Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold245
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: 689785
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 23636 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:7457 original size:13 final size:13
Alignment explanation
Indices: 7441--7475 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
7431 ACTAAAATTT
7441 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
7454 TCAAAAGCACTTT
1 TCAAAAGCACTTC
7467 TCAAAAGCA
1 TCAAAAGCA
7476 TTGCCAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.23
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:7969 original size:22 final size:23
Alignment explanation
Indices: 7938--8006 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
7928 TATGCATTAT
7938 TAAACAGAGAGCACTAAA-GTG-
1 TAAACAGAGAGCACTAAATGTGC
*
7959 TCATACAGAGAGCAC-AAATGTGC
1 T-AAACAGAGAGCACTAAATGTGC
* *
7982 TAAACGGAGAGCACT-AATATGC
1 TAAACAGAGAGCACTAAATGTGC
8004 TAA
1 TAA
8007 TAATCGGAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.10
22 35 0.88
23 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (23 bp):
TAAACAGAGAGCACTAAATGTGC
Found at i:8017 original size:25 final size:25
Alignment explanation
Indices: 7966--8061 Score: 128
Period size: 25 Copynumber: 4.0 Consensus size: 25
7956 GTGTCATACA
*
7966 GAGAGCACAAATGTGCT-A-AA-CG
1 GAGAGCACTAATGTGCTAATAATCG
*
7988 GAGAGCACTAATATGCTAATAATCG
1 GAGAGCACTAATGTGCTAATAATCG
*
8013 GAGAGCACTAACGTGCTAATAATCG
1 GAGAGCACTAATGTGCTAATAATCG
8038 GAGAGCACTAACT-TGCTAATAATC
1 GAGAGCACTAA-TGTGCTAATAATC
8062 AGATAGCGCT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
22 15 0.23
23 1 0.02
24 2 0.03
25 47 0.72
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.21
Consensus pattern (25 bp):
GAGAGCACTAATGTGCTAATAATCG
Found at i:9348 original size:18 final size:17
Alignment explanation
Indices: 9315--9353 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
9305 TTTTATAAAT
9315 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
9333 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
9350 TGTG
1 TGTG
9354 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:9532 original size:12 final size:12
Alignment explanation
Indices: 9515--9539 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9505 AGTATATATA
9515 TATTTTAAAATT
1 TATTTTAAAATT
9527 TATTTTAAAATT
1 TATTTTAAAATT
9539 T
1 T
9540 TTAGTACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTAAAATT
Found at i:23087 original size:31 final size:33
Alignment explanation
Indices: 23043--23119 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 33
23033 ATAGGACAAG
* *
23043 AAACAGATTAAGCAAAATTA-T-GGAC-AGTGAA
1 AAACCGATAAAGCAAAATTACTGGGACAAGT-AA
23074 AAACCGATAAAGC--AATTACTGGGACAAGTAA
1 AAACCGATAAAGCAAAATTACTGGGACAAGTAA
*
23105 AAACCAATAAAGCAA
1 AAACCGATAAAGCAA
23120 GATGTTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 5 0.13
30 1 0.03
31 29 0.76
32 3 0.08
ACGTcount: A:0.53, C:0.14, G:0.17, T:0.16
Consensus pattern (33 bp):
AAACCGATAAAGCAAAATTACTGGGACAAGTAA
Found at i:28091 original size:28 final size:27
Alignment explanation
Indices: 28055--28312 Score: 299
Period size: 28 Copynumber: 9.4 Consensus size: 27
28045 CATGATTTTT
28055 AATTAAATTAGGTTAGGATTTTTAATTA
1 AATTAAATTAGGTTAGG-TTTTTAATTA
28083 AATTAAATTAGGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTA-GGTTTTTAATTA
** *
28111 AATTAGGTTAGGGTTAGGGATTTTAATTA
1 AATTAAATTA-GGTTA-GGTTTTTAATTA
**
28140 AATTAGGTTAGGTTAGAGTTTTTAATTA
1 AATTAAATTAGGTTAG-GTTTTTAATTA
28168 AATTAAATTAGGTTAGGTTTTTAATTA
1 AATTAAATTAGGTTAGGTTTTTAATTA
* * *
28195 AGTTAAGTTA-G---GGTTTCTAATTA
1 AATTAAATTAGGTTAGGTTTTTAATTA
* *
28218 AACTAAATTATGTTAGGTTTTTAATTA
1 AATTAAATTAGGTTAGGTTTTTAATTA
*
28245 AATTAAATTAGGTTAGGGTTTTAATTAA
1 AATTAAATTAGGTTAGGTTTTTAATT-A
** *
28273 AATTAGGTTAGGTTAGGGTTTTTAATTT
1 AATTAAATTAGGTTA-GGTTTTTAATTA
28301 AATTAAATTAGG
1 AATTAAATTAGG
28313 GTTTTTAATT
Statistics
Matches: 199, Mismatches: 22, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
23 18 0.09
24 1 0.01
26 1 0.01
27 54 0.27
28 86 0.43
29 39 0.20
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.45
Consensus pattern (27 bp):
AATTAAATTAGGTTAGGTTTTTAATTA
Found at i:28204 original size:22 final size:23
Alignment explanation
Indices: 28168--28324 Score: 75
Period size: 23 Copynumber: 6.3 Consensus size: 23
28158 TTTTTAATTA
* *
28168 AATTAAATTAGGTTA-GGTTTTT
1 AATTAAATTAAGTTAGGGTTTCT
*
28190 AATTAAGTTAAGTTAGGGTTTCT
1 AATTAAATTAAGTTAGGGTTTCT
* * *
28213 AATTAAACTAAATTATGTTAGGTTTTT
1 AATTAAATTAAGTTA-G---GGTTTCT
28240 AATTAAATTAAATTAGGTTAGGGTTT-T
1 AATTAAATT--A--A-GTTAGGGTTTCT
*
28267 AATTAAAATTAGGTTAGGTTAGGGTTTTT
1 AATT-AAATTA----A-GTTAGGGTTTCT
* * *
28296 AATTTAATTAAATTAGGGTTTTT
1 AATTAAATTAAGTTAGGGTTTCT
28319 AATTAA
1 AATTAA
28325 GTAGGGTTAG
Statistics
Matches: 109, Mismatches: 12, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
22 13 0.12
23 34 0.31
24 2 0.02
26 1 0.01
27 19 0.17
28 29 0.27
29 6 0.06
31 2 0.02
32 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.46
Consensus pattern (23 bp):
AATTAAATTAAGTTAGGGTTTCT
Found at i:28299 original size:23 final size:22
Alignment explanation
Indices: 28273--28344 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 22
28263 TTTTAATTAA
28273 AATTAGGTTAGGTTAGGGTTTTT
1 AATTA-GTTAGGTTAGGGTTTTT
* **
28296 AATTTAATTAAATTAGGGTTTTT
1 AA-TTAGTTAGGTTAGGGTTTTT
*
28319 AATTAAG-TAGGGTTAGGGATTTT
1 AATT-AGTTA-GGTTAGGGTTTTT
28342 AAT
1 AAT
28345 CAAATAATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
22 4 0.10
23 32 0.82
24 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.46
Consensus pattern (22 bp):
AATTAGTTAGGTTAGGGTTTTT
Found at i:28331 original size:17 final size:18
Alignment explanation
Indices: 28298--28332 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28288 GGGTTTTTAA
*
28298 TTTAATTAAATTAGGGTT
1 TTTAATTAAAGTAGGGTT
28316 TTTAATT-AAGTAGGGTT
1 TTTAATTAAAGTAGGGTT
28333 AGGGATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTAATTAAAGTAGGGTT
Found at i:28456 original size:18 final size:18
Alignment explanation
Indices: 28429--28469 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
28419 NNNNNAATTA
*
28429 AATTAGGTTAGGGTTTTT
1 AATTAAGTTAGGGTTTTT
28447 AATTAAGTTAGGGTTTTT
1 AATTAAGTTAGGGTTTTT
28465 AATTA
1 AATTA
28470 TATTAAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (18 bp):
AATTAAGTTAGGGTTTTT
Found at i:28457 original size:23 final size:23
Alignment explanation
Indices: 28424--28495 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
28414 NNNNNNNNNN
*
28424 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTTTT
28447 AATTAAGTTAGGGTT----TTTAATT
1 AATTAAGTTA-GGTTAGGGTTT--TT
28469 ATATTAAGTTAGGTTAGGGTTTTT
1 A-ATTAAGTTAGGTTAGGGTTTTT
28493 AAT
1 AAT
28496 CAAATAATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 16
0.70 0.02 0.28
Matches are distributed among these distances:
20 3 0.08
22 7 0.17
23 20 0.50
24 7 0.17
26 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (23 bp):
AATTAAGTTAGGTTAGGGTTTTT
Found at i:31632 original size:17 final size:16
Alignment explanation
Indices: 31605--31657 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
31595 ATGTACTATA
*
31605 AAATATAAAATATTAT
1 AAATAAAAAATATTAT
31621 AAATAAATAAATATT-T
1 AAATAAA-AAATATTAT
*
31637 AAATAAAAAACATATAT
1 AAATAAAAAATAT-TAT
31654 AAAT
1 AAAT
31658 TTTTTAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 5 0.16
16 15 0.47
17 12 0.38
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAAAAATATTAT
Found at i:38473 original size:44 final size:44
Alignment explanation
Indices: 38409--38497 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
38399 ACATGGATGT
*
38409 CTTTAAAGCTACAATCGATCATTTACCATAATCCAACCTGTTAA
1 CTTTAAAGCTACAATCGATCATTTACCATAATCCAACCCGTTAA
* *
38453 CTTTAAAGCTACAATTGATCATTTGCCATAATCCAACCCGTTAA
1 CTTTAAAGCTACAATCGATCATTTACCATAATCCAACCCGTTAA
38497 C
1 C
38498 AACCATATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (44 bp):
CTTTAAAGCTACAATCGATCATTTACCATAATCCAACCCGTTAA
Found at i:43722 original size:14 final size:14
Alignment explanation
Indices: 43703--43742 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
43693 ATAGAGAGAG
43703 GAAAGAAGGAAAAA
1 GAAAGAAGGAAAAA
*
43717 GAAAGAAAG-AAAA
1 GAAAGAAGGAAAAA
43730 GAAA-AAGGAAAAA
1 GAAAGAAGGAAAAA
43743 TAGGGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 3 0.13
13 12 0.52
14 8 0.35
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
GAAAGAAGGAAAAA
Found at i:45253 original size:25 final size:27
Alignment explanation
Indices: 45225--45283 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
45215 GTATATGAAT
*
45225 TGAAATGAAT-TATTGGAA-TGAGAT-G
1 TGAAAT-AATCTAATGGAATTGAGATAG
45250 TGAAA-AATCTAATGGAATTGAGATAG
1 TGAAATAATCTAATGGAATTGAGATAG
45276 TGAAATAA
1 TGAAATAA
45284 GGTATGAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 3 0.10
24 7 0.24
25 11 0.38
26 6 0.21
27 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.24, T:0.29
Consensus pattern (27 bp):
TGAAATAATCTAATGGAATTGAGATAG
Found at i:46114 original size:42 final size:42
Alignment explanation
Indices: 46018--46138 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
46008 GCACATAAGC
* * * *
46018 GCTAAACAGAAACCTGTAAGGGTTAAACGGAAGCTCATAGAA
1 GCTAAACTGAAACCCGTAAGGGTTAAACTGAAGCTCAAAGAA
* * *
46060 GTTGAA-TGGAAACCCGTAAGGGTTAATCTGAAGCTCAGAAG-A
1 GCTAAACT-GAAACCCGTAAGGGTTAAACTGAAGCTCA-AAGAA
*
46102 GCTAAACTGAAACCCAG-AAGGGTTAAACTGAAACTCA
1 GCTAAACTGAAACCC-GTAAGGGTTAAACTGAAGCTCA
46139 TATGAGTTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.18
Consensus pattern (42 bp):
GCTAAACTGAAACCCGTAAGGGTTAAACTGAAGCTCAAAGAA
Found at i:46160 original size:20 final size:21
Alignment explanation
Indices: 46098--46175 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 21
46088 TGAAGCTCAG
*
46098 AAGAGCTAAACTGAAACCCAG
1 AAGAGCTAAACTGAAACCCAT
* * *
46119 AAGGGTTAAACTGAAACTCAT
1 AAGAGCTAAACTGAAACCCAT
* * *
46140 ATGAG-TTAACTGAAGCCCAT
1 AAGAGCTAAACTGAAACCCAT
46160 AAGAGCTAAACTGAAA
1 AAGAGCTAAACTGAAA
46176 GCAAAAACAG
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (21 bp):
AAGAGCTAAACTGAAACCCAT
Found at i:48299 original size:22 final size:24
Alignment explanation
Indices: 48272--48318 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
48262 TTTCTTTGAA
*
48272 TTTTTTCTTT-A-CTATTTTCCTT
1 TTTTTTCTTTCATCCATTTTCCTT
*
48294 TTTTTTGTTTCATCCATTTTCCTT
1 TTTTTTCTTTCATCCATTTTCCTT
48318 T
1 T
48319 CTGCCAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 1 0.05
24 11 0.52
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTTTCTTTCATCCATTTTCCTT
Found at i:50937 original size:21 final size:21
Alignment explanation
Indices: 50902--50987 Score: 88
Period size: 21 Copynumber: 4.2 Consensus size: 21
50892 ATACGCCAAT
*
50902 AGAAGCTCG--AGAGCTGAAT
1 AGAAGCTCGTAAGAGCTGAAC
50921 AGGAA-CTCGTAAGAGCTGAAC
1 A-GAAGCTCGTAAGAGCTGAAC
* *
50942 AGAAGCTCGTAAGAGCTTATC
1 AGAAGCTCGTAAGAGCTGAAC
* * *
50963 AGAAGTTCATAAGAGCTAAAC
1 AGAAGCTCGTAAGAGCTGAAC
50984 AGAA
1 AGAA
50988 AGTAAAACAC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
19 5 0.09
20 6 0.11
21 45 0.80
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.17
Consensus pattern (21 bp):
AGAAGCTCGTAAGAGCTGAAC
Found at i:56807 original size:8 final size:8
Alignment explanation
Indices: 56794--56838 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
56784 CCATGAGAAA
56794 ATATATAT
1 ATATATAT
56802 ATATATAT
1 ATATATAT
*
56810 AGATATAT
1 ATATATAT
*
56818 ATAGATAT
1 ATATATAT
*
56826 ATAGATAT
1 ATATATAT
*
56834 GTATA
1 ATATA
56839 AAAAAATATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (8 bp):
ATATATAT
Found at i:56817 original size:18 final size:18
Alignment explanation
Indices: 56794--56838 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
56784 CCATGAGAAA
*
56794 ATATATATATATATATAG
1 ATATATATAGATATATAG
56812 ATATATATAGATATATAG
1 ATATATATAGATATATAG
*
56830 ATATGTATA
1 ATATATATA
56839 AAAAAATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
ATATATATAGATATATAG
Found at i:56838 original size:10 final size:10
Alignment explanation
Indices: 56794--56828 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
56784 CCATGAGAAA
*
56794 ATATATATAT
1 ATATATAGAT
56804 ATATATAGAT
1 ATATATAGAT
56814 ATATATAGAT
1 ATATATAGAT
56824 ATATA
1 ATATA
56829 GATATGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (10 bp):
ATATATAGAT
Found at i:57095 original size:3 final size:3
Alignment explanation
Indices: 57043--57082 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
57033 AAATAAAAAC
* *
57043 TAA TAA TAA TTAA TAA TAG TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57083 GGTTAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:59940 original size:16 final size:16
Alignment explanation
Indices: 59916--59955 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
59906 TAGAATTGAA
* *
59916 TTATAAATTTATCATT
1 TTATTAATTTAACATT
59932 TTATTAATTTAACATT
1 TTATTAATTTAACATT
59948 TTA-TAATT
1 TTATTAATT
59956 CTAAGAGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATTAATTTAACATT
Found at i:67495 original size:23 final size:23
Alignment explanation
Indices: 67434--67492 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
67424 TGGTAATATA
*
67434 TATAA-TAAATTAATAACAAAAT
1 TATAATTAAATTAATAAAAAAAT
*
67456 TATATTTAAATTAATAAAAAAAT
1 TATAATTAAATTAATAAAAAAAT
67479 TATAATTATAATTA
1 TATAATTA-AATTA
67493 TAATTATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 4 0.12
23 23 0.72
24 5 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TATAATTAAATTAATAAAAAAAT
Found at i:67520 original size:6 final size:6
Alignment explanation
Indices: 67476--67503 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
67466 TTAATAAAAA
67476 AATTAT AATTAT AATTAT AATTAT AATT
1 AATTAT AATTAT AATTAT AATTAT AATT
67504 GTGGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:67812 original size:19 final size:20
Alignment explanation
Indices: 67788--67825 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
67778 TAAGAAGTAT
67788 TTTTGAGA-TAAAAAAACAC
1 TTTTGAGATTAAAAAAACAC
*
67807 TTTTGAGATTAAGAAAACA
1 TTTTGAGATTAAAAAAACA
67826 TTCCTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (20 bp):
TTTTGAGATTAAAAAAACAC
Found at i:71066 original size:7 final size:7
Alignment explanation
Indices: 71056--71090 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
71046 TCTTTTATCT
71056 TTTATGA
1 TTTATGA
71063 TTTATGA
1 TTTATGA
*
71070 TTTATGT
1 TTTATGA
71077 TTTATGA
1 TTTATGA
71084 TTTATGA
1 TTTATGA
71091 AGAGTAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (7 bp):
TTTATGA
Found at i:71074 original size:21 final size:21
Alignment explanation
Indices: 71049--71090 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
71039 TCTTCTATCT
71049 TTTATCTTTTATGATTTATGA
1 TTTATCTTTTATGATTTATGA
*
71070 TTTATGTTTTATGATTTATGA
1 TTTATCTTTTATGATTTATGA
71091 AGAGTAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.62
Consensus pattern (21 bp):
TTTATCTTTTATGATTTATGA
Found at i:74188 original size:8 final size:7
Alignment explanation
Indices: 74156--74192 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
74146 GACTTGGGGA
74156 CCAAAAC
1 CCAAAAC
*
74163 TCAAAAC
1 CCAAAAC
74170 CCAAAAC
1 CCAAAAC
74177 CCAAATAC
1 CCAAA-AC
74185 CCAAAAC
1 CCAAAAC
74192 C
1 C
74193 AATACCAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.54, C:0.41, G:0.00, T:0.05
Consensus pattern (7 bp):
CCAAAAC
Found at i:74194 original size:14 final size:14
Alignment explanation
Indices: 74156--74198 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
74146 GACTTGGGGA
74156 CCAAAACTCAAA-AC
1 CCAAAAC-CAAATAC
74170 CCAAAACCCAAATAC
1 CCAAAA-CCAAATAC
74185 CCAAAACC-AATAC
1 CCAAAACCAAATAC
74198 C
1 C
74199 AATCCAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.22
14 12 0.44
15 9 0.33
ACGTcount: A:0.53, C:0.40, G:0.00, T:0.07
Consensus pattern (14 bp):
CCAAAACCAAATAC
Found at i:74391 original size:19 final size:20
Alignment explanation
Indices: 74367--74407 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
74357 GCCTTTAGCA
74367 GCCACCAACTC-CTGCCACC
1 GCCACCAACTCTCTGCCACC
**
74386 GCCACCTGCTCTCTGCCACC
1 GCCACCAACTCTCTGCCACC
74406 GC
1 GC
74408 TGTCGTCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (20 bp):
GCCACCAACTCTCTGCCACC
Found at i:75417 original size:3 final size:3
Alignment explanation
Indices: 75409--75445 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
75399 ATAAATTTGA
75409 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
75446 TACTCATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:76094 original size:72 final size:72
Alignment explanation
Indices: 75986--76199 Score: 392
Period size: 72 Copynumber: 3.0 Consensus size: 72
75976 CTTTTCAAAT
* * *
75986 TCAAGTTTTAAACTATCTCGAGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATAATCCTT
1 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATAATCCTT
76051 TTTTTTC
66 TTTTTTC
76058 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATAATCCTT
1 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATAATCCTT
76123 TTTTTTC
66 TTTTTTC
*
76130 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATAATCCCT
1 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATAATCCTT
76195 TTTTT
66 TTTTT
76200 AAATCCGAGA
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 138 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (72 bp):
TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATAATCCTT
TTTTTTC
Found at i:80862 original size:7 final size:7
Alignment explanation
Indices: 80850--80878 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
80840 ATAAACGAAG
80850 ATAATAA
1 ATAATAA
80857 ATAATAA
1 ATAATAA
80864 ATAATAA
1 ATAATAA
80871 ATAATAA
1 ATAATAA
80878 A
1 A
80879 CAAAAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAA
Found at i:82404 original size:50 final size:50
Alignment explanation
Indices: 82281--82406 Score: 121
Period size: 50 Copynumber: 2.5 Consensus size: 50
82271 ATAGGATTAG
* * * *
82281 TAGCTTCAGTCTGCTCCACTGCAACT-TCAGGGAGATAAGATTCGCCGTTG
1 TAGCTTCAATCTGTTCCACTGCAA-TGTCAGGGAGACAAGATTCGCCGTTA
* * ** * * *
82331 TGGCTTCAATCTTTTTAATTGCAATGTCGGGGA-AGCAAGATTCGTCGTTA
1 TAGCTTCAATCTGTTCCACTGCAATGTCAGGGAGA-CAAGATTCGCCGTTA
82381 TAGCTTCAATCTGTTCCACTGCAATG
1 TAGCTTCAATCTGTTCCACTGCAATG
82407 CCAAAGAGAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
49 2 0.03
50 56 0.97
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (50 bp):
TAGCTTCAATCTGTTCCACTGCAATGTCAGGGAGACAAGATTCGCCGTTA
Found at i:84491 original size:2 final size:2
Alignment explanation
Indices: 84486--84510 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
84476 ATTTTATCAT
84486 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
84511 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:91433 original size:29 final size:30
Alignment explanation
Indices: 91400--91456 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
91390 AGAGGTAAGT
91400 AAAAGATATA-TAAAAAATA-TAAAAAAACA
1 AAAAGA-ATACTAAAAAATACTAAAAAAACA
**
91429 AAAAGAATACTAGCAAATACTAAAAAAA
1 AAAAGAATACTAAAAAATACTAAAAAAA
91457 TTTATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 13 0.54
30 8 0.33
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (30 bp):
AAAAGAATACTAAAAAATACTAAAAAAACA
Found at i:92156 original size:11 final size:11
Alignment explanation
Indices: 92126--92167 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
92116 GTATGAGTCG
*
92126 GAAAGAAAACA
1 GAAAGAAAAAA
*
92137 GAATG-AAAAA
1 GAAAGAAAAAA
92147 GAAAGAAAAAA
1 GAAAGAAAAAA
92158 GAAA-AAAAAA
1 GAAAGAAAAAA
92168 CCTTTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 14 0.52
11 13 0.48
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (11 bp):
GAAAGAAAAAA
Found at i:92166 original size:21 final size:21
Alignment explanation
Indices: 92126--92167 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
92116 GTATGAGTCG
* **
92126 GAAAGAAAACAGAATGAAAAA
1 GAAAGAAAAAAGAAAAAAAAA
92147 GAAAGAAAAAAGAAAAAAAAA
1 GAAAGAAAAAAGAAAAAAAAA
92168 CCTTTTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (21 bp):
GAAAGAAAAAAGAAAAAAAAA
Found at i:106011 original size:119 final size:120
Alignment explanation
Indices: 105877--106115 Score: 471
Period size: 119 Copynumber: 2.0 Consensus size: 120
105867 GAAGGCATAA
105877 TAATGGAAGTGTTAAATACATAAATTAAATTAATAAGGCATTTGATTTTGATTTTGATTTTTTAT
1 TAATGGAAGTGTTAAATACATAAATTAAATTAATAAGGCATTTGATTTTGATTTTGATTTTTTAT
105942 ATATAAAAAAAATTAAACAAAATAAAAATAACAAACATTTTTTTTTCTAAAAATG
66 ATATAAAAAAAATTAAACAAAATAAAAATAACAAACATTTTTTTTTCTAAAAATG
105997 TAATGGAAGT-TTAAATACATAAATTAAATTAATAAGGCATTTGATTTTGATTTTGATTTTTTAT
1 TAATGGAAGTGTTAAATACATAAATTAAATTAATAAGGCATTTGATTTTGATTTTGATTTTTTAT
106061 ATATAAAAAAAATTAAACAAAATAAAAATAACAAACATTTTTTTTTCTAAAAATG
66 ATATAAAAAAAATTAAACAAAATAAAAATAACAAACATTTTTTTTTCTAAAAATG
106116 ATTTAAAAAA
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 109 0.92
120 10 0.08
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (120 bp):
TAATGGAAGTGTTAAATACATAAATTAAATTAATAAGGCATTTGATTTTGATTTTGATTTTTTAT
ATATAAAAAAAATTAAACAAAATAAAAATAACAAACATTTTTTTTTCTAAAAATG
Found at i:112266 original size:2 final size:2
Alignment explanation
Indices: 112259--112287 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
112249 CATCAATGGC
112259 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
112288 TACATAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:115350 original size:25 final size:25
Alignment explanation
Indices: 115320--115373 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
115310 TTTCTCAACT
115320 TTCAAATTCTCAGACAGTGCAGAAA
1 TTCAAATTCTCAGACAGTGCAGAAA
*
115345 TTCAAATTCTCAGACAGTTCAGAAA
1 TTCAAATTCTCAGACAGTGCAGAAA
115370 TTCA
1 TTCA
115374 TAGTTTAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (25 bp):
TTCAAATTCTCAGACAGTGCAGAAA
Found at i:116208 original size:21 final size:21
Alignment explanation
Indices: 116184--116336 Score: 247
Period size: 21 Copynumber: 7.3 Consensus size: 21
116174 GGTTCCTCGA
116184 CTTCTTTTCCACTGTCCTTTT
1 CTTCTTTTCCACTGTCCTTTT
116205 CTTCTTTTCCAAC-GTCCTTTT
1 CTTCTTTTCC-ACTGTCCTTTT
116226 CTTCTTTTCCAAC-GTCCTTTT
1 CTTCTTTTCC-ACTGTCCTTTT
*
116247 CTTCTTTTCCAATGTCCTTTT
1 CTTCTTTTCCACTGTCCTTTT
*
116268 CTTCTTTTCCATTGTCCTTTT
1 CTTCTTTTCCACTGTCCTTTT
*
116289 CTTCTTTTCCAATGTCCTTTT
1 CTTCTTTTCCACTGTCCTTTT
116310 CTTCTTTTCCACTGTCCTTTT
1 CTTCTTTTCCACTGTCCTTTT
116331 CTTCTT
1 CTTCTT
116337 CTTCTGTAGC
Statistics
Matches: 126, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
20 1 0.01
21 123 0.98
22 2 0.02
ACGTcount: A:0.07, C:0.31, G:0.05, T:0.57
Consensus pattern (21 bp):
CTTCTTTTCCACTGTCCTTTT
Found at i:116231 original size:42 final size:42
Alignment explanation
Indices: 116184--116336 Score: 272
Period size: 42 Copynumber: 3.6 Consensus size: 42
116174 GGTTCCTCGA
*
116184 CTTCTTTTCCACTGTCCTTTTCTTCTTTTCCAACGTCCTTTT
1 CTTCTTTTCCACTGTCCTTTTCTTCTTTTCCAATGTCCTTTT
116226 CTTCTTTTCCAAC-GTCCTTTTCTTCTTTTCCAATGTCCTTTT
1 CTTCTTTTCC-ACTGTCCTTTTCTTCTTTTCCAATGTCCTTTT
*
116268 CTTCTTTTCCATTGTCCTTTTCTTCTTTTCCAATGTCCTTTT
1 CTTCTTTTCCACTGTCCTTTTCTTCTTTTCCAATGTCCTTTT
116310 CTTCTTTTCCACTGTCCTTTTCTTCTT
1 CTTCTTTTCCACTGTCCTTTTCTTCTT
116337 CTTCTGTAGC
Statistics
Matches: 106, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
41 1 0.01
42 103 0.97
43 2 0.02
ACGTcount: A:0.07, C:0.31, G:0.05, T:0.57
Consensus pattern (42 bp):
CTTCTTTTCCACTGTCCTTTTCTTCTTTTCCAATGTCCTTTT
Found at i:128619 original size:93 final size:93
Alignment explanation
Indices: 128470--128646 Score: 228
Period size: 93 Copynumber: 1.9 Consensus size: 93
128460 ATTTGGTGAG
* * * * * * *
128470 GGACCTGATTTTCCATAAACAGAGGTATGCCCTGTAACGTTACCACCGATGACTGGTGCTGACGA
1 GGACATGATTCTCCATAAACAGAGGTATACCCTGTAACGTTACAACCGATAACTGGTGCAGAAGA
* *
128535 ATGTTCAGTAGGAAGCACATTTGGAGGA
66 ATGGTCAGTAGGAACCACATTTGGAGGA
* * **
128563 GGACATGATTCTCCATAAACAGGGGTATACCCTTTCGCGTTACAACCGATAACTGGTGCAGAAGA
1 GGACATGATTCTCCATAAACAGAGGTATACCCTGTAACGTTACAACCGATAACTGGTGCAGAAGA
*
128628 ATGGTCGGTAGGAACCACA
66 ATGGTCAGTAGGAACCACA
128647 CGAGCTGCAA
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.23
Consensus pattern (93 bp):
GGACATGATTCTCCATAAACAGAGGTATACCCTGTAACGTTACAACCGATAACTGGTGCAGAAGA
ATGGTCAGTAGGAACCACATTTGGAGGA
Found at i:131771 original size:45 final size:45
Alignment explanation
Indices: 131716--131833 Score: 157
Period size: 44 Copynumber: 2.6 Consensus size: 45
131706 AAGACTTGTA
* * *
131716 TCTTCGATCTACTTCACCACCGGTATGGGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATATGCTT
* ***
131761 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATATGCTT
1 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATATGCTT
*
131805 TCTTTGATCTACTCCACCACCAGTATGGG
1 TCTTTGATCTACTTCACCACCAGTATGGG
131834 GAGATAGAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 37 0.62
45 23 0.38
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (45 bp):
TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATATGCTT
Found at i:132048 original size:50 final size:50
Alignment explanation
Indices: 131940--132148 Score: 159
Period size: 50 Copynumber: 4.2 Consensus size: 50
131930 GATCTGTAAT
* * * * * ** * * *
131940 CTTCAATTTGTTCAACTGCAATGTTGGGGAAGCCAGATCTGCCGTCGTAG
1 CTTCAATCTATTCCACTGCACTGTTAGGGAAGTAAGATCCGCCGTTGTGG
* * * * *
131990 CTTAAATCTATCCCACCGCACCGTTAGGGAAGTAAGATCCGCCATTGTGG
1 CTTCAATCTATTCCACTGCACTGTTAGGGAAGTAAGATCCGCCGTTGTGG
* * * * * * * * *
132040 CTTCAATCTTTTCAATTGTAATATCAGGGAAGCT-AGATCCGCCGTCGTAG
1 CTTCAATCTATTCCACTGCACTGTTAGGGAAG-TAAGATCCGCCGTTGTGG
* * *
132090 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTATTCCACTGCACTGTTAGGGAAGTAAGATCCGCCGTTGTGG
132140 CTTCAATCT
1 CTTCAATCT
132149 TTTACTTTTC
Statistics
Matches: 117, Mismatches: 40, Indels: 4
0.73 0.25 0.02
Matches are distributed among these distances:
49 1 0.01
50 115 0.98
51 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (50 bp):
CTTCAATCTATTCCACTGCACTGTTAGGGAAGTAAGATCCGCCGTTGTGG
Found at i:132121 original size:100 final size:100
Alignment explanation
Indices: 131966--132151 Score: 282
Period size: 100 Copynumber: 1.9 Consensus size: 100
131956 TGCAATGTTG
* * *
131966 GGGAAGCCAGATCTGCCGTCGTAGCTTAAATCTATCCCACCGCACCGTTAGGGAAGTAAGATCCG
1 GGGAAGCCAGATCCGCCGTCGTAGCTTAAATCTATCCCACCGCACCGCTAAGGAAGTAAGATCCG
132031 CCATTGTGGCTTCAATCTTTTCAATTGTAATATCA
66 CCATTGTGGCTTCAATCTTTTCAATTGTAATATCA
* * * * * *
132066 GGGAAGCTAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCG
1 GGGAAGCCAGATCCGCCGTCGTAGCTTAAATCTATCCCACCGCACCGCTAAGGAAGTAAGATCCG
*
132131 CCGTTGTGGCTTCAATCTTTT
66 CCATTGTGGCTTCAATCTTTT
132152 ACTTTTCAAC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 76 1.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (100 bp):
GGGAAGCCAGATCCGCCGTCGTAGCTTAAATCTATCCCACCGCACCGCTAAGGAAGTAAGATCCG
CCATTGTGGCTTCAATCTTTTCAATTGTAATATCA
Found at i:133010 original size:10 final size:9
Alignment explanation
Indices: 132994--133020 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
132984 TAGCCTCTCC
132994 ATTTTTTTT
1 ATTTTTTTT
133003 ATTTTTTTT
1 ATTTTTTTT
133012 ATTTTTTTT
1 ATTTTTTTT
133021 GAAATCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:139723 original size:20 final size:20
Alignment explanation
Indices: 139698--139737 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
139688 AAAAGGTCTT
* *
139698 TAATGCATGTGATGTGATGC
1 TAATGCATATGATGCGATGC
139718 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
139738 ATGAGGTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:148797 original size:14 final size:14
Alignment explanation
Indices: 148778--148813 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
148768 TTGTTTCACT
*
148778 GAAAATGGTTTCCG
1 GAAAATGATTTCCG
*
148792 GAAAATGATTTCTG
1 GAAAATGATTTCCG
148806 GAAAATGA
1 GAAAATGA
148814 CTTACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (14 bp):
GAAAATGATTTCCG
Found at i:151543 original size:13 final size:13
Alignment explanation
Indices: 151527--151561 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
151517 ACCAAATTTT
151527 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
151540 TCAAAAGCACTTT
1 TCAAAAGCACTTC
151553 TCAAAAGCA
1 TCAAAAGCA
151562 TTGCTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.23
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:156520 original size:23 final size:23
Alignment explanation
Indices: 156501--156614 Score: 167
Period size: 23 Copynumber: 5.0 Consensus size: 23
156491 CCACACTAAT
* *
156501 ATGTAGCCGAAGCTACCACTCAT
1 ATGTAGCCGAAGCTACCACTGAA
156524 ATGTAGCCGACA-CTACCACTGAA
1 ATGTAGCCGA-AGCTACCACTGAA
*
156547 ATGTAGCCAAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
*
156570 ATGTAGCCGAAGCTAACACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
*
156593 ACGTAGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
156615 TCAATAACAC
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
22 1 0.01
23 80 0.98
24 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:160674 original size:24 final size:23
Alignment explanation
Indices: 160635--160680 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
160625 TGTTTATTCC
*
160635 TTTTCTTTTCTTTTTATTATATA
1 TTTTCTTTTCTTTTTATAATATA
160658 TTTTCTTTT-TTGCTTTATAATAT
1 TTTTCTTTTCTT--TTTATAATAT
160681 TCAAAGATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 9 0.45
24 9 0.45
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTCTTTTCTTTTTATAATATA
Found at i:161990 original size:16 final size:18
Alignment explanation
Indices: 161952--161991 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
161942 AAAATAGAAC
161952 GTAT-AAATAGTTGAATT
1 GTATAAAATAGTTGAATT
161969 GT-TAAAATA-TT-AATT
1 GTATAAAATAGTTGAATT
161984 GTATAAAA
1 GTATAAAA
161992 AAATTTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 8 0.38
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (18 bp):
GTATAAAATAGTTGAATT
Found at i:164539 original size:15 final size:15
Alignment explanation
Indices: 164519--164550 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
164509 AAACTGTATA
164519 TAATTAAGAGACTTG
1 TAATTAAGAGACTTG
164534 TAATTAAGAGACTTG
1 TAATTAAGAGACTTG
164549 TA
1 TA
164551 TAGGTTGATG
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:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (15 bp):
TAATTAAGAGACTTG
Found at i:171772 original size:2 final size:2
Alignment explanation
Indices: 171759--171800 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
171749 GTATTATAAC
*
171759 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
171801 TGAGACAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:172976 original size:14 final size:14
Alignment explanation
Indices: 172957--172983 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
172947 TAATTGATGC
172957 ATATATATACATGT
1 ATATATATACATGT
172971 ATATATATACATG
1 ATATATATACATG
172984 CATGGCAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATATATACATGT
Found at i:176423 original size:38 final size:38
Alignment explanation
Indices: 176372--176451 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
176362 GGTACACTTC
176372 AAAGCTAATAAAGATTAGCCACTAATAAGGGTCTATTT
1 AAAGCTAATAAAGATTAGCCACTAATAAGGGTCTATTT
176410 AAAGCTAATAAAGATTAGCCACTAATAAGGGTCTATTT
1 AAAGCTAATAAAGATTAGCCACTAATAAGGGTCTATTT
176448 AAAG
1 AAAG
176452 TCTATATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (38 bp):
AAAGCTAATAAAGATTAGCCACTAATAAGGGTCTATTT
Found at i:176835 original size:12 final size:11
Alignment explanation
Indices: 176816--176865 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 11
176806 TTTATATTTT
176816 TTAAAAAATTC
1 TTAAAAAATTC
176827 TTAAAAAAATTC
1 TT-AAAAAATTC
*
176839 -TAAAAAATATA
1 TTAAAAAAT-TC
176850 TTAAAAAATT-
1 TTAAAAAATTC
176860 TTAAAA
1 TTAAAA
176866 TTTTTCTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
10 13 0.37
11 5 0.14
12 17 0.49
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAAAAATTC
Found at i:176843 original size:22 final size:22
Alignment explanation
Indices: 176817--176865 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
176807 TTATATTTTT
*
176817 TAAAAAAT-TCTTAAAAAAATTC
1 TAAAAAATATATT-AAAAAATTC
*
176839 TAAAAAATATATTAAAAAATTT
1 TAAAAAATATATTAAAAAATTC
176861 TAAAA
1 TAAAA
176866 TTTTTCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAAATATATTAAAAAATTC
Found at i:186807 original size:36 final size:36
Alignment explanation
Indices: 186767--186840 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
186757 TGAAAATGGA
**
186767 ATTTTACAAAAAGAAAAGAAAGCTAAGTATTTTTTG
1 ATTTTACAAAAAGAAAAGAAAGCTAAAAATTTTTTG
*
186803 ATTTTTCAAAAAGAAAAGAAAGCTAAAAATTTTTTG
1 ATTTTACAAAAAGAAAAGAAAGCTAAAAATTTTTTG
186839 AT
1 AT
186841 GCCTATACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (36 bp):
ATTTTACAAAAAGAAAAGAAAGCTAAAAATTTTTTG
Found at i:193287 original size:26 final size:26
Alignment explanation
Indices: 193251--193300 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
193241 ATATAAATAT
193251 ATAAATTTTATCAAGATTTGTTTCTG
1 ATAAATTTTATCAAGATTTGTTTCTG
* *
193277 ATAATTTTTATCAGGATTTGTTTC
1 ATAAATTTTATCAAGATTTGTTTC
193301 CTTTTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (26 bp):
ATAAATTTTATCAAGATTTGTTTCTG
Found at i:194245 original size:3 final size:3
Alignment explanation
Indices: 194237--194273 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
194227 TCCTGATTTA
194237 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
194274 TATAACCTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:194938 original size:17 final size:16
Alignment explanation
Indices: 194918--194960 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
194908 GAGAGATCAG
194918 AGAAGAAAGAAGATAAC
1 AGAAGAAAGAAG-TAAC
*
194935 AGAAGAAGAGAAGTAAT
1 AGAAGAA-AGAAGTAAC
194952 AGAGAGAAA
1 AGA-AGAAA
194961 TTAGGAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.63, C:0.02, G:0.28, T:0.07
Consensus pattern (16 bp):
AGAAGAAAGAAGTAAC
Found at i:196508 original size:17 final size:17
Alignment explanation
Indices: 196486--196518 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
196476 GTATATACAT
196486 TTTATTGTTAGAAATAA
1 TTTATTGTTAGAAATAA
*
196503 TTTATTGTTTGAAATA
1 TTTATTGTTAGAAATA
196519 TAATATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (17 bp):
TTTATTGTTAGAAATAA
Found at i:200158 original size:135 final size:135
Alignment explanation
Indices: 199907--200232 Score: 627
Period size: 135 Copynumber: 2.4 Consensus size: 135
199897 GGTAAGCTTA
*
199907 CCTAGACCC-TAATTGACTGAAATGACTGTATGACTGATATGAATAAGCATGATGATTATGATAT
1 CCTAGACCCTTAATTGACTGAGATGACTGTATGACTGATATGAATAAGCATGATGATTATGATAT
199971 TATGTTATAGTATATCGTATTTGTATACTGCATTGCATTGGGTTGGGGGTTTATTTTGATCGGAG
66 TATGTTATAGTATATCGTATTTGTATACTGCATTGCATTGGGTTGGGGGTTTATTTTGATCGGAG
200036 GAAGT
131 GAAGT
200041 CCTAGACCCTTAATTGACTGAGATGACTGTATGACTGATATGAATAAGCATGATGATTATGATAT
1 CCTAGACCCTTAATTGACTGAGATGACTGTATGACTGATATGAATAAGCATGATGATTATGATAT
200106 TATGTTATAGTATATCGTATTTGTATACTGCATTGCATTGGGTTGGGGGTTTATTTTGATCGGAG
66 TATGTTATAGTATATCGTATTTGTATACTGCATTGCATTGGGTTGGGGGTTTATTTTGATCGGAG
200171 GAAGT
131 GAAGT
*
200176 CCTAGACCCTTAATTGACTGAGATGACTGTATGACTGATATAAATAAGCATGATGAT
1 CCTAGACCCTTAATTGACTGAGATGACTGTATGACTGATATGAATAAGCATGATGAT
200233 GATCCACTGA
Statistics
Matches: 189, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
134 9 0.05
135 180 0.95
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.36
Consensus pattern (135 bp):
CCTAGACCCTTAATTGACTGAGATGACTGTATGACTGATATGAATAAGCATGATGATTATGATAT
TATGTTATAGTATATCGTATTTGTATACTGCATTGCATTGGGTTGGGGGTTTATTTTGATCGGAG
GAAGT
Found at i:210374 original size:24 final size:24
Alignment explanation
Indices: 210342--210388 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
210332 TTCCATTACT
210342 ATTATTATTA-CATTATTTACTATC
1 ATTATTATTATCA-TATTTACTATC
*
210366 ATTATTATTATCATATTTTCTAT
1 ATTATTATTATCATATTTACTAT
210389 ACATATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTATCATATTTACTATC
Found at i:210379 original size:12 final size:12
Alignment explanation
Indices: 210342--210379 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
210332 TTCCATTACT
210342 ATTATTATTA-C
1 ATTATTATTATC
*
210353 ATTATTTACTATC
1 ATTA-TTATTATC
210366 ATTATTATTATC
1 ATTATTATTATC
210378 AT
1 AT
210380 ATTTTCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.17
12 14 0.61
13 5 0.22
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:213885 original size:9 final size:9
Alignment explanation
Indices: 213871--213896 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
213861 ATAATATACA
213871 AATAGTATT
1 AATAGTATT
213880 AATAGTATT
1 AATAGTATT
213889 AATAGTAT
1 AATAGTAT
213897 CAACATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (9 bp):
AATAGTATT
Found at i:213977 original size:3 final size:3
Alignment explanation
Indices: 213969--214004 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
213959 GGACTATAGC
213969 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
214005 TCTAATGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:215689 original size:44 final size:44
Alignment explanation
Indices: 215633--215744 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 44
215623 TTCAATCTAT
* * ** * *
215633 TCCACTACAACTTTAGGGATATAGGATTTGTAGCTTCATCTTGC
1 TCCACTGCAACTTTAGGGAGATAAAATTTGCAGCTTCATCTCGC
*
215677 TCCATTGCAACTTTAGGGAGATAAAATTTGCAGCTTCATCTCGC
1 TCCACTGCAACTTTAGGGAGATAAAATTTGCAGCTTCATCTCGC
* *
215721 TCCACTGCGACTTTATGGAGATAA
1 TCCACTGCAACTTTAGGGAGATAA
215745 GATTCGCTAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (44 bp):
TCCACTGCAACTTTAGGGAGATAAAATTTGCAGCTTCATCTCGC
Found at i:215824 original size:138 final size:137
Alignment explanation
Indices: 215634--216052 Score: 450
Period size: 138 Copynumber: 3.0 Consensus size: 137
215624 TCAATCTATT
* * * * * * * *
215634 CCACTACAACTTTAGGGATATAGGATTTGTAGCTTC-ATCTTGCTCCATTGCAACTTTAGGGAGA
1 CCACTACAATTTTAGGG-TATAGAAATTGTAGCTTCAATC-CGATCCACTGCAACTTCAGGGATA
* * * * * * * *
215698 TAAAATTTGCAGCTTCATCTCGCTCCACTGCGACTTTATGGAGATAAGATTCGCTACT-GTAGTT
64 TAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTA-TGGCAGAT
* *
215762 TTATTCCA-AC
128 TAAAT-CAGAC
* *
215772 CCACTACAATTTTAGGAGTATAGAAATTGTAGTTTCAATCCGATCCACTGCAACTTCAGGAATAT
1 CCACTACAATTTTAGG-GTATAGAAATTGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATAT
*
215837 AAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGCAGATTA
65 AAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATGGCAGATTA
215902 AATCAGAC
130 AATCAGAC
* * * * * * *
215910 CCAATGCAATTTCAGGGGTATAGAAATTATAACTTCAATCCGGTCCACTGCAACCTCAGGGATAT
1 CCACTACAATTTTA-GGGTATAGAAATTGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATAT
* * * * *
215975 AGGATTTGTAGCTTCATCTTGCTCCACTGCAACTCCAAGGAGATAAGATTTGTTATGGCAGATTC
65 AAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATGGCAGATTA
216040 AATCCA-AC
130 AAT-CAGAC
216048 CCACT
1 CCACT
216053 GCAACTTAAG
Statistics
Matches: 239, Mismatches: 36, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
137 3 0.01
138 228 0.95
139 8 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (137 bp):
CCACTACAATTTTAGGGTATAGAAATTGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATATA
AGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATGGCAGATTAA
ATCAGAC
Found at i:215990 original size:44 final size:44
Alignment explanation
Indices: 215798--216027 Score: 151
Period size: 44 Copynumber: 5.1 Consensus size: 44
215788 AGTATAGAAA
* *
215798 TTGTAGTTTCAATCCGATCCACTGCAACTTCAGGAATATAAGAT
1 TTGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATATAAGAT
* * *
215842 TTGTAGCTTC-ATCTTGCTCCACTGCAACTTCAGGGAGATAAGAT
1 TTGTAGCTTCAATC-CGATCCACTGCAACTTCAGGGATATAAGAT
* * * * * * * *
215886 TCGCTATGGCAGATTAAATCAGACCCAATGCAATTTCAGGGGTAT-AGAAA
1 TTG-TA--GC---TTCAATCCGATCCACTGCAACTTCAGGGATATAAG-AT
* * * * *
215936 TTATAACTTCAATCCGGTCCACTGCAACCTCAGGGATATAGGAT
1 TTGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATATAAGAT
* * * * *
215980 TTGTAGCTTC-ATCTTGCTCCACTGCAACTCCAAGGAGATAAGAT
1 TTGTAGCTTCAATC-CGATCCACTGCAACTTCAGGGATATAAGAT
216024 TTGT
1 TTGT
216028 TATGGCAGAT
Statistics
Matches: 138, Mismatches: 37, Indels: 22
0.70 0.19 0.11
Matches are distributed among these distances:
43 6 0.04
44 97 0.70
45 3 0.02
47 3 0.02
49 4 0.03
50 22 0.16
51 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
TTGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATATAAGAT
Found at i:216056 original size:138 final size:138
Alignment explanation
Indices: 215697--216056 Score: 454
Period size: 138 Copynumber: 2.6 Consensus size: 138
215687 CTTTAGGGAG
* * * * * * * *
215697 ATAAAATTTGCAGCTTCATCTCGCTCCACTGCGACTTTATGGAGATAAGATTCGCTACT-GTAGT
1 ATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTA-TGGCAGA
* * * * * **
215761 TTTATTCCAACCCACTACAATTTTAGGAGTATAGAAATTGTAGTTTCAATCCGATCCACTGCAAC
65 TTAAATCCAACCCACTGCAATTTCAGGAGTATAGAAATTATAACTTCAATCCGATCCACTGCAAC
*
215826 TTCAGGAAT
130 CTCAGGAAT
*
215835 ATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGCAGAT
1 ATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATGGCAGAT
* * *
215900 TAAAT-CAGACCCAATGCAATTTCAGGGGTATAGAAATTATAACTTCAATCCGGTCCACTGCAAC
66 TAAATCCA-ACCCACTGCAATTTCAGGAGTATAGAAATTATAACTTCAATCCGATCCACTGCAAC
*
215964 CTCAGGGAT
130 CTCAGGAAT
* * * *
215973 ATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTCCAAGGAGATAAGATTTGTTATGGCAGAT
1 ATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATGGCAGAT
*
216038 TCAATCCAACCCACTGCAA
66 TAAATCCAACCCACTGCAA
216057 CTTAAGGGAT
Statistics
Matches: 192, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
137 3 0.02
138 187 0.97
139 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (138 bp):
ATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATGGCAGAT
TAAATCCAACCCACTGCAATTTCAGGAGTATAGAAATTATAACTTCAATCCGATCCACTGCAACC
TCAGGAAT
Found at i:216494 original size:3 final size:3
Alignment explanation
Indices: 216486--216535 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
216476 AACAAAACTG
216486 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
216534 TT
1 TT
216536 GTTTGTGCCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:251988 original size:15 final size:15
Alignment explanation
Indices: 251968--252003 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
251958 ATATAATAAA
*
251968 TATTTTTTTATTTTT
1 TATTTTTTAATTTTT
251983 TATTTTTTAATTTTT
1 TATTTTTTAATTTTT
*
251998 AATTTT
1 TATTTT
252004 AAAATACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TATTTTTTAATTTTT
Found at i:256869 original size:43 final size:42
Alignment explanation
Indices: 256805--256931 Score: 152
Period size: 43 Copynumber: 3.0 Consensus size: 42
256795 AGGATTTTCA
256805 ATATGTG-TTATCATGTAAGACCGCGTCTGGGACGTTGGCATCG
1 ATATGTGATTA-CATGTAAGACC-CGTCTGGGACGTTGGCATCG
* *
256848 ACT-TGTGTTTACGTGTAAGACCCTGTCTGGGACAG-TGGCATCG
1 A-TATGTGATTACATGTAAGACCC-GTCTGGGAC-GTTGGCATCG
*
256891 ATATGTGATTACATGTAAAACCACGTCTGGGACGTTGGCAT
1 ATATGTGATTACATGTAAGACC-CGTCTGGGACGTTGGCAT
256932 TATACGAGCT
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
42 3 0.04
43 64 0.88
44 6 0.08
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (42 bp):
ATATGTGATTACATGTAAGACCCGTCTGGGACGTTGGCATCG
Found at i:259341 original size:13 final size:12
Alignment explanation
Indices: 259323--259360 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
259313 AGACTTATTG
259323 CCAACGAGATGTA
1 CCAACGAG-TGTA
259336 CCAACGAGTTGTA
1 CCAACGAG-TGTA
259349 CCAACGAGTGTA
1 CCAACGAGTGTA
259361 ACGATTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (12 bp):
CCAACGAGTGTA
Found at i:262732 original size:21 final size:24
Alignment explanation
Indices: 262708--262753 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 24
262698 ACCTAATTAA
*
262708 TAATTT-TAAA-ATTTAT-TATAT
1 TAATTTATAAAGATATATATATAT
262729 TAATTTATAAAGATATATATATAT
1 TAATTTATAAAGATATATATATAT
262753 T
1 T
262754 CTTAAGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 4 0.19
23 5 0.24
24 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TAATTTATAAAGATATATATATAT
Found at i:263313 original size:233 final size:234
Alignment explanation
Indices: 263046--263513 Score: 920
Period size: 233 Copynumber: 2.0 Consensus size: 234
263036 TAATAATTTT
263046 TTGAAAGTTCGGTTAACGGTTAATATATATTTTATATACATTTTACATATATTAAATTCGATTAA
1 TTGAAAGTTC-GTTAACGGTTAATATATATTTTATATACATTTTACATATATTAAATTCGATTAA
263111 TTCAGTTAATTTTTTTATATGTTTTATAATTATTTTAACCAATAAATAAAAAAATATAAATTTCG
65 TTCAGTTAATTTTTTTATATGTTTTATAATTATTTTAACCAATAAATAAAAAAATATAAATTTCG
263176 ATTAATTTGGTTAGCTGACCGAATTAACCGAAAAAATTTGGTTCGGTTAATTTTTTTAAAAAATT
130 ATTAATTTGGTTAGCTGACCGAATTAACCGAAAAAATTTGGTTCGGTTAATTTTTTTAAAAAATT
263241 CCGGTTCGATTAATGGTTAAAGGTTTAACAAATTCGATTA
195 CCGGTTCGATTAATGGTTAAAGGTTTAACAAATTCGATTA
263281 TTGAAAGTTC-TTAACGGTTAATATATATTTTATATACATTTTACATATATTAAATTCGATTAAT
1 TTGAAAGTTCGTTAACGGTTAATATATATTTTATATACATTTTACATATATTAAATTCGATTAAT
263345 TCAGTTAATTTTTTTATATGTTTTATAATTATTTTAACCAATAAATAAAAAAATATAAATTTCGA
66 TCAGTTAATTTTTTTATATGTTTTATAATTATTTTAACCAATAAATAAAAAAATATAAATTTCGA
263410 TTAATTTGGTTAGCTGACCGAATTAACCGAAAAAATTTGGTTCGGTTAATTTTTTTAAAAAATTC
131 TTAATTTGGTTAGCTGACCGAATTAACCGAAAAAATTTGGTTCGGTTAATTTTTTTAAAAAATTC
263475 CGGTTCGATTAATGGTTAAAGGTTTAACAAATTCGATTA
196 CGGTTCGATTAATGGTTAAAGGTTTAACAAATTCGATTA
263514 ATTCAATATG
Statistics
Matches: 233, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
233 223 0.96
235 10 0.04
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (234 bp):
TTGAAAGTTCGTTAACGGTTAATATATATTTTATATACATTTTACATATATTAAATTCGATTAAT
TCAGTTAATTTTTTTATATGTTTTATAATTATTTTAACCAATAAATAAAAAAATATAAATTTCGA
TTAATTTGGTTAGCTGACCGAATTAACCGAAAAAATTTGGTTCGGTTAATTTTTTTAAAAAATTC
CGGTTCGATTAATGGTTAAAGGTTTAACAAATTCGATTA
Found at i:264211 original size:17 final size:16
Alignment explanation
Indices: 264191--264228 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
264181 TAGGGTTTTG
*
264191 TTTTGTTTATATTACTT
1 TTTTG-TTAGATTACTT
264208 TTTTG-TAGATTACTT
1 TTTTGTTAGATTACTT
264223 TTTTGT
1 TTTTGT
264229 GTTCAGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 14 0.74
17 5 0.26
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (16 bp):
TTTTGTTAGATTACTT
Found at i:266003 original size:2 final size:2
Alignment explanation
Indices: 265998--266028 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
265988 ATTATATATA
265998 TG 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 TG T
266029 TATTATTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:275637 original size:42 final size:42
Alignment explanation
Indices: 275591--275671 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
275581 TTTTTTTTTA
*
275591 GGTTTAATGCAAATGGAGATATTTTGGAGAGATGAAATGGAT
1 GGTTTAATGCAAATGGAGATATTTTGGAGAGAAGAAATGGAT
*
275633 GGTTTAATGCAAATGGAGATTTTTTGGAGAGAAGAAATG
1 GGTTTAATGCAAATGGAGATATTTTGGAGAGAAGAAATG
275672 AATATAAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.36, C:0.02, G:0.31, T:0.31
Consensus pattern (42 bp):
GGTTTAATGCAAATGGAGATATTTTGGAGAGAAGAAATGGAT
Found at i:275748 original size:17 final size:17
Alignment explanation
Indices: 275728--275791 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
275718 ATTTCAAGAC
*
275728 TTATGTAATGTTTTTAA
1 TTATGTAGTGTTTTTAA
** *
275745 TTATGTAGTGATTCAAATAC
1 TTATGTAGTG-TT--TTTAA
275765 TTATGTAGTGTTTTTAA
1 TTATGTAGTGTTTTTAA
275782 TTATGTAGTG
1 TTATGTAGTG
275792 ATTCAATTCG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
17 21 0.57
18 2 0.05
19 2 0.05
20 12 0.32
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (17 bp):
TTATGTAGTGTTTTTAA
Found at i:275767 original size:37 final size:37
Alignment explanation
Indices: 275726--275797 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
275716 TAATTTCAAG
275726 ACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAT
1 ACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAT
*
275763 ACTTATGTAGTGTTTTTAATTATGTAGTGATTCAA
1 ACTTATGTAATGTTTTTAATTATGTAGTGATTCAA
275798 TTCGGTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.49
Consensus pattern (37 bp):
ACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAT
Found at i:276793 original size:2 final size:2
Alignment explanation
Indices: 276786--276812 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
276776 TTTTAGTCCC
276786 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
276813 TTGTGAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:277831 original size:27 final size:27
Alignment explanation
Indices: 277755--277831 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 27
277745 TCATAAATTT
* *
277755 AATTTTTTTATAATTAATATAAAATAC
1 AATTTTTATATAATTAATTTAAAATAC
* *
277782 AATATATTAATATTAATACAATTTAAAAATA-
1 AAT-T-TTTATA-TAAT-TAATTT-AAAATAC
277813 AATTTTTATATAATTAATT
1 AATTTTTATATAATTAATT
277832 ATTACCAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
27 7 0.18
28 5 0.13
29 9 0.23
30 5 0.13
31 7 0.18
32 6 0.15
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (27 bp):
AATTTTTATATAATTAATTTAAAATAC
Found at i:290787 original size:21 final size:21
Alignment explanation
Indices: 290763--290803 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
290753 TTAATTTCTC
*
290763 TATTTT-TTCTAATTGTAAGAA
1 TATTTTGTTCAAATT-TAAGAA
290784 TATTTTGTTCAAATTTAAGA
1 TATTTTGTTCAAATTTAAGA
290804 TTTAATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (21 bp):
TATTTTGTTCAAATTTAAGAA
Found at i:299805 original size:2 final size:2
Alignment explanation
Indices: 299798--299830 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
299788 ATGGTCTTAT
299798 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
299831 TCAAACTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:305541 original size:12 final size:12
Alignment explanation
Indices: 305524--305553 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
305514 CTTGCTTAGT
*
305524 TCCTCGTAGATA
1 TCCTCGTAGAAA
305536 TCCTCGTAGAAA
1 TCCTCGTAGAAA
305548 TCCTCG
1 TCCTCG
305554 AAATGTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (12 bp):
TCCTCGTAGAAA
Found at i:310448 original size:195 final size:192
Alignment explanation
Indices: 309894--310453 Score: 582
Period size: 193 Copynumber: 2.9 Consensus size: 192
309884 TCTTAAAACA
* * ** *
309894 GTATGGCAATGAGTGATCTTTTCTATAACATATTAGAATCATTCAGAAAATGA-AAAACTCACCA
1 GTATGTCAATGAGTGAAC-TTT-TATAACATACCAGAATCATTCAGAAAAT-ACAAAGCTCACC-
** *
309958 ATAAATTTATGATGTTATGAACTTATGATAATTTTTCATAAAGCTAAATCTGAATGATATTTAC-
62 ATAAATTTATGATGTTATGAAC-TATGATAATTCATCATAGAGCTAAATCTGAATG-TATTTACT
* *** * * * *
310022 TTTCA--CT-GGCACCCGA-AACAAGCAGATTAAACTGAGCTTAAGGATCAGCTAGCACAGTTAA
125 TTTCACCCTCGTCA-AAAACAACAAGCAGACTAAGCTGAGTTTAAGGATCAGCTAGCACAGCTAA
310083 ATCT
189 ATCT
*
310087 GTATGTCAATGAGTGAACTTTTCAATAACATACCAGAATCATTCAGAAAATGCAAAGCTCACCAT
1 GTATGTCAATGAGTGAACTTTT--ATAACATACCAGAATCATTCAGAAAATACAAAGCTCACCAT
* * * ** * *
310152 GAAGTTTATGCTGCTATGAACTAATGGCAATTCATCATTGAGCTAAATCTGAATGGTATCTACTT
64 -AAATTTATGATGTTATGAACT-ATGATAATTCATCATAGAGCTAAATCTGAAT-GTATTTACTT
* * *
310217 TTCACCCTCATCAAAAACGACAAGCAGACAAAGCTGAGTTTAAGGATCAGCTAGCGA-AGCTAAA
126 TTCACCCTCGTCAAAAACAACAAGCAGACTAAGCTGAGTTTAAGGATCAGCTAGC-ACAGCTAAA
310281 TCT
190 TCT
* *
310284 GTATAG-CAATTAGTGAAC-TTTATAACATAGCAGAATCATTCAGAAAATACAAAGCTCACCACT
1 GTAT-GTCAATGAGTGAACTTTTATAACATACCAGAATCATTCAGAAAATACAAAGCTCACCA-T
* * *
310347 AACTGTAT-AGTGTTATGAACGTATGATAAATTCATCATAGAGATAAATCTGAATAGTATTTACT
64 AAATTTATGA-TGTTATGAAC-TATGAT-AATTCATCATAGAGCTAAATCTGAAT-GTATTTACT
*
310411 TTTCACCCTCGTCAAAAACAACAAACAGACTAAGCTGAGTTTA
125 TTTCACCCTCGTCAAAAACAACAAGCAGACTAAGCTGAGTTTA
310454 CAGATCGCTA
Statistics
Matches: 306, Mismatches: 44, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
191 1 0.00
192 6 0.02
193 98 0.32
194 62 0.20
195 73 0.24
196 6 0.02
197 58 0.19
198 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (192 bp):
GTATGTCAATGAGTGAACTTTTATAACATACCAGAATCATTCAGAAAATACAAAGCTCACCATAA
ATTTATGATGTTATGAACTATGATAATTCATCATAGAGCTAAATCTGAATGTATTTACTTTTCAC
CCTCGTCAAAAACAACAAGCAGACTAAGCTGAGTTTAAGGATCAGCTAGCACAGCTAAATCT
Found at i:312220 original size:123 final size:124
Alignment explanation
Indices: 312000--312284 Score: 455
Period size: 123 Copynumber: 2.3 Consensus size: 124
311990 ATTTATTAAG
**
312000 GAAATCGCTCCTACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCTACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAAGTTGAC
312065 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
* * * * *
312124 GAAATCACTCCCACATGGACGCGCTTTTGCTACAGTAGGTCTTG-AAAAGTAATTTCAAGTTGAC
1 GAAATCGCTCCTACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAAGTTGAC
* *
312188 GTTTCTGAGCAAATAGTATAGAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
* * *
312247 GAAATCGCTCCTATGTGGACGCGTTTTTGTTACAGTAG
1 GAAATCGCTCCTACGTGGACGCGCTTTTGCTACAGTAG
312285 AATGTTGGGC
Statistics
Matches: 146, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
123 106 0.73
124 40 0.27
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (124 bp):
GAAATCGCTCCTACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAAGTTGAC
GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
Found at i:315605 original size:48 final size:48
Alignment explanation
Indices: 315327--315580 Score: 499
Period size: 48 Copynumber: 5.3 Consensus size: 48
315317 NNNNNNNNNN
315327 TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
1 TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
315375 TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
1 TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
315423 TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
1 TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
315471 TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
1 TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
315519 TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
1 TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
315567 GTATTTTATTACAT
1 -TATTTTATTACAT
315581 TAAAATAAAC
Statistics
Matches: 205, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
48 192 0.94
49 13 0.06
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.44
Consensus pattern (48 bp):
TATTTTATTACATCAAATAATATCAAATTATTCAAAATAAACTATTTT
Found at i:315737 original size:21 final size:22
Alignment explanation
Indices: 315713--315760 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
315703 GCGGGGGTTG
*
315713 TGGTTGC-TCCGG-CGGGGACTC
1 TGGTTGCATCCGGTAGGGGA-TC
315734 TGGTT-CATCCGGTAGGGGATC
1 TGGTTGCATCCGGTAGGGGATC
315755 TGGTTG
1 TGGTTG
315761 TCGGTGTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.08, C:0.21, G:0.42, T:0.29
Consensus pattern (22 bp):
TGGTTGCATCCGGTAGGGGATC
Found at i:317921 original size:22 final size:22
Alignment explanation
Indices: 317879--317928 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
317869 TCTTTTAAAT
* *
317879 AGAAATTTGAGAGGAATTTGAG
1 AGAAATTAGAGAGGAAATTGAG
317901 AGAATATTAGAGA-GAAATTGAG
1 AGAA-ATTAGAGAGGAAATTGAG
317923 AGAAAT
1 AGAAAT
317929 GATTTAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.64
23 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (22 bp):
AGAAATTAGAGAGGAAATTGAG
Found at i:317923 original size:10 final size:10
Alignment explanation
Indices: 317879--317928 Score: 55
Period size: 10 Copynumber: 4.6 Consensus size: 10
317869 TCTTTTAAAT
317879 AGAAATTTGAG
1 AGAAA-TTGAG
*
317890 AGGAATTTGAG
1 A-GAAATTGAG
317901 AGAATATTAGAG
1 AGAA-ATT-GAG
317913 AGAAATTGAG
1 AGAAATTGAG
317923 AGAAAT
1 AGAAAT
317929 GATTTAGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 12 0.35
11 12 0.35
12 10 0.29
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (10 bp):
AGAAATTGAG
Found at i:318590 original size:45 final size:44
Alignment explanation
Indices: 318526--318618 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
318516 ATAAAGTTAT
* *
318526 AATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAGACGTAATAGT-ATT-AATGTGTTTGGTTGAATGA
*
318571 AATGGAATAGA-ACTGTAATAGTATTATTGTGTTTGGTTGAATGA
1 AATGGAATAGAGAC-GTAATAGTATTAATGTGTTTGGTTGAATGA
318615 AATG
1 AATG
318619 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 2 0.05
44 22 0.51
45 19 0.44
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGACGTAATAGTATTAATGTGTTTGGTTGAATGA
Found at i:319666 original size:30 final size:30
Alignment explanation
Indices: 319632--319690 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
319622 TTCAGTATTA
*
319632 AGCCAAGATAAAGTAGGCAATACCTGAATT
1 AGCCAAGATAAAGTAGGCAATAACTGAATT
319662 AGCCAAGATAAAGTAGGCAATAACTGAAT
1 AGCCAAGATAAAGTAGGCAATAACTGAAT
319691 AGTGATGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (30 bp):
AGCCAAGATAAAGTAGGCAATAACTGAATT
Found at i:321824 original size:18 final size:18
Alignment explanation
Indices: 321801--321840 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
321791 AGATTTGGAA
321801 AAGAAGGAAACGTAGGAG
1 AAGAAGGAAACGTAGGAG
*
321819 AAGAAGGAAATGTAGGAG
1 AAGAAGGAAACGTAGGAG
321837 AAGA
1 AAGA
321841 TGCTGAGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.53, C:0.03, G:0.38, T:0.07
Consensus pattern (18 bp):
AAGAAGGAAACGTAGGAG
Found at i:328630 original size:20 final size:21
Alignment explanation
Indices: 328602--328656 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
328592 ACGTGCTAAC
328602 AAGAGCAGAAAAA-CGTGTCAA
1 AAGA-CAGAAAAAGCGTGTCAA
328623 AAGACAGAGAAAAGCGTGTCAA
1 AAGACAGA-AAAAGCGTGTCAA
328645 AAGACAGAAAAA
1 AAGACAGAAAAA
328657 AATTCGTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 4 0.12
21 12 0.38
22 16 0.50
ACGTcount: A:0.56, C:0.13, G:0.24, T:0.07
Consensus pattern (21 bp):
AAGACAGAAAAAGCGTGTCAA
Found at i:334494 original size:18 final size:16
Alignment explanation
Indices: 334459--334536 Score: 68
Period size: 18 Copynumber: 4.4 Consensus size: 16
334449 TTTTATGTTT
334459 TTTTTA-ATTTTATAAAA
1 TTTTTATATTTT-T-AAA
334476 TTTTTATATGCTTTTAAA
1 TTTTTATAT--TTTTAAA
*
334494 TTTTTACTTTTTTTAATA
1 TTTTTA-TATTTTTAA-A
334512 TTTTTATGATTTTTAAA
1 TTTTTAT-ATTTTTAAA
334529 TTATTTAT
1 TT-TTTAT
334537 TGTCAATATG
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
17 16 0.31
18 30 0.58
19 3 0.06
20 3 0.06
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTTATATTTTTAAA
Found at i:334515 original size:36 final size:36
Alignment explanation
Indices: 334466--334535 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
334456 TTTTTTTTAA
334466 TTTTATAAAATTTTTAT-ATGCTTTTAAATT-TTTACT
1 TTTTATAAAATTTTTATGAT--TTTTAAATTATTTACT
* *
334502 TTTTTTAATATTTTTATGATTTTTAAATTATTTA
1 TTTTATAAAATTTTTATGATTTTTAAATTATTTA
334536 TTGTCAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 9 0.30
36 19 0.63
37 2 0.07
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (36 bp):
TTTTATAAAATTTTTATGATTTTTAAATTATTTACT
Found at i:336076 original size:46 final size:46
Alignment explanation
Indices: 336025--336174 Score: 104
Period size: 49 Copynumber: 3.1 Consensus size: 46
336015 ATTATAGTTG
336025 AGGGTTACTTGAGCAAATTAATTATAAATTTTTAAAAAATTAGATT
1 AGGGTTACTTGAGCAAATTAATTATAAATTTTTAAAAAATTAGATT
* * **** * * *** *
336071 AGGGTTTAGTGTTAAGGGTTTTTAA-GAAAAAAAATTAAATAAATTAGGGCTT
1 AGGG-TTA--CTTGA-GCAAATTAATTATAAATTTTTAAA-AAATTA--GATT
* *
336123 AGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAGATT
1 AGGGTTACTTGAGCAAATTAATTATAAATTTTTAAAAAATTAGATT
336169 AGGGTT
1 AGGGTT
336175 TAGGGTTTTT
Statistics
Matches: 71, Mismatches: 25, Indels: 16
0.63 0.22 0.14
Matches are distributed among these distances:
46 13 0.18
47 3 0.04
48 11 0.15
49 23 0.32
50 11 0.15
51 3 0.04
52 7 0.10
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (46 bp):
AGGGTTACTTGAGCAAATTAATTATAAATTTTTAAAAAATTAGATT
Found at i:336145 original size:98 final size:96
Alignment explanation
Indices: 335895--336177 Score: 336
Period size: 98 Copynumber: 2.9 Consensus size: 96
335885 TTGAGTTTTT
* * ** * * **
335895 GGTTTTAAAGAAAAAAATTAAATAAATAAGGGATTAGGGTTTTTTAATTAAATTAATTATAAAAA
1 GGTTTTTAAGAAAAAAATTAAATAAATTAGGG-TTAGGGTTACTTGAGTAAATTAATTATAAATT
* * * * *
335960 ATT-CAAAATTAGATTAGGGTTTTGTGTTTAT
65 TTTAAAAAATTAGATTAGGGTTTAGTGTTAAG
* * * ** *
335991 GG-TTTTAAGGAAAAAATCAATTAAATTATAGTTGAGGGTTACTTGAGCAAATTAATTATAAATT
1 GGTTTTTAAGAAAAAAATTAAATAAATTAGGGTT-AGGGTTACTTGAGTAAATTAATTATAAATT
336055 TTTAAAAAATTAGATTAGGGTTTAGTGTTAAG
65 TTTAAAAAATTAGATTAGGGTTTAGTGTTAAG
336087 GGTTTTTAAGAAAAAAAATTAAATAAATTAGGGCTTAGGGTTACTTGAGTAAATTAATTATAAAT
1 GGTTTTTAAG-AAAAAAATTAAATAAATTAGGG-TTAGGGTTACTTGAGTAAATTAATTATAAAT
*
336152 TTTAAAAAAATTAGATTAGGGTTTAG
64 TTTTAAAAAATTAGATTAGGGTTTAG
336178 GGTTTTTAAG
Statistics
Matches: 156, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
94 2 0.01
95 47 0.30
96 28 0.18
97 7 0.04
98 70 0.45
99 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (96 bp):
GGTTTTTAAGAAAAAAATTAAATAAATTAGGGTTAGGGTTACTTGAGTAAATTAATTATAAATTT
TTAAAAAATTAGATTAGGGTTTAGTGTTAAG
Found at i:336230 original size:98 final size:95
Alignment explanation
Indices: 335895--336209 Score: 283
Period size: 98 Copynumber: 3.3 Consensus size: 95
335885 TTGAGTTTTT
* * * ** * *
335895 GGTTTTAAAG-AAAAAAATTAAATAAATAAGGGATTAGGGTTTTTTAATTAAATTAATTATAAAA
1 GGTTTTTAAGAAAAAAAATTAAATAAATTAGGGCTTAGGGTTACTTGAGTAAATTAATTAT-AAA
** * * *
335959 AATT--CAAAATTAGATTAGGGTTTTGTGTTTAT
65 TTTTAAAAAAATTAGATTAGGG---TGTGTTAAG
* * * ** *
335991 GG-TTTTAAG-GAAAAAATCAATTAAATTATAG-TTGAGGGTTACTTGAGCAAATTAATTATAAA
1 GGTTTTTAAGAAAAAAAATTAAATAAATTAGGGCTT-AGGGTTACTTGAGTAAATTAATTATAAA
*
336053 TTTTTAAAAAATTAGATTAGGGTTTAGTGTTAAG
65 TTTTAAAAAAATTAGATTAGGG--T-GTGTTAAG
336087 GGTTTTTAAGAAAAAAAATTAAATAAATTAGGGCTTAGGGTTACTTGAGTAAATTAATTATAAAT
1 GGTTTTTAAGAAAAAAAATTAAATAAATTAGGGCTTAGGGTTACTTGAGTAAATTAATTATAAAT
336152 TTTAAAAAAATTAGATTA-GG-GT-TT-AG
66 TTTAAAAAAATTAGATTAGGGTGTGTTAAG
* * *
336178 GGTTTTTAAG-GAAAAACTCAAATAAATTAGGG
1 GGTTTTTAAGAAAAAAAATTAAATAAATTAGGG
336210 TTTGGGGGTT
Statistics
Matches: 185, Mismatches: 27, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
90 19 0.10
91 12 0.06
92 2 0.01
93 2 0.01
94 7 0.04
95 45 0.24
96 25 0.14
97 9 0.05
98 62 0.34
99 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.37
Consensus pattern (95 bp):
GGTTTTTAAGAAAAAAAATTAAATAAATTAGGGCTTAGGGTTACTTGAGTAAATTAATTATAAAT
TTTAAAAAAATTAGATTAGGGTGTGTTAAG
Found at i:336430 original size:126 final size:126
Alignment explanation
Indices: 336256--336543 Score: 459
Period size: 126 Copynumber: 2.3 Consensus size: 126
336246 TAATTTAAAA
* * *
336256 AAGCTCCCACGTGGACACTTTTTTGCTACAGTAGTTACTGAAAAAATAATTTTGAGAAGACGTTT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTACTGAAAAAATAATTTCGAGAAGACGTTT
* * *
336321 CTGAGCAAATTGTGGCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTTCTGAAAG
66 CTGAGCAAATAGTGGCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAAG
* * *
336382 AAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTTCTGAAACAATAATTTCGAGAAGACGTTT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTACTGAAAAAATAATTTCGAGAAGACGTTT
* * *
336447 CTGAGCAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTGTCAGCAAAAGTACTGAAAT
66 CTGAGCAAATAGTGGCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAAG
*
336508 AAGCTCCCACGTGGACGCTCTTTTGCTACCGTAGTT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTT
336544 CCTATTTGGC
Statistics
Matches: 148, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 148 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTACTGAAAAAATAATTTCGAGAAGACGTTT
CTGAGCAAATAGTGGCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAAG
Found at i:337656 original size:30 final size:30
Alignment explanation
Indices: 337622--337682 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
337612 TGTTGGGTCG
* * *
337622 GGTGACTGTGTATGTGCTGTTGCTGGGCCT
1 GGTGACTGTGTAGGCGCTGTTGATGGGCCT
* *
337652 GGTGATTGTGTGGGCGCTGTTGATGGGCCT
1 GGTGACTGTGTAGGCGCTGTTGATGGGCCT
337682 G
1 G
337683 TGTCGTCGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.07, C:0.15, G:0.44, T:0.34
Consensus pattern (30 bp):
GGTGACTGTGTAGGCGCTGTTGATGGGCCT
Found at i:341270 original size:10 final size:10
Alignment explanation
Indices: 341244--341300 Score: 60
Period size: 10 Copynumber: 5.3 Consensus size: 10
341234 GAATTTTAGA
*
341244 AGAATTTGAG
1 AGAATATGAG
341254 AGAAATATGAG
1 AG-AATATGAG
341265 AGAATATTGGAG
1 AGAATA-T-GAG
341277 AGAAATATGAG
1 AG-AATATGAG
*
341288 AGAATTTGAG
1 AGAATATGAG
341298 AGA
1 AGA
341301 CATGATTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 16 0.39
11 15 0.37
12 6 0.15
13 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (10 bp):
AGAATATGAG
Found at i:341281 original size:23 final size:21
Alignment explanation
Indices: 341244--341300 Score: 96
Period size: 23 Copynumber: 2.6 Consensus size: 21
341234 GAATTTTAGA
341244 AGAATTTGAGAGAAATATGAG
1 AGAATTTGAGAGAAATATGAG
341265 AGAATATTGGAGAGAAATATGAG
1 AGAAT-TT-GAGAGAAATATGAG
341288 AGAATTTGAGAGA
1 AGAATTTGAGAGA
341301 CATGATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.32
22 4 0.12
23 19 0.56
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (21 bp):
AGAATTTGAGAGAAATATGAG
Found at i:359125 original size:2 final size:2
Alignment explanation
Indices: 359118--359142 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
359108 TACTATACAT
359118 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
359143 TTATCTCATT
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:362902 original size:42 final size:42
Alignment explanation
Indices: 362854--362950 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
362844 CTCGGTGTCA
*
362854 CACACTTAGTGCCCGTTATTCAACATCATCATATTAATTTCT-
1 CACACTTAGTGCCCATTATTCAACATCATCATATTAATTT-TG
* * *
362896 CACACTTAGTGCCCATTATTCAACATCGTCATTTTAGTTTTG
1 CACACTTAGTGCCCATTATTCAACATCATCATATTAATTTTG
362938 CACACTTAGTGCC
1 CACACTTAGTGCC
362951 ATTCATATAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (42 bp):
CACACTTAGTGCCCATTATTCAACATCATCATATTAATTTTG
Found at i:373974 original size:21 final size:21
Alignment explanation
Indices: 373948--373992 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
373938 CCGATGACTT
373948 CTTGAAAACGATTGGCAATGG
1 CTTGAAAACGATTGGCAATGG
*
373969 CTTGAAAATGATTGGCAATGG
1 CTTGAAAACGATTGGCAATGG
373990 CTT
1 CTT
373993 TAGCAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (21 bp):
CTTGAAAACGATTGGCAATGG
Found at i:380436 original size:49 final size:49
Alignment explanation
Indices: 380382--380478 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
380372 GTTTATATTA
380382 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
380431 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTT
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTT
380479 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.47
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
Found at i:383583 original size:30 final size:31
Alignment explanation
Indices: 383544--383603 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
383534 GGAGGTGGGA
*
383544 TGGGAAGGGAATAAAAGTTTTAGGAGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGAGAAAAG
* * *
383575 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGAGAAAA
383604 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGAGAAAAG
Found at i:383913 original size:9 final size:9
Alignment explanation
Indices: 383899--383929 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
383889 TTGAGTTGAT
383899 TCGAATAAC
1 TCGAATAAC
383908 TCGAATAAC
1 TCGAATAAC
383917 TCGAATAAC
1 TCGAATAAC
383926 TCGA
1 TCGA
383930 TTCGTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (9 bp):
TCGAATAAC
Found at i:384374 original size:125 final size:125
Alignment explanation
Indices: 384141--384553 Score: 666
Period size: 125 Copynumber: 3.3 Consensus size: 125
384131 CCCAAATATG
* * *
384141 CTACTGTAGCAAAAAACGCGTCCACGTGGGAGAGATTTCAGAAATTTTTCTGATAAAGCATCTTG
1 CTACTGTAGC-AAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCTTG
*
384206 TTTGAAGCG-TTTTTATACTATTTGCTCAGAAGCGTCAACTCGAAATTATTTTTTCAGGAC
65 CTTGAAGCGTTTTTTATACTATTTGCTCAGAAGCGTCAACTCGAAATTATTTTTTCAGGAC
* *
384266 CTACTGTAGCAAAAGCGCGTCCACGTAGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCTTGC
* *
384331 TTCAAGCGTTTTTTATACTATTTGCTCAGAAGCGTCAACTCGAAATTATTTTTTTAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAGCGTCAACTCGAAATTATTTTTTCAGGAC
* * *
384391 CTACTGTAGTAAAAGCGCGTCCACGTGGGAGCGATTTTAAAAATTCTTCTGATAAAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCTTGC
* * *
384456 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAGCGTCAACTCGAAATTATTTTTTCAGGAC
* *
384516 CTACTGTAGTAAAAGCGCGTCCACGTGGTAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
384554 CTTAATAAAT
Statistics
Matches: 267, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
124 56 0.21
125 211 0.79
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCTTGC
TTGAAGCGTTTTTTATACTATTTGCTCAGAAGCGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:384765 original size:21 final size:21
Alignment explanation
Indices: 384736--384777 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
384726 CCCTAAAAAT
* *
384736 CCTAAAAACCCTAACCCTAAC
1 CCTAAAAACCCAAAACCTAAC
*
384757 CCTAGAAACCCAAAACCTAAC
1 CCTAAAAACCCAAAACCTAAC
384778 ATGGGAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.40, G:0.02, T:0.12
Consensus pattern (21 bp):
CCTAAAAACCCAAAACCTAAC
Done.