Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 12 of 250
Found at i:3435334 original size:21 final size:21
Alignment explanation
Indices: 3435310--3435361 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
3435300 GTATTTTTTG
3435310 AATTTTTAATCTAAAAATTGT-
1 AATTTTTAATCTAAAAATT-TC
3435331 AATTTTTAATCTAAAAATTTC
1 AATTTTTAATCTAAAAATTTC
3435352 AATTTTTAAT
1 AATTTTTAAT
3435362 ATTTATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (21 bp):
AATTTTTAATCTAAAAATTTC
Found at i:3435614 original size:11 final size:10
Alignment explanation
Indices: 3435580--3435661 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 10
3435570 ATATTTTATG
*
3435580 TATTATTTTA
1 TATTATTTAA
3435590 TCATTATATT-A
1 T-ATTAT-TTAA
3435601 TATTATTTAAA
1 TATTATTT-AA
* *
3435612 TATTCATGTAT
1 TATT-ATTTAA
3435623 TATTATATT-A
1 TATTAT-TTAA
3435633 TATTATTTAAA
1 TATTATTT-AA
* *
3435644 TATAATTTAT
1 TATTATTTAA
3435654 TATTATTT
1 TATTATTT
3435662 TTAAAATTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
9 4 0.07
10 22 0.39
11 26 0.46
12 5 0.09
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (10 bp):
TATTATTTAA
Found at i:3435614 original size:16 final size:16
Alignment explanation
Indices: 3435595--3435646 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
3435585 TTTTATCATT
3435595 ATATTATATTATTTAA
1 ATATTATATTATTTAA
3435611 ATATTCATGTATTA-TT--
1 ATATT-A--TATTATTTAA
3435627 ATATTATATTATTTAA
1 ATATTATATTATTTAA
3435643 ATAT
1 ATAT
3435647 AATTTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
13 5 0.17
14 2 0.07
15 1 0.03
16 14 0.47
17 1 0.03
18 2 0.07
19 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
ATATTATATTATTTAA
Found at i:3435632 original size:32 final size:31
Alignment explanation
Indices: 3435592--3435659 Score: 109
Period size: 32 Copynumber: 2.2 Consensus size: 31
3435582 TTATTTTATC
*
3435592 ATTATATTATATTATTTAAATATTCATGTATT
1 ATTATATTATATTATTTAAATA-TAATGTATT
*
3435624 ATTATATTATATTATTTAAATATAATTTATT
1 ATTATATTATATTATTTAAATATAATGTATT
3435655 ATTAT
1 ATTAT
3435660 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (31 bp):
ATTATATTATATTATTTAAATATAATGTATT
Found at i:3435730 original size:9 final size:9
Alignment explanation
Indices: 3435660--3435736 Score: 52
Period size: 9 Copynumber: 8.2 Consensus size: 9
3435650 TTATTATTAT
3435660 TTTTAAA-A
1 TTTTAAATA
3435668 TTTTAAAATA
1 TTTT-AAATA
* *
3435678 TGTTATATA
1 TTTTAAATA
3435687 TTATTAAAT-
1 TT-TTAAATA
*
3435696 TTATAAATAA
1 TTTTAAAT-A
3435706 TTTACTAAA-A
1 TTT--TAAATA
3435716 TATTTAAATA
1 T-TTTAAATA
3435726 TTTTAAATA
1 TTTTAAATA
3435735 TT
1 TT
3435737 GTCTAAAATG
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
8 9 0.17
9 24 0.44
10 15 0.28
11 2 0.04
12 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (9 bp):
TTTTAAATA
Found at i:3437267 original size:51 final size:51
Alignment explanation
Indices: 3437208--3437315 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 51
3437198 ATCCTTAAAG
* * *
3437208 TTTACACATTCTATTAATTTGGTCTTAATTTAATAAATTTAACCTACAATA
1 TTTACACATTCTATCAATTTAGTCTTAATTTAACAAATTTAACCTACAATA
* * *
3437259 TTTACACATTCTGTCAATTTAGTCTTAATTTAACAAATTTAGCTTACAATA
1 TTTACACATTCTATCAATTTAGTCTTAATTTAACAAATTTAACCTACAATA
3437310 TTTACA
1 TTTACA
3437316 TAGAATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (51 bp):
TTTACACATTCTATCAATTTAGTCTTAATTTAACAAATTTAACCTACAATA
Found at i:3437988 original size:13 final size:12
Alignment explanation
Indices: 3437968--3438009 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
3437958 TAATTAAATG
3437968 TTTT-AATTTTT
1 TTTTAAATTTTT
3437979 TTTGTAAATTTTT
1 TTT-TAAATTTTT
*
3437992 TTTTATATTTTT
1 TTTTAAATTTTT
*
3438004 TGTTAA
1 TTTTAA
3438010 TGTGGTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 3 0.12
12 13 0.50
13 10 0.38
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTAAATTTTT
Found at i:3439926 original size:16 final size:16
Alignment explanation
Indices: 3439904--3439938 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3439894 AAAATTAAAT
*
3439904 TTAAAAAAAAAGAATTG
1 TTAAAAATAAA-AATTG
3439921 TTAAAAATAAAAATTG
1 TTAAAAATAAAAATTG
3439937 TT
1 TT
3439939 TCAGTTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (16 bp):
TTAAAAATAAAAATTG
Found at i:3440977 original size:12 final size:12
Alignment explanation
Indices: 3440960--3440985 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3440950 AAAGATATAT
3440960 AATATATTCCTA
1 AATATATTCCTA
3440972 AATATATTCCTA
1 AATATATTCCTA
3440984 AA
1 AA
3440986 AGATATACAA
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATATTCCTA
Found at i:3448336 original size:88 final size:86
Alignment explanation
Indices: 3448228--3448565 Score: 306
Period size: 87 Copynumber: 3.9 Consensus size: 86
3448218 TATCACCCGA
* * * ** *
3448228 AAACAAAA-TAAAATCAAATAAAATCTTATTAAACGGTAGGAATAAATCTCGAAACAAATTTTAT
1 AAACAAAATTAAAAT-GAATAAAATC-CATTGAACGGCGGGAATAAATCCCGAAACAAATTTTAT
3448292 TTAATTTTAATTTCTCGTTTTGG
64 TTAATTTTAATTTCTCGTTTTGG
* * * * *
3448315 CAACAAAATTAAAATGTAAT-AAATTCGTTGAACGGCTGGAATAAATCCCGAAACAGATTTTATT
1 AAACAAAATTAAAATG-AATAAAATCCATTGAACGGCGGGAATAAATCCCGAAACAAATTTTA-T
* *
3448379 TTAATTTTAA-TACTCATTTTGG
64 TTAATTTTAATTTCTCGTTTTGG
* * * * * * *
3448401 AAATAAAATCAAAATTGGAATAAAATCTATTGAACGACGGGAATAAAACCCGAAGCGAATTTTAT
1 AAACAAAATTAAAA-T-GAATAAAATCCATTGAACGGCGGGAATAAATCCCGAAACAAATTTTAT
* * *
3448466 TTAACTTTAATTCCCCG-TTTGG
64 TTAATTTTAATTTCTCGTTTTGG
* * * * **
3448488 AAATAAAATAGAAAATAGAATAAAATCCGTTGAACGGCGGGAATAAATACCGAAACGGATTTTAT
1 AAACAAAAT-TAAAAT-GAATAAAATCCATTGAACGGCGGGAATAAATCCCGAAACAAATTTTAT
*
3448553 TTACTTTTAATTT
64 TTAATTTTAATTT
3448566 GGAAACAAAA
Statistics
Matches: 203, Mismatches: 40, Indels: 16
0.78 0.15 0.06
Matches are distributed among these distances:
86 51 0.25
87 102 0.50
88 50 0.25
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (86 bp):
AAACAAAATTAAAATGAATAAAATCCATTGAACGGCGGGAATAAATCCCGAAACAAATTTTATTT
AATTTTAATTTCTCGTTTTGG
Found at i:3448358 original size:86 final size:85
Alignment explanation
Indices: 3448266--3448565 Score: 307
Period size: 87 Copynumber: 3.5 Consensus size: 85
3448256 TTAAACGGTA
* * * *
3448266 GGAATAAATCTCGAAACAAATTTTATTTAATTTTAATTTCTCGTTTTGGCAACAAAATTAAAATG
1 GGAATAAATCCCGAAACAAATTTTATTTAATTTTAATTTCTCGTTTTGGAAATAAAATCAAAATG
*
3448331 TAATAAATTCGTTGAACGGCT
66 -AATAAATTCGTTGAACGGCG
* * *
3448352 GGAATAAATCCCGAAACAGATTTTATTTTAATTTTAA-TACTCATTTTGGAAATAAAATCAAAAT
1 GGAATAAATCCCGAAACAAATTTTA-TTTAATTTTAATTTCTCGTTTTGGAAATAAAATCAAAA-
* * *
3448416 TGGAATAAAATCTATTGAACGACG
64 T-GAATAAATTC-GTTGAACGGCG
* * * * * * *
3448440 GGAATAAAACCCGAAGCGAATTTTATTTAACTTTAATTCCCCG-TTTGGAAATAAAATAGAAAAT
1 GGAATAAATCCCGAAACAAATTTTATTTAATTTTAATTTCTCGTTTTGGAAATAAAAT-CAAAAT
*
3448504 AGAATAAAATCCGTTGAACGGCG
65 -GAAT-AAATTCGTTGAACGGCG
* ** *
3448527 GGAATAAATACCGAAACGGATTTTATTTACTTTTAATTT
1 GGAATAAATCCCGAAACAAATTTTATTTAATTTTAATTT
3448566 GGAAACAAAA
Statistics
Matches: 175, Mismatches: 32, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
86 44 0.25
87 90 0.51
88 41 0.23
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (85 bp):
GGAATAAATCCCGAAACAAATTTTATTTAATTTTAATTTCTCGTTTTGGAAATAAAATCAAAATG
AATAAATTCGTTGAACGGCG
Found at i:3451591 original size:12 final size:12
Alignment explanation
Indices: 3451574--3451603 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
3451564 AAAAAAGAAG
3451574 TTTTTTTTTT-C
1 TTTTTTTTTTCC
3451585 TTTTTTTTTTCC
1 TTTTTTTTTTCC
3451597 TTTTTTT
1 TTTTTTT
3451604 GACCAGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTTCC
Found at i:3457732 original size:9 final size:9
Alignment explanation
Indices: 3457718--3457747 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3457708 AATGTTAGAA
3457718 AAGAAAAAG
1 AAGAAAAAG
3457727 AAGAAAAAG
1 AAGAAAAAG
3457736 AAGAAGAAAG
1 AAGAA-AAAG
3457746 AA
1 AA
3457748 TAGGGAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:3466613 original size:13 final size:13
Alignment explanation
Indices: 3466595--3466619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3466585 TTATAATTTT
3466595 AAAATATTTTTAA
1 AAAATATTTTTAA
3466608 AAAATATTTTTA
1 AAAATATTTTTA
3466620 TTTTTCAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATATTTTTAA
Found at i:3467731 original size:23 final size:25
Alignment explanation
Indices: 3467699--3467744 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3467689 CTAATTAAAT
*
3467699 TTTTTAATAAAT-TTTATTTTTTAA
1 TTTTTAATAAATATTAATTTTTTAA
3467723 TTTTT-ATAAATATTAATTTTTT
1 TTTTTAATAAATATTAATTTTTT
3467745 TAATAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTTAATAAATATTAATTTTTTAA
Found at i:3479796 original size:21 final size:21
Alignment explanation
Indices: 3479758--3479830 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
3479748 ATAAACCCTC
** *
3479758 AATCCTAAATTTTGAGCCTTA
1 AATCCTAAACCTTAAGCCTTA
* *
3479779 AATCGTAAACCTTAAGCCCTA
1 AATCCTAAACCTTAAGCCTTA
* * *
3479800 AGTCCTAAACTTTAAACCTTA
1 AATCCTAAACCTTAAGCCTTA
3479821 AA-CCTAAACC
1 AATCCTAAACC
3479831 ATACATCTTA
Statistics
Matches: 40, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 7 0.17
21 33 0.82
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (21 bp):
AATCCTAAACCTTAAGCCTTA
Found at i:3479900 original size:41 final size:41
Alignment explanation
Indices: 3479855--3479946 Score: 116
Period size: 41 Copynumber: 2.2 Consensus size: 41
3479845 CTCAACCTTC
* *
3479855 AACCTTAACTC-TAAACCCTCAGTCTTGAGCCCTAAATCTT-A
1 AACCTTAA-TCAT-AACCCTAAGTCGTGAGCCCTAAATCTTAA
*
3479896 AACCTTGAATCATATCCCTAAGTCGTGAGCCCTAAATCTTAA
1 AACCTT-AATCATAACCCTAAGTCGTGAGCCCTAAATCTTAA
3479938 AACCTTAAT
1 AACCTTAAT
3479947 TTTTTAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 35 0.78
42 10 0.22
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.29
Consensus pattern (41 bp):
AACCTTAATCATAACCCTAAGTCGTGAGCCCTAAATCTTAA
Found at i:3484797 original size:101 final size:102
Alignment explanation
Indices: 3484672--3484880 Score: 354
Period size: 101 Copynumber: 2.1 Consensus size: 102
3484662 CAACCACACC
3484672 ATAAAA-TTTAAAATTTTAACTATTTAAAGATTAAGGATAAATAATATTTTAAATATTTTGACTG
1 ATAAAATTTTAAAATTTTAACTATTTAAAGATTAAGGATAAATAATATTTTAAATATTTTGACTG
*
3484736 TTTTAATTTTAAGGAT-AACATATTATTTATCC-TTCA
66 TTTTAATTTTAAGG-TCAAAATATTATTTATCCTTTCA
* *
3484772 ATAAAATTTTAAAATTTTAACTATTTAAATATTAAGGATAAATAATATTTTAAATATTTTGATTG
1 ATAAAATTTTAAAATTTTAACTATTTAAAGATTAAGGATAAATAATATTTTAAATATTTTGACTG
3484837 TTTTAATTTTAAGGTCAAAATATTATTTATCCTTTCA
66 TTTTAATTTTAAGGTCAAAATATTATTTATCCTTTCA
3484874 A-AAAATT
1 ATAAAATT
3484881 CAAAAAATAT
Statistics
Matches: 103, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
100 7 0.07
101 91 0.88
102 5 0.05
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (102 bp):
ATAAAATTTTAAAATTTTAACTATTTAAAGATTAAGGATAAATAATATTTTAAATATTTTGACTG
TTTTAATTTTAAGGTCAAAATATTATTTATCCTTTCA
Found at i:3484888 original size:31 final size:31
Alignment explanation
Indices: 3484853--3484911 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
3484843 TTTTAAGGTC
3484853 AAAATATTATTTATCCTTTCAAAAAATTCAA
1 AAAATATTATTTATCCTTTCAAAAAATTCAA
*
3484884 AAAATATTATTTATCCTTTCATAAAATT
1 AAAATATTATTTATCCTTTCAAAAAATT
3484912 TTAACGGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (31 bp):
AAAATATTATTTATCCTTTCAAAAAATTCAA
Found at i:3485008 original size:32 final size:31
Alignment explanation
Indices: 3484968--3485029 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
3484958 TTTGAAGGAT
*
3484968 AAAATATTATTTATCCTTTCATCAAATTTTA
1 AAAATATTATTTATCCTTTCATAAAATTTTA
* *
3484999 AAAACTATTATTTCTCTTTTCATAAAATTTT
1 AAAA-TATTATTTATCCTTTCATAAAATTTT
3485030 CAAATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (31 bp):
AAAATATTATTTATCCTTTCATAAAATTTTA
Found at i:3485299 original size:41 final size:42
Alignment explanation
Indices: 3485215--3485307 Score: 95
Period size: 41 Copynumber: 2.3 Consensus size: 42
3485205 CATAGGTGTT
* * * *
3485215 AACCTTAAA-CCCTAAGCTCTAAACCATAAATCTTTACCTTA
1 AACCTTAAATCCCTAACCTCTAAACCATAAACCTTGACCCTA
*
3485256 AACCTTAAATCCC-AACCTCTAAACCCT-AACCTTGAGCCCTA
1 AACCTTAAATCCCTAACCTCTAAACCATAAACCTTGA-CCCTA
3485297 AA-CTATAAATC
1 AACCT-TAAATC
3485308 ATAAAGCATG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
40 8 0.18
41 33 0.75
42 3 0.07
ACGTcount: A:0.39, C:0.32, G:0.03, T:0.26
Consensus pattern (42 bp):
AACCTTAAATCCCTAACCTCTAAACCATAAACCTTGACCCTA
Found at i:3485409 original size:21 final size:21
Alignment explanation
Indices: 3485366--3485456 Score: 119
Period size: 21 Copynumber: 4.3 Consensus size: 21
3485356 TTTTGAGCCG
* * *
3485366 TAAATCTTAAGCCCTAAGTCT
1 TAAATCTTAAACCTTAAATCT
* *
3485387 TAAGTCTTAAACCTTAAACCT
1 TAAATCTTAAACCTTAAATCT
*
3485408 TAAACCTTAAACCTTAAATCT
1 TAAATCTTAAACCTTAAATCT
*
3485429 TAAATCTTAAATCTTAAATCT
1 TAAATCTTAAACCTTAAATCT
3485450 TAAATCT
1 TAAATCT
3485457 AAATCCTAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (21 bp):
TAAATCTTAAACCTTAAATCT
Found at i:3485465 original size:7 final size:7
Alignment explanation
Indices: 3485384--3485461 Score: 104
Period size: 7 Copynumber: 11.3 Consensus size: 7
3485374 AAGCCCTAAG
*
3485384 TCTTAAG
1 TCTTAAA
3485391 TCTTAAA
1 TCTTAAA
*
3485398 CCTTAAA
1 TCTTAAA
*
3485405 CCTTAAA
1 TCTTAAA
*
3485412 CCTTAAA
1 TCTTAAA
*
3485419 CCTTAAA
1 TCTTAAA
3485426 TCTTAAA
1 TCTTAAA
3485433 TCTTAAA
1 TCTTAAA
3485440 TCTTAAA
1 TCTTAAA
3485447 TCTTAAA
1 TCTTAAA
3485454 TC-TAAA
1 TCTTAAA
3485460 TC
1 TC
3485462 CTAAGCCCTA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
6 6 0.09
7 62 0.91
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (7 bp):
TCTTAAA
Found at i:3487733 original size:3 final size:3
Alignment explanation
Indices: 3487725--3487772 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
3487715 TCAATGACTG
* * * *
3487725 TTC TTC TTC TTT TTC TTT TTC TT- TTT TTC TTC TTC TTC TCC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3487772 T
1 T
3487773 CTGTTAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:3490306 original size:41 final size:41
Alignment explanation
Indices: 3490249--3490331 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
3490239 CCTGGCGCAT
*
3490249 AATTTCTCATATCAAACACTTATGAAATTACACAAATTTAA
1 AATTTCTCATATCAAACACTTAAGAAATTACACAAATTTAA
* *
3490290 AATTTCTCATGTCAAACACTTAAGGAATTACACAAATTTAA
1 AATTTCTCATATCAAACACTTAAGAAATTACACAAATTTAA
3490331 A
1 A
3490332 GGGGAAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.33
Consensus pattern (41 bp):
AATTTCTCATATCAAACACTTAAGAAATTACACAAATTTAA
Found at i:3491215 original size:96 final size:96
Alignment explanation
Indices: 3491038--3491225 Score: 225
Period size: 96 Copynumber: 2.0 Consensus size: 96
3491028 CCATATTTTT
* ** * ** *
3491038 TGGTACACAAACTCCATGGTGATCACTATCAACATGATCACCGACTCTCCCTGCTAGTGGGATCA
1 TGGTACACAAACTCCATGGTGATCACTACCAACACAATCACCAACTCTCCCAACTAGTGAGATCA
* *
3491103 ACGTATCATGGCTTAATGGTAGAATATGAGA
66 ACGGATAATGGCTTAATGGTAGAATATGAGA
* * * *
3491134 TGGTACACAAGCTCCATGGTGATCACTACCAACACAATCAGCAACTC-CCACAATTGGTGAGATC
1 TGGTACACAAACTCCATGGTGATCACTACCAACACAATCACCAACTCTCC-CAACTAGTGAGATC
* *
3491198 AAGGGATAATGGTTTAATGGTAGAATAT
65 AACGGATAATGGCTTAATGGTAGAATAT
3491226 TATATGGAAG
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
95 2 0.03
96 74 0.97
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (96 bp):
TGGTACACAAACTCCATGGTGATCACTACCAACACAATCACCAACTCTCCCAACTAGTGAGATCA
ACGGATAATGGCTTAATGGTAGAATATGAGA
Found at i:3492387 original size:133 final size:132
Alignment explanation
Indices: 3492223--3492600 Score: 427
Period size: 133 Copynumber: 2.8 Consensus size: 132
3492213 TTTTAAATTG
*
3492223 AATATTTTGACTATTTTAATTTTAA-AGATAAAATATCT-TTTATCCTTTCATAAAATTTTAAAA
1 AATATTTTGACTGTTTTAA-TTTAAGA-ATAAAATAT-TATTTATCCTTTCATAAAATTTTAAAA
*
3492286 CATATTACTTATCCTTTCATAAAATTTTAAAACTTTAACTATTTAAATATTAAAGATAAATAATA
63 CATATTATTTATCCTTTCATAAAATTTTAAAA-TTTAACTATTTAAATATTAAAGATAAATAATA
3492351 TCTT-A
127 TCTTAA
* * *
3492356 AATATTTTGATTGTTTTAAGTTTAAGAATAAAATATTATTTATCCTTTAATAAAATTTTAAAAAA
1 AATATTTTGACTGTTTTAA-TTTAAGAATAAAATATTATTTATCCTTTCATAAAATTTTAAAACA
* *
3492421 TATTATTTAT-CTATTCATAAAA-TTT----TTTAAC-AGTTAAAATATTAAGGATAAATAATAT
65 TATTATTTATCCT-TTCATAAAATTTTAAAATTTAACTA-TTTAAATATTAAAGATAAATAATAT
*
3492479 TTTAA
128 CTTAA
* * *
3492484 AATATTTTGACTGTTTTAATTTGAAGGATAAAATATTATTATTTATCATTTCATCAAATTTTAGA
1 AATATTTTGACTGTTTTAATTT-AAGAAT-AAA-A-TATTATTTATCCTTTCATAAAATTTTA-A
* * * *
3492549 AAC-TATTATTTCTCTTTTCTTAAAATTTTCAAAATTTAACTGTTTAAATATT
61 AACATATTATTTATCCTTTCATAAAATTTT-AAAATTTAACTATTTAAATATT
3492601 TTAAATATTT
Statistics
Matches: 207, Mismatches: 20, Indels: 32
0.80 0.08 0.12
Matches are distributed among these distances:
126 1 0.00
127 34 0.16
128 24 0.12
129 3 0.01
130 1 0.00
131 41 0.20
132 13 0.06
133 74 0.36
134 1 0.00
137 15 0.07
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.47
Consensus pattern (132 bp):
AATATTTTGACTGTTTTAATTTAAGAATAAAATATTATTTATCCTTTCATAAAATTTTAAAACAT
ATTATTTATCCTTTCATAAAATTTTAAAATTTAACTATTTAAATATTAAAGATAAATAATATCTT
AA
Found at i:3492423 original size:32 final size:32
Alignment explanation
Indices: 3492385--3492446 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
3492375 GTTTAAGAAT
3492385 AAAATATTATTTATCCT-TTAATAAAATTTTAA
1 AAAATATTATTTAT-CTATTAATAAAATTTTAA
*
3492417 AAAATATTATTTATCTATTCATAAAATTTT
1 AAAATATTATTTATCTATTAATAAAATTTT
3492447 TTAACAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (32 bp):
AAAATATTATTTATCTATTAATAAAATTTTAA
Found at i:3495127 original size:14 final size:15
Alignment explanation
Indices: 3495098--3495130 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3495088 CCGTAAAAAT
*
3495098 AAATAAATATAATAA
1 AAATAAATAAAATAA
3495113 AAATAAA-AAAATAA
1 AAATAAATAAAATAA
3495127 AAAT
1 AAAT
3495131 TTATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAAATAAAATAA
Found at i:3496751 original size:21 final size:21
Alignment explanation
Indices: 3496727--3496766 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3496717 TATATGATAG
3496727 TTATCATATTA-TTATATTTCA
1 TTAT-ATATTATTTATATTTCA
*
3496748 TTATATTTTATTTATATTT
1 TTATATATTATTTATATTT
3496767 TTTATTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATATATTATTTATATTTCA
Found at i:3496795 original size:10 final size:10
Alignment explanation
Indices: 3496727--3496799 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
3496717 TATATGATAG
3496727 TTATCATATTA
1 TTAT-ATATTA
3496738 TTATAT-TTCA
1 TTATATATT-A
*
3496748 TTATATTTTA
1 TTATATATTA
3496758 TT-TATATT-
1 TTATATATTA
* *
3496766 TTTTATTACATA
1 TTATA-TA-TTA
*
3496778 TCATATATTA
1 TTATATATTA
3496788 TTATATATTA
1 TTATATATTA
3496798 TT
1 TT
3496800 CCCTATATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
8 2 0.04
9 9 0.18
10 27 0.54
11 9 0.18
12 3 0.06
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATATATTA
Found at i:3496831 original size:7 final size:7
Alignment explanation
Indices: 3496817--3496852 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
3496807 TTATCTTCCT
3496817 TTTATTA
1 TTTATTA
*
3496824 TATATTA
1 TTTATTA
3496831 TTTCATTA
1 TTT-ATTA
3496839 TTTATTA
1 TTTATTA
3496846 TTTATTA
1 TTTATTA
3496853 GTATAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTATTA
Found at i:3496844 original size:15 final size:14
Alignment explanation
Indices: 3496817--3496857 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
3496807 TTATCTTCCT
3496817 TTTATTATATATTA
1 TTTATTATATATTA
*
3496831 TTTCATTATTTATTA
1 TTT-ATTATATATTA
3496846 TTTATTAGTATA
1 TTTATTA-TATA
3496858 AAAATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTATTATATATTA
Found at i:3508736 original size:44 final size:44
Alignment explanation
Indices: 3508671--3509265 Score: 753
Period size: 44 Copynumber: 13.5 Consensus size: 44
3508661 GATACAATGT
*
3508671 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * * * *
3508715 AAATCGAAGAGAACAGATTTGGTGTCTCTATATTGTCAGAGAGT
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * *
3508759 AGATCGAACATAGCAGATTTGACGTCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * * *
3508803 AAATCGAAGAGAACAGATTTGGTGTCTCTATATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * *
3508847 AGATCGAACATAGCAGATTTGACGTCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * * *
3508891 AAATCGAAGATAGCAGATTTGGCATCTCTATATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* *
3508935 AGATCGAAGAGAACAGATTTGGCGTCTCTATATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* ** *
3508979 AGATCGAAGATAGCAGATTTGGCACCTCTGTATTGTCAGAGAAC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
*
3509023 AGATCGAAAATAGA-AGATTTGGCGTCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATA-ACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
**
3509067 AGATCGAAGATAACAGATTTGGCACCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * * * *
3509111 ATATCAAAGATAGC-GAATTTGGCATCTCTGTATTGTCAGAGAGT
1 AGATCGAAGATAACAG-ATTTGGCGTCTCTGTATTGTCAGAGAGC
* * **
3509155 AGATCAAATATAACAGATTTGGTATCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* ** * *
3509199 AGATCAAAGATAACAGATTCAGCGTCTCTGTATTGTCAAAAAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* *
3509243 AGGTCGGAGATAACAGATTTGGC
1 AGATCGAAGATAACAGATTTGGC
3509266 ATTCTTAAGT
Statistics
Matches: 474, Mismatches: 73, Indels: 8
0.85 0.13 0.01
Matches are distributed among these distances:
43 2 0.00
44 471 0.99
45 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (44 bp):
AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
Found at i:3510901 original size:18 final size:18
Alignment explanation
Indices: 3510867--3510919 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
3510857 TATAAAATAA
*
3510867 TATATATTATT-TTTTATT
1 TATATATTATTATTATA-T
3510885 TATATATTATTCATTATAT
1 TATATATTATT-ATTATAT
*
3510904 TAT-TTTTATTATTATA
1 TATATATTATTATTATA
3510920 CATTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 6 0.19
18 17 0.55
19 4 0.13
20 4 0.13
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TATATATTATTATTATAT
Found at i:3511199 original size:7 final size:7
Alignment explanation
Indices: 3511185--3511220 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
3511175 TTATCTTCCT
3511185 TTTATTA
1 TTTATTA
*
3511192 TATATTA
1 TTTATTA
3511199 TTTCATTA
1 TTT-ATTA
3511207 TTTATTA
1 TTTATTA
3511214 TTTATTA
1 TTTATTA
3511221 GTATAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTATTA
Found at i:3511206 original size:15 final size:14
Alignment explanation
Indices: 3511185--3511225 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
3511175 TTATCTTCCT
3511185 TTTATTATATATTA
1 TTTATTATATATTA
*
3511199 TTTCATTATTTATTA
1 TTT-ATTATATATTA
3511214 TTTATTAGTATA
1 TTTATTA-TATA
3511226 AAAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTATTATATATTA
Found at i:3513049 original size:16 final size:16
Alignment explanation
Indices: 3513028--3513061 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3513018 TCCCAGAAAA
3513028 GTTAATTTTTGATAAT
1 GTTAATTTTTGATAAT
3513044 GTTAATTTTTGATAAT
1 GTTAATTTTTGATAAT
3513060 GT
1 GT
3513062 GCTACTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (16 bp):
GTTAATTTTTGATAAT
Found at i:3515844 original size:21 final size:21
Alignment explanation
Indices: 3515814--3515863 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3515804 TATGAGCTCC
* *
3515814 TTTATGTTTTGT-TTTTCCAAA
1 TTTATTTTTTGTATTAT-CAAA
3515835 TTTATTTTTTGTATTATCAAA
1 TTTATTTTTTGTATTATCAAA
3515856 TTTATTTT
1 TTTATTTT
3515864 AATAAAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (21 bp):
TTTATTTTTTGTATTATCAAA
Found at i:3515952 original size:27 final size:27
Alignment explanation
Indices: 3515921--3515995 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
3515911 AAAAAGTTAT
* * *
3515921 ACCCTAAATCATAAGTCTTAAGTTTTA
1 ACCCTAAATCATAAATCTTAAATCTTA
*
3515948 ACCCTAAATCCTAAATCTTAAATCTTA
1 ACCCTAAATCATAAATCTTAAATCTTA
* *
3515975 ACACTAAA-CTTTAAATCTTAA
1 ACCCTAAATC-ATAAATCTTAA
3515996 CCTTTAAGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.02
27 40 0.98
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (27 bp):
ACCCTAAATCATAAATCTTAAATCTTA
Found at i:3517741 original size:64 final size:64
Alignment explanation
Indices: 3517586--3517844 Score: 218
Period size: 68 Copynumber: 3.9 Consensus size: 64
3517576 TGGATGATAC
* ** * ** * *
3517586 AGATAGTATGTAGCTAGGTCACATGTATGGTGCTGGGTGCACATCATGT-GTACAAGAGAGCTAC
1 AGATA-TATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGCTAC
3517650 AAG
64 --G
* *
3517653 ACATTATTATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAC
1 AGA-TA-TATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTAC
3517718 G
64 G
* * * * * *
3517719 GGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTA
1 AGATATATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTA
3517784 CG
63 CG
* * * * *
3517786 AGATAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 AGATATATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
3517845 CGAACTATAT
Statistics
Matches: 156, Mismatches: 30, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
62 1 0.01
63 19 0.12
64 26 0.17
65 2 0.01
66 24 0.15
67 34 0.22
68 49 0.31
69 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (64 bp):
AGATATATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACG
Found at i:3519674 original size:7 final size:7
Alignment explanation
Indices: 3519664--3519736 Score: 51
Period size: 7 Copynumber: 10.6 Consensus size: 7
3519654 CATTGAGCCC
3519664 TAAACCT
1 TAAACCT
*
3519671 TAAACCA
1 TAAACCT
*
3519678 TAAATCT
1 TAAACCT
*
3519685 TAAATCT
1 TAAACCT
3519692 TAAA-CT
1 TAAACCT
*
3519698 TAAACCC
1 TAAACCT
* *
3519705 TAAGCCA
1 TAAACCT
3519712 TAAACC-
1 TAAACCT
**
3519718 TAAAATT
1 TAAACCT
3519725 CTAAACCT
1 -TAAACCT
3519733 TAAA
1 TAAA
3519737 TCATAGACCC
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
6 10 0.19
7 37 0.71
8 5 0.10
ACGTcount: A:0.48, C:0.23, G:0.01, T:0.27
Consensus pattern (7 bp):
TAAACCT
Found at i:3519681 original size:14 final size:13
Alignment explanation
Indices: 3519662--3519868 Score: 53
Period size: 14 Copynumber: 15.2 Consensus size: 13
3519652 AACATTGAGC
3519662 CCTAAACCTTAAA
1 CCTAAACCTTAAA
*
3519675 CCATAAATCTTAAA
1 CC-TAAACCTTAAA
*
3519689 TCTTAAA-CTTAAA
1 -CCTAAACCTTAAA
* *
3519702 CCCTAAGCCATAAA
1 -CCTAAACCTTAAA
**
3519716 CCTAAAATTCTAAA
1 CCTAAACCT-TAAA
* * *
3519730 CCTTAAATCATAGAC
1 CC-TAAACCTTA-AA
* *
3519745 CCTAAATCTTAAG
1 CCTAAACCTTAAA
3519758 CTCTAAACC-TAAA
1 C-CTAAACCTTAAA
* *
3519771 CCCTACACCTTACAC
1 -CCTAAACCTTA-AA
*
3519786 CCTCAACCTT-AA
1 CCTAAACCTTAAA
* *
3519798 CTCGAACCCTCTAAA
1 C-CTAAACCT-TAAA
*
3519813 CCTTAAGCAC-TAAA
1 CC-TAAAC-CTTAAA
* * *
3519827 CTTACACCTTAAG
1 CCTAAACCTTAAA
* * *
3519840 CCATCAAGCTTAAC
1 CC-TAAACCTTAAA
3519854 CCTAAACCTTAAA
1 CCTAAACCTTAAA
3519867 CC
1 CC
3519869 ATATTCTCTA
Statistics
Matches: 137, Mismatches: 40, Indels: 34
0.65 0.19 0.16
Matches are distributed among these distances:
12 3 0.02
13 50 0.36
14 68 0.50
15 15 0.11
16 1 0.01
ACGTcount: A:0.40, C:0.32, G:0.03, T:0.25
Consensus pattern (13 bp):
CCTAAACCTTAAA
Found at i:3523153 original size:16 final size:16
Alignment explanation
Indices: 3523129--3523166 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3523119 TGGATTTAAT
3523129 TTAGAACTCTAAACGA
1 TTAGAACTCTAAACGA
* *
3523145 TTAGGACTCTAAATGA
1 TTAGAACTCTAAACGA
3523161 TTAGAA
1 TTAGAA
3523167 TGGAACTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAGAACTCTAAACGA
Found at i:3523545 original size:26 final size:26
Alignment explanation
Indices: 3523516--3523565 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3523506 AAAAATTGTT
3523516 AAAACTCTT-ATAAAAAAAACTCAATA
1 AAAACTCTTGA-AAAAAAAACTCAATA
* *
3523542 AAAATTCTTGAAAAGAAAACTCAA
1 AAAACTCTTGAAAAAAAAACTCAA
3523566 AGAGAATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.60, C:0.14, G:0.04, T:0.22
Consensus pattern (26 bp):
AAAACTCTTGAAAAAAAAACTCAATA
Found at i:3525452 original size:7 final size:7
Alignment explanation
Indices: 3525444--3525511 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
3525434 GTCATATTTG
*
3525444 GGGTTTG
1 GGGTTTT
3525451 GGGTTTT
1 GGGTTTT
*
3525458 AGGTTTT
1 GGGTTTT
3525465 GGGTTTT
1 GGGTTTT
3525472 GGGTTTAT
1 GGGTTT-T
*
3525480 -GGTTAT
1 GGGTTTT
3525486 -GGTTTT
1 GGGTTTT
*
3525492 GAG-TTT
1 GGGTTTT
3525498 GAGGTTTT
1 G-GGTTTT
*
3525506 GAGTTT
1 GGGTTT
3525512 GAGGTCAGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 10 0.20
7 34 0.69
8 5 0.10
ACGTcount: A:0.09, C:0.00, G:0.38, T:0.53
Consensus pattern (7 bp):
GGGTTTT
Found at i:3525468 original size:14 final size:14
Alignment explanation
Indices: 3525445--3525516 Score: 58
Period size: 14 Copynumber: 5.2 Consensus size: 14
3525435 TCATATTTGG
*
3525445 GGTTTGGGGTTTTA
1 GGTTTTGGGTTTTA
*
3525459 GGTTTTGGGTTTTG
1 GGTTTTGGGTTTTA
*
3525473 GGTTTAT-GGTTAT-
1 GGTTT-TGGGTTTTA
* *
3525486 GGTTTTGAGTTTGA
1 GGTTTTGGGTTTTA
* *
3525500 GGTTTTGAGTTTGA
1 GGTTTTGGGTTTTA
3525514 GGT
1 GGT
3525517 CAGGTTTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
12 1 0.02
13 8 0.16
14 39 0.80
15 1 0.02
ACGTcount: A:0.10, C:0.00, G:0.39, T:0.51
Consensus pattern (14 bp):
GGTTTTGGGTTTTA
Found at i:3525592 original size:28 final size:28
Alignment explanation
Indices: 3525529--3525631 Score: 79
Period size: 28 Copynumber: 3.7 Consensus size: 28
3525519 GGTTTAATGT
3525529 TTTAGGGTTTAAGG-TTTTGTA-TTTCA-AG
1 TTTAGGGTTT-AGGATTTTG-AGTTT-AGAG
* *
3525557 TCTT-GGGTTTTGGATTTTGAGTTTTGAG
1 T-TTAGGGTTTAGGATTTTGAGTTTAGAG
** * *
3525585 TTTAGGGTTTACAATTTAGAGTTTAGTG
1 TTTAGGGTTTAGGATTTTGAGTTTAGAG
*
3525613 TTTAAGGTTTAGGATTTTG
1 TTTAGGGTTTAGGATTTTG
3525632 GGCTTCGAGT
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
27 5 0.09
28 51 0.88
29 2 0.03
ACGTcount: A:0.19, C:0.03, G:0.27, T:0.50
Consensus pattern (28 bp):
TTTAGGGTTTAGGATTTTGAGTTTAGAG
Found at i:3525663 original size:21 final size:21
Alignment explanation
Indices: 3525542--3525664 Score: 65
Period size: 21 Copynumber: 5.9 Consensus size: 21
3525532 AGGGTTTAAG
* * *
3525542 GTTTTGTATTTCAAGTCTTGG
1 GTTTTGTGTTTCAAGTTTTGA
**
3525563 GTTTTG-GATTTTGAGTTTTGA
1 GTTTTGTG-TTTCAAGTTTTGA
* * *
3525584 GTTTAGGGTTTACAA-TTTAGA
1 GTTTTGTGTTT-CAAGTTTTGA
* *
3525605 GTTTAGTGTTT-AAGGTTT-A
1 GTTTTGTGTTTCAAGTTTTGA
* * *
3525624 GGATTTTGGGCTTCGAGTTTTGA
1 -G-TTTTGTGTTTCAAGTTTTGA
3525647 GTTTTGTGTTTCAAGTTT
1 GTTTTGTGTTTCAAGTTT
3525665 CAAGCTTTGA
Statistics
Matches: 74, Mismatches: 20, Indels: 16
0.67 0.18 0.15
Matches are distributed among these distances:
19 3 0.04
20 3 0.04
21 59 0.80
22 8 0.11
23 1 0.01
ACGTcount: A:0.17, C:0.05, G:0.27, T:0.51
Consensus pattern (21 bp):
GTTTTGTGTTTCAAGTTTTGA
Found at i:3526357 original size:35 final size:35
Alignment explanation
Indices: 3526318--3526402 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
3526308 TAAGAATTAG
* *
3526318 AGTTTAAGGTTCAAGGTTCAGGGTTCATGGTTAAA
1 AGTTTAAGGTTCAAGGTTAAGGGTTCAAGGTTAAA
* *
3526353 AGTTTAGGGCTT-AAGGTTAAGGGTTCAAGGTTTAA
1 AGTTTAAGG-TTCAAGGTTAAGGGTTCAAGGTTAAA
*
3526388 AGTTTAGTGGTTCAA
1 AGTTTA-AGGTTCAA
3526403 CAACCACTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
35 36 0.86
36 6 0.14
ACGTcount: A:0.28, C:0.07, G:0.29, T:0.35
Consensus pattern (35 bp):
AGTTTAAGGTTCAAGGTTAAGGGTTCAAGGTTAAA
Found at i:3528215 original size:30 final size:31
Alignment explanation
Indices: 3528179--3528238 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3528169 CCCCACCTAT
3528179 ATTTTTAA-AA-TATATATTATTTTTAATTTA
1 ATTTTTAATAATTATAT-TTATTTTTAATTTA
* *
3528209 ATTTTTAATAATTTTATTTATTTTTTATTT
1 ATTTTTAATAATTATATTTATTTTTAATTT
3528239 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 14 0.54
32 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
ATTTTTAATAATTATATTTATTTTTAATTTA
Found at i:3528726 original size:18 final size:18
Alignment explanation
Indices: 3528677--3528742 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
3528667 AATTTTAGAA
*
3528677 TTTTTATTTTTTTAAATCT
1 TTTTTA-TTTTTTAAATAT
*
3528696 TTTTT-TGAATTTTAAATAT
1 TTTTTAT--TTTTTAAATAT
3528715 TTTTTATTTTTTCAAA-AT
1 TTTTTATTTTTT-AAATAT
3528733 TTTTTATTTT
1 TTTTTATTTT
3528743 ATTTTAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.03
18 16 0.40
19 22 0.55
20 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTTATTTTTTAAATAT
Found at i:3528736 original size:36 final size:35
Alignment explanation
Indices: 3528664--3528737 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 35
3528654 TTAGAAAACA
* * *
3528664 TTGAATTTTAGAATTTTTATTTTTTTAAATCTTTTT
1 TTGAATTTTAAAATTTTTATTTTTTCAAA-CATTTT
3528700 TTGAATTTTAAATATTTTTTATTTTTTCAAA-ATTTT
1 TTGAATTTTAAA-A-TTTTTATTTTTTCAAACATTTT
3528736 TT
1 TT
3528738 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 17 0.52
37 1 0.03
38 15 0.45
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (35 bp):
TTGAATTTTAAAATTTTTATTTTTTCAAACATTTT
Found at i:3529250 original size:15 final size:15
Alignment explanation
Indices: 3529209--3529257 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
3529199 GTTTAATCAT
*
3529209 TTTAATTTAATTTAA
1 TTTAATTAAATTTAA
*
3529224 TTTAATTTAATTTAA
1 TTTAATTAAATTTAA
3529239 TTT-ATTAAAATTTATA
1 TTTAATT-AAATTTA-A
3529255 TTT
1 TTT
3529258 TATTTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
14 3 0.10
15 24 0.77
16 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAATTAAATTTAA
Found at i:3529261 original size:5 final size:5
Alignment explanation
Indices: 3529209--3529242 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
3529199 GTTTAATCAT
3529209 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
3529243 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:3529327 original size:27 final size:27
Alignment explanation
Indices: 3529293--3529347 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
3529283 TTTTTTTATA
*
3529293 ATTTTTATTTTAAAATGAAAAAAAATT
1 ATTTTTATTTAAAAATGAAAAAAAATT
3529320 ATTTTTATTTAAAAATGAAAAAAAATT
1 ATTTTTATTTAAAAATGAAAAAAAATT
3529347 A
1 A
3529348 AAAATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (27 bp):
ATTTTTATTTAAAAATGAAAAAAAATT
Found at i:3532753 original size:47 final size:47
Alignment explanation
Indices: 3532678--3532801 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 47
3532668 TTCGACCTCG
* ** *
3532678 AGTCAATGAGGCACTATAAGTGTCGTACTGTTACTG-TTACTTTGGTTTA
1 AGTCGATGAGGCAC--TAAGTACCGTACTGTTACTGTTTACTTCGG-TTA
* *
3532727 A-TCTGATGAGGTACTGAGTACCGTACTGTTACTGTTTACTTCGGTTA
1 AGTC-GATGAGGCACTAAGTACCGTACTGTTACTGTTTACTTCGGTTA
*
3532774 AGTCGATGAGGCACTAAGTGCCGTACTG
1 AGTCGATGAGGCACTAAGTACCGTACTG
3532802 ATGTGTTGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
47 42 0.67
48 12 0.19
49 9 0.14
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (47 bp):
AGTCGATGAGGCACTAAGTACCGTACTGTTACTGTTTACTTCGGTTA
Found at i:3535284 original size:17 final size:17
Alignment explanation
Indices: 3535254--3535286 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3535244 AACCCAGCAG
3535254 ACCCGTTACTACCCAAA
1 ACCCGTTACTACCCAAA
3535271 ACCCGGTTAC-ACCCAA
1 ACCC-GTTACTACCCAA
3535287 GCTCGAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.33, C:0.42, G:0.09, T:0.15
Consensus pattern (17 bp):
ACCCGTTACTACCCAAA
Found at i:3536464 original size:18 final size:17
Alignment explanation
Indices: 3536441--3536474 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3536431 TTTTGAATTT
3536441 TATTATGTATTTAATATA
1 TATTAT-TATTTAATATA
*
3536459 TATTATTATTTTATAT
1 TATTATTATTTAATAT
3536475 TAAAATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTATTATTTAATATA
Found at i:3536770 original size:17 final size:17
Alignment explanation
Indices: 3536748--3536799 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
3536738 GTTTTCATAT
3536748 TATTTTATTACATATTA
1 TATTTTATTACATATTA
* * *
3536765 TATTTTACTCCATATGA
1 TATTTTATTACATATTA
*
3536782 TA-TTT-TTATATATTA
1 TATTTTATTACATATTA
3536797 TAT
1 TAT
3536800 ACATTTTATC
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
15 8 0.30
16 3 0.11
17 16 0.59
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTTATTACATATTA
Found at i:3536799 original size:15 final size:15
Alignment explanation
Indices: 3536705--3536823 Score: 59
Period size: 15 Copynumber: 7.4 Consensus size: 15
3536695 CTTATATACA
3536705 TTTTATATATTTCACTAT
1 TTTTATATA-TT-A-TAT
*
3536723 ATTTATATATTAT-T
1 TTTTATATATTATAT
3536737 TGTTT-TCATATTAT-T
1 T-TTTAT-ATATTATAT
*
3536752 TTATTACATATTATA-
1 TT-TTATATATTATAT
*
3536767 TTTTACTCCATATGATAT
1 TTTTA-T--ATATTATAT
3536785 TTTTATATATTATAT
1 TTTTATATATTATAT
3536800 ACATTTTATCATA-TATAT
1 ---TTTTAT-ATATTATAT
3536818 TTTTAT
1 TTTTAT
3536824 TTTATTTATC
Statistics
Matches: 82, Mismatches: 6, Indels: 29
0.70 0.05 0.25
Matches are distributed among these distances:
14 6 0.07
15 38 0.46
16 1 0.01
17 10 0.12
18 24 0.29
19 3 0.04
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTTATATATTATAT
Found at i:3539657 original size:22 final size:22
Alignment explanation
Indices: 3539627--3539671 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3539617 TTACTTTTAC
*
3539627 TATTGAATTTGAATAGA-AATAA
1 TATTGAATTT-AATAAATAATAA
*
3539649 TATTTAATTTAATAAATAATAA
1 TATTGAATTTAATAAATAATAA
3539671 T
1 T
3539672 CTATCCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (22 bp):
TATTGAATTTAATAAATAATAA
Found at i:3541018 original size:16 final size:15
Alignment explanation
Indices: 3540972--3541018 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3540962 CGAAAAATTT
*
3540972 TAATTATTTATATAA
1 TAATAATTTATATAA
*
3540987 AAATAATGTT-TATAA
1 TAATAAT-TTATATAA
3541002 TAATACATTTATATAA
1 TAATA-ATTTATATAA
3541018 T
1 T
3541019 CTAATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TAATAATTTATATAA
Found at i:3542386 original size:98 final size:98
Alignment explanation
Indices: 3542261--3542445 Score: 336
Period size: 98 Copynumber: 1.9 Consensus size: 98
3542251 CGGTCACACG
* *
3542261 GCCCAAATTGGTCTTACTCGTGTGGATCACACGGCCTGGCTCAAATTCCCATACGCCC-GTGTGG
1 GCCCAAATTGGTCTTACTCGTGTGGATCACACGGCCTGGCCCAAATTCCCACACGCCCTGTG-GG
3542325 CCCACACGGCCTATTTGCTTGAGGCACGCACATA
65 CCCACACGGCCTATTTGCTTGAGGCACGCACATA
3542359 GCCCAAATTGGTCTTACTCGTGTGGATCACACGGCCTGGCCCAAATTCCCACACGCCCTGTGGGC
1 GCCCAAATTGGTCTTACTCGTGTGGATCACACGGCCTGGCCCAAATTCCCACACGCCCTGTGGGC
3542424 CCACACGGCCTATTTGCTTGAG
66 CCACACGGCCTATTTGCTTGAG
3542446 TCTGTGCCTC
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
98 81 0.96
99 3 0.04
ACGTcount: A:0.19, C:0.34, G:0.24, T:0.23
Consensus pattern (98 bp):
GCCCAAATTGGTCTTACTCGTGTGGATCACACGGCCTGGCCCAAATTCCCACACGCCCTGTGGGC
CCACACGGCCTATTTGCTTGAGGCACGCACATA
Found at i:3543859 original size:17 final size:17
Alignment explanation
Indices: 3543826--3543875 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
3543816 TCTAAATATG
3543826 ATTTTTTAAATCA--TAA
1 ATTTTTTAAA-CATTTAA
3543842 ATTTTTTAAACATTTAA
1 ATTTTTTAAACATTTAA
* * *
3543859 ATATTATAAAAATTTAA
1 ATTTTTTAAACATTTAA
3543876 TGATCATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 10 0.34
17 17 0.59
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTTTAAACATTTAA
Found at i:3544039 original size:2 final size:2
Alignment explanation
Indices: 3544032--3544064 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3544022 TAATTGGTGT
3544032 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3544065 CCCTTTTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3545843 original size:16 final size:15
Alignment explanation
Indices: 3545821--3545858 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
3545811 TAATTTGATC
*
3545821 AATTTTAATTTTTAA
1 AATTTTAAATTTTAA
3545836 ATATTTTAAATTTTAA
1 A-ATTTTAAATTTTAA
3545852 AATTTTA
1 AATTTTA
3545859 GTCTTAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AATTTTAAATTTTAA
Found at i:3552291 original size:22 final size:22
Alignment explanation
Indices: 3552266--3552330 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
3552256 GTTAAGGGTT
3552266 AAATTTACTATTATGTCATTAG
1 AAATTTACTATTATGTCATTAG
* * * *
3552288 AAA--TCCAATT-T-T-ACTAT
1 AAATTTACTATTATGTCATTAG
3552305 AAATTTACTATTATGTCATTAG
1 AAATTTACTATTATGTCATTAG
3552327 AAAT
1 AAAT
3552331 CCAATTTTAC
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 6 0.20
18 1 0.03
19 6 0.20
20 6 0.20
21 1 0.03
22 10 0.33
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (22 bp):
AAATTTACTATTATGTCATTAG
Found at i:3552319 original size:39 final size:39
Alignment explanation
Indices: 3552265--3552343 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3552255 TGTTAAGGGT
3552265 TAAATTTACTATTATGTCATTAGAAATCCAATTTTACTA
1 TAAATTTACTATTATGTCATTAGAAATCCAATTTTACTA
3552304 TAAATTTACTATTATGTCATTAGAAATCCAATTTTACTA
1 TAAATTTACTATTATGTCATTAGAAATCCAATTTTACTA
3552343 T
1 T
3552344 TGGTAAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (39 bp):
TAAATTTACTATTATGTCATTAGAAATCCAATTTTACTA
Found at i:3560359 original size:27 final size:27
Alignment explanation
Indices: 3560329--3560526 Score: 224
Period size: 27 Copynumber: 7.4 Consensus size: 27
3560319 TGAGTCCGCT
* * * *
3560329 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* *
3560356 CACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
3560383 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAGTCAAA-TCGCA
** * *
3560411 CACTTAGTGCCGCATGGTCAATTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* **
3560438 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAGTCAAATCGCA
*
3560465 CACTTAGTGCAACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
3560492 CACTTAGTGCTACATAGTC-AATCG--
1 CACTTAGTGCTACATAGTCAAATCGCA
3560516 CACTTAGTGCT
1 CACTTAGTGCT
3560527 GTACAATTTA
Statistics
Matches: 150, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
24 11 0.07
26 5 0.03
27 110 0.73
28 24 0.16
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
CACTTAGTGCTACATAGTCAAATCGCA
Found at i:3560471 original size:82 final size:80
Alignment explanation
Indices: 3560346--3560526 Score: 233
Period size: 82 Copynumber: 2.2 Consensus size: 80
3560336 TGCTATATAA
* *
3560346 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAA-TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
* *
3560411 CACTTAGTGCCGCATGG
64 CACTTAGTGCCACATAG
* **
3560428 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAA-TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
*
3560492 CACTTAGTGCTACATAG
64 CACTTAGTGCCACATAG
3560509 TCAATCG--CACTTAGTGCT
1 TCAATCGCACACTTAGTGCT
3560527 GTACAATTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
78 10 0.11
80 3 0.03
81 24 0.27
82 51 0.58
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (80 bp):
TCAATCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACA
CTTAGTGCCACATAG
Found at i:3568457 original size:27 final size:27
Alignment explanation
Indices: 3568419--3568599 Score: 240
Period size: 27 Copynumber: 6.8 Consensus size: 27
3568409 AGTGCTATAT
* * *
3568419 TCAACTCGCACACTTAGTGCTACGTAA
1 TCAAATCGCACACTTAGTGCTACATAG
3568446 TCAAATCGCACACTTAGTGCTACATAG
1 TCAAATCGCACACTTAGTGCTACATAG
* ** *
3568473 TCAAACCGCACACTTAGTGCCGCATGG
1 TCAAATCGCACACTTAGTGCTACATAG
* *
3568500 TCAATTCGCAC-CTTAGTGCT-CATAT
1 TCAAATCGCACACTTAGTGCTACATAG
** *
3568525 TCATTTCGCACACTTAGTGCAACATAG
1 TCAAATCGCACACTTAGTGCTACATAG
3568552 TCAAATCGCACACTTAGTGCTACATAG
1 TCAAATCGCACACTTAGTGCTACATAG
3568579 TCAAATCGCACACTTAGTGCT
1 TCAAATCGCACACTTAGTGCT
3568600 GTACAATTTA
Statistics
Matches: 134, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
25 13 0.10
26 16 0.12
27 105 0.78
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
TCAAATCGCACACTTAGTGCTACATAG
Found at i:3568540 original size:79 final size:81
Alignment explanation
Indices: 3568419--3568599 Score: 249
Period size: 79 Copynumber: 2.3 Consensus size: 81
3568409 AGTGCTATAT
* * *
3568419 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACCGCAC
1 TCAAATCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCAC
* *
3568484 ACTTAGTGCCGCATGG
66 ACTTAGTGCCACATAG
* * ** *
3568500 TCAATTCGCAC-CTTAGTGCT-CATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAAATCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCAC
*
3568563 ACTTAGTGCTACATAG
66 ACTTAGTGCCACATAG
3568579 TCAAATCGCACACTTAGTGCT
1 TCAAATCGCACACTTAGTGCT
3568600 GTACAATTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
79 60 0.68
80 18 0.20
81 10 0.11
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAAATCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCAC
ACTTAGTGCCACATAG
Found at i:3568556 original size:106 final size:105
Alignment explanation
Indices: 3568409--3568598 Score: 317
Period size: 106 Copynumber: 1.8 Consensus size: 105
3568399 CCGCTCACTC
* *
3568409 AGTGCTATATTCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGT
1 AGTGCTATATTCAACTCGCACACTTAGTGCAACATAATCAAATCGCACACTTAGTGCTACATAGT
3568474 CAAACCGCACACTTAGTGCCGCATGGTCAATTCGCACCTT
66 CAAACCGCACACTTAGTGCCGCATGGTCAATTCGCACCTT
** *
3568514 AGTGCTCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCTACATAG
1 AGTGCT-ATATTCAACTCGCACACTTAGTGCAACATAATCAAATCGCACACTTAGTGCTACATAG
*
3568579 TCAAATCGCACACTTAGTGC
65 TCAAACCGCACACTTAGTGC
3568599 TGTACAATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
105 6 0.08
106 72 0.92
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (105 bp):
AGTGCTATATTCAACTCGCACACTTAGTGCAACATAATCAAATCGCACACTTAGTGCTACATAGT
CAAACCGCACACTTAGTGCCGCATGGTCAATTCGCACCTT
Found at i:3571874 original size:18 final size:17
Alignment explanation
Indices: 3571825--3571877 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
3571815 ATAAATAAAT
*
3571825 AATTCAAATAATTTTTAA
1 AATTCAAA-AATTTATAA
3571843 AATTCAAAATATTTATAA
1 AATTCAAAA-ATTTATAA
*
3571861 AAGTTCCAAAATTTATA
1 AA-TTCAAAAATTTATA
3571878 TATTTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 24 0.77
19 6 0.19
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (17 bp):
AATTCAAAAATTTATAA
Found at i:3572916 original size:19 final size:19
Alignment explanation
Indices: 3572890--3572932 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3572880 TTTTTTTTTA
3572890 TTTA-GAAAATTTTAGAAT
1 TTTATGAAAATTTTAGAAT
* *
3572908 TTTATGAAACTTTTATAAT
1 TTTATGAAAATTTTAGAAT
3572927 TTTATG
1 TTTATG
3572933 GTATTTTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (19 bp):
TTTATGAAAATTTTAGAAT
Found at i:3574558 original size:18 final size:19
Alignment explanation
Indices: 3574532--3574569 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3574522 TTATTACTAC
* *
3574532 TATTGTCACT-GTTATTAT
1 TATTATCACTCGTTAATAT
3574550 TATTATCACTCGTTAATAT
1 TATTATCACTCGTTAATAT
3574569 T
1 T
3574570 TTCATACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.53
Consensus pattern (19 bp):
TATTATCACTCGTTAATAT
Found at i:3574883 original size:17 final size:17
Alignment explanation
Indices: 3574863--3574918 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
3574853 AATGTTTTTC
3574863 TTATTTCATTATTCTTA
1 TTATTTCATTATTCTTA
*
3574880 TTATTTCTTTATTCTTTA
1 TTATTTCATTATTC-TTA
* *
3574898 TT-TGTCATTATTGTTA
1 TTATTTCATTATTCTTA
3574914 TTATT
1 TTATT
3574919 ATTATTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 5 0.16
17 22 0.69
18 5 0.16
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.68
Consensus pattern (17 bp):
TTATTTCATTATTCTTA
Found at i:3575253 original size:17 final size:16
Alignment explanation
Indices: 3575227--3575261 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3575217 ATTTACATAA
*
3575227 ATATTTTATTATTTTT
1 ATATTTTATTATTATT
3575243 ATATCTTTATTATTATT
1 ATAT-TTTATTATTATT
3575260 AT
1 AT
3575262 TATTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
ATATTTTATTATTATT
Found at i:3576462 original size:17 final size:17
Alignment explanation
Indices: 3576442--3576482 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
3576432 AATTTTTTAT
3576442 TTTTTATAATTTCTAAG
1 TTTTTATAATTTCTAAG
*
3576459 TTTTATATATTTTCTAAG
1 TTTT-TATAATTTCTAAG
*
3576477 ATTTTA
1 TTTTTA
3576483 AGGAATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTTTATAATTTCTAAG
Found at i:3577095 original size:29 final size:30
Alignment explanation
Indices: 3577063--3577129 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
3577053 CAGCGTACCT
**
3577063 AATATTTAATCTA-TAATTTAAAATTATAA
1 AATATTTAATAAATTAATTTAAAATTATAA
**
3577092 AATATTTAATAAATTAATTTAATTTTATAA
1 AATATTTAATAAATTAATTTAAAATTATAA
3577122 AAT-TTTAA
1 AATATTTAA
3577130 AAACCACACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
AATATTTAATAAATTAATTTAAAATTATAA
Found at i:3581036 original size:33 final size:34
Alignment explanation
Indices: 3580994--3581059 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
3580984 ATGATGTTCG
3580994 TTGCTCTCTAAAT-ATCTGATT-CAAGGTGGAGTT
1 TTGCTCTCTAAATAATCTGATTAC-AGGTGGAGTT
* *
3581027 TTGCTCTCTACATAATCTTATTACAGGTGGAGT
1 TTGCTCTCTAAATAATCTGATTACAGGTGGAGT
3581060 AGTGTTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 12 0.41
34 16 0.55
35 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (34 bp):
TTGCTCTCTAAATAATCTGATTACAGGTGGAGTT
Found at i:3586533 original size:27 final size:27
Alignment explanation
Indices: 3586503--3586707 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
3586493 ATATTGAGTC
* * * *
3586503 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
3586530 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
3586557 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
3586585 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
3586612 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
3586639 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
3586666 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
3586693 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3586708 GTACAATTTA
Statistics
Matches: 157, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 24 0.15
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:3590022 original size:18 final size:18
Alignment explanation
Indices: 3589985--3590038 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
3589975 ATAATAAAAT
*
3589985 AATTCAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAA
3590004 AATTCAAAATATTTATAA
1 AATTCAAAATATTTATAA
*
3590022 AAGTTCCAAA-ATTTATA
1 AA-TTCAAAATATTTATA
3590039 TATTTTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:3591015 original size:17 final size:17
Alignment explanation
Indices: 3590993--3591026 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3590983 CAAAACTTCA
*
3590993 AAAAAAAATTAAGAAAT
1 AAAAAAAATTAAAAAAT
*
3591010 AAAAAAATTTAAAAAAT
1 AAAAAAAATTAAAAAAT
3591027 TGTTTGGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAAAAATTAAAAAAT
Found at i:3591094 original size:21 final size:19
Alignment explanation
Indices: 3591053--3591097 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
3591043 TTTTTTTTTA
3591053 TTTA-GAAAATTTTAGAAT
1 TTTATGAAAATTTTAGAAT
*
3591071 TTTATGAAAACTTTTAATAAT
1 TTTATGAAAA-TTTT-AGAAT
3591092 TTTATG
1 TTTATG
3591098 GTATTTTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 5 0.22
20 4 0.17
21 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (19 bp):
TTTATGAAAATTTTAGAAT
Found at i:3592781 original size:14 final size:15
Alignment explanation
Indices: 3592762--3592802 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3592752 ATTTTCATAA
3592762 CTATTATTTA-TACT
1 CTATTATTTATTACT
3592776 CTATTA-TTATTACT
1 CTATTATTTATTACT
3592790 -TATTATTTTATTA
1 CTATTA-TTTATTA
3592803 TTGTTATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.33
14 10 0.42
15 6 0.25
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (15 bp):
CTATTATTTATTACT
Found at i:3592781 original size:45 final size:44
Alignment explanation
Indices: 3592732--3592843 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 44
3592722 TCACTGTTAT
*
3592732 TATTATTATCACTCGTTATTATTTTCATAACTATTAT-TTATACT-C
1 TATTATTATCACTC-TTATTATTTT-ATAACTATTATCTAATA-TAC
* * * *
3592777 TATTATTATTA--CTTATTATTTTATTATTGTTATCTAATATAC
1 TATTATTATCACTCTTATTATTTTATAACTATTATCTAATATAC
*
3592819 TATTATTATCACTATTATTATTTTA
1 TATTATTATCACTCTTATTATTTTA
3592844 CTATTGTAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
41 9 0.16
42 25 0.45
43 1 0.02
44 11 0.20
45 10 0.18
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (44 bp):
TATTATTATCACTCTTATTATTTTATAACTATTATCTAATATAC
Found at i:3592783 original size:3 final size:3
Alignment explanation
Indices: 3592777--3592886 Score: 73
Period size: 3 Copynumber: 36.7 Consensus size: 3
3592767 ATTTATACTC
* * *
3592777 TAT TAT TAT TACT TAT TAT T-T TAT TAT TGT TAT CTAA TA- TAC TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * * * * *
3592822 TAT TAT CAC TAT TAT TAT T-T TAC TAT TGT AACT TAA TAT TTT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
3592867 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
3592887 AACTAATTAA
Statistics
Matches: 82, Mismatches: 19, Indels: 12
0.73 0.17 0.11
Matches are distributed among these distances:
2 6 0.07
3 69 0.84
4 7 0.09
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3592840 original size:18 final size:18
Alignment explanation
Indices: 3592717--3592840 Score: 73
Period size: 18 Copynumber: 7.1 Consensus size: 18
3592707 TTATTACTAC
* *
3592717 TATTGTCACTGTTATTAT
1 TATTATCACTATTATTAT
*
3592735 TATTATCACTCGTTATTAT
1 TATTATCACT-ATTATTAT
*
3592754 T-TTCATAACTATTA-T-T
1 TATT-ATCACTATTATTAT
*
3592770 TA-TA-CTCTATTATTAT
1 TATTATCACTATTATTAT
* *
3592786 TACTTATTA-TTTTATTAT
1 TA-TTATCACTATTATTAT
* * *
3592804 TGTTATCTAATA-TACTAT
1 TATTATC-ACTATTATTAT
3592822 TATTATCACTATTATTAT
1 TATTATCACTATTATTAT
3592840 T
1 T
3592841 TTACTATTGT
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
14 6 0.08
15 2 0.03
16 6 0.08
17 8 0.10
18 43 0.54
19 15 0.19
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTATCACTATTATTAT
Found at i:3592859 original size:44 final size:42
Alignment explanation
Indices: 3592776--3592860 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 42
3592766 TATTTATACT
* * *
3592776 CTATTATTATTACTTATTATTTTATTATTGTTATCTAATATA
1 CTATTATTATCACTTATTATTTTACTATTGTAATCTAATATA
3592818 CTATTATTATCACTATTATTATTTTACTATTGTAA-CTTAATAT
1 CTATTATTATCAC--TTATTATTTTACTATTGTAATC-TAATAT
3592861 TTTTGTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 12 0.32
43 1 0.03
44 24 0.65
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.56
Consensus pattern (42 bp):
CTATTATTATCACTTATTATTTTACTATTGTAATCTAATATA
Found at i:3593141 original size:3 final size:3
Alignment explanation
Indices: 3593049--3593131 Score: 62
Period size: 3 Copynumber: 27.3 Consensus size: 3
3593039 ATTCCAAATG
* * * *
3593049 TTA TTC TTA TT- TTCA TTA TTC TTA TTA TT- TCTA TTA TTCT TTA TTG
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA T-TA TTA TT-A TTA TTA
* * *
3593095 TCA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3593132 AGCTATTATT
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
2 3 0.05
3 53 0.87
4 5 0.08
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3593446 original size:3 final size:3
Alignment explanation
Indices: 3593431--3593469 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
3593421 TACATAATAT
*
3593431 TTA TTA TTT TTA TTA TCT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
3593470 AAAAATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3593453 original size:18 final size:18
Alignment explanation
Indices: 3593430--3593464 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3593420 TTACATAATA
*
3593430 TTTATTATTTTTATTATC
1 TTTATTATTATTATTATC
3593448 TTTATTATTATTATTAT
1 TTTATTATTATTATTAT
3593465 TATTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTATTATTATTATC
Found at i:3594662 original size:18 final size:18
Alignment explanation
Indices: 3594641--3594682 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3594631 TTTTTTTATT
3594641 TTTTTATAATTTTCTAAG-
1 TTTTTAT-ATTTTCTAAGA
*
3594659 TTTTAATATTTTCTAAGA
1 TTTTTATATTTTCTAAGA
3594677 TTTTTA
1 TTTTTA
3594683 AGGAATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTTATATTTTCTAAGA
Found at i:3599140 original size:33 final size:33
Alignment explanation
Indices: 3599098--3599163 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3599088 TGATGATTCG
*
3599098 TTGCTCTCTAAATAATCTGATTCAAGGTGGAGT
1 TTGCTCTCTAAATAATCTAATTCAAGGTGGAGT
*
3599131 TTGCTCTCTACATAATCTAATTCAAGGTGGAGT
1 TTGCTCTCTAAATAATCTAATTCAAGGTGGAGT
3599164 AGTGTTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (33 bp):
TTGCTCTCTAAATAATCTAATTCAAGGTGGAGT
Found at i:3601063 original size:3 final size:3
Alignment explanation
Indices: 3601055--3601079 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3601045 AAAGGTTTAG
3601055 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3601080 TATTCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3603123 original size:36 final size:36
Alignment explanation
Indices: 3603080--3603151 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3603070 GCAACTAAAG
3603080 GACAAGCCGAATACTACATCCTTTTCTTTTACTTTT
1 GACAAGCCGAATACTACATCCTTTTCTTTTACTTTT
3603116 GACAAGCCGAATACTACATCCTTTTCTTTTACTTTT
1 GACAAGCCGAATACTACATCCTTTTCTTTTACTTTT
3603152 TCCCTTGCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42
Consensus pattern (36 bp):
GACAAGCCGAATACTACATCCTTTTCTTTTACTTTT
Found at i:3604467 original size:34 final size:34
Alignment explanation
Indices: 3604425--3604519 Score: 104
Period size: 34 Copynumber: 2.8 Consensus size: 34
3604415 TTGTTTTCAT
*
3604425 ACTG-TACTGAAAAGGGCTGAGGCCCAGACTGTC-
1 ACTGTTACTGAAAAGGGCTAAGGCCCAGACTG-CG
* * *
3604458 ACTGTTACTGAAATGGGCTCAGGCCAAGACTGCG
1 ACTGTTACTGAAAAGGGCTAAGGCCCAGACTGCG
*
3604492 ACTATTACTGAAAAAGAGGCTAAGGCCC
1 ACTGTTACTG-AAAAG-GGCTAAGGCCC
3604520 CTAACTGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
33 5 0.10
34 33 0.65
35 4 0.08
36 9 0.18
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (34 bp):
ACTGTTACTGAAAAGGGCTAAGGCCCAGACTGCG
Found at i:3609706 original size:40 final size:40
Alignment explanation
Indices: 3609644--3609888 Score: 318
Period size: 40 Copynumber: 6.2 Consensus size: 40
3609634 AAACCAAGTA
* * *
3609644 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
3609683 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
3609723 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
3609763 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * *
3609803 CCTTCGAGACTTAGCTCAGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* * *
3609843 CCTTCGGGACTTAGCTCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
3609883 CCTTCG
1 CCTTCG
3609889 TTATCATCCG
Statistics
Matches: 189, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
39 14 0.07
40 175 0.93
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:3616542 original size:22 final size:22
Alignment explanation
Indices: 3616517--3616598 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
3616507 TTTATTATTC
*
3616517 TTATTTATTTTTATTATATTTA
1 TTATTTATTCTTATTATATTTA
*
3616539 TTATCCTT-TT-TT-TGTATTTTTA
1 TTAT--TTATTCTTAT-TATATTTA
* *
3616561 TTTTTTTATTCTTATTATGTTTA
1 -TTATTTATTCTTATTATATTTA
3616584 TTATTTATTCTTATT
1 TTATTTATTCTTATT
3616599 TTAGCTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
21 3 0.06
22 29 0.59
23 14 0.29
24 3 0.06
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (22 bp):
TTATTTATTCTTATTATATTTA
Found at i:3616577 original size:45 final size:48
Alignment explanation
Indices: 3616495--3616587 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 48
3616485 TTTCTTTTTC
*
3616495 CCTTTTTATTTATTTATTATTCTTATTTATTTTTATTATATTTATTAT
1 CCTTTTTATTTATTTATTATTCTTATTTATTCTTATTATATTTATTAT
*
3616543 CCTTTTT-TTGTATTT-TTATT-TT-TTTATTCTTATTATGTTTATTAT
1 CCTTTTTATT-TATTTATTATTCTTATTTATTCTTATTATATTTATTAT
3616588 TTATTCTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
45 21 0.50
46 2 0.05
47 7 0.17
48 12 0.29
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.72
Consensus pattern (48 bp):
CCTTTTTATTTATTTATTATTCTTATTTATTCTTATTATATTTATTAT
Found at i:3619141 original size:34 final size:34
Alignment explanation
Indices: 3619068--3619145 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
3619058 AGTGACAGCC
*
3619068 CAGTATCAGTGTGGGCCTTAGCCCATATCAGTAG
1 CAGTATCAGTGTGGGCCTTAGCCCATATCAGTAA
* * *
3619102 TAGTATTATTGTGGGCCTTAGCCCAT-TACAGTAA
1 CAGTATCAGTGTGGGCCTTAGCCCATAT-CAGTAA
3619136 CAGTATCAGT
1 CAGTATCAGT
3619146 AATGCAACAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 1 0.03
34 35 0.97
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (34 bp):
CAGTATCAGTGTGGGCCTTAGCCCATATCAGTAA
Found at i:3630370 original size:21 final size:21
Alignment explanation
Indices: 3630336--3630378 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3630326 AGCTTGATTG
3630336 AGATTAAGAACGAAAGAAATC
1 AGATTAAGAACGAAAGAAATC
* * *
3630357 AGATTTAGATCGAAGGAAATC
1 AGATTAAGAACGAAAGAAATC
3630378 A
1 A
3630379 AAAGTTATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (21 bp):
AGATTAAGAACGAAAGAAATC
Found at i:3637490 original size:21 final size:21
Alignment explanation
Indices: 3637456--3637498 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3637446 AGCTTGATTG
3637456 AGATTAAGAACGAAAGAAATC
1 AGATTAAGAACGAAAGAAATC
* * *
3637477 AGATTTAGATCGAAGGAAATC
1 AGATTAAGAACGAAAGAAATC
3637498 A
1 A
3637499 AAAGTTATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (21 bp):
AGATTAAGAACGAAAGAAATC
Found at i:3640002 original size:50 final size:50
Alignment explanation
Indices: 3639878--3640126 Score: 266
Period size: 50 Copynumber: 4.8 Consensus size: 50
3639868 GATAATAACA
* * ** * *
3639878 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* * *
3639929 TGCCCATGCCACGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
3639979 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
3640029 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* * *
3640084 ATGTCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
3640127 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:3640057 original size:100 final size:104
Alignment explanation
Indices: 3639877--3640126 Score: 339
Period size: 100 Copynumber: 2.4 Consensus size: 104
3639867 TGATAATAAC
**
3639877 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCACG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCACG
* *
3639942 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
3639979 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCACG
3640042 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* * *
3640084 ATGTCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
3640127 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCACGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:3640242 original size:13 final size:13
Alignment explanation
Indices: 3640221--3640252 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3640211 GCTTGGATCA
*
3640221 TCATCAAATAAAT
1 TCATAAAATAAAT
3640234 TCATAAAATAAAT
1 TCATAAAATAAAT
3640247 TCATAA
1 TCATAA
3640253 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:3645618 original size:50 final size:50
Alignment explanation
Indices: 3645494--3645741 Score: 275
Period size: 49 Copynumber: 4.8 Consensus size: 50
3645484 GATAATAACA
* * ** * *
3645494 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
3645545 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
3645595 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
3645644 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
3645699 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
3645742 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
49 46 0.27
50 45 0.27
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:3645669 original size:99 final size:104
Alignment explanation
Indices: 3645493--3645734 Score: 343
Period size: 99 Copynumber: 2.3 Consensus size: 104
3645483 TGATAATAAC
**
3645493 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACAT-GGATCCTCTCGTGATGGTGCCCATGCCATG
* *
3645558 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
3645595 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGA-CCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGATCCTCTCGTGAT-GGTGCCCATGCCATG
3645657 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
*
3645699 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGG
3645735 GATCTCTTTA
Statistics
Matches: 126, Mismatches: 7, Indels: 11
0.88 0.05 0.08
Matches are distributed among these distances:
98 1 0.01
99 50 0.40
100 3 0.02
101 32 0.25
102 3 0.02
103 1 0.01
104 2 0.02
105 34 0.27
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGATCCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:3645857 original size:13 final size:13
Alignment explanation
Indices: 3645836--3645867 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3645826 GCTTGGATCA
*
3645836 TCATCAAATAAAT
1 TCATAAAATAAAT
3645849 TCATAAAATAAAT
1 TCATAAAATAAAT
3645862 TCATAA
1 TCATAA
3645868 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:3646115 original size:30 final size:30
Alignment explanation
Indices: 3646079--3646135 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3646069 CCTCGACTCT
*
3646079 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
3646109 AACTTTTACATAATTACATTTTTGCCC
1 AACTTTTACAAAATTACAATTTTGCCC
3646136 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:3651334 original size:13 final size:13
Alignment explanation
Indices: 3651316--3651341 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3651306 GCAGGGGAGA
3651316 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
3651329 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
3651342 GGGGAAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:3657612 original size:16 final size:16
Alignment explanation
Indices: 3657591--3657628 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3657581 TTGAAAGTCT
3657591 CTGATGGTTACATAGA
1 CTGATGGTTACATAGA
3657607 CTGATGGTTACATAGA
1 CTGATGGTTACATAGA
3657623 CT-ATGG
1 CTGATGG
3657629 AATGAGCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (16 bp):
CTGATGGTTACATAGA
Found at i:3660269 original size:44 final size:44
Alignment explanation
Indices: 3660219--3660318 Score: 109
Period size: 45 Copynumber: 2.3 Consensus size: 44
3660209 CGAAATAATC
*
3660219 AATATATCAATACAAATTA-AACAT-AAATAAT-AATATTTCATGCG
1 AATATATC-ATA-AAATAACAACATAAAATAATCAAT-TTTCATGCG
* *
3660263 AATATATTCTTAAAATAACAACATAAAATGATCAATTTTCATGCG
1 AATATA-TCATAAAATAACAACATAAAATAATCAATTTTCATGCG
3660308 AATATAT-ATAA
1 AATATATCATAA
3660319 CAATGAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
43 8 0.17
44 14 0.29
45 23 0.48
46 3 0.06
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (44 bp):
AATATATCATAAAATAACAACATAAAATAATCAATTTTCATGCG
Found at i:3660688 original size:17 final size:16
Alignment explanation
Indices: 3660659--3660713 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
3660649 TAATATAGGG
3660659 AATA-ATATATAATAA
1 AATATATATATAATAA
* *
3660674 TATATGATATGTAATAA
1 AATAT-ATATATAATAA
3660691 AATATATATATAAATAA
1 AATATATATAT-AATAA
3660708 AATATA
1 AATATA
3660714 ATGAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.09
16 5 0.15
17 25 0.76
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (16 bp):
AATATATATATAATAA
Found at i:3660928 original size:12 final size:11
Alignment explanation
Indices: 3660858--3660959 Score: 55
Period size: 12 Copynumber: 9.0 Consensus size: 11
3660848 AAACACAAGG
3660858 AATAATATATA
1 AATAATATATA
* * *
3660869 TATAGTAAAATA
1 AATAAT-ATATA
*
3660881 TATAATATATA
1 AATAATATATA
** *
3660892 CTTAATTTATA
1 AATAATATATA
*
3660903 AATAA-A-ATG
1 AATAATATATA
*
3660912 TATAATAATATA
1 AATAAT-ATATA
*
3660924 AATAATATAATG
1 AATAATAT-ATA
3660936 AATAATATATAAA
1 AATAATATAT--A
3660949 AATAATATATA
1 AATAATATATA
3660960 CTATTTTATA
Statistics
Matches: 67, Mismatches: 17, Indels: 14
0.68 0.17 0.14
Matches are distributed among these distances:
9 6 0.09
11 25 0.37
12 26 0.39
13 10 0.15
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (11 bp):
AATAATATATA
Found at i:3670582 original size:14 final size:15
Alignment explanation
Indices: 3670565--3670602 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
3670555 GCTTAGATAT
3670565 GATATG-CAATCTTA
1 GATATGACAATCTTA
3670579 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
3670596 GATATGA
1 GATATGA
3670603 TTGCAATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
17 14 0.67
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:3670641 original size:17 final size:19
Alignment explanation
Indices: 3670544--3670634 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
3670534 ATAATCTTCA
*
3670544 ATGATATGCAAGCTTAGAT
1 ATGATATGCAATCTTAGAT
3670563 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
3670582 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
3670599 ATGAT-TGCAATCTTATAT
1 ATGATATGCAATCTTAGAT
3670617 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
3670635 AGATATGATT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 15 0.23
19 35 0.53
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:3670957 original size:18 final size:17
Alignment explanation
Indices: 3670926--3670959 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3670916 TTTCCCGGAT
*
3670926 TTTTTTATATATTTTAA
1 TTTTTTATAAATTTTAA
3670943 TTTTTTACTAAATTTTA
1 TTTTTTA-TAAATTTTA
3670960 GTATCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTATAAATTTTAA
Done.