Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold114
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: 3219552
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 36736 characters in sequence are not A, C, G, or T
File 5 of 13
Found at i:1089682 original size:21 final size:21
Alignment explanation
Indices: 1089656--1089696 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1089646 TAAATAATGA
1089656 AAAAAATATTTTTAAATTAAT
1 AAAAAATATTTTTAAATTAAT
1089677 AAAAAATATTTTTAAATTAA
1 AAAAAATATTTTTAAATTAA
1089697 ATCAATAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAAATATTTTTAAATTAAT
Found at i:1091210 original size:10 final size:10
Alignment explanation
Indices: 1091195--1091228 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
1091185 AAAAGATGAT
1091195 ATAATTGCAA
1 ATAATTGCAA
1091205 ATAATTGCAA
1 ATAATTGCAA
1091215 TATAATTGCAA
1 -ATAATTGCAA
1091226 ATA
1 ATA
1091229 GGAATCACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (10 bp):
ATAATTGCAA
Found at i:1091221 original size:11 final size:11
Alignment explanation
Indices: 1091193--1091225 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
1091183 AAAAAAGATG
1091193 ATATAATTGCA
1 ATATAATTGCA
1091204 A-ATAATTGCA
1 ATATAATTGCA
1091214 ATATAATTGCA
1 ATATAATTGCA
1091225 A
1 A
1091226 ATAGGAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.33
Consensus pattern (11 bp):
ATATAATTGCA
Found at i:1095570 original size:13 final size:13
Alignment explanation
Indices: 1095552--1095584 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1095542 ATCAGTTGAA
1095552 AAGTTCCCTTTGC
1 AAGTTCCCTTTGC
1095565 AAGTTCCCTTTGC
1 AAGTTCCCTTTGC
1095578 AAGTTCC
1 AAGTTCC
1095585 TACATCCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.30, G:0.15, T:0.36
Consensus pattern (13 bp):
AAGTTCCCTTTGC
Found at i:1111134 original size:14 final size:14
Alignment explanation
Indices: 1111115--1111142 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1111105 AAGCTCCTAC
1111115 TTCCCATCTAATGA
1 TTCCCATCTAATGA
1111129 TTCCCATCTAATGA
1 TTCCCATCTAATGA
1111143 CTTAATCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
TTCCCATCTAATGA
Found at i:1122805 original size:21 final size:21
Alignment explanation
Indices: 1122781--1122851 Score: 54
Period size: 22 Copynumber: 3.3 Consensus size: 21
1122771 CATTAGTAAC
1122781 TTTCTCCAGAACATTTCCTCA
1 TTTCTCCAGAACATTTCCTCA
* ** * *
1122802 TTTCT-CAGCCAAAAACTGCTAA
1 TTTCTCCAG--AACATTTCCTCA
*
1122824 CTTTCTCCAGAACATTTCCTCC
1 -TTTCTCCAGAACATTTCCTCA
1122846 TTTCTC
1 TTTCTC
1122852 AGCCAAAAAC
Statistics
Matches: 35, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
20 3 0.09
21 11 0.31
22 13 0.37
23 5 0.14
24 3 0.09
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.37
Consensus pattern (21 bp):
TTTCTCCAGAACATTTCCTCA
Found at i:1122840 original size:44 final size:44
Alignment explanation
Indices: 1122777--1122864 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
1122767 TTTTCATTAG
1122777 TAACTTTCTCCAGAACATTTCCTCATTTCTCAGCCAAAAACTGC
1 TAACTTTCTCCAGAACATTTCCTCATTTCTCAGCCAAAAACTGC
*
1122821 TAACTTTCTCCAGAACATTTCCTCCTTTCTCAGCCAAAAACTGC
1 TAACTTTCTCCAGAACATTTCCTCATTTCTCAGCCAAAAACTGC
1122865 ATAGAAAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.32
Consensus pattern (44 bp):
TAACTTTCTCCAGAACATTTCCTCATTTCTCAGCCAAAAACTGC
Found at i:1126245 original size:104 final size:103
Alignment explanation
Indices: 1126112--1126320 Score: 337
Period size: 104 Copynumber: 2.0 Consensus size: 103
1126102 ACTCTTTCAC
* *
1126112 CAGTTTCCGATTTAGTACTAGTACAAGTCAACCGCCTTCTACATCCAACTGTTAAAAAAATGTTC
1 CAGTTTCCGATTTAGTACTAGTACAAGTCAACCGCCATCTACACCCAACTGTT-AAAAAATGTTC
* *
1126177 TCCACAAAACAAGATACACATAAGGCAAAACGCAAAAGT
65 TCCACAAAACAAGATACACACAAGGCAAAACACAAAAGT
*
1126216 CAGTTTCCGATTTAGTACTAGTACTAGTCAACCGCCATCTACACCCAACTGTTAAAAAATGTTCT
1 CAGTTTCCGATTTAGTACTAGTACAAGTCAACCGCCATCTACACCCAACTGTTAAAAAATGTTCT
* * *
1126281 CCATAAATCAAGATACACACAAGGCAAAACACAGAAGT
66 CCACAAAACAAGATACACACAAGGCAAAACACAAAAGT
1126319 CA
1 CA
1126321 AGAATGCTAA
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
103 47 0.48
104 50 0.52
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (103 bp):
CAGTTTCCGATTTAGTACTAGTACAAGTCAACCGCCATCTACACCCAACTGTTAAAAAATGTTCT
CCACAAAACAAGATACACACAAGGCAAAACACAAAAGT
Found at i:1126902 original size:6 final size:6
Alignment explanation
Indices: 1126886--1126914 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1126876 GGAGTGTAGT
1126886 GGAGT- GGAGTG GGAGTG GGAGTG GGAGTG
1 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG
1126915 CGACGAAAGT
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:0.17, C:0.00, G:0.66, T:0.17
Consensus pattern (6 bp):
GGAGTG
Found at i:1135073 original size:21 final size:21
Alignment explanation
Indices: 1135025--1135074 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
1135015 AGACTACTGG
* *
1135025 ATTAAACTTTGTCAAATATAA
1 ATTAAAATTTGTCAAAAATAA
*
1135046 ATT--AATTTGTTAAAAATAA
1 ATTAAAATTTGTCAAAAATAA
1135065 ATTAAAATTT
1 ATTAAAATTT
1135075 TTATCAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 16 0.67
21 8 0.33
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (21 bp):
ATTAAAATTTGTCAAAAATAA
Found at i:1139660 original size:2 final size:2
Alignment explanation
Indices: 1139645--1139684 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1139635 ACTTACTTAC
* *
1139645 AT AT AT AC AA AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1139685 ATTTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1139901 original size:17 final size:15
Alignment explanation
Indices: 1139880--1139923 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1139870 TTTTTATATA
*
1139880 AATATAATTTTTAATT
1 AATAT-ATTTTAAATT
1139896 ATATATATTTTAAATT
1 A-ATATATTTTAAATT
1139912 AATAT-TTTTAAA
1 AATATATTTTAAA
1139924 AATATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.27
15 4 0.15
16 11 0.42
17 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATATTTTAAATT
Found at i:1139916 original size:13 final size:14
Alignment explanation
Indices: 1139878--1139931 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
1139868 ATTTTTTATA
1139878 TAAATATAAT-TTT
1 TAAATATAATATTT
*
1139891 TAATTATATATATTT
1 TAAATATA-ATATTT
1139906 TAAAT-TAATATTT
1 TAAATATAATATTT
*
1139919 TTAA-A-AATATTT
1 TAAATATAATATTT
1139931 T
1 T
1139932 TTATTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
12 8 0.23
13 16 0.46
14 4 0.11
15 7 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAAATATAATATTT
Found at i:1139929 original size:12 final size:13
Alignment explanation
Indices: 1139886--1139932 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 13
1139876 TATAAATATA
*
1139886 ATTTTTAATTATAT
1 ATTTTTAAATA-AT
1139900 ATATTTTAAATTAAT
1 AT-TTTTAAA-TAAT
1139915 ATTTTTAAA-AAT
1 ATTTTTAAATAAT
1139927 ATTTTT
1 ATTTTT
1139933 TATTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 9 0.30
14 9 0.30
15 10 0.33
16 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTTTAAATAAT
Found at i:1139932 original size:13 final size:14
Alignment explanation
Indices: 1139867--1139934 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 14
1139857 TAATTATTTT
*
1139867 TATTTTTTATATAAA
1 TATTTTTTAAAT-AA
*
1139882 TATAATTTTTAATTATA
1 TAT--TTTTTAAATA-A
*
1139899 TATATTTTAAATTAA
1 TATTTTTTAAA-TAA
1139914 TA-TTTTTAAA-AA
1 TATTTTTTAAATAA
1139926 TATTTTTTA
1 TATTTTTTA
1139935 TTTTTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
12 4 0.09
13 6 0.14
14 7 0.16
15 12 0.28
16 3 0.07
17 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTTTAAATAA
Found at i:1143278 original size:32 final size:32
Alignment explanation
Indices: 1143266--1143328 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1143256 ATATTCTGTT
*
1143266 TCTTAATATTTTTGTATATACATATATTCATA
1 TCTTAATATTTTTATATATACATATATTCATA
* * *
1143298 TCTTAATATTTTTTTATACACATGTATTCAT
1 TCTTAATATTTTTATATATACATATATTCAT
1143329 TAAAAATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.54
Consensus pattern (32 bp):
TCTTAATATTTTTATATATACATATATTCATA
Found at i:1150264 original size:11 final size:11
Alignment explanation
Indices: 1150209--1150287 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 11
1150199 ATTACACATT
1150209 AAAATTTAAAA
1 AAAATTTAAAA
* *
1150220 AAAAATCAAAA
1 AAAATTTAAAA
1150231 AAAATATT--AA
1 AAAAT-TTAAAA
*
1150241 AAAA--TAGATA
1 AAAATTTA-AAA
* *
1150251 AAAGTTGAAAA
1 AAAATTTAAAA
1150262 AAAATTTAAAA
1 AAAATTTAAAA
*
1150273 AAATTTTAAAA
1 AAAATTTAAAA
1150284 AAAA
1 AAAA
1150288 ATTACCTCAG
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
7 1 0.02
10 10 0.20
11 37 0.74
12 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:1152441 original size:102 final size:105
Alignment explanation
Indices: 1152256--1152453 Score: 285
Period size: 102 Copynumber: 1.9 Consensus size: 105
1152246 AGAAAGTATG
* * * *
1152256 AATATATTGCAACCAAACATATTTGAGATAAATGCTAGTCATTATCTTGCAGGAAATAGAATAAG
1 AATATATTGCAACCAAACATATTTGAGAGAAA-GCTAGACATTATCTTCCAGGAAATAAAATAAG
* **
1152321 CTAAGATACCAATGGACTATTTTAACCAAAACATCTGAAGA
65 CTAAGACACCAACAGACTATTTTAACCAAAACATCTGAAGA
* *
1152362 AATATTTTGCAACCAAACATATTT-A-AGACA-CTAGACATTATCTTCCAGGAAATAAAATAAGC
1 AATATATTGCAACCAAACATATTTGAGAGAAAGCTAGACATTATCTTCCAGGAAATAAAATAAGC
1152424 TAAGACACCAACAGACTATTTTAACCAAAA
66 TAAGACACCAACAGACTATTTTAACCAAAA
1152454 TATACAGACC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
102 56 0.67
104 3 0.04
105 1 0.01
106 23 0.28
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (105 bp):
AATATATTGCAACCAAACATATTTGAGAGAAAGCTAGACATTATCTTCCAGGAAATAAAATAAGC
TAAGACACCAACAGACTATTTTAACCAAAACATCTGAAGA
Found at i:1158186 original size:20 final size:20
Alignment explanation
Indices: 1158161--1158212 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1158151 ATATTTAAAT
* * *
1158161 TTTTTATTATATTATTTTTA
1 TTTTTATTATATGAGTTATA
*
1158181 TTTTTATTAAATGAGTTATA
1 TTTTTATTATATGAGTTATA
1158201 TTTTTA-TATATG
1 TTTTTATTATATG
1158213 TTTATTAGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (20 bp):
TTTTTATTATATGAGTTATA
Found at i:1158606 original size:23 final size:23
Alignment explanation
Indices: 1158578--1158625 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1158568 TGTTTATATC
1158578 ATATTTTATTATATTATAATTAT
1 ATATTTTATTATATTATAATTAT
1158601 ATATTTTATTATATTATAATTAT
1 ATATTTTATTATATTATAATTAT
1158624 AT
1 AT
1158626 TTAAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATTTTATTATATTATAATTAT
Found at i:1158609 original size:20 final size:19
Alignment explanation
Indices: 1158586--1158676 Score: 67
Period size: 16 Copynumber: 5.2 Consensus size: 19
1158576 TCATATTTTA
1158586 TTATATTATAATTATATAT
1 TTATATTATAATTATATAT
1158605 TT-TATTAT-ATTATA-A-
1 TTATATTATAATTATATAT
*
1158620 TTATATT-TAA-AATAT-T
1 TTATATTATAATTATATAT
*
1158636 TTATATT-TATATTATATTT
1 TTATATTATA-ATTATATAT
1158655 TTATGTATTAT-ATTATAT-T
1 TTA--TATTATAATTATATAT
1158674 TTA
1 TTA
1158677 ATTTTTTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
15 6 0.10
16 15 0.25
17 7 0.12
18 10 0.17
19 10 0.17
20 7 0.12
21 4 0.07
22 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (19 bp):
TTATATTATAATTATATAT
Found at i:1158610 original size:28 final size:30
Alignment explanation
Indices: 1158579--1158645 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
1158569 GTTTATATCA
*
1158579 TATTTTATTAT-ATTATAATT-ATATATTT
1 TATTTTATTATAATTATAATTAAAATATTT
* *
1158607 TATTATATTATAATTATATTTAAAATATTT
1 TATTTTATTATAATTATAATTAAAATATTT
1158637 TATATTTAT
1 TAT-TTTAT
1158646 ATTATATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 10 0.31
29 8 0.25
30 10 0.31
31 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TATTTTATTATAATTATAATTAAAATATTT
Found at i:1158616 original size:5 final size:5
Alignment explanation
Indices: 1158571--1158673 Score: 72
Period size: 5 Copynumber: 20.4 Consensus size: 5
1158561 TTGTTACTGT
* *
1158571 TTATA TCATA TTTTA TTATA TTATAA TTATA -TAT- TT-TA TTATA TTATAA
1 TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTAT-A
* * *
1158620 TTATA TTTAAA ATATT TTATA TTTATA TTATA TT-T- TTATGTA TTATA
1 TTATA -TTATA TTATA TTATA -TTATA TTATA TTATA TTA--TA TTATA
1158667 TTATA TT
1 TTATA TT
1158674 TTAATTTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
3 3 0.04
4 7 0.09
5 44 0.57
6 20 0.26
7 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:1158688 original size:20 final size:20
Alignment explanation
Indices: 1158581--1158688 Score: 67
Period size: 20 Copynumber: 5.3 Consensus size: 20
1158571 TTATATCATA
*
1158581 TTTTATTATATTATAATTATAT
1 TTTTATTATATTTTAATT-T-T
* *
1158603 ATTTTATTATATTATAATTAT
1 -TTTTATTATATTTTAATTTT
* ** *
1158624 ATTTAAAATATTTT-A-TAT
1 TTTTATTATATTTTAATTTT
* * * *
1158642 TTATATTATATTTTTATGTA
1 TTTTATTATATTTTAATTTT
*
1158662 TTATATTATATTTTAATTTT
1 TTTTATTATATTTTAATTTT
1158682 TTTTATT
1 TTTTATT
1158689 CTCGTATAAT
Statistics
Matches: 67, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
18 13 0.19
19 2 0.03
20 33 0.49
21 1 0.01
23 18 0.27
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (20 bp):
TTTTATTATATTTTAATTTT
Found at i:1166600 original size:12 final size:11
Alignment explanation
Indices: 1166582--1166618 Score: 58
Period size: 10 Copynumber: 3.4 Consensus size: 11
1166572 AATCAAATCA
1166582 AATTAATTAAT
1 AATTAATTAAT
1166593 ATATTAATTAA-
1 A-ATTAATTAAT
1166604 AATTAATTAAT
1 AATTAATTAAT
1166615 AATT
1 AATT
1166619 CGATTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.38
11 6 0.25
12 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTAATTAAT
Found at i:1166795 original size:44 final size:43
Alignment explanation
Indices: 1166708--1166797 Score: 101
Period size: 44 Copynumber: 2.1 Consensus size: 43
1166698 TTTGAATTGA
* * * *
1166708 ATTTATAAAAAATTAATTTAATTTTTATATTTTTAAATATTTT
1 ATTTATAAAAAATGAATTTAATATTTAAATATTTAAATATTTT
* *
1166751 ATTTATAAATAATGAGATTTAAATATTTAAATATTT-AATTTTTT
1 ATTTATAAAAAATGA-ATTT-AATATTTAAATATTTAAATATTTT
1166795 ATT
1 ATT
1166798 AAAGATTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
43 13 0.33
44 14 0.36
45 12 0.31
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (43 bp):
ATTTATAAAAAATGAATTTAATATTTAAATATTTAAATATTTT
Found at i:1166864 original size:35 final size:36
Alignment explanation
Indices: 1166773--1166877 Score: 90
Period size: 38 Copynumber: 2.9 Consensus size: 36
1166763 TGAGATTTAA
*
1166773 ATATTTAAATATTTAATTTTTTATTAAAGATTATATT
1 ATATTT-AATATTTATTTTTTTATTAAAGATTATATT
* * **
1166810 ATTAAATTAA-ATATAATTTTTTTATTAATTATTA-ATT
1 A-T-ATTTAATAT-TTATTTTTTTATTAAAGATTATATT
**
1166847 ATATTTAATATTTATTTTAATATTAAA-ATTA
1 ATATTTAATATTTATTTTTTTATTAAAGATTA
1166878 ATGCTTAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
34 4 0.07
35 17 0.31
36 3 0.06
37 7 0.13
38 20 0.37
39 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (36 bp):
ATATTTAATATTTATTTTTTTATTAAAGATTATATT
Found at i:1170184 original size:21 final size:21
Alignment explanation
Indices: 1170158--1170201 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1170148 ATGGCAGTCA
1170158 CAATTCTTCTATAATGGTTCC
1 CAATTCTTCTATAATGGTTCC
**
1170179 CAATTCTTCTATGGTGGTTCC
1 CAATTCTTCTATAATGGTTCC
1170200 CA
1 CA
1170202 TGGGGATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (21 bp):
CAATTCTTCTATAATGGTTCC
Found at i:1171764 original size:2 final size:2
Alignment explanation
Indices: 1171757--1171783 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1171747 TTGTATTACT
1171757 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1171784 CTGTTTTTCT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1175446 original size:5 final size:5
Alignment explanation
Indices: 1175436--1175469 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
1175426 AAACTTCCAT
*
1175436 GAAAA GAAAA GAAAA GAAAG GAAAA GAAAA -AAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1175470 ATTCATGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:1175657 original size:2 final size:2
Alignment explanation
Indices: 1175650--1175678 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1175640 CAAAACTTTA
1175650 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1175679 ATAAGTTTTC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1177938 original size:22 final size:22
Alignment explanation
Indices: 1177912--1177954 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177902 TCTTAAACAC
1177912 AAAAAGAA-AGACTTGGAGAAAA
1 AAAAAGAAGAGACTT-GAGAAAA
*
1177934 AAAAAGAAGAGTCTTGAGAAA
1 AAAAAGAAGAGACTTGAGAAA
1177955 GAACTCAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.60, C:0.05, G:0.23, T:0.12
Consensus pattern (22 bp):
AAAAAGAAGAGACTTGAGAAAA
Found at i:1178954 original size:36 final size:35
Alignment explanation
Indices: 1178914--1178999 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 35
1178904 AATTTTTAAG
*
1178914 TTTAAATTAAATTAAATTTAAAACATA-ATATTATTA
1 TTTAAATTAAATTAAA-TTAAAA-ATATATATTAATA
* *
1178950 TTTAAAATAATATCAAATTAAAAATATATATTAATA
1 TTTAAATTAA-ATTAAATTAAAAATATATATTAATA
1178986 TTTATAATTAAATT
1 TTTA-AATTAAATT
1179000 TTAATAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
35 3 0.07
36 29 0.69
37 10 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (35 bp):
TTTAAATTAAATTAAATTAAAAATATATATTAATA
Found at i:1180229 original size:2 final size:2
Alignment explanation
Indices: 1180222--1180255 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1180212 AGAAATGACC
1180222 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
1180256 CCATGTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1188351 original size:18 final size:16
Alignment explanation
Indices: 1188336--1188369 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
1188326 TATGTATTAA
1188336 ATATTTTATTTATATT
1 ATATTTTATTTATATT
1188352 ATATTTGTATATTATATT
1 ATATTT-TAT-TTATATT
1188370 TAAAAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
ATATTTTATTTATATT
Found at i:1188364 original size:13 final size:13
Alignment explanation
Indices: 1188346--1188370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1188336 ATATTTTATT
1188346 TATATTATATTTG
1 TATATTATATTTG
1188359 TATATTATATTT
1 TATATTATATTT
1188371 AAAAATATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TATATTATATTTG
Found at i:1189057 original size:28 final size:27
Alignment explanation
Indices: 1189011--1189125 Score: 116
Period size: 25 Copynumber: 4.3 Consensus size: 27
1189001 TTAAGAGTAA
*
1189011 ATTTAATA-ATTTATTTATTTATATTAT
1 ATTTAATATA-TTATATATTTATATTAT
1189038 ATTTATTATATATTA-ATA-TTATAATTAT
1 ATTTA--ATATATTATATATTTAT-ATTAT
* *
1189066 ATTTAAAATATTATATATTTAT-CTAT
1 ATTTAATATATTATATATTTATATTAT
*
1189092 -TTTAATAAATTATATATTTATATTAT
1 ATTTAATATATTATATATTTATATTAT
1189118 A-TTAATAT
1 ATTTAATAT
1189126 TAGAAGTGGC
Statistics
Matches: 73, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
25 19 0.26
26 19 0.26
27 12 0.16
28 16 0.22
29 6 0.08
30 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTAATATATTATATATTTATATTAT
Found at i:1189120 original size:11 final size:11
Alignment explanation
Indices: 1189022--1189068 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
1189012 TTTAATAATT
1189022 TATT-TATTTA
1 TATTATATTTA
1189032 TATTATATTTA
1 TATTATATTTA
*
1189043 T-TATATATTAA
1 TAT-TATATTTA
*
1189054 TATTATAATTA
1 TATTATATTTA
1189065 TATT
1 TATT
1189069 TAAAATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 5 0.16
11 25 0.81
12 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATATTTA
Found at i:1191273 original size:129 final size:131
Alignment explanation
Indices: 1191128--1191402 Score: 322
Period size: 129 Copynumber: 2.1 Consensus size: 131
1191118 GAAGTTAGTT
* * ** * * * *
1191128 TTGGTGGTGCATCAGCTGGAGCTGCCGTTTTGGGTTACTCGTCTGCTCAAGAAGATT-CACATTT
1 TTGGTGCTGTATCAGCTGGAGCTGCCGTTAGGGGTTACTCATCTCCGCAAGAA-ATTCCAAATTT
* * * * * *
1191192 AGTTGGCCATAGATGGGATGCTTC-T-GGCATTAGCCCAAGTGCTTGAGTTTATCCTGAACCCAG
65 AGTTGGCCAAAGATGAGATGCTTCTTAGGCATTAGCCCAAGTGCTGGACTTCATCCCGAACCCAG
1191255 CC
130 CC
* * *
1191257 TTGGTGCTGTATCAGCTGGAGCTGCCGTTAGGGGTTATTCATCTCCGCTAGAACTTCCAAATTTA
1 TTGGTGCTGTATCAGCTGGAGCTGCCGTTAGGGGTTACTCATCTCCGCAAGAAATTCCAAATTTA
* *
1191322 GTTGGCCAAAGATGAGATGTTTCTTTAGGCATTAGTCCAAGTGCTGGACTTCATCCCGAACCCAG
66 GTTGGCCAAAGATGAGATGCTTC-TTAGGCATTAGCCCAAGTGCTGGACTTCATCCCGAACCCAG
*
1191387 CG
130 CC
*
1191389 TTGATGCTGTATCA
1 TTGGTGCTGTATCA
1191403 AATGGAGAAA
Statistics
Matches: 121, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
128 2 0.02
129 71 0.59
131 1 0.01
132 47 0.39
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (131 bp):
TTGGTGCTGTATCAGCTGGAGCTGCCGTTAGGGGTTACTCATCTCCGCAAGAAATTCCAAATTTA
GTTGGCCAAAGATGAGATGCTTCTTAGGCATTAGCCCAAGTGCTGGACTTCATCCCGAACCCAGC
C
Found at i:1195814 original size:29 final size:29
Alignment explanation
Indices: 1195772--1195830 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1195762 CCAGACATTA
1195772 ATACTTCCCCAATATATTATAACAACATC
1 ATACTTCCCCAATATATTATAACAACATC
*
1195801 ATACTTCTCCAATATATTATAACAACATC
1 ATACTTCCCCAATATATTATAACAACATC
1195830 A
1 A
1195831 ATACATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.32
Consensus pattern (29 bp):
ATACTTCCCCAATATATTATAACAACATC
Found at i:1198334 original size:29 final size:29
Alignment explanation
Indices: 1198287--1198346 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1198277 AATAAAAAAT
*
1198287 ATAAAAATTAAATAATTATA-TTATTAAA
1 ATAAAAATAAAATAATTATATTTATTAAA
* *
1198315 ATAAAAATAAAAATATTTATATTTGTTAAA
1 ATAAAAAT-AAAATAATTATATTTATTAAA
1198345 AT
1 AT
1198347 TTTTATACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 8 0.30
29 10 0.37
30 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
ATAAAAATAAAATAATTATATTTATTAAA
Found at i:1199145 original size:21 final size:21
Alignment explanation
Indices: 1199120--1199182 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 21
1199110 CATTGTTTTA
*
1199120 TATTAT-TTTTTATATTAAATG
1 TATTATATATTTATA-TAAATG
1199141 TATTATATATTTATATAAAT-
1 TATTATATATTTATATAAATG
1199161 T-TTA-ATATATTA-ATAAAT-
1 TATTATATAT-TTATATAAATG
1199179 TATT
1 TATT
1199183 TTATGTAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
18 11 0.29
19 8 0.21
20 1 0.03
21 11 0.29
22 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TATTATATATTTATATAAATG
Found at i:1199146 original size:26 final size:28
Alignment explanation
Indices: 1199099--1199152 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1199089 GACTCTCGAA
*
1199099 TTTATATTATACATTGTTTTATATTATTT
1 TTTATATTATACATTGTATTATA-TATTT
1199128 TTTATATTA-A-A-TGTATTATATATTT
1 TTTATATTATACATTGTATTATATATTT
1199153 ATATAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 8 0.33
27 1 0.04
28 1 0.04
29 9 0.38
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTATATTATACATTGTATTATATATTT
Found at i:1211687 original size:2 final size:2
Alignment explanation
Indices: 1211680--1211714 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1211670 ATAAAAGTAA
1211680 AG 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 AG A
1211715 AGTGGATGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1211934 original size:4 final size:4
Alignment explanation
Indices: 1211909--1211951 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
1211899 TCTTTAGGTA
* *
1211909 TATG TATA TATG TATA TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1211952 ACCCAGAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1219497 original size:3 final size:3
Alignment explanation
Indices: 1219489--1219519 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1219479 CTTGAAGATG
*
1219489 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1219520 AAGTATTGTG
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:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1228193 original size:18 final size:18
Alignment explanation
Indices: 1228150--1228198 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1228140 AATTAACACT
*
1228150 ATATATTTTTATGTATTA
1 ATATATTTTTATTTATTA
*
1228168 TTATATTTTTATTTATTTA
1 ATATATTTTTATTTA-TTA
*
1228187 ATA-ATTTATATT
1 ATATATTTTTATT
1228199 ACGTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
ATATATTTTTATTTATTA
Found at i:1234939 original size:2 final size:2
Alignment explanation
Indices: 1234932--1234961 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1234922 AGTTTTGCTT
1234932 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
1234962 CACAATTGAG
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:1236464 original size:3 final size:3
Alignment explanation
Indices: 1236456--1236480 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1236446 AACACCCAAA
1236456 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1236481 CCATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1236601 original size:16 final size:17
Alignment explanation
Indices: 1236571--1236604 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1236561 TTTTAAAAGT
*
1236571 TAAAAATATATATTTTA
1 TAAAAATATAAATTTTA
1236588 TAAAAATA-AAATTTTA
1 TAAAAATATAAATTTTA
1236604 T
1 T
1236605 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAAATATAAATTTTA
Found at i:1238762 original size:2 final size:2
Alignment explanation
Indices: 1238755--1238779 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1238745 TTCATTTGAT
1238755 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1238780 TTTTCTATTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1247411 original size:18 final size:19
Alignment explanation
Indices: 1247371--1247411 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1247361 TAAATTAAAT
* *
1247371 TTAAGTTTATTTTGATTTA
1 TTAAATTTATTTTGATTAA
1247390 -TAAATTTATTTT-ATTAA
1 TTAAATTTATTTTGATTAA
1247407 TTAAA
1 TTAAA
1247412 AATATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTAAATTTATTTTGATTAA
Found at i:1251012 original size:21 final size:21
Alignment explanation
Indices: 1250982--1251559 Score: 133
Period size: 21 Copynumber: 26.9 Consensus size: 21
1250972 TCAATAATAT
1250982 ATTATCAAAATTATATTAAAA
1 ATTATCAAAATTATATTAAAA
*
1251003 ATTATTAAAATTATA-TAAAA
1 ATTATCAAAATTATATTAAAA
* * *
1251023 CGTTAT-AAAATTTTATTAAAT
1 -ATTATCAAAATTATATTAAAA
* *
1251044 ATTATCAAACTTATATGATTCAAA
1 ATTATCAAA-AT-TAT-ATTAAAA
*
1251068 ATTAT-ATTAAATGT-TCA-AAAAA
1 ATTATCA--AAAT-TAT-ATTAAAA
* *
1251090 ACTTATCAAATTTACA-TAAAA
1 A-TTATCAAAATTATATTAAAA
* * * **
1251111 GGA-TACCAAAATTAT-CTCAGT
1 --ATTATCAAAATTATATTAAAA
* * *
1251132 GTTATCAGAATTATAGTAAAA
1 ATTATCAAAATTATATTAAAA
* * * *
1251153 AATAACAAAATCATATAAAAA
1 ATTATCAAAATTATATTAAAA
* ** *
1251174 ATCA-CTAAAACCATTTTAAAA
1 ATTATC-AAAATTATATTAAAA
* * * * *
1251195 GTTATTAATATCATATTAAAT
1 ATTATCAAAATTATATTAAAA
* * *
1251216 ATTAACAAAAAAATATTTTAAAA
1 ATTATC--AAAATTATATTAAAA
* *
1251239 ATTATTAAAATTATATAAAAA
1 ATTATCAAAATTATATTAAAA
1251260 ATTATCAAAATTATA-TAAAA
1 ATTATCAAAATTATATTAAAA
**
1251280 ATTTATCAAAATTATTAAAAAAAA
1 A-TTATCAAAATTA-T-ATTAAAA
* **
1251304 ATTTATAAAAATT-TACCAAAA
1 A-TTATCAAAATTATATTAAAA
1251325 CTATTAATATCAAAA-T-TATTACAAA
1 --A-T--TATCAAAATTATATTA-AAA
* *
1251350 TTATCAAATCAAAATTATATTAAAT
1 --AT--TATCAAAATTATATTAAAA
* * *
1251375 ATTAACATAAA-TATATCAAGA
1 ATTATCA-AAATTATATTAAAA
*
1251396 ATTACTCAAAATTATATAAAAAA
1 ATTA-TCAAAATTATAT-TAAAA
1251419 ATTACTC-AAA-T-TA-TAAAA
1 ATTA-TCAAAATTATATTAAAA
*
1251437 TTTATCAAAATTATA-TATAAA
1 ATTATCAAAATTATATTA-AAA
* *
1251458 ATTATCAAAA--CTGTTAAAA
1 ATTATCAAAATTATATTAAAA
** *
1251477 ATTTAAAAAAATTATATTCAAA
1 A-TTATCAAAATTATATTAAAA
* * *
1251499 ATTTTTAAAA--CTATTACAAA
1 ATTATCAAAATTATATTA-AAA
* * *
1251519 ATTA-CTAATATTGTATAAAAA
1 ATTATC-AAAATTATATTAAAA
1251540 ATTATCAAAATTAATATTAA
1 ATTATCAAAATT-ATATTAA
1251560 CTAAGATATT
Statistics
Matches: 402, Mismatches: 106, Indels: 97
0.66 0.18 0.16
Matches are distributed among these distances:
17 2 0.00
18 10 0.02
19 10 0.02
20 57 0.14
21 179 0.45
22 40 0.10
23 40 0.10
24 42 0.10
25 17 0.04
26 5 0.01
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.35
Consensus pattern (21 bp):
ATTATCAAAATTATATTAAAA
Found at i:1251236 original size:44 final size:44
Alignment explanation
Indices: 1251159--1251269 Score: 118
Period size: 44 Copynumber: 2.6 Consensus size: 44
1251149 AAAAAATAAC
* * ** *
1251159 AAAATCATATAAAAAA-TCAC-TAAAACCATTTTAAAAGTTATT
1 AAAATCATATAAAAAATTAACAAAAAAATATTTTAAAAATTATT
* * *
1251201 AATATCATATTAAATATTAACAAAAAAATATTTTAAAAATTATT
1 AAAATCATATAAAAAATTAACAAAAAAATATTTTAAAAATTATT
* *
1251245 AAAATTATATAAAAAATTATCAAAA
1 AAAATCATATAAAAAATTAACAAAA
1251270 TTATATAAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 13 0.24
43 3 0.06
44 38 0.70
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (44 bp):
AAAATCATATAAAAAATTAACAAAAAAATATTTTAAAAATTATT
Found at i:1251246 original size:10 final size:10
Alignment explanation
Indices: 1251233--1251300 Score: 61
Period size: 10 Copynumber: 6.7 Consensus size: 10
1251223 AAAAAATATT
1251233 TTAAAAATTA
1 TTAAAAATTA
1251243 TT-AAAATTA
1 TTAAAAATTA
1251252 TATAAAAAATTA
1 T-T-AAAAATTA
*
1251264 -TCAAAATTA
1 TTAAAAATTA
1251273 TATAAAAATT-
1 T-TAAAAATTA
*
1251283 TATCAAAATTA
1 T-TAAAAATTA
1251294 TTAAAAA
1 TTAAAAA
1251301 AAAATTTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
9 15 0.31
10 18 0.38
11 8 0.17
12 7 0.15
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:1251250 original size:9 final size:9
Alignment explanation
Indices: 1251236--1251299 Score: 56
Period size: 9 Copynumber: 6.4 Consensus size: 9
1251226 AAATATTTTA
1251236 AAAATTATT
1 AAAATTATT
1251245 AAAATTATAT
1 AAAATTAT-T
*
1251255 AAAAAATTATC
1 --AAAATTATT
1251266 AAAATTATAT
1 AAAATTAT-T
*
1251276 AAAAATTTATC
1 -AAAA-TTATT
1251287 AAAATTATT
1 AAAATTATT
1251296 AAAA
1 AAAA
1251300 AAAAATTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
9 24 0.53
10 5 0.11
11 4 0.09
12 12 0.27
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATTATT
Found at i:1251313 original size:10 final size:10
Alignment explanation
Indices: 1251224--1251318 Score: 66
Period size: 11 Copynumber: 8.9 Consensus size: 10
1251214 ATATTAACAA
*
1251224 AAAAATATTTT
1 AAAAAT-TTAT
1251235 AAAAA-TTAT
1 AAAAATTTAT
*
1251244 TAAAATTATAT
1 AAAAATT-TAT
*
1251255 AAAAAATTAT
1 AAAAATTTAT
*
1251265 CAAAATTATAT
1 AAAAATT-TAT
1251276 AAAAATTTAT
1 AAAAATTTAT
* *
1251286 CAAAATTATTAAAA
1 -AAAA--ATT-TAT
1251300 AAAAATTTAT
1 AAAAATTTAT
1251310 AAAAATTTA
1 AAAAATTTA
1251319 CCAAAACTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
9 7 0.11
10 22 0.33
11 29 0.44
13 7 0.11
14 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:1251314 original size:34 final size:35
Alignment explanation
Indices: 1251266--1251331 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
1251256 AAAAATTATC
* *
1251266 AAAATTATATAAAAATTTATCAAAATTATTAAAAA
1 AAAATTATATAAAAATTTACCAAAACTATTAAAAA
1251301 AAAATT-TATAAAAATTTACCAAAACTATTAA
1 AAAATTATATAAAAATTTACCAAAACTATTAA
1251332 TATCAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 23 0.79
35 6 0.21
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (35 bp):
AAAATTATATAAAAATTTACCAAAACTATTAAAAA
Found at i:1254781 original size:13 final size:14
Alignment explanation
Indices: 1254759--1254790 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1254749 TATATAAATT
1254759 TAAA-TATATTA-A
1 TAAATTATATTATA
1254771 TAAATTATATTATA
1 TAAATTATATTATA
1254785 TAAATT
1 TAAATT
1254791 TTAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.22
13 7 0.39
14 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATTATATTATA
Found at i:1254785 original size:32 final size:32
Alignment explanation
Indices: 1254743--1254814 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
1254733 TTAAAATATT
*
1254743 TTATTTTATATAAA-TTTAAATATATTAATAAA
1 TTATATTATATAAATTTTAAA-ATATTAATAAA
* *
1254775 TTATATTATATAAATTTTAAAATATTTATATA
1 TTATATTATATAAATTTTAAAATATTAATAAA
1254807 TTAATATT
1 TT-ATATT
1254815 TTTTTATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 24 0.69
33 11 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TTATATTATATAAATTTTAAAATATTAATAAA
Found at i:1256240 original size:23 final size:22
Alignment explanation
Indices: 1256185--1256250 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 22
1256175 AAATATTTTA
1256185 TAAATTAAA-ATTAATAATTATT
1 TAAATTAAATA-TAATAATTATT
*
1256207 TTAA-T-AATATAATAATTATT
1 TAAATTAAATATAATAATTATT
* *
1256227 TAAATTAAATTATAAAAATAATT
1 TAAATTAAA-TATAATAATTATT
1256250 T
1 T
1256251 TTTAAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
20 16 0.44
21 3 0.08
22 5 0.14
23 12 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTAAATATAATAATTATT
Found at i:1256261 original size:23 final size:26
Alignment explanation
Indices: 1256217--1256280 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 26
1256207 TTAATAATAT
*
1256217 AATAATTATTTAAATTAAATTA-TAAA
1 AATAATTTTTTAAATT-AATTATTAAA
*
1256243 AATAATTTTTTAAA-T-ATTATTATA
1 AATAATTTTTTAAATTAATTATTAAA
* *
1256267 AACATTTTTTTAAA
1 AATAATTTTTTAAA
1256281 AAAAATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 4 0.12
24 15 0.45
25 1 0.03
26 13 0.39
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATAATTTTTTAAATTAATTATTAAA
Found at i:1256288 original size:24 final size:25
Alignment explanation
Indices: 1256233--1256288 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
1256223 TATTTAAATT
*
1256233 AAATTATAAAAATAATTTTTTAAATA
1 AAATTATAAAAAT-ATTTTTTAAAAA
** *
1256259 TTATTATAAACAT-TTTTTTAAAAA
1 AAATTATAAAAATATTTTTTAAAAA
1256283 AAATTA
1 AAATTA
1256289 AATATAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 14 0.58
26 10 0.42
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
AAATTATAAAAATATTTTTTAAAAA
Found at i:1258247 original size:15 final size:17
Alignment explanation
Indices: 1258227--1258259 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1258217 TTCACGCGAA
1258227 AATGAAA-TAAAA-ATT
1 AATGAAACTAAAATATT
1258242 AATGAAACTAAAATATT
1 AATGAAACTAAAATATT
1258259 A
1 A
1258260 TACTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (17 bp):
AATGAAACTAAAATATT
Found at i:1258422 original size:2 final size:2
Alignment explanation
Indices: 1258415--1258448 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1258405 CGTAAAATAC
1258415 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
1258449 TTGTATGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1259675 original size:3 final size:3
Alignment explanation
Indices: 1259667--1259696 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1259657 ACAAAAGCTA
1259667 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1259697 GTTTTTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1260073 original size:2 final size:2
Alignment explanation
Indices: 1260066--1260096 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1260056 TGCTTCAATC
1260066 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1260097 TTAAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1260908 original size:39 final size:39
Alignment explanation
Indices: 1260829--1260911 Score: 94
Period size: 41 Copynumber: 2.1 Consensus size: 39
1260819 TTAAAATTTT
* *
1260829 TATAAATATAAAATATAAAATATTTAAACATAATTTTAA
1 TATAAATATAAAATAAAAAATATTTAAACATAATTATAA
* * *
1260868 TATAAATATATAAATTAAAAAATATTAAAAAATTAATAATAA
1 TATAAATATA-AAA-TAAAAAATATTTAAACA-TAATTATAA
1260910 TA
1 TA
1260912 ATAATATTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 10 0.28
40 3 0.08
41 14 0.39
42 9 0.25
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (39 bp):
TATAAATATAAAATAAAAAATATTTAAACATAATTATAA
Found at i:1263433 original size:12 final size:13
Alignment explanation
Indices: 1263404--1263437 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1263394 TTTTAAAAGT
1263404 TAAAAAATTTAAA
1 TAAAAAATTTAAA
1263417 TAAAAAATTTAAA
1 TAAAAAATTTAAA
1263430 -AAAAAATT
1 TAAAAAATT
1263438 ATAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TAAAAAATTTAAA
Found at i:1264106 original size:14 final size:13
Alignment explanation
Indices: 1264085--1264111 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1264075 TGTGTTTTAG
1264085 GTCTAAAAAGTTA
1 GTCTAAAAAGTTA
1264098 GTCTAAAAAGTTA
1 GTCTAAAAAGTTA
1264111 G
1 G
1264112 GGGGTGAAAA
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:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (13 bp):
GTCTAAAAAGTTA
Found at i:1268859 original size:3 final size:3
Alignment explanation
Indices: 1268851--1268884 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1268841 GCTTAAAAAG
*
1268851 ATA ATA ATA ATA ATA ATA TTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1268885 AAAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1276187 original size:2 final size:2
Alignment explanation
Indices: 1276180--1276209 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1276170 AATTCACAAA
1276180 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
1276210 GCATATGATA
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):
AT
Found at i:1278270 original size:24 final size:24
Alignment explanation
Indices: 1278224--1278275 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1278214 TGAGTATAAA
**
1278224 GTTA-TATCAAAATTATTGTAAAT
1 GTTATTATCAAAATTATTACAAAT
*
1278247 GTTATTATCAAAATTGTTACAAAT
1 GTTATTATCAAAATTATTACAAAT
1278271 -TTATT
1 GTTATT
1278276 TTTACAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (24 bp):
GTTATTATCAAAATTATTACAAAT
Found at i:1278722 original size:20 final size:19
Alignment explanation
Indices: 1278707--1278765 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
1278697 ACTTAAATTG
*
1278707 TATTAAATGTTATTAAACT
1 TATTAAATGTTATTAAAAT
* * *
1278726 ATATCAAATATTATCAAAAT
1 -TATTAAATGTTATTAAAAT
1278746 TATTACAAATGTTATTAAAA
1 TATT--AAATGTTATTAAAA
1278766 GTATATCTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 3 0.10
20 15 0.50
21 12 0.40
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (19 bp):
TATTAAATGTTATTAAAAT
Found at i:1278754 original size:21 final size:21
Alignment explanation
Indices: 1278730--1278835 Score: 60
Period size: 21 Copynumber: 5.1 Consensus size: 21
1278720 TAAACTATAT
1278730 CAAATATTATCAAAATTATTA
1 CAAATATTATCAAAATTATTA
* * *
1278751 CAAATGTTATTAAAAGTA-TA
1 CAAATATTATCAAAATTATTA
* *
1278771 TC-TATGAATA-CTAAAATTATTA
1 -CAAAT-ATTATC-AAAATTATTA
* *
1278793 GAAATGTTATC-AAATTATTA
1 CAAATATTATCAAAATTATTA
* *
1278813 CAAA-ACTTATAAAAATTTTTA
1 CAAATA-TTATCAAAATTATTA
1278834 CA
1 CA
1278836 TAAGCTATTA
Statistics
Matches: 61, Mismatches: 16, Indels: 16
0.66 0.17 0.17
Matches are distributed among these distances:
20 20 0.33
21 36 0.59
22 5 0.08
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (21 bp):
CAAATATTATCAAAATTATTA
Found at i:1278822 original size:20 final size:20
Alignment explanation
Indices: 1278784--1278822 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1278774 ATGAATACTA
* **
1278784 AAATTATTAGAAATGTTATC
1 AAATTATTACAAAACTTATC
1278804 AAATTATTACAAAACTTAT
1 AAATTATTACAAAACTTAT
1278823 AAAAATTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (20 bp):
AAATTATTACAAAACTTATC
Found at i:1280754 original size:23 final size:24
Alignment explanation
Indices: 1280715--1280770 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
1280705 TTTTTATCAA
1280715 TAATTTAAATATTAAAAAATTAAT
1 TAATTTAAATATTAAAAAATTAAT
* *
1280739 TAATTTATA-ATTAAAAATTTAA-
1 TAATTTAAATATTAAAAAATTAAT
*
1280761 AAATTTAAAT
1 TAATTTAAAT
1280771 TTATTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 7 0.26
23 12 0.44
24 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATTTAAATATTAAAAAATTAAT
Found at i:1280758 original size:38 final size:39
Alignment explanation
Indices: 1280679--1280770 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 39
1280669 AAAAATCAGA
* * *
1280679 TTAAAAATTAAATTAAATTAATAAATTTTTTATCAATAAT
1 TTAAAAATTAAA-TAAATTAATAAATTTATAATCAAAAAT
* * *
1280719 TTAAATATTAAA-AAATTAATTAATTTATAATTAAAAAT
1 TTAAAAATTAAATAAATTAATAAATTTATAATCAAAAAT
1280757 TTAAAAATTTAAAT
1 TTAAAAA-TTAAAT
1280771 TTATTTATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 27 0.63
39 5 0.12
40 11 0.26
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (39 bp):
TTAAAAATTAAATAAATTAATAAATTTATAATCAAAAAT
Found at i:1281414 original size:2 final size:2
Alignment explanation
Indices: 1281403--1281438 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1281393 TGAATAAAAC
1281403 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1281439 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1282719 original size:6 final size:6
Alignment explanation
Indices: 1282708--1282732 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1282698 TGGCTTTTGG
1282708 GGTTTT GGTTTT GGTTTT GGTTTT G
1 GGTTTT GGTTTT GGTTTT GGTTTT G
1282733 AACGAGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (6 bp):
GGTTTT
Found at i:1283284 original size:2 final size:2
Alignment explanation
Indices: 1283277--1283304 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1283267 ACATTCTGTC
1283277 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
1283305 GTAGAGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1286713 original size:33 final size:32
Alignment explanation
Indices: 1286641--1286713 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 32
1286631 AATGATAAGA
** * *
1286641 ATATATATATATATATATCTTTCAATTTTCCT
1 ATATATATATATATATATCTTAAAACTATCCT
1286673 ATAATATATATATATATATCTTAAAAGACTATCC-
1 AT-ATATATATATATATATCTT-AAA-ACTATCCT
1286707 ATATATA
1 ATATATA
1286714 ATTCTTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
32 2 0.06
33 24 0.71
34 3 0.09
35 5 0.15
ACGTcount: A:0.42, C:0.11, G:0.01, T:0.45
Consensus pattern (32 bp):
ATATATATATATATATATCTTAAAACTATCCT
Found at i:1288339 original size:6 final size:7
Alignment explanation
Indices: 1288320--1288371 Score: 59
Period size: 7 Copynumber: 6.9 Consensus size: 7
1288310 TAATGCACCC
1288320 TATTTTT
1 TATTTTT
1288327 TATTTTT
1 TATTTTT
1288334 TATTTTT
1 TATTTTT
1288341 TATTTTT
1 TATTTTT
*
1288348 AATTTCCTT
1 TATTT--TT
1288357 TCATTTTT
1 T-ATTTTT
1288365 GTATTTT
1 -TATTTT
1288372 GGCAGTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
7 25 0.64
8 7 0.18
9 3 0.08
10 4 0.10
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (7 bp):
TATTTTT
Found at i:1293762 original size:70 final size:69
Alignment explanation
Indices: 1293658--1293807 Score: 264
Period size: 70 Copynumber: 2.1 Consensus size: 69
1293648 TTTTAAACCT
*
1293658 TTGAGACTCGAAATTTGATTAAGTTCAATTGAGTATAACTTTTCAATCTTGACTTTCAACTTGTA
1 TTGA-ACTCGAAATTTGATTAAGTTCAATTGAGTATAACTTTTCAATCTTGACTCTCAACTTGTA
1293723 ATTAC
65 ATTAC
*
1293728 TTGAACTCGAAATTTGATTCAAGTTCAATTGAGTATAGCTTTTCAATCTTGACTCTCAACTTGTA
1 TTGAACTCGAAATTTGATT-AAGTTCAATTGAGTATAACTTTTCAATCTTGACTCTCAACTTGTA
1293793 ATTAC
65 ATTAC
1293798 TTGAACTCGA
1 TTGAACTCGA
1293808 TGTGATAGAT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
69 15 0.19
70 62 0.81
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (69 bp):
TTGAACTCGAAATTTGATTAAGTTCAATTGAGTATAACTTTTCAATCTTGACTCTCAACTTGTAA
TTAC
Found at i:1294857 original size:7 final size:8
Alignment explanation
Indices: 1294833--1294858 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1294823 CCCCTAAAGG
1294833 AAATCAAA
1 AAATCAAA
1294841 AAATCAAA
1 AAATCAAA
1294849 AAATCAAA
1 AAATCAAA
1294857 AA
1 AA
1294859 GTTTGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATCAAA
Found at i:1296047 original size:2 final size:2
Alignment explanation
Indices: 1296040--1296064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1296030 CAATACATAC
1296040 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 A
1296065 GAAATCAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1296935 original size:24 final size:24
Alignment explanation
Indices: 1296886--1296932 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1296876 AAATTATTAA
* *
1296886 AATATATATTAATATATTAATATT
1 AATATATATTAATATAATAAAATT
*
1296910 AATATATATT-TTATAATAAAATT
1 AATATATATTAATATAATAAAATT
1296933 TAAATTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATATATATTAATATAATAAAATT
Found at i:1296968 original size:18 final size:18
Alignment explanation
Indices: 1296945--1297005 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1296935 AATTAAATAA
1296945 TAATTTAAATAATCAAAT
1 TAATTTAAATAATCAAAT
* * * *
1296963 TAATTTGAATTATAAAAA
1 TAATTTAAATAATCAAAT
* *
1296981 TATATTTTAA-ACTCAAAT
1 TA-ATTTAAATAATCAAAT
1296999 TAATTTA
1 TAATTTA
1297006 TATTAAATTT
Statistics
Matches: 32, Mismatches: 10, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
17 4 0.12
18 22 0.69
19 6 0.19
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATTTAAATAATCAAAT
Found at i:1297360 original size:3 final size:3
Alignment explanation
Indices: 1297352--1297385 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1297342 ACCAAACAAA
1297352 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1297386 TTATTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1297390 original size:3 final size:3
Alignment explanation
Indices: 1297384--1297409 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1297374 ATAATAATAA
1297384 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1297410 AAATGGACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1297799 original size:20 final size:20
Alignment explanation
Indices: 1297776--1297816 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1297766 TTAAATTTAA
*
1297776 AAATTTTACTTAATTTATTT
1 AAATTTAACTTAATTTATTT
*
1297796 AAATTTAATTTAATTTATTT
1 AAATTTAACTTAATTTATTT
1297816 A
1 A
1297817 TAAAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
AAATTTAACTTAATTTATTT
Found at i:1297859 original size:16 final size:16
Alignment explanation
Indices: 1297835--1297892 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
1297825 TTTAATAAAG
*
1297835 TTAATTTAAAAATAAT
1 TTAAATTAAAAATAAT
*
1297851 TTAAATTAAAAATAAA
1 TTAAATTAAAAATAAT
*
1297867 TAAAATTAAAAATAAT
1 TTAAATTAAAAATAAT
*
1297883 TTAATTTAAA
1 TTAAATTAAA
1297893 TATTAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAATTAAAAATAAT
Found at i:1297869 original size:37 final size:36
Alignment explanation
Indices: 1297835--1297914 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 36
1297825 TTTAATAAAG
1297835 TTAATTTAAAAATAATTTAAATTAAA-AATAAATAA
1 TTAATTTAAAAATAATTTAAATTAAATAATAAATAA
* *
1297870 --AA-TTAAAAATAATTTAATTTAAATATTAAATTTAA
1 TTAATTTAAAAATAATTTAAATTAAATAATAAA--TAA
1297905 TTAATTTAAA
1 TTAATTTAAA
1297915 TCTAATTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
32 20 0.54
33 7 0.19
35 3 0.08
37 2 0.05
38 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (36 bp):
TTAATTTAAAAATAATTTAAATTAAATAATAAATAA
Found at i:1297897 original size:23 final size:22
Alignment explanation
Indices: 1297867--1297915 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1297857 TAAAAATAAA
1297867 TAAA-ATTAAAAATAATTTAATT
1 TAAATATTAAAAATAA-TTAATT
**
1297889 TAAATATTAAATTTAATTAATT
1 TAAATATTAAAAATAATTAATT
1297911 TAAAT
1 TAAAT
1297916 CTAATTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATATTAAAAATAATTAATT
Found at i:1300434 original size:42 final size:42
Alignment explanation
Indices: 1300372--1300455 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
1300362 CCAAACCAAC
* *
1300372 CCTTCGCCCTTCAGCAGACATCTCACGTCTATGAGCAGTGGT
1 CCTTCGCCCTTCAGCAGACATCTCACATCCATGAGCAGTGGT
* *
1300414 CCTTCGCCCTTCAGCGGACATCTCACATCCGTGAGCAGTGGT
1 CCTTCGCCCTTCAGCAGACATCTCACATCCATGAGCAGTGGT
1300456 TAAACATCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.18, C:0.35, G:0.23, T:0.25
Consensus pattern (42 bp):
CCTTCGCCCTTCAGCAGACATCTCACATCCATGAGCAGTGGT
Found at i:1305016 original size:19 final size:19
Alignment explanation
Indices: 1304992--1305038 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1304982 ATTAAATCTT
*
1304992 AAATAAATATATATAATAA
1 AAATAAATATAAATAATAA
* *
1305011 AAATAAATTTAAATATTAA
1 AAATAAATATAAATAATAA
1305030 ATAATAAAT
1 A-AATAAAT
1305039 TTTTTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATAAATATAAATAATAA
Found at i:1305548 original size:18 final size:18
Alignment explanation
Indices: 1305527--1305580 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
1305517 TTTAATTTAA
1305527 TTAATTTATATAATTATT
1 TTAATTTATATAATTATT
1305545 TTAA---A-A-AA-TATT
1 TTAATTTATATAATTATT
1305557 TTAATATT-TATAATTATT
1 TTAAT-TTATATAATTATT
1305575 TTAATT
1 TTAATT
1305581 CAAATTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 15
0.66 0.00 0.34
Matches are distributed among these distances:
12 8 0.28
13 2 0.07
14 1 0.03
15 1 0.03
16 1 0.03
17 3 0.10
18 13 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATTTATATAATTATT
Found at i:1307634 original size:2 final size:2
Alignment explanation
Indices: 1307627--1307653 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1307617 GGAAAATTTT
1307627 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 A
1307654 TATAGAGTGC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1308808 original size:20 final size:20
Alignment explanation
Indices: 1308765--1308817 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1308755 TTTAAAATAT
*
1308765 TATATATTAATATAAATTTT
1 TATATATTAATATAAATTTA
*
1308785 TATATATT-ATTTATAATTTA
1 TATATATTAATATA-AATTTA
1308805 TATA-ATATAATAT
1 TATATAT-TAATAT
1308818 TTAAAAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 6 0.22
20 18 0.67
21 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATTAATATAAATTTA
Found at i:1308819 original size:16 final size:16
Alignment explanation
Indices: 1308736--1308833 Score: 55
Period size: 16 Copynumber: 6.2 Consensus size: 16
1308726 AGTAATTTAT
* *
1308736 ATATTTATGTATTATA
1 ATATTTATATAATATA
1308752 ATATTTA-A-AATAT-
1 ATATTTATATAATATA
*
1308765 -TATATAT-TAATATAA
1 ATATTTATATAATAT-A
* * *
1308780 ATTTTTATATATTATTT
1 ATATTTATATAATA-TA
1308797 ATAATTTATATAATATA
1 AT-ATTTATATAATATA
*
1308814 ATATTTA-AAAATGATA
1 ATATTTATATAAT-ATA
1308830 ATAT
1 ATAT
1308834 ATTTTGATTA
Statistics
Matches: 62, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
12 5 0.08
13 5 0.08
14 4 0.06
15 4 0.06
16 24 0.39
17 9 0.15
18 11 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATTTATATAATATA
Found at i:1309287 original size:13 final size:14
Alignment explanation
Indices: 1309269--1309308 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1309259 TTTTATCGAA
1309269 TATATAAATATT-T
1 TATATAAATATTAT
1309282 TATATAAATATTAT
1 TATATAAATATTAT
* *
1309296 TAAATAATTATTA
1 TATATAAATATTA
1309309 ATATGATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATAAATATTAT
Found at i:1315235 original size:9 final size:9
Alignment explanation
Indices: 1315223--1315303 Score: 55
Period size: 9 Copynumber: 9.2 Consensus size: 9
1315213 AAAATTTTTA
1315223 AAATTAATT
1 AAATTAATT
*
1315232 AAATTAAAT
1 AAATTAATT
*
1315241 AAATTTA-T
1 AAATTAATT
1315249 AAATTTAA-T
1 AAA-TTAATT
**
1315258 AAAAAAATT
1 AAATTAATT
1315267 -AA--AATT
1 AAATTAATT
*
1315273 AAAATAATT
1 AAATTAATT
1315282 AAATTAAATTT
1 AAATT-AA-TT
1315293 AAATTAATT
1 AAATTAATT
1315302 AA
1 AA
1315304 TTTTAAGATT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
6 4 0.07
7 2 0.03
8 8 0.14
9 34 0.58
10 4 0.07
11 7 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AAATTAATT
Found at i:1315238 original size:5 final size:5
Alignment explanation
Indices: 1315223--1315303 Score: 52
Period size: 5 Copynumber: 17.4 Consensus size: 5
1315213 AAAATTTTTA
* * *
1315223 AAATT -AATT AAATT AAA-T AAATT -TA-T AAATT TAA-T AAA-A AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT
*
1315267 AAAATT AAAAT -AATT AAATT AAATTT AAATT -AATT AA
1 -AAATT AAATT AAATT AAATT AAA-TT AAATT AAATT AA
1315304 TTTTAAGATT
Statistics
Matches: 59, Mismatches: 8, Indels: 18
0.69 0.09 0.21
Matches are distributed among these distances:
3 1 0.02
4 23 0.39
5 25 0.42
6 10 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:1315245 original size:27 final size:27
Alignment explanation
Indices: 1315214--1315290 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
1315204 TTGAATTTTA
1315214 AAATTTTTAAAATTAATTAAATTAAAT
1 AAATTTTTAAAATTAATTAAATTAAAT
* * *
1315241 AAATTTATAAATTTAA-TAAA-AAAATT
1 AAATTTTTAAAATTAATTAAATTAAA-T
*
1315267 AAA--ATTAAAA-TAATTAAATTAAAT
1 AAATTTTTAAAATTAATTAAATTAAAT
1315291 TTAAATTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
23 3 0.08
24 9 0.22
25 6 0.15
26 8 0.20
27 14 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATTTTTAAAATTAATTAAATTAAAT
Found at i:1315285 original size:20 final size:20
Alignment explanation
Indices: 1315262--1315303 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1315252 TTTAATAAAA
1315262 AAATTAAAATTAAAATAATT
1 AAATTAAAATTAAAATAATT
* *
1315282 AAATTAAATTTAAATTAATT
1 AAATTAAAATTAAAATAATT
1315302 AA
1 AA
1315304 TTTTAAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTAAAATTAAAATAATT
Found at i:1315784 original size:75 final size:74
Alignment explanation
Indices: 1315667--1315949 Score: 284
Period size: 75 Copynumber: 3.8 Consensus size: 74
1315657 GTTTGTCAGA
* * * * * * * *
1315667 GATT-CATTTTTTTGGCGACCAAAATTTAAGTGACGAGCACAGGTTTGGCAGCTAGAATGAGTGT
1 GATTCCATCTTTTTGGCGATCAAGATTTATGTGACGAGTACAGGTCTGGCAGCCAGAATGAATGT
**
1315731 TGTTTATCAG
66 TGGCTA-CAG
** * * ** *
1315741 GATTCTGTCTTTTTGGCGA-CTAGGATTTATGTGGCGAGTACAGGTCTGGCAATCAGAGTGAATG
1 GATTCCATCTTTTTGGCGATC-AAGATTTATGTGACGAGTACAGGTCTGGCAGCCAGAATGAATG
1315805 TTGGCTACTAG
65 TTGGCTAC-AG
* * * *
1315816 GATTCCATCTTTCTAGCGATCAAGATTTATGTGACGAGTACAGGTCTGACAGCCAGAATAAATGT
1 GATTCCATCTTTTTGGCGATCAAGATTTATGTGACGAGTACAGGTCTGGCAGCCAGAATGAATGT
1315881 TGGCTACCAG
66 TGGCTA-CAG
* * *
1315891 GATTCCAT-TTTTCTGGCGATCAGGATTTATGTAACGAGTACAGGTCTAGCAGCCAGAAT
1 GATTCCATCTTTT-TGGCGATCAAGATTTATGTGACGAGTACAGGTCTGGCAGCCAGAAT
1315950 AAGTATCGGC
Statistics
Matches: 170, Mismatches: 33, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
74 9 0.05
75 159 0.94
76 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (74 bp):
GATTCCATCTTTTTGGCGATCAAGATTTATGTGACGAGTACAGGTCTGGCAGCCAGAATGAATGT
TGGCTACAG
Found at i:1316462 original size:78 final size:78
Alignment explanation
Indices: 1316333--1316705 Score: 345
Period size: 78 Copynumber: 4.8 Consensus size: 78
1316323 TATTACCAAT
* * * * * *
1316333 GTGGCGAGC-AGAATGGGAGTGACTTAGTGTCACTGATAATATTAATGCCGTGGTAGCGATTAGG
1 GTGGCGAGCAAG-ATCGGAGTGACTTGGTGTCACTGACAGTATTGATGCCGTGGTAGCGATCAGG
* * *
1316397 ATCGTGGTGCTATA
65 ATCGTAGTGCCATG
* * * * * *
1316411 GTGGCGAGCAGGGTCGGAGTGACTTGGTGCCACTGACAGTATTGATGCCGTGGTGGCAATCATGA
1 GTGGCGAGCAAGATCGGAGTGACTTGGTGTCACTGACAGTATTGATGCCGTGGTAGCGATCAGGA
1316476 TCGTAGTGCCATG
66 TCGTAGTGCCATG
* ** * * * * * * *
1316489 GTGGCTAGCAAGATCAAAGTGCCATAGTGTCACTAATAGTATTGATGCCATGGTAGCGATCAGAA
1 GTGGCGAGCAAGATCGGAGTGACTTGGTGTCACTGACAGTATTGATGCCGTGGTAGCGATCAGGA
** *
1316554 TTATAGTGACATG
66 TCGTAGTGCCATG
* * * * *
1316567 GTGGCTAGCAAGATCGGAGTGCCATGGTGTCAGTGACAGTATTGATGCCATGGT-GACGATCAGG
1 GTGGCGAGCAAGATCGGAGTGACTTGGTGTCACTGACAGTATTGATGCCGTGGTAG-CGATCAGG
1316631 ATCGTAGTGCCATG
65 ATCGTAGTGCCATG
** * * * * * *
1316645 GTGGAAAGCAAAATTGGATTGACTTGGTGTCACTGACAATACTGATGTCGTGGTAGCGATC
1 GTGGCGAGCAAGATCGGAGTGACTTGGTGTCACTGACAGTATTGATGCCGTGGTAGCGATC
1316706 GAAGTGACTT
Statistics
Matches: 236, Mismatches: 56, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
77 1 0.00
78 233 0.99
79 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.26
Consensus pattern (78 bp):
GTGGCGAGCAAGATCGGAGTGACTTGGTGTCACTGACAGTATTGATGCCGTGGTAGCGATCAGGA
TCGTAGTGCCATG
Found at i:1316503 original size:26 final size:26
Alignment explanation
Indices: 1316456--1316595 Score: 63
Period size: 26 Copynumber: 5.4 Consensus size: 26
1316446 ACAGTATTGA
* * * *
1316456 TGCCGTGGTGGCAATCATGATCGTAG
1 TGCCATGGTGGCTAGCAAGATCGTAG
**
1316482 TGCCATGGTGGCTAGCAAGATCAAAG
1 TGCCATGGTGGCTAGCAAGATCGTAG
* * * *
1316508 TGCCATAGTGTC-A-CTA-ATAGTATTG
1 TGCCATGGTGGCTAGCAAGATCGTA--G
* * * **
1316533 ATGCCATGGTAGCGATC-AGAATTATAG
1 -TGCCATGGTGGCTAGCAAG-ATCGTAG
* *
1316560 TGACATGGTGGCTAGCAAGATCGGAG
1 TGCCATGGTGGCTAGCAAGATCGTAG
1316586 TGCCATGGTG
1 TGCCATGGTG
1316596 TCAGTGACAG
Statistics
Matches: 81, Mismatches: 25, Indels: 16
0.66 0.20 0.13
Matches are distributed among these distances:
23 3 0.04
24 2 0.02
25 2 0.02
26 64 0.79
27 5 0.06
28 1 0.01
29 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (26 bp):
TGCCATGGTGGCTAGCAAGATCGTAG
Found at i:1316675 original size:156 final size:156
Alignment explanation
Indices: 1316350--1316705 Score: 390
Period size: 156 Copynumber: 2.3 Consensus size: 156
1316340 GCAGAATGGG
* * * * *
1316350 AGTGACTTAGTGTCACTGATAATATTAATGCCGTGGTAGCGATTAGGATCGTGGTGCTATAGTGG
1 AGTGACTTAGTGTCACTGATAATATTGATGCCGTGGTAGCGATCAGAATCATAGTGCTATAGTGG
* * * * * *
1316415 CGAGCAGGGTCGGAGTGACTTGGTGCCACTGACAGTATTGATGCCGTGGTGGCAATCATGATCGT
66 CGAGCAAGATCGGAGTGACATGGTGCCACTGACAGTATTGATGCCATGGTGACAATCAGGATCGT
** *
1316480 AGTGCCATGGTGGCTAGCAAGATCAA
131 AGTGCCATGGTGGAAAGCAAAATCAA
* * * * * * *
1316506 AGTGCCATAGTGTCACTAATAGTATTGATGCCATGGTAGCGATCAGAATTATAGTGAC-ATGGTG
1 AGTGACTTAGTGTCACTGATAATATTGATGCCGTGGTAGCGATCAGAATCATAGTG-CTATAGTG
* * * * *
1316570 GCTAGCAAGATCGGAGTGCCATGGTGTCAGTGACAGTATTGATGCCATGGTGACGATCAGGATCG
65 GCGAGCAAGATCGGAGTGACATGGTGCCACTGACAGTATTGATGCCATGGTGACAATCAGGATCG
***
1316635 TAGTGCCATGGTGGAAAGCAAAATTGG
130 TAGTGCCATGGTGGAAAGCAAAATCAA
* * * * *
1316662 ATTGACTTGGTGTCACTGACAATACTGATGTCGTGGTAGCGATC
1 AGTGACTTAGTGTCACTGATAATATTGATGCCGTGGTAGCGATC
1316706 GAAGTGACTT
Statistics
Matches: 160, Mismatches: 39, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
156 159 0.99
157 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (156 bp):
AGTGACTTAGTGTCACTGATAATATTGATGCCGTGGTAGCGATCAGAATCATAGTGCTATAGTGG
CGAGCAAGATCGGAGTGACATGGTGCCACTGACAGTATTGATGCCATGGTGACAATCAGGATCGT
AGTGCCATGGTGGAAAGCAAAATCAA
Found at i:1316750 original size:46 final size:46
Alignment explanation
Indices: 1316664--1316751 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
1316654 AAAATTGGAT
* * *
1316664 TGACTTGGTGTCACTGACAATACTGATGTCGTGGTAGCGATCGAAG
1 TGACTTGGTGTCACTGACAATACTGATGCCATGATAGCGATCGAAG
* * *
1316710 TGACTTGGTGTCACTGACAGTATTGATGCCATGATGGCGATC
1 TGACTTGGTGTCACTGACAATACTGATGCCATGATAGCGATC
1316752 AGGATCGTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (46 bp):
TGACTTGGTGTCACTGACAATACTGATGCCATGATAGCGATCGAAG
Found at i:1316772 original size:26 final size:26
Alignment explanation
Indices: 1316736--1316794 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
1316726 ACAGTATTGA
* **
1316736 TGCCATGATGGCGATCAGGATCGTAG
1 TGCCATGATGGCGAGCAGGATCAAAG
*
1316762 TGCCATGATGGCTAGCAGGATCAAAG
1 TGCCATGATGGCGAGCAGGATCAAAG
1316788 TGCCATG
1 TGCCATG
1316795 GTGTCACTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.22
Consensus pattern (26 bp):
TGCCATGATGGCGAGCAGGATCAAAG
Found at i:1316828 original size:124 final size:124
Alignment explanation
Indices: 1316591--1316829 Score: 291
Period size: 124 Copynumber: 1.9 Consensus size: 124
1316581 CGGAGTGCCA
* * *
1316591 TGGTGTCAGTGACAGTATTGATGCCATGGTGACGATCAGGATCGTAGTGCCATGGTGGAAAGCAA
1 TGGTGTCACTGACAGTATTGATGCCATGATGACGATCAGGATCGTAGTGCCATGATGGAAAGCAA
*** * * * *
1316656 AATTGGATTGACTTGGTGTCACTGACAATACTGATGTCGTGGTAGCGATCGAAGTGACT
66 AATCAAAGTGACATGGTGTCACTGACAATACTGATCTCATGGTAGCGATCGAAGTGACT
* ** *
1316715 TGGTGTCACTGACAGTATTGATGCCATGATGGCGATCAGGATCGTAGTGCCATGATGGCTAGCAG
1 TGGTGTCACTGACAGTATTGATGCCATGATGACGATCAGGATCGTAGTGCCATGATGGAAAGCAA
* * * * *
1316780 GATCAAAGTGCCATGGTGTCACTGACATTAGTGATACT-ATGGTGGCGATC
66 AATCAAAGTGACATGGTGTCACTGACAATACTGAT-CTCATGGTAGCGATC
1316830 AGGATCGTGG
Statistics
Matches: 95, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
124 94 0.99
125 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (124 bp):
TGGTGTCACTGACAGTATTGATGCCATGATGACGATCAGGATCGTAGTGCCATGATGGAAAGCAA
AATCAAAGTGACATGGTGTCACTGACAATACTGATCTCATGGTAGCGATCGAAGTGACT
Found at i:1316836 original size:78 final size:78
Alignment explanation
Indices: 1316715--1316867 Score: 216
Period size: 78 Copynumber: 2.0 Consensus size: 78
1316705 CGAAGTGACT
* * * *
1316715 TGGTGTCACTGACAGTATTGATGCCATGATGGCGATCAGGATCGTAGTGCCATGATGGCTAGCAG
1 TGGTGTCACTGACAGTAGTGATACCATGATGGCGATCAGGATCGTAGTGCCATGATGGCGAGCAA
1316780 GATCAAAGTGCCA
66 GATCAAAGTGCCA
* * * * *
1316793 TGGTGTCACTGACATTAGTGATACTATGGTGGCGATCAGGATCGTGGTGCCATGGTGGCGAGCAA
1 TGGTGTCACTGACAGTAGTGATACCATGATGGCGATCAGGATCGTAGTGCCATGATGGCGAGCAA
*
1316858 GATCAGAGTG
66 GATCAAAGTG
1316868 ACTTGGAATT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (78 bp):
TGGTGTCACTGACAGTAGTGATACCATGATGGCGATCAGGATCGTAGTGCCATGATGGCGAGCAA
GATCAAAGTGCCA
Found at i:1318403 original size:27 final size:27
Alignment explanation
Indices: 1318365--1318419 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1318355 CCAAGTATAA
1318365 ATCTGACAATTAGAGTGAATATTGACT
1 ATCTGACAATTAGAGTGAATATTGACT
1318392 ATCTGACAATTAGAGTGAATATTGACT
1 ATCTGACAATTAGAGTGAATATTGACT
1318419 A
1 A
1318420 CTAAGATTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (27 bp):
ATCTGACAATTAGAGTGAATATTGACT
Found at i:1318544 original size:22 final size:23
Alignment explanation
Indices: 1318519--1318573 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
1318509 AATTTAAAAA
* *
1318519 ATATTTTATTAAAAAT-AATTAT
1 ATATTATATTAAAAATAAATAAT
* *
1318541 ATATTATATTTATAATAAATAAT
1 ATATTATATTAAAAATAAATAAT
1318564 ATATTA-ATTA
1 ATATTATATTA
1318574 TAATTAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTATATTAAAAATAAATAAT
Found at i:1318595 original size:13 final size:13
Alignment explanation
Indices: 1318569--1318598 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1318559 ATAATATATT
1318569 AATTATAATTAAA
1 AATTATAATTAAA
1318582 AATTA-AATTAAA
1 AATTATAATTAAA
1318594 AATTA
1 AATTA
1318599 CTTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATTATAATTAAA
Found at i:1318624 original size:28 final size:26
Alignment explanation
Indices: 1318574--1318687 Score: 73
Period size: 28 Copynumber: 4.6 Consensus size: 26
1318564 ATATTAATTA
1318574 TAATT-AA-AAATTA-AATTAAAAAT
1 TAATTAAATAAATTATAATTAAAAAT
* * *
1318597 TACTTAATTTAATTATAATTAATCAAAT
1 TAATTAAATAAATTATAATTAA--AAAT
** * *
1318625 TAATTAAATAAATTATTTTTTATAAT
1 TAATTAAATAAATTATAATTAAAAAT
* *
1318651 TAA-TAAAT--TTTAAAATT--AAAT
1 TAATTAAATAAATTATAATTAAAAAT
1318672 TAATTAAATAAATTAT
1 TAATTAAATAAATTAT
1318688 TTTTTATAAT
Statistics
Matches: 66, Mismatches: 17, Indels: 15
0.67 0.17 0.15
Matches are distributed among these distances:
21 6 0.09
22 5 0.08
23 9 0.14
24 4 0.06
25 10 0.15
26 12 0.18
28 20 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TAATTAAATAAATTATAATTAAAAAT
Found at i:1318627 original size:19 final size:18
Alignment explanation
Indices: 1318555--1318659 Score: 72
Period size: 18 Copynumber: 5.8 Consensus size: 18
1318545 TATATTTATA
* *
1318555 ATAAATAATATATTAATT
1 ATAATTAATAAATTAATT
1318573 ATAATTAA-AAATTAAATT
1 ATAATTAATAAATT-AATT
* * *
1318591 AAAAATTACTTAATTTAATT
1 -ATAATTA-ATAAATTAATT
1318611 ATAATTAATCAAATTAATT
1 ATAATTAAT-AAATTAATT
* * **
1318630 A-AATAAAT-TATTTTTT
1 ATAATTAATAAATTAATT
1318646 ATAATTAATAAATT
1 ATAATTAATAAATT
1318660 TTAAAATTAA
Statistics
Matches: 66, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
16 6 0.09
17 10 0.15
18 21 0.32
19 21 0.32
20 4 0.06
21 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTAATAAATTAATT
Found at i:1318638 original size:9 final size:9
Alignment explanation
Indices: 1318574--1318686 Score: 61
Period size: 9 Copynumber: 13.7 Consensus size: 9
1318564 ATATTAATTA
1318574 TAATTAAA-
1 TAATTAAAT
1318582 -AATTAAAT
1 TAATTAAAT
1318590 TAA--AAAT
1 TAATTAAAT
* *
1318597 TACTTAATT
1 TAATTAAAT
1318606 TAATTATAAT
1 TAATTA-AAT
*
1318616 TAATCAAAT
1 TAATTAAAT
1318625 TAATTAAAT
1 TAATTAAAT
*
1318634 AAATT--AT
1 TAATTAAAT
**
1318641 TTTTTATAAT
1 TAATTA-AAT
1318651 TAA-TAAAT
1 TAATTAAAT
1318659 T--TT-AA-
1 TAATTAAAT
1318664 -AATTAAAT
1 TAATTAAAT
1318672 TAATTAAAT
1 TAATTAAAT
*
1318681 AAATTA
1 TAATTA
1318687 TTTTTTATAA
Statistics
Matches: 78, Mismatches: 13, Indels: 27
0.66 0.11 0.23
Matches are distributed among these distances:
6 4 0.05
7 20 0.26
8 4 0.05
9 40 0.51
10 10 0.13
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
TAATTAAAT
Found at i:1318655 original size:21 final size:22
Alignment explanation
Indices: 1318625--1318706 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 22
1318615 TTAATCAAAT
1318625 TAATTAAATAAATTATTTTTTA
1 TAATTAAATAAATTATTTTTTA
**
1318647 TAATT-AATAAATT-TTAAAATTAAA
1 TAATTAAATAAATTATT----TTTTA
1318671 TTAATTAAATAAATTATTTTTTA
1 -TAATTAAATAAATTATTTTTTA
*
1318694 TAA-TCAATAAATT
1 TAATTAAATAAATT
1318707 TTAAAAACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
20 2 0.04
21 17 0.35
22 8 0.17
23 3 0.06
24 3 0.06
25 5 0.10
26 8 0.17
27 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATTAAATAAATTATTTTTTA
Done.