Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009589.1 Hibiscus syriacus cultivar Beakdansim tig00116968_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 660543
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 3
Found at i:1732 original size:18 final size:18
Alignment explanation
Indices: 1709--1743 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1699 TTCCATCCGG
*
1709 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1727 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1744 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:2954 original size:32 final size:33
Alignment explanation
Indices: 2907--2978 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 33
2897 CGATCCGGCT
*
2907 CGGCTCCGGCTCAGCTCAAACGGCTC-GCTTAAA
1 CGGCT-CGGCTCAGCTCAAACGGCTCGGCTCAAA
*
2940 CGGCTCGGCTCAGCTCAAGCGGCTCGGCTCAAA
1 CGGCTCGGCTCAGCTCAAACGGCTCGGCTCAAA
2973 CGGCTC
1 CGGCTC
2979 CTCAGGCTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 19 0.53
33 17 0.47
ACGTcount: A:0.18, C:0.38, G:0.28, T:0.17
Consensus pattern (33 bp):
CGGCTCGGCTCAGCTCAAACGGCTCGGCTCAAA
Found at i:2964 original size:19 final size:19
Alignment explanation
Indices: 2907--2970 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
2897 CGATCCGGCT
2907 CGGCTCCGGCTCAGCTCAAA
1 CGGCT-CGGCTCAGCTCAAA
2927 CGGCTC-GCT----T-AAA
1 CGGCTCGGCTCAGCTCAAA
*
2940 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
2959 CGGCTCGGCTCA
1 CGGCTCGGCTCA
2971 AACGGCTCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 9 0.24
14 4 0.11
18 4 0.11
19 15 0.41
20 5 0.14
ACGTcount: A:0.17, C:0.38, G:0.28, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:2971 original size:14 final size:14
Alignment explanation
Indices: 2913--2951 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
2903 GGCTCGGCTC
2913 CGGCTCAGCTCAAA
1 CGGCTCAGCTCAAA
*
2927 CGGCTC-GCTTAAA
1 CGGCTCAGCTCAAA
*
2940 CGGCTCGGCTCA
1 CGGCTCAGCTCA
2952 GCTCAAGCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.18
Consensus pattern (14 bp):
CGGCTCAGCTCAAA
Found at i:2976 original size:14 final size:14
Alignment explanation
Indices: 2902--2978 Score: 63
Period size: 14 Copynumber: 5.4 Consensus size: 14
2892 CGGCTCGATC
2902 CGGCTCGGCTC---
1 CGGCTCGGCTCAAA
*
2913 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
*
2927 CGGCTC-GCTTAAA
1 CGGCTCGGCTCAAA
2940 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
2958 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
2973 CGGCTC
1 CGGCTC
2979 CTCAGGCTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
11 10 0.19
13 12 0.22
14 16 0.30
15 2 0.04
18 2 0.04
19 12 0.22
ACGTcount: A:0.17, C:0.38, G:0.29, T:0.17
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:6733 original size:18 final size:18
Alignment explanation
Indices: 6710--6744 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6700 TTCCATCCGG
*
6710 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
6728 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
6745 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:8090 original size:19 final size:19
Alignment explanation
Indices: 8068--8150 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
8058 CTAGGCGGCT
*
8068 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
8087 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
8106 CGGCTCGGCT----T-AAA
1 CGGCTCGGCTCAGCTCAAA
*
8120 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
8139 CGGCTCGGCTCA
1 CGGCTCGGCTCA
8151 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:8097 original size:14 final size:14
Alignment explanation
Indices: 8092--8158 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
8082 TCAAACGGCT
*
8092 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
*
8106 CGGCTCGGCTTAAA
1 CGGCTCGGCTCAAA
8120 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
8138 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
8153 CGGCTC
1 CGGCTC
8159 CTCAGGCTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 29 0.64
15 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.19, C:0.36, G:0.28, T:0.16
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:8121 original size:33 final size:33
Alignment explanation
Indices: 8074--8158 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
8064 GGCTCGGCTT
*
8074 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
* *
8107 GGCTCGGCTTAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
8140 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
8159 CTCAGGCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.16
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:10282 original size:2 final size:2
Alignment explanation
Indices: 10275--10301 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10265 TATGATATTT
10275 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
10302 TACTTTCATT
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:19376 original size:15 final size:15
Alignment explanation
Indices: 19356--19401 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
19346 TATTAGAATA
19356 ATTTATTTAAATATT
1 ATTTATTTAAATATT
* *
19371 ATTTATATCAATATT
1 ATTTATTTAAATATT
*
19386 A-TTATTAAAATATT
1 ATTTATTTAAATATT
19400 AT
1 AT
19402 ATCTACAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTTAAATATT
Found at i:19397 original size:14 final size:14
Alignment explanation
Indices: 19358--19507 Score: 59
Period size: 14 Copynumber: 11.0 Consensus size: 14
19348 TTAGAATAAT
*
19358 TTATTTAAATATTA
1 TTATTAAAATATTA
*
19372 TT-TATATCAATATTA
1 TTAT-TA-AAATATTA
19387 TTATTAAAATATTA
1 TTATTAAAATATTA
* *
19401 -TATCTACAATTTTA
1 TTAT-TAAAATATTA
* *
19415 TAAATAAAA-A-TA
1 TTATTAAAATATTA
**
19427 TTACGAAAAT-TATA
1 TTATTAAAATAT-TA
**
19441 TTCTATTAAAATAAAA
1 -T-TATTAAAATATTA
*
19457 TTATTATAA-ATTA
1 TTATTAAAATATTA
*
19470 -TATT-AATTA-T-
1 TTATTAAAATATTA
*
19480 TTATTAAAATAATA
1 TTATTAAAATATTA
19494 TTATTAAAATATTA
1 TTATTAAAATATTA
19508 AAAATTATAA
Statistics
Matches: 97, Mismatches: 23, Indels: 32
0.64 0.15 0.21
Matches are distributed among these distances:
11 6 0.06
12 17 0.18
13 7 0.07
14 44 0.45
15 14 0.14
16 9 0.09
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (14 bp):
TTATTAAAATATTA
Found at i:19466 original size:16 final size:17
Alignment explanation
Indices: 19444--19499 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 17
19434 AATTATATTC
19444 TATTAAAATAAAATTAT
1 TATTAAAATAAAATTAT
*
19461 TA-TAAATTATATTAATTATT
1 TATTAAA--ATA-AAATTA-T
*
19481 TATTAAAATAATATTAT
1 TATTAAAATAAAATTAT
19498 TA
1 TA
19500 AAATATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
16 4 0.13
17 5 0.16
18 7 0.23
19 8 0.26
20 3 0.10
21 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAAAATAAAATTAT
Found at i:19508 original size:8 final size:8
Alignment explanation
Indices: 19495--19535 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
19485 AAAATAATAT
19495 TATTAAAA
1 TATTAAAA
19503 TATTAAAA
1 TATTAAAA
*
19511 -ATTATAA
1 TATTAAAA
19518 TATTAAAA
1 TATTAAAA
19526 TATTAAAA
1 TATTAAAA
19534 TA
1 TA
19536 AGAATATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TATTAAAA
Found at i:19514 original size:15 final size:16
Alignment explanation
Indices: 19495--19535 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
19485 AAAATAATAT
19495 TATTAAAATATTAAAA
1 TATTAAAATATTAAAA
*
19511 -ATTATAATATTAAAA
1 TATTAAAATATTAAAA
19526 TATTAAAATA
1 TATTAAAATA
19536 AGAATATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TATTAAAATATTAAAA
Found at i:19521 original size:23 final size:23
Alignment explanation
Indices: 19481--19544 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
19471 ATTAATTATT
*
19481 TATT-AAAATAATATTATTAAAA
1 TATTAAAAATAATAATATTAAAA
*
19503 TATTAAAAATTATAATATTAAAA
1 TATTAAAAATAATAATATTAAAA
*
19526 TATT-AAAATAAGAATATTA
1 TATTAAAAATAATAATATTA
19545 CATTATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 17 0.46
23 20 0.54
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TATTAAAAATAATAATATTAAAA
Found at i:19522 original size:37 final size:37
Alignment explanation
Indices: 19421--19527 Score: 101
Period size: 37 Copynumber: 2.8 Consensus size: 37
19411 TTTATAAATA
*
19421 AAAATATTACGAAAATTATATTCTATTAAAATAAAATTATT
1 AAAATATTA--AAAATTATA--ATATTAAAATAAAATTATT
** * *
19462 ATAAAT-TATATTAATTAT-TTATTAAAATAATATTATT
1 A-AAATAT-TAAAAATTATAATATTAAAATAAAATTATT
19499 AAAATATTAAAAATTATAATATTAAAATA
1 AAAATATTAAAAATTATAATATTAAAATA
19528 TTAAAATAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
36 12 0.22
37 29 0.53
40 6 0.11
41 2 0.04
42 6 0.11
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (37 bp):
AAAATATTAAAAATTATAATATTAAAATAAAATTATT
Found at i:19695 original size:48 final size:48
Alignment explanation
Indices: 19607--19711 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
19597 AAATTAATAA
* * *
19607 ATAATATTA-ATTTTATTAATAATTATCATATATCATTAAAATAAAAGT
1 ATAATATTATATATTATTAATAATTATCATATAACAATAAAATAAAA-T
* *
19655 ATAATATTATATATTA-TAATAA-TATGATTATAACAATAAAATATAAT
1 ATAATATTATATATTATTAATAATTATCA-TATAACAATAAAATAAAAT
*
19702 ATCATATTAT
1 ATAATATTAT
19712 TAAAATTATC
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
47 14 0.29
48 30 0.61
49 5 0.10
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (48 bp):
ATAATATTATATATTATTAATAATTATCATATAACAATAAAATAAAAT
Found at i:43761 original size:29 final size:30
Alignment explanation
Indices: 43727--43788 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
43717 CAGAAATTGT
*
43727 AATTAAAATATATG-AACAAATAT-TTATAA
1 AATTAAAACATATGCAACAAAT-TGTTATAA
* *
43756 AATTAAAGCATATGCTACAAATTGTTATAA
1 AATTAAAACATATGCAACAAATTGTTATAA
43786 AAT
1 AAT
43789 CAAGAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (30 bp):
AATTAAAACATATGCAACAAATTGTTATAA
Found at i:44350 original size:20 final size:20
Alignment explanation
Indices: 44325--44363 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
44315 GCAGAGATTT
44325 CATCCCAAATGGCTAGAAAA
1 CATCCCAAATGGCTAGAAAA
*
44345 CATCCCCAATGGCTAGAAA
1 CATCCCAAATGGCTAGAAA
44364 CGGCTACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.15
Consensus pattern (20 bp):
CATCCCAAATGGCTAGAAAA
Found at i:50566 original size:20 final size:20
Alignment explanation
Indices: 50504--50566 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
50494 GGTACCAAAG
* *
50504 AGGG-GTATCGATACCAACCA
1 AGGGAGTATCGATA-CTACTA
* **
50524 AGGGAAGTATCGGTACTGTTA
1 AGGG-AGTATCGATACTACTA
50545 AGGGAGTATCGATACTACTA
1 AGGGAGTATCGATACTACTA
50565 AG
1 AG
50567 TATGAAATGA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 19 0.58
21 6 0.18
22 8 0.24
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (20 bp):
AGGGAGTATCGATACTACTA
Found at i:51154 original size:24 final size:24
Alignment explanation
Indices: 51126--51183 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
51116 TTCAGGATAT
51126 TTCTACGTGGTCCTTAGGGACAAA
1 TTCTACGTGGTCCTTAGGGACAAA
*** * *
51150 TTCTACGCAATCCTTCGGGGCAAA
1 TTCTACGTGGTCCTTAGGGACAAA
51174 TTCTACGTGG
1 TTCTACGTGG
51184 CATTTCGGTG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (24 bp):
TTCTACGTGGTCCTTAGGGACAAA
Found at i:79189 original size:2 final size:2
Alignment explanation
Indices: 79182--79212 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
79172 TACTCTCATT
79182 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
79213 TCGTATGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79556 original size:58 final size:58
Alignment explanation
Indices: 79466--79583 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
79456 AGTTGGGGAC
79466 AAGTGGATCACTTGATGGGCAGCAAAGGTTGGTTGTGAAGGGAAGGTTTGCGCCCAAA
1 AAGTGGATCACTTGATGGGCAGCAAAGGTTGGTTGTGAAGGGAAGGTTTGCGCCCAAA
79524 AAGTGGATCACTTGATGGGCAGCAAAGGTTGGTTGTGAAGGGAAGGTTTGCGCCCAAA
1 AAGTGGATCACTTGATGGGCAGCAAAGGTTGGTTGTGAAGGGAAGGTTTGCGCCCAAA
79582 AA
1 AA
79584 TTTTGAAGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.22
Consensus pattern (58 bp):
AAGTGGATCACTTGATGGGCAGCAAAGGTTGGTTGTGAAGGGAAGGTTTGCGCCCAAA
Found at i:89365 original size:3 final size:3
Alignment explanation
Indices: 89357--89504 Score: 235
Period size: 3 Copynumber: 49.7 Consensus size: 3
89347 TTTTTATCCA
*
89357 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
89405 TAT TAT TAT TAA TAT TAT TAT CAT TAT TAA TAT TAT TAT TAA TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
89453 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
89500 TAT TA
1 TAT TA
89505 AATATATTAA
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
2 2 0.02
3 130 0.98
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:102290 original size:1 final size:1
Alignment explanation
Indices: 102284--102310 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
102274 TATTATGCTT
102284 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
102311 GAGGGTCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:102655 original size:16 final size:17
Alignment explanation
Indices: 102636--102680 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
102626 CTATTTCAAG
*
102636 TTCAATTTATTT-GAGA
1 TTCAATTTATTTGGAAA
*
102652 TTCAATTATTTTTGGAAA
1 TTCAATT-TATTTGGAAA
102670 TTCAATTTATT
1 TTCAATTTATT
102681 CTTTTCTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 10 0.42
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (17 bp):
TTCAATTTATTTGGAAA
Found at i:103726 original size:52 final size:52
Alignment explanation
Indices: 103462--103706 Score: 481
Period size: 52 Copynumber: 4.7 Consensus size: 52
103452 AATATGCTCA
103462 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
103514 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
103566 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
*
103618 AACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
103670 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
103707 AATTGGATAG
Statistics
Matches: 191, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 191 1.00
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.38
Consensus pattern (52 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
Found at i:104673 original size:119 final size:116
Alignment explanation
Indices: 104344--105142 Score: 1222
Period size: 119 Copynumber: 6.9 Consensus size: 116
104334 TAGCAAAGAT
104344 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAA--C-TC
* *
104409 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
63 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
104463 TTAAATTCATC-ACTTGATGGATCATTCTTTTCCAGA-GAAG-GTTCATAATGAGAAGAACTCAT
1 TTGAATTCATCAAATTGATGGATCA-TCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCAT
104525 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
104577 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATCATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAA--C-TC
* *
104642 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
63 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
104696 TTAAATTCATC-ATTTGATGGATCATTCTTTTCCAGA-GAAG-GTTCATAATGAGAAGAACTCAT
1 TTGAATTCATCAAATTGATGGATCA-TCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCAT
*
104758 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACCTTTTGC
65 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
104810 TTGAATTCATCAAATTGATGGATCATCATTTTCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAA--C-TC
*
104875 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGT
63 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
104929 TTAAATTCATCAAACTGATGGATCATCATTTCCAGAGGTAA-AGTTCATAATGAGAAGAACTCAT
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGG-AAGAGTTCATAATGAGAAGAACTCAT
*
104993 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * *
105045 TTGAATTCATC-ATTTGATGGATCAACATTACCAG-GTAA-AGTTCATAATGAGAAGAACTCATC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATC
*
105107 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
66 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
105143 CATCAAGAGC
Statistics
Matches: 628, Mismatches: 37, Indels: 36
0.90 0.05 0.05
Matches are distributed among these distances:
113 60 0.10
114 147 0.23
115 53 0.08
116 97 0.15
117 34 0.05
118 34 0.05
119 201 0.32
120 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (116 bp):
TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATC
TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:104751 original size:233 final size:233
Alignment explanation
Indices: 104344--105140 Score: 1383
Period size: 233 Copynumber: 3.4 Consensus size: 233
104334 TAGCAAAGAT
104344 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
104409 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATC
*
104474 ACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
131 AATTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
104539 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
196 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
104577 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATCATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
104642 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATC
*
104707 ATTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
131 AATTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
*
104772 AGAAGTTCATAATGAGAAGAACTTCTTCAACCTTTTGC
196 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
104810 TTGAATTCATCAAATTGATGGATCATCATTTTCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
*
104875 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATC
* * *
104940 AAACTGATGGATCA-TCATTTCCAGAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
131 -AATTGATGGATCATTCTTTTCCAGA-G-AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
105004 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
193 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * *
105045 TTGAATTCATC-ATTTGATGGATCAACATTACCAG-GTAA-AGTTCATAATGAGAAGAA--C-TC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
*
105104 ATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAA
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
105141 CTCATCAAGA
Statistics
Matches: 543, Mismatches: 18, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
229 38 0.07
230 1 0.00
232 18 0.03
233 370 0.68
234 31 0.06
235 85 0.16
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (233 bp):
TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATC
AATTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:105011 original size:352 final size:345
Alignment explanation
Indices: 104347--105142 Score: 1244
Period size: 352 Copynumber: 2.3 Consensus size: 345
104337 CAAAGATTTG
*
104347 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATC-ATTTGATGGATCATCATTTCCAGA-GAAG-GTTCATAATGAGAAGAA--C-TCATC
* * * *
104412 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCACT
60 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACCTTTTGCTTAAATTCATCAAT
104477 TGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
125 TGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
104542 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAATTGATGGATCATCATT
190 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAAACTGATGGATCATCATT
*
104607 TCCAGAGGAAGAGTTCATCATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
255 TCCAGAGGAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
104672 AGAAGAATTTGTTCAACCTTTTGTTTA
319 AGAAGAATTTGTTCAACCTTTTGCTTA
*
104699 AATTCATCATTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCATTTGATGGATCA-TCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
*
104764 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACCTTTTGCTTGAATTCATCAAATTGAT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACCTTTTGCTTAAATTCATC-AATTGAT
104829 GGATCA-TCATTTT-CAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAA
129 GGATCATTC-TTTTCCAGA-GAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAA
*
104892 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCAAACTGATGGATCATCA
188 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAAACTGATGGATCATCA
104957 TTTCCAGAGGTAA-AGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGAAGTTCATAA
253 TTTCCAGAGG-AAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAAGTTCATAA
*
105019 TGAGAAGAATTTGTTCAACCTTTTGCTTG
317 TGAGAAGAATTTGTTCAACCTTTTGCTTA
* * *
105048 AATTCATCATTTGATGGATCAACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCATTTGATGGATCATCATTTCCAGAG-AAGGTTCATAATGAGAAGAACTCATCTGAAG
*
105112 AAGGAAGAAAAAGTTCATAATGAGAAGAACT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACT
105143 CATCAAGAGC
Statistics
Matches: 416, Mismatches: 18, Indels: 24
0.91 0.04 0.05
Matches are distributed among these distances:
347 70 0.17
348 88 0.21
349 95 0.23
350 18 0.04
351 17 0.04
352 126 0.30
353 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (345 bp):
AATTCATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACCTTTTGCTTAAATTCATCAATTGATGG
ATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAAACTGATGGATCATCATTTCCAGA
GGAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
TTTGTTCAACCTTTTGCTTA
Found at i:105396 original size:3 final size:3
Alignment explanation
Indices: 105388--105528 Score: 214
Period size: 3 Copynumber: 47.7 Consensus size: 3
105378 TTTTTATCCA
*
105388 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
105436 TAT TAT TAA TAT TAT TAT CAT TAT TAA TAT TAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
105484 TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT T-T T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
105529 AATATATTAA
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
2 4 0.03
3 121 0.97
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:106978 original size:23 final size:25
Alignment explanation
Indices: 106929--106981 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
106919 TGTTTTAGTG
**
106929 ATATTTTTATTTTATTATATTGTTAA
1 ATATTTTTA-TTTATTATATTCATAA
106955 ATATTTTTA-TTA-TATATTCATAA
1 ATATTTTTATTTATTATATTCATAA
106978 ATAT
1 ATAT
106982 ACATATAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.52
24 3 0.12
26 9 0.36
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
ATATTTTTATTTATTATATTCATAA
Found at i:108533 original size:60 final size:58
Alignment explanation
Indices: 108464--108618 Score: 168
Period size: 60 Copynumber: 2.6 Consensus size: 58
108454 ATATGTATTA
** **
108464 TTTTATTAAGTCCTTCAACTGCTAAAAGTTATAAAATGATTC-TCTAACTATAGAATGTTG
1 TTTTATTAAGT-C-TCAACTATTAAAAGTTATAAAATGA-TCATCTAACTATAGAACATTG
* * * *
108524 TTTTATTAAGTTCATCGACTATTAAAATTTATAAAATTATCATTTAACTATAGAACATTG
1 TTTTATTAAG-TC-TCAACTATTAAAAGTTATAAAATGATCATCTAACTATAGAACATTG
* *
108584 TTTTATGAAGTCTCAACTATTAAAAGTTAAAAAAT
1 TTTTATTAAGTCTCAACTATTAAAAGTTATAAAAT
108619 TATTTTACAT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
58 20 0.25
59 4 0.05
60 55 0.69
61 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (58 bp):
TTTTATTAAGTCTCAACTATTAAAAGTTATAAAATGATCATCTAACTATAGAACATTG
Found at i:111760 original size:15 final size:15
Alignment explanation
Indices: 111727--111775 Score: 73
Period size: 15 Copynumber: 3.2 Consensus size: 15
111717 GTTAAATTAG
111727 TTTAGGTTTTAGCTTA
1 TTTAGGTTTTAG-TTA
111743 TTTAGGTTTTAGTTA
1 TTTAGGTTTTAGTTA
111758 TTTAGGTTTATA-TTA
1 TTTAGGTTT-TAGTTA
111773 TTT
1 TTT
111776 CTTTGGGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 18 0.56
16 14 0.44
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.61
Consensus pattern (15 bp):
TTTAGGTTTTAGTTA
Found at i:123437 original size:8 final size:7
Alignment explanation
Indices: 123401--123542 Score: 71
Period size: 7 Copynumber: 19.7 Consensus size: 7
123391 AAGAAGAAAT
*
123401 AAAAGGA
1 AAAAAGA
123408 AAAAA-A
1 AAAAAGA
*
123414 AACAA-A
1 AAAAAGA
*
123420 AAAACGA
1 AAAAAGA
*
123427 AAAATGA
1 AAAAAGA
123434 AAAAA-A
1 AAAAAGA
*
123440 AAATAA-T
1 AAA-AAGA
*
123447 AAAATGA
1 AAAAAGA
123454 GAAAAAG-
1 -AAAAAGA
123461 AAAAAGA
1 AAAAAGA
123468 AGAAAAGA
1 A-AAAAGA
123476 AGAAAAGA
1 A-AAAAGA
123484 AAAAATGA
1 AAAAA-GA
123492 GAAAAA-A
1 -AAAAAGA
123499 TAAAAATGAAA
1 -AAAAA-G--A
123510 AAAAAGA
1 AAAAAGA
*
123517 AAAAATA
1 AAAAAGA
*
123524 AAAGAGA
1 AAAAAGA
*
123531 AAAATGA
1 AAAAAGA
123538 AAAAA
1 AAAAA
123543 AAGAAATAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
6 20 0.19
7 52 0.49
8 22 0.21
9 6 0.06
10 5 0.05
11 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.06
Consensus pattern (7 bp):
AAAAAGA
Found at i:123457 original size:22 final size:22
Alignment explanation
Indices: 123401--123553 Score: 75
Period size: 23 Copynumber: 6.7 Consensus size: 22
123391 AAGAAGAAAT
* *
123401 AAAAGGAAAAAAAAACAAAAAAACG
1 AAAA-GAAGAAAAAA-AAAATAA-G
* *
123426 AAAA-ATGAAAAAAAAAATAAT
1 AAAAGAAGAAAAAAAAAATAAG
*
123447 AAAATG-AGAAAAAGAAAAAGAAG
1 AAAA-GAAGAAAAA-AAAAATAAG
*
123470 AAAAGAAGAAAAGAAAAAATGAG
1 AAAAGAAGAAAA-AAAAAATAAG
* *
123493 AAAA-AATAAAAATGAAAAAAAAG
1 AAAAGAAGAAAAA--AAAAATAAG
*
123516 AAAA-AATAAAAGAGAAAAATGAA-
1 AAAAGAAGAAAA-A-AAAAAT-AAG
*
123539 AAAA-AAGAAATAAAA
1 AAAAGAAGAAAAAAAA
123554 GGGGTTCAAG
Statistics
Matches: 104, Mismatches: 15, Indels: 22
0.74 0.11 0.16
Matches are distributed among these distances:
21 8 0.08
22 20 0.19
23 68 0.65
24 4 0.04
25 4 0.04
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.07
Consensus pattern (22 bp):
AAAAGAAGAAAAAAAAAATAAG
Found at i:123536 original size:46 final size:45
Alignment explanation
Indices: 123407--123544 Score: 133
Period size: 46 Copynumber: 3.1 Consensus size: 45
123397 AAATAAAAGG
* * *
123407 AAAA-AAAAACAAAAAAACGAAAA-ATGAAAA-AAAAAAT-AATAA
1 AAAATAAAAAGAAAAAAAAGAAAAGAAGAAAAGAAAAAATGAA-AA
* * * *
123449 AATGAGAAAAAGAAAAAGAAGAAAAGAAGAAAAGAAAAAATGAGAA
1 AA-AATAAAAAGAAAAAAAAGAAAAGAAGAAAAGAAAAAATGAAAA
*
123495 AAAATAAAAATGAAAAAAAAGAAAA-AATAAAAGAGAAAAATGAAAA
1 AAAATAAAAA-GAAAAAAAAGAAAAGAAGAAAAGA-AAAAATGAAAA
123541 AAAA
1 AAAA
123545 GAAATAAAAG
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
42 2 0.03
43 1 0.01
44 16 0.21
45 20 0.26
46 38 0.49
47 1 0.01
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.07
Consensus pattern (45 bp):
AAAATAAAAAGAAAAAAAAGAAAAGAAGAAAAGAAAAAATGAAAA
Found at i:124784 original size:51 final size:51
Alignment explanation
Indices: 124723--125235 Score: 873
Period size: 51 Copynumber: 10.0 Consensus size: 51
124713 GAAGCAAATT
124723 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
*
124774 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
*
124825 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
124876 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
124927 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
*
124978 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
125029 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
*
125080 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* * *
125131 AGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* ** * * *
125182 TGTTTATTGAAGATTTTTTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 AGTTCGTTGAAGA----TTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
125236 CCGTTTTATT
Statistics
Matches: 440, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
51 407 0.93
55 33 0.08
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (51 bp):
AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
Found at i:126476 original size:16 final size:16
Alignment explanation
Indices: 126455--126497 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
126445 GTTAAATTAG
126455 TTTAGGTTTTAGCTTA
1 TTTAGGTTTTAGCTTA
*
126471 TTTAGGTTTTAGTTTA
1 TTTAGGTTTTAGCTTA
126487 TTTAGGTTTTA
1 TTTAGGTTTTA
126498 TATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.19, C:0.02, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTAGGTTTTAGCTTA
Found at i:126503 original size:16 final size:16
Alignment explanation
Indices: 126450--126505 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
126440 GTGAAGTTAA
*
126450 ATTAGTTTAGGTTTTAG
1 ATTA-TTTAGGTTTTAT
*
126467 CTTATTTAGGTTTTAGT
1 ATTATTTAGGTTTTA-T
126484 -TTATTTAGGTTTTAT
1 ATTATTTAGGTTTTAT
126499 ATTATTT
1 ATTATTT
126506 CTTTTGGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 1 0.03
16 31 0.89
17 3 0.09
ACGTcount: A:0.21, C:0.02, G:0.16, T:0.61
Consensus pattern (16 bp):
ATTATTTAGGTTTTAT
Found at i:128666 original size:16 final size:17
Alignment explanation
Indices: 128630--128669 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
128620 GATAGATCGA
128630 TAAATTTAATGATAATT
1 TAAATTTAATGATAATT
128647 TAAATTTAA-G-TAAGTT
1 TAAATTTAATGATAA-TT
128663 TAAATTT
1 TAAATTT
128670 TAGTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 10 0.45
17 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
TAAATTTAATGATAATT
Found at i:130052 original size:14 final size:13
Alignment explanation
Indices: 130035--130068 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
130025 AGGATTATGG
130035 TTTAGGGTTTGTAA
1 TTTAGGGTTT-TAA
130049 TTTAGGGTTTTAA
1 TTTAGGGTTTTAA
*
130062 GTTAGGG
1 TTTAGGG
130069 CTAGAGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (13 bp):
TTTAGGGTTTTAA
Found at i:130068 original size:13 final size:14
Alignment explanation
Indices: 130036--130068 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
130026 GGATTATGGT
*
130036 TTAGGGTTTGTAAT
1 TTAGGGTTTGTAAG
130050 TTAGGGTTT-TAAG
1 TTAGGGTTTGTAAG
130063 TTAGGG
1 TTAGGG
130069 CTAGAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTGTAAG
Found at i:131526 original size:31 final size:31
Alignment explanation
Indices: 131488--131641 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
131478 GGGTCGAGGG
*
131488 TTACCTATGTTCTTCGGGACATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
131519 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
131550 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
131581 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
131612 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
131642 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:135897 original size:31 final size:31
Alignment explanation
Indices: 135859--136074 Score: 371
Period size: 31 Copynumber: 7.0 Consensus size: 31
135849 GGGTCGAGGG
*
135859 TTACCTATGTTCTTCGGGACATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
135890 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
135921 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
135952 TTACCTATGTTCTTCGGGACATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
135983 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
136014 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
136045 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
136075 GTCCTTCGGG
Statistics
Matches: 178, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 177 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:137611 original size:21 final size:20
Alignment explanation
Indices: 137572--137612 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
137562 TAATTAATAA
**
137572 ATATATGTATATGAATGGTT
1 ATATATGTATAAAAATGGTT
137592 ATATATGTATTAAAAATGGTT
1 ATATATGTA-TAAAAATGGTT
137613 TGTTACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (20 bp):
ATATATGTATAAAAATGGTT
Found at i:138356 original size:14 final size:14
Alignment explanation
Indices: 138333--138362 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
138323 ATTATTTAAT
*
138333 TTTAATATAAAACA
1 TTTAAAATAAAACA
138347 TTTAAAATAAAACA
1 TTTAAAATAAAACA
138361 TT
1 TT
138363 AAATTATCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTAAAATAAAACA
Found at i:147042 original size:22 final size:19
Alignment explanation
Indices: 147014--147067 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 19
147004 GAACTTTACG
147014 ATATAAAATTTATAATTTTAA
1 ATATAAAATTTATAA--TTAA
* *
147035 ATTTTAAAATTCATAATTAA
1 A-TATAAAATTTATAATTAA
147055 ATATAAAATTTAT
1 ATATAAAATTTAT
147068 TTTGGTGGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 10 0.36
20 5 0.18
21 1 0.04
22 12 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAAAATTTATAATTAA
Found at i:147890 original size:2 final size:2
Alignment explanation
Indices: 147883--147920 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
147873 AAAAACAAGA
147883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
147921 TAATTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:152706 original size:19 final size:19
Alignment explanation
Indices: 152682--152723 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
152672 TTCCAGTTCG
152682 CGTTGCGATTTTCTAAATT
1 CGTTGCGATTTTCTAAATT
152701 CGTTGCGATTTTCTAAATT
1 CGTTGCGATTTTCTAAATT
152720 CGTT
1 CGTT
152724 ACGAAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCTAAATT
Found at i:152842 original size:5 final size:5
Alignment explanation
Indices: 152826--152879 Score: 99
Period size: 5 Copynumber: 10.6 Consensus size: 5
152816 CGTATTACCA
152826 CGACC ACGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC
1 CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGACC
152877 CGA
1 CGA
152880 GACGAGACGG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 43 0.90
6 5 0.10
ACGTcount: A:0.22, C:0.57, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:153420 original size:6 final size:6
Alignment explanation
Indices: 153373--153411 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
153363 TCTCGTCTCG
*
153373 GGTCTT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
153412 GGTCGTGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.15, G:0.49, T:0.36
Consensus pattern (6 bp):
GGTCGT
Found at i:153602 original size:21 final size:21
Alignment explanation
Indices: 153559--153602 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
153549 ACAACTGTAG
** *
153559 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
153580 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
153601 AC
1 AC
153603 GCGAATTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:160354 original size:30 final size:33
Alignment explanation
Indices: 160320--160390 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 33
160310 GTTTACAATT
*
160320 AAATAATCA-AATAAT-AAAAAA-TAAATACTA
1 AAATAATAATAATAATAAAAAAATTAAATACTA
* *
160350 AAATAA-AATAATAATAAAAAAATTAATTACTT
1 AAATAATAATAATAATAAAAAAATTAAATACTA
160382 AAATAATAA
1 AAATAATAA
160391 AAAAATTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 1 0.03
30 12 0.35
31 6 0.18
32 13 0.38
33 2 0.06
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (33 bp):
AAATAATAATAATAATAAAAAAATTAAATACTA
Found at i:169681 original size:37 final size:37
Alignment explanation
Indices: 169640--169715 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
169630 AGTTGGATAA
169640 ATTTTCGAAGGGAAATAGATGAATTATGGGTAAGGGT
1 ATTTTCGAAGGGAAATAGATGAATTATGGGTAAGGGT
169677 ATTTTCGAAGGGAAATAGATGAATTATGGGTAAGGGT
1 ATTTTCGAAGGGAAATAGATGAATTATGGGTAAGGGT
169714 AT
1 AT
169716 CGGTACTGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.03, G:0.32, T:0.30
Consensus pattern (37 bp):
ATTTTCGAAGGGAAATAGATGAATTATGGGTAAGGGT
Found at i:173740 original size:31 final size:31
Alignment explanation
Indices: 173702--173762 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
173692 GTTGAGAGGG
* *
173702 GACTAAAATTGAACGGATCGATAATGTTAGA
1 GACTAAAATCGAACGGATCGATAACGTTAGA
*
173733 GACTAAAATCGAACTGATCGATAACGTTAG
1 GACTAAAATCGAACGGATCGATAACGTTAG
173763 GACCATTCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (31 bp):
GACTAAAATCGAACGGATCGATAACGTTAGA
Found at i:175008 original size:21 final size:21
Alignment explanation
Indices: 174983--175022 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
174973 CCTTCCAGAT
*
174983 TCTCTTCTCTATCTCTCTCTC
1 TCTCTTCCCTATCTCTCTCTC
*
175004 TCTCTTCCCTTTCTCTCTC
1 TCTCTTCCCTATCTCTCTC
175023 CCTTCGTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.53
Consensus pattern (21 bp):
TCTCTTCCCTATCTCTCTCTC
Found at i:187046 original size:20 final size:20
Alignment explanation
Indices: 187023--187061 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
187013 CTTGAAACAA
*
187023 AAAGTGTGAAGAAAG-GAAGG
1 AAAGTG-GAAAAAAGTGAAGG
187043 AAAGTGGAAAAAAGTGAAG
1 AAAGTGGAAAAAAGTGAAG
187062 AAGAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.36, T:0.10
Consensus pattern (20 bp):
AAAGTGGAAAAAAGTGAAGG
Found at i:194123 original size:31 final size:31
Alignment explanation
Indices: 194050--194120 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
194040 ACTATCGACC
* *
194050 CGTCCAATTTAAGTCTCTAACGTTATTAATT
1 CGTCCGATTTAAGTCTCTAACGTTATCAATT
*
194081 CGTCCGATTTAAGTC-CTAACGTTATCAGTT
1 CGTCCGATTTAAGTCTCTAACGTTATCAATT
*
194111 CGTTCGATTT
1 CGTCCGATTT
194121 TAATCCCTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 22 0.61
31 14 0.39
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (31 bp):
CGTCCGATTTAAGTCTCTAACGTTATCAATT
Found at i:195607 original size:41 final size:41
Alignment explanation
Indices: 195550--195628 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
195540 AATTTACTTC
195550 TTTGCTTCTAAGATCGAAGCTTTTACTTAAAATGAACTTAT
1 TTTGCTTCTAAGATCGAAGCTTTTACTTAAAATGAACTTAT
195591 TTTGCTTCTAAGATCGAAGCTTTTACTTAAAATGAACT
1 TTTGCTTCTAAGATCGAAGCTTTTACTTAAAATGAACT
195629 AGATTATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (41 bp):
TTTGCTTCTAAGATCGAAGCTTTTACTTAAAATGAACTTAT
Found at i:199663 original size:2 final size:2
Alignment explanation
Indices: 199656--199692 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
199646 GTCTTAATCT
199656 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
199693 TATTCGATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:217569 original size:29 final size:29
Alignment explanation
Indices: 217527--217588 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
217517 GCAACACTAG
217527 TTGGCTCAATAACTGGCTCGGGTTTAATA
1 TTGGCTCAATAACTGGCTCGGGTTTAATA
217556 TTGGCTCAATAACTGGCTCGGGTTTAATA
1 TTGGCTCAATAACTGGCTCGGGTTTAATA
217585 TTGG
1 TTGG
217589 ATACCGACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (29 bp):
TTGGCTCAATAACTGGCTCGGGTTTAATA
Found at i:220079 original size:41 final size:43
Alignment explanation
Indices: 220034--220132 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
220024 ACATAGTTCC
* *
220034 ATGCAAAATTAAGACGAGGA-T-TGCCCTCCATAGAGGATTCT
1 ATGCAGAATTAAGACGAGGATTATGCCCTCCATAGAGGATCCT
* *
220075 ATGCAGAATTAGGACGAGGATTATGCCCTCCGTAGAGGATCCT
1 ATGCAGAATTAAGACGAGGATTATGCCCTCCATAGAGGATCCT
*
220118 ATGCAGAATCAAGAC
1 ATGCAGAATTAAGAC
220133 AGAGATATTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
41 18 0.36
42 1 0.02
43 31 0.62
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (43 bp):
ATGCAGAATTAAGACGAGGATTATGCCCTCCATAGAGGATCCT
Found at i:220589 original size:29 final size:29
Alignment explanation
Indices: 220555--220613 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
220545 CCTAAATTAA
220555 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
220584 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
220613 T
1 T
220614 AGGTGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:224878 original size:28 final size:28
Alignment explanation
Indices: 224846--224902 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
224836 ACCTAAATTA
224846 TTTGATGTCATTGC-TACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAA-TTAGT
224874 TTTGATGTCATTGCTTACATCAATTAGT
1 TTTGATGTCATTGCTTACATCAATTAGT
224902 T
1 T
224903 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (28 bp):
TTTGATGTCATTGCTTACATCAATTAGT
Found at i:225738 original size:36 final size:37
Alignment explanation
Indices: 225678--225751 Score: 141
Period size: 36 Copynumber: 2.0 Consensus size: 37
225668 GATATGAATA
225678 TTAGCCACTTTCTTTTTTTCTTTTTCACTGTTTGCCT
1 TTAGCCACTTTCTTTTTTTCTTTTTCACTGTTTGCCT
225715 TTAGCCACTTTC-TTTTTTCTTTTTCACTGTTTGCCT
1 TTAGCCACTTTCTTTTTTTCTTTTTCACTGTTTGCCT
225751 T
1 T
225752 AGTTTCTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 25 0.68
37 12 0.32
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.59
Consensus pattern (37 bp):
TTAGCCACTTTCTTTTTTTCTTTTTCACTGTTTGCCT
Found at i:226671 original size:42 final size:42
Alignment explanation
Indices: 226490--226712 Score: 241
Period size: 43 Copynumber: 5.2 Consensus size: 42
226480 AAGGTAATTA
*
226490 GCGGCGTTTGTATCCAAAAACGTCGCTATAGATATGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTT
* * * *
226533 GCGGCGTTTGTATCTAAAAACGCCTCTATAGATCTGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTT
* * * * * * *
226576 GCGACGTTTATTCCAAAAATGCCGTTATAAATATCAACTTTAT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTT-T
* *
226619 ACGGCGTTTGTT-CAAAAACGCCGCTATAGATATCGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTT
* * *
226661 GCGGCATTTGTTCCAAAAACGCCGCTATAGATCTTGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGAT-ATGACCTTTT
226704 GCGGCGTTT
1 GCGGCGTTT
226713 TTTGTTCTCA
Statistics
Matches: 147, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
42 50 0.34
43 96 0.65
44 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTT
Found at i:226709 original size:85 final size:85
Alignment explanation
Indices: 226490--226712 Score: 252
Period size: 85 Copynumber: 2.6 Consensus size: 85
226480 AAGGTAATTA
*
226490 GCGGCGTTTGTATCCAAAAACGTCGCTATAGATATGACCTTTTGCGGCGTTTGTATCTAAAAACG
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCTAAAAACG
* * * *
226555 CCTCTATAGATCTGACTTTTT
65 CCGCTATAGATATGACCTATT
* * * * * * * *
226576 GCGACGTTTATTCCAAAAATGCCGTTATAAATATCAACTTTATACGGCGTTTGT-TC-AAAAACG
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTT-TGCGGCGTTTGTATCTAAAAACG
226639 CCGCTATAGATATCGACCTATT
65 CCGCTATAGATAT-GACCTATT
* * *
226661 GCGGCATTTGTTCCAAAAACGCCGCTATAGATCTTGACCTATTGCGGCGTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGAT-ATGACCTTTTGCGGCGTTT
226713 TTTGTTCTCA
Statistics
Matches: 110, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
84 18 0.16
85 67 0.61
86 25 0.23
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (85 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCTAAAAACGC
CGCTATAGATATGACCTATT
Found at i:240655 original size:30 final size:30
Alignment explanation
Indices: 240619--240781 Score: 290
Period size: 30 Copynumber: 5.4 Consensus size: 30
240609 TCCGAAGGAC
240619 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
240649 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
240679 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
240709 CTATCCAGATGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
240739 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
240769 CTGTCCATAGGTC
1 CTATCCAGAGGTC
240782 CCGAAGAACC
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 127 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:240798 original size:90 final size:91
Alignment explanation
Indices: 240619--240803 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 91
240609 TCCGAAGGAC
240619 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
240684 CAAAGGTCATAAAGATCCTCGGT-AA
66 CAAAGGTCACAAAGAACCTAGGTAAA
* *
240709 CTATCCAGATGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
240774 CATAGGTCCCGAAGAACCTAGGTAAA
66 CAAAGGTCACAAAGAACCTAGGTAAA
240800 CTAT
1 CTAT
240804 TTATATGTTC
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 80 0.93
91 6 0.07
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (91 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
CAAAGGTCACAAAGAACCTAGGTAAA
Found at i:241049 original size:4 final size:4
Alignment explanation
Indices: 241033--241197 Score: 303
Period size: 4 Copynumber: 41.2 Consensus size: 4
241023 ATATAACCAT
* *
241033 TACA TAAA TACA TACA TACA TACA TACA TACA TACA TACA TATA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
241081 TATA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
241129 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
241177 TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA T
241198 GTCATCATTT
Statistics
Matches: 155, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 155 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:242128 original size:21 final size:21
Alignment explanation
Indices: 242104--242146 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
242094 TCATATTCAT
* *
242104 TTGAGGGGGAATCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
* *
242125 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
242146 T
1 T
242147 AGCCCATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Found at i:245515 original size:30 final size:30
Alignment explanation
Indices: 245479--245641 Score: 299
Period size: 30 Copynumber: 5.4 Consensus size: 30
245469 TCCGAAGGAC
245479 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
245509 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
245539 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
245569 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
245599 CTATCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
245629 CTGTCCATAGGTC
1 CTATCCAGAGGTC
245642 CCGAAGAACC
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 131 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:245658 original size:30 final size:30
Alignment explanation
Indices: 245495--245668 Score: 105
Period size: 30 Copynumber: 5.8 Consensus size: 30
245485 AGAGGTCATA
* * * ***
245495 AAGATCCTCGGTAACTATCCAGAGGTCATA
1 AAGAACCTAGGTAACTATCCATAGGTCCCG
* * * ***
245525 AAGATCCTCGGTAACTATCCAGAGGTCATA
1 AAGAACCTAGGTAACTATCCATAGGTCCCG
* * * ***
245555 AAGATCCTCGGTAACTATCCAGAGGTCATA
1 AAGAACCTAGGTAACTATCCATAGGTCCCG
* * ***
245585 AAGATCCTCGGTAACTATCCATAGGTCATA
1 AAGAACCTAGGTAACTATCCATAGGTCCCG
* * *
245615 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTATCCATAGGTCCCG
245645 AAGAACCTAGGTAAACTATCCATA
1 AAGAACCTAGGT-AACTATCCATA
245669 TGTTCCTTAG
Statistics
Matches: 135, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
30 125 0.93
31 10 0.07
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
AAGAACCTAGGTAACTATCCATAGGTCCCG
Found at i:245658 original size:90 final size:91
Alignment explanation
Indices: 245479--245666 Score: 297
Period size: 90 Copynumber: 2.1 Consensus size: 91
245469 TCCGAAGGAC
245479 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
245544 CAGAGGTCATAAAGATCCTCGGT-AA
66 CAGAGGTCACAAAGAACCTAGGTAAA
* *
245569 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCATAGGTCATAAAGATCCTCGGTAACTGTC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
245634 CATAGGTCCCGAAGAACCTAGGTAAA
66 CAGAGGTCACAAAGAACCTAGGTAAA
245660 CTATCCA
1 CTATCCA
245667 TATGTTCCTT
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 80 0.90
91 9 0.10
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (91 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCACAAAGAACCTAGGTAAA
Found at i:245715 original size:31 final size:30
Alignment explanation
Indices: 245624--245719 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
245614 AAAGATCCTC
* * *
245624 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
245654 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
245685 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
245716 GGTA
1 GGTA
245720 GTTCTTCGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:259492 original size:31 final size:31
Alignment explanation
Indices: 259457--259543 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
259447 CCAATAAAGT
259457 TTAAAAAATTATAAAATAATTATTAAATTTA
1 TTAAAAAATTATAAAATAATTATTAAATTTA
* * *
259488 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAATAATTATTAAATTTA
* *
259519 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAATAATTATTA
259544 TATTATCGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 47 0.98
32 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (31 bp):
TTAAAAAATTATAAAATAATTATTAAATTTA
Found at i:261721 original size:17 final size:18
Alignment explanation
Indices: 261689--261723 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
261679 AGGTATAAGA
*
261689 ATTTATTTAGAATTAATT
1 ATTTATTTAAAATTAATT
261707 ATTTA-TTAAAATTAATT
1 ATTTATTTAAAATTAATT
261724 TTAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTATTTAAAATTAATT
Found at i:262927 original size:22 final size:21
Alignment explanation
Indices: 262890--262930 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
262880 AATTTAATAA
262890 TTATTTAAATGTTTATAAATT
1 TTATTTAAATGTTTATAAATT
262911 TTATATTAAAT-TATTATAAA
1 TTAT-TTAAATGT-TTATAAA
262931 AAATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTATTTAAATGTTTATAAATT
Found at i:263014 original size:23 final size:24
Alignment explanation
Indices: 262960--263014 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
262950 ATGAAATTAT
*
262960 TTTAAAAT-CATATTATTTATTTA
1 TTTAAAATACATATTAATTATTTA
**
262983 TTTGGAATAC-TATTAATTATTTA
1 TTTAAAATACATATTAATTATTTA
263006 TTTAAAATA
1 TTTAAAATA
263015 ATAATATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTAAAATACATATTAATTATTTA
Found at i:263053 original size:19 final size:18
Alignment explanation
Indices: 263022--263057 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
263012 ATAATAATAT
*
263022 TTTTAAATTATATATTTAA
1 TTTTAAATAATAT-TTTAA
263041 TTTTAAATAATATTTTA
1 TTTTAAATAATATTTTA
263058 CGAAACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAAATAATATTTTAA
Found at i:265131 original size:3 final size:3
Alignment explanation
Indices: 265123--265256 Score: 234
Period size: 3 Copynumber: 44.7 Consensus size: 3
265113 TTTTTATCCA
265123 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
*
265171 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
265218 TAA TAT TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA
265257 AATATATTAA
Statistics
Matches: 125, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.02
3 120 0.96
4 3 0.02
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:266022 original size:13 final size:13
Alignment explanation
Indices: 266004--266032 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
265994 ACCACCGTTA
266004 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
266017 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
266030 CGG
1 CGG
266033 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:266630 original size:19 final size:19
Alignment explanation
Indices: 266592--266627 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
266582 CAATTTAGTC
266592 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
266611 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
266628 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:279054 original size:52 final size:52
Alignment explanation
Indices: 278976--279481 Score: 922
Period size: 52 Copynumber: 9.7 Consensus size: 52
278966 TATGTGCTCA
*
278976 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
279028 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
279080 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
279132 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
279184 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
279236 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
279288 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
279340 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * *
279392 ATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATGGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
279444 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
279482 CGAAGAAGTG
Statistics
Matches: 440, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 440 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:280281 original size:113 final size:113
Alignment explanation
Indices: 280042--281273 Score: 2054
Period size: 113 Copynumber: 10.9 Consensus size: 113
280032 GATTCAAATT
* * *
280042 CATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
280106 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* * * *
280154 CATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
280219 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
280267 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
***
280332 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
280380 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
280445 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
280493 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* ***
280558 AGAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
280605 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
280670 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
280718 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* ***
280783 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
280831 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
280896 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* *
280944 CATCATTTGGTGGATCATCTTTTCCAGAAAAAGTCCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
281009 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
*
281057 CATCATTTGGTGGATCATATTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *** * *
281122 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* * * ** *
281170 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGG
**
281235 AAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
281274 GTTTGATATC
Statistics
Matches: 1056, Mismatches: 61, Indels: 4
0.94 0.05 0.00
Matches are distributed among these distances:
112 166 0.16
113 827 0.78
114 63 0.06
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (113 bp):
CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
Found at i:280884 original size:451 final size:452
Alignment explanation
Indices: 280042--281279 Score: 2167
Period size: 451 Copynumber: 2.7 Consensus size: 452
280032 GATTCAAATT
* * *
280042 CATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
280106 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
* *
280171 ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
131 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
280236 AGAAGAATTTGTTCAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGT
196 AGAAGAATTTGTTCAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGT
*
280301 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC
261 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
280366 CTTTTGTTTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACT
326 CTTTTGTTTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACT
280431 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
391 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
280493 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
280558 AGAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATCCATCATTTGGTGGATCA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
280622 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
131 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
280687 AGAAGAATTTGTTCAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGT
196 AGAAGAATTTGTTCAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGT
280752 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
261 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
280817 CTTTTGTTTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACT
326 CTTTTGTTTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACT
280882 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
391 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
* *
280944 CATCATTTGGTGGATCATCTTTTCCAGAAAAAGTCCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
281009 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
*
281074 TATTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
131 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * *** * ** * * * ** *
281139 AGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATGGCCAAAGAAAGT
196 AGAAGAATTTGTTCAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGT
*
281204 TCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA
261 TCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
281269 CC-TTTGTTTGA
325 CCTTTTGTTTGA
281280 TATCATTTGA
Statistics
Matches: 751, Mismatches: 33, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
451 500 0.67
452 190 0.25
453 61 0.08
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (452 bp):
CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAATTTGTTCAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGT
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
CTTTTGTTTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACT
CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
Found at i:281576 original size:3 final size:3
Alignment explanation
Indices: 281568--281680 Score: 192
Period size: 3 Copynumber: 37.7 Consensus size: 3
281558 TTTTTATCCA
281568 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
*
281616 TAT TAT TAT TAT TAT TAT TAT CAT TAT TA- TAT TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
281661 TAT TAT TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
281681 ATATATTAAA
Statistics
Matches: 104, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.02
3 99 0.95
4 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:282448 original size:13 final size:13
Alignment explanation
Indices: 282430--282458 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
282420 ACCACCGTTA
282430 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
282443 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
282456 CGG
1 CGG
282459 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:283053 original size:18 final size:19
Alignment explanation
Indices: 283020--283055 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
283010 AATTTAGTCA
283020 TTATTTTATATGTTTTAAT
1 TTATTTTATATGTTTTAAT
283039 TTATTTTAT-TGTTTTAA
1 TTATTTTATATGTTTTAA
283056 ATATATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (19 bp):
TTATTTTATATGTTTTAAT
Found at i:283062 original size:19 final size:19
Alignment explanation
Indices: 283021--283062 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
283011 ATTTAGTCAT
*
283021 TATTTTATATGTTTTAATT
1 TATTTTATATGTTTTAATA
283040 TATTTTAT-TGTTTTAAATA
1 TATTTTATATGTTTT-AATA
283059 TATT
1 TATT
283063 GTTTTAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
TATTTTATATGTTTTAATA
Found at i:283117 original size:19 final size:20
Alignment explanation
Indices: 283081--283120 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
283071 AGAATTATTC
**
283081 TTTTATTATATTGTTAAATA
1 TTTTATTATATTCATAAATA
283101 TTTTA-TATATTCATAAATA
1 TTTTATTATATTCATAAATA
283120 T
1 T
283121 ATATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATTATATTCATAAATA
Found at i:288842 original size:17 final size:17
Alignment explanation
Indices: 288802--288844 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
288792 TAAAAAGCAT
288802 TAATATAAATTTCTAAA
1 TAATATAAATTTCTAAA
288819 -AATTATATAATTTC-AAA
1 TAA-TATA-AATTTCTAAA
288836 TAATATAAA
1 TAATATAAA
288845 GAAATTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATATAAATTTCTAAA
Found at i:288995 original size:2 final size:2
Alignment explanation
Indices: 288988--289021 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
288978 TTGTACTTCT
288988 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
289022 CTAGAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:291823 original size:31 final size:31
Alignment explanation
Indices: 291777--291848 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
291767 CCCATCGTTT
*
291777 ATGATAAGTGGTCATATCTTAATTAAAACGAA
1 ATGA-AAGTGATCATATCTTAATTAAAACGAA
* *
291809 ATGAAAGTGATCATATTTTAATTAAAATGAA
1 ATGAAAGTGATCATATCTTAATTAAAACGAA
*
291840 ACGAAAGTG
1 ATGAAAGTG
291849 TCTACGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 32 0.89
32 4 0.11
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.31
Consensus pattern (31 bp):
ATGAAAGTGATCATATCTTAATTAAAACGAA
Found at i:296293 original size:35 final size:35
Alignment explanation
Indices: 296254--296328 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
296244 GAAACATCGA
296254 ACTTTCGATACAAGTAGAACGAAA-GGAGACATAAC
1 ACTTTCGATACAAGTAGAAC-AAATGGAGACATAAC
* ** *
296289 ACTTTTGATTTAAGTAGAACAAATGGAGGCATAAC
1 ACTTTCGATACAAGTAGAACAAATGGAGACATAAC
296324 ACTTT
1 ACTTT
296329 TAATTCTCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 3 0.09
35 32 0.91
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (35 bp):
ACTTTCGATACAAGTAGAACAAATGGAGACATAAC
Found at i:296358 original size:112 final size:112
Alignment explanation
Indices: 296188--296405 Score: 323
Period size: 112 Copynumber: 1.9 Consensus size: 112
296178 TTGTCGTCTA
* * * *
296188 AAGTAGAACGAAAGGAGTCATAACACTTTTGATTCTCATCTAAAGTAGTACGGAAGGAAACATCG
1 AAGTAGAACGAAAGGAGGCATAACACTTTTAATTCTCATCTAAAGTAGAACGAAAGGAAACATCG
*
296253 AACTTTCGATACAAGTAGAACGAAAGGAGACATAACACTTTTGATTT
66 AACTTTCAATACAAGTAGAACGAAAGGAGACATAACACTTTTGATTT
*
296300 AAGTAGAAC-AAATGGAGGCATAACACTTTTAATTCTCGTCTAAAGTAGAAC-AATAGGAAACAT
1 AAGTAGAACGAAA-GGAGGCATAACACTTTTAATTCTCATCTAAAGTAGAACGAA-AGGAAACAT
* * *
296363 CGCACTTTCAATTCAAGTAGAACGAAAGGAGGCATAACACTTT
64 CGAACTTTCAATACAAGTAGAACGAAAGGAGACATAACACTTT
296406 CAAATTCGCA
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
111 4 0.04
112 91 0.96
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (112 bp):
AAGTAGAACGAAAGGAGGCATAACACTTTTAATTCTCATCTAAAGTAGAACGAAAGGAAACATCG
AACTTTCAATACAAGTAGAACGAAAGGAGACATAACACTTTTGATTT
Found at i:303388 original size:22 final size:22
Alignment explanation
Indices: 303354--303396 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
303344 TTAGCCCTTG
* * *
303354 TATGAACTTCTGAGTAAATTAT
1 TATGAAATCCTGAATAAATTAT
303376 TATGAAATCCTGAATAAATTA
1 TATGAAATCCTGAATAAATTA
303397 AAATACAAAT
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:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (22 bp):
TATGAAATCCTGAATAAATTAT
Found at i:307611 original size:30 final size:30
Alignment explanation
Indices: 307577--307633 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
307567 GGAGCTAGCT
307577 CAACTTATTGGAAAATTCATCTTTGGTGGC
1 CAACTTATTGGAAAATTCATCTTTGGTGGC
307607 CAACTTATTGGAAAATTCATCTTTGGT
1 CAACTTATTGGAAAATTCATCTTTGGT
307634 AGGGAACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.39
Consensus pattern (30 bp):
CAACTTATTGGAAAATTCATCTTTGGTGGC
Found at i:308846 original size:16 final size:16
Alignment explanation
Indices: 308825--308858 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
308815 TTTTACTAGA
*
308825 TTAAAAACCGGTTTTT
1 TTAAAAACCAGTTTTT
*
308841 TTAAAAATCAGTTTTT
1 TTAAAAACCAGTTTTT
308857 TT
1 TT
308859 CAAACCGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (16 bp):
TTAAAAACCAGTTTTT
Found at i:309123 original size:31 final size:31
Alignment explanation
Indices: 309085--309147 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
309075 CATTTCAAAG
309085 ATAGAATTTCTACTAATATATAATTGGAGTA
1 ATAGAATTTCTACTAATATATAATTGGAGTA
309116 ATAGAATTTCTACTAATATATAATTGGAGTA
1 ATAGAATTTCTACTAATATATAATTGGAGTA
309147 A
1 A
309148 CTGACTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (31 bp):
ATAGAATTTCTACTAATATATAATTGGAGTA
Found at i:317699 original size:18 final size:18
Alignment explanation
Indices: 317676--317710 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
317666 TTCCATCCGG
*
317676 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
317694 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
317711 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:318844 original size:13 final size:13
Alignment explanation
Indices: 318826--318855 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
318816 GCCGGTCAAC
*
318826 GGTCAACGGGTCG
1 GGTCAACAGGTCG
318839 GGTCAACAGGTCG
1 GGTCAACAGGTCG
318852 GGTC
1 GGTC
318856 GGGTCAACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:318855 original size:18 final size:18
Alignment explanation
Indices: 318832--318909 Score: 102
Period size: 18 Copynumber: 4.3 Consensus size: 18
318822 CAACGGTCAA
* *
318832 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTAAACGGGT
* *
318850 CGGGTCGGGTCAACTGGT
1 CGGGTCGGGTAAACGGGT
*
318868 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTAAACGGGT
*
318886 CGGTTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
318904 CGGGTC
1 CGGGTC
318910 AGGTTGTGAC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.14, C:0.19, G:0.46, T:0.21
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:322660 original size:18 final size:18
Alignment explanation
Indices: 322637--322671 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
322627 TTCCATCCGG
*
322637 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
322655 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
322672 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:323790 original size:15 final size:16
Alignment explanation
Indices: 323760--323793 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
323750 GGTCAACATT
323760 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
323777 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
323792 GG
1 GG
323794 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:323814 original size:18 final size:18
Alignment explanation
Indices: 323791--323868 Score: 102
Period size: 18 Copynumber: 4.3 Consensus size: 18
323781 AACGGGTCAA
* *
323791 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTAAACGGGT
* *
323809 CGGGTCGGGTCAACTGGT
1 CGGGTCGGGTAAACGGGT
*
323827 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTAAACGGGT
*
323845 CGGTTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
323863 CGGGTC
1 CGGGTC
323869 AGGTTGTGAC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.14, C:0.19, G:0.46, T:0.21
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:323832 original size:13 final size:13
Alignment explanation
Indices: 323783--323814 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
323773 CAACGGTCAA
*
323783 CGGGTCAACGGGT
1 CGGGTCAACAGGT
323796 CGGGTCAACAGGT
1 CGGGTCAACAGGT
323809 CGGGTC
1 CGGGTC
323815 GGGTCAACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.25, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACAGGT
Found at i:325298 original size:28 final size:28
Alignment explanation
Indices: 325240--325298 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
325230 ACATATTTAA
* *
325240 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAATATAGTACC
** *
325268 AAGTAAACAATAAAACATGTATATTACC
1 AAGTAAACAATAAAACAAATATAGTACC
325296 AAG
1 AAG
325299 GAAAGATACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAGTACC
Found at i:325359 original size:14 final size:14
Alignment explanation
Indices: 325340--325369 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
325330 TATGTTGTTG
325340 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
325354 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
325368 AC
1 AC
325370 AATCAACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.30, G:0.07, T:0.53
Consensus pattern (14 bp):
ACTTGTTCTTTCTC
Found at i:336787 original size:7 final size:7
Alignment explanation
Indices: 336775--336840 Score: 109
Period size: 7 Copynumber: 9.7 Consensus size: 7
336765 TGGAGAGGAA
336775 GAGAAGG
1 GAGAAGG
336782 GAGAAGG
1 GAGAAGG
336789 GAGAAGG
1 GAGAAGG
336796 GAGAAGG
1 GAGAAGG
336803 GAGAAGG
1 GAGAAGG
336810 GAGAAGG
1 GAGAAGG
336817 GAGAA--
1 GAGAAGG
*
336822 AAGAAGG
1 GAGAAGG
336829 GAGAAGG
1 GAGAAGG
336836 GAGAA
1 GAGAA
336841 AGTGAAGAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 4 0.07
7 51 0.93
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (7 bp):
GAGAAGG
Found at i:340658 original size:2 final size:2
Alignment explanation
Indices: 340653--340694 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
340643 TATATGATAG
340653 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
340695 AGTTTTCCGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:342488 original size:32 final size:32
Alignment explanation
Indices: 342412--342488 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
342402 GTCGTCTTCG
* * *
342412 TCCTCACTCCATGGATGCTTCAATAGTCGTCC
1 TCCTCACTCCATTGATGCTGCAATAGTCGTCA
* *
342444 TCCTCACTCCATTGATGCTGCAATTGTCGTTA
1 TCCTCACTCCATTGATGCTGCAATAGTCGTCA
*
342476 TCCTCGCTCCATT
1 TCCTCACTCCATT
342489 TACGCTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.17, C:0.34, G:0.14, T:0.35
Consensus pattern (32 bp):
TCCTCACTCCATTGATGCTGCAATAGTCGTCA
Found at i:343130 original size:15 final size:12
Alignment explanation
Indices: 343099--343140 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
343089 GGTATTCTAT
343099 ATATTATTCGCC
1 ATATTATTCGCC
343111 ATATTATTCGCC
1 ATATTATTCGCC
343123 -TAATTATT-GCC
1 AT-ATTATTCGCC
343134 ATATTAT
1 ATATTAT
343141 CACCCTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (12 bp):
ATATTATTCGCC
Found at i:362357 original size:28 final size:29
Alignment explanation
Indices: 362326--362395 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
362316 TGAATTATTA
*
362326 GAATTTGAATTACTGGAA-TTG-ATTACTG
1 GAATTTGAATTACTGAAATTTGAATT-CTG
362354 GAATTTGAATTACTGAAATTTGAATTCTG
1 GAATTTGAATTACTGAAATTTGAATTCTG
**
362383 GAAAATGAATTAC
1 GAATTTGAATTAC
362396 ATTTCAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.46
29 17 0.46
30 3 0.08
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (29 bp):
GAATTTGAATTACTGAAATTTGAATTCTG
Found at i:362361 original size:14 final size:15
Alignment explanation
Indices: 362316--362395 Score: 94
Period size: 15 Copynumber: 5.5 Consensus size: 15
362306 TTTCGGAAAA
* *
362316 TGAATTATTAGAATT
1 TGAATTACTGGAATT
362331 TGAATTACTGGAA-T
1 TGAATTACTGGAATT
362345 TG-ATTACTGGAATT
1 TGAATTACTGGAATT
*
362359 TGAATTACTGAAATT
1 TGAATTACTGGAATT
**
362374 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
362388 TGAATTAC
1 TGAATTAC
362396 ATTTCAGGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
13 10 0.18
14 17 0.30
15 29 0.52
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:362391 original size:29 final size:28
Alignment explanation
Indices: 362331--362395 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
362321 TATTAGAATT
* **
362331 TGAATTACTGGAATTGATTACTGGAATT
1 TGAATTACTGAAATTGATTACTGGAAAA
362359 TGAATTACTGAAATTTGAATT-CTGGAAAA
1 TGAATTACTGAAA-TTG-ATTACTGGAAAA
362388 TGAATTAC
1 TGAATTAC
362396 ATTTCAGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 12 0.38
29 17 0.53
30 3 0.09
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (28 bp):
TGAATTACTGAAATTGATTACTGGAAAA
Found at i:362405 original size:20 final size:20
Alignment explanation
Indices: 362382--362427 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
362372 TTTGAATTCT
362382 GGAAAATGAATTACATTTCA
1 GGAAAATGAATTACATTTCA
*
362402 GGAAAATGAATTACATTTCT
1 GGAAAATGAATTACATTTCA
362422 GGAAAA
1 GGAAAA
362428 CATCTGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (20 bp):
GGAAAATGAATTACATTTCA
Found at i:362586 original size:26 final size:26
Alignment explanation
Indices: 362519--362606 Score: 71
Period size: 26 Copynumber: 3.5 Consensus size: 26
362509 TTATTACAAA
*
362519 TATTAAATATAATAAGTAATATTATTTAT
1 TATTAAATAT--TAAATAAT-TTATTTAT
* *
362548 CA-TAAA-ATTTAAT-A-TTA-TTAT
1 TATTAAATATTAAATAATTTATTTAT
362569 T-TTAAAATATTAAATAATTTATTTAT
1 TATT-AAATATTAAATAATTTATTTAT
362595 TATTAAATATTA
1 TATTAAATATTA
362607 TTTTTATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 17
0.68 0.07 0.25
Matches are distributed among these distances:
21 5 0.11
22 6 0.13
23 6 0.13
24 2 0.04
25 6 0.13
26 13 0.28
27 4 0.09
28 4 0.09
29 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (26 bp):
TATTAAATATTAAATAATTTATTTAT
Done.