ATTATTATTATTA
1218910 ATTATTATTATTA
1 ATTATTATTATTA
*
1218923 AGTATTATTATTA
1 ATTATTATTATTA
* *
1218936 CTTATTGTTAATTA
1 ATTATTATT-ATTA
*
1218950 TTGTTATTATTATTA
1 --ATTATTATTATTA
* *
1218965 ATTGTTATTATTG
1 ATTATTATTATTA
*
1218978 ATTGTTATTATT-
1 ATTATTATTATTA
1218990 ATTAT
1 ATTAT
1218995 AATCATAAGT
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
12 7 0.09
13 60 0.73
14 4 0.05
15 4 0.05
16 7 0.09
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.60
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:1218929 original size:16 final size:15
Alignment explanation
Indices: 1218883--1218994 Score: 75
Period size: 16 Copynumber: 7.2 Consensus size: 15
1218873 ATAATACTAA
1218883 TATTATTATTAATTAT
1 TATTATTATTAA-TAT
*
1218899 TATTAGTATT-A-AT
1 TATTATTATTAATAT
1218912 TATTATTATTAAGTAT
1 TATTATTATTAA-TAT
* *
1218928 TATTATTACTTATTGT
1 TATTATTA-TTAATAT
* *
1218944 TAATTATTGTTATTAT
1 T-ATTATTATTAATAT
* *
1218960 TATTAATTGTTATTAT
1 TATT-ATTATTAATAT
* *
1218976 TGATTGTTATTATTAT
1 T-ATTATTATTAATAT
1218992 TAT
1 TAT
1218995 AATCATAAGT
Statistics
Matches: 81, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
13 11 0.14
14 1 0.01
15 6 0.07
16 51 0.63
17 12 0.15
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (15 bp):
TATTATTATTAATAT
Found at i:1221490 original size:10 final size:10
Alignment explanation
Indices: 1221475--1221504 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1221465 TGGCAACTCC
1221475 AATTCAAAAT
1 AATTCAAAAT
*
1221485 AATTCAAACT
1 AATTCAAAAT
1221495 AATTCAAAAT
1 AATTCAAAAT
1221505 CCCAATTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (10 bp):
AATTCAAAAT
Found at i:1230515 original size:13 final size:13
Alignment explanation
Indices: 1230497--1230530 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1230487 GGACAATCTT
*
1230497 AGACACGACTTTG
1 AGACACAACTTTG
1230510 AGACACAACTTTG
1 AGACACAACTTTG
1230523 AGACACAA
1 AGACACAA
1230531 TTCACAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (13 bp):
AGACACAACTTTG
Found at i:1230868 original size:3 final size:3
Alignment explanation
Indices: 1230860--1230895 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1230850 TTCGATTAAT
1230860 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1230896 CTCGAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1235406 original size:134 final size:135
Alignment explanation
Indices: 1235232--1235500 Score: 515
Period size: 134 Copynumber: 2.0 Consensus size: 135
1235222 CACCTTCATT
1235232 GGAGAATTTGTACCATTTTGAATCTAGAGTACCTAACGAAATTAGATTTCTACTCAAACTTGGAA
1 GGAGAATTTGTACCATTTTGAATCTAGAGTACCTAACGAAATTAGATTTCTACTCAAACTTGGAA
1235297 CATGTCTCACATTACCAAGTGTTCGAACAATCCCATCAAACATCTTAATC-TAATTGTGACAATA
66 C-TGTCTCACATTACCAAGTGTTCGAACAATCCCATCAAACATCTTAATCTTAATTGTGACAATA
1235361 TCTGTG
130 TCTGTG
1235367 GGAGAATTTGTACCA-TTTGAATCTAGAGTACCTAACGAAATTAGATTTCTACTCAAACTTGGAA
1 GGAGAATTTGTACCATTTTGAATCTAGAGTACCTAACGAAATTAGATTTCTACTCAAACTTGGAA
1235431 CTGTCTCACATTACCAAGTGTTCGAACAATCCCATCAAACATCTTAATCTTAATTGTGACAATAT
66 CTGTCTCACATTACCAAGTGTTCGAACAATCCCATCAAACATCTTAATCTTAATTGTGACAATAT
1235496 CTGTG
131 CTGTG
1235501 ACTTTACAAG
Statistics
Matches: 133, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
133 48 0.36
134 70 0.53
135 15 0.11
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (135 bp):
GGAGAATTTGTACCATTTTGAATCTAGAGTACCTAACGAAATTAGATTTCTACTCAAACTTGGAA
CTGTCTCACATTACCAAGTGTTCGAACAATCCCATCAAACATCTTAATCTTAATTGTGACAATAT
CTGTG
Found at i:1242865 original size:194 final size:198
Alignment explanation
Indices: 1242530--1242924 Score: 735
Period size: 194 Copynumber: 2.0 Consensus size: 198
1242520 TCTAGTTATT
1242530 ATAGCATACATATATTCTATGGATATAACTGTTTGAACTTGGGTTTTCTAGTTTTTTTTATTATA
1 ATAGCATACATATATTCTATGGATATAACTGTTTGAACTTGGGTTTTCTAGTTTTTTTTATTATA
1242595 TTCTTACTAATAAGGCCTCGCAATGCATTTTAATTTTCATTGTTTTGATATAGTTAGAAGTGATT
66 -T-TTACTAATAAGGCCTCGCAATGCATTTTAATTTTCATTGTTTTGATATAGTTAGAAGTGATT
1242660 TATGGGAAATGATTGCAGGTGCGATAGGATACTGTGGAAAGGCGAAGGACTGAAGCAAATATGGT
129 TATGGGAAATGATTGCAGGTGCGATAGGATACTGTGGAAAGGCGAAGGACTGAAGCAAATATGGT
1242725 ACTCA
194 ACTCA
1242730 ATAGCATACATATATTCTATGGATATAACTGTTTGAACTTGGGTTTTCTAGTTTTTTTTA-T-TA
1 ATAGCATACATATATTCTATGGATATAACTGTTTGAACTTGGGTTTTCTAGTTTTTTTTATTATA
*
1242793 -TTA-TACTAAGGCCTCGCAATGCATTTTAATTTTCATTGTTTTGATATAGTTAGAAGTGATTTA
66 TTTACTAATAAGGCCTCGCAATGCATTTTAATTTTCATTGTTTTGATATAGTTAGAAGTGATTTA
1242856 TGGGAAATGATTGCAGGTGCGATAGGATACTGTGGAAAGGCGAAGGACTGAAGCAAATATGGTAC
131 TGGGAAATGATTGCAGGTGCGATAGGATACTGTGGAAAGGCGAAGGACTGAAGCAAATATGGTAC
1242921 TCA
196 TCA
1242924 A
1 A
1242925 GGGGCGAGTC
Statistics
Matches: 194, Mismatches: 1, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
194 128 0.66
195 3 0.02
198 2 0.01
199 1 0.01
200 60 0.31
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (198 bp):
ATAGCATACATATATTCTATGGATATAACTGTTTGAACTTGGGTTTTCTAGTTTTTTTTATTATA
TTTACTAATAAGGCCTCGCAATGCATTTTAATTTTCATTGTTTTGATATAGTTAGAAGTGATTTA
TGGGAAATGATTGCAGGTGCGATAGGATACTGTGGAAAGGCGAAGGACTGAAGCAAATATGGTAC
TCA
Found at i:1244034 original size:29 final size:30
Alignment explanation
Indices: 1244000--1244058 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
1243990 ATAGGATATT
1244000 CTTTGTT-GTCTCTCGACTA-TAAGAAGTTG
1 CTTTGTTAGTCTCTCGACTATTAA-AAGTTG
1244029 CTTTGTTGAGTCTCTCGACTATTAAAAGTT
1 CTTTGTT-AGTCTCTCGACTATTAAAAGTT
1244059 ACAAAATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 7 0.26
31 17 0.63
32 3 0.11
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (30 bp):
CTTTGTTAGTCTCTCGACTATTAAAAGTTG
Found at i:1245535 original size:20 final size:21
Alignment explanation
Indices: 1245488--1245537 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1245478 TTGGAGCGTG
1245488 GGGGGAATCGGTACCTCCTAT
1 GGGGGAATCGGTACCTCCTAT
1245509 GGGGGAATCGGTACCTCCTAT
1 GGGGGAATCGGTACCTCCTAT
1245530 -GGGGAATC
1 GGGGGAATC
1245538 AGTTCCCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.22
Consensus pattern (21 bp):
GGGGGAATCGGTACCTCCTAT
Found at i:1248118 original size:20 final size:20
Alignment explanation
Indices: 1248081--1248119 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1248071 AGATTGAGTG
* * *
1248081 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
1248101 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
1248120 AGTTTAAGAG
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:1248346 original size:21 final size:21
Alignment explanation
Indices: 1248275--1248357 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
1248265 CAGAACCCCA
* **
1248275 GGGGGGTATCGATTCCCTTGT
1 GGGGGGAATCGATTCCCTCAT
* * *
1248296 GGGGGGAATTGGTTCCCCTTCAA
1 GGGGGGAATCGATT-CCC-TCAT
* *
1248319 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGAATCGATTCCCTCAT
1248340 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
1248358 TGCACCAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
20 11 0.22
21 19 0.39
22 6 0.12
23 13 0.27
ACGTcount: A:0.14, C:0.23, G:0.36, T:0.27
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAT
Found at i:1248349 original size:20 final size:20
Alignment explanation
Indices: 1248320--1248357 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1248310 CCCCTTCAAA
*
1248320 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
1248340 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1248358 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:1252107 original size:21 final size:20
Alignment explanation
Indices: 1252073--1252112 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1252063 TGAGTTGTTT
1252073 TCATTTTTCAATTTTGAAAAA
1 TCATTTTTCAATTTT-AAAAA
1252094 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1252113 TAATTTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (20 bp):
TCATTTTTCAATTTTAAAAA
Found at i:1264061 original size:24 final size:23
Alignment explanation
Indices: 1264021--1264091 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 23
1264011 AAATATATTT
*
1264021 AATAATATAATATATTATTGTTAC
1 AATAATATAATATATTA-TATTAC
* *
1264045 AATAATATACTCA-ATTATATTAT
1 AATAATATAAT-ATATTATATTAC
1264068 AATAATATATGATACTATTATATT
1 AATAATATA--ATA-TATTATATT
1264092 CTTATTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 13 0.34
24 15 0.39
25 2 0.05
26 8 0.21
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (23 bp):
AATAATATAATATATTATATTAC
Found at i:1264249 original size:23 final size:22
Alignment explanation
Indices: 1264222--1264274 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1264212 TAGTCTAATA
1264222 ATATTA-TAAAAATTCCTTAAAAT
1 ATATTATTAAAAATT--TTAAAAT
*
1264245 ATATTATTAATAATTTTAAAAT
1 ATATTATTAAAAATTTTAAAAT
*
1264267 ATAATATT
1 ATATTATT
1264275 TTATTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 14 0.52
23 6 0.22
24 7 0.26
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTATTAAAAATTTTAAAAT
Found at i:1264280 original size:20 final size:21
Alignment explanation
Indices: 1264238--1264283 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1264228 TAAAAATTCC
*
1264238 TTAAAATATATTATTAATAATT
1 TTAAAATATAATATT-ATAATT
* *
1264260 TTAAAATATAATATTTTATTT
1 TTAAAATATAATATTATAATT
1264281 TTA
1 TTA
1264284 TAGATATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAAAATATAATATTATAATT
Found at i:1264469 original size:22 final size:20
Alignment explanation
Indices: 1264417--1264470 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
1264407 ATTATTCTAA
*
1264417 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
1264437 TAAGTTTTTATAATAAATAATAT
1 T-A-TTTTTATAAT-AATAATAT
1264460 TATTTATTATA
1 TATTT-TTATA
1264471 TTTTTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 15 0.52
23 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:1273113 original size:184 final size:183
Alignment explanation
Indices: 1272709--1273545 Score: 943
Period size: 183 Copynumber: 4.6 Consensus size: 183
1272699 GATACAAATA
* * ** * * * *
1272709 AAAAATGTATCG--ACACATATAATATATCATATAAAAATATGA-GAAATCGGGTTCAATATGAC
1 AAAAATGTATCGATACACA-ACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGAC
** * ** * *
1272771 AAAACCAATAAAGCGCTACCGGATATGTTGAAAGTATTAATTACATTGAAATAAGTATTAACACT
65 AAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTGAAATAAGTATCAACACT
* * * * * * *
1272836 TTTGAAATTTAAAAGAAAAGTAGTACTAGCGCCTAAAAAGTATAGATAATTTAT
130 TTTGGAATTCAAAAGAAAAATAGTAATAGCGCCTATAAAGTATTGATACTTTAT
* * *
1272890 AAAAATATATCGATACACAACAATATAACAGGTAAAAATATGATAAAAATGGTTTCATTATGACA
1 AAAAATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGACA
* * *
1272955 AAACCGGTAAAGCGCTACCAGATATATTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTT
66 AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTGAAATAAGTATCAACACTT
* * *
1273020 TTGGAATTTAAAAAGAAAAATAGTACTAGCGCCTA-AATAGTATCGATGA-TTTAT
131 TTGGAA-TTCAAAAGAAAAATAGTAATAGCGCCTATAA-AGTATTGAT-ACTTTAT
* * *
1273074 AAAAATGTATCAATATACAACAATATAACAGGTAAAAATATGATAAAAACGGTTTCATTATGACA
1 AAAAATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGACA
* * * * * * *
1273139 AAACCAGTAAAACACTACCAGATATGTTGAAAGTTTCGATTTCATTTAAACAAGTATCAACACTT
66 AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTGAAATAAGTATCAACACTT
* * *
1273204 TTGGAATTCAAAAGAAAAATAATAATAGCGTCTATAAAGTGTTGATACTTTAT
131 TTGGAATTCAAAAGAAAAATAGTAATAGCGCCTATAAAGTATTGATACTTTAT
* * * ** * *
1273257 ATAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATTGGTTTCACTATGATT
1 AAAAATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGA-C
* * * *
1273322 AAAA-TGGTAAAGCGATATC-GAATATGTTGAAAGTATCGATTCCATTGAAATAAGTATCGACAC
65 AAAACCGGTAAAGCGCTACCAG-ATATGTTGAAAGTATCGATTCCATTGAAATAAGTATCAACAC
* *
1273385 TTTTGGAATTCAAAAGAAAAGA-AGTAATAACGCCTATAAAGTGTTGATACTTTAT
129 TTTTGGAATTCAAAAGAAAA-ATAGTAATAGCGCCTATAAAGTATTGATACTTTAT
** * * * *
1273440 AAAATATGCGTCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATTTCATTATGAC
1 AAAA-ATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGAC
* * * *
1273505 AAAACCGGTAAAGCGCTATCGGATATGTTGAATGTGTCGAT
65 AAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGAT
1273546 ACTTTAATAA
Statistics
Matches: 564, Mismatches: 78, Indels: 25
0.85 0.12 0.04
Matches are distributed among these distances:
181 11 0.02
182 22 0.04
183 276 0.49
184 253 0.45
185 2 0.00
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (183 bp):
AAAAATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGACA
AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTGAAATAAGTATCAACACTT
TTGGAATTCAAAAGAAAAATAGTAATAGCGCCTATAAAGTATTGATACTTTAT
Found at i:1273465 original size:367 final size:366
Alignment explanation
Indices: 1272740--1273545 Score: 1005
Period size: 367 Copynumber: 2.2 Consensus size: 366
1272730 ATATATCATA
* * * * *
1272740 TAAAAATATGAGAAATCGGGTTCAATATGACAAAACCAATAAAGCGCTACCGGATATGTTGAAAG
1 TAAAAATATGAAAAAACGGTTTCATTATGACAAAACCAGTAAAGCGCTACCGGATATGTTGAAAG
* * * * * * *
1272805 TATT-AATTACATTGAAATAAGTATTAACACTTTTGAAATTTAAAAGAAAAGTAGTACTAGCGCC
66 T-TTCGATTACATTGAAACAAGTATCAACACTTTTGAAATTCAAAAGAAAAATAATAATAGCGCC
*
1272869 TAAAAAGTATAGATAATTTATAAAAATATATCGATACACAACAATATAACAGGTAAAAATATGAT
130 TAAAAAGTATAGATAATTTATAAAAATATATCGATACACAACAATATAACAGGTAAAAATATGAC
* *
1272934 AAAAATGGTTTCATTATGACAAAACCGGTAAAGCGCTACCAGATATATTGAAAGTATCGATTCCA
195 AAAAATGGTTTCACTATGACAAAACCGGTAAAGCGATACCAGATATATTGAAAGTATCGATTCCA
* * *
1272999 TTTAAATAAGTATCGACACTTTTGGAATTTAAAAAGAAAAATAGTACTAGCGCCTAAATAGTATC
260 TTGAAATAAGTATCGACACTTTTGGAATTTAAAAAGAAAAATAGTAATAACGCCTAAATAGTATC
* *
1273064 GATGATTTATAAAAATGTATCAATATACAACAATATAACAGG
325 GATGATTTATAAAAATGCATCAATACACAACAATATAACAGG
* * *
1273106 TAAAAATATGATAAAAACGGTTTCATTATGACAAAACCAGTAAAACACTACCAGATATGTTGAAA
1 TAAAAATATGA-AAAAACGGTTTCATTATGACAAAACCAGTAAAGCGCTACCGGATATGTTGAAA
* * * *
1273171 GTTTCGATTTCATTTAAACAAGTATCAACACTTTTGGAATTCAAAAGAAAAATAATAATAGCGTC
65 GTTTCGATTACATTGAAACAAGTATCAACACTTTTGAAATTCAAAAGAAAAATAATAATAGCGCC
* * * * * * * *
1273236 TATAAAGTGTTGATACTTTATATAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAC
130 TAAAAAGTATAGATAATTTATAAAAATATATCGATACACAACAATATAACAGGTAAAAATATGAC
* * * * *
1273301 AAAATTGGTTTCACTATGATTAAAA-TGGTAAAGCGATATC-GAATATGTTGAAAGTATCGATTC
195 AAAAATGGTTTCACTATGA-CAAAACCGGTAAAGCGATACCAG-ATATATTGAAAGTATCGATTC
*
1273364 CATTGAAATAAGTATCGACACTTTTGGAA-TTCAAAAGAAAAGA-AGTAATAACGCCTATAA-AG
258 CATTGAAATAAGTATCGACACTTTTGGAATTTAAAAAGAAAA-ATAGTAATAACGCCTA-AATAG
* * * * * *
1273426 TGTTGAT-ACTTTATAAAATATGCGTCGATCCATAACAATATAACAGG
321 TATCGATGA-TTTATAAAA-ATGCATCAATACACAACAATATAACAGG
* * * * *
1273473 TAAAAATATGACAAAACCGATTTCATTATGACAAAACCGGTAAAGCGCTATCGGATATGTTGAAT
1 TAAAAATATGA-AAAAACGGTTTCATTATGACAAAACCAGTAAAGCGCTACCGGATATGTTGAAA
*
1273538 GTGTCGAT
65 GTTTCGAT
1273546 ACTTTAATAA
Statistics
Matches: 375, Mismatches: 57, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
365 1 0.00
366 53 0.14
367 317 0.85
368 4 0.01
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (366 bp):
TAAAAATATGAAAAAACGGTTTCATTATGACAAAACCAGTAAAGCGCTACCGGATATGTTGAAAG
TTTCGATTACATTGAAACAAGTATCAACACTTTTGAAATTCAAAAGAAAAATAATAATAGCGCCT
AAAAAGTATAGATAATTTATAAAAATATATCGATACACAACAATATAACAGGTAAAAATATGACA
AAAATGGTTTCACTATGACAAAACCGGTAAAGCGATACCAGATATATTGAAAGTATCGATTCCAT
TGAAATAAGTATCGACACTTTTGGAATTTAAAAAGAAAAATAGTAATAACGCCTAAATAGTATCG
ATGATTTATAAAAATGCATCAATACACAACAATATAACAGG
Found at i:1273962 original size:17 final size:16
Alignment explanation
Indices: 1273940--1274008 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
1273930 CCGTGTCCCG
*
1273940 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
1273957 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
1273972 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
* * *
1273989 ACACGG-TAATAGGGT
1 ACCCGGATATTCGGGT
1274004 ACCCG
1 ACCCG
1274009 ATACCCGGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
15 19 0.46
16 6 0.15
17 16 0.39
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.22
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:1273972 original size:15 final size:15
Alignment explanation
Indices: 1273952--1274008 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1273942 CCGGATGTTA
1273952 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
1273967 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
*
1273983 GCGGGTACACGGTAAT
1 -CGGGTACCCGGTAAT
*
1273999 AGGGTACCCG
1 CGGGTACCCG
1274009 ATACCCGGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 19 0.58
16 4 0.12
17 10 0.30
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:1273976 original size:32 final size:32
Alignment explanation
Indices: 1273940--1274008 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
1273930 CCGTGTCCCG
* *
1273940 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACACGGTAATAGGGT
* *
1273972 ACCCGGATTTTGCGGGTACACGGTAATAGGGT
1 ACCCGGATGTTACGGGTACACGGTAATAGGGT
1274004 ACCCG
1 ACCCG
1274009 ATACCCGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACACGGTAATAGGGT
Found at i:1275600 original size:36 final size:36
Alignment explanation
Indices: 1275550--1275621 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1275540 GCTATTGGGA
* * *
1275550 AGGGGGTTGTTGTGAGGGGACTATGAGGATGTCATT
1 AGGGGGCTGCTGTGAGGGAACTATGAGGATGTCATT
1275586 AGGGGGCTGCTGTGAGGGAACTATGAGGATGTCATT
1 AGGGGGCTGCTGTGAGGGAACTATGAGGATGTCATT
1275622 TGTATGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.21, C:0.08, G:0.43, T:0.28
Consensus pattern (36 bp):
AGGGGGCTGCTGTGAGGGAACTATGAGGATGTCATT
Found at i:1279117 original size:15 final size:15
Alignment explanation
Indices: 1279097--1279126 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1279087 TAGTAGGGTA
1279097 GGATGAAGGTGAGGG
1 GGATGAAGGTGAGGG
*
1279112 GGATGACGGTGAGGG
1 GGATGAAGGTGAGGG
1279127 AAAACAAAGT
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:0.23, C:0.03, G:0.60, T:0.13
Consensus pattern (15 bp):
GGATGAAGGTGAGGG
Found at i:1283477 original size:199 final size:199
Alignment explanation
Indices: 1283123--1284462 Score: 1821
Period size: 199 Copynumber: 6.7 Consensus size: 199
1283113 ATATAATGTA
* * *
1283123 TCGATA-ATTTTAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGTTA
1 TCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTA
* * * * *
1283187 AATTTACAATGTAACCGATA-AGAATATACCGGTTTTATGACAGAATAGGTCAACATATTGTGTC
66 AATTTACAATGTAACCGGTAGA-AATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATC
** * * * * *
1283251 GATTCTTTTTAAAATTATGTTGATACTTTTGGTCCATAATGAATGCCCAACGAGATGCACACATA
130 GACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATA
1283316 AAGTG
195 AAGTG
* * *
1283321 TCGATACATTTAAAATTGTATCAATCCCGAAAACATCGAAACCGATAATTACAATGTAATAGGTA
1 TCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTA
* * * * * *
1283386 AATTTACAATATAACCAGTAGAAATATACCGGTTTAATTAGAAAATAGGTTAACATAATGTATCA
66 AATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATCG
** *
1283451 ACACTTTTTAAATTTGTGTCGATACTTTTTATCCCGAATGAATGCCCAACGA-AGTGCACGCATA
131 ACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGA-TGCACGCATA
1283515 AAGTG
195 AAGTG
* * *
1283520 TTGATACATTTAAAATTGTATCGATCCTAAAAACATCGAAACCTATAATTATAATGTAATAGGTA
1 TCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTA
** * * * * *
1283585 AATTTACAATGTAACCGGTAGAAATATA--TTTTCTTAATTAGAAAATTGGTCCATATAATGTAG
66 AATTTACAATGTAACCGGTAGAAATATACCGGTT-TT-ATGAGAAAATAGGTCAACATAATGTAT
*
1283648 CGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGTACGCAT
129 CGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCAT
1283713 AAAGTG
194 AAAGTG
* *
1283719 TCGATACATTTAAAATTGTATCGATCCCAAAAATATCGAACCCGATAATTATAATGTAATAGGTA
1 TCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTA
* ** * *
1283784 AATTTACAATGTAACCGGTATAAATATACCAATTTTATGAGAAAATATGTCAAAATAATGTATCG
66 AATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATCG
* * * *
1283849 AAACTTTTTAAATTTGTGTCGATACTTTTGGTCTAGAATGAATGCCCAACGAGGTGCATGCATAA
131 ACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATAA
1283914 AGTG
196 AGTG
* *
1283918 TCGATACATTTAAAATTGTATCGATCCCAAAAACATC-AAACCCGGTAATTATAATGTAATAAGT
1 TCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAA-CCGATAATTATAATGTAATAGGT
* ** * *
1283982 AAATTTACAATATAACCAATAGAAATATACCGGTTTTATGAGAAAATATGTCAACATAATGAATC
65 AAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATC
* * **
1284047 GACACTTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGGCCAACGAGGTGCACATAT
130 GACAC-TTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCAT
1284112 AAAGTG
194 AAAGTG
* *
1284118 TCGATACATTTAAAATTGTATCGATCCCAAAAACATTGAACCCGATAATTATAATGTAATAGGTA
1 TCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTA
* * * * *
1284183 AATTAACAATGTAACCGGTAGAAATATATCAGTTTTATGAGAAATTAGGTCAACATAATGTATCA
66 AATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATCG
* * *
1284248 ATACTTTTTAAATTTGTGTCGATACTTTTGGTCTAGAATGAATGCCCAACGAGGTGCACGCATAA
131 ACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATAA
1284313 AGTG
196 AGTG
* * * * *
1284317 TGGATACATTTAAAATTGTATCGATCCAAAAAAAAAATCAAAACCAATAATTATAATGTAATAGG
1 TCGATACATTTAAAATTGTATCGATCC--CAAAAACATCGAAACCGATAATTATAATGTAATAGG
* * * * * * *
1284382 TAAATTTACAATGTAACCGGTAAAAATATATC-GTTTTATGATATAATATGTAAACATATTGTAT
64 TAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTAT
1284446 CGACACTTTTTAAATTT
129 CGACACTTTTTAAATTT
1284463 TATCGATTTT
Statistics
Matches: 1008, Mismatches: 121, Indels: 24
0.87 0.10 0.02
Matches are distributed among these distances:
197 2 0.00
198 10 0.01
199 711 0.71
200 221 0.22
201 64 0.06
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (199 bp):
TCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTA
AATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATCG
ACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATAA
AGTG
Found at i:1285882 original size:6 final size:6
Alignment explanation
Indices: 1285842--1285881 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
1285832 CAAGCACTCA
* *
1285842 ATGAAG ATGACG ATGAAG ATGAAG ATGAAG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
1285882 TAATCTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:1287294 original size:30 final size:30
Alignment explanation
Indices: 1287260--1287317 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1287250 TTTCATGTTC
1287260 ATTTCATATTT-AATTGGAGTTTGAATTTAA
1 ATTTCA-ATTTGAATTGGAGTTTGAATTTAA
* *
1287290 ATTTCAATTTGAGTTTGAGTTTGAATTT
1 ATTTCAATTTGAATTGGAGTTTGAATTT
1287318 CAATATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (30 bp):
ATTTCAATTTGAATTGGAGTTTGAATTTAA
Found at i:1287298 original size:24 final size:24
Alignment explanation
Indices: 1287267--1287321 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1287257 TTCATTTCAT
1287267 ATTT-AATTGGAGTTTGAATTTAA
1 ATTTCAATTGGAGTTTGAATTTAA
* * *
1287290 ATTTCAATTTGAGTTTGAGTTTGA
1 ATTTCAATTGGAGTTTGAATTTAA
1287314 ATTTCAAT
1 ATTTCAAT
1287322 ATAAATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (24 bp):
ATTTCAATTGGAGTTTGAATTTAA
Found at i:1289095 original size:200 final size:200
Alignment explanation
Indices: 1288747--1289220 Score: 661
Period size: 200 Copynumber: 2.4 Consensus size: 200
1288737 GTATCGACAT
* *
1288747 ATTTATTGTAAGTATCGATCCC-AAAATCATCTAAACCGATAATTATAAAGTAATAGGTAAATTT
1 ATTTATTGTAAGTATCGATCCCAAAAAT-ATCGAAACCGATAATTATAATGTAATAGGTAAATTT
* * * * * *
1288811 ACAAAGTAACCGGTAAAAATATACCCGTTTTATGACAAAATAGTTCAACAAAATGTATCGATACT
65 ACAATGTAACCAGTAAAAATATACCCGTTTAATGACAAAATAGGTCAACAAAATATATCGATAAT
* *
1288876 TTTTAAATTTGTATCGATACTTTTGGTCCAGAATGAATGTCCAACGAGGTGCCCACATAAAGTGT
130 TTTTAAATTTGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGT
1288941 CGATAC
195 CGATAC
*
1288947 ATTTATTGTAAGTATTGATCCCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTTA
1 ATTTATTGTAAGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTTA
* * * * * *
1289012 CAATTTAACTAGTAGAAATATA-CCGATTTAATTAGAAAATAGGTCAACATAATATATCGATAAT
66 CAATGTAACCAGTAAAAATATACCCG-TTTAATGACAAAATAGGTCAACAAAATATATCGATAAT
* * *
1289076 TTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAATGAGGTGCACGCATAAAGTGT
130 TTTTAAATTTGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGT
1289141 CGATAC
195 CGATAC
* * * *
1289147 ATTTAAATT-T--GTATCAATCCCAAAAACATCGAACCCAATAATTATAATGTAATAGGTAAATT
1 ATTT--ATTGTAAGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATT
1289209 TACAATGTAACC
64 TACAATGTAACC
1289221 GGTAGATGTA
Statistics
Matches: 243, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
199 60 0.25
200 174 0.72
201 6 0.02
202 3 0.01
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.32
Consensus pattern (200 bp):
ATTTATTGTAAGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTTA
CAATGTAACCAGTAAAAATATACCCGTTTAATGACAAAATAGGTCAACAAAATATATCGATAATT
TTTAAATTTGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTC
GATAC
Found at i:1289336 original size:164 final size:163
Alignment explanation
Indices: 1289066--1289390 Score: 560
Period size: 164 Copynumber: 2.0 Consensus size: 163
1289056 CAACATAATA
* *
1289066 TATCGATAATTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAATGAGGTGCACG
1 TATCGATAATTTTTAAATTTATGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACG
*
1289131 CATAAAGTGTCGATACATTTAAATTTGTATCAATCCCAAAAACATCGAACCCAATAATTATAATG
66 CATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCCAATAATTATAATG
1289196 TAATAGGTAAATTTACAATGTAACCGGTAGATG
131 TAATAGGTAAATTTACAATGTAACCGGTAGATG
* *
1289229 TATCGATACTTTTTAAAATTTATGTCGATACTTTTGGTCCAGAATGAATGCCTAACGAGGTGCAC
1 TATCGATAATTTTT-AAATTTATGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCAC
**
1289294 GCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCTGATAATTATAAT
65 GCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCCAATAATTATAAT
* *
1289359 GTAATATGTAAATTTACAATGTAACTGGTAGA
130 GTAATAGGTAAATTTACAATGTAACCGGTAGA
1289391 AATATACCAG
Statistics
Matches: 152, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
163 13 0.09
164 139 0.91
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (163 bp):
TATCGATAATTTTTAAATTTATGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACG
CATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCCAATAATTATAATG
TAATAGGTAAATTTACAATGTAACCGGTAGATG
Found at i:1289562 original size:365 final size:363
Alignment explanation
Indices: 1288863--1289591 Score: 1160
Period size: 365 Copynumber: 2.0 Consensus size: 363
1288853 GTTCAACAAA
*
1288863 ATGTATCGATACTTTTTAAATTTGTATCGATACTTTTGGTCCAGAATGAATGTCCAACGAGGTGC
1 ATGTATCGATACTTTTTAAATTTATATCGATACTTTTGGTCCAGAATGAATGTCCAACGAGGTGC
* *** ** *
1288928 CCACATAAAGTGTCGATACATTTATTGTAAGTATTGATCCCAAAAATATCGAAACCGATAATTAT
66 ACACATAAAGTGTCGATACATTTAAAATAAGTATCAATCCCAAAAACATCGAAACCGATAATTAT
*
1288993 AATGTAATAGGTAAATTTACAATTTAACTAGTAGAAATATACCGATTTAATTAGAAAATAGGTCA
131 AATGTAATAGGTAAATTTACAATGTAACTAGTAGAAATATACCGATTTAATTAGAAAATAGGTCA
* * *
1289058 ACATAATATATCGATAATTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAATGA
196 ACATAATATATCGATAATTTTTAAATTTGTGTCGATACTTTTGGTACAAAATGAATGCCCAACGA
*
1289123 GGTGCACGCATAAAGTGTCGATACATTTAAATTTGTATCAATCCCAAAAACATCGAACCCAATAA
261 GGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCCAATAA
1289188 TTATAATGTAATAGGTAAATTTACAATGTAACCGGTAG
326 TTATAATGTAATAGGTAAATTTACAATGTAACCGGTAG
*
1289226 ATGTATCGATACTTTTTAAAATTTATGTCGATACTTTTGGTCCAGAATGAATG-CCTAACGAGGT
1 ATGTATCGATACTTTTT-AAATTTATATCGATACTTTTGGTCCAGAATGAATGTCC-AACGAGGT
* *
1289290 GCACGCATAAAGTGTCGATACATTTAAAAT-TGTATCAATCCCAAAAACATCG-AACCTGATAAT
64 GCACACATAAAGTGTCGATACATTTAAAATAAGTATCAATCCCAAAAACATCGAAACC-GATAAT
* * *
1289353 TATAATGTAATATGTAAATTTACAATGTAACTGGTAGAAATATACC-AGTTTAATTAGAAAATAT
128 TATAATGTAATAGGTAAATTTACAATGTAACTAGTAGAAATATACCGA-TTTAATTAGAAAATAG
* *
1289417 GTCAACATAATGTATCGATACTTTTTTAAAATTTGTGTCGATACTTTTGGTACAAAATGAATGCC
192 GTCAACATAATATATCGATA-ATTTTT-AAATTTGTGTCGATACTTTTGGTACAAAATGAATGCC
*
1289482 TAACGAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACC
255 CAACGAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACC
* *
1289547 CGATAATTATAATGTAATAGGTAAATTTACAATGTAACTGGTAG
320 CAATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAG
1289591 A
1 A
1289592 AATATACCAG
Statistics
Matches: 336, Mismatches: 24, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
362 5 0.01
363 120 0.36
364 71 0.21
365 140 0.42
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (363 bp):
ATGTATCGATACTTTTTAAATTTATATCGATACTTTTGGTCCAGAATGAATGTCCAACGAGGTGC
ACACATAAAGTGTCGATACATTTAAAATAAGTATCAATCCCAAAAACATCGAAACCGATAATTAT
AATGTAATAGGTAAATTTACAATGTAACTAGTAGAAATATACCGATTTAATTAGAAAATAGGTCA
ACATAATATATCGATAATTTTTAAATTTGTGTCGATACTTTTGGTACAAAATGAATGCCCAACGA
GGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCCAATAA
TTATAATGTAATAGGTAAATTTACAATGTAACCGGTAG
Found at i:1289751 original size:199 final size:200
Alignment explanation
Indices: 1289226--1289913 Score: 1076
Period size: 201 Copynumber: 3.5 Consensus size: 200
1289216 TAACCGGTAG
* * *
1289226 ATGTATCGATACTTTTTAAAATTTATGTCGATACTTTTGGTCCAGAATGAATGCCTAACGAGGTG
1 ATGTATCGACACTTTTTAAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTG
*
1289291 CACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCTGATAATTAT
66 CACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCCGATAATTAT
* *
1289356 AATGTAATATGTAAATTTACAATGTAACTGGTAGAAATATACCAGTTTAATTAGAAAATATGTCA
131 AATGTAATAGGTAAATTTACAATGTAACTGGTAGAAATATACCAGTTTAATTAGAAAATAGGTCA
1289421 ACATA
196 ACATA
* * * *
1289426 ATGTATCGATACTTTTTTAAAATTTGTGTCGATACTTTTGGTACAAAATGAATGCCTAACGAGGT
1 ATGTATCGACAC-TTTTTAAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGT
1289491 GCACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCCGATAATTA
65 GCACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCCGATAATTA
1289556 TAATGTAATAGGTAAATTTACAATGTAACTGGTAGAAATATACCAGTTTAATTAGAAAATAGGTC
130 TAATGTAATAGGTAAATTTACAATGTAACTGGTAGAAATATACCAGTTTAATTAGAAAATAGGTC
1289621 AACATA
195 AACATA
* * *
1289627 ATGTATCGACACTTTTT-AAATTTGTGTCGATACTTTTTGTCCAGAATGAATACCCAACGAGGTA
1 ATGTATCGACACTTTTTAAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTG
* * *
1289691 CACGCATAAAGTATCGATACATTTAAAATTGTATCGATCCCAAAAACATCTAACCCGATAATTAT
66 CACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCCGATAATTAT
* * ** * * * *
1289756 AATGTAATAGGTAAATTTACAATGTAACAGGTAAAAATATACTGGTTTTATGAGAGAATAGGTAA
131 AATGTAATAGGTAAATTTACAATGTAACTGGTAGAAATATACCAGTTTAATTAGAAAATAGGTCA
1289821 ACATA
196 ACATA
* ** *
1289826 TTGTATCGACACTTTTT-AAA-TTGTAACGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTG
1 ATGTATCGACACTTTTTAAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTG
* *
1289889 CACACATAAAGTGTCGATACCTTTA
66 CACGCATAAAGTGTCGATACATTTA
1289914 TTGTAAGTAT
Statistics
Matches: 455, Mismatches: 32, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
198 61 0.13
199 184 0.40
200 17 0.04
201 193 0.42
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (200 bp):
ATGTATCGACACTTTTTAAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTG
CACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATCGAACCCGATAATTAT
AATGTAATAGGTAAATTTACAATGTAACTGGTAGAAATATACCAGTTTAATTAGAAAATAGGTCA
ACATA
Found at i:1289850 original size:20 final size:20
Alignment explanation
Indices: 1289825--1289862 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1289815 AGGTAAACAT
*
1289825 ATTGTATCGACACTTTTTAA
1 ATTGTAACGACACTTTTTAA
*
1289845 ATTGTAACGATACTTTTT
1 ATTGTAACGACACTTTTT
1289863 GTCCAGAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (20 bp):
ATTGTAACGACACTTTTTAA
Found at i:1292439 original size:45 final size:45
Alignment explanation
Indices: 1292340--1292443 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
1292330 AATTGTTCAG
* *
1292340 TGTGTATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
1 TGTGTATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATT
* * * **
1292385 AGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTGATT
1 TGTGTATCGATGCA-CCCATTAAAAATGAAAACATCGAAGGCAATT
1292430 TGTGTATCGATGCA
1 TGTGTATCGATGCA
1292444 TGGGTAGTGC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 44 0.90
46 5 0.10
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (45 bp):
TGTGTATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATT
Found at i:1294279 original size:2 final size:2
Alignment explanation
Indices: 1294272--1294296 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1294262 CCACACGTAT
1294272 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 T
1294297 TCCATACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1294760 original size:23 final size:23
Alignment explanation
Indices: 1294731--1294791 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1294721 TATGTAATTA
1294731 ACCTATTTTATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
* ***
1294754 AGCTATTACGTTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
*
1294777 ACCTAATATTATTAT
1 ACCT-ATTTTATTAT
1294792 GTTTGATAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (23 bp):
ACCTATTTTATTATATAAGCGCT
Found at i:1294923 original size:156 final size:157
Alignment explanation
Indices: 1294596--1294923 Score: 505
Period size: 156 Copynumber: 2.1 Consensus size: 157
1294586 ATAATGTGCA
* * **
1294596 ACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATA-GTTATTATGCTTGATAATATTAACAGTAATTAA
** *
1294661 CCGGTTATGTTATCATTGATAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTATGT
65 CCGACTATGTTATCATTGATAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
1294726 AATTAACCTATTTTATTATATAAGCGCT
130 AATTAACCTATTTTATTATATAAGCGCT
* * *
1294754 AGCTATTACGTTATATAAGCGCTACCTAATA-TTATTATGTTTGATAATATTAACGGTAATTAAC
1 ACCTATTACGTTATATAAGCGCTACCTAATAGTTATTATGCTTGATAATATTAACAGTAATTAAC
* * *
1294818 CGACTATGTTATCCTTGGTAATATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTA
66 CGACTATGTTATCATTGATAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTA
1294883 ATTAACCTATTTTATTATATAAGCGCT
131 ATTAACCTATTTTATTATATAAGCGCT
* *
1294910 ACCTAATATGTTAT
1 ACCTATTACGTTAT
1294924 TATGCTTGAT
Statistics
Matches: 154, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
156 125 0.81
158 29 0.19
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (157 bp):
ACCTATTACGTTATATAAGCGCTACCTAATAGTTATTATGCTTGATAATATTAACAGTAATTAAC
CGACTATGTTATCATTGATAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTA
ATTAACCTATTTTATTATATAAGCGCT
Found at i:1295656 original size:18 final size:20
Alignment explanation
Indices: 1295615--1295657 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1295605 TATGACCATA
1295615 AATTATCAAAAAAATAACGC
1 AATTATCAAAAAAATAACGC
*
1295635 AATTATCAAAATAA-AACG-
1 AATTATCAAAAAAATAACGC
1295653 AATTA
1 AATTA
1295658 AAAATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 4 0.18
20 13 0.59
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (20 bp):
AATTATCAAAAAAATAACGC
Found at i:1296180 original size:29 final size:25
Alignment explanation
Indices: 1296110--1296180 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 25
1296100 TTTTAAAAAA
1296110 TATTAAAAATATATTAAATTTTAATTT
1 TATTAAAAATA-A-TAAATTTTAATTT
1296137 TATTAAAAATGAATACACATTATTAATTTT
1 TATTAAAAAT-AATA-A-ATT-TTAA-TTT
1296167 TATTAAAAATAATA
1 TATTAAAAATAATA
1296181 TTTAATGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
26 2 0.05
27 12 0.31
28 4 0.10
29 8 0.21
30 13 0.33
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (25 bp):
TATTAAAAATAATAAATTTTAATTT
Found at i:1305034 original size:24 final size:24
Alignment explanation
Indices: 1305002--1305055 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1304992 CAGACAAAAA
1305002 GAATGAGAACAAGGAAGTCGCTGT
1 GAATGAGAACAAGGAAGTCGCTGT
1305026 GAATGAGAACAAGGAAGTCGCTGT
1 GAATGAGAACAAGGAAGTCGCTGT
1305050 GAATGA
1 GAATGA
1305056 CTTCTGCCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.33, T:0.17
Consensus pattern (24 bp):
GAATGAGAACAAGGAAGTCGCTGT
Found at i:1306322 original size:22 final size:19
Alignment explanation
Indices: 1306275--1306349 Score: 71
Period size: 18 Copynumber: 3.8 Consensus size: 19
1306265 ATATGCCTTA
* * *
1306275 GGGTATCGGTACCATCTGAG
1 GGGTATCGATACCTTATG-G
1306295 GGGTATCGATACCATTGCATGG
1 GGGTATCGATACC-TT--ATGG
1306317 GGGTATCGATA-CTTATGG
1 GGGTATCGATACCTTATGG
*
1306335 GGGTATCGGTACCTT
1 GGGTATCGATACCTT
1306350 TTGAATATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 14 0.30
19 3 0.06
20 14 0.30
21 2 0.04
22 12 0.26
23 2 0.04
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.29
Consensus pattern (19 bp):
GGGTATCGATACCTTATGG
Found at i:1306336 original size:18 final size:21
Alignment explanation
Indices: 1306275--1306347 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 21
1306265 ATATGCCTTA
*
1306275 GGGTATCGGTACCA-TC-TGAG
1 GGGTATCGATACCATTCATG-G
1306295 GGGTATCGATACCATTGCATGG
1 GGGTATCGATACCATT-CATGG
1306317 GGGTATCGATA-C-TT-ATGG
1 GGGTATCGATACCATTCATGG
*
1306335 GGGTATCGGTACC
1 GGGTATCGATACC
1306348 TTTTGAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
18 14 0.30
19 1 0.02
20 15 0.32
21 2 0.04
22 13 0.28
23 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (21 bp):
GGGTATCGATACCATTCATGG
Found at i:1309076 original size:23 final size:23
Alignment explanation
Indices: 1309045--1309148 Score: 103
Period size: 23 Copynumber: 4.7 Consensus size: 23
1309035 TTGTACCATT
1309045 AGGGGGTATCGATACCCATTC-A
1 AGGGGGTATCGATACCCATTCAA
*
1309067 AGGGAGGTATCGATACCTATTGC--
1 AGGG-GGTATCGATACCCATT-CAA
**
1309090 A-GGGGTATCGATACTTATTCAA
1 AGGGGGTATCGATACCCATTCAA
**
1309112 AGGGGGTATCGATA-CCATTCTC
1 AGGGGGTATCGATACCCATTCAA
1309134 A-GGGGTATCGATACC
1 AGGGGGTATCGATACC
1309149 TTATGCACAA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
20 1 0.01
21 27 0.39
22 13 0.19
23 28 0.40
24 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (23 bp):
AGGGGGTATCGATACCCATTCAA
Found at i:1309096 original size:44 final size:44
Alignment explanation
Indices: 1309047--1309148 Score: 145
Period size: 44 Copynumber: 2.3 Consensus size: 44
1309037 GTACCATTAG
1309047 GGGGTATCGATACCCATTC-AAGGGAGGTATCGATACCTATT-GCA
1 GGGGTATCGATACCCATTCAAAGGG-GGTATCGATACC-ATTCGCA
** *
1309091 GGGGTATCGATACTTATTCAAAGGGGGTATCGATACCATTCTCA
1 GGGGTATCGATACCCATTCAAAGGGGGTATCGATACCATTCGCA
1309135 GGGGTATCGATACC
1 GGGGTATCGATACC
1309149 TTATGCACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
43 3 0.06
44 44 0.85
45 5 0.10
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (44 bp):
GGGGTATCGATACCCATTCAAAGGGGGTATCGATACCATTCGCA
Found at i:1309098 original size:21 final size:22
Alignment explanation
Indices: 1309045--1309149 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 22
1309035 TTGTACCATT
*
1309045 AGGGGGTATCGATACCCATTCA
1 AGGGGGTATCGATACCTATTCA
1309067 AGGGAGGTATCGATACCTATTGC-
1 AGGG-GGTATCGATACCTATT-CA
*
1309090 A-GGGGTATCGATACTTATTCAA
1 AGGGGGTATCGATACCTATTC-A
*
1309112 AGGGGGTATCGATACC-ATTCTC
1 AGGGGGTATCGATACCTATTC-A
1309134 A-GGGGTATCGATACCT
1 AGGGGGTATCGATACCT
1309150 TATGCACAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.01
21 29 0.40
22 12 0.17
23 29 0.40
24 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (22 bp):
AGGGGGTATCGATACCTATTCA
Found at i:1312970 original size:22 final size:21
Alignment explanation
Indices: 1312928--1312967 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1312918 GAGCTTATTT
*
1312928 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1312949 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1312968 ACAATTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1314610 original size:21 final size:20
Alignment explanation
Indices: 1314565--1314637 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
1314555 ATATGCCTTA
*
1314565 GGGTATCGGTACCATCTGAG
1 GGGTATCGATACCATCTGAG
1314585 GGGTATCGATACCAT-TGCATG
1 GGGTATCGATACCATCTG-A-G
* *
1314606 GGGTATCGATACC-TATGGG
1 GGGTATCGATACCATCTGAG
*
1314625 GGGTATCGGTACC
1 GGGTATCGATACC
1314638 TTTCGAGCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
19 15 0.32
20 16 0.34
21 16 0.34
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCATCTGAG
Found at i:1314625 original size:17 final size:19
Alignment explanation
Indices: 1314565--1314618 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
1314555 ATATGCCTTA
*
1314565 GGGTATCGGTACCATC-TGAG
1 GGGTATCGATACCATCAT--G
1314585 GGGTATCGATACCATTGCATG
1 GGGTATCGATACCA-T-CATG
1314606 GGGTATCGATACC
1 GGGTATCGATACC
1314619 TATGGGGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 13 0.43
21 15 0.50
22 1 0.03
23 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.26
Consensus pattern (19 bp):
GGGTATCGATACCATCATG
Found at i:1314629 original size:19 final size:19
Alignment explanation
Indices: 1314565--1314638 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
1314555 ATATGCCTTA
* *
1314565 GGGTATCGGTACCATCTGAG
1 GGGTATCGATACC-TATGAG
1314585 GGGTATCGATACC-ATTGCATG
1 GGGTATCGATACCTA-TG-A-G
*
1314606 GGGTATCGATACCTATGGG
1 GGGTATCGATACCTATGAG
*
1314625 GGGTATCGGTACCT
1 GGGTATCGATACCT
1314639 TTCGAGCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
19 16 0.35
20 13 0.28
21 16 0.35
22 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.27
Consensus pattern (19 bp):
GGGTATCGATACCTATGAG
Found at i:1316732 original size:21 final size:20
Alignment explanation
Indices: 1316706--1316803 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
1316696 TCAGTTTCCA
*
1316706 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
1316727 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
1316748 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
1316769 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
1316789 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1316804 ACACATAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:1316832 original size:20 final size:20
Alignment explanation
Indices: 1316770--1316963 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
1316760 CGATTTTCCA
* ** *
1316770 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1316790 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1316810 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1316830 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1316850 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1316870 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1316890 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* ***
1316910 AAATCGCAACG-ATAATAAAT
1 AAATCGCAACGCGT-ATCCGT
1316930 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1316951 AAATCGCAACGCG
1 AAATCGCAACGCG
1316964 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1316854 original size:60 final size:60
Alignment explanation
Indices: 1316770--1316963 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
1316760 CGATTTTCCA
* ** * * *
1316770 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* * *** *
1316830 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* **
1316890 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATAAATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAAT-AAATCGCAACGCGTATCCGT
1316951 AAATCGCAACGCG
1 AAATCGCAACGCG
1316964 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
Found at i:1317373 original size:30 final size:30
Alignment explanation
Indices: 1317339--1317403 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
1317329 TTCACTTAGA
*
1317339 TTTCATTTCGCGTTACGATTCTGTCGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGCGAT
* *
1317369 TTTCATTTCGCGTTGCTATTCTCTCGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGCGAT
1317399 TTTCA
1 TTTCA
1317404 AGTTAGTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (30 bp):
TTTCATTTCGCGTTACGATTCTCTCGCGAT
Found at i:1317525 original size:20 final size:20
Alignment explanation
Indices: 1317481--1317590 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
1317471 TGCAGAAGAG
*
1317481 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1317502 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1317522 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1317543 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
1317557 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
1317576 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1317591 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1317538 original size:41 final size:38
Alignment explanation
Indices: 1317474--1317590 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
1317464 TTCAATTTGC
* *
1317474 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1317512 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1317553 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1317586 AGAAT
1 AGAAT
1317591 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:1317560 original size:14 final size:14
Alignment explanation
Indices: 1317541--1317597 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1317531 GAGAAATGAA
1317541 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1317555 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1317574 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1317588 AATCGCAACG
1 AATCGCAACG
1317598 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1317573 original size:33 final size:33
Alignment explanation
Indices: 1317533--1317613 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1317523 CGCAACGAGA
1317533 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1317566 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1317599 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1317614 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1317631 original size:19 final size:19
Alignment explanation
Indices: 1317609--1317673 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
1317599 GAAACCAAAA
*
1317609 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1317628 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1317642 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
1317661 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1317674 CTCTCGTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 10 0.27
16 2 0.05
17 3 0.08
19 22 0.59
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1317650 original size:14 final size:14
Alignment explanation
Indices: 1317631--1317687 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1317621 TTTCATTTCG
1317631 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1317645 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
1317664 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1317678 CGTTGCGATT
1 CGTTGCGATT
1317688 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1317660 original size:33 final size:33
Alignment explanation
Indices: 1317614--1317695 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
1317604 CAAAATCGCA
1317614 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1317647 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1317680 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1317696 AACCAAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1319792 original size:185 final size:183
Alignment explanation
Indices: 1319387--1319853 Score: 891
Period size: 185 Copynumber: 2.5 Consensus size: 183
1319377 TAGATTGCTT
*
1319387 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1319452 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1319517 GTGTTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1319571 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1319636 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
1319701 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TG--TTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1319756 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1319821 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAAT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAT
1319854 GCAATCCATT
Statistics
Matches: 280, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
183 36 0.13
184 102 0.36
185 142 0.51
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (183 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1319826 original size:93 final size:93
Alignment explanation
Indices: 1319387--1319852 Score: 895
Period size: 93 Copynumber: 5.1 Consensus size: 93
1319377 TAGATTGCTT
*
1319387 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1319452 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1319480 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTG--TTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1319543 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1319571 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1319636 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1319664 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1319728 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1319756 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1319821 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1319848 AGTAA
1 AGTAA
1319853 TGCAATCCAT
Statistics
Matches: 369, Mismatches: 1, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
91 91 0.25
92 98 0.27
93 180 0.49
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1319940 original size:19 final size:19
Alignment explanation
Indices: 1319900--1320028 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1319890 TAGTTTACTT
* *
1319900 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1319920 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1319939 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1319958 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
*
1319972 TCGTAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1319991 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1320005 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1320024 TCGCA
1 TCGCA
1320029 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1319980 original size:33 final size:32
Alignment explanation
Indices: 1319936--1320028 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
1319926 CGCGAAACCA
**
1319936 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
1319968 AGAATCGTAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1320001 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1320029 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1320026 original size:52 final size:52
Alignment explanation
Indices: 1319900--1320028 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
1319890 TAGTTTACTT
**
1319900 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * * *
1319952 T-G-AAAATCGCAACGACAGAATCGTAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1320005 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1320029 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 40 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1320046 original size:19 final size:19
Alignment explanation
Indices: 1320024--1320158 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1320014 GAAACCAAAA
*
1320024 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1320043 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1320059 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1320076 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1320092 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1320109 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1320128 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1320148 TCGTGTTGCGA
1 TCGCGTTGCGA
1320159 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1320065 original size:14 final size:14
Alignment explanation
Indices: 1320046--1320102 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1320036 TTTCATTTCG
1320046 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1320060 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1320077 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1320093 CGTTGCGATT
1 CGTTGCGATT
1320103 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1320071 original size:33 final size:33
Alignment explanation
Indices: 1320029--1320121 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1320019 CAAAATCGCA
*
1320029 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1320062 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1320095 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1320122 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1322098 original size:14 final size:14
Alignment explanation
Indices: 1322079--1322114 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1322069 ATTGTTTAAT
1322079 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1322093 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1322107 TGATTTGT
1 TGATTTGT
1322115 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1322237 original size:19 final size:19
Alignment explanation
Indices: 1322221--1322317 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
1322211 AAAAATGACT
1322221 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1322240 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1322259 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1322273 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1322292 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
1322311 ATCGCAA
1 ATCGCAA
1322318 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 48 0.69
20 6 0.09
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1322299 original size:52 final size:52
Alignment explanation
Indices: 1322221--1322335 Score: 214
Period size: 52 Copynumber: 2.2 Consensus size: 52
1322211 AAAAATGACT
1322221 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGA
1322273 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
1322325 ATCGCAATGCG
1 ATCGCAATGCG
1322336 TTTATATTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 56 0.90
53 6 0.10
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
Found at i:1322387 original size:19 final size:19
Alignment explanation
Indices: 1322363--1322541 Score: 173
Period size: 19 Copynumber: 10.4 Consensus size: 19
1322353 GATTCTCTCG
1322363 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1322382 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1322401 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1322415 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1322434 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1322448 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1322467 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1322481 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1322501 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
1322515 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1322534 TTGCGATT
1 TTGCGATT
1322542 CTCTCGTTGC
Statistics
Matches: 131, Mismatches: 8, Indels: 42
0.72 0.04 0.23
Matches are distributed among these distances:
14 29 0.22
16 23 0.18
17 20 0.15
18 3 0.02
19 44 0.34
20 12 0.09
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1322403 original size:52 final size:52
Alignment explanation
Indices: 1322341--1322541 Score: 222
Period size: 52 Copynumber: 3.9 Consensus size: 52
1322331 ATGCGTTTAT
1322341 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1322393 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* * * * * *
1322443 -TCTCG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* *
1322492 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATT
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATT
1322542 CTCTCGTTGC
Statistics
Matches: 123, Mismatches: 13, Indels: 25
0.76 0.08 0.16
Matches are distributed among these distances:
45 9 0.07
46 5 0.04
47 17 0.14
49 7 0.06
50 5 0.04
51 2 0.02
52 47 0.38
53 19 0.15
54 5 0.04
55 6 0.05
56 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1322419 original size:33 final size:33
Alignment explanation
Indices: 1322382--1322555 Score: 305
Period size: 33 Copynumber: 5.2 Consensus size: 33
1322372 TCATTTCGCA
1322382 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1322415 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1322448 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1322481 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1322515 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1322548 TTGCGATT
1 TTGCGATT
1322556 GTAATTTTCG
Statistics
Matches: 134, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
32 1 0.01
33 103 0.77
34 29 0.22
35 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1322420 original size:14 final size:14
Alignment explanation
Indices: 1322401--1322488 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
1322391 TCATTTCGCA
1322401 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1322415 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1322432 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
1322448 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1322465 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1322481 TTGCGATT
1 TTGCGATT
1322489 TTCATTTCCG
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.33
16 14 0.23
17 14 0.23
19 12 0.20
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1322538 original size:67 final size:66
Alignment explanation
Indices: 1322382--1322555 Score: 305
Period size: 67 Copynumber: 2.6 Consensus size: 66
1322372 TCATTTCGCA
1322382 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1322447 G
66 G
*
1322448 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTCTC-
1322513 T-G
64 TCG
*
1322515 TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1322556 GTAATTTTCG
Statistics
Matches: 104, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
66 48 0.46
67 55 0.53
68 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (66 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
G
Found at i:1325788 original size:20 final size:20
Alignment explanation
Indices: 1325760--1325989 Score: 228
Period size: 20 Copynumber: 11.5 Consensus size: 20
1325750 AAATTTCAGT
* * *
1325760 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1325780 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1325800 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1325820 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1325840 GTTGCAATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1325860 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1325880 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1325900 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1325920 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1325940 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1325960 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1325980 GTTGCGATTT
1 GTTGCGATTT
1325990 TGGAAAATCG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1326006 original size:21 final size:21
Alignment explanation
Indices: 1325976--1326058 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1325966 ATTTTCATAT
*
1325976 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1325997 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1326018 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1326039 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1326059 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1326049 original size:42 final size:43
Alignment explanation
Indices: 1325956--1326054 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1325946 ATTTATGTGT
* *
1325956 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1325997 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1326039 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1326055 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1327392 original size:19 final size:19
Alignment explanation
Indices: 1327349--1327392 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1327339 AAATGATCAA
*
1327349 CAAATTCACAACGCGATCT
1 CAAATTCACAACGCGAACT
*
1327368 CAAATTCACAATGCGAACT
1 CAAATTCACAACGCGAACT
*
1327387 CTAATT
1 CAAATT
1327393 TCGCAACTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (19 bp):
CAAATTCACAACGCGAACT
Found at i:1327470 original size:20 final size:20
Alignment explanation
Indices: 1327445--1327522 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
1327435 GCAACACAAA
* *
1327445 AGTCAAATTTGTAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
1327465 AGTCAAAATCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
1327485 AGTCAAATTCGCAATGCGAT
1 AGTCAAATTCGCAACGCGAT
1327505 AGTCAAATTCGCAACGCG
1 AGTCAAATTCGCAACGCG
1327523 TAATTTCAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:1327520 original size:40 final size:40
Alignment explanation
Indices: 1327430--1327540 Score: 125
Period size: 40 Copynumber: 2.8 Consensus size: 40
1327420 GCGAATCTGT
* ** * * *
1327430 AAATCGCAACACAAAAGTCAAATTTGTAACGCGATAGTCA
1 AAATCGCAACGCGTAAGTCAAATTCGCAATGCGATAGTCA
1327470 AAATCGCAACGCG-ATAGTCAAATTCGCAATGCGATAGTCA
1 AAATCGCAACGCGTA-AGTCAAATTCGCAATGCGATAGTCA
* *
1327510 AATTCGCAACGCGTAATTTCAAATTCGCAAT
1 AAATCGCAACGCGTAA-GTCAAATTCGCAAT
1327541 TGAATTTCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
39 1 0.02
40 46 0.75
41 14 0.23
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.23
Consensus pattern (40 bp):
AAATCGCAACGCGTAAGTCAAATTCGCAATGCGATAGTCA
Found at i:1327751 original size:16 final size:15
Alignment explanation
Indices: 1327716--1327754 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1327706 TCCCCATCTC
*
1327716 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1327731 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1327747 TAATTTTT
1 TAATTTTT
1327755 CATTGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1328329 original size:12 final size:12
Alignment explanation
Indices: 1328308--1328341 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1328298 ACCACATTTC
*
1328308 CAATACCAAACA
1 CAATATCAAACA
1328320 CAATATCAAACA
1 CAATATCAAACA
*
1328332 CAATCTCAAA
1 CAATATCAAA
1328342 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1330807 original size:12 final size:12
Alignment explanation
Indices: 1330790--1330830 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1330780 AGCAAAAGGA
*
1330790 AATCAAAATCGC
1 AATCAAAATCAC
*
1330802 AATCAAAATCAA
1 AATCAAAATCAC
*
1330814 AATCAAAATCCC
1 AATCAAAATCAC
1330826 AATCA
1 AATCA
1330831 CAACCGGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:1330811 original size:6 final size:6
Alignment explanation
Indices: 1330789--1330823 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1330779 AAGCAAAAGG
* *
1330789 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
1330824 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:1331675 original size:24 final size:24
Alignment explanation
Indices: 1331623--1331675 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1331613 TTTCATATGT
* *
1331623 AATTGGAGTTTGAATTTAAATTTA
1 AATTTGAGTTTGAATTTAAATATA
*
1331647 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1331671 AATTT
1 AATTT
1331676 CGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1332035 original size:39 final size:39
Alignment explanation
Indices: 1331978--1332064 Score: 131
Period size: 39 Copynumber: 2.2 Consensus size: 39
1331968 TTCGATGCTC
* *
1331978 ATCAGAATCTAAAGCTCATATGGT-TCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGT-CAAGCAAAAGGAA
*
1332017 ATCAAAATCCAAATCTCATATGGTGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
1332056 ATCAAAATC
1 ATCAAAATC
1332065 TACAACTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 43 0.98
40 1 0.02
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
Found at i:1333888 original size:21 final size:21
Alignment explanation
Indices: 1333864--1333962 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
1333854 ACGGGCAGGA
*
1333864 CCTCTTGAACGATGATAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
1333885 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
1333906 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
**
1333927 CCTCTTGAACGAT-AGGAGGCA
1 CCTCTTGAACGATGA-GAGGGG
*
1333948 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
1333963 TAGGTGCATC
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:1333960 original size:42 final size:41
Alignment explanation
Indices: 1333844--1333962 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 41
1333834 GTGAATTGGG
* * *
1333844 CTCTTGAACGACGGGCAGGACCTCTTGAACGATGATAGGGGC
1 CTCTTGAACGATGGG-AGGACCTCTTGAATGATGAGAGGGGC
* * *
1333886 CTCTTGAACGGTGGGAGGGGCTTCTTCG-ATGATGAGAGGGGC
1 CTCTTGAACGATGGGA-GGACCTCTT-GAATGATGAGAGGGGC
*
1333928 CTCTTGAACGATAGGAGGCACCTCTTGAATGATGA
1 CTCTTGAACGATGGGAGG-ACCTCTTGAATGATGA
1333963 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
41 4 0.06
42 58 0.92
43 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGATGGGAGGACCTCTTGAATGATGAGAGGGGC
Found at i:1334122 original size:12 final size:12
Alignment explanation
Indices: 1334103--1334144 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1334093 ATCGGGCCGA
1334103 AAATAAATTAAT
1 AAATAAATTAAT
* *
1334115 ACATAAATTAGT
1 AAATAAATTAAT
*
1334127 AAATAAATAAAT
1 AAATAAATTAAT
1334139 AAATAA
1 AAATAA
1334145 TGTCGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:1334395 original size:21 final size:21
Alignment explanation
Indices: 1334367--1334416 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1334357 ACCATTATCT
1334367 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
*
1334388 TGACGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
1334409 TCACGTAA
1 TCACGTAA
1334417 TTCCCCTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGTACCGACCTCA
Found at i:1336602 original size:39 final size:39
Alignment explanation
Indices: 1336509--1336672 Score: 301
Period size: 39 Copynumber: 4.2 Consensus size: 39
1336499 GATTTTCGCT
*
1336509 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTATTGCG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACT-TTGTG
1336549 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTGTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTGTG
1336588 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTGTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTGTG
1336627 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTT-TGTG
1336667 TTGCGA
1 TTGCGA
1336673 TTTACAAATT
Statistics
Matches: 122, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
39 78 0.64
40 44 0.36
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.40
Consensus pattern (39 bp):
TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTGTG
Found at i:1336670 original size:59 final size:61
Alignment explanation
Indices: 1336494--1336672 Score: 251
Period size: 59 Copynumber: 3.0 Consensus size: 61
1336484 TCGCGTAAAA
* * *
1336494 AATTTGATTTTCGCTTTGCGAATTTGACTATCGCGTTGCGAATTTGACTAT-TGCGTTGCG
1 AATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCTGCGTTGCG
* *
1336554 AATTTGACTATCGCGTTGCGAATTTGACT-TTGTGTTGCGAATTTGACTATC-GCGTTGCG
1 AATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCTGCGTTGCG
* * *
1336613 AATTTGACT-TTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT-TCTGTGTTGCG
1 AATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCTGCGTTGCG
1336672 A
1 A
1336673 TTTACAAATT
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
58 19 0.18
59 61 0.58
60 26 0.25
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (61 bp):
AATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCTGCGTTGCG
Found at i:1336672 original size:20 final size:20
Alignment explanation
Indices: 1336494--1336660 Score: 248
Period size: 20 Copynumber: 8.4 Consensus size: 20
1336484 TCGCGTAAAA
* * *
1336494 AATTTGATTTTCGCTTTGCG
1 AATTTGACTATCGCGTTGCG
1336514 AATTTGACTATCGCGTTGCG
1 AATTTGACTATCGCGTTGCG
*
1336534 AATTTGACTATTGCGTTGCG
1 AATTTGACTATCGCGTTGCG
1336554 AATTTGACTATCGCGTTGCG
1 AATTTGACTATCGCGTTGCG
* *
1336574 AATTTGACT-TTGTGTTGCG
1 AATTTGACTATCGCGTTGCG
1336593 AATTTGACTATCGCGTTGCG
1 AATTTGACTATCGCGTTGCG
* *
1336613 AATTTGACT-TTGTGTTGCG
1 AATTTGACTATCGCGTTGCG
1336632 AATTTGACTATCGCGTTGCG
1 AATTTGACTATCGCGTTGCG
1336652 AATTTGACT
1 AATTTGACT
1336661 TCTGTGTTGC
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
19 34 0.26
20 98 0.74
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (20 bp):
AATTTGACTATCGCGTTGCG
Found at i:1336689 original size:20 final size:20
Alignment explanation
Indices: 1336666--1336712 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1336656 TGACTTCTGT
1336666 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
1336686 GTTGTGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
1336706 GTTGCGA
1 GTTGCGA
1336713 AATTGGAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:1336749 original size:20 final size:21
Alignment explanation
Indices: 1336701--1336753 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1336691 GATTTACAGA
1336701 TTCGCGTTGCGAAATTGGAAG
1 TTCGCGTTGCGAAATTGGAAG
* *
1336722 CTAG-GTTGCGAAATTGG-AG
1 TTCGCGTTGCGAAATTGGAAG
1336741 TTCGCGTTGCGAA
1 TTCGCGTTGCGAA
1336754 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 21 0.78
21 2 0.07
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (21 bp):
TTCGCGTTGCGAAATTGGAAG
Found at i:1337076 original size:21 final size:21
Alignment explanation
Indices: 1337054--1337115 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1337044 TCAATAAATT
*
1337054 AATTTATAAATTTTAAATTTTA
1 AATTT-TAAATTATAAATTTTA
*
1337076 AATTTTAAATTATAAAATATTA
1 AATTTTAAATTATAA-ATTTTA
*
1337098 AA-TATATAATTATAAATT
1 AATTTTA-AATTATAAATT
1337116 ACTAAAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 14 0.41
22 20 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTTTAAATTATAAATTTTA
Found at i:1337121 original size:8 final size:7
Alignment explanation
Indices: 1337057--1337121 Score: 60
Period size: 7 Copynumber: 9.0 Consensus size: 7
1337047 ATAAATTAAT
1337057 TTATAAA
1 TTATAAA
*
1337064 TTTTAAA
1 TTATAAA
*
1337071 TTTTAAA
1 TTATAAA
*
1337078 TTTTAAA
1 TTATAAA
1337085 TTATAAA
1 TTATAAA
*
1337092 ATATTAAA
1 TTA-TAAA
1337100 -TATATAA
1 TTATA-AA
1337107 TTATAAA
1 TTATAAA
1337114 TTACTAAA
1 TTA-TAAA
1337122 AATCAAAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
6 2 0.04
7 37 0.73
8 12 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (7 bp):
TTATAAA
Found at i:1341117 original size:24 final size:23
Alignment explanation
Indices: 1341086--1341132 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
1341076 AAACACAATA
1341086 ATTTG-AAAATTAACATTTTTTTT
1 ATTTGAAAAATTAA-ATTTTTTTT
1341109 ATTTCGAAAAATTAAATTTTTTTT
1 ATTT-GAAAAATTAAATTTTTTTT
1341133 GAAAATTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
24 10 0.45
25 8 0.36
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (23 bp):
ATTTGAAAAATTAAATTTTTTTT
Done.