Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 93 of 143
Found at i:28912139 original size:16 final size:16
Alignment explanation
Indices: 28912101--28912139 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28912091 TAACAAAAAT
28912101 AAAATAATTTAATTCA
1 AAAATAATTTAATTCA
* * *
28912117 AATATAATTTATTTTA
1 AAAATAATTTAATTCA
28912133 AAAATAA
1 AAAATAA
28912140 ATTCAACTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATAATTTAATTCA
Found at i:28912738 original size:26 final size:25
Alignment explanation
Indices: 28912709--28912771 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
28912699 TATAAAAATG
* *
28912709 TATAAAATTATTAAATTTTAAAATAA
1 TATAAAATAATT-AATTTTAAAAAAA
* *
28912735 TATAATATAATTATTTTTAAAAAAA
1 TATAAAATAATTAATTTTAAAAAAA
*
28912760 TAAAAAAATAAT
1 T-ATAAAATAAT
28912772 ATAAGTGAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 12 0.40
26 18 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TATAAAATAATTAATTTTAAAAAAA
Found at i:28920879 original size:21 final size:21
Alignment explanation
Indices: 28920849--28920900 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
28920839 GTGCAGATTA
* *
28920849 CTACCTATACAAGTGACAGTT
1 CTACCAATACAAGTGACAATT
*
28920870 CTACCGATACAAGTGACAATT
1 CTACCAATACAAGTGACAATT
28920891 CTACCAATAC
1 CTACCAATAC
28920901 CTGTCTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.25
Consensus pattern (21 bp):
CTACCAATACAAGTGACAATT
Found at i:28920990 original size:21 final size:24
Alignment explanation
Indices: 28920966--28921016 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
28920956 CAACTTCTAC
28920966 CGATACAAGCA-TC-C-TAACTAT
1 CGATACAAGCATTCACATAACTAT
28920987 CGATACAAGCATTCACATAACTAT
1 CGATACAAGCATTCACATAACTAT
28921011 CGATAC
1 CGATAC
28921017 CTACTATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.41
22 2 0.07
23 1 0.04
24 13 0.48
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (24 bp):
CGATACAAGCATTCACATAACTAT
Found at i:28925545 original size:23 final size:23
Alignment explanation
Indices: 28925519--28925722 Score: 282
Period size: 23 Copynumber: 8.8 Consensus size: 23
28925509 GTGTTCTTAT
*
28925519 ATTTATGCTTAAATATTAATATG
1 ATTTATGCTTAAATATTAATGTG
* *
28925542 ATTTGTGCTAAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTG
*
28925565 ATTTATGTTTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTG
* *
28925588 ATTTGTGCTTAAATATTAATATG
1 ATTTATGCTTAAATATTAATGTG
* *
28925611 ATTTGTGCTCAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTG
*
28925634 ATTTATGCTTAAATATTGATGTG
1 ATTTATGCTTAAATATTAATGTG
* *
28925657 ATTTATGCCTAAATATTAATATG
1 ATTTATGCTTAAATATTAATGTG
*
28925680 ATTTATGATTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTG
*
28925703 ATTTGTGCTTAAATAATTAA
1 ATTTATGCTTAAAT-ATTAA
28925723 GATGTGATAT
Statistics
Matches: 158, Mismatches: 22, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 153 0.97
24 5 0.03
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (23 bp):
ATTTATGCTTAAATATTAATGTG
Found at i:28925606 original size:69 final size:69
Alignment explanation
Indices: 28925519--28925722 Score: 318
Period size: 69 Copynumber: 2.9 Consensus size: 69
28925509 GTGTTCTTAT
*
28925519 ATTTATGCTTAAATATTAATATGATTTGTGCTAAAATATTAATGTGATTTATGTTTAAATATTAA
1 ATTTATGCTTAAATATTAATATGATTTGTGCTAAAATATTAATGTGATTTATGCTTAAATATTAA
28925584 TGTG
66 TGTG
* * *
28925588 ATTTGTGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTATGCTTAAATATTGA
1 ATTTATGCTTAAATATTAATATGATTTGTGCTAAAATATTAATGTGATTTATGCTTAAATATTAA
28925653 TGTG
66 TGTG
* * * * *
28925657 ATTTATGCCTAAATATTAATATGATTTATGATTAAATATTAATGTGATTTGTGCTTAAATAATTA
1 ATTTATGCTTAAATATTAATATGATTTGTGCTAAAATATTAATGTGATTTATGCTTAAAT-ATTA
28925722 A
65 A
28925723 GATGTGATAT
Statistics
Matches: 123, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
69 119 0.97
70 4 0.03
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (69 bp):
ATTTATGCTTAAATATTAATATGATTTGTGCTAAAATATTAATGTGATTTATGCTTAAATATTAA
TGTG
Found at i:28925825 original size:36 final size:36
Alignment explanation
Indices: 28925785--28925897 Score: 147
Period size: 36 Copynumber: 3.1 Consensus size: 36
28925775 TGATGACTGT
*
28925785 TGTGAAAGTGAATATGTGGGTATGTTCTTCATGCCA
1 TGTGAAAGAGAATATGTGGGTATGTTCTTCATGCCA
* * * *
28925821 TGTGACAGAAAATATATGGGTATGTGT-TTCATGTCA
1 TGTGAAAGAGAATATGTGGGTATGT-TCTTCATGCCA
* *
28925857 TGTGATAGAGAATATGTGGGTACGTTCTTCATGCCA
1 TGTGAAAGAGAATATGTGGGTATGTTCTTCATGCCA
28925893 TGTGA
1 TGTGA
28925898 CTGATTAGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
35 1 0.02
36 63 0.97
37 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (36 bp):
TGTGAAAGAGAATATGTGGGTATGTTCTTCATGCCA
Found at i:28926411 original size:18 final size:17
Alignment explanation
Indices: 28926388--28926426 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
28926378 ATGAATATGT
28926388 TGTATGATTG-TTGATTTA
1 TGTATGA-TGATTG-TTTA
28926406 TGTATGATGATTGTTTA
1 TGTATGATGATTGTTTA
28926423 TGTA
1 TGTA
28926427 GTAGTTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (17 bp):
TGTATGATGATTGTTTA
Found at i:28930845 original size:5 final size:5
Alignment explanation
Indices: 28930835--28930867 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
28930825 TGCACATAGG
28930835 AGATC AGATC AGATC AGATC AGATC AGATC AGA
1 AGATC AGATC AGATC AGATC AGATC AGATC AGA
28930868 AGAAGATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.18
Consensus pattern (5 bp):
AGATC
Found at i:28941909 original size:20 final size:20
Alignment explanation
Indices: 28941884--28941933 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
28941874 CGATCCATTC
**
28941884 AAATTCATTAAAGATTTCTT
1 AAATTCATTAAAGACCTCTT
28941904 AAATTCAAATTAAAGACCTCTT
1 AAATTC--ATTAAAGACCTCTT
*
28941926 AATTTCAT
1 AAATTCAT
28941934 CAAAATAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 8 0.32
22 17 0.68
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (20 bp):
AAATTCATTAAAGACCTCTT
Found at i:28941925 original size:22 final size:22
Alignment explanation
Indices: 28941890--28941932 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28941880 ATTCAAATTC
**
28941890 ATTAAAGATTTCTTAAATTCAA
1 ATTAAAGACCTCTTAAATTCAA
*
28941912 ATTAAAGACCTCTTAATTTCA
1 ATTAAAGACCTCTTAAATTCA
28941933 TCAAAATAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTAAAGACCTCTTAAATTCAA
Found at i:28942166 original size:25 final size:24
Alignment explanation
Indices: 28942124--28942174 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
28942114 TGATGAAATT
* *
28942124 TTGAAAAATCATGTGAAA-GAATAA
1 TTGAAAAATCAAGAGAAATG-ATAA
28942148 TTGAAAAATCAAAGAGAAATGATAA
1 TTGAAAAATC-AAGAGAAATGATAA
28942173 TT
1 TT
28942175 TTCTTTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.43
25 12 0.52
26 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (24 bp):
TTGAAAAATCAAGAGAAATGATAA
Found at i:28943691 original size:17 final size:17
Alignment explanation
Indices: 28943656--28943697 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
28943646 GGAAAAAGTA
*
28943656 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
28943674 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
28943691 GTTAAAG
1 GTTAAAG
28943698 GTCAAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:28943697 original size:24 final size:24
Alignment explanation
Indices: 28943670--28943717 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28943660 CAAGAATATG
* *
28943670 AAAGGTTAAAGAAGATGGAAGGTT
1 AAAGGTCAAAGAAGATGAAAGGTT
* *
28943694 AAAGGTCAAGGGAGATGAAAGGTT
1 AAAGGTCAAAGAAGATGAAAGGTT
28943718 GAACATCCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.35, T:0.19
Consensus pattern (24 bp):
AAAGGTCAAAGAAGATGAAAGGTT
Found at i:28949077 original size:17 final size:17
Alignment explanation
Indices: 28949042--28949084 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
28949032 GGAAAAAGTA
*
28949042 GTTATAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
28949060 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
28949077 GTTAAAGA
1 GTTAAAGA
28949085 TCAAGGGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:28950542 original size:29 final size:29
Alignment explanation
Indices: 28950510--28950649 Score: 96
Period size: 29 Copynumber: 4.8 Consensus size: 29
28950500 AATTTGGGGT
28950510 TAAAAATAGAATTTTGGAAAGTTCAAGGG
1 TAAAAATAGAATTTTGGAAAGTTCAAGGG
* *
28950539 T-AAAATGGTAATTTTGGTGAAA--TC-GGGG
1 TAAAAATAG-AATTTT-G-GAAAGTTCAAGGG
* *
28950567 TTAAAAAT-GAAATTTTGGAAAGTTTAGGGG
1 -TAAAAATAG-AATTTTGGAAAGTTCAAGGG
* *
28950597 TAAAACGATA-ATTTTTGG-AAGTTTCAAGGT
1 TAAAA--ATAGAATTTTGGAAAG-TTCAAGGG
*
28950627 TAAAAATGGAATTTTGGAAAGTT
1 TAAAAATAGAATTTTGGAAAGTT
28950650 TGGGGGTAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 28
0.70 0.08 0.22
Matches are distributed among these distances:
27 4 0.05
28 12 0.14
29 35 0.40
30 30 0.34
31 6 0.07
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (29 bp):
TAAAAATAGAATTTTGGAAAGTTCAAGGG
Found at i:28950570 original size:58 final size:58
Alignment explanation
Indices: 28950505--28950888 Score: 427
Period size: 58 Copynumber: 6.6 Consensus size: 58
28950495 GAGAAAATTT
* * * *
28950505 GGGGTTAAAAATAGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTGGTGAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGATAATTTTGGTGAAATC
* * * *
28950563 GGGGTTAAAAATGAAATTTTGGAAAGTTTAGGGGTAAAACGATAATTTTTG-GAAGTTTC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGATAATTTTGGTGAA--ATC
** * * * *
28950622 AAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTGGGTAAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGATAATTTTGGTGAAATC
* * * * * * * *
28950680 AGGGTTAAAAATGAAAGTTTAGAAAGTTTAGGGGTAAATTGGTAATTTTTGGTAAAATT
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGATAA-TTTTGGTGAAATC
*
28950739 GGGGTT-AAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGATAATTTTGGGTGAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGATAATTTT-GGTGAAATC
* * *
28950797 GGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGATAATTTT--TAGAAGTTTC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGATAATTTTGGT-GAA--ATC
*
28950856 GGGGTCAAAAATGGAATTTTGGAAAGTTT-GGGG
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGG
28950889 ACTAGAGAGC
Statistics
Matches: 276, Mismatches: 41, Indels: 18
0.82 0.12 0.05
Matches are distributed among these distances:
56 1 0.00
57 10 0.04
58 134 0.49
59 129 0.47
60 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (58 bp):
GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGATAATTTTGGTGAAATC
Found at i:28950685 original size:117 final size:117
Alignment explanation
Indices: 28950505--28950884 Score: 539
Period size: 117 Copynumber: 3.2 Consensus size: 117
28950495 GAGAAAATTT
* * *
28950505 GGGGTTAAAAATAGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTA
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTGGGTGAAATCGGGGTTA
* *
28950570 AAAATGAAATTTTGGAAAGTTTAGGGGTAAAACGATAATTTTTGGAAGTTTC
66 AAAATGAAATTTTAGAAAGTTTAGGGGTAAAATGATAATTTTTGGAAGTTTC
** ** * *
28950622 AAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTGGGTAAAATCAGGGTTA
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTGGGTGAAATCGGGGTTA
* * * **
28950687 AAAATGAAAGTTTAGAAAGTTTAGGGGTAAATTGGTAATTTTTGGTAAAATT-
66 AAAATGAAATTTTAGAAAGTTTAGGGGTAAAATGATAATTTTTGG-AAGTTTC
*
28950739 GGGGTT-AAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGATAATTTTGGGTGAAATCGGGGTT
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAA-TTTGGGTGAAATCGGGGTT
* * *
28950803 AAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGATAATTTTTAGAAGTTTC
65 AAAAATGAAATTTTAGAAAGTTTAGGGGTAAAATGATAATTTTTGGAAGTTTC
*
28950856 GGGGTCAAAAATGGAATTTTGGAAAGTTT
1 GGGGTTAAAAATGGAATTTTGGAAAGTTT
28950885 GGGGACTAGA
Statistics
Matches: 227, Mismatches: 32, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
116 39 0.17
117 162 0.71
118 26 0.11
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (117 bp):
GGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTGGGTGAAATCGGGGTTA
AAAATGAAATTTTAGAAAGTTTAGGGGTAAAATGATAATTTTTGGAAGTTTC
Found at i:28951211 original size:32 final size:32
Alignment explanation
Indices: 28951153--28951215 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
28951143 TTACTGGGTC
* *
28951153 AAATTAAAAATAATTAAAAGTATGAAAAGGACT
1 AAATTAAAAACAATTAAAAATATG-AAAGGACT
*
28951186 AAATT-AAAACAATTAAAAATGTGAAAGGAC
1 AAATTAAAAACAATTAAAAATATGAAAGGAC
28951216 CAAACGCGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 7 0.26
32 15 0.56
33 5 0.19
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (32 bp):
AAATTAAAAACAATTAAAAATATGAAAGGACT
Found at i:28952682 original size:17 final size:16
Alignment explanation
Indices: 28952671--28952739 Score: 50
Period size: 17 Copynumber: 4.0 Consensus size: 16
28952661 TATTTAAGCT
28952671 AAATTTAAATTTAGAAC
1 AAATTTAAATTTA-AAC
* *
28952688 AAATTTAATTTTAAAA
1 AAATTTAAATTTAAAC
*
28952704 ATGAATTTTAAATTTAAATTT
1 A--AA-TTTAAATTTAAA--C
28952725 AAA-TTAAATTTAAAC
1 AAATTTAAATTTAAAC
28952740 TTAGAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
16 3 0.07
17 23 0.55
18 2 0.05
19 13 0.31
21 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
AAATTTAAATTTAAAC
Found at i:28952731 original size:11 final size:12
Alignment explanation
Indices: 28952670--28952738 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 12
28952660 ATATTTAAGC
28952670 TAAATTTAAATT
1 TAAATTTAAATT
*
28952682 TAGAA--CAAATT
1 TA-AATTTAAATT
* *
28952693 TAATTTTAAAAAT
1 TAAATTT-AAATT
* *
28952706 GAATTTTAAATT
1 TAAATTTAAATT
28952718 TAAATTTAAA-T
1 TAAATTTAAATT
28952729 TAAATTTAAA
1 TAAATTTAAA
28952739 CTTAGAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
10 1 0.02
11 18 0.40
12 14 0.31
13 12 0.27
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:28952733 original size:5 final size:6
Alignment explanation
Indices: 28952670--28952738 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
28952660 ATATTTAAGC
* * * * *
28952670 TAAATT TAAATT TAGAA-- CAAATT TAATTT TAAAAAT GAATTT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT TAAATT
28952718 TAAATT TAAA-T TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAA
28952739 CTTAGAAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
4 2 0.04
5 6 0.12
6 35 0.73
7 5 0.10
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:28952753 original size:42 final size:42
Alignment explanation
Indices: 28952670--28952753 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
28952660 ATATTTAAGC
** *
28952670 TAAATTTAAATTTAGAACAAATTTAATTTTAAAAATGAATTT
1 TAAATTTAAATTTAGAACAAATTTAAACTTAAAAATAAATTT
* *
28952712 TAAATTTAAATTTA-AATTAAATTTAAACTTAGAAATAAATTT
1 TAAATTTAAATTTAGAA-CAAATTTAAACTTAAAAATAAATTT
28952754 GAAACCAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (42 bp):
TAAATTTAAATTTAGAACAAATTTAAACTTAAAAATAAATTT
Found at i:28958757 original size:21 final size:20
Alignment explanation
Indices: 28958718--28958757 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28958708 GGGTTCATGG
*
28958718 TATATTTGTTTTTAAAGAAA
1 TATATTTATTTTTAAAGAAA
*
28958738 TATATTTATTGTTTATAGAA
1 TATATTTATT-TTTAAAGAA
28958758 CTGACATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (20 bp):
TATATTTATTTTTAAAGAAA
Found at i:28958790 original size:20 final size:21
Alignment explanation
Indices: 28958765--28958803 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
28958755 GAACTGACAT
28958765 AATAATAATCA-TTGTTATAA
1 AATAATAATCACTTGTTATAA
28958785 AATAATAATCACTTGTTAT
1 AATAATAATCACTTGTTAT
28958804 TTAATATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (21 bp):
AATAATAATCACTTGTTATAA
Found at i:28958809 original size:21 final size:20
Alignment explanation
Indices: 28958763--28958809 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
28958753 TAGAACTGAC
28958763 ATAATAATAATCATTGTTAT
1 ATAATAATAATCATTGTTAT
*
28958783 AAAATAATAATCACTTGTTAT
1 ATAATAATAATCA-TTGTTAT
*
28958804 TTAATA
1 ATAATA
28958810 TTCAATAGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (20 bp):
ATAATAATAATCATTGTTAT
Found at i:28961099 original size:29 final size:29
Alignment explanation
Indices: 28961067--28961128 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
28961057 CGAGTAGCGA
* *
28961067 ATAATAAG-AGA-AATTAGATATGAAGCAAT
1 ATAATAAGCAGATAAATA-ATATGAA-AAAT
28961096 ATAATAAGCAGATAAATAATATGAAAAAT
1 ATAATAAGCAGATAAATAATATGAAAAAT
28961125 ATAA
1 ATAA
28961129 AATACAGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 15 0.52
30 10 0.34
31 4 0.14
ACGTcount: A:0.60, C:0.03, G:0.13, T:0.24
Consensus pattern (29 bp):
ATAATAAGCAGATAAATAATATGAAAAAT
Found at i:28961261 original size:29 final size:30
Alignment explanation
Indices: 28961218--28961495 Score: 125
Period size: 30 Copynumber: 9.5 Consensus size: 30
28961208 ATTCGGAGGC
*
28961218 AAAATGGTAATTTTGGTGAAATCGAGGTTT
1 AAAATGGTAATTTTGGTGAAATCGAGGGTT
*
28961248 AAAATGG-AATTTT-G-GAAAGTTC-AGGGGT
1 AAAATGGTAATTTTGGTGAAA--TCGAGGGTT
* *
28961276 ATAATGGTAATTTTCGGTGAAACCG-GGGTT
1 AAAATGGTAATTTT-GGTGAAATCGAGGGTT
* *
28961306 AAGAATGG-AATTTT--AGAAAGTTCG-GGGGT
1 AA-AATGGTAATTTTGGTGAAA--TCGAGGGTT
28961335 AAAATGGTAATTTTTGGTGAAATC-AGGGTT
1 AAAATGGTAA-TTTTGGTGAAATCGAGGGTT
*
28961365 AAAAATGG-AATTTT-G-GAAAGTTTG-GGAG-T
1 -AAAATGGTAATTTTGGTGAAA--TCGAGG-GTT
* *
28961394 AAAACGGTAATTTTTGGTGAAACCG-GGGTT
1 AAAATGGTAA-TTTTGGTGAAATCGAGGGTT
* *
28961424 AAAAATGG-AATTTT--AGAAAGTTTG-GGG-T
1 -AAAATGGTAATTTTGGTGAAA--TCGAGGGTT
* *
28961452 AAAATAGTAATTTTCGGTGAAATC-AAGGTT
1 AAAATGGTAATTTT-GGTGAAATCGAGGGTT
28961482 AAAAATGG-AATTTT
1 -AAAATGGTAATTTT
28961496 AGAAAGTTAG
Statistics
Matches: 189, Mismatches: 24, Indels: 70
0.67 0.08 0.25
Matches are distributed among these distances:
27 22 0.12
28 30 0.16
29 46 0.24
30 49 0.26
31 30 0.16
32 12 0.06
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTGAAATCGAGGGTT
Found at i:28961313 original size:59 final size:58
Alignment explanation
Indices: 28961218--28961523 Score: 407
Period size: 59 Copynumber: 5.2 Consensus size: 58
28961208 ATTCGGAGGC
* * *
28961218 AAAATGGTAATTTT-GGTGAAATCGAGGTTTAAAATGGAATTTTGGAAAGTTCAGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT-AGGGGT
* * * *
28961276 ATAATGGTAATTTTCGGTGAAACCGGGGTTAAGAATGGAATTTTAGAAAGTTCGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT-AGGGGT
* * * *
28961335 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGAGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTAGGG-GT
* * * *
28961394 AAAACGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTAGGGGT
* **
28961452 AAAATAGTAATTTTCGGTGAAATCAAGGTTAAAAATGGAATTTTAGAAAGTTAGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTA-GGGGT
28961511 AAAATGGTAATTT
1 AAAATGGTAATTT
28961524 CTGGACTGTT
Statistics
Matches: 219, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
58 64 0.29
59 155 0.71
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTAGGGGT
Found at i:28961436 original size:30 final size:31
Alignment explanation
Indices: 28961218--28961495 Score: 129
Period size: 29 Copynumber: 9.5 Consensus size: 31
28961208 ATTCGGAGGC
* *
28961218 AAAATGGTAA-TTTTGGTGAAATCGAGGTTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
28961248 AAAATGG-AA-TTTT-G-GAAAGTTCAGGGG-T-
1 AAAATGGTAATTTTTGGTGAAA--TC-GGGGTTA
* * *
28961276 ATAATGGTAATTTTCGGTGAAACCGGGGTTA
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
* * *
28961307 AGAATGG-AA-TTTT--AGAAAGTTCGGGGGT-
1 AAAATGGTAATTTTTGGTGAAA--TCGGGGTTA
*
28961335 AAAATGGTAATTTTTGGTGAAATCAGGGTTA
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
*
28961366 AAAATGG-AA-TTTT-G-GAAAGTTTGGGAG-T-
1 AAAATGGTAATTTTTGGTGAAA--TCGGG-GTTA
* *
28961394 AAAACGGTAATTTTTGGTGAAACCGGGGTTA
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
* *
28961425 AAAATGG-AA-TTTT--AGAAAGTTTGGGG-T-
1 AAAATGGTAATTTTTGGTGAAA--TCGGGGTTA
* * **
28961452 AAAATAGTAATTTTCGGTGAAATCAAGGTTA
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
28961483 AAAATGG-AATTTT
1 AAAATGGTAATTTT
28961496 AGAAAGTTAG
Statistics
Matches: 186, Mismatches: 29, Indels: 66
0.66 0.10 0.23
Matches are distributed among these distances:
27 22 0.12
28 23 0.12
29 51 0.27
30 47 0.25
31 31 0.17
32 12 0.06
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTA
Found at i:28961513 original size:117 final size:117
Alignment explanation
Indices: 28961209--28961523 Score: 463
Period size: 118 Copynumber: 2.7 Consensus size: 117
28961199 CTTTTGGATA
* * * *
28961209 TTCGGAGGCAAAATGGTAATTTTGGTGAAATCGAGGTTTAAAATGGAATTTTGGAAAGTTCA-GG
1 TTCGGGGGTAAAATGGTAATTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTT-AGGG
* *
28961273 GGTATAATGGTAATTTTCGGTGAAACCGGGGTTAAGAATGGAATTTTAGAAAG
65 GGTAAAATGGTAATTTTCGGTGAAACCGGGGTTAAAAATGGAATTTTAGAAAG
* *
28961326 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTGGG
1 TTCGGGGGTAAAATGGTAA-TTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTAGGG
* * *
28961391 AGTAAAACGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTAGAAAG
65 GGTAAAATGGTAATTTTCGGTGAAACCGGGGTTAAAAATGGAATTTTAGAAAG
* * *
28961444 TT-TGGGGTAAAATAGTAATTTTCGGTGAAATCAAGGTTAAAAATGGAATTTTAGAAAGTTAGGG
1 TTCGGGGGTAAAATGGTAATTTT-GGTGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTAGGG
28961508 GGTAAAATGGTAATTT
65 GGTAAAATGGTAATTT
28961524 CTGGACTGTT
Statistics
Matches: 177, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
116 4 0.02
117 83 0.47
118 90 0.51
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (117 bp):
TTCGGGGGTAAAATGGTAATTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTAGGGG
GTAAAATGGTAATTTTCGGTGAAACCGGGGTTAAAAATGGAATTTTAGAAAG
Found at i:28962641 original size:3 final size:3
Alignment explanation
Indices: 28962633--28962666 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28962623 AATTAATATC
28962633 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
28962667 ACACCATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:28963408 original size:17 final size:17
Alignment explanation
Indices: 28963381--28963464 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 17
28963371 TTAAATTTTC
28963381 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
28963399 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* ** * *
28963416 ACTCCAAACAAGTTTTAA
1 ATTTAAAATAA-ATTTAA
* *
28963434 ATTTATAACAAATTTAA
1 ATTTAAAATAAATTTAA
*
28963451 ATTTAAAATGAATT
1 ATTTAAAATAAATT
28963465 AAGAATCTAA
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
17 36 0.69
18 16 0.31
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:28963519 original size:3 final size:3
Alignment explanation
Indices: 28963511--28963543 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28963501 ATTGGGCTTC
28963511 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28963544 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28963548 original size:3 final size:3
Alignment explanation
Indices: 28963542--28963570 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28963532 AATAATAATA
28963542 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28963571 GGTATAGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:28970214 original size:105 final size:106
Alignment explanation
Indices: 28969916--28970214 Score: 339
Period size: 106 Copynumber: 2.8 Consensus size: 106
28969906 TTCGAATAAT
* * * * * *
28969916 AGAGTTGATGAAATTCTAAATAAACCAAACAAAACCCGTCACTCATTTACAAATTTTTAGTCTTG
1 AGAGTTCACGAAATTCTAAATAAACCAAACAAAACCCATCACTTATTTAC-AACTTTTAGTCTTC
* * * *
28969981 CTTTCAGAATGTATCAAGCCATGGAGTCTGCAATTGCAATGTC
65 CTTTCAGAATGTATC-AGCCATGGAATCAGCAAATGCAATATC
* * * * * * *
28970024 AGAGTTGATGAAATTTTAAATAAACCAAACAAAACCAATAACTTATTTACGACATTTAGTCTTCC
1 AGAGTTCACGAAATTCTAAATAAACCAAACAAAACCCATCACTTATTTACAACTTTTAGTCTTCC
* * * *
28970089 ATTCAGTATGTATCAACCATGGAATCAGCAAATGCAATATT
66 TTTCAGAATGTATCAGCCATGGAATCAGCAAATGCAATATC
** * *
28970130 TTAGTTCACGAAATTCTAAATAAACCAAAC-AAACCCATCACTTATTCACAACTTTTAGTCTTTC
1 AGAGTTCACGAAATTCTAAATAAACCAAACAAAACCCATCACTTATTTACAACTTTTAGTCTTCC
*
28970194 TTTCAGAATGTATCGGCCATG
66 TTTCAGAATGTATCAGCCATG
28970215 TAGTCTGCAA
Statistics
Matches: 159, Mismatches: 32, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
105 45 0.28
106 46 0.29
107 23 0.14
108 45 0.28
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (106 bp):
AGAGTTCACGAAATTCTAAATAAACCAAACAAAACCCATCACTTATTTACAACTTTTAGTCTTCC
TTTCAGAATGTATCAGCCATGGAATCAGCAAATGCAATATC
Found at i:28972429 original size:15 final size:15
Alignment explanation
Indices: 28972395--28972443 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
28972385 TTTATGAATG
*
28972395 TTTTTAATTGTATATAA
1 TTTTTAATT-T-TTTAA
*
28972412 TTTTTATTTTTTTAA
1 TTTTTAATTTTTTAA
*
28972427 TTTTTAATTTTTAAA
1 TTTTTAATTTTTTAA
28972442 TT
1 TT
28972444 AATTATTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 19 0.68
16 1 0.04
17 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTTTAATTTTTTAA
Found at i:28978484 original size:71 final size:71
Alignment explanation
Indices: 28978368--28978510 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
28978358 TTTGTTTAAA
28978368 TGTGAAGATGCTTCATTTATTAGTTTCTTGTTGATTTGATACTTATTATTTCACTTTAACATCTA
1 TGTGAAGATGCTTCATTTATTAGTTTCTTGTTGATTTGATACTTATTATTTCACTTTAACATCTA
28978433 TTGAGT
66 TTGAGT
*
28978439 TGTGAAGATGCTTCATTTATTAGTTTCTTGTTGATTTGATACTTATTATTTCACTTTATCATCTA
1 TGTGAAGATGCTTCATTTATTAGTTTCTTGTTGATTTGATACTTATTATTTCACTTTAACATCTA
28978504 TTGAGT
66 TTGAGT
28978510 T
1 T
28978511 CTTTATTAGG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (71 bp):
TGTGAAGATGCTTCATTTATTAGTTTCTTGTTGATTTGATACTTATTATTTCACTTTAACATCTA
TTGAGT
Found at i:28980295 original size:17 final size:16
Alignment explanation
Indices: 28980270--28980313 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
28980260 TTTAATTGTG
* *
28980270 CATAGTTTTTTT-TTC
1 CATAATTTTTTTCTTT
28980285 CATATATTTTTTTCTTT
1 CATA-ATTTTTTTCTTT
28980302 CATAATTTTTTT
1 CATAATTTTTTT
28980314 ATCCTACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 15 0.60
17 6 0.24
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.68
Consensus pattern (16 bp):
CATAATTTTTTTCTTT
Found at i:28985999 original size:21 final size:21
Alignment explanation
Indices: 28985975--28986021 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
28985965 TTGCCTTTTG
*
28985975 CCTTTAAACCTTTGTTTTATA
1 CCTTTAAACCCTTGTTTTATA
28985996 CCTTTAAACCCTTGTTTTATA
1 CCTTTAAACCCTTGTTTTATA
*
28986017 ACTTT
1 CCTTT
28986022 TGATTGGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.04, T:0.51
Consensus pattern (21 bp):
CCTTTAAACCCTTGTTTTATA
Found at i:28990295 original size:9 final size:8
Alignment explanation
Indices: 28990281--28990320 Score: 50
Period size: 7 Copynumber: 5.4 Consensus size: 8
28990271 AAATGATGCA
*
28990281 TTTTAAAT
1 TTTTTAAT
28990289 TTTTTAA-
1 TTTTTAAT
28990296 TTTTTAA-
1 TTTTTAAT
28990303 TTTTTAA-
1 TTTTTAAT
28990310 TTTTTAAT
1 TTTTTAAT
28990318 TTT
1 TTT
28990321 CTCGTAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 21 0.70
8 9 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTTAAT
Found at i:28990297 original size:8 final size:7
Alignment explanation
Indices: 28990289--28990320 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
28990279 CATTTTAAAT
28990289 TTTTTAA
1 TTTTTAA
28990296 TTTTTAA
1 TTTTTAA
28990303 TTTTTAA
1 TTTTTAA
28990310 TTTTTAA
1 TTTTTAA
28990317 TTTT
1 TTTT
28990321 CTCGTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTAA
Found at i:28990304 original size:15 final size:15
Alignment explanation
Indices: 28990280--28990320 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
28990270 TAAATGATGC
*
28990280 ATTTTAAATTTTTTA
1 ATTTTTAATTTTTTA
28990295 ATTTTTAA-TTTTTA
1 ATTTTTAATTTTTTA
28990309 ATTTTTAATTTT
1 ATTTTTAATTTT
28990321 CTCGTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTTAATTTTTTA
Found at i:28996921 original size:32 final size:31
Alignment explanation
Indices: 28996867--28996930 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
28996857 GTTTAATTAG
* * *
28996867 ACTTTTAATAAATATTTATAATTATAAATTTT
1 ACTTTTAATAAAAATATATAATT-GAAATTTT
28996899 ACTTTTAGATAAAAATAT-TAATTGAAATTTT
1 ACTTTTA-ATAAAAATATATAATTGAAATTTT
28996930 A
1 A
28996931 TGTATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 8 0.29
32 12 0.43
33 8 0.29
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (31 bp):
ACTTTTAATAAAAATATATAATTGAAATTTT
Found at i:29000471 original size:3 final size:3
Alignment explanation
Indices: 29000463--29000521 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
29000453 GATTGGCTAT
29000463 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29000511 ATA ATA ATA AT
1 ATA ATA ATA AT
29000522 GATGTCTCGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:29004344 original size:29 final size:27
Alignment explanation
Indices: 29004318--29004425 Score: 71
Period size: 28 Copynumber: 3.9 Consensus size: 27
29004308 AAAAATTTAA
*
29004318 CTATATTTTATTAA-ATTTTTTATATTT
1 CTATATTTT-TTAATAATTTTTATATTT
*
29004345 TTATATTTTTTAATAATTTTTATAAGTTT
1 CTATATTTTTTAATAATTTTTAT-A-TTT
* *
29004374 -TATCA-ATTTTCATAATTTTTGATAATTTT
1 CTAT-ATTTTTTAATAATTTTT-AT-A-TTT
* *
29004403 TTATATTTTTGAAT-ATTTTTATA
1 CTATATTTTTTAATAATTTTTATA
29004426 AAAAAATAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
26 4 0.06
27 17 0.26
28 19 0.29
29 18 0.27
30 8 0.12
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (27 bp):
CTATATTTTTTAATAATTTTTATATTT
Found at i:29004346 original size:10 final size:9
Alignment explanation
Indices: 29004319--29004422 Score: 75
Period size: 10 Copynumber: 11.0 Consensus size: 9
29004309 AAAATTTAAC
29004319 TATATTTTAT
1 TATATTTT-T
*
29004329 TAAATTTTT
1 TATATTTTT
29004338 TATA-TTTT
1 TATATTTTT
29004346 TATATTTTT
1 TATATTTTT
*
29004355 TAATAATTTT
1 T-ATATTTTT
**
29004365 TATAAGTTT
1 TATATTTTT
*
29004374 TATCAATTTT
1 TAT-ATTTTT
*
29004384 CATAATTTTT
1 TAT-ATTTTT
*
29004394 GATAATTTTT
1 TAT-ATTTTT
29004404 TATATTTTT
1 TATATTTTT
*
29004413 GAATATTTTT
1 -TATATTTTT
29004423 ATAAAAAAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
8 8 0.10
9 25 0.32
10 46 0.58
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (9 bp):
TATATTTTT
Found at i:29004374 original size:19 final size:19
Alignment explanation
Indices: 29004331--29004426 Score: 92
Period size: 19 Copynumber: 5.1 Consensus size: 19
29004321 TATTTTATTA
*
29004331 AATTTTTTAT-ATTTTTAT
1 AATTTTTAATAATTTTTAT
*
29004349 ATTTTTTAATAATTTTTAT
1 AATTTTTAATAATTTTTAT
* *
29004368 AAGTTTT-ATCAATTTTCAT
1 AATTTTTAAT-AATTTTTAT
*
29004387 AATTTTTGATAATTTTT-T
1 AATTTTTAATAATTTTTAT
29004405 ATATTTTTGAAT-ATTTTTAT
1 A-ATTTTT-AATAATTTTTAT
29004425 AA
1 AA
29004427 AAAAATAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
18 12 0.19
19 46 0.72
20 6 0.09
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (19 bp):
AATTTTTAATAATTTTTAT
Found at i:29007285 original size:11 final size:13
Alignment explanation
Indices: 29007258--29007291 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
29007248 TTAATTTTAA
29007258 ATAATAAAAATAT
1 ATAATAAAAATAT
29007271 ATAATAAAAATAT
1 ATAATAAAAATAT
*
29007284 AAAATAAA
1 ATAATAAA
29007292 TTGAGTCAAA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAATAAAAATAT
Found at i:29009788 original size:14 final size:15
Alignment explanation
Indices: 29009769--29009798 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29009759 AAGCTTTTTA
29009769 AATTTTTAAT-TAAT
1 AATTTTTAATATAAT
29009783 AATTTTTAATATAAT
1 AATTTTTAATATAAT
29009798 A
1 A
29009799 GTTCTTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTTTAATATAAT
Found at i:29009891 original size:129 final size:132
Alignment explanation
Indices: 29009716--29010056 Score: 371
Period size: 129 Copynumber: 2.6 Consensus size: 132
29009706 CGTGGGTTCA
** * **
29009716 ATTCCTCTTTTACTCACATTTGCATTCTTTTTCATGTTGCTTCAAGCTTTTTAAATTTTTAATTA
1 ATTCCTCTACTACTCACATTTGTATT-TTTTTCATGTTGCTTCAAGCTTTTTAAAGATTTAATTA
* *
29009781 ATAATTTTTAATATAATAGTTCTTTGGTTAGATGGTT-ATA-A-TTACA-TCTTTCAGTCTCGAG
65 ATAATTTTTAACATAATAATTCTTTGGTTAGATGGTTAATATAGTTACATTC-TTCAGTCTCGAG
*
29009842 TTTT
129 TTTG
* * *
29009846 ATTCCTCTCCTACTCATATTTGTATTTTTTTCGTGTTGCTTCAAGCTTTTTAAAGATTTAATTAA
1 ATTCCTCTACTACTCACATTTGTATTTTTTTCATGTTGCTTCAAGCTTTTTAAAGATTTAATTAA
* ** * *
29009911 TATTTTTTAACATTTTAATTCTTTTGTTAGATGGTTAGATAGTTGTAGTTACATTCTTGAGTCTC
66 TAATTTTTAACATAATAATTCTTTGGTTAGATGGTTA-ATA----TAGTTACATTCTTCAGTCTC
29009976 GAGTTTG
126 GAGTTTG
*
29009983 ATTCCTCTACTACTCACATTTGTATTTTTTTTTAATGTTGCTTCAAG-TTTTT-----TTTAATT
1 ATTCCTCTACTACTCACATTTGTA--TTTTTTTCATGTTGCTTCAAGCTTTTTAAAGATTTAATT
29010042 AAT-ATTTTTAACATA
64 AATAATTTTTAACATA
29010057 TTAGCTCATC
Statistics
Matches: 179, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
129 66 0.37
130 22 0.12
131 3 0.02
132 10 0.06
133 10 0.06
136 1 0.01
137 41 0.23
138 7 0.04
139 19 0.11
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.52
Consensus pattern (132 bp):
ATTCCTCTACTACTCACATTTGTATTTTTTTCATGTTGCTTCAAGCTTTTTAAAGATTTAATTAA
TAATTTTTAACATAATAATTCTTTGGTTAGATGGTTAATATAGTTACATTCTTCAGTCTCGAGTT
TG
Found at i:29010271 original size:37 final size:37
Alignment explanation
Indices: 29010201--29010271 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
29010191 TGATGATATT
* *
29010201 TTTTTAACTATTTTTATTTTTAAATAATGTATTTTTA
1 TTTTTAACTATTTTTATTTTAAAATAATATATTTTTA
29010238 TTTTTAACT-TTTTTATTTATAAAATTAA-ATATTT
1 TTTTTAACTATTTTTATTT-TAAAA-TAATATATTT
29010272 ACTGCAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 9 0.30
37 18 0.60
38 3 0.10
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (37 bp):
TTTTTAACTATTTTTATTTTAAAATAATATATTTTTA
Found at i:29020420 original size:6 final size:6
Alignment explanation
Indices: 29020409--29020443 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
29020399 ACACCTCTCT
29020409 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
29020444 TTCCTTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.51
Consensus pattern (6 bp):
TCTTCA
Found at i:29020676 original size:16 final size:16
Alignment explanation
Indices: 29020639--29020679 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
29020629 TTAGGGTTTA
* *
29020639 AAATTTTTAATTAATT
1 AAATATTTATTTAATT
29020655 -AA-ATTTATTTAATT
1 AAATATTTATTTAATT
29020669 AAATATTTATT
1 AAATATTTATT
29020680 CTCATTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.48
15 4 0.19
16 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATATTTATTTAATT
Found at i:29021667 original size:13 final size:13
Alignment explanation
Indices: 29021649--29021673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29021639 CTTATGAGCT
29021649 CAAAATTTGCTAC
1 CAAAATTTGCTAC
29021662 CAAAATTTGCTA
1 CAAAATTTGCTA
29021674 TCATATAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
CAAAATTTGCTAC
Found at i:29030578 original size:104 final size:105
Alignment explanation
Indices: 29030397--29030594 Score: 337
Period size: 104 Copynumber: 1.9 Consensus size: 105
29030387 CCTTGTTGGG
*
29030397 ACACATGTGAAAAAAACACTCTTAATCCAAGATCCACTCAGATGTAAGTTCAGAGTTTTCTCTTA
1 ACACATGTGAAAAAAACACTCTTAATCCAAGATCCACTCAAATGTAAGTTCAGAGTTTTCTCTTA
*
29030462 TTAACACAAACAAGAAATCATCGCTCTTGTCATCAATCAA
66 TTAACACAAACAAGAAATCATCACTCTTGTCATCAATCAA
29030502 ACACATGTGGAAAAAAAC-C-CTTAATCCAAGATCCACTCAAATGTAAGTTCAGAGTTTTCTCTT
1 ACACATGT-GAAAAAAACACTCTTAATCCAAGATCCACTCAAATGTAAGTTCAGAGTTTTCTCTT
* *
29030565 GTTGACACAAACAAGAAATCATCACTCTTG
65 ATTAACACAAACAAGAAATCATCACTCTTG
29030595 AGATCAGTCA
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
104 70 0.80
105 9 0.10
106 9 0.10
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (105 bp):
ACACATGTGAAAAAAACACTCTTAATCCAAGATCCACTCAAATGTAAGTTCAGAGTTTTCTCTTA
TTAACACAAACAAGAAATCATCACTCTTGTCATCAATCAA
Found at i:29032519 original size:13 final size:13
Alignment explanation
Indices: 29032489--29032521 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29032479 AATTATTTTT
*
29032489 ATTTATTTTTGTA
1 ATTTATTTTTATA
29032502 A-TTATTTTTATA
1 ATTTATTTTTATA
29032514 ATTTATTT
1 ATTTATTT
29032522 AATCCTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
ATTTATTTTTATA
Found at i:29033315 original size:42 final size:42
Alignment explanation
Indices: 29033240--29033320 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
29033230 GTGAGTAAAG
* *
29033240 GCATGGAGCAAGTCAAAAGTTAGCATCAATGATGGGAATAGT
1 GCATGGAGCAAGTAAAAAATTAGCATCAATGATGGGAATAGT
* * *
29033282 GCATGGTGCAAGTAAAAAATTAGTATCATTGATGGGAAT
1 GCATGGAGCAAGTAAAAAATTAGCATCAATGATGGGAAT
29033321 GGTACGTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (42 bp):
GCATGGAGCAAGTAAAAAATTAGCATCAATGATGGGAATAGT
Found at i:29037124 original size:16 final size:16
Alignment explanation
Indices: 29037085--29037139 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
29037075 CTTTGGTTCA
* *
29037085 CTGTAATAGAATAAAG
1 CTGTAATGGAATAGAG
*
29037101 CTGCAATGGAATAGAG
1 CTGTAATGGAATAGAG
* *
29037117 TTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
29037133 CTGTAAT
1 CTGTAAT
29037140 CAATAATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.27
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:29037373 original size:58 final size:59
Alignment explanation
Indices: 29037311--29037461 Score: 200
Period size: 58 Copynumber: 2.6 Consensus size: 59
29037301 TTTTAATAAG
* *
29037311 ATTATAATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTTTTAACATA
* * *
29037369 ATTATTATTAAATACAATTTAAT-AAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTTTTAACATA
* *
29037427 ATTATTATTAAAATATGAA-TTAGTAAAAATTATAA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAA
29037462 TATATAATAT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
57 22 0.28
58 39 0.49
59 9 0.11
60 10 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTTTTAACATA
Found at i:29037459 original size:25 final size:24
Alignment explanation
Indices: 29037430--29037480 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
29037420 TAATATAATT
*
29037430 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
29037455 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
29037479 AT
1 AT
29037481 AATACATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:29037470 original size:58 final size:55
Alignment explanation
Indices: 29037291--29037470 Score: 170
Period size: 58 Copynumber: 3.1 Consensus size: 55
29037281 AGATGATTAT
* * *
29037291 TATTATTAA-ATTTTAATA-AGATTATAATTAAATATAATTTAATAAAAATAATAAA
1 TATTAATAATATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATTAT-AA
* * *
29037346 TAATTTAATTATATTTTAACATAATTATTATTAAATACAATTTAATAAAATAATATATAA
1 T-A-TTAATAATATTTTAATATAATTATTATTAAATATAATTTAAT-AAA-AAT-TATAA
*
29037406 T-TTAATAATATTTTTAATATAATTATTATTAAAATATGAA-TTAGTAAAAATTATAA
1 TATTAATAATA-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAATTATAA
29037462 TATATAATA
1 TAT-TAATA
29037471 TTAGAAAAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
55 1 0.01
56 7 0.07
57 17 0.17
58 55 0.53
59 13 0.13
60 8 0.08
61 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (55 bp):
TATTAATAATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATTATAA
Found at i:29041956 original size:15 final size:15
Alignment explanation
Indices: 29041910--29041943 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29041900 CCACTGCTAC
* *
29041910 CGCCGTCGATGCCGA
1 CGCCATCGACGCCGA
29041925 CGCCATCGACGCCGA
1 CGCCATCGACGCCGA
29041940 CGCC
1 CGCC
29041944 GACGCCATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.47, G:0.29, T:0.09
Consensus pattern (15 bp):
CGCCATCGACGCCGA
Found at i:29042089 original size:20 final size:18
Alignment explanation
Indices: 29042050--29042085 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29042040 TCTACAAAAA
29042050 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
29042068 TAAACTATATATTTAAAT
1 TAAAATATATATTTAAAT
29042086 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:29044682 original size:7 final size:7
Alignment explanation
Indices: 29044667--29044702 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
29044657 AATTTTCATG
*
29044667 TATACAT
1 TATAAAT
29044674 TATAAAT
1 TATAAAT
29044681 TATAAAT
1 TATAAAT
29044688 TATAAAT
1 TATAAAT
29044695 TATCAAAT
1 TAT-AAAT
29044703 AGTTTCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
7 23 0.85
8 4 0.15
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (7 bp):
TATAAAT
Found at i:29047282 original size:18 final size:19
Alignment explanation
Indices: 29047261--29047300 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
29047251 TAAAAATTAT
*
29047261 AAATTAAAAAG-TTTAAAA
1 AAATCAAAAAGTTTTAAAA
*
29047279 AAATCATAAAGTTTTAAAA
1 AAATCAAAAAGTTTTAAAA
29047298 AAA
1 AAA
29047301 AATACAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATCAAAAAGTTTTAAAA
Found at i:29062357 original size:2 final size:2
Alignment explanation
Indices: 29062350--29062386 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29062340 ACATCCACAA
29062350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29062387 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29062391 original size:2 final size:2
Alignment explanation
Indices: 29062386--29062462 Score: 100
Period size: 2 Copynumber: 38.5 Consensus size: 2
29062376 ATATATATAT
* *
29062386 AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG GG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
29062428 AT AA AG AG AG AG AG AC AG AG AG GG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29062463 TGAAAATTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.49, C:0.03, G:0.47, T:0.01
Consensus pattern (2 bp):
AG
Found at i:29062436 original size:34 final size:34
Alignment explanation
Indices: 29062386--29062463 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
29062376 ATATATATAT
* *
29062386 AGAGAGAGAGAGAGAGAGAGAGACAGAGAGGGAG
1 AGAGAGAGATAAAGAGAGAGAGACAGAGAGGGAG
29062420 AGAGAGAGATAAAGAGAGAGAGACAGAGAGGGAG
1 AGAGAGAGATAAAGAGAGAGAGACAGAGAGGGAG
29062454 AGAGAGAGAT
1 AGAGAGAGAT
29062464 GAAAATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.49, C:0.03, G:0.46, T:0.03
Consensus pattern (34 bp):
AGAGAGAGATAAAGAGAGAGAGACAGAGAGGGAG
Found at i:29066926 original size:25 final size:26
Alignment explanation
Indices: 29066875--29066928 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
29066865 TAAAAGTAAT
* *
29066875 TTTTTTTTAATTAATTATGTAAATAA
1 TTTTTTTTAATTAAATACGTAAATAA
29066901 TTTTTTTT-ATTAAATACG-AAATTAA
1 TTTTTTTTAATTAAATACGTAAA-TAA
29066926 TTT
1 TTT
29066929 AAAATCTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 14 0.56
26 8 0.32
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTTTTTTAATTAAATACGTAAATAA
Found at i:29070620 original size:15 final size:16
Alignment explanation
Indices: 29070602--29070631 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29070592 TCTATCTCTC
29070602 ATCTATCTA-TTTTTT
1 ATCTATCTACTTTTTT
29070617 ATCTATCTACTTTTT
1 ATCTATCTACTTTTT
29070632 CTTTAGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (16 bp):
ATCTATCTACTTTTTT
Found at i:29071321 original size:21 final size:21
Alignment explanation
Indices: 29071292--29071331 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29071282 ATTTAATATA
29071292 AATTAAATAG-AATAAGAATAG
1 AATTAAATAGTAAT-AGAATAG
*
29071313 AATTTAATAGTAATAGAAT
1 AATTAAATAGTAATAGAAT
29071332 TTTCTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
AATTAAATAGTAATAGAATAG
Found at i:29072273 original size:16 final size:16
Alignment explanation
Indices: 29072252--29072302 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
29072242 TTTCTAGTAT
*
29072252 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTA
29072268 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
29072284 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
29072300 TTT
1 TTT
29072303 GCTCTTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.53
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:29074101 original size:12 final size:12
Alignment explanation
Indices: 29074084--29074109 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29074074 AATTTGTTTG
29074084 TTGTTTTAATAT
1 TTGTTTTAATAT
29074096 TTGTTTTAATAT
1 TTGTTTTAATAT
29074108 TT
1 TT
29074110 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:29074482 original size:70 final size:71
Alignment explanation
Indices: 29074365--29074499 Score: 213
Period size: 71 Copynumber: 1.9 Consensus size: 71
29074355 GGGCTACCAC
*
29074365 TTTAATTAAATAAATTTTTTTAATTATTTTTATTTATATTTTTAAAAT-AATTTTAAATTTTTTT
1 TTTAATTAAAT-AATTTTTTTAAATATTTTTATTTATATTTTTAAAATAAATTTTAAATTTTTTT
29074429 GGCACCT
65 GGCACCT
29074436 TTTAATTAAAT-ATTTTTTTAAAATAGTTTTT-TTTATATTTTTAAAATAAATTTTAAATTTTTT
1 TTTAATTAAATAATTTTTTT-AAATA-TTTTTATTTATATTTTTAAAATAAATTTTAAATTTTTT
29074499 T
64 T
29074500 ATGATGTCAT
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
69 8 0.13
70 20 0.33
71 32 0.53
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (71 bp):
TTTAATTAAATAATTTTTTTAAATATTTTTATTTATATTTTTAAAATAAATTTTAAATTTTTTTG
GCACCT
Found at i:29074537 original size:92 final size:95
Alignment explanation
Indices: 29074436--29074661 Score: 280
Period size: 95 Copynumber: 2.4 Consensus size: 95
29074426 TTTGGCACCT
* * *
29074436 TTTAATTAAAT-ATTTTTTTAAAATAGTTTTT-TTTATATTTTTAAAATAAATTTTAAATT-TTT
1 TTTAATTAAATAATTTTTTTAAAATATTTTTTATTTATAATTTTAAAATAAATTTAAAATTCTTT
* * *
29074498 TTATGATGTCATATTAAATGACGTCACCAC
66 TGATGATGCCATATTAAATGACGCCACCAC
*
29074528 TTTAATTAAATAATTTTGTT-AAATGATTTTTTATTTATAATTTTAAAATAAATTTAAAATTCTT
1 TTTAATTAAATAATTTTTTTAAAAT-ATTTTTTATTTATAATTTTAAAATAAATTTAAAATTCTT
* * * * **
29074592 TTGGTGGTGCCATATTAGATGGCGCCACCTT
65 TTGATGATGCCATATTAAATGACGCCACCAC
*
29074623 TTTAATTAAATAAATTTTTTAAAATTATTTTTTATTTAT
1 TTTAATTAAATAATTTTTTTAAAA-TATTTTTTATTTAT
29074662 TATATAATAT
Statistics
Matches: 113, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
92 15 0.13
93 13 0.12
94 26 0.23
95 42 0.37
96 16 0.14
97 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (95 bp):
TTTAATTAAATAATTTTTTTAAAATATTTTTTATTTATAATTTTAAAATAAATTTAAAATTCTTT
TGATGATGCCATATTAAATGACGCCACCAC
Found at i:29074691 original size:18 final size:18
Alignment explanation
Indices: 29074670--29074705 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29074660 ATTATATAAT
29074670 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
*
29074688 ATTTAAATATATATTTTA
1 ATTTAAATATATAGTTTA
29074706 TTTTTGGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:29074789 original size:27 final size:27
Alignment explanation
Indices: 29074759--29074826 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
29074749 AATTTTTTTG
**
29074759 TTTATTATTTATTTTTTAAATTTTAAA
1 TTTATTATTTATTTTAAAAATTTTAAA
*
29074786 TTTATT-TTTAATTTAAAAATTTTAAA
1 TTTATTATTTATTTTAAAAATTTTAAA
*
29074812 -ATATTATTTTATTTT
1 TTTATTA-TTTATTTT
29074827 GGTGGAGCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.12
26 17 0.50
27 13 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTATTATTTATTTTAAAAATTTTAAA
Found at i:29074795 original size:26 final size:27
Alignment explanation
Indices: 29074759--29074826 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
29074749 AATTTTTTTG
**
29074759 TTTATTATTTATTTTTTAAATTTT-AAA
1 TTTATT-TTTATTTTAAAAATTTTAAAA
*
29074786 TTTATTTTTAATTTAAAAATTTTAAAA
1 TTTATTTTTATTTTAAAAATTTTAAAA
29074813 TATTA-TTTTATTTT
1 T-TTATTTTTATTTT
29074827 GGTGGAGCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.40
27 18 0.51
28 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTATTTTTATTTTAAAAATTTTAAAA
Found at i:29074807 original size:19 final size:20
Alignment explanation
Indices: 29074765--29074803 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
29074755 TTTGTTTATT
*
29074765 ATTTATTTTTTAAATTTTAA
1 ATTTATTTTTTAAATTTAAA
29074785 ATTTA-TTTTT-AATTTAAA
1 ATTTATTTTTTAAATTTAAA
29074803 A
1 A
29074804 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 5 0.28
20 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTATTTTTTAAATTTAAA
Found at i:29078124 original size:22 final size:22
Alignment explanation
Indices: 29078099--29078141 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29078089 AAATATTTAG
* *
29078099 TGAAATTATATTATATAACACT
1 TGAAATTATATGACATAACACT
29078121 TGAAATTATATGACATAACAC
1 TGAAATTATATGACATAACAC
29078142 CTAAAATTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (22 bp):
TGAAATTATATGACATAACACT
Found at i:29078148 original size:22 final size:22
Alignment explanation
Indices: 29078101--29078149 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
29078091 ATATTTAGTG
* * * *
29078101 AAATTATATTATATAACACTTG
1 AAATTATATGACATAACACCTA
29078123 AAATTATATGACATAACACCTA
1 AAATTATATGACATAACACCTA
29078145 AAATT
1 AAATT
29078150 GGACTAAACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (22 bp):
AAATTATATGACATAACACCTA
Found at i:29080569 original size:19 final size:20
Alignment explanation
Indices: 29080531--29080574 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29080521 TTAATATGTA
*
29080531 TTTAATTTAATATGAAAATT
1 TTTAATGTAATATGAAAATT
*
29080551 TTTAATGTAATGT-AAAATT
1 TTTAATGTAATATGAAAATT
*
29080570 ATTAA
1 TTTAA
29080575 ATACTTTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (20 bp):
TTTAATGTAATATGAAAATT
Found at i:29081082 original size:14 final size:13
Alignment explanation
Indices: 29081060--29081094 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
29081050 AAACAACAAC
*
29081060 AAAAAACAAATTA
1 AAAAAACAAAATA
29081073 AAAAAGACAAAATA
1 AAAAA-ACAAAATA
29081087 AAAAAACA
1 AAAAAACA
29081095 GTATAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.80, C:0.09, G:0.03, T:0.09
Consensus pattern (13 bp):
AAAAAACAAAATA
Found at i:29081609 original size:11 final size:11
Alignment explanation
Indices: 29081572--29081614 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
29081562 CCCAACTTGG
29081572 ATTTTAAATTA
1 ATTTTAAATTA
*
29081583 AGTTTGAAATTA
1 A-TTTTAAATTA
*
29081595 ATTTTAAATTT
1 ATTTTAAATTA
29081606 A-TTTAAATT
1 ATTTTAAATT
29081615 TAAATTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.29
11 10 0.36
12 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:29081614 original size:17 final size:17
Alignment explanation
Indices: 29081574--29081636 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
29081564 CAACTTGGAT
*
29081574 TTTAAA-TTAAGTTTGAA
1 TTTAAATTTAAATTTG-A
* *
29081591 ATTAATTTTAAATTT-A
1 TTTAAATTTAAATTTGA
*
29081607 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGA
29081624 TTTAAATTTAAAT
1 TTTAAATTTAAAT
29081637 ACATTTGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
16 14 0.37
17 17 0.45
18 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTGA
Found at i:29081619 original size:27 final size:28
Alignment explanation
Indices: 29081580--29081656 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
29081570 GGATTTTAAA
*
29081580 TTAAGTTTGAAATTAATTTTAAATTTAT
1 TTAAATTTGAAATTAATTTTAAATTTAT
** *
29081608 TTAAATTT-AAATTTGTTTTAAATTTAA
1 TTAAATTTGAAATTAATTTTAAATTTAT
* * *
29081635 ATACATTTGAAA-TAACTTTAAA
1 TTAAATTTGAAATTAATTTTAAA
29081657 CTTAAAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
27 29 0.74
28 10 0.26
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (28 bp):
TTAAATTTGAAATTAATTTTAAATTTAT
Found at i:29082534 original size:16 final size:17
Alignment explanation
Indices: 29082496--29082541 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
29082486 AAGTACACAT
*
29082496 TAAAT-ATATTTAATAA
1 TAAATAATATTAAATAA
29082512 TAAATAATATTAAAT-A
1 TAAATAATATTAAATAA
*
29082528 TAAATAATAATAAA
1 TAAATAATATTAAA
29082542 AAAGAAGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAATAATATTAAATAA
Found at i:29083317 original size:32 final size:33
Alignment explanation
Indices: 29083275--29083343 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 33
29083265 TTATTTACGC
* *
29083275 ATTTGGTCCTTCCGCAT-TTTTTAATTATT-TTA
1 ATTTAGTCCTT-CGCATACTTTTAATTATTCTTA
**
29083307 ATTTAGTCCTTTTCATACTTTTAATTATTCTTA
1 ATTTAGTCCTTCGCATACTTTTAATTATTCTTA
29083340 ATTT
1 ATTT
29083344 GACTCGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 3 0.10
32 21 0.68
33 7 0.23
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (33 bp):
ATTTAGTCCTTCGCATACTTTTAATTATTCTTA
Found at i:29083813 original size:116 final size:116
Alignment explanation
Indices: 29083609--29083906 Score: 433
Period size: 117 Copynumber: 2.6 Consensus size: 116
29083599 CTTGAACTGT
* *
29083609 CCAAAAATTA-CATTTTAACCCTCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAA
1 CCAAAAATTACCATTTT-ACCCTCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC-AA
* * *
29083673 AATTACCATTTTACCCCGAACTTTCTAAAATCCCA-TTTTAACC-CTAATTTTA
64 AACTACCATTTTACCCCGAACTTTCCAAAATCCCATTTTTAACCTC-AATTTCA
*
29083725 CCAAAAATTACCATTTTACCC-CTAAACTTTCTAAAATCCCATTTTTAACCCCGATTTCACCAAA
1 CCAAAAATTACCATTTTACCCTC-AAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAA
*
29083789 ACTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCA
65 ACTACCATTTTA-CCCCGAACTTTCCAAAATCCCATTTTTAACCTCAATTTCA
* * *
29083842 CCTAAAATTACCATTTTACCCTCAAACTTTCCAAAATCCTATTTTTAACCCCGATTTCACAAAAA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAA
29083907 ATTACCGTTT
Statistics
Matches: 165, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
115 15 0.09
116 70 0.42
117 78 0.47
118 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.33
Consensus pattern (116 bp):
CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAA
CTACCATTTTACCCCGAACTTTCCAAAATCCCATTTTTAACCTCAATTTCA
Found at i:29083880 original size:59 final size:58
Alignment explanation
Indices: 29083609--29083912 Score: 425
Period size: 59 Copynumber: 5.2 Consensus size: 58
29083599 CTTGAACTGT
*
29083609 CCAAAAATTA-CATTTTAACCCTCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTT-ACCC-CGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* ** *
29083668 CCAAAAATTACCATTTTACCCCGAACTTTCTAAAATCCCA-TTTTAACCCTAATTTTA
1 CCAAAAATTACCATTTTACCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* *
29083725 CCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATCCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCC-GAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* *
29083784 CC-AAAACTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTA-CCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* * *
29083842 CCTAAAATTACCATTTTACCCTCAAACTTTCCAAAATCCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCC-CGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
*
29083901 CAAAAAATTACC
1 CCAAAAATTACC
29083913 GTTTACCTCG
Statistics
Matches: 220, Mismatches: 19, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
57 35 0.16
58 87 0.40
59 92 0.42
60 6 0.03
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.33
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
Found at i:29083906 original size:29 final size:28
Alignment explanation
Indices: 29083757--29083906 Score: 89
Period size: 29 Copynumber: 5.1 Consensus size: 28
29083747 TAAACTTTCT
29083757 AAAATCCCATTTTTAACCCCGATTTCACCA
1 AAAAT-CCATTTTTAACCCCGATTTCA-CA
* *
29083787 AAACTACCA-TTTTACCCCCGAACTTTC-C-
1 AAAAT-CCATTTTTAACCCCG-A-TTTCACA
*
29083815 AAAATCCCATTTTTAACCTCGATTTCACCTA
1 AAAAT-CCATTTTTAACCCCGATTTCA-C-A
* *
29083846 AAATTACCA-TTTT-ACCCTCAAACTTTC-C-
1 AAAAT-CCATTTTTAACCC-C-GA-TTTCACA
29083874 AAAATCCTATTTTTAACCCCGATTTCACA
1 AAAATCC-ATTTTTAACCCCGATTTCACA
29083903 AAAA
1 AAAA
29083907 ATTACCGTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 31
0.68 0.10 0.23
Matches are distributed among these distances:
27 10 0.11
28 15 0.16
29 33 0.36
30 18 0.20
31 12 0.13
32 4 0.04
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAATCCATTTTTAACCCCGATTTCACA
Found at i:29084063 original size:20 final size:20
Alignment explanation
Indices: 29084010--29084063 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 20
29084000 CACTAAATAC
29084010 TTGCATT-TATTTTAATCATT
1 TTGCATTCTATTTTAAT-ATT
29084030 TTGCACTTGC-ATTTTACAT-TT
1 TTGCA-TT-CTATTTTA-ATATT
29084051 TTGCATTCTATTT
1 TTGCATTCTATTT
29084064 ATCTGCTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
19 1 0.03
20 11 0.38
21 9 0.31
22 6 0.21
23 2 0.07
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (20 bp):
TTGCATTCTATTTTAATATT
Found at i:29096243 original size:200 final size:200
Alignment explanation
Indices: 29095889--29096287 Score: 609
Period size: 200 Copynumber: 2.0 Consensus size: 200
29095879 GTTCAACGAA
* * * *
29095889 CAAGCGAGGCGGTCATCTTCCTAAGGAGATACAGAGAAGAATACTAATTCAACGCTCAATACGAG
1 CAAGCGAGACGGTCATCTTCCTAAGGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAG
* *
29095954 CAAATCTTCGAACTCAGCTTCCTGATGAGACACTAAGAAGCAGGCCGAAACAATAAAATGGTTAG
66 CAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGCCGAAACAATAAAAAGGTTAG
* * *
29096019 CCTCCTGATGAGACACAGAGAAGTGGATCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAAT
131 CCTCCTGATGAGACACACAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAACCGAAT
29096084 TAAAG
196 TAAAG
* * * *
29096089 CAAGCGAGACGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAATGCTCAACGCGAG
1 CAAGCGAGACGGTCATCTTCCTAAGGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAG
* * *
29096154 CAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAG
66 CAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGCCGAAACAATAAAAAGGTTAG
* * * * *
29096219 CTTCCTGATGGGACACACAGAAGTGGGCCAAATTTGTCTTCTTGAGGAGATCCAGAGAACCGAAT
131 CCTCCTGATGAGACACACAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAACCGAAT
29096284 TAAA
196 TAAA
29096288 ACAGATGATT
Statistics
Matches: 178, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
200 178 1.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (200 bp):
CAAGCGAGACGGTCATCTTCCTAAGGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAG
CAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGCCGAAACAATAAAAAGGTTAG
CCTCCTGATGAGACACACAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAACCGAAT
TAAAG
Found at i:29096714 original size:11 final size:11
Alignment explanation
Indices: 29096677--29096719 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
29096667 CCCAACTTGG
29096677 ATTTTAAATTA
1 ATTTTAAATTA
*
29096688 AGTTTGAAATTA
1 A-TTTTAAATTA
*
29096700 ATTTTAAATTT
1 ATTTTAAATTA
29096711 A-TTTAAATT
1 ATTTTAAATT
29096720 TAAATTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.29
11 10 0.36
12 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:29096719 original size:17 final size:17
Alignment explanation
Indices: 29096679--29096741 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
29096669 CAACTTGGAT
*
29096679 TTTAAA-TTAAGTTTGAA
1 TTTAAATTTAAATTTG-A
* *
29096696 ATTAATTTTAAATTT-A
1 TTTAAATTTAAATTTGA
*
29096712 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGA
29096729 TTTAAATTTAAAT
1 TTTAAATTTAAAT
29096742 ACATTTGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
16 14 0.37
17 17 0.45
18 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTGA
Found at i:29096724 original size:27 final size:28
Alignment explanation
Indices: 29096685--29096761 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
29096675 GGATTTTAAA
*
29096685 TTAAGTTTGAAATTAATTTTAAATTTAT
1 TTAAATTTGAAATTAATTTTAAATTTAT
** *
29096713 TTAAATTT-AAATTTGTTTTAAATTTAA
1 TTAAATTTGAAATTAATTTTAAATTTAT
* * *
29096740 ATACATTTGAAA-TAACTTTAAA
1 TTAAATTTGAAATTAATTTTAAA
29096762 CTTAAAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
27 29 0.74
28 10 0.26
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (28 bp):
TTAAATTTGAAATTAATTTTAAATTTAT
Found at i:29097185 original size:16 final size:17
Alignment explanation
Indices: 29097147--29097192 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
29097137 AAGTACACAT
*
29097147 TAAAT-ATATTTAATAA
1 TAAATAATATTAAATAA
29097163 TAAATAATATTAAAT-A
1 TAAATAATATTAAATAA
*
29097179 TAAATAATAATAAA
1 TAAATAATATTAAA
29097193 AAAGAAGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAATAATATTAAATAA
Found at i:29098335 original size:29 final size:29
Alignment explanation
Indices: 29098303--29098390 Score: 67
Period size: 29 Copynumber: 3.0 Consensus size: 29
29098293 TCAACTTTTT
29098303 GAAATCCCATTTTTAACCCCGATTTCATC
1 GAAATCCCATTTTTAACCCCGATTTCATC
* *
29098332 GAAAATTACCA-TTTT-ACCCCTAAACTTTC--C
1 G-AAA-TCCCATTTTTAACCCC--GA-TTTCATC
* *
29098362 AAAATCCCATTTTTAACCCTGATTTCATC
1 GAAATCCCATTTTTAACCCCGATTTCATC
29098391 AAAAATTACC
Statistics
Matches: 44, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
27 4 0.09
28 5 0.11
29 14 0.32
30 12 0.27
31 5 0.11
32 4 0.09
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.35
Consensus pattern (29 bp):
GAAATCCCATTTTTAACCCCGATTTCATC
Found at i:29098351 original size:59 final size:59
Alignment explanation
Indices: 29098275--29098818 Score: 667
Period size: 59 Copynumber: 9.3 Consensus size: 59
29098265 AACTGTCCAG
*** * * *
29098275 AAATTA-CATTTTGACCCCTCAACTTTTTGAAATCCCATTTTTAACCCCGATTTCATCGA
1 AAATTACCATTTT-ACCCCTCAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
* *
29098334 AAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCATCAA
1 AAATTACCATTTTACCCCTCAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
** *
29098393 AAATTACCATTTTA-CCCTCAAACTTTCCAAAATATCATTTTTAACCTTGATTTCACCAA
1 AAATTACCATTTTACCCCTC-AACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
* * * *
29098452 AAATTACCATTTTACCCCTAAACTTTCCAAAATCTCATTTTTAATCCTGATTTTACCAA
1 AAATTACCATTTTACCCCTCAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
* *
29098511 AAATTACCA-TTTACCCCTAAAATTTCCAAAATCCCATTTTTAA-CCTCGATTTCACCAA
1 AAATTACCATTTTACCCCTCAACTTTCCAAAATCCCATTTTTAACCCT-GATTTCACCAA
*
29098569 AAATTACCATTTTA-CCCTCGAACTTTCTAAAATCCCATTTTTAACCCTGATTTCACCAA
1 AAATTACCATTTTACCCCTC-AACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
* * * *
29098628 AAACTACCATTTTACCCC-CAAACTTTCTAAAATCTCATTTTTAACCCTAATTTCACC-A
1 AAATTACCATTTTACCCCTC-AACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
* * *
29098686 AAACTACCATTTTA-CCCTCGAACTTTCCAAAATCCCA-TTTTAACCCCGATTTCACCCA
1 AAATTACCATTTTACCCCTC-AACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
* * * * * *
29098744 AAATTGCCATTTTACCCTTAAACTTTCTAAAATCCTATTTTTAA-CCTCGGTTTCACCAA
1 AAATTACCATTTTACCCCTCAACTTTCCAAAATCCCATTTTTAACCCT-GATTTCACCAA
*
29098803 AAATTACCGTTTTACC
1 AAATTACCATTTTACC
29098819 TCGGAGGTCA
Statistics
Matches: 430, Mismatches: 42, Indels: 26
0.86 0.08 0.05
Matches are distributed among these distances:
57 23 0.05
58 120 0.28
59 271 0.63
60 16 0.04
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (59 bp):
AAATTACCATTTTACCCCTCAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
Found at i:29098572 original size:176 final size:174
Alignment explanation
Indices: 29098275--29098818 Score: 736
Period size: 176 Copynumber: 3.1 Consensus size: 174
29098265 AACTGTCCAG
* * * * * *
29098275 AAATTA-CATTTTGACCCCTCAACTTTTTGAAATCCCATTTTTAACCCCGATTTCATCGAAAATT
1 AAATTACCATTTT-ACCCCTAAACTTTCTAAAATCTCATTTTTAACCCTGATTTCA-CCAAAATT
*
29098339 ACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCATCAAAAATTACCATT
64 ACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCC-GATTTCACCAAAAATTACCATT
* *
29098404 TTACCCTCAAACTTTCCAAAATATCATTTTTAACCTTGATTTCACCAA
128 TTACCCTCAAACTTTCTAAAAT-CCATTTTTAACCTTGATTTCACCAA
* * *
29098452 AAATTACCATTTTACCCCTAAACTTTCCAAAATCTCATTTTTAATCCTGATTTTACCAAAAATTA
1 AAATTACCATTTTACCCCTAAACTTTCTAAAATCTCATTTTTAACCCTGATTTCACC-AAAATTA
*
29098517 CCA-TTTACCCCTAAAATTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTT
65 CCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACC-CGATTTCACCAAAAATTACCATTT
* *
29098581 TACCCTCGAACTTTCTAAAATCCCATTTTTAACCCTGATTTCACCAA
129 TACCCTCAAACTTTCTAAAAT-CCATTTTTAACCTTGATTTCACCAA
* * * *
29098628 AAACTACCATTTTACCCCCAAACTTTCTAAAATCTCATTTTTAACCCTAATTTCACCAAAACTAC
1 AAATTACCATTTTACCCCTAAACTTTCTAAAATCTCATTTTTAACCCTGATTTCACCAAAATTAC
* * *
29098693 CATTTTA-CCCTCGAACTTTCCAAAATCCCA-TTTTAACCCCGATTTCACCCAAAATTGCCATTT
66 CATTTTACCCCT-AAACTTTCCAAAATCCCATTTTTAA-CCCGATTTCACCAAAAATTACCATTT
* * *
29098756 TACCCTTAAACTTTCTAAAATCCTATTTTTAACCTCGGTTTCACCAA
129 TACCCTCAAACTTTCTAAAATCC-ATTTTTAACCTTGATTTCACCAA
*
29098803 AAATTACCGTTTTACC
1 AAATTACCATTTTACC
29098819 TCGGAGGTCA
Statistics
Matches: 326, Mismatches: 34, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
174 2 0.01
175 94 0.29
176 173 0.53
177 51 0.16
178 6 0.02
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (174 bp):
AAATTACCATTTTACCCCTAAACTTTCTAAAATCTCATTTTTAACCCTGATTTCACCAAAATTAC
CATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCGATTTCACCAAAAATTACCATTTTA
CCCTCAAACTTTCTAAAATCCATTTTTAACCTTGATTTCACCAA
Found at i:29098601 original size:117 final size:118
Alignment explanation
Indices: 29098275--29098818 Score: 699
Period size: 117 Copynumber: 4.6 Consensus size: 118
29098265 AACTGTCCAG
* *** * * *
29098275 AAATTA-CATTTTGACCCCTCAACTTTTTGAAATCCCATTTTTAACCCCGATTTCATCGAAAATT
1 AAATTACCATTTT-ACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATT
*
29098339 ACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCATCAA
65 ACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
** *
29098393 AAATTACCATTTTA-CCCTCAAACTTTCCAAAATATCATTTTTAACCTTGATTTCACCAAAAATT
1 AAATTACCATTTTACCCCT-AAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATT
* * *
29098457 ACCATTTTACCCCTAAACTTTCCAAAATCTCATTTTTAATCCTGATTTTACCAA
65 ACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
*
29098511 AAATTACCA-TTTACCCCTAAAATTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTA
1 AAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTA
* *
29098575 CCATTTTA-CCCTCGAACTTTCTAAAATCCCATTTTTAACCCTGATTTCACCAA
66 CCATTTTACCCCT-AAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
* * * * * *
29098628 AAACTACCATTTTACCCCCAAACTTTCTAAAATCTCATTTTTAACC-CTAATTTCACC-AAAACT
1 AAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTC-GATTTCACCAAAAATT
* * *
29098691 ACCATTTTA-CCCTCGAACTTTCCAAAATCCCA-TTTTAACCCCGATTTCACCCA
65 ACCATTTTACCCCT-AAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
* * * * *
29098744 AAATTGCCATTTTACCCTTAAACTTTCTAAAATCCTATTTTTAACCTCGGTTTCACCAAAAATTA
1 AAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTA
*
29098809 CCGTTTTACC
66 CCATTTTACC
29098819 TCGGAGGTCA
Statistics
Matches: 374, Mismatches: 43, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
116 70 0.19
117 152 0.41
118 146 0.39
119 6 0.02
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (118 bp):
AAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTA
CCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAA
Found at i:29098962 original size:20 final size:20
Alignment explanation
Indices: 29098909--29098962 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 20
29098899 CACTAAATAC
29098909 TTGCATT-TATTTTAATCATT
1 TTGCATTCTATTTTAAT-ATT
29098929 TTGCACTTGC-ATTTT-ATATTT
1 TTGCA-TT-CTATTTTAATA-TT
29098950 TTGCATTCTATTT
1 TTGCATTCTATTT
29098963 ATCTGCTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 11 0.38
22 5 0.17
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.59
Consensus pattern (20 bp):
TTGCATTCTATTTTAATATT
Found at i:29101445 original size:13 final size:13
Alignment explanation
Indices: 29101403--29101458 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
29101393 TATAGTTTAA
*
29101403 AAAATTAAATACT
1 AAAATTAAATAAT
* ** *
29101416 AATATTTTATTAT
1 AAAATTAAATAAT
29101429 AAAA-TATAATAAT
1 AAAATTA-AATAAT
29101442 AAAATTAAATAAT
1 AAAATTAAATAAT
29101455 AAAA
1 AAAA
29101459 AAGAAAAAGG
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
12 1 0.03
13 29 0.91
14 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTAAATAAT
Found at i:29101754 original size:28 final size:29
Alignment explanation
Indices: 29101710--29101773 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
29101700 TAGATTTTAG
* *
29101710 GTTATTTTCGTATTTAA-TAAAAAAATGA
1 GTTATTTACGTAATTAATTAAAAAAATGA
29101738 GTTATTTACGTAATTAATTAAAAAAATGA
1 GTTATTTACGTAATTAATTAAAAAAATGA
29101767 GTTATTT
1 GTTATTT
29101774 TTATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (29 bp):
GTTATTTACGTAATTAATTAAAAAAATGA
Found at i:29105869 original size:33 final size:33
Alignment explanation
Indices: 29105811--29105997 Score: 184
Period size: 33 Copynumber: 5.7 Consensus size: 33
29105801 GTGTGTTGGT
*
29105811 TTGA-TAGCTCTTACGA-CATACCATGTAATGA
1 TTGATTAGCTCTTACGAGCATACCATGTACTGA
*
29105842 TTGGA-TAGCTTTTACGAGCATACCATGTACTGA
1 TT-GATTAGCTCTTACGAGCATACCATGTACTGA
** * * *
29105875 TTGATTAGCTCTTATAAGCATATCGTGTACTAA
1 TTGATTAGCTCTTACGAGCATACCATGTACTGA
29105908 TTGATTAGCTCTTACGAGCATA-CAGTGTACTGA
1 TTGATTAGCTCTTACGAGCATACCA-TGTACTGA
* * ** * *
29105941 TTTATTAGCCCTTACGAGCATACTGTGTATTACA
1 TTGATTAGCTCTTACGAGCATACCATGTACT-GA
* *
29105975 TTGATGAGCTCTTATGAGCATAC
1 TTGATTAGCTCTTACGAGCATAC
29105998 TGTGAATTTA
Statistics
Matches: 128, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
31 2 0.02
32 16 0.12
33 90 0.70
34 20 0.16
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (33 bp):
TTGATTAGCTCTTACGAGCATACCATGTACTGA
Found at i:29105957 original size:99 final size:98
Alignment explanation
Indices: 29105811--29105996 Score: 225
Period size: 99 Copynumber: 1.9 Consensus size: 98
29105801 GTGTGTTGGT
** *
29105811 TTGATAGCTCTTACGACATACCATGTAATGATTGGATAGCTTTTACGAGCATACCATGTACT-GA
1 TTGATAGCTCTTACGACATACCATGTAATGATTGGATAGCCCTTACGAGCATACCATGTACTACA
*
29105875 TTGATTAGCTCTTATAAGCATATCGTGTACTAA
66 TTGATGAGCTCTTATAAGCATATCGTGTACTAA
* * ** *
29105908 TTGATTAGCTCTTACGAGCATA-CAGTGTACTGATT-TATTAGCCCTTACGAGCATACTGTGTAT
1 TTGA-TAGCTCTTACGA-CATACCA-TGTAATGATTGGA-TAGCCCTTACGAGCATACCATGTAC
*
29105971 TACATTGATGAGCTCTTATGAGCATA
62 TACATTGATGAGCTCTTATAAGCATA
29105997 CTGTGAATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
97 4 0.05
98 15 0.20
99 34 0.46
100 21 0.28
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (98 bp):
TTGATAGCTCTTACGACATACCATGTAATGATTGGATAGCCCTTACGAGCATACCATGTACTACA
TTGATGAGCTCTTATAAGCATATCGTGTACTAA
Found at i:29108021 original size:19 final size:20
Alignment explanation
Indices: 29107975--29108021 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
29107965 GGACTAAAGG
29107975 ATCGATACTTATATCAGAGT
1 ATCGATACTTATATCAGAGT
* *
29107995 ATCAATACTT-TA-CAAGGGT
1 ATCGATACTTATATC-AGAGT
29108014 ATCGATAC
1 ATCGATAC
29108022 AATTGATCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 13 0.57
20 9 0.39
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (20 bp):
ATCGATACTTATATCAGAGT
Found at i:29111065 original size:23 final size:23
Alignment explanation
Indices: 29111038--29111139 Score: 150
Period size: 23 Copynumber: 4.4 Consensus size: 23
29111028 ATCTTAATTC
*
29111038 TTTAAGCACAAATCAAATTAATA
1 TTTAAGCACAAATCATATTAATA
* *
29111061 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCATATTAATA
* *
29111084 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATA
*
29111107 TTTAAGCACAAAGCATATTAATA
1 TTTAAGCACAAATCATATTAATA
29111130 TTTAAGCACA
1 TTTAAGCACA
29111140 GATATAAGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCATATTAATA
Found at i:29113108 original size:25 final size:26
Alignment explanation
Indices: 29113074--29113122 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
29113064 GTTACTAAGC
* *
29113074 AAACAAATAT-TTTTGTTTTAAAAAA
1 AAACAAATATCTTTTATCTTAAAAAA
29113099 AAACAAATATCTTTTATCTTAAAA
1 AAACAAATATCTTTTATCTTAAAA
29113123 CGAATCCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (26 bp):
AAACAAATATCTTTTATCTTAAAAAA
Found at i:29121704 original size:23 final size:21
Alignment explanation
Indices: 29121654--29121705 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
29121644 AATGCATATT
29121654 TTTTTTATTTTTCAAAAATAA
1 TTTTTTATTTTTCAAAAATAA
* *
29121675 ATATTTATTTTTCAATTAAATAA
1 TTTTTTATTTTTCAA--AAATAA
29121698 TTTTTTAT
1 TTTTTTAT
29121706 CCTAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 13 0.52
23 12 0.48
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTTATTTTTCAAAAATAA
Found at i:29121914 original size:6 final size:6
Alignment explanation
Indices: 29121903--29121933 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
29121893 TGCAAATAGA
*
29121903 TCATTT TCATTT TCATTT TCATTT CCATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT T
29121934 TTGAGAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (6 bp):
TCATTT
Found at i:29127859 original size:2 final size:2
Alignment explanation
Indices: 29127813--29127841 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29127803 ATAATAAGTA
29127813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29127842 ATCAAATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29134253 original size:36 final size:36
Alignment explanation
Indices: 29134206--29134289 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
29134196 GGTGCCGGTG
* * *
29134206 CTTCAATCGGTGGGGCGAATTTCTCTTCTTCCTTGA
1 CTTCAACCGGTGGGGCGAACTCCTCTTCTTCCTTGA
**
29134242 CTTCAACCGGTGGGGCGGCCTCCTCTTCTTCCTTGA
1 CTTCAACCGGTGGGGCGAACTCCTCTTCTTCCTTGA
*
29134278 CTTCAACGGGTG
1 CTTCAACCGGTG
29134290 CGGGTGCTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.12, C:0.30, G:0.25, T:0.33
Consensus pattern (36 bp):
CTTCAACCGGTGGGGCGAACTCCTCTTCTTCCTTGA
Found at i:29143406 original size:31 final size:31
Alignment explanation
Indices: 29143368--29143435 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
29143358 CTAATTAAAA
29143368 TAAAATCAATGTTTTTTATTTTCATGTTATG
1 TAAAATCAATGTTTTTTATTTTCATGTTATG
29143399 TAAAATCAATGTTTTTTATTTTCATGTTATG
1 TAAAATCAATGTTTTTTATTTTCATGTTATG
29143430 TAAAAT
1 TAAAAT
29143436 TTCAATTAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (31 bp):
TAAAATCAATGTTTTTTATTTTCATGTTATG
Found at i:29145109 original size:12 final size:12
Alignment explanation
Indices: 29145092--29145138 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
29145082 TCACGAACAA
29145092 GCTCGTTTATTG
1 GCTCGTTTATTG
**
29145104 GCTCGTTTATAA
1 GCTCGTTTATTG
*
29145116 GTTCGTTTATTG
1 GCTCGTTTATTG
*
29145128 ACTCGTTTATT
1 GCTCGTTTATT
29145139 TATTAATGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.51
Consensus pattern (12 bp):
GCTCGTTTATTG
Found at i:29145297 original size:47 final size:47
Alignment explanation
Indices: 29145228--29145343 Score: 223
Period size: 47 Copynumber: 2.5 Consensus size: 47
29145218 TCATTAACAT
*
29145228 TGTTCGTGAACATGTTCAATTATATGTTCATGAATATGTTTGTTTAA
1 TGTTCGTGAACATGTTCAATTATATGCTCATGAATATGTTTGTTTAA
29145275 TGTTCGTGAACATGTTCAATTATATGCTCATGAATATGTTTGTTTAA
1 TGTTCGTGAACATGTTCAATTATATGCTCATGAATATGTTTGTTTAA
29145322 TGTTCGTGAACATGTTCAATTA
1 TGTTCGTGAACATGTTCAATTA
29145344 AGTTAAATGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (47 bp):
TGTTCGTGAACATGTTCAATTATATGCTCATGAATATGTTTGTTTAA
Found at i:29145344 original size:23 final size:23
Alignment explanation
Indices: 29145228--29145361 Score: 117
Period size: 23 Copynumber: 5.7 Consensus size: 23
29145218 TCATTAACAT
*
29145228 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
* ***
29145252 TGTTCATGAATATGTTTGTTTAA
1 TGTTCATGAACATGTTCAATTAA
*
29145275 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
* * ***
29145299 TGCTCATGAATATGTTTGTTTAA
1 TGTTCATGAACATGTTCAATTAA
*
29145322 TGTTCGTGAACATGTTCAATTAA
1 TGTTCATGAACATGTTCAATTAA
*
29145345 -GTTAAATGAACATGTTC
1 TGTT-CATGAACATGTTC
29145362 GTGAACCTTA
Statistics
Matches: 84, Mismatches: 24, Indels: 5
0.74 0.21 0.04
Matches are distributed among these distances:
22 3 0.04
23 47 0.56
24 34 0.40
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:29146969 original size:15 final size:15
Alignment explanation
Indices: 29146945--29146974 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29146935 CAATAGGATA
29146945 ATTTACATTGTGATG
1 ATTTACATTGTGATG
*
29146960 ATTTATATTGTGATG
1 ATTTACATTGTGATG
29146975 TGAAAAATAG
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:0.27, C:0.03, G:0.20, T:0.50
Consensus pattern (15 bp):
ATTTACATTGTGATG
Found at i:29149686 original size:46 final size:42
Alignment explanation
Indices: 29149570--29149821 Score: 154
Period size: 43 Copynumber: 5.8 Consensus size: 42
29149560 ACACTCTAGT
* * *
29149570 TTGTGAATGAAACACCAGTATTTGCAGAT--AACTTCTAGTAGG
1 TTGTGGATG-AACAACA-TATTTGCAGATAAAACTGCTAGTAGG
* *
29149612 TTGTGGATGCACAACATATTTGCAGATAAAAGCTGCTAGTAAGT
1 TTGTGGATGAACAACATATTTGCAGATAAAA-CTGCTAGT-AGG
* * * *
29149656 TTGTGGATGAACAACTAATATTTGCAGAT-AAATTTCCAATAGG
1 TTGTGGATGAACAAC--ATATTTGCAGATAAAACTGCTAGTAGG
* ** * * **
29149699 TTGTGAATGCTCAACATATTTACAAATAAAAGCTGCTAGTAATT
1 TTGTGGATGAACAACATATTTGCAGATAAAA-CTGCTAGT-AGG
* * * * *
29149743 TTGTGTATAAACCACCAGTGTTTGCAGAT-AAACTGCCAGTAGG
1 TTGTGGATGAA-CAACA-TATTTGCAGATAAAACTGCTAGTAGG
* *
29149786 TTGT-GAGTGCACAACATATTTACAGATAAAAGCTGC
1 TTGTGGA-TGAACAACATATTTGCAGATAAAA-CTGC
29149822 CAATAATTTC
Statistics
Matches: 157, Mismatches: 39, Indels: 27
0.70 0.17 0.12
Matches are distributed among these distances:
40 11 0.07
41 24 0.15
42 21 0.13
43 36 0.23
44 35 0.22
45 10 0.06
46 20 0.13
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (42 bp):
TTGTGGATGAACAACATATTTGCAGATAAAACTGCTAGTAGG
Done.