Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 12 of 332
Found at i:3426623 original size:20 final size:20
Alignment explanation
Indices: 3426600--3426661 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
3426590 AAAATTACAA
3426600 AAAAAAATTAAAATATTTAT
1 AAAAAAATTAAAATATTTAT
*
3426620 -AAAAATTCTAAAATA--TAT
1 AAAAAAAT-TAAAATATTTAT
* *
3426638 AAAGGAAATTAAAA-ATTTTT
1 AAA-AAAATTAAAATATTTAT
3426658 AAAA
1 AAAA
3426662 GTTCTAGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 11
0.67 0.10 0.23
Matches are distributed among these distances:
18 4 0.12
19 13 0.41
20 15 0.47
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAAAATTAAAATATTTAT
Found at i:3426633 original size:39 final size:38
Alignment explanation
Indices: 3426590--3426672 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 38
3426580 TTTCTCAACA
3426590 AAAAT-TACAAAAAAAAATTAAAATATTTATAAAAATTCT
1 AAAATATA-AAAAAAAAATTAAAA-ATTTATAAAAATTCT
* ** * *
3426629 AAAATATATAAAGGAAATTAAAAATTTTTAAAAGTTCT
1 AAAATATAAAAAAAAAATTAAAAATTTATAAAAATTCT
*
3426667 AGAATA
1 AAAATA
3426673 ATATTTTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
38 18 0.49
39 17 0.46
40 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (38 bp):
AAAATATAAAAAAAAAATTAAAAATTTATAAAAATTCT
Found at i:3429780 original size:21 final size:22
Alignment explanation
Indices: 3429751--3429797 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3429741 CAGAAGGAGT
*
3429751 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3429773 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3429794 GAGT
1 GAGT
3429798 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:3434720 original size:23 final size:25
Alignment explanation
Indices: 3434658--3434720 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 25
3434648 TTGTTAAAAA
3434658 ATATTT-ATTTTA-ATATTTTTTAT
1 ATATTTAATTTTATATATTTTTTAT
*
3434681 ATATTTAA-TGTATTATATTTTTTA-
1 ATATTTAATTTTA-TATATTTTTTAT
3434705 A-ATTTAATTTTATATA
1 ATATTTAATTTTATATA
3434721 AAAATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 19 0.56
24 5 0.15
25 10 0.29
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
ATATTTAATTTTATATATTTTTTAT
Found at i:3435769 original size:24 final size:24
Alignment explanation
Indices: 3435737--3435784 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3435727 TATATTTTAT
3435737 AACAAATGATTATGAGTGGATCCG
1 AACAAATGATTATGAGTGGATCCG
3435761 AACAAATGATTATGAGTGGATCCG
1 AACAAATGATTATGAGTGGATCCG
3435785 TAAAAAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (24 bp):
AACAAATGATTATGAGTGGATCCG
Found at i:3436956 original size:22 final size:22
Alignment explanation
Indices: 3436931--3436979 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3436921 TGGTGTAAAA
*
3436931 TATATAAACAAATTAATGAAAT
1 TATATAAACAAATAAATGAAAT
* * *
3436953 TATAAAAATAAATAAATTAAAT
1 TATATAAACAAATAAATGAAAT
3436975 TATAT
1 TATAT
3436980 CAAAATTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TATATAAACAAATAAATGAAAT
Found at i:3437373 original size:22 final size:23
Alignment explanation
Indices: 3437325--3437377 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3437315 AAATTTTTAT
3437325 AAATTTAAGAGTTTAATGAGAAA
1 AAATTTAAGAGTTTAATGAGAAA
* * *
3437348 AAATTTAGGGGTTTAATTA-AAA
1 AAATTTAAGAGTTTAATGAGAAA
3437370 AAATTTAA
1 AAATTTAA
3437378 ATTTTTGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (23 bp):
AAATTTAAGAGTTTAATGAGAAA
Found at i:3440670 original size:33 final size:32
Alignment explanation
Indices: 3440621--3440703 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 32
3440611 GTACGCTATA
* *
3440621 TGTGTACACTTGAAAAGGTTATGTGCACTTCG
1 TGTGTACACTTGAAAAGGGTATGTACACTTCG
*
3440653 TGTGTACAAATTGAAAAGGGTATGTACACTTCG
1 TGTGTAC-ACTTGAAAAGGGTATGTACACTTCG
3440686 TGTGTACGACTTGAAAAG
1 TGTGTAC-ACTTGAAAAG
3440704 AGAATGTGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 7 0.16
33 38 0.84
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (32 bp):
TGTGTACACTTGAAAAGGGTATGTACACTTCG
Found at i:3442937 original size:17 final size:17
Alignment explanation
Indices: 3442903--3442937 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3442893 TTTTTATTAC
* *
3442903 ATTTGCAATTTTACTTT
1 ATTTGCAATTTAAATTT
3442920 ATTTGCAATTTAAATTT
1 ATTTGCAATTTAAATTT
3442937 A
1 A
3442938 AATTTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (17 bp):
ATTTGCAATTTAAATTT
Found at i:3445256 original size:4 final size:4
Alignment explanation
Indices: 3445247--3445283 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
3445237 CCCTTTTCTA
3445247 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
3445284 CACGTTTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:3448791 original size:12 final size:12
Alignment explanation
Indices: 3448774--3448802 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3448764 CCACGCCCGT
3448774 GCGCCGACCATA
1 GCGCCGACCATA
3448786 GCGCCGACCATA
1 GCGCCGACCATA
3448798 GCGCC
1 GCGCC
3448803 ATCTTTGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.45, G:0.28, T:0.07
Consensus pattern (12 bp):
GCGCCGACCATA
Found at i:3453903 original size:34 final size:34
Alignment explanation
Indices: 3453860--3453926 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
3453850 ACTATGAAGG
3453860 TTAAAGGTTAAGTCATAGGAATTTTGGTGATATT
1 TTAAAGGTTAAGTCATAGGAATTTTGGTGATATT
3453894 TTAAAGGTTAAGTCATAGGAATTTTGGTGATAT
1 TTAAAGGTTAAGTCATAGGAATTTTGGTGATAT
3453927 ACATATTCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.40
Consensus pattern (34 bp):
TTAAAGGTTAAGTCATAGGAATTTTGGTGATATT
Found at i:3454673 original size:45 final size:45
Alignment explanation
Indices: 3454609--3454783 Score: 232
Period size: 45 Copynumber: 4.0 Consensus size: 45
3454599 TATCGTACGG
* * * *
3454609 TACTATTCGAGCCTTTGAGCCTAGCAGGTTATGATGTCGGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGTTATAATGCCGGTGAGA
* *
3454654 TACTATTCGGGCCTTTGAGCCTAGCAGGTTATAATACCGGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGTTATAATGCCGGTGAGA
* *
3454699 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGTTATAATGCCGGTGAGA
*
3454744 TGA-TA-TCGGG-CTTCGAGCCTAGCAGGTGA-AATGCCGGTGA
1 T-ACTATTCGGGCCTTCGAGCCTAGCAGGTTATAATGCCGGTGA
3454784 ATGAATTCAG
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
42 11 0.09
43 17 0.14
44 5 0.04
45 85 0.71
46 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (45 bp):
TACTATTCGGGCCTTCGAGCCTAGCAGGTTATAATGCCGGTGAGA
Found at i:3456148 original size:64 final size:63
Alignment explanation
Indices: 3456044--3456170 Score: 173
Period size: 64 Copynumber: 2.0 Consensus size: 63
3456034 TTATTTTTCT
* * *
3456044 AGTTAAGTGACTTGTTCAATTCAATCTCGATTTTAGCCTTTTTCTTTCAGCTTCTAACCACACC
1 AGTTAAGTGACTTGTTCAATTCAATATCGATTCTAACC-TTTTCTTTCAGCTTCTAACCACACC
* * * * *
3456108 AGTTAGGTGATTTGTTCAATTCGATATCGATTCTAACCTTTTCTTTCAGCTTCTGACGACACC
1 AGTTAAGTGACTTGTTCAATTCAATATCGATTCTAACCTTTTCTTTCAGCTTCTAACCACACC
3456171 CCCTAACCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 23 0.42
64 32 0.58
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (63 bp):
AGTTAAGTGACTTGTTCAATTCAATATCGATTCTAACCTTTTCTTTCAGCTTCTAACCACACC
Found at i:3465011 original size:53 final size:53
Alignment explanation
Indices: 3464913--3465032 Score: 170
Period size: 53 Copynumber: 2.3 Consensus size: 53
3464903 TATTCCAGAC
* *
3464913 ATGGTCTTATACGGAATCACATTATCACATTATACTGATGCCATAGTC-CAGCT
1 ATGGTCTTATACGGAATCACATTATCACATTACACCGATGCCATAG-CACAGCT
* * *
3464966 ATGGTCTTATACGGAGTCACATTATCACATTGCACCGATGTCATAGCACAGCT
1 ATGGTCTTATACGGAATCACATTATCACATTACACCGATGCCATAGCACAGCT
*
3465019 ATGGTCTTAAACGG
1 ATGGTCTTATACGG
3465033 GCGCACTTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 1 0.02
53 59 0.98
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (53 bp):
ATGGTCTTATACGGAATCACATTATCACATTACACCGATGCCATAGCACAGCT
Found at i:3468181 original size:21 final size:21
Alignment explanation
Indices: 3468155--3468308 Score: 105
Period size: 21 Copynumber: 7.3 Consensus size: 21
3468145 AAGCCCGATG
*
3468155 GCTAAACAGAAGCTCATGAGA
1 GCTAAACAGAAGCTCATAAGA
* * *
3468176 GCTAAACAGAAACCCATAAGG
1 GCTAAACAGAAGCTCATAAGA
* * * ** *
3468197 GTTGAACGGAAGCTTGTAAGC
1 GCTAAACAGAAGCTCATAAGA
* *
3468218 GCTAAACAGAAAC-CTGTAAGA
1 GCTAAACAGAAGCTC-ATAAGA
*
3468239 GTTAAACAGAAGCTCAATAA-A
1 GCTAAACAGAAGCTC-ATAAGA
* * * *
3468260 GCTGAACGGAAACTCATATGA
1 GCTAAACAGAAGCTCATAAGA
* *
3468281 GTTAAACAGAAGCTCGTAAGA
1 GCTAAACAGAAGCTCATAAGA
3468302 GCTAAAC
1 GCTAAAC
3468309 GAAAAGTAAA
Statistics
Matches: 96, Mismatches: 34, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
20 3 0.03
21 89 0.93
22 4 0.04
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (21 bp):
GCTAAACAGAAGCTCATAAGA
Found at i:3468251 original size:42 final size:42
Alignment explanation
Indices: 3468157--3468312 Score: 156
Period size: 42 Copynumber: 3.7 Consensus size: 42
3468147 GCCCGATGGC
* * *
3468157 TAAACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAACAGAAACCTATAAGAGT
* * ** * *
3468199 TGAACGGAAGCTTGTAAGCGCTAAACAGAAACCTGTAAGAGT
1 TAAACAGAAGCTCATAAGAGCTAAACAGAAACCTATAAGAGT
* * *
3468241 TAAACAGAAGCTCAATAA-AGCTGAACGGAAA-CTCATATGAGT
1 TAAACAGAAGCTC-ATAAGAGCTAAACAGAAACCT-ATAAGAGT
*
3468283 TAAACAGAAGCTCGTAAGAGCTAAAC-GAAA
1 TAAACAGAAGCTCATAAGAGCTAAACAGAAA
3468313 AGTAAACACG
Statistics
Matches: 91, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
41 9 0.10
42 79 0.87
43 3 0.03
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
TAAACAGAAGCTCATAAGAGCTAAACAGAAACCTATAAGAGT
Found at i:3474123 original size:15 final size:16
Alignment explanation
Indices: 3474093--3474125 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3474083 TTTTAGATTA
3474093 ATTTTTATTTAGAAAT
1 ATTTTTATTTAGAAAT
*
3474109 ATTTTTTTTTA-AAAT
1 ATTTTTATTTAGAAAT
3474124 AT
1 AT
3474126 AATATACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTTTATTTAGAAAT
Found at i:3481494 original size:15 final size:15
Alignment explanation
Indices: 3481476--3481529 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
3481466 AAAAAGTTTA
3481476 ATAAATAAAAAATAT
1 ATAAATAAAAAATAT
*
3481491 ATAAAATTAATAAATAT
1 AT-AAA-TAAAAAATAT
*
3481508 -TAAATTAAAAATAAT
1 ATAAATAAAAAAT-AT
3481523 ATAAATA
1 ATAAATA
3481530 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 6 0.19
15 7 0.23
16 9 0.29
17 9 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAATAAAAAATAT
Found at i:3481505 original size:17 final size:16
Alignment explanation
Indices: 3481478--3481527 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
3481468 AAAGTTTAAT
*
3481478 AAATAAAAAATATATA
1 AAATTAAAAATATATA
3481494 AAATTAATAAATAT-T-
1 AAATTAA-AAATATATA
3481509 AAATTAAAAATAATATA
1 AAATTAAAAAT-ATATA
3481526 AA
1 AA
3481528 TATATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 8 0.28
17 8 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTAAAAATATATA
Found at i:3481921 original size:25 final size:24
Alignment explanation
Indices: 3481893--3481955 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
3481883 TAATAAAATT
* * *
3481893 TATTTTTAAATTTTTTTAAATAGTA
1 TATTTTTAAATATTATTAAACA-TA
*
3481918 TATTTTTCAATATTATTAAACATA
1 TATTTTTAAATATTATTAAACATA
* *
3481942 TATATTTAATTATT
1 TATTTTTAAATATT
3481956 TATATTTAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTTTAAATATTATTAAACATA
Found at i:3481997 original size:25 final size:25
Alignment explanation
Indices: 3481969--3482024 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
3481959 ATTTAGTCAC
3481969 ATAATAAATTATTATT-ATAAATAAT
1 ATAATAAATTATT-TTAATAAATAAT
** *
3481994 ATAATTTATTATTTTAATAAATTAT
1 ATAATAAATTATTTTAATAAATAAT
*
3482019 TTAATA
1 ATAATA
3482025 TTTTAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATAATAAATTATTTTAATAAATAAT
Found at i:3482064 original size:16 final size:16
Alignment explanation
Indices: 3482020--3482064 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 16
3482010 ATAAATTATT
3482020 TAAT-ATTTT-AATAA
1 TAATAATTTTAAATAA
3482034 TAA-AA-TTTAAA-AA
1 TAATAATTTTAAATAA
3482047 TAATAATTTTAAATAA
1 TAATAATTTTAAATAA
3482063 TA
1 TA
3482065 TTCTTCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 8 0.31
14 8 0.31
15 6 0.23
16 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAATTTTAAATAA
Found at i:3482107 original size:14 final size:15
Alignment explanation
Indices: 3482083--3482119 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3482073 ATATTATTGA
3482083 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
3482096 TAATATTTTAATAAT
1 AAATATTTTAATAAT
3482111 AAATATTTT
1 AAATATTTT
3482120 GTAGTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 4 0.20
14 6 0.30
15 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:3490200 original size:30 final size:30
Alignment explanation
Indices: 3490161--3490230 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
3490151 CTTTATTTAC
*
3490161 TTTTTAATTATTT-ATTAATGGCTTAATTGA
1 TTTTTAATTATTTCATTAA-GACTTAATTGA
* *
3490191 TTTTCAATTATTTCATTAAGATTTAATTGA
1 TTTTTAATTATTTCATTAAGACTTAATTGA
3490221 TTTTTAATTA
1 TTTTTAATTA
3490231 CTTTTTGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.57
Consensus pattern (30 bp):
TTTTTAATTATTTCATTAAGACTTAATTGA
Found at i:3490891 original size:61 final size:63
Alignment explanation
Indices: 3490825--3490949 Score: 157
Period size: 62 Copynumber: 2.0 Consensus size: 63
3490815 AAATTTAATT
* * *
3490825 ATTTTTACAGGG-TTATTTTAGCCTGGCCATATACTTATTACCA-TTCTAATTTTCAA-CAATA
1 ATTTTTACAGGGATTATTTTAGCATGACCATATACTTATTACCATTTC-AAGTTTCAACCAATA
* * * *
3490886 ATTTTTACAGGGATTTTTTTAGCATGATCATATATTTATTTCCATTTCAAGTTTCAACCAATA
1 ATTTTTACAGGGATTATTTTAGCATGACCATATACTTATTACCATTTCAAGTTTCAACCAATA
3490949 A
1 A
3490950 CCATCACCTG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 12 0.22
62 33 0.61
63 9 0.17
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (63 bp):
ATTTTTACAGGGATTATTTTAGCATGACCATATACTTATTACCATTTCAAGTTTCAACCAATA
Found at i:3493900 original size:14 final size:14
Alignment explanation
Indices: 3493881--3493909 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3493871 ACCACAGACT
3493881 ATCTCAATGCTGAA
1 ATCTCAATGCTGAA
3493895 ATCTCAATGCTGAA
1 ATCTCAATGCTGAA
3493909 A
1 A
3493910 GAACTGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (14 bp):
ATCTCAATGCTGAA
Found at i:3498819 original size:31 final size:32
Alignment explanation
Indices: 3498755--3498829 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
3498745 TCTGAACTCG
**
3498755 AAATTGACCCAAACCTGAATGACCTGGAGTCA
1 AAATTGACCCAAACCTGAATGACCCAGAGTCA
3498787 AAATTGACCCAAA-CTGAAGTGACCCAGA-TCA
1 AAATTGACCCAAACCTGAA-TGACCCAGAGTCA
*
3498818 AAACTTAACCCA
1 AAA-TTGACCCA
3498830 TTCCGCTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 11 0.29
32 27 0.71
ACGTcount: A:0.41, C:0.27, G:0.15, T:0.17
Consensus pattern (32 bp):
AAATTGACCCAAACCTGAATGACCCAGAGTCA
Found at i:3504046 original size:21 final size:21
Alignment explanation
Indices: 3504004--3504049 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3503994 AATCTTAATA
* *
3504004 TTAAATTTTAGACTTTGAATC
1 TTAAATTTTAGAATTTCAATC
3504025 TTAAATTTTA-AATTTCATATC
1 TTAAATTTTAGAATTTCA-ATC
3504046 TTAA
1 TTAA
3504050 CTTGAATCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (21 bp):
TTAAATTTTAGAATTTCAATC
Found at i:3511578 original size:22 final size:21
Alignment explanation
Indices: 3511538--3511598 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
3511528 GTACTTTAAA
* **
3511538 ATTTAATAATACTTTTAATTT
1 ATTTAATAATATTTTTAATAG
3511559 ATTTAATAATATTTTTTAATAG
1 ATTTAATAATA-TTTTTAATAG
3511581 ATTTAATAATACTTTTTA
1 ATTTAATAATA-TTTTTA
3511599 TACAAGTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 11 0.31
22 24 0.69
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTAATAATATTTTTAATAG
Found at i:3517611 original size:21 final size:21
Alignment explanation
Indices: 3517585--3517646 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
3517575 CTCTCTCAAC
3517585 AAAAATTACAAAATAATTT-T-A
1 AAAAATT-CAAAAT-ATTTATAA
3517606 AAAAATTCAAAATATTTATAA
1 AAAAATTCAAAATATTTATAA
3517627 AAAAATTCAAAAT-TTTATAA
1 AAAAATTCAAAATATTTATAA
3517647 TTTTTTACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.10
20 14 0.36
21 21 0.54
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATTCAAAATATTTATAA
Found at i:3517694 original size:48 final size:48
Alignment explanation
Indices: 3517601--3517694 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 48
3517591 TACAAAATAA
* * *
3517601 TTTTAAAAAATTCAAAATATTTATAAAAAAATTCAAAATTTTATAATT
1 TTTTAAAAAATTCAAAATATTTATAAAAAAATTAAAAAATATATAATT
* *
3517649 TTTTACAAAATT-ATAAATATTTCA-AAAAAATTTAAAAAATATATAA
1 TTTTAAAAAATTCA-AAATATTT-ATAAAAAAATTAAAAAATATATAA
3517695 AGAAAGTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
47 1 0.03
48 37 0.95
49 1 0.03
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.39
Consensus pattern (48 bp):
TTTTAAAAAATTCAAAATATTTATAAAAAAATTAAAAAATATATAATT
Found at i:3519246 original size:4 final size:4
Alignment explanation
Indices: 3519239--3519264 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3519229 ATATATCTAT
3519239 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
3519265 AATGATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:3528505 original size:16 final size:16
Alignment explanation
Indices: 3528486--3528523 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3528476 AATATAAAAC
*
3528486 ATATTTAAAGTAAATA
1 ATATTTAAAATAAATA
*
3528502 ATATTAAAAATAAATA
1 ATATTTAAAATAAATA
3528518 ATATTT
1 ATATTT
3528524 TCTGAATAAA
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:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATTTAAAATAAATA
Found at i:3529594 original size:29 final size:30
Alignment explanation
Indices: 3529535--3529604 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
3529525 CAAGTAAACT
*
3529535 TAAATTTTAAAATATAAAAAGTAGAAAGAC
1 TAAATTTTAAAATATAAAAAGTACAAAGAC
* *
3529565 TAAATTCTTAAAA-AT-ACAAGTACAATGAC
1 TAAATT-TTAAAATATAAAAAGTACAAAGAC
*
3529594 TGAAATATTAA
1 T-AAATTTTAA
3529605 TTTTTGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 16 0.47
30 12 0.35
31 6 0.18
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.29
Consensus pattern (30 bp):
TAAATTTTAAAATATAAAAAGTACAAAGAC
Found at i:3534275 original size:23 final size:23
Alignment explanation
Indices: 3534249--3534323 Score: 132
Period size: 23 Copynumber: 3.3 Consensus size: 23
3534239 ATAAGTGCAA
*
3534249 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
3534272 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
3534295 CACTGAAACGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
3534318 CACTGA
1 CACTGA
3534324 TCAATAACAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.17
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:3541653 original size:23 final size:23
Alignment explanation
Indices: 3541627--3541701 Score: 132
Period size: 23 Copynumber: 3.3 Consensus size: 23
3541617 ATAAGTGCAA
*
3541627 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
3541650 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
3541673 CACTGAAACGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
3541696 CACTGA
1 CACTGA
3541702 TCAATAACAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.17
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:3552971 original size:17 final size:19
Alignment explanation
Indices: 3552937--3552971 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3552927 TTGAAAGAGT
3552937 TTGAACAAATATATTTAAC
1 TTGAACAAATATATTTAAC
3552956 TTGAA-AAATA-ATTTAA
1 TTGAACAAATATATTTAA
3552972 AAAAATTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (19 bp):
TTGAACAAATATATTTAAC
Found at i:3554284 original size:15 final size:15
Alignment explanation
Indices: 3554264--3554292 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3554254 AAAAGCATGT
3554264 TAGAGAAATTCACAC
1 TAGAGAAATTCACAC
3554279 TAGAGAAATTCACA
1 TAGAGAAATTCACA
3554293 TTGACTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (15 bp):
TAGAGAAATTCACAC
Found at i:3557661 original size:21 final size:21
Alignment explanation
Indices: 3557635--3557675 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3557625 ATCTGCTCAA
* *
3557635 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3557656 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3557676 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3569958 original size:16 final size:17
Alignment explanation
Indices: 3569927--3569960 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3569917 TATTTATAAA
3569927 TTTTAAATTTTATTATG
1 TTTTAAATTTTATTATG
*
3569944 TTTTTAATTTT-TTATG
1 TTTTAAATTTTATTATG
3569960 T
1 T
3569961 ATAAAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTTAAATTTTATTATG
Found at i:3577005 original size:15 final size:16
Alignment explanation
Indices: 3576976--3577005 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3576966 TAATTTCTAT
3576976 ATTGTTTTGTATATTG
1 ATTGTTTTGTATATTG
3576992 ATTGTTTT-TATATT
1 ATTGTTTTGTATATT
3577006 ATTCCATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (16 bp):
ATTGTTTTGTATATTG
Found at i:3579480 original size:3 final size:3
Alignment explanation
Indices: 3579460--3579517 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
3579450 ATTTTTATAC
* * * * *
3579460 TAT TAA TAT TAC TAT TAT TAT TAT TAT TAT TAT TAG TAG TAG TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
3579509 TTT TAT TAT
1 TAT TAT TAT
3579518 ATGCGCGTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3579838 original size:11 final size:11
Alignment explanation
Indices: 3579818--3579865 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
3579808 TATGTTTTCT
3579818 TATA-TATGTA
1 TATATTATGTA
3579828 TATATTATGTA
1 TATATTATGTA
3579839 T-T-TTA--TA
1 TATATTATGTA
3579846 TATATTATGTA
1 TATATTATGTA
3579857 TATTATTAT
1 TA-TATTAT
3579866 TTTTATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
7 3 0.09
8 1 0.03
9 6 0.19
10 5 0.16
11 11 0.34
12 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (11 bp):
TATATTATGTA
Found at i:3579871 original size:18 final size:18
Alignment explanation
Indices: 3579826--3579862 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3579816 CTTATATATG
*
3579826 TATATATTATGTATTTTA
1 TATATATTATGTATATTA
3579844 TATATATTATGTATATTA
1 TATATATTATGTATATTA
3579862 T
1 T
3579863 TATTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
TATATATTATGTATATTA
Found at i:3579875 original size:30 final size:30
Alignment explanation
Indices: 3579818--3579889 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
3579808 TATGTTTTCT
3579818 TATA-TATGTATA-TATTATGTATTTTATA
1 TATATTATGTATATTATTATGTATTTTATA
*
3579846 TATATTATGTATATTATTAT-TTTTATTATA
1 TATATTATGTATATTATTATGTATT-TTATA
* *
3579876 CATATTACGTATAT
1 TATATTATGTATAT
3579890 ATCAAATATC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 4 0.11
29 11 0.29
30 23 0.61
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.57
Consensus pattern (30 bp):
TATATTATGTATATTATTATGTATTTTATA
Found at i:3580051 original size:24 final size:25
Alignment explanation
Indices: 3580024--3580083 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
3580014 TTATGTGTAC
*
3580024 ATATTATGTAAATGTTTTA-ATATT
1 ATATCATGTAAATGTTTTATATATT
* **
3580048 ATATCGTGTGTATGTTTTATATATT
1 ATATCATGTAAATGTTTTATATATT
*
3580073 ATGAACATGTA
1 AT-ATCATGTA
3580084 TTTTCAATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 15 0.56
25 7 0.26
26 5 0.19
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (25 bp):
ATATCATGTAAATGTTTTATATATT
Found at i:3582134 original size:18 final size:18
Alignment explanation
Indices: 3582111--3582145 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3582101 GCTGCAGTAA
3582111 AAACCACAGGCAAACATG
1 AAACCACAGGCAAACATG
3582129 AAACCACAGGCAAACAT
1 AAACCACAGGCAAACAT
3582146 CCCGTTAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.29, G:0.14, T:0.06
Consensus pattern (18 bp):
AAACCACAGGCAAACATG
Found at i:3582850 original size:20 final size:19
Alignment explanation
Indices: 3582827--3582889 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
3582817 AAATTTTAAT
*
3582827 AAAAGATATTAAAAATTAG
1 AAAAAATATTAAAAATTAG
*
3582846 AAAAAAAATTATAAAATTAG
1 AAAAAATATTA-AAAATTAG
*
3582866 TAAGAAAATATAAAAAATT-G
1 -AA-AAAATATTAAAAATTAG
3582886 AAAA
1 AAAA
3582890 TTTTTATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.05
19 11 0.30
20 9 0.24
21 8 0.22
22 7 0.19
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (19 bp):
AAAAAATATTAAAAATTAG
Found at i:3582882 original size:21 final size:21
Alignment explanation
Indices: 3582827--3582889 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 21
3582817 AAATTTTAAT
* *
3582827 AAAAGATATTAAAAATTAGAA
1 AAAAAATATAAAAAATTAGAA
* *
3582848 AAAAAAT-TATAAAATTAGTA
1 AAAAAATATAAAAAATTAGAA
*
3582868 AGAAAATATAAAAAATT-GAA
1 AAAAAATATAAAAAATTAGAA
3582888 AA
1 AA
3582890 TTTTTATAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (21 bp):
AAAAAATATAAAAAATTAGAA
Found at i:3583165 original size:21 final size:22
Alignment explanation
Indices: 3583139--3583182 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3583129 AAATTACGAA
3583139 TTTTAT-A-TTTCTTTACAATTT
1 TTTTATAATTTTC-TTACAATTT
3583160 TTTTATAATTTTCTTACAATTT
1 TTTTATAATTTTCTTACAATTT
3583182 T
1 T
3583183 ATAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATAATTTTCTTACAATTT
Found at i:3583229 original size:9 final size:9
Alignment explanation
Indices: 3583178--3583275 Score: 62
Period size: 9 Copynumber: 10.6 Consensus size: 9
3583168 TTTTCTTACA
3583178 ATTTTATA-
1 ATTTTATAT
3583186 ATTTTATAGTT
1 ATTTTATA--T
*
3583197 TTTTTATAT
1 ATTTTATAT
3583206 ATTTCTATAT
1 ATTT-TATAT
3583216 ATTTTATAGT
1 ATTTTATA-T
*
3583226 -TTTTATAAA
1 ATTTTAT-AT
3583235 ATTTTATA-
1 ATTTTATAT
*
3583243 ATTTTTTTACT
1 A-TTTTATA-T
3583254 ATTTT-TAT
1 ATTTTATAT
3583262 AATTTT-TAT
1 -ATTTTATAT
3583271 ATTTT
1 ATTTT
3583276 GTTAAAATTT
Statistics
Matches: 75, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
8 15 0.20
9 31 0.41
10 21 0.28
11 8 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
ATTTTATAT
Found at i:3583238 original size:19 final size:20
Alignment explanation
Indices: 3583216--3583271 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
3583206 ATTTCTATAT
*
3583216 ATTTTATAGTTTTTATA-AA
1 ATTTTATAATTTTTATACAA
* *
3583235 ATTTTATAATTTTTTTACTA
1 ATTTTATAATTTTTATACAA
*
3583255 TTTTTATAATTTTTATA
1 ATTTTATAATTTTTATA
3583272 TTTTGTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTATAATTTTTATACAA
Found at i:3583251 original size:30 final size:30
Alignment explanation
Indices: 3583150--3583275 Score: 90
Period size: 30 Copynumber: 4.4 Consensus size: 30
3583140 TTTATATTTC
* * *
3583150 TTTACAATTTTTTTATAATTTTCT-TACAAT
1 TTTATAATTTTTTTATAGTTTT-TATAAAAT
* *
3583180 TTTATAA---TTTTATAGTTTTTTTATATAT
1 TTTATAATTTTTTTATAGTTTTTATA-AAAT
*
3583208 TTCTAT-A-TATTTTATAGTTTTTATAAAAT
1 TT-TATAATTTTTTTATAGTTTTTATAAAAT
*
3583237 TTTATAATTTTTTTACTA-TTTTTAT-AATT
1 TTTATAATTTTTTTA-TAGTTTTTATAAAAT
3583266 TTTAT-ATTTT
1 TTTATAATTTT
3583276 GTTAAAATTT
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
26 1 0.01
27 13 0.16
28 13 0.16
29 17 0.21
30 34 0.43
31 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (30 bp):
TTTATAATTTTTTTATAGTTTTTATAAAAT
Found at i:3583272 original size:57 final size:57
Alignment explanation
Indices: 3583160--3583275 Score: 141
Period size: 57 Copynumber: 2.1 Consensus size: 57
3583150 TTTACAATTT
* * *
3583160 TTTTATAATTTTCTTACAATTTTATAATTTTATAGTTTTTTTATATATTTCTATATA
1 TTTTATAATTTTCTTAAAATTTTATAATTTTATACTATTTTTATATATTTCTATATA
* *
3583217 TTTTATAGTTTT-TATAAAATTTTATAATTTTTTTACTATTTTTATA-ATTT-T-TATA
1 TTTTATAATTTTCT-TAAAATTTTATAA-TTTTATACTATTTTTATATATTTCTATATA
3583272 TTTT
1 TTTT
3583276 GTTAAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
55 8 0.15
56 2 0.04
57 27 0.52
58 15 0.29
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (57 bp):
TTTTATAATTTTCTTAAAATTTTATAATTTTATACTATTTTTATATATTTCTATATA
Found at i:3589591 original size:22 final size:22
Alignment explanation
Indices: 3589566--3589610 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3589556 TTATGCTTTA
3589566 ATTTTTTTATTGTTTGGAAGTT
1 ATTTTTTTATTGTTTGGAAGTT
*
3589588 ATTTTTTTATTGTTTGGATGTT
1 ATTTTTTTATTGTTTGGAAGTT
3589610 A
1 A
3589611 CTTATGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (22 bp):
ATTTTTTTATTGTTTGGAAGTT
Found at i:3593557 original size:51 final size:50
Alignment explanation
Indices: 3593497--3593592 Score: 183
Period size: 51 Copynumber: 1.9 Consensus size: 50
3593487 AGAAAAACTA
3593497 TTTTATATTGTATTGTATGCATAATTGAGTTGAAAATTTATCATTTAATTG
1 TTTTATATTGTATTGTATGCATAATTGAGTTG-AAATTTATCATTTAATTG
3593548 TTTTATATTGTATTGTATGCATAATTGAGTTGAAATTTATCATTT
1 TTTTATATTGTATTGTATGCATAATTGAGTTGAAATTTATCATTT
3593593 GGTAGTATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 13 0.29
51 32 0.71
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (50 bp):
TTTTATATTGTATTGTATGCATAATTGAGTTGAAATTTATCATTTAATTG
Found at i:3594439 original size:30 final size:30
Alignment explanation
Indices: 3594405--3594469 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
3594395 AAAAATATAC
* *
3594405 AAAAATCATTAA-AAATTGTATAAACA-TTTT
1 AAAAATAATTAAGAAA-T-TATAAAAATTTTT
3594435 AAAAATAATTAAGAAATTATAAAAATTTTT
1 AAAAATAATTAAGAAATTATAAAAATTTTT
3594465 AAAAA
1 AAAAA
3594470 ATGTTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 7 0.23
30 21 0.68
31 3 0.10
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAAATAATTAAGAAATTATAAAAATTTTT
Found at i:3598339 original size:30 final size:31
Alignment explanation
Indices: 3598273--3598341 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
3598263 TAACGTTTAG
* * **
3598273 GTGACTAAAATAAAAATACCCTAAAAGTTGA
1 GTGACCAAAATAAAAACACCCTAAAAAATGA
* *
3598304 ATGACCAAAATGAAAACA-CCTAAAAAATGA
1 GTGACCAAAATAAAAACACCCTAAAAAATGA
3598334 GTGACCAA
1 GTGACCAA
3598342 CTAGATAGTT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.17
Consensus pattern (31 bp):
GTGACCAAAATAAAAACACCCTAAAAAATGA
Found at i:3599547 original size:6 final size:6
Alignment explanation
Indices: 3599536--3599568 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3599526 TCACGTCACC
*
3599536 ATATGT ATATGT ATATGT ATATGT ATATTT ATA
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATA
3599569 CATAAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (6 bp):
ATATGT
Found at i:3602559 original size:14 final size:15
Alignment explanation
Indices: 3602519--3602559 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
3602509 GAAGTTAAAT
*
3602519 TATATAATATATAAA
1 TATATAATATATTAA
*
3602534 TATAT-ATATATTGA
1 TATATAATATATTAA
3602548 TATATAAT-TATT
1 TATATAATATATT
3602560 TAAATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TATATAATATATTAA
Found at i:3627739 original size:53 final size:53
Alignment explanation
Indices: 3627583--3627748 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
3627573 GACGAAAAAT
* **
3627583 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
3627635 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
3627688 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
3627742 TATGTGA
1 -ATGTGA
3627749 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:3629776 original size:19 final size:19
Alignment explanation
Indices: 3629752--3629794 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3629742 AAAGGTGGTA
** *
3629752 AAAGAAGATGAAGAGAAAG
1 AAAGAAGAAAAAGAAAAAG
3629771 AAAGAAGAAAAAGAAAAAG
1 AAAGAAGAAAAAGAAAAAG
3629790 AAAGA
1 AAAGA
3629795 TAATGAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (19 bp):
AAAGAAGAAAAAGAAAAAG
Found at i:3634025 original size:20 final size:19
Alignment explanation
Indices: 3633981--3634027 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
3633971 CATCCAAACA
3633981 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
*
3634000 CTAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCA-TTT
3634020 CCAGAAAA
1 CCAGAAAA
3634028 TATTTTACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:3635392 original size:23 final size:23
Alignment explanation
Indices: 3635348--3635392 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3635338 AAAGCTGAAT
* *
3635348 TTTAATTTTAATTGGTATATAAC
1 TTTAATATTAATTAGTATATAAC
3635371 TTTAATATTAATTAAGTA-ATAA
1 TTTAATATTAATT-AGTATATAA
3635393 TTAACATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (23 bp):
TTTAATATTAATTAGTATATAAC
Found at i:3643391 original size:201 final size:201
Alignment explanation
Indices: 3643042--3643443 Score: 768
Period size: 201 Copynumber: 2.0 Consensus size: 201
3643032 TTGAAGATTT
*
3643042 TCCCTCCTTTTTTCACTTCTTGGCTAGTTCATTTATCAGTTACATGTACCTTTATGAAACTCAAT
1 TCCCTCCTTTTTTCACTGCTTGGCTAGTTCATTTATCAGTTACATGTACCTTTATGAAACTCAAT
3643107 TATTCTTATAGGTTGGAAATTATGAGGATAAAGATGTAATGGACTATGACAATGATCCTAAAACA
66 TATTCTTATAGGTTGGAAATTATGAGGATAAAGATGTAATGGACTATGACAATGATCCTAAAACA
* *
3643172 GAGTTTCAACGCTTCATCAGGCTAATAAGAGAGGGTATGTATACTTTTCATATTTTCTAATTATT
131 GAGTTTCAACGATTCATCAGGCTAATAAGAGAGGGTATGTATACTTTTCATATTTGCTAATTATT
3643237 TATATA
196 TATATA
*
3643243 TCCCTCCTTTTTTCACTGCTTGGCTAGTTCATTTATCAGTTACATGTACCTTTATGTAACTCAAT
1 TCCCTCCTTTTTTCACTGCTTGGCTAGTTCATTTATCAGTTACATGTACCTTTATGAAACTCAAT
3643308 TATTCTTATAGGTTGGAAATTATGAGGATAAAGATGTAATGGACTATGACAATGATCCTAAAACA
66 TATTCTTATAGGTTGGAAATTATGAGGATAAAGATGTAATGGACTATGACAATGATCCTAAAACA
3643373 GAGTTTCAACGATTCATCAGGCTAATAAGAGAGGGTATGTATACTTTTCATATTTGCTAATTATT
131 GAGTTTCAACGATTCATCAGGCTAATAAGAGAGGGTATGTATACTTTTCATATTTGCTAATTATT
3643438 TATATA
196 TATATA
3643444 CATTCTCTGA
Statistics
Matches: 197, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 197 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (201 bp):
TCCCTCCTTTTTTCACTGCTTGGCTAGTTCATTTATCAGTTACATGTACCTTTATGAAACTCAAT
TATTCTTATAGGTTGGAAATTATGAGGATAAAGATGTAATGGACTATGACAATGATCCTAAAACA
GAGTTTCAACGATTCATCAGGCTAATAAGAGAGGGTATGTATACTTTTCATATTTGCTAATTATT
TATATA
Found at i:3645806 original size:15 final size:15
Alignment explanation
Indices: 3645783--3645815 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3645773 GACAAACTTA
*
3645783 ATACGTTCATGTAAC
1 ATACATTCATGTAAC
3645798 ATACATTCATGTAAC
1 ATACATTCATGTAAC
3645813 ATA
1 ATA
3645816 TTGTCTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (15 bp):
ATACATTCATGTAAC
Found at i:3652837 original size:105 final size:105
Alignment explanation
Indices: 3652588--3652960 Score: 633
Period size: 105 Copynumber: 3.6 Consensus size: 105
3652578 TAACCGTTAT
* * **
3652588 TGGTGGATCTCGCACTTAGCACCACCGTTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
3652653 AATCAGTACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* *
3652692 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
3652756 GAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
3652797 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
3652862 AATCAGCACATAGCAACCCCCTTTTTACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
**
3652902 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
3652961 TTATATACAA
Statistics
Matches: 256, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
104 80 0.31
105 175 0.68
106 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (105 bp):
TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:3653321 original size:29 final size:29
Alignment explanation
Indices: 3653288--3653351 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
3653278 TAATCCACCA
3653288 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
3653317 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
3653347 CCCAA
1 CCCAA
3653352 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:3653325 original size:30 final size:30
Alignment explanation
Indices: 3653295--3653351 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3653285 CCACCCAACT
3653295 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
3653324 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
3653352 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:3659346 original size:13 final size:13
Alignment explanation
Indices: 3659328--3659354 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3659318 AAAAGAATGC
3659328 ACGTTTTTATTTA
1 ACGTTTTTATTTA
3659341 ACGTTTTTATTTA
1 ACGTTTTTATTTA
3659354 A
1 A
3659355 TGCATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (13 bp):
ACGTTTTTATTTA
Found at i:3662005 original size:156 final size:155
Alignment explanation
Indices: 3661758--3662561 Score: 892
Period size: 156 Copynumber: 5.1 Consensus size: 155
3661748 ACAAAAGAAA
* *
3661758 TGTTCATAGTTTCATTATCCTTGATTTGACTTTTATA-TCTCTATCTCCATTCCTCAAACACACG
1 TGTTCGTAG-TTCATTATCCTTGATTTGACTTTTATATTC-CTATCT-CA-TCCTCAAACACACA
* * * * *
3661822 ACTCAAAATAAAAATACAAGCACAAGAAAATACCATTTTTTCCTTGGGGAATAATTTCTCAGATG
62 ACTCAAAATATAAATACATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATG
* * *
3661887 GCTTCCTTGATATAGTTTCCTGAAAAGGA
127 GCTTCCTCGATACAGTTTCCTGAAAAGGG
* *
3661916 TGCTCGTAGTTTATTATCCTTGATTTGACTTTTATATTCCTATCTACATCCTCAAACACACAACT
1 TGTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCT-CATCCTCAAACACACAACT
* * *
3661981 CAAAATATAAATATATGCACAAGAACATACCATTTTCTCCTTGGGGATTAATTTCTCAGTTGGCT
65 CAAAATATAAATACATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATGG--
3662046 TCTTCCTCGATACAGTTTCCTG-AAAGGG
128 -CTTCCTCGATACAGTTTCCTGAAAAGGG
* * * * * * *
3662074 TGTTTC-TAGCTCATCATCCTTGATTTGAC-CTTATGTACTTATCTCAATCCTAAAACACACAAC
1 TG-TTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTC-ATCCTCAAACACACAAC
* * *
3662137 TCCAAATATAAATACAAGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCCCAGATGGT
64 TCAAAATATAAATACATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATGG-
* *
3662202 TTCTTCCTCGATACGGTTTCCTGAAAAGGC
128 --CTTCCTCGATACAGTTTCCTGAAAAGGG
* ** * * * *
3662232 TGTTCCTAGTTCATTATCCTTGATTTGACTTTTACGTTCCTGTCTCCCTCCTCTAACGCACAACT
1 TGTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCT-CATCCTCAAACACACAACT
* * *
3662297 -AAAAGTATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGAC
65 CAAAA-TATAAATACATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATGGC
* * * *
3662361 TTCCTCCATTCAATTTCCTGAAAAAGG
129 TTCCTCGATACAGTTTCCTGAAAAGGG
* *
3662388 TGTTCGTAGTTCGTTATCCTTGATTTGACATTTATATTCCTATCTCTATCCTCAAACACACAACT
1 TGTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTC-ATCCTCAAACACACAACT
* ** * * **
3662453 CAAGATATAAATATGTACACAATAAGAACATACCATTTTCTCCTTGGAGAGTAATCCCTCAGATG
65 CAAAATATAAATACATGCAC---AAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATG
*
3662518 GC-T--TCGATACAATTTCCTGAAAAGGG
127 GCTTCCTCGATACAGTTTCCTGAAAAGGG
3662544 TGCTT-GTAGTT-A-TATCCT
1 TG-TTCGTAGTTCATTATCCT
3662562 ATCTCCATCC
Statistics
Matches: 551, Mismatches: 78, Indels: 38
0.83 0.12 0.06
Matches are distributed among these distances:
154 6 0.01
155 1 0.00
156 189 0.34
157 149 0.27
158 68 0.12
159 137 0.25
160 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.35
Consensus pattern (155 bp):
TGTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCATCCTCAAACACACAACTC
AAAATATAAATACATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATGGCTT
CCTCGATACAGTTTCCTGAAAAGGG
Found at i:3662663 original size:133 final size:132
Alignment explanation
Indices: 3662419--3662673 Score: 345
Period size: 133 Copynumber: 1.9 Consensus size: 132
3662409 GATTTGACAT
* * *
3662419 TTATATTCCTATCTCTATCCTCAAACACACAACTCAAGATATAAATATGTACACAATAAGAACAT
1 TTATATTCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATACGTACAC-A-AAGAACAT
*
3662484 ACCATTTTCTCCTTGGAGAGTAATCCCTCAGATGGCTTCGATACAATTTCCTGAAAAGGGTGCTT
64 ACCATTTTCTCCTTGGAGAGTAATCCCTCAGATGGCTTCAATACAATTTCCTGAAAAGGGTGCTT
3662549 GTAG
129 GTAG
* *
3662553 TTATA-TCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATGCGTGCAC-AAGAACATAC
1 TTATATTCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATACGTACACAAAGAACATAC
* * * *
3662616 CGTTTTCTCCTTGGAGAGTAA-CTTCTTAGATGGTTTGCTCAATACAATTTCCTGAAAA
66 CATTTTCTCCTTGGAGAGTAATC-CCTCAGATGG-CT--TCAATACAATTTCCTGAAAA
3662674 AGATGCAGAG
Statistics
Matches: 107, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
129 1 0.01
130 38 0.36
131 1 0.01
133 62 0.58
134 5 0.05
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.31
Consensus pattern (132 bp):
TTATATTCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATACGTACACAAAGAACATAC
CATTTTCTCCTTGGAGAGTAATCCCTCAGATGGCTTCAATACAATTTCCTGAAAAGGGTGCTTGT
AG
Found at i:3667867 original size:39 final size:39
Alignment explanation
Indices: 3667758--3667889 Score: 167
Period size: 39 Copynumber: 3.4 Consensus size: 39
3667748 ATCGGTGGAT
3667758 TCTGGTATGGTGTTTGATGATCTATTATGCTACTTTCAG
1 TCTGGTATGGTGTTTGATGATCTATTATGCTACTTTCAG
* * * * *
3667797 TCTGATAAGGTGTTTTATGATATATTTTGCTACTTTCAG
1 TCTGGTATGGTGTTTGATGATCTATTATGCTACTTTCAG
* * * *
3667836 TCTGGTATGAG-GTTTGATCATCTGTTCTGCTAATTTCAG
1 TCTGGTATG-GTGTTTGATGATCTATTATGCTACTTTCAG
3667875 TCTGGTATGGTGTTT
1 TCTGGTATGGTGTTT
3667890 TACTGATGGT
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 76 0.97
40 1 0.01
ACGTcount: A:0.18, C:0.12, G:0.23, T:0.47
Consensus pattern (39 bp):
TCTGGTATGGTGTTTGATGATCTATTATGCTACTTTCAG
Found at i:3668132 original size:27 final size:28
Alignment explanation
Indices: 3668102--3668161 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
3668092 TTAATAATGT
*
3668102 TAAAATTATATTTTAA-CC-TCAAAAATA
1 TAAAATT-TAATTTAATCCTTCAAAAATA
*
3668129 TAAAAATTTAATTTAATCCTTTAAAAATA
1 T-AAAATTTAATTTAATCCTTCAAAAATA
3668158 TAAA
1 TAAA
3668162 GATATAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
27 8 0.29
28 11 0.39
29 9 0.32
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAAATTTAATTTAATCCTTCAAAAATA
Found at i:3671060 original size:21 final size:21
Alignment explanation
Indices: 3671034--3671074 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3671024 ATCTGCTCAA
* *
3671034 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3671055 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3671075 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3675717 original size:21 final size:21
Alignment explanation
Indices: 3675686--3675726 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3675676 TCTTAATTTA
*
3675686 TTTATTTATTACTTTTTTTTGC
1 TTTATTTATTA-TTTATTTTGC
3675708 TTTA-TTATTATTTATTTTG
1 TTTATTTATTATTTATTTTG
3675727 AATTTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTATTTATTATTTATTTTGC
Found at i:3676052 original size:18 final size:19
Alignment explanation
Indices: 3676014--3676052 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3676004 TTTGTTTTTG
* *
3676014 TTATTGTTTTATTATTTAT
1 TTATGGTTTTATTATTCAT
3676033 TTATGGTTTT-TTATTCAT
1 TTATGGTTTTATTATTCAT
3676051 TT
1 TT
3676053 TAAATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.72
Consensus pattern (19 bp):
TTATGGTTTTATTATTCAT
Found at i:3677558 original size:16 final size:16
Alignment explanation
Indices: 3677537--3677588 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
3677527 TAATTACATA
*
3677537 AATTTTGATTTTATGT
1 AATTTTGATTTTATAT
*
3677553 AATTTT-A-TATATAT
1 AATTTTGATTTTATAT
* *
3677567 AATTTTGATTTGATTT
1 AATTTTGATTTTATAT
3677583 AATTTT
1 AATTTT
3677589 TATAAATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 11 0.38
15 2 0.07
16 16 0.55
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (16 bp):
AATTTTGATTTTATAT
Found at i:3680350 original size:29 final size:29
Alignment explanation
Indices: 3680165--3680337 Score: 256
Period size: 29 Copynumber: 6.0 Consensus size: 29
3680155 TTGTGTGTAC
* * * *
3680165 AATGTGAAAAGCGATAGTTTCGGCTGTCG
1 AATGTGAAAAGGGATAGCTTCGGCTATCA
*
3680194 AATGTGAAAAGGGATAGCTTTGGCTATCA
1 AATGTGAAAAGGGATAGCTTCGGCTATCA
* *
3680223 AATGTGAAAAGAGATAGCTTCGGCTATCG
1 AATGTGAAAAGGGATAGCTTCGGCTATCA
* * *
3680252 AATGTGAAAATGGATAGCTTTGACTATCA
1 AATGTGAAAAGGGATAGCTTCGGCTATCA
3680281 AATGTGAAAAGGGATAGCTTCGGCTATCA
1 AATGTGAAAAGGGATAGCTTCGGCTATCA
3680310 AATGTGAAAAGGGATAGCTTCGGCTATC
1 AATGTGAAAAGGGATAGCTTCGGCTATC
3680338 GAATTTGGAA
Statistics
Matches: 128, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 128 1.00
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.27
Consensus pattern (29 bp):
AATGTGAAAAGGGATAGCTTCGGCTATCA
Found at i:3680377 original size:33 final size:33
Alignment explanation
Indices: 3680340--3680505 Score: 233
Period size: 33 Copynumber: 5.0 Consensus size: 33
3680330 CGGCTATCGA
*
3680340 ATTTGGAAAGGAAAGGTATACTTTGTGTATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
**
3680373 ATTTGAAAAGGTTAGGTATACTTTGTGTATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
**
3680406 ATTTGAAAAGGTTAGGTATACTTTGTGTATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
*
3680439 ATTTGAAAAGGAAAGGTATACTTTGTGTATATC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
* ** * *
3680472 ATATGAAAATAAAAAGTATACTTTGTGTGTACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
3680505 A
1 A
3680506 CTCGGAAAGA
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 121 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (33 bp):
ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
Found at i:3684153 original size:60 final size:59
Alignment explanation
Indices: 3684080--3684201 Score: 219
Period size: 59 Copynumber: 2.1 Consensus size: 59
3684070 ATATAAAAAT
3684080 TATTAATTTAAAGTTATTTAAATTCAA-ATATATACAAATGATTAATAAAAGTTATATATA
1 TATTAATTTAAAGTTATTTAAATT-AATATATAT-CAAATGATTAATAAAAGTTATATATA
3684140 TATTAATTTAAAGTTATTTAAATTAATATATATCAAATGATTAATAAAAGTTATATATA
1 TATTAATTTAAAGTTATTTAAATTAATATATATCAAATGATTAATAAAAGTTATATATA
3684199 TAT
1 TAT
3684202 AAACTTGGAG
Statistics
Matches: 61, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
59 31 0.51
60 30 0.49
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.43
Consensus pattern (59 bp):
TATTAATTTAAAGTTATTTAAATTAATATATATCAAATGATTAATAAAAGTTATATATA
Found at i:3684166 original size:20 final size:22
Alignment explanation
Indices: 3684127--3684166 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
3684117 ATGATTAATA
*
3684127 AAAGTTATATATATATTAATTT
1 AAAGTTATATATAAATTAATTT
3684149 AAAGTTAT-T-TAAATTAAT
1 AAAGTTATATATAAATTAAT
3684167 ATATATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
AAAGTTATATATAAATTAATTT
Found at i:3684330 original size:22 final size:21
Alignment explanation
Indices: 3684302--3684348 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
3684292 TTTCAGATGT
* *
3684302 AATTTTTATTAATTAATTTTAA
1 AATTTTTAATAAAT-ATTTTAA
3684324 AATTTTTTAATAAATATTTTAA
1 AA-TTTTTAATAAATATTTTAA
3684346 AAT
1 AAT
3684349 ATATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 1 0.05
22 11 0.50
23 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTTTTAATAAATATTTTAA
Found at i:3686013 original size:32 final size:31
Alignment explanation
Indices: 3685963--3686037 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
3685953 TATAAAGTTC
* *
3685963 AATTAATTGATATGAGTT-ATCAAATTAAATT
1 AATTAATTTATATGAGTTAAT-AAATTAAAGT
*
3685994 AATTAATTTATCATGAGTTAATAAATTCAAGT
1 AATTAATTTAT-ATGAGTTAATAAATTAAAGT
3686026 AATTAATTTATA
1 AATTAATTTATA
3686038 AGTTTATGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 11 0.28
32 26 0.67
33 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (31 bp):
AATTAATTTATATGAGTTAATAAATTAAAGT
Found at i:3694403 original size:19 final size:19
Alignment explanation
Indices: 3694367--3694405 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3694357 ACCGACGTTG
3694367 AAGTCCTTTATTAATTATT
1 AAGTCCTTTATTAATTATT
*
3694386 AAGT-CTTTACTTATTTATT
1 AAGTCCTTTA-TTAATTATT
3694405 A
1 A
3694406 CTGCATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (19 bp):
AAGTCCTTTATTAATTATT
Found at i:3694463 original size:25 final size:25
Alignment explanation
Indices: 3694451--3694504 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
3694441 GATTCTTTCC
3694451 ATTATATCATTTATAATCTCGTCCA
1 ATTATATCATTTATAATCTCGTCCA
*
3694476 ATTATATCATTTATAATCTCGTCTA
1 ATTATATCATTTATAATCTCGTCCA
3694501 ATTA
1 ATTA
3694505 AGAGAGGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTATATCATTTATAATCTCGTCCA
Found at i:3695618 original size:19 final size:19
Alignment explanation
Indices: 3695581--3695618 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3695571 TATATATTCT
*
3695581 ATTTTAAATATTGAATATA
1 ATTTTAAATATTCAATATA
3695600 ATTTTAAA-ATTCAACTATA
1 ATTTTAAATATTCAA-TATA
3695619 TAATAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTTTAAATATTCAATATA
Found at i:3701758 original size:22 final size:22
Alignment explanation
Indices: 3701730--3701773 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3701720 AAATTTTCTC
*
3701730 TAGATGTGTTTGGATACCATAA
1 TAGATGTGTTCGGATACCATAA
3701752 TAGATGTGTTCGGATACCATAA
1 TAGATGTGTTCGGATACCATAA
3701774 AATGATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (22 bp):
TAGATGTGTTCGGATACCATAA
Found at i:3701885 original size:17 final size:18
Alignment explanation
Indices: 3701863--3701901 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3701853 TATTGTAATT
*
3701863 ATATTTTAA-AAAAATAA
1 ATATTTAAATAAAAATAA
3701880 ATATTTAAATAAAAATAA
1 ATATTTAAATAAAAATAA
3701898 ATAT
1 ATAT
3701902 ATTCAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATTTAAATAAAAATAA
Found at i:3701903 original size:20 final size:19
Alignment explanation
Indices: 3701862--3701910 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
3701852 ATATTGTAAT
*
3701862 TATATTTTAA-AAAAATAA
1 TATATTTAAATAAAAATAA
3701880 -ATATTTAAATAAAAATAAA
1 TATATTTAAATAAAAAT-AA
*
3701899 TATATTCAAATA
1 TATATTTAAATA
3701911 TACTTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 8 0.31
18 6 0.23
19 2 0.08
20 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATTTAAATAAAAATAA
Found at i:3703805 original size:41 final size:41
Alignment explanation
Indices: 3703760--3703840 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
3703750 AATAATGAAA
* *
3703760 CATACTTCAAAAATTTAACACATTGTACAAGAACAGACAAT
1 CATACTTCAAAAATTCAACACATTGTACAAGAACAAACAAT
*
3703801 CATACTTCAAAAATTCAACACATTGTTCAAGAACAAACAA
1 CATACTTCAAAAATTCAACACATTGTACAAGAACAAACAA
3703841 ATCAACAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.49, C:0.21, G:0.06, T:0.23
Consensus pattern (41 bp):
CATACTTCAAAAATTCAACACATTGTACAAGAACAAACAAT
Found at i:3704166 original size:17 final size:17
Alignment explanation
Indices: 3704144--3704182 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3704134 TTGGAAATGA
*
3704144 TTTTGT-CCAAAACATAT
1 TTTTGTCCCAAAA-ATAC
3704161 TTTTGTCCCAAAAATAC
1 TTTTGTCCCAAAAATAC
3704178 TTTTG
1 TTTTG
3704183 AAAAGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.44
Consensus pattern (17 bp):
TTTTGTCCCAAAAATAC
Found at i:3708186 original size:26 final size:24
Alignment explanation
Indices: 3708156--3708205 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
3708146 AAATAAAAAA
*
3708156 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
3708182 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
3708206 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:3708225 original size:21 final size:21
Alignment explanation
Indices: 3708176--3708234 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
3708166 ATAATAAATC
*
3708176 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
3708196 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
3708218 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
3708235 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:3708311 original size:15 final size:16
Alignment explanation
Indices: 3708281--3708313 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3708271 AAATGGTTAT
3708281 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
3708298 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
3708313 A
1 A
3708314 AAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:3708821 original size:30 final size:30
Alignment explanation
Indices: 3708785--3708843 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
3708775 ATCTAAACTC
* *
3708785 TAAAAATTCAAATCAACATATTTAAATTTT
1 TAAAAATTCAAAACAACATATCTAAATTTT
*
3708815 TAAAAATTCAAAACAATATATCTAAATTT
1 TAAAAATTCAAAACAACATATCTAAATTT
3708844 CCAAAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (30 bp):
TAAAAATTCAAAACAACATATCTAAATTTT
Found at i:3709028 original size:27 final size:29
Alignment explanation
Indices: 3708999--3709051 Score: 85
Period size: 26 Copynumber: 1.9 Consensus size: 29
3708989 AAATTAAGGT
3708999 TTTTTTATTTTT-TAAA-A-TTTAAATAC
1 TTTTTTATTTTTATAAATATTTTAAATAC
3709025 TTTTTTATTTTTATAAATATTTTAAAT
1 TTTTTTATTTTTATAAATATTTTAAAT
3709052 TTTTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 12 0.50
27 4 0.17
28 1 0.04
29 7 0.29
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTTTATTTTTATAAATATTTTAAATAC
Found at i:3709047 original size:19 final size:20
Alignment explanation
Indices: 3709018--3709058 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3709008 TTTTAAAATT
**
3709018 TAAATACTTTTTTATTTTTA
1 TAAATACTTTTAAATTTTTA
3709038 TAAATA-TTTTAAATTTTTA
1 TAAATACTTTTAAATTTTTA
3709057 TA
1 TA
3709059 TATTATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TAAATACTTTTAAATTTTTA
Found at i:3710260 original size:23 final size:22
Alignment explanation
Indices: 3710209--3710268 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
3710199 ATTGATATGA
3710209 AATAAAAATAGATAAAAGAAAG
1 AATAAAAATAGATAAAAGAAAG
* * *
3710231 AACTAAAAATATATTAAAGTAAAT
1 AA-TAAAAATAGATAAAAG-AAAG
*
3710255 AATAAATAT-GATAA
1 AATAAAAATAGATAA
3710269 TAATATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 5 0.17
23 20 0.67
24 5 0.17
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (22 bp):
AATAAAAATAGATAAAAGAAAG
Found at i:3710894 original size:13 final size:12
Alignment explanation
Indices: 3710875--3710913 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
3710865 AAAAACATAG
3710875 ATATAAAATATA
1 ATATAAAATATA
3710887 ATACTAAAATATA
1 ATA-TAAAATATA
*
3710900 CATATAATATATA
1 -ATATAAAATATA
3710913 A
1 A
3710914 GGATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.17
13 17 0.71
14 3 0.12
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:3710993 original size:27 final size:27
Alignment explanation
Indices: 3710956--3711007 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3710946 TACAAGATAT
* * *
3710956 ATATATAATATGATGTTAAGAGTATAC
1 ATATAAAATATAATGTTAAAAGTATAC
3710983 ATATAAAATATAATGTTAAAAGTAT
1 ATATAAAATATAATGTTAAAAGTAT
3711008 GTATGCATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.37
Consensus pattern (27 bp):
ATATAAAATATAATGTTAAAAGTATAC
Found at i:3713430 original size:28 final size:26
Alignment explanation
Indices: 3713380--3713440 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
3713370 ATTCTTTCTT
*
3713380 ATTTATATAATATTTTTCATTTATAA
1 ATTTTTATAATATTTTTCATTTATAA
*
3713406 TAGTTTTTATAATATTATTT-TTTTATAA
1 -A-TTTTTATAATATT-TTTCATTTATAA
3713434 ATTTTTA
1 ATTTTTA
3713441 CACTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 6 0.20
27 2 0.07
28 19 0.63
29 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTTTATAATATTTTTCATTTATAA
Found at i:3713463 original size:16 final size:16
Alignment explanation
Indices: 3713448--3713478 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3713438 TTACACTTTA
3713448 ATAT-TTTTATTATTT
1 ATATGTTTTATTATTT
3713463 ATATGTTTTATTATTT
1 ATATGTTTTATTATTT
3713479 TCTATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
ATATGTTTTATTATTT
Found at i:3713484 original size:19 final size:18
Alignment explanation
Indices: 3713454--3713528 Score: 64
Period size: 19 Copynumber: 4.1 Consensus size: 18
3713444 TTTAATATTT
3713454 TTATTATTTATATGTTTTA
1 TTATT-TTTATATGTTTTA
* *
3713473 TTATTTTCTATATTTTTTG
1 TTATTTT-TATATGTTTTA
* *
3713492 TT-TTATTATATTTTTTA
1 TTATTTTTATATGTTTTA
3713509 TTGATTTTTA-ATGATTTTA
1 TT-ATTTTTATATG-TTTTA
3713528 T
1 T
3713529 AAATAATACA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
17 12 0.26
18 7 0.15
19 27 0.59
ACGTcount: A:0.23, C:0.01, G:0.05, T:0.71
Consensus pattern (18 bp):
TTATTTTTATATGTTTTA
Found at i:3713488 original size:17 final size:16
Alignment explanation
Indices: 3713410--3713510 Score: 64
Period size: 17 Copynumber: 6.1 Consensus size: 16
3713400 TTATAATAGT
*
3713410 TTTTATAATATTATTT-
1 TTTTAT-ATATTTTTTA
* *
3713426 TTTTATAAATTTTTACA
1 TTTTATATATTTTT-TA
*
3713443 CTTTA-ATA-TTTTTA
1 TTTTATATATTTTTTA
*
3713457 TTATTTATATGTTTTATTA
1 -T-TTTATATATTTT-TTA
* *
3713476 TTTTCTATATTTTTTG
1 TTTTATATATTTTTTA
3713492 TTTTATTATATTTTTTA
1 TTTTA-TATATTTTTTA
3713509 TT
1 TT
3713511 GATTTTTAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
14 1 0.02
15 10 0.16
16 18 0.28
17 28 0.44
18 4 0.06
19 3 0.05
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTATATATTTTTTA
Found at i:3713493 original size:24 final size:25
Alignment explanation
Indices: 3713444--3713510 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
3713434 ATTTTTACAC
*
3713444 TTTAATATTTTTATTATTTATATGT
1 TTTATTATTTTTATTATTTATATGT
*
3713469 TTTATTATTTTCTA-TATTT-TTTGT
1 TTTATTATTTT-TATTATTTATATGT
3713493 TTTATTATATTTT-TTATT
1 TTTATTAT-TTTTATTATT
3713511 GATTTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
24 17 0.46
25 18 0.49
26 2 0.05
ACGTcount: A:0.22, C:0.01, G:0.03, T:0.73
Consensus pattern (25 bp):
TTTATTATTTTTATTATTTATATGT
Found at i:3718107 original size:24 final size:24
Alignment explanation
Indices: 3718041--3718110 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
3718031 TTCTTTAAAA
*
3718041 ATTATAAAAATATA-AACTATTAA-A
1 ATTATAAAAATATATAA-T-TTAATT
* *
3718065 ATAAT-AAAAT-TATATTTTAATT
1 ATTATAAAAATATATAATTTAATT
3718087 ATTATAAAAATATATAATTTAATT
1 ATTATAAAAATATATAATTTAATT
3718111 CTTAATTTCG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
23 11 0.30
24 15 0.41
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTATAAAAATATATAATTTAATT
Found at i:3718624 original size:21 final size:21
Alignment explanation
Indices: 3718599--3718664 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 21
3718589 TATGATAATC
*
3718599 TTTATAATTTTTTTTACGA-AT
1 TTTATAATTTTCTTTAC-ATAT
3718620 TTTAT-A-TTTCTTTACATAT
1 TTTATAATTTTCTTTACATAT
*
3718639 TTTATAATTTTC-TTACA-AC
1 TTTATAATTTTCTTTACATAT
3718658 TTTATAA
1 TTTATAA
3718665 AATTTTATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 1 0.03
19 23 0.57
20 7 0.17
21 9 0.22
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTATAATTTTCTTTACATAT
Found at i:3718698 original size:10 final size:10
Alignment explanation
Indices: 3718678--3718741 Score: 67
Period size: 10 Copynumber: 6.3 Consensus size: 10
3718668 TTTATCATTA
*
3718678 TTTTCTATAT
1 TTTTATATAT
*
3718688 TTCTATATAT
1 TTTTATATAT
3718698 TTTTATAT-T
1 TTTTATATAT
*
3718707 TTTTTTATGAT
1 TTTTATAT-AT
*
3718718 TTATATATAT
1 TTTTATATAT
3718728 TTTTATATTAT
1 TTTTATA-TAT
3718739 TTT
1 TTT
3718742 ATTAAAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
9 8 0.18
10 23 0.52
11 13 0.30
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTTATATAT
Found at i:3718704 original size:8 final size:9
Alignment explanation
Indices: 3718666--3718743 Score: 57
Period size: 10 Copynumber: 7.8 Consensus size: 9
3718656 ACTTTATAAA
3718666 ATTTTATCATT
1 ATTTTAT-A-T
*
3718677 ATTTTCTAT
1 ATTTTATAT
3718686 ATTTCTATAT
1 ATTT-TATAT
3718696 ATTTTTATAT
1 A-TTTTATAT
* *
3718706 TTTTTTTAT
1 ATTTTATAT
3718715 GATTTATATAT
1 -ATTT-TATAT
3718726 ATTTTTATATT
1 A-TTTTATA-T
3718737 ATTTTAT
1 ATTTTAT
3718744 TAAAATTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
9 12 0.22
10 25 0.45
11 18 0.33
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (9 bp):
ATTTTATAT
Found at i:3718725 original size:30 final size:30
Alignment explanation
Indices: 3718667--3718764 Score: 112
Period size: 30 Copynumber: 3.2 Consensus size: 30
3718657 CTTTATAAAA
* *
3718667 TTTTATCATTATTTTCTATATTTCTATATAT
1 TTTTAT-ATTATTTTTTATATTTATATATAT
3718698 TTTTATATT-TTTTTTATGATTTATATATAT
1 TTTTATATTATTTTTTAT-ATTTATATATAT
*
3718728 TTTTATATTATTTTATTAAAATTTA-ATAT-T
1 TTTTATATTATTTT-TT-ATATTTATATATAT
3718758 TTTTATA
1 TTTTATA
3718765 ACTTTTATTT
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
29 7 0.12
30 31 0.52
31 14 0.23
32 7 0.12
33 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (30 bp):
TTTTATATTATTTTTTATATTTATATATAT
Found at i:3718742 original size:10 final size:10
Alignment explanation
Indices: 3718666--3718743 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 10
3718656 ACTTTATAAA
3718666 ATTTTATCATT
1 ATTTTAT-ATT
*
3718677 ATTTTCTA-T
1 ATTTTATATT
3718686 ATTTCTATA-T
1 ATTT-TATATT
3718696 ATTTTTATATT
1 A-TTTTATATT
* *
3718707 -TTTTTTATG
1 ATTTTATATT
3718716 A-TTTATATAT
1 ATTTTATAT-T
3718726 ATTTTTATATT
1 A-TTTTATATT
3718737 ATTTTAT
1 ATTTTAT
3718744 TAAAATTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
9 18 0.33
10 17 0.31
11 12 0.22
12 7 0.13
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (10 bp):
ATTTTATATT
Found at i:3718756 original size:29 final size:32
Alignment explanation
Indices: 3718691--3718773 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 32
3718681 TCTATATTTC
* *
3718691 TATATATTTTTATATT-TTTT-TTATGATTTA
1 TATATATTTTTATATTATTTTATTATAAATTA
3718721 TATATATTTTTATATTATTTTATTA-AAATT-
1 TATATATTTTTATATTATTTTATTATAAATTA
*
3718751 TA-ATATTTTT-TATAACTTTTATT
1 TATATATTTTTATATTA-TTTTATT
3718774 TTTTTATCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
28 4 0.09
29 15 0.32
30 18 0.38
31 7 0.15
32 3 0.06
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (32 bp):
TATATATTTTTATATTATTTTATTATAAATTA
Found at i:3721266 original size:16 final size:16
Alignment explanation
Indices: 3721245--3721283 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3721235 GATTATCTAT
*
3721245 GTAATGGAATAGAGGC
1 GTAATGGAATAGAAGC
3721261 GTAATGGAATAGAAGC
1 GTAATGGAATAGAAGC
3721277 GTAATGG
1 GTAATGG
3721284 GTAATTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (16 bp):
GTAATGGAATAGAAGC
Found at i:3721350 original size:44 final size:46
Alignment explanation
Indices: 3721263--3721355 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 46
3721253 ATAGAGGCGT
*
3721263 AATGGAATAGAAGCGTAATGGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAAGCGTAATGGGTAATTCTTGTGTTTGGTTGAATGG
3721309 AATGGAATAGAAGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAAGCGTAATGGGTAATTCTTGTGTTTGGTTGAATGG
3721353 AAT
1 AAT
3721356 AGAGGTGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 24 0.52
45 3 0.07
46 19 0.41
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAAGCGTAATGGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:3728879 original size:8 final size:8
Alignment explanation
Indices: 3728868--3728941 Score: 53
Period size: 8 Copynumber: 8.5 Consensus size: 8
3728858 CATAAAAATT
3728868 ATATAAAA
1 ATATAAAA
3728876 ATATAAAA
1 ATATAAAA
3728884 ATTATATAAA
1 A-TATA-AAA
*
3728894 ATTATGAAA
1 A-TATAAAA
3728903 ATCAT-AAA
1 AT-ATAAAA
3728911 ATATAAAA
1 ATATAAAA
3728919 A-ATGCAAAA
1 ATAT--AAAA
3728928 ATTATGAAAA
1 A-TAT-AAAA
3728938 ATAT
1 ATAT
3728942 TGTAGAAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
7 4 0.07
8 19 0.34
9 18 0.32
10 13 0.23
11 2 0.04
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (8 bp):
ATATAAAA
Found at i:3728881 original size:19 final size:19
Alignment explanation
Indices: 3728853--3728921 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
3728843 TTTTATATTT
3728853 AAAATCATAAAAATTATATA
1 AAAAT-ATAAAAATTATATA
3728873 AAAATATAAAAATTATATA
1 AAAATATAAAAATTATATA
* * *
3728892 AAATTATGAAAATCATA-A
1 AAAATATAAAAATTATATA
*
3728910 AATATA-AAAAAT
1 AAAATATAAAAAT
3728922 GCAAAAATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
17 5 0.12
18 5 0.12
19 28 0.65
20 5 0.12
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (19 bp):
AAAATATAAAAATTATATA
Found at i:3728937 original size:10 final size:9
Alignment explanation
Indices: 3728853--3728939 Score: 70
Period size: 9 Copynumber: 9.6 Consensus size: 9
3728843 TTTTATATTT
*
3728853 AAAATCATA
1 AAAATTATA
3728862 AAAATTATA
1 AAAATTATA
*
3728871 TAAAAATATA
1 -AAAATTATA
3728881 AAAATTATA
1 AAAATTATA
*
3728890 TAAAATTATG
1 -AAAATTATA
*
3728900 AAAATCAT-
1 AAAATTATA
3728908 AAAA-TATA
1 AAAATTATA
* **
3728916 AAAAATGCA
1 AAAATTATA
3728925 AAAATTATGA
1 AAAATTAT-A
3728935 AAAAT
1 AAAAT
3728940 ATTGTAGAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
7 2 0.03
8 8 0.13
9 30 0.48
10 22 0.35
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAATTATA
Found at i:3728939 original size:18 final size:18
Alignment explanation
Indices: 3728889--3728939 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
3728879 TAAAAATTAT
3728889 ATAAAATTATG-AAAATC
1 ATAAAATTATGAAAAATC
*
3728906 ATAAAA-TATAAAAAATGC
1 ATAAAATTATGAAAAAT-C
3728924 A-AAAATTATGAAAAAT
1 ATAAAATTATGAAAAAT
3728940 ATTGTAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 3 0.10
17 15 0.52
18 11 0.38
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAATTATGAAAAATC
Done.