Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 4 of 32
Found at i:1460127 original size:2 final size:2
Alignment explanation
Indices: 1460122--1460150 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1460112 TCTCTCTCTC
1460122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1460151 CCAAGTACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1464413 original size:3 final size:3
Alignment explanation
Indices: 1464398--1464441 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1464388 ATTAATACTC
*
1464398 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1464442 TTGAAGTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1469385 original size:23 final size:25
Alignment explanation
Indices: 1469350--1469401 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
1469340 CTCGATAATT
*
1469350 TGTAGTAAGAATGATTTT-CTTTTA-
1 TGTAATAAGAATG-TTTTACTTTTAC
1469374 TGTAATAA-AATGTTTTACTTTTAC
1 TGTAATAAGAATGTTTTACTTTTAC
1469398 TGTA
1 TGTA
1469402 CTTCACTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 10 0.40
24 11 0.44
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (25 bp):
TGTAATAAGAATGTTTTACTTTTAC
Found at i:1475899 original size:30 final size:29
Alignment explanation
Indices: 1475863--1475930 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
1475853 AATCATTAAT
* **
1475863 TATAAAATTTTATTTGATTTAAAATAAAAA
1 TATAAAATTTTAATT-AAATAAAATAAAAA
*
1475893 TATAAAAATTTTAATTAAATATAATAAAAA
1 TAT-AAAATTTTAATTAAATAAAATAAAAA
1475923 TA-AAAATT
1 TATAAAATT
1475931 ACTTAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.18
30 16 0.48
31 11 0.33
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (29 bp):
TATAAAATTTTAATTAAATAAAATAAAAA
Found at i:1475905 original size:22 final size:22
Alignment explanation
Indices: 1475879--1475923 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1475869 ATTTTATTTG
*
1475879 ATTTAAAATAAAAAT-ATAAAA
1 ATTTTAAATAAAAATAATAAAA
* *
1475900 ATTTTAATTAAATATAATAAAA
1 ATTTTAAATAAAAATAATAAAA
1475922 AT
1 AT
1475924 AAAAATTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTTTAAATAAAAATAATAAAA
Found at i:1475936 original size:26 final size:26
Alignment explanation
Indices: 1475881--1475940 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1475871 TTTATTTGAT
*
1475881 TTAAA-ATAAAAATATAAAAATTTTAA
1 TTAAATATAAAAAAATAAAAA-TTTAA
*
1475907 TTAAATATAATAAAAATAAAAA-TTAC
1 TTAAATATAA-AAAAATAAAAATTTAA
1475933 TTAAATAT
1 TTAAATAT
1475941 TTTTAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 16 0.53
27 4 0.13
28 10 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAAATATAAAAAAATAAAAATTTAA
Found at i:1476586 original size:26 final size:26
Alignment explanation
Indices: 1476557--1476611 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
1476547 AAATAAATTT
*
1476557 TTAAATAA-ATTATAAT-TAATAATTAA
1 TTAAATAATATTA-AATAAAAT-ATTAA
*
1476583 TTAATTAATATTAAATAAAATATTAA
1 TTAAATAATATTAAATAAAATATTAA
1476609 TTA
1 TTA
1476612 TTATGTCACG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TTAAATAATATTAAATAAAATATTAA
Found at i:1476587 original size:15 final size:14
Alignment explanation
Indices: 1476569--1476611 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 14
1476559 AAATAAATTA
1476569 TAATTAATAATTAAT
1 TAATTAAT-ATTAAT
*
1476584 TAATTAATATTAAA
1 TAATTAATATTAAT
1476598 TAA--AATATTAAT
1 TAATTAATATTAAT
1476610 TA
1 TA
1476612 TTATGTCACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 10 0.38
14 8 0.31
15 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATTAATATTAAT
Found at i:1476758 original size:14 final size:14
Alignment explanation
Indices: 1476736--1476769 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1476726 ATATTTTAAT
1476736 TAATAAATTAATAA
1 TAATAAATTAATAA
* *
1476750 TAATTAATTATTAA
1 TAATAAATTAATAA
1476764 TAATAA
1 TAATAA
1476770 TAATTTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATAAATTAATAA
Found at i:1476778 original size:17 final size:17
Alignment explanation
Indices: 1476732--1476774 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
1476722 AGTGATATTT
*
1476732 TAATTAATAAATTAATAA
1 TAATTAAT-TATTAATAA
1476750 TAATTAATTATTAATAA
1 TAATTAATTATTAATAA
1476767 TAA-TAATT
1 TAATTAATT
1476775 TATTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 11 0.46
18 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTAATTATTAATAA
Found at i:1478275 original size:22 final size:21
Alignment explanation
Indices: 1478233--1478276 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1478223 TTTTTATTTC
*
1478233 TTTTAATCAAAAAATTTTTTA
1 TTTTAATCAAAAAATTGTTTA
1478254 TTTTAGATCAAATAAA-TGTTTA
1 TTTTA-ATCAAA-AAATTGTTTA
1478276 T
1 T
1478277 AATTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 12 0.60
23 3 0.15
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTTAATCAAAAAATTGTTTA
Found at i:1478485 original size:29 final size:28
Alignment explanation
Indices: 1478453--1478521 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
1478443 TATTAGAAAT
*
1478453 ATTTATTTAATTTAA-AATTAAAATATAAAA
1 ATTTATTTAATGTAATAA--AAAA-ATAAAA
* *
1478483 TTTTGATTGAATGTAATAAAAAAATAAAA
1 ATTT-ATTTAATGTAATAAAAAAATAAAA
1478512 ATTTATTTAA
1 ATTTATTTAA
1478522 ATTTTTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 5 0.16
29 9 0.28
30 7 0.22
31 9 0.28
32 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (28 bp):
ATTTATTTAATGTAATAAAAAAATAAAA
Found at i:1478920 original size:32 final size:32
Alignment explanation
Indices: 1478884--1478948 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1478874 TTTTTTTCTT
1478884 TCCTTTCATTTACATTGTATGTCTAACCTTTC
1 TCCTTTCATTTACATTGTATGTCTAACCTTTC
1478916 TCCTTTCATTTACATTGTATGTCTAACCTTTC
1 TCCTTTCATTTACATTGTATGTCTAACCTTTC
1478948 T
1 T
1478949 GAAGTCTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.06, T:0.51
Consensus pattern (32 bp):
TCCTTTCATTTACATTGTATGTCTAACCTTTC
Found at i:1493335 original size:23 final size:23
Alignment explanation
Indices: 1493305--1493355 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
1493295 TTCAACCCCG
*
1493305 AGGCAAAAGTCTTAGCCTACAGT
1 AGGCAAAAGTCTTAGCCTACACT
*
1493328 AGGCAAAAGTCTTAGCCTATACT
1 AGGCAAAAGTCTTAGCCTACACT
1493351 AGGCA
1 AGGCA
1493356 CAGACTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (23 bp):
AGGCAAAAGTCTTAGCCTACACT
Found at i:1494129 original size:48 final size:43
Alignment explanation
Indices: 1494067--1494168 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 43
1494057 ATTATTTTAA
1494067 ATATATAATTTTTAAATAATTT-TAATTATATACAAAATTATTAATTTT
1 ATATATAATTTTT-AATAATTTAT-ATT-T-TAC-AAATTA-TAATTTT
* *
1494115 ATATATTATTTTTAATTATTTATATTTTACAAATTATAATTTT
1 ATATATAATTTTTAATAATTTATATTTTACAAATTATAATTTT
*
1494158 ATATGTAATTT
1 ATATATAATTT
1494169 CATATTTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
43 16 0.33
44 6 0.12
45 3 0.06
46 1 0.02
47 10 0.20
48 13 0.27
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (43 bp):
ATATATAATTTTTAATAATTTATATTTTACAAATTATAATTTT
Found at i:1507644 original size:8 final size:8
Alignment explanation
Indices: 1507627--1507661 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1507617 TGTTGAAGGA
1507627 AGACAGAG
1 AGACAGAG
*
1507635 AGACACAG
1 AGACAGAG
*
1507643 AGAGAGAG
1 AGACAGAG
1507651 AGACAGAG
1 AGACAGAG
1507659 AGA
1 AGA
1507662 GGGTCTTAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.51, C:0.11, G:0.37, T:0.00
Consensus pattern (8 bp):
AGACAGAG
Found at i:1507650 original size:14 final size:14
Alignment explanation
Indices: 1507631--1507662 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1507621 GAAGGAAGAC
1507631 AGAGAGACACAGAG
1 AGAGAGACACAGAG
*
1507645 AGAGAGAGACAGAG
1 AGAGAGACACAGAG
1507659 AGAG
1 AGAG
1507663 GGTCTTAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.41, T:0.00
Consensus pattern (14 bp):
AGAGAGACACAGAG
Found at i:1516793 original size:15 final size:16
Alignment explanation
Indices: 1516767--1516804 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1516757 AACTCTATTG
* *
1516767 ATATGTACATTTTTTT
1 ATATGTAAATTTTGTT
1516783 A-ATGTAAATTTTGTT
1 ATATGTAAATTTTGTT
1516798 ATATGTA
1 ATATGTA
1516805 TATATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.55
Consensus pattern (16 bp):
ATATGTAAATTTTGTT
Found at i:1534679 original size:2 final size:2
Alignment explanation
Indices: 1534672--1534707 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1534662 TTGTCCTCTA
1534672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1534708 TAAGAATGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1538966 original size:2 final size:2
Alignment explanation
Indices: 1538959--1538983 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1538949 CAAACCTATG
1538959 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1538984 TATGTACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1540602 original size:26 final size:27
Alignment explanation
Indices: 1540565--1540619 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1540555 ATGATCAAAA
*
1540565 ATAAAAATAAAT-AAATTTAATTAAAT
1 ATAAAAATAAATAAAAATTAATTAAAT
*
1540591 ATAATAAA-AAATAAAAATTATTTAAAT
1 ATAA-AAATAAATAAAAATTAATTAAAT
1540618 AT
1 AT
1540620 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
ATAAAAATAAATAAAAATTAATTAAAT
Found at i:1540632 original size:19 final size:20
Alignment explanation
Indices: 1540605--1540646 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1540595 TAAAAAATAA
* *
1540605 AAATTATTTAAATA-TTTTT
1 AAATAATTTAAAAACTTTTT
1540624 AAATAATTTAAAAACTTTTT
1 AAATAATTTAAAAACTTTTT
1540644 AAA
1 AAA
1540647 ACATTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATAATTTAAAAACTTTTT
Found at i:1548852 original size:16 final size:16
Alignment explanation
Indices: 1548833--1548870 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1548823 TTATATTTTC
*
1548833 ATTAAAAATTTAATAT
1 ATTAAAAATTTAATAA
*
1548849 ATTAATAATTTAATAA
1 ATTAAAAATTTAATAA
1548865 ATTAAA
1 ATTAAA
1548871 CACTAATATT
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:0.00, T:0.42
Consensus pattern (16 bp):
ATTAAAAATTTAATAA
Found at i:1563994 original size:17 final size:17
Alignment explanation
Indices: 1563969--1564008 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1563959 ATTTATAATT
1563969 GTATCGGATTAGATTAA
1 GTATCGGATTAGATTAA
* *
1563986 GTATTGGATTGGATTAA
1 GTATCGGATTAGATTAA
1564003 GTATCG
1 GTATCG
1564009 AAAGCATATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.38
Consensus pattern (17 bp):
GTATCGGATTAGATTAA
Found at i:1564292 original size:17 final size:18
Alignment explanation
Indices: 1564251--1564292 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1564241 TAAATTAATA
*
1564251 TAAGAAATGTATATTTAT
1 TAAGAAATCTATATTTAT
*
1564269 TTA-AAATCTATA-TTAT
1 TAAGAAATCTATATTTAT
1564285 TAAGAAAT
1 TAAGAAAT
1564293 ATGTTGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 6 0.30
17 12 0.60
18 2 0.10
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (18 bp):
TAAGAAATCTATATTTAT
Found at i:1569340 original size:20 final size:21
Alignment explanation
Indices: 1569302--1569343 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
1569292 AACGAGGGAA
1569302 ATGATTAATAATAGTTAAGGT
1 ATGATTAATAATAGTTAAGGT
1569323 ATGATTAA-AATA-TATAAGGT
1 ATGATTAATAATAGT-TAAGGT
1569343 A
1 A
1569344 AGTAGTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.36
Consensus pattern (21 bp):
ATGATTAATAATAGTTAAGGT
Found at i:1577342 original size:4 final size:4
Alignment explanation
Indices: 1577326--1577355 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1577316 GGACTACTGT
*
1577326 GGGA GGGA AGGA GGGA GGGA GGGA GGGA GG
1 GGGA GGGA GGGA GGGA GGGA GGGA GGGA GG
1577356 AGCAGGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (4 bp):
GGGA
Found at i:1578434 original size:25 final size:25
Alignment explanation
Indices: 1578406--1578482 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
1578396 TATTATTTTT
* *
1578406 TAAAAATAAAAT-AAAATATATAATA
1 TAAAAATATAATAAAAATA-AAAATA
*
1578431 TAAAAATATATTAAAAATAAAAATA
1 TAAAAATATAATAAAAATAAAAATA
*
1578456 TAAAATTATAATAAAAATAAAAATA
1 TAAAAATATAATAAAAATAAAAATA
1578481 TA
1 TA
1578483 TATATGACAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 40 0.87
26 6 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAAAATATAATAAAAATAAAAATA
Found at i:1578435 original size:19 final size:19
Alignment explanation
Indices: 1578411--1578484 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
1578401 TTTTTTAAAA
1578411 ATAAAATAAAATATATAAT
1 ATAAAATAAAATATATAAT
* * *
1578430 ATAAAAATATATTA-AAAAT
1 AT-AAAATAAAATATATAAT
*
1578449 AAAAATATAAAAT-TATAAT
1 ATAAA-ATAAAATATATAAT
1578468 A-AAAATAAAAATATATA
1 ATAAAAT-AAAATATATA
1578485 TATGACATTC
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
17 2 0.05
18 11 0.26
19 21 0.49
20 9 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAAATAAAATATATAAT
Found at i:1578441 original size:17 final size:17
Alignment explanation
Indices: 1578413--1578457 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1578403 TTTTAAAAAT
1578413 AAAAT-AAAATATA-T-
1 AAAATAAAAATATATTA
*
1578427 AATATAAAAATATATTA
1 AAAATAAAAATATATTA
1578444 AAAATAAAAATATA
1 AAAATAAAAATATA
1578458 AAATTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 1 0.04
17 13 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAAAATATATTA
Found at i:1578848 original size:15 final size:16
Alignment explanation
Indices: 1578801--1578863 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 16
1578791 AAATGATTTT
**
1578801 ATTTAAAATATTTTTTA
1 ATTT-AAATATTTAATA
1578818 ATTTAATACTATTTAATA
1 ATTTAA-A-TATTTAATA
1578836 ATTTAAATA-TTAATA
1 ATTTAAATATTTAATA
*
1578851 TTTTAAATTATTT
1 ATTTAAA-TATTT
1578864 TTTAAGTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 12 0.31
16 6 0.15
17 8 0.21
18 13 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTAAATATTTAATA
Found at i:1620620 original size:43 final size:43
Alignment explanation
Indices: 1620559--1620640 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
1620549 AAAGATATGC
*
1620559 TCGTATTCCTTTTTAAAACTGCATACAGCTTACTCATAGATGA
1 TCGTATTCCTTCTTAAAACTGCATACAGCTTACTCATAGATGA
1620602 TCGTATTCCTTCTTAAAACTGCATACAGCTTACTCATAG
1 TCGTATTCCTTCTTAAAACTGCATACAGCTTACTCATAG
1620641 TGAAGTTTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (43 bp):
TCGTATTCCTTCTTAAAACTGCATACAGCTTACTCATAGATGA
Found at i:1623487 original size:50 final size:51
Alignment explanation
Indices: 1623422--1623561 Score: 210
Period size: 51 Copynumber: 2.8 Consensus size: 51
1623412 CCCGGCAGGG
*
1623422 TGCCAACAGGGGCGCACATCACAAGCCCTTGGGCAAGCTGT-CCGACGGGA
1 TGCCAACAGGGGCGCACATCACAGGCCCTTGGGCAAGCTGTCCCGACGGGA
1623472 TGCCAACAGGGGCGCACATCACAGGCCCTTGGGCAAGCTGTCCCGACGGGA
1 TGCCAACAGGGGCGCACATCACAGGCCCTTGGGCAAGCTGTCCCGACGGGA
** * * * *
1623523 TGCCATTAGGGGCGTACAGCACAGGCCCCTGGGCGAGCT
1 TGCCAACAGGGGCGCACATCACAGGCCCTTGGGCAAGCT
1623562 AGCCCTACAG
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 40 0.49
51 42 0.51
ACGTcount: A:0.21, C:0.32, G:0.34, T:0.13
Consensus pattern (51 bp):
TGCCAACAGGGGCGCACATCACAGGCCCTTGGGCAAGCTGTCCCGACGGGA
Found at i:1623730 original size:70 final size:70
Alignment explanation
Indices: 1623651--1623837 Score: 218
Period size: 69 Copynumber: 2.7 Consensus size: 70
1623641 CCATGGTTAC
** * *
1623651 GCGGCACGCAGGCCCGGGGCCGCCGACCCAGCAAGGGTGCGTGGCACG-CAGGGACGCAGAGCAT
1 GCGGCACGCAGGCCCGGGGCCGCCGACCCAGCAAGGGTGCGCAGCACGTAAGGG-CGCACAGCAT
1623715 GGGCGCA
65 GGGCG-A
* * * * * *
1623722 -CGGTACGCAGGCCCAGGGCCTCCG-GCCAGCAGGGGTGCGCAGCACGTAAGTGCGCACAGCATG
1 GCGGCACGCAGGCCCGGGGCCGCCGACCCAGCAAGGGTGCGCAGCACGTAAGGGCGCACAGCATG
1623785 GGCGA
66 GGCGA
* * *
1623790 GCGGCACGCAGGCTCGGGGCCGCCGACCCAACAAGGGTGTGCAGCACG
1 GCGGCACGCAGGCCCGGGGCCGCCGACCCAGCAAGGGTGCGCAGCACG
1623838 CAAGTACGTG
Statistics
Matches: 95, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
68 1 0.01
69 52 0.55
70 42 0.44
ACGTcount: A:0.19, C:0.34, G:0.41, T:0.06
Consensus pattern (70 bp):
GCGGCACGCAGGCCCGGGGCCGCCGACCCAGCAAGGGTGCGCAGCACGTAAGGGCGCACAGCATG
GGCGA
Found at i:1624074 original size:33 final size:34
Alignment explanation
Indices: 1624019--1624086 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
1624009 ACCCATGTAG
*
1624019 TGAGCTGCTGGAAATTTCAGCTTTCCCTC-CAAA
1 TGAGCTGCTAGAAATTTCAGCTTTCCCTCTCAAA
*
1624052 TGAGCTTCTAGAAACTTT-AGCTTTCCCTCTCAAA
1 TGAGCTGCTAGAAA-TTTCAGCTTTCCCTCTCAAA
1624086 T
1 T
1624087 TTTTTGAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 23 0.74
34 8 0.26
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (34 bp):
TGAGCTGCTAGAAATTTCAGCTTTCCCTCTCAAA
Found at i:1624154 original size:13 final size:15
Alignment explanation
Indices: 1624083--1624150 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
1624073 TTTCCCTCTC
* * *
1624083 AAATTTTTTGAAGGG
1 AAATATTTTGGAGAG
* *
1624098 AAATCTTTTGGAGGG
1 AAATATTTTGGAGAG
**
1624113 AAATGCTTTGGAGAG
1 AAATATTTTGGAGAG
1624128 AAATATTTTGGAGAG
1 AAATATTTTGGAGAG
1624143 AAATATTT
1 AAATATTT
1624151 GAGAACCTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (15 bp):
AAATATTTTGGAGAG
Found at i:1628545 original size:3 final size:3
Alignment explanation
Indices: 1628539--1628573 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1628529 TCAAGAAGAA
* *
1628539 AAC AAC AAC AAC AAC AAC AAC AAT AAC AAG AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1628574 GTTTTTTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.69, C:0.26, G:0.03, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:1629970 original size:6 final size:6
Alignment explanation
Indices: 1629954--1629982 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1629944 AGAAAAGAGA
1629954 TTTTC- TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1629983 CAAAGGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:1631430 original size:18 final size:16
Alignment explanation
Indices: 1631396--1631437 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
1631386 TTAAAAATTA
1631396 ATATTAAATTTTTTAT
1 ATATTAAATTTTTTAT
*
1631412 ATTTTAATATTTATTTAT
1 ATATTAA-ATTT-TTTAT
1631430 ATATTAAA
1 ATATTAAA
1631438 CACTGTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 5 0.23
18 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTAAATTTTTTAT
Found at i:1636745 original size:19 final size:19
Alignment explanation
Indices: 1636723--1636781 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 19
1636713 AAATAATAAT
1636723 AATAATAATTAAAAATATA
1 AATAATAATTAAAAATATA
* *
1636742 AAT-A-AATTAAAAGT-TT
1 AATAATAATTAAAAATATA
*
1636758 AATATTAAATTAAAAAATATA
1 AATAAT-AATT-AAAAATATA
1636779 AAT
1 AAT
1636782 TTAGTATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 4 0.13
17 9 0.30
18 1 0.03
19 7 0.23
20 5 0.17
21 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AATAATAATTAAAAATATA
Found at i:1637436 original size:37 final size:36
Alignment explanation
Indices: 1637395--1637476 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
1637385 AAGTTTTGAC
*
1637395 TTTTTAATAAAATATTAAATTATAAAAATATTGTTAT
1 TTTTTAATAAAATATTAAATTATAAAAATA-TATTAT
* * *
1637432 TTTTTAAT--AATATTTAATTATTAATATATATTAT
1 TTTTTAATAAAATATTAAATTATAAAAATATATTAT
*
1637466 TTTTTCATAAA
1 TTTTTAATAAA
1637477 TCACTTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
34 12 0.32
35 17 0.45
36 1 0.03
37 8 0.21
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (36 bp):
TTTTTAATAAAATATTAAATTATAAAAATATATTAT
Found at i:1643623 original size:2 final size:2
Alignment explanation
Indices: 1643616--1643644 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1643606 ATAAACATAC
1643616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1643645 CACACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1645367 original size:25 final size:25
Alignment explanation
Indices: 1645339--1645387 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1645329 AAATGATATT
*
1645339 TTAATTGATAATAA-TTATTTAATTA
1 TTAATT-ATAAAAATTTATTTAATTA
1645364 TTAATTATAAAAATTTATTTAATT
1 TTAATTATAAAAATTTATTTAATT
1645388 TAAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TTAATTATAAAAATTTATTTAATTA
Found at i:1649052 original size:2 final size:2
Alignment explanation
Indices: 1649045--1649075 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1649035 TTTGAACATG
*
1649045 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1649076 ATAATGACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1652947 original size:3 final size:3
Alignment explanation
Indices: 1652939--1652981 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
1652929 AGTATCTTTG
1652939 CTT CTT CTT CTT CTT CTT CTT CTT -TT CTT CTTT CTT -TT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CT
1652982 CCTTTTCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
CTT
Found at i:1652956 original size:12 final size:11
Alignment explanation
Indices: 1652940--1652989 Score: 73
Period size: 12 Copynumber: 4.4 Consensus size: 11
1652930 GTATCTTTGC
1652940 TTCTTCTTCTT
1 TTCTTCTTCTT
1652951 CTTCTTCTTCTT
1 -TTCTTCTTCTT
1652963 TTCTTCTTTCTT
1 TTCTTC-TTCTT
*
1652975 TTCTTCTCCTT
1 TTCTTCTTCTT
1652986 TTCT
1 TTCT
1652990 ATTCTAAGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
11 14 0.39
12 22 0.61
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
TTCTTCTTCTT
Found at i:1652966 original size:20 final size:20
Alignment explanation
Indices: 1652943--1652981 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1652933 TCTTTGCTTC
1652943 TTCTTC-TTCTTCTTCTTCTT
1 TTCTTCTTTCTT-TTCTTCTT
1652963 TTCTTCTTTCTTTTCTTCT
1 TTCTTCTTTCTTTTCTTCT
1652982 CCTTTTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTTCTTTCTTTTCTTCTT
Found at i:1652966 original size:23 final size:23
Alignment explanation
Indices: 1652940--1652989 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1652930 GTATCTTTGC
*
1652940 TTCTTC-TTCTTCTTCTTCTTCTT
1 TTCTTCTTTCTT-TTCTTCTCCTT
1652963 TTCTTCTTTCTTTTCTTCTCCTT
1 TTCTTCTTTCTTTTCTTCTCCTT
1652986 TTCT
1 TTCT
1652990 ATTCTAAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCTTCTTTCTTTTCTTCTCCTT
Found at i:1653443 original size:3 final size:3
Alignment explanation
Indices: 1653435--1653463 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1653425 GCAAAGAGGA
1653435 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1653464 GTTTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1656187 original size:2 final size:2
Alignment explanation
Indices: 1656180--1656206 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1656170 TGCCAACCTG
1656180 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1656207 CACCAAGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1666472 original size:2 final size:2
Alignment explanation
Indices: 1666460--1666490 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1666450 GCTGTTGGTG
*
1666460 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1666491 GATCATTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1707385 original size:14 final size:14
Alignment explanation
Indices: 1707366--1707394 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1707356 CGTCTAGCTC
1707366 CTTTAATATAATCT
1 CTTTAATATAATCT
1707380 CTTTAATATAATCT
1 CTTTAATATAATCT
1707394 C
1 C
1707395 AATAGTCCCA
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:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (14 bp):
CTTTAATATAATCT
Found at i:1712693 original size:27 final size:27
Alignment explanation
Indices: 1712663--1712714 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1712653 TTATTTTATT
*
1712663 TTTAAAATATTAATAATTTATAATTTA
1 TTTAAAATATTAATAATTGATAATTTA
* *
1712690 TTTAAAATGTTAATCATTGATAATT
1 TTTAAAATATTAATAATTGATAATT
1712715 CAAATTTTAA
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:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (27 bp):
TTTAAAATATTAATAATTGATAATTTA
Found at i:1712813 original size:12 final size:12
Alignment explanation
Indices: 1712789--1712822 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1712779 TTATTTATAA
1712789 TTTAAATATTATT
1 TTTAAA-ATTATT
*
1712802 TTTTAAATTATT
1 TTTAAAATTATT
1712814 TTTAAAATT
1 TTTAAAATT
1712823 TAAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTAAAATTATT
Found at i:1712821 original size:26 final size:27
Alignment explanation
Indices: 1712758--1712835 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 27
1712748 GTAATCATTA
*
1712758 ATATTTTAAAATATTAATATTTTATTT
1 ATATTTTAAAATATTAATATTTTAATT
* *
1712785 ATAATTT-AAATATT-ATTTTTTAAATT
1 ATATTTTAAAATATTAATATTTT-AATT
* *
1712811 AT-TTTTAAAAT-TTAAAATATTAATT
1 ATATTTTAAAATATTAATATTTTAATT
1712836 TTTTACACTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
25 15 0.37
26 20 0.49
27 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATATTTTAAAATATTAATATTTTAATT
Found at i:1713687 original size:22 final size:22
Alignment explanation
Indices: 1713670--1713728 Score: 86
Period size: 21 Copynumber: 2.7 Consensus size: 22
1713660 TATATTATGA
*
1713670 GATTAGTTTTTAGGTATTGCGT
1 GATTAGTTTTTAGGTATTACGT
1713692 GATTAG-TTTTAGGTATTACGT
1 GATTAGTTTTTAGGTATTACGT
1713713 GATT-GATTTTTAGGTA
1 GATTAG-TTTTTAGGTA
1713729 ATGTCTAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.03
21 18 0.53
22 15 0.44
ACGTcount: A:0.22, C:0.03, G:0.25, T:0.49
Consensus pattern (22 bp):
GATTAGTTTTTAGGTATTACGT
Found at i:1713782 original size:23 final size:23
Alignment explanation
Indices: 1713739--1713806 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1713729 ATGTCTAAGT
**
1713739 CACAATACC-TAAAAACTAGTCA
1 CACAATACCTTATTAACTAGTCA
*
1713761 CGCAATACCTTATTAACTAGTCA
1 CACAATACCTTATTAACTAGTCA
** *
1713784 CACAATGTCTTATTAACCAGTCA
1 CACAATACCTTATTAACTAGTCA
1713807 TGTAATATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 8 0.21
23 30 0.79
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (23 bp):
CACAATACCTTATTAACTAGTCA
Found at i:1724756 original size:12 final size:12
Alignment explanation
Indices: 1724739--1724763 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1724729 GGTATGTGTC
1724739 ACAGAGAGAGAG
1 ACAGAGAGAGAG
1724751 ACAGAGAGAGAG
1 ACAGAGAGAGAG
1724763 A
1 A
1724764 GAAAAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.40, T:0.00
Consensus pattern (12 bp):
ACAGAGAGAGAG
Found at i:1736278 original size:2 final size:2
Alignment explanation
Indices: 1736271--1736296 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1736261 TTGGCATTGG
1736271 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1736297 TGTTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1736713 original size:33 final size:33
Alignment explanation
Indices: 1736649--1736715 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1736639 TATACCATAC
**
1736649 AATATTGACATAACATATTAACATACTATAATA
1 AATATTGACATAACATATTAACATAAAATAATA
* *
1736682 AATATTGACATAAGATATTAATATAAAATAATA
1 AATATTGACATAACATATTAACATAAAATAATA
1736715 A
1 A
1736716 CATTACTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (33 bp):
AATATTGACATAACATATTAACATAAAATAATA
Found at i:1736861 original size:31 final size:29
Alignment explanation
Indices: 1736826--1736902 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
1736816 AATATTAATT
1736826 TAAAAAATCTATTTAATTTAAAATAAAAATA
1 TAAAAAAT-TATTTAATTTAAAATAAAAA-A
* * *
1736857 TAAAAACTTAATTTAA--CATAATAAAAAA
1 TAAAAAATT-ATTTAATTTAAAATAAAAAA
*
1736885 TAAAAATTTATTTAATTT
1 TAAAAAATTATTTAATTT
1736903 TTTTTAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
27 6 0.16
28 9 0.24
29 9 0.24
30 1 0.03
31 13 0.34
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAAAAATTATTTAATTTAAAATAAAAAA
Found at i:1736869 original size:26 final size:25
Alignment explanation
Indices: 1736838--1736900 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
1736828 AAAAATCTAT
1736838 TTAATTTAA-AATAAAAATATAAAAA
1 TTAATTTAATAATAAAAA-ATAAAAA
1736863 CTTAATTTAACATAATAAAAAATAAAAA
1 -TTAATTT-A-ATAATAAAAAATAAAAA
*
1736891 TTTATTTAAT
1 TTAATTTAAT
1736901 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
25 2 0.06
26 8 0.24
27 7 0.21
28 8 0.24
29 8 0.24
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAATTTAATAATAAAAAATAAAAA
Found at i:1744528 original size:54 final size:53
Alignment explanation
Indices: 1744425--1744528 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 53
1744415 TTTTTATTTG
* *
1744425 ATATCAAATATGGTGATTTCTAAATCTCGATATTAATGATTACCAAGTAAAATT
1 ATATCAAATATGGTGATTTCTAAATCAC-ATAGTAATGATTACCAAGTAAAATT
1744479 ATATCAAATATGGTGATTT-TAAATCAC-TAGTAATGACATTACCATAGTAA
1 ATATCAAATATGGTGATTTCTAAATCACATAGTAATG--ATTACCA-AGTAA
1744529 TAAGATCACT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
51 7 0.16
53 14 0.31
54 24 0.53
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (53 bp):
ATATCAAATATGGTGATTTCTAAATCACATAGTAATGATTACCAAGTAAAATT
Found at i:1757949 original size:20 final size:20
Alignment explanation
Indices: 1757924--1757986 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
1757914 TTATGAATGG
*
1757924 ATATTTTTAATTTAAAAAAT
1 ATATTTTAAATTTAAAAAAT
**
1757944 ATA-TTTAAAAATAAAAAAT
1 ATATTTTAAATTTAAAAAAT
*
1757963 ATTATTTATAAATTTAAAATAT
1 A-TATTT-TAAATTTAAAAAAT
1757985 AT
1 AT
1757987 TTCGTCTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 14 0.41
20 5 0.15
21 3 0.09
22 12 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTTTAAATTTAAAAAAT
Found at i:1757960 original size:19 final size:19
Alignment explanation
Indices: 1757936--1757988 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
1757926 ATTTTTAATT
1757936 TAAAAAATATATTTAAAAA
1 TAAAAAATATATTTAAAAA
*
1757955 TAAAAAATATTATTTATAAA
1 TAAAAAATA-TATTTAAAAA
**
1757975 TTTAAAATATATTT
1 TAAAAAATATATTT
1757989 CGTCTTTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAAAATATATTTAAAAA
Found at i:1774932 original size:21 final size:21
Alignment explanation
Indices: 1774906--1774945 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1774896 TCAAACCCTG
1774906 AAAACATGACCACTCGTTTGT
1 AAAACATGACCACTCGTTTGT
1774927 AAAACATGACCACTCGTTT
1 AAAACATGACCACTCGTTT
1774946 ACGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (21 bp):
AAAACATGACCACTCGTTTGT
Found at i:1778321 original size:2 final size:2
Alignment explanation
Indices: 1778314--1778355 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1778304 CCCCATAGAA
1778314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1778356 GTATTAGCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1780352 original size:2 final size:2
Alignment explanation
Indices: 1780345--1780377 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1780335 NNNNNNNNNN
1780345 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
1780378 AAGCATATGT
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:1789422 original size:28 final size:29
Alignment explanation
Indices: 1789377--1789431 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1789367 ATTTAATAAT
* *
1789377 ATTTAAATAAATTTTTATTTTTTTATTAC
1 ATTTAAATAAATTCTTATATTTTTATTAC
*
1789406 ATTT-AATAAGTTCTTATATTTTTATT
1 ATTTAAATAAATTCTTATATTTTTATT
1789432 TCAAATCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (29 bp):
ATTTAAATAAATTCTTATATTTTTATTAC
Found at i:1798269 original size:2 final size:2
Alignment explanation
Indices: 1798262--1798288 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1798252 AAACATTGAT
1798262 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1798289 GAATGCTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1805915 original size:2 final size:2
Alignment explanation
Indices: 1805908--1805946 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1805898 ATCATGGAGA
1805908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1805947 CCATAAGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1810326 original size:2 final size:2
Alignment explanation
Indices: 1810321--1810350 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1810311 CACACACATT
1810321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1810351 AAATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1824769 original size:9 final size:9
Alignment explanation
Indices: 1824751--1824781 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1824741 CGTTAATGGT
1824751 TTATTGTTA
1 TTATTGTTA
*
1824760 TTATTATTA
1 TTATTGTTA
1824769 TTATTGTTA
1 TTATTGTTA
1824778 TTAT
1 TTAT
1824782 CAAACAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (9 bp):
TTATTGTTA
Found at i:1828146 original size:14 final size:14
Alignment explanation
Indices: 1828127--1828156 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1828117 ATCTTAAATT
1828127 ATAGTTTAATTATA
1 ATAGTTTAATTATA
*
1828141 ATAGTTTAATTTTA
1 ATAGTTTAATTATA
1828155 AT
1 AT
1828157 TAAACTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (14 bp):
ATAGTTTAATTATA
Found at i:1828721 original size:11 final size:11
Alignment explanation
Indices: 1828694--1828733 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
1828684 GTTTTATTAA
*
1828694 AAATATTTTTA
1 AAATATTTTTT
1828705 ATAATATTTTTT
1 A-AATATTTTTT
1828717 AAATATTTTTT
1 AAATATTTTTT
1828728 AAATAT
1 AAATAT
1828734 AATTTCGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
AAATATTTTTT
Found at i:1831691 original size:26 final size:25
Alignment explanation
Indices: 1831662--1831721 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
1831652 TCCTTTTTCC
* *
1831662 TTTTTTTTTTTAATTTTTGTTTTTT
1 TTTTTTTTTTTAATTTCTCTTTTTT
* *
1831687 GTTTTTTTTGTTCATTTCTCTTTTTT
1 -TTTTTTTTTTTAATTTCTCTTTTTT
*
1831713 TTCTTTTTT
1 TTTTTTTTT
1831722 CCTTTTCTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.83
Consensus pattern (25 bp):
TTTTTTTTTTTAATTTCTCTTTTTT
Found at i:1832387 original size:22 final size:22
Alignment explanation
Indices: 1832358--1832406 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1832348 TCCTCCATTC
* * *
1832358 ATTTTTTTTACTTTATTTTTTTT
1 ATTTTTTTAACCTT-TTTTTGTT
1832381 ATTTTTTTAACCTTTTTTTGTT
1 ATTTTTTTAACCTTTTTTTGTT
1832403 ATTT
1 ATTT
1832407 ACTGGATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (22 bp):
ATTTTTTTAACCTTTTTTTGTT
Found at i:1840521 original size:23 final size:19
Alignment explanation
Indices: 1840477--1840539 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
1840467 AAAGTTTATT
1840477 TAAA-ATATT-ATAATAA-A
1 TAAATATATTAAT-ATAATA
*
1840494 TAATATATTTTAATATTAATTA
1 TAA-ATATATTAATA-TAA-TA
1840516 TAAATATATTAATATAATA
1 TAAATATATTAATATAATA
1840535 TAAAT
1 TAAAT
1840540 TTTATTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 3 0.08
18 1 0.03
19 12 0.32
20 8 0.21
21 10 0.26
22 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATATATTAATATAATA
Found at i:1882953 original size:16 final size:17
Alignment explanation
Indices: 1882927--1882959 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1882917 TATAAACACG
1882927 ATATAATCATATTATTA
1 ATATAATCATATTATTA
1882944 ATAT-ATCATATTATTA
1 ATATAATCATATTATTA
1882960 TTCATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATAATCATATTATTA
Found at i:1893299 original size:17 final size:17
Alignment explanation
Indices: 1893269--1893302 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1893259 TATATTTTTA
1893269 TTTTAAATTAAATAAAT
1 TTTTAAATTAAATAAAT
1893286 TTTTATAATT-AATAAAT
1 TTTTA-AATTAAATAAAT
1893303 AATTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAATTAAATAAAT
Found at i:1906741 original size:17 final size:17
Alignment explanation
Indices: 1906700--1906731 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1906690 CCTGGATTGC
1906700 CCACCACC-CCACACCA
1 CCACCACCACCACACCA
1906716 CCACCACCACCACACC
1 CCACCACCACCACACC
1906732 CCCCCAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (17 bp):
CCACCACCACCACACCA
Found at i:1910689 original size:38 final size:38
Alignment explanation
Indices: 1910637--1910709 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
1910627 GTAATAATAA
* *
1910637 AAAACCATTTCTATTCCAGTTAATGTAACAATGCCTAC
1 AAAACCATTCCTATTCCAGTTAAGGTAACAATGCCTAC
1910675 AAAACCATTCCTATTCCAGTTAAGGTAACAATGCC
1 AAAACCATTCCTATTCCAGTTAAGGTAACAATGCC
1910710 ACTGTGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.29
Consensus pattern (38 bp):
AAAACCATTCCTATTCCAGTTAAGGTAACAATGCCTAC
Found at i:1917555 original size:2 final size:2
Alignment explanation
Indices: 1917548--1917581 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1917538 ACTCGAGCGC
* *
1917548 CT CT CT CT CT CT CT CT CT CT CT CT TT AT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1917582 GCATTTATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1923610 original size:16 final size:16
Alignment explanation
Indices: 1923585--1923615 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1923575 GACATGGTAG
1923585 CGGTGAGGAGAGAGAA
1 CGGTGAGGAGAGAGAA
*
1923601 CGGTGGGGAGAGAGA
1 CGGTGAGGAGAGAGA
1923616 GGAGACTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.55, T:0.06
Consensus pattern (16 bp):
CGGTGAGGAGAGAGAA
Found at i:1925171 original size:3 final size:3
Alignment explanation
Indices: 1925157--1925187 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1925147 TTAATGATTA
*
1925157 AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1925188 TAAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1952468 original size:21 final size:19
Alignment explanation
Indices: 1952427--1952470 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1952417 TCATAGGTTT
*
1952427 TATAATTTTATAATAATAA
1 TATAATTTTATAATAAAAA
*
1952446 TATAATTAATTATATTAAAAA
1 TATAATT--TTATAATAAAAA
1952467 TATA
1 TATA
1952471 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATAATTTTATAATAAAAA
Found at i:1953286 original size:30 final size:29
Alignment explanation
Indices: 1953250--1953349 Score: 112
Period size: 30 Copynumber: 3.4 Consensus size: 29
1953240 ATCGTTAATG
1953250 ATAAAAATTTATTTAACTTAAAATAAAAAT
1 ATAAAAATTTATTTAA-TTAAAATAAAAAT
* *
1953280 ATAAAAATTTATATGATTTAAAATAAAAAT
1 ATAAAAATTTAT-TTAATTAAAATAAAAAT
* * *
1953310 ATAATAATTTAATTAA-AAATAATAAAAAT
1 ATAAAAATTTATTTAATTAA-AATAAAAAT
*
1953339 ATAATAATTTA
1 ATAAAAATTTA
1953350 ATTATTATAC
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
28 2 0.03
29 22 0.36
30 35 0.57
31 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (29 bp):
ATAAAAATTTATTTAATTAAAATAAAAAT
Found at i:1953319 original size:21 final size:21
Alignment explanation
Indices: 1953280--1953330 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1953270 AAATAAAAAT
* *
1953280 ATAAAAATTTATATGATTTAAA
1 ATAAAAATATATATAATTT-AA
1953302 ATAAAAATATA-ATAATTTAA
1 ATAAAAATATATATAATTTAA
*
1953322 TTAAAAATA
1 ATAAAAATA
1953331 ATAAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 10 0.38
21 6 0.23
22 10 0.38
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAAAAATATATATAATTTAA
Found at i:1953334 original size:21 final size:20
Alignment explanation
Indices: 1953303--1953343 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1953293 TGATTTAAAA
* *
1953303 TAAAAATATAATAATTTAAT
1 TAAAAATATAAAAATATAAT
1953323 TAAAAATAATAAAAATATAAT
1 TAAAAAT-ATAAAAATATAAT
1953344 AATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAATATAAAAATATAAT
Found at i:1954284 original size:21 final size:21
Alignment explanation
Indices: 1954260--1954299 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1954250 TATATACGGT
*
1954260 TAAATTTTTATGAATTAATAA
1 TAAAATTTTATGAATTAATAA
*
1954281 TAAAATTTTATTAATTAAT
1 TAAAATTTTATGAATTAAT
1954300 TAAGATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TAAAATTTTATGAATTAATAA
Found at i:1959980 original size:18 final size:20
Alignment explanation
Indices: 1959957--1959995 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1959947 GAGAATAAGT
*
1959957 TCAGATT-T-TATATCAGAA
1 TCAGATTATCTATAACAGAA
1959975 TCAGATTATCTATAACAGAA
1 TCAGATTATCTATAACAGAA
1959995 T
1 T
1959996 GCAATATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (20 bp):
TCAGATTATCTATAACAGAA
Found at i:1962889 original size:11 final size:11
Alignment explanation
Indices: 1962873--1962898 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1962863 AGAACATTTC
1962873 ATAATTTTATA
1 ATAATTTTATA
1962884 ATAATTTTATA
1 ATAATTTTATA
1962895 ATAA
1 ATAA
1962899 ATTATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATAATTTTATA
Found at i:1963002 original size:39 final size:39
Alignment explanation
Indices: 1962958--1963043 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
1962948 TTCTCTCATC
1962958 CTTAATAAATATCTATTTTTCTCATTATTTATCTCATTT
1 CTTAATAAATATCTATTTTTCTCATTATTTATCTCATTT
1962997 CTTAATAAATATCTATTTTTCTCATTATTTATCTCATTT
1 CTTAATAAATATCTATTTTTCTCATTATTTATCTCATTT
1963036 CTT-ATAAA
1 CTTAATAAA
1963044 AAATAGGTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 5 0.11
39 42 0.89
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (39 bp):
CTTAATAAATATCTATTTTTCTCATTATTTATCTCATTT
Found at i:1963029 original size:20 final size:21
Alignment explanation
Indices: 1962967--1963035 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 21
1962957 CCTTAATAAA
1962967 TATCT-ATTTTTCTCATTATT
1 TATCTCATTTTTCTCATTATT
* * **
1962987 TATCTCA--TTTCTTAATAAA
1 TATCTCATTTTTCTCATTATT
1963006 TATCT-ATTTTTCTCATTATT
1 TATCTCATTTTTCTCATTATT
1963026 TATCTCATTT
1 TATCTCATTT
1963036 CTTATAAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
18 1 0.03
19 13 0.35
20 18 0.49
21 5 0.14
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (21 bp):
TATCTCATTTTTCTCATTATT
Found at i:1963423 original size:11 final size:11
Alignment explanation
Indices: 1963407--1963437 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1963397 AAGTTAAAAG
1963407 AATAAAATTTT
1 AATAAAATTTT
1963418 AATAAAATTTT
1 AATAAAATTTT
*
1963429 ATTAAAATT
1 AATAAAATT
1963438 CCTCATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AATAAAATTTT
Found at i:1967942 original size:7 final size:7
Alignment explanation
Indices: 1967930--1967956 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1967920 TTTCACTCGC
1967930 TTTCCAT
1 TTTCCAT
1967937 TTTCCAT
1 TTTCCAT
1967944 TTTCCAT
1 TTTCCAT
1967951 TTTCCA
1 TTTCCA
1967957 ACGCAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTCCAT
Found at i:1981141 original size:9 final size:9
Alignment explanation
Indices: 1981127--1981151 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1981117 GAAGATCAAT
1981127 ATGTTTAAC
1 ATGTTTAAC
1981136 ATGTTTAAC
1 ATGTTTAAC
1981145 ATGTTTA
1 ATGTTTA
1981152 TGTTTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (9 bp):
ATGTTTAAC
Found at i:1991240 original size:57 final size:57
Alignment explanation
Indices: 1991176--1991295 Score: 161
Period size: 57 Copynumber: 2.1 Consensus size: 57
1991166 TGTTGATTCA
* * * *
1991176 GACTCCCGGGGGCTAACCAGCTTCTTCTCAGGAATTTCAAGCTTAGTCATGACTGAT
1 GACTCCCGAGGACTAACCAACTTCTTCTCAAGAATTTCAAGCTTAGTCATGACTGAT
** * *
1991233 GACTCCCGAGGACTAACCAACTTCTTCTCAAGAATTTCGGGCTTTGTCATGGCTGAT
1 GACTCCCGAGGACTAACCAACTTCTTCTCAAGAATTTCAAGCTTAGTCATGACTGAT
1991290 G-CTCCC
1 GACTCCC
1991296 ATGCGAGCTC
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
56 5 0.09
57 50 0.91
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (57 bp):
GACTCCCGAGGACTAACCAACTTCTTCTCAAGAATTTCAAGCTTAGTCATGACTGAT
Found at i:1996137 original size:20 final size:21
Alignment explanation
Indices: 1996096--1996137 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1996086 TTTAAATTAA
*
1996096 TAATATCAATCTATTTTCTTT
1 TAATATCAATCTATTATCTTT
1996117 TAATAT-AATCTAATTAT-TTT
1 TAATATCAATCT-ATTATCTTT
1996137 T
1 T
1996138 CATTTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATCAATCTATTATCTTT
Found at i:2005778 original size:30 final size:27
Alignment explanation
Indices: 2005711--2005778 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
2005701 TTTAAAAATT
* *
2005711 TTAAATAAATTTTTATTTTTTATTACA
1 TTAAATAAATCTTTATTTTTTATTAAA
*
2005738 TTCAATTAAATCTTTATATTTTTATTTCAAA
1 TT-AAATAAATCTTTAT-TTTTTA-TT-AAA
2005769 TTAAATAAAT
1 TTAAATAAAT
2005779 TCTTACGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 2 0.06
28 12 0.36
29 6 0.18
30 9 0.27
31 4 0.12
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAAATAAATCTTTATTTTTTATTAAA
Found at i:2006682 original size:15 final size:15
Alignment explanation
Indices: 2006659--2006689 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2006649 CATAATTTTT
2006659 TATAAATGAAAAAAA
1 TATAAATGAAAAAAA
*
2006674 TATATATGAAAAAAA
1 TATAAATGAAAAAAA
2006689 T
1 T
2006690 CCTTTTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
TATAAATGAAAAAAA
Found at i:2044619 original size:30 final size:31
Alignment explanation
Indices: 2044559--2044619 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2044549 ATGAAAGGAG
*
2044559 TTTTTTTTAAAAATTATGTCAATTTTTTAAA
1 TTTTTTTTAAAAATTATGTCAATTTATTAAA
*
2044590 TTTTTTTTAAAAA-TGTGCTC-ATTTATTAAA
1 TTTTTTTTAAAAATTATG-TCAATTTATTAAA
2044620 AATAATCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (31 bp):
TTTTTTTTAAAAATTATGTCAATTTATTAAA
Found at i:2044741 original size:13 final size:14
Alignment explanation
Indices: 2044725--2044757 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2044715 TAAATAATTT
*
2044725 ATTTATTAAAA-AA
1 ATTTATAAAAATAA
2044738 ATTTATAAAAATAA
1 ATTTATAAAAATAA
2044752 ATTTAT
1 ATTTAT
2044758 CATACAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTTATAAAAATAA
Found at i:2047767 original size:16 final size:16
Alignment explanation
Indices: 2047734--2047764 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2047724 ATTAATTTTT
2047734 TATATTTTAATTATAA
1 TATATTTTAATTATAA
2047750 TATA-TTTAATTATAA
1 TATATTTTAATTATAA
2047765 ATAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTTTAATTATAA
Found at i:2047793 original size:49 final size:49
Alignment explanation
Indices: 2047698--2047793 Score: 108
Period size: 49 Copynumber: 2.0 Consensus size: 49
2047688 TTTATAAAAT
* * *
2047698 TAATATTTTAAATTAAAAATTAAAAAATTAATTTTTTATATTTTAATTA
1 TAATATTTTAAATTAAAAATTAAAAAATTAATTTTTAAAATATTAATTA
*
2047747 TAATATATTT-AATTATAAA-TAAAATAA-TAATATTTTAAAATATTAAT
1 TAATAT-TTTAAATTAAAAATTAAAA-AATTAAT-TTTTAAAATATTAAT
2047794 CTTTAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
48 9 0.22
49 28 0.70
50 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (49 bp):
TAATATTTTAAATTAAAAATTAAAAAATTAATTTTTAAAATATTAATTA
Found at i:2047800 original size:15 final size:16
Alignment explanation
Indices: 2047766--2047807 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2047756 TAATTATAAA
* *
2047766 TAAAATAATAATATTT
1 TAAAATATTAATACTT
2047782 TAAAATATTAAT-CTT
1 TAAAATATTAATACTT
*
2047797 TAAATTATTAA
1 TAAAATATTAA
2047808 GTGAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATATTAATACTT
Found at i:2047967 original size:17 final size:17
Alignment explanation
Indices: 2047934--2047967 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2047924 TTAAAAGTAT
*
2047934 TAATATTTTAATCATAA
1 TAATATTTAAATCATAA
*
2047951 TAATATTTAAATTATAA
1 TAATATTTAAATCATAA
2047968 ATTAAATTAC
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTAAATCATAA
Found at i:2048075 original size:24 final size:24
Alignment explanation
Indices: 2048017--2048083 Score: 84
Period size: 22 Copynumber: 2.9 Consensus size: 24
2048007 TAAATTATAA
* * *
2048017 ATAAAATATTAATACTTAAATAAT
1 ATAAATTATTAATATTTAAAAAAT
*
2048041 CT--ATTATTAATATTTAAAAAAT
1 ATAAATTATTAATATTTAAAAAAT
2048063 ATAAATTATTAATATTTAAAA
1 ATAAATTATTAATATTTAAAA
2048084 GATCAAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 18 0.50
24 18 0.50
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (24 bp):
ATAAATTATTAATATTTAAAAAAT
Found at i:2048179 original size:156 final size:163
Alignment explanation
Indices: 2047942--2048242 Score: 404
Period size: 156 Copynumber: 1.9 Consensus size: 163
2047932 ATTAATATTT
* *
2047942 TAATCATAATAATATTTAAATTATAAATTAAATTACCAATTATAGTATTTTATAATATTAATTAT
1 TAATCATAATAACATTTAAATTATAAATTAAATT---AATTATA-TATTTTATAATATTAATCAT
* * *
2048007 TAAATTATAAATAAAATATTAATACTTAA-ATAATCTATTATT-AATA-TTTAAA-AAA-TATAA
62 TAAAGTATAAACAAAATATTAATACTTAAGAT-ATCAATT-TTGAATATTTTAAATAAATTATAA
*
2048067 ATTATTAATATTTAAAAGATCAAATTAAATAAAAATAAA
125 ATTATAAATATTTAAAAGATCAAATTAAATAAAAATAAA
2048106 TAATCATAATAACATTTAAATTATAAATTAAA-T-ATTAT-TATTTT-TAATATTAATCATTAAA
1 TAATCATAATAACATTTAAATTATAAATTAAATTAATTATATATTTTATAATATTAATCATTAAA
* * *
2048167 GTATAAACAAAATATTAATATTTAAGCTATCAATTTTGAATATTTTAAATAAATTGTAAATTATA
66 GTATAAACAAAATATTAATACTTAAGATATCAATTTTGAATATTTTAAATAAATTATAAATTATA
2048232 AATATTTAAAA
131 AATATTTAAAA
2048243 ATAAAAAAAC
Statistics
Matches: 123, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
155 2 0.02
156 48 0.39
157 13 0.11
158 3 0.02
159 25 0.20
163 1 0.01
164 31 0.25
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (163 bp):
TAATCATAATAACATTTAAATTATAAATTAAATTAATTATATATTTTATAATATTAATCATTAAA
GTATAAACAAAATATTAATACTTAAGATATCAATTTTGAATATTTTAAATAAATTATAAATTATA
AATATTTAAAAGATCAAATTAAATAAAAATAAA
Found at i:2048330 original size:20 final size:20
Alignment explanation
Indices: 2048263--2048344 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 20
2048253 ATAATAACAT
2048263 TTAA-ATTATAAATAAAATA
1 TTAATATTATAAATAAAATA
* * **
2048282 TTAGTATTTTATAATGTTAATGA
1 TTAATATTATA-AAT-AAAAT-A
2048305 TT-ATATTATAAATAAAATA
1 TTAATATTATAAATAAAATA
*
2048324 TTAATATTTAAAAATAAAATA
1 TTAATA-TTATAAATAAAATA
2048345 AAATAATTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
19 6 0.12
20 11 0.23
21 19 0.40
22 9 0.19
23 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (20 bp):
TTAATATTATAAATAAAATA
Found at i:2048380 original size:142 final size:142
Alignment explanation
Indices: 2048096--2048367 Score: 325
Period size: 142 Copynumber: 1.9 Consensus size: 142
2048086 TCAAATTAAA
* * * *
2048096 TAAAAATAAATAATCATAATAACATTTAAATTATAAATTAAATATTATTATTTTTAATATTAATC
1 TAAAAATAAAAAAACATAATAACATTTAAATTATAAATAAAATATTAGTATTTTTAATATTAATC
** ** ** * **
2048161 ATTAAAGTATAAACAAAATATTAATATTTAAGCTATCAATTTTGAATATTTTAAATAAATTGTAA
66 ATTAAAGTATAAACAAAATATTAATATTTAAGAAATCAAAATAAAATATATTAAATAAATAATAA
*
2048226 ATTATAAATATT
131 AGTATAAATATT
*
2048238 TAAAAATAAAAAAACATAATAACATTTAAATTATAAATAAAATATTAGTATTTTATAATGTTAAT
1 TAAAAATAAAAAAACATAATAACATTTAAATTATAAATAAAATATTAGTATTTT-TAATATTAAT
* * * * * *
2048303 GATTATATTATAAATAAAATATTAATATTTAA-AAAT-AAAATAAAATA-ATTAATTATATAATA
65 CATTAAAGTATAAACAAAATATTAATATTTAAGAAATCAAAATAAAATATATTAAATAAATAATA
2048365 AAG
130 AAG
2048368 GGTAGTTTTA
Statistics
Matches: 108, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
140 12 0.11
141 7 0.06
142 52 0.48
143 37 0.34
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (142 bp):
TAAAAATAAAAAAACATAATAACATTTAAATTATAAATAAAATATTAGTATTTTTAATATTAATC
ATTAAAGTATAAACAAAATATTAATATTTAAGAAATCAAAATAAAATATATTAAATAAATAATAA
AGTATAAATATT
Found at i:2050093 original size:21 final size:22
Alignment explanation
Indices: 2050069--2050125 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
2050059 TTCCTCTTTG
2050069 TCTTTTCTTTCTTTCTGTC-AC
1 TCTTTTCTTTCTTTCTGTCTAC
* * *
2050090 TCTTTTCTTTTTTTCTTTCTTC
1 TCTTTTCTTTCTTTCTGTCTAC
*
2050112 TCTTTTCGTTCTTT
1 TCTTTTCTTTCTTT
2050126 TCCTTGTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.02, C:0.25, G:0.04, T:0.70
Consensus pattern (22 bp):
TCTTTTCTTTCTTTCTGTCTAC
Found at i:2050135 original size:23 final size:22
Alignment explanation
Indices: 2050089--2050135 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
2050079 CTTTCTGTCA
* *
2050089 CTCTTTTCTTTTTTTCTTTCTT
1 CTCTTTTCTTCTTTTCCTTCTT
*
2050111 CTCTTTTCGTTCTTTTCCTTGTT
1 CTCTTTTC-TTCTTTTCCTTCTT
2050134 CT
1 CT
2050136 TGCATTTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.00, C:0.26, G:0.04, T:0.70
Consensus pattern (22 bp):
CTCTTTTCTTCTTTTCCTTCTT
Found at i:2056898 original size:2 final size:2
Alignment explanation
Indices: 2056891--2056927 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2056881 ATTTCCCAAT
2056891 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2056928 CTAAGATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2067356 original size:30 final size:30
Alignment explanation
Indices: 2067312--2067434 Score: 155
Period size: 30 Copynumber: 4.1 Consensus size: 30
2067302 TTTATTACAT
2067312 TAAAC-CTTTATATTTTTATTTTAAA-CTAAA
1 TAAACTCTTT-TATTTTTATTTTAAATC-AAA
2067342 TAAACTCTTTTATTTTTATTTTAAATCAAA
1 TAAACTCTTTTATTTTTATTTTAAATCAAA
** *
2067372 TAAACTCTTAAATTTTTATTTTAAATTAAA
1 TAAACTCTTTTATTTTTATTTTAAATCAAA
2067402 TAAA-T-TTTTATTTTTTTATTTTAAATCAAA
1 TAAACTCTTTTA--TTTTTATTTTAAATCAAA
2067432 TAA
1 TAA
2067435 GTCTTTATGA
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
28 3 0.04
29 1 0.01
30 74 0.89
31 5 0.06
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (30 bp):
TAAACTCTTTTATTTTTATTTTAAATCAAA
Found at i:2100504 original size:24 final size:24
Alignment explanation
Indices: 2100477--2100527 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2100467 ATGAATTAAA
* * *
2100477 TATTTAGGTATTACTTAAATTATT
1 TATTTAAGTATTAATTAAATAATT
*
2100501 TATTTAATTATTAATTAAATAATT
1 TATTTAAGTATTAATTAAATAATT
2100525 TAT
1 TAT
2100528 AACTTGCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (24 bp):
TATTTAAGTATTAATTAAATAATT
Found at i:2119395 original size:12 final size:12
Alignment explanation
Indices: 2119374--2119411 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2119364 AGCTAAGGAA
*
2119374 GAGAAGAAAGAT
1 GAGAAAAAAGAT
2119386 GAGAAAAAAGAT
1 GAGAAAAAAGAT
2119398 GA-AAATAAAGAT
1 GAGAAA-AAAGAT
2119410 GA
1 GA
2119412 AAAGAACTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (12 bp):
GAGAAAAAAGAT
Found at i:2119412 original size:12 final size:11
Alignment explanation
Indices: 2119380--2119414 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
2119370 GGAAGAGAAG
2119380 AAAGATGAGAAA
1 AAAGATGA-AAA
2119392 AAAGATGAAAA
1 AAAGATGAAAA
2119403 TAAAGATGAAAA
1 -AAAGATGAAAA
2119415 GAACTAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 3 0.14
12 19 0.86
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (11 bp):
AAAGATGAAAA
Found at i:2122380 original size:24 final size:24
Alignment explanation
Indices: 2122348--2122394 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2122338 CAAAAGGGTC
2122348 GATCTTTGCTGAGTTAAACAACCT
1 GATCTTTGCTGAGTTAAACAACCT
2122372 GATCTTTGCTGAGTTAAACAACC
1 GATCTTTGCTGAGTTAAACAACC
2122395 CTGTTTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (24 bp):
GATCTTTGCTGAGTTAAACAACCT
Found at i:2123703 original size:2 final size:2
Alignment explanation
Indices: 2123698--2123728 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2123688 TACAAGTGTG
2123698 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2123729 GAACCTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.