Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 4 of 185
Found at i:1059498 original size:24 final size:23
Alignment explanation
Indices: 1059456--1059535 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 23
1059446 AATAGTAAGG
*
1059456 ATAATAATAAATAAA-ATAATAAA
1 ATAATAA-AAACAAATATAATAAA
* *
1059479 ACTAATAAAACCAAATATAATGAAT
1 A-TAATAAAAACAAATATAAT-AAA
* *
1059504 ATAATAAAAATAAATAAAAT-AA
1 ATAATAAAAACAAATATAATAAA
1059526 ATAATAAAAA
1 ATAATAAAAA
1059536 GAAAAAGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 11 0.23
23 6 0.13
24 27 0.57
25 3 0.06
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (23 bp):
ATAATAAAAACAAATATAATAAA
Found at i:1064541 original size:20 final size:21
Alignment explanation
Indices: 1064513--1064558 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1064503 AATTAGAATG
*
1064513 AAAAA-ATTAAA-TAAATATT
1 AAAAATATTAAATTAAAAATT
1064532 AAAAATATTAAATTAAAAATT
1 AAAAATATTAAATTAAAAATT
1064553 AAAAAT
1 AAAAAT
1064559 GGCTAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 5 0.21
20 6 0.25
21 13 0.54
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATATTAAATTAAAAATT
Found at i:1064569 original size:21 final size:20
Alignment explanation
Indices: 1064520--1064569 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1064510 ATGAAAAAAT
* *
1064520 TAAATAAATATTAAAAATAT
1 TAAATAAAAATTAAAAATAC
*
1064540 TAAATTAAAAATTAAAAATGGC
1 TAAA-TAAAAATTAAAAAT-AC
1064562 TAAATAAA
1 TAAATAAA
1064570 TGAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (20 bp):
TAAATAAAAATTAAAAATAC
Found at i:1075882 original size:16 final size:15
Alignment explanation
Indices: 1075861--1075890 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1075851 ATTCACCCTA
1075861 AATATTGATTTAATTT
1 AATATTG-TTTAATTT
1075877 AATATTGTTTAATT
1 AATATTGTTTAATT
1075891 ATTTAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
AATATTGTTTAATTT
Found at i:1077233 original size:25 final size:25
Alignment explanation
Indices: 1077199--1077248 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1077189 TTTAAAGTAT
1077199 TAGGGTTTTTCCATTGATGAATATG
1 TAGGGTTTTTCCATTGATGAATATG
1077224 TAGGGTTTTTCCATTGATGAATATG
1 TAGGGTTTTTCCATTGATGAATATG
1077249 CTTGAAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (25 bp):
TAGGGTTTTTCCATTGATGAATATG
Found at i:1078732 original size:3 final size:3
Alignment explanation
Indices: 1078724--1078777 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
1078714 GTGAGGTAAG
1078724 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1078772 TAT TAT
1 TAT TAT
1078778 GAGTGAGAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1080684 original size:25 final size:25
Alignment explanation
Indices: 1080639--1080690 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1080629 CACACCACAA
* *
1080639 CTCGTATGAGCTTCCTAATTTGCAG
1 CTCGTATGAACTTCCTAATTTACAG
*
1080664 CTCGTATGAACTT-CTCGATTTACAG
1 CTCGTATGAACTTCCT-AATTTACAG
1080689 CT
1 CT
1080691 TGTGAGAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (25 bp):
CTCGTATGAACTTCCTAATTTACAG
Found at i:1088571 original size:20 final size:21
Alignment explanation
Indices: 1088546--1088587 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1088536 TAGATTTGAA
1088546 TGTTTAACA-TAAATTGAATG
1 TGTTTAACATTAAATTGAATG
* *
1088566 TGTTTAGCATTAAATTGCATG
1 TGTTTAACATTAAATTGAATG
1088587 T
1 T
1088588 ATAAGTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (21 bp):
TGTTTAACATTAAATTGAATG
Found at i:1091325 original size:19 final size:20
Alignment explanation
Indices: 1091288--1091327 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1091278 TCAAGGTAGA
1091288 ATATGATTGCTTTGGTCTGC
1 ATATGATTGCTTTGGTCTGC
*
1091308 ATATGATT-CTTTGTTCTGC
1 ATATGATTGCTTTGGTCTGC
1091327 A
1 A
1091328 GACTGAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.47
Consensus pattern (20 bp):
ATATGATTGCTTTGGTCTGC
Found at i:1095634 original size:15 final size:15
Alignment explanation
Indices: 1095614--1095644 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1095604 CAAAAATTTT
1095614 AAAAAACTACCAAAA
1 AAAAAACTACCAAAA
*
1095629 AAAAAAGTACCAAAA
1 AAAAAACTACCAAAA
1095644 A
1 A
1095645 TTGAGAGATT
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:0.74, C:0.16, G:0.03, T:0.06
Consensus pattern (15 bp):
AAAAAACTACCAAAA
Found at i:1096927 original size:3 final size:3
Alignment explanation
Indices: 1096919--1096953 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1096909 ATGTTTAAAT
1096919 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1096954 TTTTTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1100544 original size:23 final size:24
Alignment explanation
Indices: 1100500--1100553 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
1100490 ATAATTTTAG
1100500 AATTTTTTTAAGATTTAAATAATAT
1 AATTTTTTTAAGATTT-AATAATAT
*
1100525 AATTTTTTTAGGATTT-ATAATAT
1 AATTTTTTTAAGATTTAATAATAT
1100548 AATTTT
1 AATTTT
1100554 AGAAAGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 13 0.46
25 15 0.54
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (24 bp):
AATTTTTTTAAGATTTAATAATAT
Found at i:1107033 original size:19 final size:19
Alignment explanation
Indices: 1107009--1107059 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
1106999 TTAAATTGAT
1107009 AATAATTTTATCTCA-TTTA
1 AATAATTTTAT-TCACTTTA
1107028 AATAATTTGT-TTCACTTTA
1 AATAATTT-TATTCACTTTA
1107047 ATATAATTTTATT
1 A-ATAATTTTATT
1107060 TTAAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.11
19 15 0.54
20 10 0.36
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (19 bp):
AATAATTTTATTCACTTTA
Found at i:1107242 original size:16 final size:15
Alignment explanation
Indices: 1107221--1107271 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
1107211 TACCAAACCT
1107221 AAATGACTCGAACATG
1 AAATGACTCGAAC-TG
* *
1107237 AAATGATTCAAACTCG
1 AAATGACTCGAACT-G
1107253 AAATGACTCGAACTTG
1 AAATGACTCGAAC-TG
1107269 AAA
1 AAA
1107272 CTAACCCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (15 bp):
AAATGACTCGAACTG
Found at i:1129314 original size:8 final size:8
Alignment explanation
Indices: 1129301--1129335 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
1129291 CAGCCTCTAC
1129301 AAAAAACA
1 AAAAAACA
1129309 AAAAAACA
1 AAAAAACA
1129317 AAAAAACA
1 AAAAAACA
1129325 AAAAAACA
1 AAAAAACA
1129333 AAA
1 AAA
1129336 CTTGAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:1134670 original size:31 final size:29
Alignment explanation
Indices: 1134635--1134693 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1134625 ATTGTCATGT
1134635 TTGAGTTGGCAAAATTTGGCAACAAATTATC
1 TTGAGTT-G-AAAATTTGGCAACAAATTATC
* *
1134666 TTGAGTTGTAATTTTGGCAACAAATTAT
1 TTGAGTTGAAAATTTGGCAACAAATTAT
1134694 TTTGGGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 18 0.69
30 1 0.04
31 7 0.27
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (29 bp):
TTGAGTTGAAAATTTGGCAACAAATTATC
Found at i:1140175 original size:21 final size:22
Alignment explanation
Indices: 1140140--1140187 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1140130 CAAATGTGTT
1140140 AAAATTATTAATTAAAAATAA-A
1 AAAATTATTAATT-AAAATAAGA
*
1140162 AAAATTATT-TTTAAAATAAGA
1 AAAATTATTAATTAAAATAAGA
1140183 AAAAT
1 AAAAT
1140188 GTGTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 8 0.33
22 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATTATTAATTAAAATAAGA
Found at i:1140177 original size:20 final size:22
Alignment explanation
Indices: 1140140--1140187 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
1140130 CAAATGTGTT
1140140 AAAATTATTAATTAAAAATAA-A
1 AAAATTATT-ATTAAAAATAAGA
*
1140162 AAAATTATT-TTTAAAATAAGA
1 AAAATTATTATTAAAAATAAGA
1140183 AAAAT
1 AAAAT
1140188 GTGTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 6 0.25
22 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATTATTATTAAAAATAAGA
Found at i:1140568 original size:43 final size:43
Alignment explanation
Indices: 1140520--1140691 Score: 272
Period size: 43 Copynumber: 4.0 Consensus size: 43
1140510 TCAAAAGTAC
* * * *
1140520 TTCTCAAAATCATTTTTCAAAAGCATTTTTTACAAGAACTTCT
1 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGCACTTCT
1140563 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGCACTTCT
1 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGCACTTCT
* *
1140606 TTCTCAAAATTATTTTTCGAATGCACTTTTTAAAAGCACTTCT
1 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGCACTTCT
* *
1140649 TTCTCAAAATTATTTTTCGAAAGCACTTTTTAAAAGCAATTCT
1 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGCACTTCT
1140692 CAAAAGCAAT
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 121 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (43 bp):
TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGCACTTCT
Found at i:1140623 original size:86 final size:86
Alignment explanation
Indices: 1140520--1140870 Score: 329
Period size: 86 Copynumber: 4.0 Consensus size: 86
1140510 TCAAAAGTAC
* *
1140520 TTCTCAAAATCATTTTTCAAAAGCATTTTTTACAAGAACTTCTTTCTCAAAATCATTTTTCGAAA
1 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGAACTTCTTTCTCAAAATCATTTTTCGAAA
*
1140585 GCACTTTTTAAAAGCACTTCT
66 GCACTTTTTAAAAGCAATTCT
* * * * *
1140606 TTCTCAAAATTATTTTTCGAATGCACTTTTTAAAAGCACTTCTTTCTCAAAATTATTTTTCGAAA
1 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGAACTTCTTTCTCAAAATCATTTTTCGAAA
1140671 GCACTTTTTAAAAGCAA----
66 GCACTTTTTAAAAGCAATTCT
* * ** * ** *
1140688 TTCTCAAAAGCAATGCT-AAACACTCAAATCTTAAACCA-AACTTTTCAAAAGTACTTCTCAAAA
1 TTCTCAAAATCATTTTTCAAA-A-GCACTTTTTAAA--AGAAC--TTC-----T--TTCTCAAAA
* * *
1140751 TCATTTTTCAAAAGCACTTTTTAAAAGTACTTCT
53 TCATTTTTCGAAAGCACTTTTTAAAAGCAATTCT
* *
1140785 TTCTCAAAATCATTTTTCGAAAA-CACTTTTTAAAAGCACTTCTTTCTCAAAATCAATTTTCGAA
1 TTCTCAAAATCATTTTTC-AAAAGCACTTTTTAAAAGAACTTCTTTCTCAAAATCATTTTTCGAA
*
1140849 AGCACTTTTTAAAAGCACTTCT
65 AGCACTTTTTAAAAGCAATTCT
1140871 CAAAAGCAAT
Statistics
Matches: 210, Mismatches: 35, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
81 2 0.01
82 12 0.06
83 8 0.04
84 2 0.01
85 1 0.00
86 117 0.56
88 1 0.00
91 1 0.00
93 38 0.18
94 1 0.00
95 2 0.01
96 8 0.04
97 13 0.06
98 1 0.00
99 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (86 bp):
TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGAACTTCTTTCTCAAAATCATTTTTCGAAA
GCACTTTTTAAAAGCAATTCT
Found at i:1140644 original size:13 final size:14
Alignment explanation
Indices: 1140507--1140878 Score: 90
Period size: 13 Copynumber: 26.9 Consensus size: 14
1140497 TAAACCAAAC
*
1140507 TTTTCAAAAGTAC-
1 TTTTCAAAAGCACT
* *
1140520 TTCTCAAAATCA-T
1 TTTTCAAAAGCACT
*
1140533 TTTTCAAAAGCATT
1 TTTTCAAAAGCACT
*
1140547 TTTTACAAGAA-CTTCT
1 TTTT-CAA-AAGC-ACT
* *
1140563 TTCTCAAAATCA-T
1 TTTTCAAAAGCACT
*
1140576 TTTTCGAAAGCACT
1 TTTTCAAAAGCACT
1140590 TTTT-AAAAGCACTT
1 TTTTCAAAAGCAC-T
**
1140604 CTTTCTCAAAATTA-T
1 -TTT-TCAAAAGCACT
* *
1140619 TTTTCGAATGCACT
1 TTTTCAAAAGCACT
1140633 TTTT-AAAAGCACTT
1 TTTTCAAAAGCAC-T
**
1140647 CTTTCTCAAAATTA-T
1 -TTT-TCAAAAGCACT
*
1140662 TTTTCGAAAGCACT
1 TTTTCAAAAGCACT
*
1140676 TTTT-AAAAGCA-A
1 TTTTCAAAAGCACT
*
1140688 TTCTCAAAAGCA--
1 TTTTCAAAAGCACT
* * *
1140700 -ATGCTAAA-CACT
1 TTTTCAAAAGCACT
*** * *
1140712 CAAATCTTAAACCAAACT
1 -TTTTC-AAAAGC-A-CT
*
1140730 T-TTCAAAAGTAC-
1 TTTTCAAAAGCACT
* *
1140742 TTCTCAAAATCA-T
1 TTTTCAAAAGCACT
1140755 TTTTCAAAAGCACT
1 TTTTCAAAAGCACT
*
1140769 TTTT-AAAAGTACTT
1 TTTTCAAAAGCAC-T
*
1140783 CTTTCTCAAAATCA-T
1 -TTT-TCAAAAGCACT
1140798 TTTTCGAAAA-CACT
1 TTTTC-AAAAGCACT
1140812 TTTT-AAAAGCACTT
1 TTTTCAAAAGCAC-T
* *
1140826 CTTTCTCAAAATCA-A
1 -TTT-TCAAAAGCACT
*
1140841 TTTTCGAAAGCACT
1 TTTTCAAAAGCACT
1140855 TTTT-AAAAGCAC-
1 TTTTCAAAAGCACT
*
1140867 TTCTCAAAAGCA
1 TTTTCAAAAGCA
1140879 ATGCTAAACT
Statistics
Matches: 262, Mismatches: 55, Indels: 84
0.65 0.14 0.21
Matches are distributed among these distances:
10 2 0.01
11 4 0.02
12 11 0.04
13 119 0.45
14 59 0.23
15 30 0.11
16 13 0.05
17 22 0.08
18 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (14 bp):
TTTTCAAAAGCACT
Found at i:1140776 original size:179 final size:179
Alignment explanation
Indices: 1140563--1140887 Score: 578
Period size: 179 Copynumber: 1.8 Consensus size: 179
1140553 AAGAACTTCT
* * *
1140563 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGCACTTCTTTCTCAAAATTATTTTTCGAAT
1 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGCACTTCTTTCTCAAAATCATTTTTCGAAA
* * *
1140628 GCACTTTTTAAAAGCACTTCTTTCTCAAAATTATTTTTCGAAAGCACTTTTTAAAAGCAATTCTC
66 ACACTTTTTAAAAGCACTTCTTTCTCAAAATCAATTTTCGAAAGCACTTTTTAAAAGCAATTCTC
1140693 AAAAGCAATGCTAAACACTCAAATCTTAAACCAAACTTTTCAAAAGTAC
131 AAAAGCAATGCTAAACACTCAAATCTTAAACCAAACTTTTCAAAAGTAC
*
1140742 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGTACTTCTTTCTCAAAATCATTTTTCGAAA
1 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGCACTTCTTTCTCAAAATCATTTTTCGAAA
*
1140807 ACACTTTTTAAAAGCACTTCTTTCTCAAAATCAATTTTCGAAAGCACTTTTTAAAAGCACTTCTC
66 ACACTTTTTAAAAGCACTTCTTTCTCAAAATCAATTTTCGAAAGCACTTTTTAAAAGCAATTCTC
1140872 AAAAGCAATGCTAAAC
131 AAAAGCAATGCTAAAC
1140888 TAACCCTAAG
Statistics
Matches: 138, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
179 138 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.36
Consensus pattern (179 bp):
TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGCACTTCTTTCTCAAAATCATTTTTCGAAA
ACACTTTTTAAAAGCACTTCTTTCTCAAAATCAATTTTCGAAAGCACTTTTTAAAAGCAATTCTC
AAAAGCAATGCTAAACACTCAAATCTTAAACCAAACTTTTCAAAAGTAC
Found at i:1140802 original size:43 final size:43
Alignment explanation
Indices: 1140742--1140870 Score: 215
Period size: 43 Copynumber: 3.0 Consensus size: 43
1140732 TCAAAAGTAC
*
1140742 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGTACTTCT
1 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGCACTTCT
1140785 TTCTCAAAATCATTTTTCGAAAA-CACTTTTTAAAAGCACTTCT
1 TTCTCAAAATCATTTTTC-AAAAGCACTTTTTAAAAGCACTTCT
* *
1140828 TTCTCAAAATCAATTTTCGAAAGCACTTTTTAAAAGCACTTCT
1 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGCACTTCT
1140871 CAAAAGCAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
42 3 0.04
43 74 0.91
44 4 0.05
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (43 bp):
TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGCACTTCT
Found at i:1144486 original size:23 final size:20
Alignment explanation
Indices: 1144458--1144509 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1144448 TCGACCTATT
*
1144458 TTTTAATAAACACCAAAAAATTA
1 TTTTAA-AAACA--AAAAAACTA
*
1144481 TTTTAAAAATAAAAAAACTA
1 TTTTAAAAACAAAAAAACTA
1144501 TTTTAAAAA
1 TTTTAAAAA
1144510 TATTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 17 0.63
22 4 0.15
23 6 0.22
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
TTTTAAAAACAAAAAAACTA
Found at i:1144496 original size:19 final size:20
Alignment explanation
Indices: 1144472--1144511 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1144462 AATAAACACC
*
1144472 AAAAAATTATTTTAAAAATA
1 AAAAAACTATTTTAAAAATA
1144492 AAAAAACTATTTTAAAAATA
1 AAAAAACTATTTTAAAAATA
1144512 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAACTATTTTAAAAATA
Found at i:1149165 original size:33 final size:33
Alignment explanation
Indices: 1149126--1149199 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
1149116 TTCCTTTTGA
* * ** *
1149126 AAATCAAGAGTTTGTTGTTGTATTTGTTGTTGG
1 AAATCAAGAGTTTGTCGTTGTATCTACTGTTGC
*
1149159 AAATCAATAGTTTGTCGTTGTATCTACTGTTGC
1 AAATCAAGAGTTTGTCGTTGTATCTACTGTTGC
1149192 AAATCAAG
1 AAATCAAG
1149200 CAGATTAGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (33 bp):
AAATCAAGAGTTTGTCGTTGTATCTACTGTTGC
Found at i:1151435 original size:19 final size:18
Alignment explanation
Indices: 1151386--1151441 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
1151376 ATTTGTTCCT
1151386 AATTAAACTCTAAAAGATA
1 AATTAAA-TCTAAAAGATA
** *
1151405 AA-TAAAGATAAAAGCTGA
1 AATTAAATCTAAAAGAT-A
*
1151423 AATTAAATCTAAAAAATA
1 AATTAAATCTAAAAGATA
1151441 A
1 A
1151442 TCCTAACAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
17 7 0.25
18 9 0.32
19 12 0.43
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.23
Consensus pattern (18 bp):
AATTAAATCTAAAAGATA
Found at i:1154263 original size:30 final size:31
Alignment explanation
Indices: 1154239--1154297 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1154229 GTAAATACTC
*
1154239 AAAATTTGAGGGGTTAA-AATGTAAATATAA
1 AAAATTTGAAGGGTTAATAATGTAAATATAA
*
1154269 AAAATTTGAAGGGTTAATAGTGTAAATAT
1 AAAATTTGAAGGGTTAATAATGTAAATAT
1154298 TTTAAGGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.32
Consensus pattern (31 bp):
AAAATTTGAAGGGTTAATAATGTAAATATAA
Found at i:1156865 original size:53 final size:54
Alignment explanation
Indices: 1156802--1156909 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
1156792 ATTGGTACAA
1156802 GAATTAAATTGTAAAGCATG-AAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1 GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1156855 GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1 GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1156909 G
1 G
1156910 CATGCATGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 20 0.37
54 34 0.63
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (54 bp):
GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
Found at i:1157440 original size:44 final size:44
Alignment explanation
Indices: 1157380--1157467 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
1157370 ATTGACTATA
1157380 AAGGTGGTTGTTATGTGATGATTCCACCGAGTATCAT-TTATTAT
1 AAGGTGGTTGTTATGTGATGATTCCACCGAGTATC-TGTTATTAT
* *
1157424 AAGGTGGTTGTTATGTGCTGATTCCACCGTGTATCTGTTATTAT
1 AAGGTGGTTGTTATGTGATGATTCCACCGAGTATCTGTTATTAT
1157468 TCCGAAGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.42
Consensus pattern (44 bp):
AAGGTGGTTGTTATGTGATGATTCCACCGAGTATCTGTTATTAT
Found at i:1162907 original size:11 final size:11
Alignment explanation
Indices: 1162891--1162915 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1162881 CTCTCCAAAG
1162891 TTTTTTTGTTT
1 TTTTTTTGTTT
1162902 TTTTTTTGTTT
1 TTTTTTTGTTT
1162913 TTT
1 TTT
1162916 GTTTAGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:1187813 original size:5 final size:5
Alignment explanation
Indices: 1187803--1187832 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1187793 GCTGGGGGCA
*
1187803 ATTGT ATTGT ATTGT ATTGT ATTGT GTTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
1187833 CTGTACACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (5 bp):
ATTGT
Found at i:1190642 original size:11 final size:10
Alignment explanation
Indices: 1190611--1190645 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
1190601 TTTCAAACAT
1190611 AAATTTTTTA
1 AAATTTTTTA
1190621 AAATTTATTTA
1 AAATTT-TTTA
1190632 ATAATTTTTTA
1 A-AATTTTTTA
1190643 AAA
1 AAA
1190646 GTTAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.35
11 10 0.43
12 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
AAATTTTTTA
Found at i:1190867 original size:22 final size:22
Alignment explanation
Indices: 1190842--1190884 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1190832 TTTTAAAATA
* *
1190842 TAAAAAATAGGGACTAAATTTC
1 TAAAAAACAAGGACTAAATTTC
*
1190864 TAAAATACAAGGACTAAATTT
1 TAAAAAACAAGGACTAAATTT
1190885 TTAATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (22 bp):
TAAAAAACAAGGACTAAATTTC
Found at i:1195014 original size:27 final size:27
Alignment explanation
Indices: 1194979--1195032 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1194969 GAAGCAACTT
* * *
1194979 TCTCGCTGTTGTTGGCTTCGTGTTGAA
1 TCTCACTGTTGTTCGCTTCATGTTGAA
1195006 TCTCACTGTTGTTCGCTTCATGTTGAA
1 TCTCACTGTTGTTCGCTTCATGTTGAA
1195033 GTTCGAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.44
Consensus pattern (27 bp):
TCTCACTGTTGTTCGCTTCATGTTGAA
Found at i:1207055 original size:26 final size:26
Alignment explanation
Indices: 1207008--1207083 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
1206998 TTTCTCACCT
*
1207008 AATTTTACCC-CAGTAAAATTTTGAC
1 AATTTTACCCTCGGTAAAATTTTGAC
1207033 AATTTTACCCTCGGTAAAATTTTGAC
1 AATTTTACCCTCGGTAAAATTTTGAC
* *
1207059 GATTTTACCACT-GATAAAATTTTGA
1 AATTTTACC-CTCGGTAAAATTTTGA
1207084 GAAAATTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 10 0.22
26 34 0.74
27 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (26 bp):
AATTTTACCCTCGGTAAAATTTTGAC
Found at i:1207403 original size:28 final size:27
Alignment explanation
Indices: 1207363--1207437 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 27
1207353 ATTTCGTTCA
1207363 TTTGTGGTGTAATATGAAAGGAAAAGC
1 TTTGTGGTGTAATATGAAAGGAAAAGC
1207390 TTTTGTGGTGTAATATGAAA--AAAAGC
1 -TTTGTGGTGTAATATGAAAGGAAAAGC
* * *
1207416 -CTGTGGCGGAATATGAAAGGAA
1 TTTGTGGTGTAATATGAAAGGAA
1207438 TGCCCTTGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 15 0.36
26 8 0.19
28 19 0.45
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.28
Consensus pattern (27 bp):
TTTGTGGTGTAATATGAAAGGAAAAGC
Found at i:1208836 original size:20 final size:19
Alignment explanation
Indices: 1208790--1208828 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1208780 TTCAAAATAT
1208790 AAATAAATAAATTTCTAAA
1 AAATAAATAAATTTCTAAA
1208809 AAATTAAATTAAATTT-TAAA
1 AAA-TAAA-TAAATTTCTAAA
1208829 TATATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 8 0.44
21 7 0.39
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAAATAAATTTCTAAA
Found at i:1209509 original size:30 final size:28
Alignment explanation
Indices: 1209429--1209509 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
1209419 CCCTTCAATG
* *
1209429 TTTACAGATTCTATCAATTTAGTCATAA
1 TTTACAAATTCTATCAATTTAGCCATAA
* *
1209457 TTCTAAAAAATCTA-CAAATTTAGCCATCAA
1 TT-TACAAATTCTATC-AATTTAGCCAT-AA
*
1209487 CTTTACACATTCTATCAATTTAG
1 -TTTACAAATTCTATCAATTTAG
1209510 TTTTATTTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
28 3 0.07
29 18 0.44
30 17 0.41
31 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (28 bp):
TTTACAAATTCTATCAATTTAGCCATAA
Found at i:1209563 original size:17 final size:17
Alignment explanation
Indices: 1209529--1209568 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1209519 TTAAAAACGC
** *
1209529 AAATTTTAAATTTTAAA
1 AAATTTTAAAAGTAAAA
1209546 AAATTTTAAAAGTAAAA
1 AAATTTTAAAAGTAAAA
1209563 AAATTT
1 AAATTT
1209569 ATTTAAAATT
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:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AAATTTTAAAAGTAAAA
Found at i:1210188 original size:20 final size:20
Alignment explanation
Indices: 1210163--1210204 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1210153 CCTTGAATTG
1210163 TTTATTTATA-AGATTATTAT
1 TTTATTTATACA-ATTATTAT
1210183 TTTATTTATACAATTATTAT
1 TTTATTTATACAATTATTAT
1210203 TT
1 TT
1210205 AAATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATTTATACAATTATTAT
Found at i:1210731 original size:27 final size:27
Alignment explanation
Indices: 1210693--1210745 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1210683 TCTATACCCC
*
1210693 TTGTAATTATCCCGAAAGGGTTTCCAT
1 TTGTAACTATCCCGAAAGGGTTTCCAT
1210720 TTGTAACTATCCCGAAAGGGTTTCCA
1 TTGTAACTATCCCGAAAGGGTTTCCA
1210746 CGTAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
TTGTAACTATCCCGAAAGGGTTTCCAT
Found at i:1214250 original size:5 final size:5
Alignment explanation
Indices: 1214240--1214267 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1214230 AAGTTTGTAA
1214240 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
1214268 GTGATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:1215609 original size:16 final size:18
Alignment explanation
Indices: 1215588--1215626 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1215578 ATAAAAAAAA
*
1215588 TAAAAATA-TAA-TACAT
1 TAAAAATACTAAGAACAT
1215604 TAAAAATACTAAGAACAT
1 TAAAAATACTAAGAACAT
1215622 TAAAA
1 TAAAA
1215627 TAAATGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 3 0.15
18 9 0.45
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAATACTAAGAACAT
Found at i:1217535 original size:20 final size:22
Alignment explanation
Indices: 1217510--1217558 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
1217500 CAAAATTTAT
1217510 ATTTAAAAAAAT-TATAAA-AA
1 ATTTAAAAAAATATATAAAGAA
*
1217530 ATTT-AAAGAATATATAAAGAA
1 ATTTAAAAAAATATATAAAGAA
*
1217551 AGTTAAAA
1 ATTTAAAA
1217559 CTTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 10 0.42
21 5 0.21
22 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
ATTTAAAAAAATATATAAAGAA
Found at i:1220277 original size:21 final size:23
Alignment explanation
Indices: 1220241--1220282 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1220231 TGTAAAAAGT
*
1220241 AAAATATACTTAA-TTTAAATCC
1 AAAATATACATAATTTTAAATCC
1220263 AAAATAT-CATAATTTTAAAT
1 AAAATATACATAATTTTAAAT
1220283 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATATACATAATTTTAAATCC
Found at i:1220353 original size:23 final size:23
Alignment explanation
Indices: 1220318--1220361 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1220308 TATAGAAAAA
1220318 AATAAAAGAGT-AAGAGTAAATTG
1 AATAAAAGAGTAAAG-GTAAATTG
* *
1220341 AATAAATGTGTAAAGGTAAAT
1 AATAAAAGAGTAAAGGTAAAT
1220362 GCTAAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (23 bp):
AATAAAAGAGTAAAGGTAAATTG
Found at i:1221265 original size:11 final size:11
Alignment explanation
Indices: 1221249--1221274 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1221239 ATTTTTTTAA
1221249 TTTTAAAATAC
1 TTTTAAAATAC
1221260 TTTTAAAATAC
1 TTTTAAAATAC
1221271 TTTT
1 TTTT
1221275 TTAAAATTTT
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:1221285 original size:11 final size:11
Alignment explanation
Indices: 1221249--1221331 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
1221239 ATTTTTTTAA
**
1221249 TTTTAAAATAC
1 TTTTAAAATTT
1221260 TTTTAAAATACTT
1 TTTTAAAAT--TT
1221273 TTTTAAAA-TT
1 TTTTAAAATTT
1221283 TTTT-AAA---
1 TTTTAAAATTT
*
1221290 TTTTAAATTTT
1 TTTTAAAATTT
1221301 TTTTAAAATACTTT
1 TTTT-AAA-A-TTT
*
1221315 TTTTTAAATTT
1 TTTTAAAATTT
1221326 TTTTAA
1 TTTTAA
1221332 TTTTAAAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
7 4 0.07
8 2 0.04
9 3 0.05
10 6 0.11
11 21 0.37
12 4 0.07
13 10 0.18
14 7 0.12
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:1221292 original size:41 final size:42
Alignment explanation
Indices: 1221239--1221346 Score: 164
Period size: 42 Copynumber: 2.6 Consensus size: 42
1221229 TTTATTTTTT
1221239 ATTTTTTTAATTTTAAAATACTTTTAAAATAC-TTTTTTAAA
1 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAAA
* * ** *
1221280 ATTTTTTAAATTTTAAATTTTTTTTAAAATACTTTTTTTTAA
1 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAAA
1221322 ATTTTTTTAATTTTAAAATACTTTT
1 ATTTTTTTAATTTTAAAATACTTTT
1221347 TTTAACTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
41 28 0.49
42 29 0.51
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (42 bp):
ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAAA
Found at i:1221315 original size:15 final size:15
Alignment explanation
Indices: 1221297--1221349 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
1221287 AAATTTTAAA
1221297 TTTTTTTTAAAATAC
1 TTTTTTTTAAAATAC
**
1221312 TTTTTTTT-AAATTT
1 TTTTTTTTAAAATAC
1221326 TTTTAATTTTAAAATAC
1 TTTT--TTTTAAAATAC
1221343 TTTTTTT
1 TTTTTTT
1221350 AACTTTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 8 0.26
15 11 0.35
16 4 0.13
17 8 0.26
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTTTTAAAATAC
Found at i:1221348 original size:32 final size:33
Alignment explanation
Indices: 1221300--1221374 Score: 111
Period size: 31 Copynumber: 2.3 Consensus size: 33
1221290 TTTTAAATTT
1221300 TTTTTAAAATACTTTTTTTTAA-ATTT-TTTTAA
1 TTTTTAAAATAC-TTTTTTTAACATTTGTTTTAA
*
1221332 -TTTTAAAATACTTTTTTTAACTTTTGTTTTAA
1 TTTTTAAAATACTTTTTTTAACATTTGTTTTAA
1221364 TTTTTAAAATA
1 TTTTTAAAATA
1221375 AATTTTTGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
30 9 0.23
31 14 0.36
32 6 0.15
33 10 0.26
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (33 bp):
TTTTTAAAATACTTTTTTTAACATTTGTTTTAA
Found at i:1221355 original size:41 final size:42
Alignment explanation
Indices: 1221239--1221368 Score: 137
Period size: 41 Copynumber: 3.1 Consensus size: 42
1221229 TTTATTTTTT
*** *
1221239 ATTTTTTTAATTTTAAAATACTTTTAAAATAC-TTTTTTAAA
1 ATTTTTTTAATTTTAAAATACTTTTTTTATACTTTTTTTTAA
*
1221280 ATTTTTTAAATTTT-AAAT--TTTTTTTAAAATACTTTTTTTTAA
1 ATTTTTTTAATTTTAAAATACTTTTTTT---ATACTTTTTTTTAA
1221322 ATTTTTTTAATTTTAAAATACTTTTTTTA-ACTTTTGTTTT-A
1 ATTTTTTTAATTTTAAAATACTTTTTTTATACTTTT-TTTTAA
1221363 ATTTTT
1 ATTTTT
1221369 AAAATAAATT
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
38 4 0.05
40 4 0.05
41 30 0.40
42 26 0.35
43 4 0.05
45 7 0.09
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (42 bp):
ATTTTTTTAATTTTAAAATACTTTTTTTATACTTTTTTTTAA
Found at i:1221773 original size:11 final size:11
Alignment explanation
Indices: 1221752--1221790 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1221742 AAACAGTAGC
*
1221752 AAACAATAACA
1 AAACAACAACA
*
1221763 AAGCAACAACA
1 AAACAACAACA
*
1221774 AAACATCAACA
1 AAACAACAACA
1221785 AAACAA
1 AAACAA
1221791 TAGTAGGGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.69, C:0.23, G:0.03, T:0.05
Consensus pattern (11 bp):
AAACAACAACA
Found at i:1222412 original size:20 final size:17
Alignment explanation
Indices: 1222379--1222430 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
1222369 TTAAAATTGA
*
1222379 TATAAAATTTATAAATAT
1 TATAAAATTAATAAA-AT
1222397 TATAATAATATAAT-AAAT
1 TATAA-AAT-TAATAAAAT
1222415 TATAAAATTAATAAAA
1 TATAAAATTAATAAAA
1222431 AATATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.13
17 6 0.20
18 12 0.40
19 5 0.17
20 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAAAATTAATAAAAT
Found at i:1222433 original size:47 final size:45
Alignment explanation
Indices: 1222344--1222441 Score: 112
Period size: 47 Copynumber: 2.2 Consensus size: 45
1222334 GATTATAAAA
* *
1222344 TATAAATATTAAATATTAAAAAATGTTAAAATTGATATAAAAT-T
1 TATAAATATTAAATATTAAAAAATGTTAAAATTAATAAAAAATAT
*
1222388 TATAAATATTATAATAATATAATAAAT-TATAAAATTAATAAAAAATAT
1 TATAAATATTA-AAT-AT-TAAAAAATGT-TAAAATTAATAAAAAATAT
1222436 T-TAAAT
1 TATAAAT
1222442 TAAAAATGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
44 11 0.24
45 3 0.07
46 3 0.07
47 27 0.59
48 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (45 bp):
TATAAATATTAAATATTAAAAAATGTTAAAATTAATAAAAAATAT
Found at i:1222487 original size:10 final size:10
Alignment explanation
Indices: 1222474--1222527 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
1222464 AAAATGCAAT
1222474 AAAAATTATA
1 AAAAATTATA
*
1222484 AAAAAATAT-
1 AAAAATTATA
1222493 AAAAATTGATA
1 AAAAATT-ATA
* *
1222504 TAAATTTATA
1 AAAAATTATA
*
1222514 AAAAATCATA
1 AAAAATTATA
1222524 AAAA
1 AAAA
1222528 CTTAAACTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
9 6 0.17
10 24 0.69
11 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:1222498 original size:30 final size:30
Alignment explanation
Indices: 1222472--1222527 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1222462 TAAAAATGCA
1222472 ATAAAAA-TTATAAAAAAAT-ATAAAAATTG
1 ATAAAAATTTAT-AAAAAATCATAAAAATTG
*
1222501 ATATAAATTTATAAAAAATCATAAAAA
1 ATAAAAATTTATAAAAAATCATAAAAA
1222528 CTTAAACTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (30 bp):
ATAAAAATTTATAAAAAATCATAAAAATTG
Found at i:1223014 original size:20 final size:21
Alignment explanation
Indices: 1222991--1223037 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
1222981 TTTTATAATT
1222991 TTTTATAAAATTTT-AATATG
1 TTTTATAAAATTTTAAATATG
*
1223011 TTTTACAAAATTTTAAATATG
1 TTTTATAAAATTTTAAATATG
1223032 TTTTAT
1 TTTTAT
1223038 TTATTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTATAAAATTTTAAATATG
Found at i:1223191 original size:20 final size:19
Alignment explanation
Indices: 1223128--1223191 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
1223118 TAATAATATT
* *
1223128 TTTTTATAATTTTATCTAA
1 TTTTTATGATTTTATATAA
1223147 TTTTTATGATTTTATATAA
1 TTTTTATGATTTTATATAA
*
1223166 TATTTATGATTTT-TAATAA
1 TTTTTATGATTTTAT-ATAA
1223185 CTTTTTA
1 -TTTTTA
1223192 AAAAAAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
18 1 0.03
19 33 0.85
20 5 0.13
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTTATGATTTTATATAA
Found at i:1228673 original size:16 final size:17
Alignment explanation
Indices: 1228640--1228675 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1228630 CATGTATATC
*
1228640 ATTTTTTTCATATATTT
1 ATTTTTTTAATATATTT
1228657 ATTTTTTTAATAT-TTT
1 ATTTTTTTAATATATTT
1228673 ATT
1 ATT
1228676 ATATCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTTTAATATATTT
Found at i:1235997 original size:25 final size:25
Alignment explanation
Indices: 1235946--1235999 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1235936 GTTACTGGAG
* *
1235946 GTTGTTAGCTATTTTCTTATTTCTA
1 GTTGTTAGCTACTTCCTTATTTCTA
*
1235971 GTTGTTAGCTGCTTCCTT-TTTCTTA
1 GTTGTTAGCTACTTCCTTATTTC-TA
1235996 GTTG
1 GTTG
1236000 AGTAGTTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.11, C:0.15, G:0.17, T:0.57
Consensus pattern (25 bp):
GTTGTTAGCTACTTCCTTATTTCTA
Found at i:1256653 original size:38 final size:38
Alignment explanation
Indices: 1256606--1256679 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
1256596 TGTTTGAAGG
*
1256606 TGACCTGAGG-GCCTAAAGATGATCTGTGGGTTTGGATA
1 TGACCTGAGGTGCC-AAAGATGATCTATGGGTTTGGATA
* * * *
1256644 TGACTTGAGGTTCCCAATATGATCTATGGGTTTGGA
1 TGACCTGAGGTGCCAAAGATGATCTATGGGTTTGGA
1256680 ATGTCTGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 28 0.93
39 2 0.07
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32
Consensus pattern (38 bp):
TGACCTGAGGTGCCAAAGATGATCTATGGGTTTGGATA
Found at i:1256745 original size:38 final size:38
Alignment explanation
Indices: 1256685--1256761 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
1256675 TTGGAATGTC
* * **
1256685 TGAATATGATCTATGGGTTTGGAAATTACTTGAGGGTT
1 TGAATATGATCTAGGGGATTGGAAACAACTTGAGGGTT
* *
1256723 TGAATATTATGTAGGGGATTGGAAACAACTTGAGGGTT
1 TGAATATGATCTAGGGGATTGGAAACAACTTGAGGGTT
1256761 T
1 T
1256762 AAAGATGACC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.29, C:0.05, G:0.30, T:0.36
Consensus pattern (38 bp):
TGAATATGATCTAGGGGATTGGAAACAACTTGAGGGTT
Found at i:1257797 original size:16 final size:18
Alignment explanation
Indices: 1257770--1257803 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1257760 AATAAACATC
1257770 TTAAATTAA-TTTCTCAA
1 TTAAATTAATTTTCTCAA
1257787 TTAAA-TAATTTTCTCAA
1 TTAAATTAATTTTCTCAA
1257804 CTCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATTAATTTTCTCAA
Found at i:1259776 original size:25 final size:26
Alignment explanation
Indices: 1259702--1259776 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
1259692 GTCCCTATAT
* * *
1259702 ATGGCTATTCGTGAGCTTCCCGATTA
1 ATGGCTCTTCGTGAGCTTTCTGATTA
* *
1259728 AAGGCTCTTTGTGAGC-TTCATGATTA
1 ATGGCTCTTCGTGAGCTTTC-TGATTA
1259754 ATGGCTCTTCG-GAGCTTTCTGAT
1 ATGGCTCTTCGTGAGCTTTCTGAT
1259777 ATGACTCGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
25 10 0.25
26 30 0.75
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (26 bp):
ATGGCTCTTCGTGAGCTTTCTGATTA
Found at i:1259877 original size:73 final size:73
Alignment explanation
Indices: 1259740--1259880 Score: 176
Period size: 73 Copynumber: 1.9 Consensus size: 73
1259730 GGCTCTTTGT
* * * *
1259740 GAGCTTCATGATTAATGGCTCTTCGGAGCTTTCTGATATGACTCGCTTGAACTTCCAGATATATG
1 GAGCTTCATGATTAATGGCTCTTCAGAGCTATCTGATATGACTCACATGAACTTCCAGATATATG
1259805 GCTATCCG
66 GCTATCCG
* * * * * *
1259813 GAGCTTCTTGATTAATGGCTCTTTAGAGCTATCTGTTATTGGCTCACATGAGCTTCCTGA-ATAT
1 GAGCTTCATGATTAATGGCTCTTCAGAGCTATCTGATA-TGACTCACATGAACTTCCAGATATAT
1259877 GGCT
65 GGCT
1259881 TTTATGAGCT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
73 41 0.72
74 16 0.28
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (73 bp):
GAGCTTCATGATTAATGGCTCTTCAGAGCTATCTGATATGACTCACATGAACTTCCAGATATATG
GCTATCCG
Found at i:1259890 original size:73 final size:73
Alignment explanation
Indices: 1259730--1259891 Score: 164
Period size: 73 Copynumber: 2.2 Consensus size: 73
1259720 CCCGATTAAA
* * * * *
1259730 GGCTCTTTGTGAGCTTCATGATTAATGGCTCTTCGGAGCTTTCTGATATGACTCGCTTGAACTTC
1 GGCT-TTTATGAGCTTCATGATTAATGGCTCTTCAGAGCTATCTGATATGACTCACATGAACTTC
1259795 CAGATATAT
65 CAGATATAT
* *** * * * * *
1259804 GGCTATCCGGAGCTTCTTGATTAATGGCTCTTTAGAGCTATCTGTTATTGGCTCACATGAGCTTC
1 GGCTTTTATGAGCTTCATGATTAATGGCTCTTCAGAGCTATCTGATA-TGACTCACATGAACTTC
*
1259869 CTGA-ATAT
65 CAGATATAT
1259877 GGCTTTTATGAGCTT
1 GGCTTTTATGAGCTT
1259892 TCCATTATAT
Statistics
Matches: 69, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
73 49 0.71
74 20 0.29
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (73 bp):
GGCTTTTATGAGCTTCATGATTAATGGCTCTTCAGAGCTATCTGATATGACTCACATGAACTTCC
AGATATAT
Found at i:1262173 original size:33 final size:33
Alignment explanation
Indices: 1262135--1262200 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1262125 TTGTTACCTA
1262135 GTTTATTAATAAAGGAATTGGCATTATTGTTAT
1 GTTTATTAATAAAGGAATTGGCATTATTGTTAT
*
1262168 GTTTATTAATAAAGGCATTGGCATTATTGTTAT
1 GTTTATTAATAAAGGAATTGGCATTATTGTTAT
1262201 CACTACTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (33 bp):
GTTTATTAATAAAGGAATTGGCATTATTGTTAT
Found at i:1266480 original size:18 final size:18
Alignment explanation
Indices: 1266438--1266486 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1266428 ACTATTAAAA
1266438 ATAATAAAAATAT-ATAT
1 ATAATAAAAATATAATAT
* **
1266455 TTTTTAAAAATATAATAT
1 ATAATAAAAATATAATAT
*
1266473 ATAATAAAATTATA
1 ATAATAAAAATATA
1266487 TAAAAATATT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATAAAAATATAATAT
Found at i:1268048 original size:34 final size:35
Alignment explanation
Indices: 1268004--1268070 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
1267994 CAGTAAAATA
1268004 TTTTCCGTAAAATGATTT-C-GGAAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGG-AAAATATTTTAC
*
1268038 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
1268071 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 17 0.57
35 11 0.37
36 2 0.07
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:1268897 original size:3 final size:3
Alignment explanation
Indices: 1268889--1268922 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1268879 CCTAAGACCA
1268889 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1268923 GTGGGAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1276001 original size:31 final size:31
Alignment explanation
Indices: 1275966--1276031 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
1275956 CACTCCAAAC
1275966 TAATATTTTCGTCCATTTTTATGCATGTAAG
1 TAATATTTTCGTCCATTTTTATGCATGTAAG
1275997 TAATATTTTCGTCCATTTTTATGCATGTAAG
1 TAATATTTTCGTCCATTTTTATGCATGTAAG
1276028 TAAT
1 TAAT
1276032 TAATTGATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (31 bp):
TAATATTTTCGTCCATTTTTATGCATGTAAG
Found at i:1277705 original size:17 final size:18
Alignment explanation
Indices: 1277683--1277717 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1277673 TTTATTTTTT
*
1277683 TATATAAT-TTTAAAAAA
1 TATATAATATGTAAAAAA
1277700 TATATAATATGTAAAAAA
1 TATATAATATGTAAAAAA
1277718 AACTAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TATATAATATGTAAAAAA
Found at i:1283751 original size:2 final size:2
Alignment explanation
Indices: 1283744--1283768 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1283734 AACAAGTAAA
1283744 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 A
1283769 AGAAGATGAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1287937 original size:6 final size:6
Alignment explanation
Indices: 1287926--1287967 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
1287916 AAAGTAATAA
1287926 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
1287968 GACAAAATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CAAAAT
Found at i:1290238 original size:16 final size:18
Alignment explanation
Indices: 1290209--1290243 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1290199 AAAATTGCTT
1290209 TTATATACATATTATAGA
1 TTATATACATATTATAGA
1290227 TTATATA-A-ATTATAGA
1 TTATATACATATTATAGA
1290243 T
1 T
1290244 AGATTTAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TTATATACATATTATAGA
Found at i:1307071 original size:20 final size:19
Alignment explanation
Indices: 1307046--1307096 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
1307036 TTTTTTATTA
* *
1307046 TTATAATTTTCAGTTTTTTT
1 TTATAATTTTCA-TATTTAT
1307066 TTATAATTTATCATATTTAT
1 TTATAATTT-TCATATTTAT
1307086 TTATAAGTTTT
1 TTATAA-TTTT
1307097 TTTTATGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
TTATAATTTTCATATTTAT
Found at i:1307191 original size:7 final size:8
Alignment explanation
Indices: 1307155--1307192 Score: 53
Period size: 7 Copynumber: 4.9 Consensus size: 8
1307145 AGTTTTAATA
1307155 ATTTTTAT
1 ATTTTTAT
1307163 ATTTTTAT
1 ATTTTTAT
1307171 GATTTTT-T
1 -ATTTTTAT
1307179 ATTTTT-T
1 ATTTTTAT
1307186 ATTTTTA
1 ATTTTTA
1307193 CTTTTTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 13 0.46
8 9 0.32
9 6 0.21
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (8 bp):
ATTTTTAT
Found at i:1317354 original size:125 final size:125
Alignment explanation
Indices: 1317152--1317401 Score: 482
Period size: 125 Copynumber: 2.0 Consensus size: 125
1317142 GTGGGCCAAG
1317152 ACTCACACACTAAGCTTTTTAGCTCACTCTGTTGTTTAACATTTTTCAAGTGATCCTCAGACTTA
1 ACTCACACACTAAGCTTTTTAGCTCACTCTGTTGTTTAACATTTTTCAAGTGATCCTCAGACTTA
*
1317217 AGATTTGGCGACGTTCCCAGAGCTTGGTTCGGTTTATTGAATTTTAGTATTTCTGAACTT
66 AGATTTGGCGACGTTCCCAGAGCTCGGTTCGGTTTATTGAATTTTAGTATTTCTGAACTT
1317277 ACTCACACACTAAGCTTTTTAGCTCACTCTGTTGTTTAACATTTTTCAAGTGATCCTCAGACTTA
1 ACTCACACACTAAGCTTTTTAGCTCACTCTGTTGTTTAACATTTTTCAAGTGATCCTCAGACTTA
*
1317342 AGATTTGGCGACGTTCCCGGAGCTCGGTTCGGTTTATTGAATTTTAGTATTTCTGAACTT
66 AGATTTGGCGACGTTCCCAGAGCTCGGTTCGGTTTATTGAATTTTAGTATTTCTGAACTT
1317402 TATATTTCAG
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 123 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (125 bp):
ACTCACACACTAAGCTTTTTAGCTCACTCTGTTGTTTAACATTTTTCAAGTGATCCTCAGACTTA
AGATTTGGCGACGTTCCCAGAGCTCGGTTCGGTTTATTGAATTTTAGTATTTCTGAACTT
Found at i:1321903 original size:23 final size:23
Alignment explanation
Indices: 1321862--1321913 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1321852 TTAATTTACA
1321862 TAAATTCAAATAAAAAAA-TAAT
1 TAAATTCAAATAAAAAAATTAAT
* *
1321884 TAAATTTAAATTAAATAAATTAAT
1 TAAATTCAAA-TAAAAAAATTAAT
*
1321908 AAAATT
1 TAAATT
1321914 ATAGATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.36
23 7 0.28
24 9 0.36
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATTCAAATAAAAAAATTAAT
Found at i:1322007 original size:22 final size:23
Alignment explanation
Indices: 1321961--1322007 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1321951 CATGTGATTT
*
1321961 TTTAAAAAAAATATTACTTATAAA
1 TTTAAAAAAAATAATAC-TATAAA
*
1321985 TTTAAATAAAATAATA-TATAAA
1 TTTAAAAAAAATAATACTATAAA
1322007 T
1 T
1322008 AACACAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TTTAAAAAAAATAATACTATAAA
Found at i:1324529 original size:12 final size:12
Alignment explanation
Indices: 1324491--1324531 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1324481 ACAATTTCAG
1324491 TACTTATTAAAT
1 TACTTATTAAAT
*
1324503 TA-TT-TTAATT
1 TACTTATTAAAT
1324513 TACTTATTAAAT
1 TACTTATTAAAT
*
1324525 AACTTAT
1 TACTTAT
1324532 ATCACTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 7 0.29
11 4 0.17
12 13 0.54
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (12 bp):
TACTTATTAAAT
Found at i:1324717 original size:18 final size:17
Alignment explanation
Indices: 1324693--1324734 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1324683 AAACTCTAAG
*
1324693 AATATAAATTTAT-AAA
1 AATATAAATCTATAAAA
*
1324709 TATATATAATCTATAAAA
1 AATATA-AATCTATAAAA
1324727 AATATAAA
1 AATATAAA
1324735 AAATAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 5 0.24
17 8 0.38
18 8 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
AATATAAATCTATAAAA
Found at i:1324740 original size:16 final size:16
Alignment explanation
Indices: 1324721--1324753 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1324711 TATATAATCT
1324721 ATAA-AAAATATAAAAA
1 ATAAGAAAA-ATAAAAA
1324737 ATAAGAAAAATAAAAA
1 ATAAGAAAAATAAAAA
1324753 A
1 A
1324754 ATTGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATAAAAA
Found at i:1341347 original size:21 final size:22
Alignment explanation
Indices: 1341308--1341349 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1341298 GATTAATACT
1341308 AAAAATAAAATAAACAAACAAG
1 AAAAATAAAATAAACAAACAAG
1341330 AAAAATTAAAA-AAA-AAACAA
1 AAAAA-TAAAATAAACAAACAA
1341350 AAAGTAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAAATAAAATAAACAAACAAG
Found at i:1346820 original size:15 final size:15
Alignment explanation
Indices: 1346800--1346831 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1346790 CTGATTCAAA
1346800 GGTTGGGTTGGGGTG
1 GGTTGGGTTGGGGTG
1346815 GGTTGGGTTGGGGTG
1 GGTTGGGTTGGGGTG
1346830 GG
1 GG
1346832 GGGACATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (15 bp):
GGTTGGGTTGGGGTG
Found at i:1352817 original size:15 final size:15
Alignment explanation
Indices: 1352792--1352826 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1352782 GACTCTATTT
*
1352792 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
1352806 TAATTAATATTAAGA
1 TAATTAATATTAAGA
1352821 TAATTA
1 TAATTA
1352827 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:1357884 original size:2 final size:2
Alignment explanation
Indices: 1357877--1357901 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1357867 TCCTTCTGTG
1357877 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
1357902 TTGTTTAAGC
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:1358128 original size:15 final size:15
Alignment explanation
Indices: 1358108--1358157 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1358098 TATTTCTTAA
1358108 TATATATTATAATAT
1 TATATATTATAATAT
1358123 TATATATT-TAACT-T
1 TATATATTATAA-TAT
*
1358137 TCATATAATATAATAT
1 T-ATATATTATAATAT
*
1358153 GATAT
1 TATAT
1358158 GAAATAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 5 0.17
15 20 0.69
16 4 0.14
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (15 bp):
TATATATTATAATAT
Found at i:1370089 original size:30 final size:30
Alignment explanation
Indices: 1370053--1370132 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
1370043 TTGTTAAACC
1370053 CAAATAAGCCCTTAAACTGT-AATTGGTACT
1 CAAATAAGCCCTTAAACT-TCAATTGGTACT
1370083 CAAATAAGCCCTTAAACTTCAATTGGTACT
1 CAAATAAGCCCTTAAACTTCAATTGGTACT
1370113 CAAATAAGCCCTTAAACTTC
1 CAAATAAGCCCTTAAACTTC
1370133 TATGGGTCCA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (30 bp):
CAAATAAGCCCTTAAACTTCAATTGGTACT
Found at i:1375179 original size:32 final size:32
Alignment explanation
Indices: 1375143--1375205 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1375133 TTTGTTAAGT
*
1375143 ATACCAGATTATTACTGGTCTGATATTTATCC
1 ATACCAGATTATTACAGGTCTGATATTTATCC
*
1375175 ATACCAGATTGTTACAGGTCTGATATTTATC
1 ATACCAGATTATTACAGGTCTGATATTTATC
1375206 GAACTGTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (32 bp):
ATACCAGATTATTACAGGTCTGATATTTATCC
Found at i:1388559 original size:40 final size:40
Alignment explanation
Indices: 1388515--1388593 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
1388505 AGTATACTAC
* * *
1388515 TAAGGCACATTGCACTTTTAAAAGAGAATACAAATTCAAA
1 TAAGGCACACTGCACTCTTAAAAGAGAACACAAATTCAAA
* *
1388555 TAAGGCACACTGCACTCTTAATAGAGAACGCAAATTCAA
1 TAAGGCACACTGCACTCTTAAAAGAGAACACAAATTCAA
1388594 TCTTAGAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (40 bp):
TAAGGCACACTGCACTCTTAAAAGAGAACACAAATTCAAA
Found at i:1391537 original size:35 final size:35
Alignment explanation
Indices: 1391498--1391658 Score: 216
Period size: 35 Copynumber: 4.6 Consensus size: 35
1391488 GTTGATATTC
1391498 TGATTCACATGTTAAGCATGTCATTATACTGATTA
1 TGATTCACATGTTAAGCATGTCATTATACTGATTA
* * *
1391533 TGATTCACATGTTAAGCATGCCATTGCT-CTGATTC
1 TGATTCACATGTTAAGCATGTCATT-ATACTGATTA
* *
1391568 TGTTTCACATGTTAAGCATGTCAGTATACTGATTA
1 TGATTCACATGTTAAGCATGTCATTATACTGATTA
* * *
1391603 TGATTCTCATGTTAAGCATGCCATTATACTGATTC
1 TGATTCACATGTTAAGCATGTCATTATACTGATTA
* *
1391638 TGATTCGCATGTTAAACATGT
1 TGATTCACATGTTAAGCATGT
1391659 TGCTATACTG
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
34 1 0.01
35 106 0.98
36 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (35 bp):
TGATTCACATGTTAAGCATGTCATTATACTGATTA
Found at i:1391575 original size:70 final size:70
Alignment explanation
Indices: 1391494--1391658 Score: 260
Period size: 70 Copynumber: 2.4 Consensus size: 70
1391484 ATTTGTTGAT
*
1391494 ATTCTGATTCACATGTTAAGCATGTCATTATACTGATTATGATTCACATGTTAAGCATGCCATTG
1 ATTCTGATTCACATGTTAAGCATGTCAGTATACTGATTATGATTCACATGTTAAGCATGCCATT-
*
1391559 CT-CTG
65 ATACTG
* *
1391564 ATTCTGTTTCACATGTTAAGCATGTCAGTATACTGATTATGATTCTCATGTTAAGCATGCCATTA
1 ATTCTGATTCACATGTTAAGCATGTCAGTATACTGATTATGATTCACATGTTAAGCATGCCATTA
1391629 TACTG
66 TACTG
* *
1391634 ATTCTGATTCGCATGTTAAACATGT
1 ATTCTGATTCACATGTTAAGCATGT
1391659 TGCTATACTG
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
69 1 0.01
70 86 0.99
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (70 bp):
ATTCTGATTCACATGTTAAGCATGTCAGTATACTGATTATGATTCACATGTTAAGCATGCCATTA
TACTG
Found at i:1391666 original size:35 final size:35
Alignment explanation
Indices: 1391494--1391678 Score: 178
Period size: 35 Copynumber: 5.3 Consensus size: 35
1391484 ATTTGTTGAT
**
1391494 ATTCTGATTCACATGTTAAGCATGTCATTATACTG
1 ATTCTGATTCACATGTTAAGCATGTCGCTATACTG
* * ** *
1391529 ATTATGATTCACATGTTAAGCATGCCATTGCT-CTG
1 ATTCTGATTCACATGTTAAGCATGTCGCT-ATACTG
*
1391564 ATTCTGTTTCACATGTTAAGCATGTCAG-TATACTG
1 ATTCTGATTCACATGTTAAGCATGTC-GCTATACTG
* * * **
1391599 ATTATGATTCTCATGTTAAGCATGCCATTATACTG
1 ATTCTGATTCACATGTTAAGCATGTCGCTATACTG
* * *
1391634 ATTCTGATTCGCATGTTAAACATGTTGCTATACTGG
1 ATTCTGATTCACATGTTAAGCATGTCGCTATACT-G
1391670 ATT-TGATTC
1 ATTCTGATTC
1391679 GCATACCTAC
Statistics
Matches: 125, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.01
35 119 0.95
36 5 0.04
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (35 bp):
ATTCTGATTCACATGTTAAGCATGTCGCTATACTG
Found at i:1391666 original size:70 final size:69
Alignment explanation
Indices: 1391494--1391678 Score: 248
Period size: 70 Copynumber: 2.6 Consensus size: 69
1391484 ATTTGTTGAT
*
1391494 ATTCTGATTCACATGTTAAGCATGTCATTATACTGATTATGATTCACATGTTAAGCATGCCATTG
1 ATTCTGATTCACATGTTAAGCATGT-AGTATACTGATTATGATTCACATGTTAAGCATGCCATTG
*
1391559 CTCTG
65 ATCTG
* *
1391564 ATTCTGTTTCACATGTTAAGCATGTCAGTATACTGATTATGATTCTCATGTTAAGCATGCCATT-
1 ATTCTGATTCACATGTTAAGCATGT-AGTATACTGATTATGATTCACATGTTAAGCATGCCATTG
1391628 ATACTG
65 AT-CTG
* * *
1391634 ATTCTGATTCGCATGTTAAACATGTTGCTATACTGGATT-TGATTC
1 ATTCTGATTCACATGTTAAGCATGTAG-TATACT-GATTATGATTC
1391679 GCATACCTAC
Statistics
Matches: 104, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
69 2 0.02
70 98 0.94
71 4 0.04
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (69 bp):
ATTCTGATTCACATGTTAAGCATGTAGTATACTGATTATGATTCACATGTTAAGCATGCCATTGA
TCTG
Found at i:1414621 original size:45 final size:45
Alignment explanation
Indices: 1414500--1414621 Score: 138
Period size: 45 Copynumber: 2.7 Consensus size: 45
1414490 ATGCCTAAAT
*
1414500 TGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGACAAAAA
1 TGAGTAAGACCATAGCTAAAAGACGTTATGGCATCATGACAAAAA
* * ** ** *
1414545 TGAGTAAGACCATGGCTGAAAGACGCCATGGCATCATGGTAAACGA
1 TGAGTAAGACCATAGCTAAAAGACGTTATGGCATCATGACAAA-AA
* *
1414591 -GATTAAGACCATAACTAAAAGACGTTATGGC
1 TGAGTAAGACCATAGCTAAAAGACGTTATGGC
1414622 TTTTTGGTAG
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
45 61 0.98
46 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.20
Consensus pattern (45 bp):
TGAGTAAGACCATAGCTAAAAGACGTTATGGCATCATGACAAAAA
Found at i:1415120 original size:12 final size:12
Alignment explanation
Indices: 1415080--1415136 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 12
1415070 TCAACTATGA
1415080 TTAAACTTAATCACT
1 TTAAA-TTAAT-A-T
1415095 TTAATATTAA-AT
1 TTAA-ATTAATAT
1415107 TTAAATTAATAT
1 TTAAATTAATAT
1415119 TTAAATTTAATA-
1 TTAAA-TTAATAT
1415131 TTAAAT
1 TTAAAT
1415137 CTTATTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.15
12 17 0.44
13 7 0.18
15 8 0.21
16 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAAATTAATAT
Found at i:1415671 original size:9 final size:9
Alignment explanation
Indices: 1415657--1415757 Score: 134
Period size: 9 Copynumber: 11.4 Consensus size: 9
1415647 TGGTTAAAAA
1415657 TTAACCGAT
1 TTAACCGAT
*
1415666 TTAACCTAT
1 TTAACCGAT
*
1415675 TTAACTGA-
1 TTAACCGAT
1415683 TTAACCGAT
1 TTAACCGAT
*
1415692 TTAACCGAC
1 TTAACCGAT
1415701 TTAACCGAT
1 TTAACCGAT
* *
1415710 CTAACCTAT
1 TTAACCGAT
1415719 TTAACCGA-
1 TTAACCGAT
1415727 TTAACCGAT
1 TTAACCGAT
*
1415736 TTAACCGAC
1 TTAACCGAT
1415745 TTAACCGAT
1 TTAACCGAT
1415754 TTAA
1 TTAA
1415758 ATCACTATAT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
8 15 0.19
9 63 0.81
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.33
Consensus pattern (9 bp):
TTAACCGAT
Found at i:1415685 original size:26 final size:26
Alignment explanation
Indices: 1415656--1415757 Score: 134
Period size: 26 Copynumber: 3.9 Consensus size: 26
1415646 TTGGTTAAAA
* *
1415656 ATTAACCGATTTAACCTATTTAACTG
1 ATTAACCGATTTAACCGATTTAACCG
*
1415682 ATTAACCGATTTAACCGACTTAACCG
1 ATTAACCGATTTAACCGATTTAACCG
*
1415708 ATCTAACCTATTTAACCGA-TTAACCG
1 AT-TAACCGATTTAACCGATTTAACCG
*
1415734 ATTTAACCGACTTAACCGATTTAA
1 A-TTAACCGATTTAACCGATTTAA
1415758 ATCACTATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 47 0.70
27 20 0.30
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (26 bp):
ATTAACCGATTTAACCGATTTAACCG
Found at i:1415707 original size:44 final size:44
Alignment explanation
Indices: 1415657--1415757 Score: 184
Period size: 44 Copynumber: 2.3 Consensus size: 44
1415647 TGGTTAAAAA
*
1415657 TTAACCGATTTAACCTATTTAACTGATTAACCGATTTAACCGAC
1 TTAACCGATTTAACCTATTTAACCGATTAACCGATTTAACCGAC
*
1415701 TTAACCGATCTAACCTATTTAACCGATTAACCGATTTAACCGAC
1 TTAACCGATTTAACCTATTTAACCGATTAACCGATTTAACCGAC
1415745 TTAACCGATTTAA
1 TTAACCGATTTAA
1415758 ATCACTATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.33
Consensus pattern (44 bp):
TTAACCGATTTAACCTATTTAACCGATTAACCGATTTAACCGAC
Found at i:1418259 original size:18 final size:19
Alignment explanation
Indices: 1418224--1418275 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1418214 AACCGACCGA
**
1418224 TTAACCGAATTCGGTCGG-
1 TTAACCGAATTTTGTCGGT
*
1418242 TTAACCGAATTTTTTCGGTT
1 TTAACCGAATTTTGTCGG-T
1418262 TTAACCGAATTTTG
1 TTAACCGAATTTTG
1418276 CACACCCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.54
20 13 0.46
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (19 bp):
TTAACCGAATTTTGTCGGT
Found at i:1427839 original size:32 final size:32
Alignment explanation
Indices: 1427803--1427863 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1427793 TTTTTTGTCC
*
1427803 AATTTGGTACCTAAACTTGACACTTTTTCCCT
1 AATTTAGTACCTAAACTTGACACTTTTTCCCT
*
1427835 AATTTAGTACCTAAATTTGACACTTTTTC
1 AATTTAGTACCTAAACTTGACACTTTTTC
1427864 TTAAGTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (32 bp):
AATTTAGTACCTAAACTTGACACTTTTTCCCT
Found at i:1427935 original size:89 final size:89
Alignment explanation
Indices: 1427747--1427937 Score: 226
Period size: 90 Copynumber: 2.1 Consensus size: 89
1427737 TTAATATAAT
* ** * *
1427747 ATTTGGTACTTAAATTTGACATTCTTTTAATTTGGTACTTAAAACTTTTTTTGTCCAATTTGGTA
1 ATTTGGTACCTAAATTTGACATTCTTTTAATTTGGTACTTAAAACTTTTTGGGACAAATTTGGTA
1427812 CCTAAACTTGACACTTTTTCCCTA
66 CCTAAACTTGACACTTTTTCCCTA
* * * *
1427836 ATTTAGTACCTAAATTTGACACTTTTTCTTAAGTTT-GTATTTAATA-TTTTTGGGACAAATTTG
1 ATTTGGTACCTAAATTTGACA-TTCTT-TTAA-TTTGGTACTTAAAACTTTTTGGGACAAATTTG
* * *
1427899 GTACCTGAACTTTACTCTTTTT-CCTA
63 GTACCTAAACTTGACACTTTTTCCCTA
1427925 ATTTGGTACCTAA
1 ATTTGGTACCTAA
1427938 TTTTTTTTGT
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
89 35 0.41
90 36 0.42
91 12 0.14
92 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (89 bp):
ATTTGGTACCTAAATTTGACATTCTTTTAATTTGGTACTTAAAACTTTTTGGGACAAATTTGGTA
CCTAAACTTGACACTTTTTCCCTA
Found at i:1431916 original size:23 final size:23
Alignment explanation
Indices: 1431890--1432011 Score: 165
Period size: 23 Copynumber: 5.3 Consensus size: 23
1431880 ATAAGTGCCT
1431890 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1431913 CACTGATATGCAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1431936 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1431959 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1431982 CACT-AAATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
*
1432005 AACTGAT
1 CACTGAT
1432012 CAATAACACT
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
22 2 0.02
23 81 0.96
24 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1431957 original size:46 final size:46
Alignment explanation
Indices: 1431890--1432011 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
1431880 ATAAGTGCCT
*
1431890 CACTGATATGTAGCCGAAGCTACCACTGATATGCAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGCAGCCGTAGCTAC
* *
1431936 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCTGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGCAGCCGTAGCTAC
*
1431982 CACT-AAATTGTAGCCGAAGCTACAACTGAT
1 CACTGAAA-TGTAGCCGAAGCTACCACTGAT
1432012 CAATAACACT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 3 0.04
46 68 0.96
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGCAGCCGTAGCTAC
Found at i:1432263 original size:18 final size:17
Alignment explanation
Indices: 1432237--1432275 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1432227 ATTTTCCTTC
1432237 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
1432254 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
1432272 CACA
1 CACA
1432276 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:1434366 original size:9 final size:9
Alignment explanation
Indices: 1434352--1434391 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1434342 ATTAAAATAT
1434352 TAATTAAAC
1 TAATTAAAC
1434361 TAATTAAAC
1 TAATTAAAC
* *
1434370 CAATTAAAG
1 TAATTAAAC
*
1434379 TAATTAACC
1 TAATTAAAC
1434388 TAAT
1 TAAT
1434392 GGAATTTCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (9 bp):
TAATTAAAC
Found at i:1435348 original size:20 final size:20
Alignment explanation
Indices: 1435323--1435372 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1435313 TGGCTTAAAA
1435323 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1435343 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1435360 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1435373 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1439986 original size:20 final size:20
Alignment explanation
Indices: 1439961--1440010 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1439951 TGGCTTAAAA
1439961 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1439981 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1439998 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1440011 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1447012 original size:16 final size:18
Alignment explanation
Indices: 1446979--1447012 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1446969 ATGGCTTTTG
1446979 AAAGTCTATTATAAAATA
1 AAAGTCTATTATAAAATA
1446997 AAAGT-TATTA-AAAATA
1 AAAGTCTATTATAAAATA
1447013 TTATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (18 bp):
AAAGTCTATTATAAAATA
Found at i:1447021 original size:12 final size:12
Alignment explanation
Indices: 1446985--1447055 Score: 51
Period size: 12 Copynumber: 6.0 Consensus size: 12
1446975 TTTGAAAGTC
1446985 TATTATAAAATAA
1 TATTATAAAA-AA
* *
1446998 AAGTTATTAAAAA
1 TA-TTATAAAAAA
1447011 TATTATAAAAAA
1 TATTATAAAAAA
1447023 -A--ATAATAAAA
1 TATTATAA-AAAA
* *
1447033 -GTTATTAAAAA
1 TATTATAAAAAA
1447044 TATTATAAAAAA
1 TATTATAAAAAA
1447056 AATAATTCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
9 4 0.09
10 4 0.09
11 5 0.11
12 21 0.47
13 4 0.09
14 7 0.16
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
TATTATAAAAAA
Found at i:1447032 original size:33 final size:33
Alignment explanation
Indices: 1446993--1447061 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1446983 TCTATTATAA
1446993 AATAAAAGTTATTAAAAATATTATAAAAAAAAT
1 AATAAAAGTTATTAAAAATATTATAAAAAAAAT
1447026 AATAAAAGTTATTAAAAATATTATAAAAAAAAT
1 AATAAAAGTTATTAAAAATATTATAAAAAAAAT
1447059 AAT
1 AAT
1447062 TCATCACAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (33 bp):
AATAAAAGTTATTAAAAATATTATAAAAAAAAT
Found at i:1447037 original size:21 final size:21
Alignment explanation
Indices: 1447013--1447053 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1447003 ATTAAAAATA
1447013 TTATAAAAAAAATAATAAAAG
1 TTATAAAAAAAATAATAAAAG
* * *
1447034 TTATTAAAAATATTATAAAA
1 TTATAAAAAAAATAATAAAA
1447054 AAAATAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TTATAAAAAAAATAATAAAAG
Found at i:1447150 original size:25 final size:28
Alignment explanation
Indices: 1447104--1447162 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 28
1447094 AGAATTTAAA
1447104 AATAAGTAATCGAAAATGTAACCAAAT-AT
1 AATAAGTAATCGAAAA-GTAA-CAAATAAT
1447133 AATAA-TAAT-GAAAA-TAACAAATAAT
1 AATAAGTAATCGAAAAGTAACAAATAAT
1447158 AATAA
1 AATAA
1447163 CAAATTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 5 0.17
25 10 0.34
27 5 0.17
28 4 0.14
29 5 0.17
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24
Consensus pattern (28 bp):
AATAAGTAATCGAAAAGTAACAAATAAT
Found at i:1447163 original size:13 final size:14
Alignment explanation
Indices: 1447145--1447193 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
1447135 TAATAATGAA
1447145 AATAACAAA-TAAT
1 AATAACAAATTAAT
1447158 AATAACAAATTAAT
1 AATAACAAATTAAT
* *
1447172 ATTAAACTAATTAAT
1 AAT-AACAAATTAAT
1447187 AA-AACAA
1 AATAACAA
1447194 TGGGCTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 13 0.43
14 6 0.20
15 11 0.37
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAACAAATTAAT
Found at i:1456801 original size:37 final size:37
Alignment explanation
Indices: 1456760--1456836 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
1456750 ATTTTTTCCC
*
1456760 AATGGTTCTTAATATAAATTTTGAACTTTTCTGGCTA
1 AATGGTTCTTAATATAAATTTTGAACTTTTCTAGCTA
1456797 AATGGTTCTTAATATAAATTTTGAACTTTTCTAGCTA
1 AATGGTTCTTAATATAAATTTTGAACTTTTCTAGCTA
1456834 AAT
1 AAT
1456837 TATTGTTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.45
Consensus pattern (37 bp):
AATGGTTCTTAATATAAATTTTGAACTTTTCTAGCTA
Found at i:1464034 original size:66 final size:66
Alignment explanation
Indices: 1463947--1464153 Score: 362
Period size: 66 Copynumber: 3.1 Consensus size: 66
1463937 CCTCATCTTC
1463947 ATGGCGTTCACCTTCTCAAGTCATGACAGGGTTCGATGGTACTCAGACCATGGACTACATGAGCG
1 ATGG-GTTCACCTTCTCAAGTCATGACAGGGTTCGATGGTACTCAGACCATGGACTACATGAGCG
1464012 GA
65 GA
* *
1464014 ATGGGTTCACCTTCTCAAGTCATGACAGGGTTCAATGGTACTCAGACAATGGACTACATGAGCGG
1 ATGGGTTCACCTTCTCAAGTCATGACAGGGTTCGATGGTACTCAGACCATGGACTACATGAGCGG
1464079 A
66 A
*
1464080 ATGGGTTCACCTTCTCAAGTCATGACAGGGTT-GAATGGTACTCCGACCATGGACTACATGAGCG
1 ATGGGTTCACCTTCTCAAGTCATGACAGGGTTCG-ATGGTACTCAGACCATGGACTACATGAGCG
1464144 GA
65 GA
1464146 ATGGGTTC
1 ATGGGTTC
1464154 TCATTATGCT
Statistics
Matches: 134, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
66 130 0.97
67 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (66 bp):
ATGGGTTCACCTTCTCAAGTCATGACAGGGTTCGATGGTACTCAGACCATGGACTACATGAGCGG
A
Found at i:1464514 original size:42 final size:42
Alignment explanation
Indices: 1464455--1464544 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
1464445 ATTGGAGTAT
1464455 GAGAGGTTTCAACCTGAAAGCAATGCAGCAGCAGCAGCTACC
1 GAGAGGTTTCAACCTGAAAGCAATGCAGCAGCAGCAGCTACC
** * *
1464497 GAGAGGTTTGGACCTGAAAGCAATGTAGCAGCAGCAGCTACT
1 GAGAGGTTTCAACCTGAAAGCAATGCAGCAGCAGCAGCTACC
1464539 GAGAGG
1 GAGAGG
1464545 AGGCAGAAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.32, C:0.21, G:0.31, T:0.16
Consensus pattern (42 bp):
GAGAGGTTTCAACCTGAAAGCAATGCAGCAGCAGCAGCTACC
Done.