Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 21
Found at i:2974116 original size:46 final size:46
Alignment explanation
Indices: 2974034--2974246 Score: 171
Period size: 46 Copynumber: 4.8 Consensus size: 46
2974024 TCGGGGAATG
**
2974034 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGCCATCTAAAGGTGATA
* * * ** *
2974080 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT--AGG-G-TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGCCATCTAAAGGTGATA
* ** *
2974122 ACACGGCTCATACGTGATGAAGAGATCTGG---TC--GGGGT-ATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGCCATCTAAAGGTGATA
**
2974162 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGCCATCTAAAGGTGATA
* * *
2974208 ACACGGTTCCTACGTGATGAGGACG-GCTGGCCATCTAAA
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGCCATCTAAA
2974247 AGTTATGGTT
Statistics
Matches: 135, Mismatches: 20, Indels: 24
0.75 0.11 0.13
Matches are distributed among these distances:
39 4 0.03
40 31 0.23
41 1 0.01
42 25 0.19
43 3 0.02
44 3 0.02
45 3 0.02
46 63 0.47
47 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGCCATCTAAAGGTGATA
Found at i:2974190 original size:128 final size:129
Alignment explanation
Indices: 2973978--2974237 Score: 486
Period size: 128 Copynumber: 2.0 Consensus size: 129
2973968 ATGAAGAGTT
* *
2973978 TGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
1 TGGTTATCTATGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
2974043 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
66 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
*
2974107 TGGTTATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGTATGACACGGCTC
1 TGGTTATCTATGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
2974171 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
66 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
2974235 TGG
1 TGG
2974238 CCATCTAAAA
Statistics
Matches: 128, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
128 118 0.92
129 10 0.08
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (129 bp):
TGGTTATCTATGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
Found at i:2974403 original size:36 final size:36
Alignment explanation
Indices: 2974363--2974437 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
2974353 GTTTCAAAGG
*
2974363 AAATGACTCAAAGATT-GTTTAAAGGAAAACTG-TCTC
1 AAATGACACAAA-ATTCGTTTAAAGGAAAA-TGATCTC
* *
2974399 AAATGAGACAAAATTCGTTTAAAGGGAAATGATCTC
1 AAATGACACAAAATTCGTTTAAAGGAAAATGATCTC
2974435 AAA
1 AAA
2974438 GATGTTTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (36 bp):
AAATGACACAAAATTCGTTTAAAGGAAAATGATCTC
Found at i:2974436 original size:63 final size:63
Alignment explanation
Indices: 2974325--2974444 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
2974315 TTTCAAAAGC
*
2974325 AACTGTCTCTTAAAAGAGACAAAATTTTGTTTCAAAGGAAATGACTCAAAGATTGTTTAAAGGAA
1 AACTGTCTC-TAAAAGAGACAAAATTTCGTTTCAAAGGAAATGACTCAAAGA-TGTTTAAAGGAA
*
2974390 AACTGTCTC-AAATGAGACAAAA-TTCGTTT-AAAGGGAAATGATCTCAAAGATGTTT
1 AACTGTCTCTAAAAGAGACAAAATTTCGTTTCAAA-GGAAATGA-CTCAAAGATGTTT
2974445 GTTTTGTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
61 3 0.06
62 19 0.37
63 20 0.39
65 9 0.18
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (63 bp):
AACTGTCTCTAAAAGAGACAAAATTTCGTTTCAAAGGAAATGACTCAAAGATGTTTAAAGGAA
Found at i:2974561 original size:27 final size:28
Alignment explanation
Indices: 2974512--2974693 Score: 190
Period size: 28 Copynumber: 6.4 Consensus size: 28
2974502 CAAAACTTTG
* * * *
2974512 TTTCAAAATAAATAGACTCAAAGATATT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
2974540 TTTCAAAAGAAAC-AACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
* *
2974567 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
* *
2974596 ATTCAAAATG-AGCAAACTCAAAGA-TTT
1 TTTCAAAA-GAAACAAACTCAAAGATTTT
* *
2974623 TTTCAAGAGGAACAAACTCAAAGATTTTTT
1 TTTCAAAAGAAACAAACTCAAAGA--TTTT
* *
2974653 TTTCAAGAGAAACAAACCCAAAGATTTTT
1 TTTCAAAAGAAACAAACTCAAAGA-TTTT
2974682 TTTCAAAAGAAA
1 TTTCAAAAGAAA
2974694 TTGTCTTTAA
Statistics
Matches: 132, Mismatches: 15, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
26 1 0.01
27 35 0.27
28 41 0.31
29 30 0.23
30 25 0.19
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:2974616 original size:84 final size:86
Alignment explanation
Indices: 2974527--2974689 Score: 226
Period size: 85 Copynumber: 1.9 Consensus size: 86
2974517 AAATAAATAG
*
2974527 ACTCAAAGATATTTTTCAAAAGAAAC-AACTCAAAGA-TTTTTATTCAAAAGGAACAAACTCC-A
1 ACTCAAAGAT-TTTTTCAAAAGAAACAAACTCAAAGATTTTTTATTCAAAAGAAACAAAC-CCAA
2974589 AGA-TTTTATTCAAAATGAGCAA
64 AGATTTTTATTCAAAATGAGCAA
* * * *
2974611 ACTCAAAGATTTTTTCAAGAGGAACAAACTCAAAGATTTTTTTTTCAAGAGAAACAAACCCAAAG
1 ACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGATTTTTTATTCAAAAGAAACAAACCCAAAG
*
2974676 ATTTTTTTTCAAAA
66 ATTTTTATTCAAAA
2974690 GAAATTGTCT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
83 13 0.19
84 22 0.32
85 23 0.33
86 11 0.16
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.29
Consensus pattern (86 bp):
ACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGATTTTTTATTCAAAAGAAACAAACCCAAAG
ATTTTTATTCAAAATGAGCAA
Found at i:2974658 original size:57 final size:55
Alignment explanation
Indices: 2974527--2974682 Score: 183
Period size: 57 Copynumber: 2.8 Consensus size: 55
2974517 AAATAAATAG
2974527 ACTCAAAGATATTT-TTCAAAAGAAAC-AACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTTATTCAAAAGAAACAAACTCAAAGA-TTTT-TTCAAAAGGAACAA
* * *
2974583 ACTCCAAGATTTTATTCAAAATG-AGCAAACTCAAAGATTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTATTCAAAA-GAAACAAACTCAAAGATTTTTTCAAAAGGAACAA
* * *
2974638 ACTCAAAGATTTTTTTTTCAAGAGAAACAAACCCAAAGATTTTTT
1 ACTCAAAGA--TTTTATTCAAAAGAAACAAACTCAAAGATTTTTT
2974683 TTCAAAAGAA
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
55 24 0.28
56 23 0.27
57 39 0.45
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.29
Consensus pattern (55 bp):
ACTCAAAGATTTTATTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:2975016 original size:36 final size:35
Alignment explanation
Indices: 2974932--2975034 Score: 113
Period size: 36 Copynumber: 3.0 Consensus size: 35
2974922 GAGAAAATGA
* *
2974932 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGA-AT
* **
2974966 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAGT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAA-T
*
2975002 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAA
2975035 ACGATTTCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
34 19 0.33
35 10 0.18
36 28 0.49
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAT
Found at i:2975708 original size:4 final size:4
Alignment explanation
Indices: 2975699--2975738 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
2975689 TGTATCATGG
2975699 ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
2975739 ATACTTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 32 0.94
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2983573 original size:11 final size:10
Alignment explanation
Indices: 2983556--2983593 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
2983546 GGGCTTCGGG
2983556 TTGTTGGGCC
1 TTGTTGGGCC
2983566 TCTGTTGGGCC
1 T-TGTTGGGCC
2983577 TTGGTTGGGCC
1 TT-GTTGGGCC
2983588 TTGTTG
1 TTGTTG
2983594 TATTGGGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.00, C:0.18, G:0.39, T:0.42
Consensus pattern (10 bp):
TTGTTGGGCC
Found at i:2983641 original size:3 final size:3
Alignment explanation
Indices: 2983627--2983683 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
2983617 ATGTAAAATG
* * **
2983627 TAA TAT TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA AAA TAA CGA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2983673 TAA TAA TAA TA
1 TAA TAA TAA TA
2983684 TACAAAAAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2989189 original size:33 final size:33
Alignment explanation
Indices: 2989147--2989209 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2989137 ATATATAAAA
*
2989147 AAATAATATATTGAATAAAATATAACAAAATTT
1 AAATAATATATTAAATAAAATATAACAAAATTT
* *
2989180 AAATAATATATTAAATAAATTTTAACAAAA
1 AAATAATATATTAAATAAAATATAACAAAA
2989210 ATTTCTTACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (33 bp):
AAATAATATATTAAATAAAATATAACAAAATTT
Found at i:2990137 original size:2 final size:2
Alignment explanation
Indices: 2990130--2990154 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2990120 TGTTGCTAAC
2990130 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2990155 CTCTCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2993262 original size:30 final size:31
Alignment explanation
Indices: 2993222--2993283 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2993212 TTAACAGGTT
*
2993222 AGTGACTAAAATGTT-A-CAATCGATAATATA
1 AGTGACTAAAAT-TTAATAAATCGATAATATA
*
2993252 AGTGAGTAAAATTTAATAAATCGATAATATA
1 AGTGACTAAAATTTAATAAATCGATAATATA
2993283 A
1 A
2993284 ATTACCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 12 0.43
31 14 0.50
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (31 bp):
AGTGACTAAAATTTAATAAATCGATAATATA
Found at i:3002291 original size:11 final size:11
Alignment explanation
Indices: 3002275--3002308 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
3002265 TGGGTATGTT
3002275 TATGGTTCAAG
1 TATGGTTCAAG
3002286 TATGGTTCAAG
1 TATGGTTCAAG
3002297 TATGGTTCAAG
1 TATGGTTCAAG
3002308 T
1 T
3002309 TTTGTGAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.38
Consensus pattern (11 bp):
TATGGTTCAAG
Found at i:3004020 original size:17 final size:17
Alignment explanation
Indices: 3004000--3004033 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3003990 TTAATTAAAA
3004000 TTATTATATAA-TATATT
1 TTATTATA-AACTATATT
3004017 TTATTATAAACTATATT
1 TTATTATAAACTATATT
3004034 ACATAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTATAAACTATATT
Found at i:3005405 original size:11 final size:11
Alignment explanation
Indices: 3005375--3005413 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3005365 TTTGTCCTTT
*
3005375 TTTATATTT-A
1 TTTATTTTTCA
3005385 TTTA-TTTTCA
1 TTTATTTTTCA
3005395 TTTATTTTTCA
1 TTTATTTTTCA
3005406 TTTATTTT
1 TTTATTTT
3005414 CGTTATCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 3 0.12
10 9 0.35
11 14 0.54
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTTTCA
Found at i:3005409 original size:21 final size:20
Alignment explanation
Indices: 3005375--3005414 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3005365 TTTGTCCTTT
3005375 TTTATATTTATTTATTTTCA
1 TTTATATTTATTTATTTTCA
*
3005395 TTTATTTTTCATTTATTTTC
1 TTTATATTT-ATTTATTTTC
3005415 GTTATCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATATTTATTTATTTTCA
Found at i:3005424 original size:21 final size:21
Alignment explanation
Indices: 3005376--3005424 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3005366 TTGTCCTTTT
* *
3005376 TTATATTT-ATTTATTTTCAT
1 TTATTTTTCATTTATTTTCAG
3005396 TTATTTTTCATTTATTTTC-G
1 TTATTTTTCATTTATTTTCAG
3005416 TTATCTTTT
1 TTAT-TTTT
3005425 TTACATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATTTTTCATTTATTTTCAG
Found at i:3005471 original size:18 final size:18
Alignment explanation
Indices: 3005434--3005476 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3005424 TTTACATTTA
*
3005434 TTCTATTTCTCTATTTAT
1 TTCTATTTCTCTATTGAT
* *
3005452 TTCTATTTCTTTCTTGAT
1 TTCTATTTCTCTATTGAT
3005470 TT-TATTT
1 TTCTATTT
3005477 ACTCATTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (18 bp):
TTCTATTTCTCTATTGAT
Found at i:3005514 original size:9 final size:9
Alignment explanation
Indices: 3005502--3005556 Score: 67
Period size: 9 Copynumber: 6.0 Consensus size: 9
3005492 ATTATCTTCA
3005502 TTATTTTAT
1 TTATTTTAT
3005511 TTATTTTAT
1 TTATTTTAT
3005520 TTACTTTTAT
1 TTA-TTTTAT
*
3005530 CTATTTT-T
1 TTATTTTAT
*
3005538 ATATTTTTAT
1 TTA-TTTTAT
3005548 TTATTTTAT
1 TTATTTTAT
3005557 CTTTTTTGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 3 0.08
9 26 0.65
10 11 0.28
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTTTAT
Found at i:3005554 original size:10 final size:10
Alignment explanation
Indices: 3005375--3005554 Score: 70
Period size: 10 Copynumber: 17.8 Consensus size: 10
3005365 TTTGTCCTTT
*
3005375 TTTATATTTA
1 TTTATTTTTA
*
3005385 TTTATTTTCA
1 TTTATTTTTA
3005395 TTTATTTTTCA
1 TTTATTTTT-A
*
3005406 TTTA-TTTTC
1 TTTATTTTTA
* *
3005415 GTTATCTTT-
1 TTTATTTTTA
**
3005424 TTTACATTTA
1 TTTATTTTTA
3005434 TTCTATTTCTCTA
1 TT-TATTT-T-TA
*
3005447 TTTATTTCTA
1 TTTATTTTTA
*
3005457 TTTCTTTCTTGA
1 TTTATTT-TT-A
*
3005469 TTTTATTTACTCA
1 -TTTATTT--TTA
* *
3005482 TTTA-GTATA
1 TTTATTTTTA
* *
3005491 TATTATCTTCA
1 T-TTATTTTTA
3005502 -TTA-TTTTA
1 TTTATTTTTA
3005510 TTTA-TTTTA
1 TTTATTTTTA
*
3005519 TTTACTTTTA
1 TTTATTTTTA
*
3005529 TCTATTTTTA
1 TTTATTTTTA
3005539 --TATTTTTA
1 TTTATTTTTA
3005547 TTTATTTT
1 TTTATTTT
3005555 ATCTTTTTTG
Statistics
Matches: 128, Mismatches: 26, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
8 11 0.09
9 26 0.20
10 55 0.43
11 12 0.09
12 11 0.09
13 11 0.09
14 2 0.02
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:3009673 original size:19 final size:20
Alignment explanation
Indices: 3009649--3009687 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3009639 ACCATTGTAT
3009649 GGGGGTATCGATACC-TCTG
1 GGGGGTATCGATACCATCTG
*
3009668 GGGGGTATCGGTACCATCTG
1 GGGGGTATCGATACCATCTG
3009688 AGCATTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.15, C:0.21, G:0.38, T:0.26
Consensus pattern (20 bp):
GGGGGTATCGATACCATCTG
Found at i:3009731 original size:18 final size:18
Alignment explanation
Indices: 3009708--3009758 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
3009698 TATTTCTCGG
3009708 AACCAAAATGTTCATCGA
1 AACCAAAATGTTCATCGA
*
3009726 AACCAAAATGTTCATCGG
1 AACCAAAATGTTCATCGA
3009744 AACCAAAATGTTCAT
1 AACCAAAATGTTCAT
3009759 AGGGGTATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.24
Consensus pattern (18 bp):
AACCAAAATGTTCATCGA
Found at i:3012574 original size:21 final size:20
Alignment explanation
Indices: 3012505--3012630 Score: 96
Period size: 21 Copynumber: 5.8 Consensus size: 20
3012495 AACCTGACAG
3012505 GGGGTATCGATACC-A-TCA
1 GGGGTATCGATACCTATTCA
3012523 GTAGGGTATCGATACAC-ATTCAAA
1 G--GGGTATCGATAC-CTATTC--A
3012547 GGGGGTATCGATACCTATTGCA
1 -GGGGTATCGATACCTATT-CA
*
3012569 GGGGTATCGATACCTATACAAA
1 GGGGTATCGATACCTATTC--A
* *
3012591 GGTGGTATCGATACCAATCTTA
1 GG-GGTATCGATACCTAT-TCA
3012613 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
3012631 GCACAAAAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 24
0.75 0.04 0.20
Matches are distributed among these distances:
18 1 0.01
20 13 0.15
21 30 0.34
22 13 0.15
23 29 0.33
24 2 0.02
25 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (20 bp):
GGGGTATCGATACCTATTCA
Found at i:3012591 original size:44 final size:43
Alignment explanation
Indices: 3012503--3012630 Score: 145
Period size: 44 Copynumber: 2.9 Consensus size: 43
3012493 TAAACCTGAC
*
3012503 AGGGGGTATCGATACCA-TCAGTAGGGTATCGATACAC-ATTCAA
1 AGGGGGTATCGATACCATTCAG--GGGTATCGATACACTATACAA
3012546 AGGGGGTATCGATACCTATTGCAGGGGTATCGATAC-CTATACAA
1 AGGGGGTATCGATACC-ATT-CAGGGGTATCGATACACTATACAA
* * *
3012590 AGGTGGTATCGATACCAATCTTAGGGGTATCGATACTCTAT
1 AGGGGGTATCGATACC-AT-TCAGGGGTATCGATACACTAT
3012631 GCACAAAAAT
Statistics
Matches: 75, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
43 17 0.23
44 49 0.65
45 6 0.08
46 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
AGGGGGTATCGATACCATTCAGGGGTATCGATACACTATACAA
Found at i:3018419 original size:18 final size:19
Alignment explanation
Indices: 3018375--3018434 Score: 77
Period size: 18 Copynumber: 3.1 Consensus size: 19
3018365 TACCTCTTGA
3018375 GGGGGTATCGATACCATTGCAT
1 GGGGGTATCGATACCA-T-C-T
3018397 GGGGGTATCGATACC-TCT
1 GGGGGTATCGATACCATCT
*
3018415 GGGGGTATCGGTACCATCT
1 GGGGGTATCGATACCATCT
3018434 G
1 G
3018435 AGCATTCTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 15 0.42
19 5 0.14
20 1 0.03
22 15 0.42
ACGTcount: A:0.18, C:0.20, G:0.35, T:0.27
Consensus pattern (19 bp):
GGGGGTATCGATACCATCT
Found at i:3019494 original size:2 final size:2
Alignment explanation
Indices: 3019487--3019537 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3019477 AGTAAGAAAG
3019487 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3019529 AT AT AT AT A
1 AT AT AT AT A
3019538 AGTATCGAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3020579 original size:20 final size:20
Alignment explanation
Indices: 3020554--3020591 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3020544 CACATGTTAA
*
3020554 AGAATGTATTGATACACTGT
1 AGAATGTACTGATACACTGT
*
3020574 AGAATGTACTGATGCACT
1 AGAATGTACTGATACACT
3020592 TCAATGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
AGAATGTACTGATACACTGT
Found at i:3021437 original size:18 final size:18
Alignment explanation
Indices: 3021414--3021512 Score: 117
Period size: 18 Copynumber: 5.5 Consensus size: 18
3021404 GTTATTAAGG
3021414 AGTGGTCCTTCGGGACAC
1 AGTGGTCCTTCGGGACAC
*
3021432 AGTGGTCATTCGGGACAC
1 AGTGGTCCTTCGGGACAC
* * *
3021450 AGTGGTCATTCAGGACAT
1 AGTGGTCCTTCGGGACAC
* *
3021468 AATGGTCCTTCGAGACAC
1 AGTGGTCCTTCGGGACAC
* * *
3021486 AGTGATCCTTCGTGACAT
1 AGTGGTCCTTCGGGACAC
3021504 AGTGGTCCT
1 AGTGGTCCT
3021513 ACAGGACAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAC
Found at i:3021475 original size:54 final size:54
Alignment explanation
Indices: 3021416--3021520 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
3021406 TATTAAGGAG
* * *
3021416 TGGTCCTTCGGGACACAGTGGTCATTCGGGACACAGTGGTCATTCAGGACATAA
1 TGGTCCTTCGAGACACAGTGATCATTCGGGACACAGTGGTCATACAGGACATAA
* * * *
3021470 TGGTCCTTCGAGACACAGTGATCCTTCGTGACATAGTGGTCCTACAGGACA
1 TGGTCCTTCGAGACACAGTGATCATTCGGGACACAGTGGTCATACAGGACA
3021521 AATTCTACGC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (54 bp):
TGGTCCTTCGAGACACAGTGATCATTCGGGACACAGTGGTCATACAGGACATAA
Found at i:3021725 original size:7 final size:7
Alignment explanation
Indices: 3021679--3021722 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
3021669 GTGAAATGCT
3021679 ATATGTG
1 ATATGTG
3021686 ATATGTG
1 ATATGTG
3021693 ATATGTG
1 ATATGTG
3021700 ATATGTG
1 ATATGTG
3021707 ATATGT-
1 ATATGTG
*
3021713 ATAAGTG
1 ATATGTG
3021720 ATA
1 ATA
3021723 AGTTAGGATC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 5 0.14
7 30 0.86
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (7 bp):
ATATGTG
Found at i:3025746 original size:20 final size:20
Alignment explanation
Indices: 3025721--3025758 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3025711 CACATGTTAA
*
3025721 AGAATGTATTGATACACTGT
1 AGAATGTACTGATACACTGT
*
3025741 AGAATGTACTGATGCACT
1 AGAATGTACTGATACACT
3025759 TCAATGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
AGAATGTACTGATACACTGT
Found at i:3026603 original size:18 final size:18
Alignment explanation
Indices: 3026580--3026678 Score: 117
Period size: 18 Copynumber: 5.5 Consensus size: 18
3026570 GTTCTTAAGG
3026580 AGTGGTCCTTCGGGACAC
1 AGTGGTCCTTCGGGACAC
*
3026598 AGTGGTCATTCGGGACAC
1 AGTGGTCCTTCGGGACAC
* * *
3026616 AGTGGTCATTCAGGACAT
1 AGTGGTCCTTCGGGACAC
* *
3026634 AATGGTCCTTCGAGACAC
1 AGTGGTCCTTCGGGACAC
* * *
3026652 AGTGATCCTTCGTGACAT
1 AGTGGTCCTTCGGGACAC
3026670 AGTGGTCCT
1 AGTGGTCCT
3026679 ACAGGACAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAC
Found at i:3026641 original size:54 final size:54
Alignment explanation
Indices: 3026582--3026686 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
3026572 TCTTAAGGAG
* * *
3026582 TGGTCCTTCGGGACACAGTGGTCATTCGGGACACAGTGGTCATTCAGGACATAA
1 TGGTCCTTCGAGACACAGTGATCATTCGGGACACAGTGGTCATACAGGACATAA
* * * *
3026636 TGGTCCTTCGAGACACAGTGATCCTTCGTGACATAGTGGTCCTACAGGACA
1 TGGTCCTTCGAGACACAGTGATCATTCGGGACACAGTGGTCATACAGGACA
3026687 AATTCTACGC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (54 bp):
TGGTCCTTCGAGACACAGTGATCATTCGGGACACAGTGGTCATACAGGACATAA
Found at i:3026857 original size:7 final size:7
Alignment explanation
Indices: 3026845--3026871 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3026835 GTGAAATGCT
3026845 ATATGTG
1 ATATGTG
3026852 ATATGTG
1 ATATGTG
3026859 ATATGTG
1 ATATGTG
3026866 ATATGT
1 ATATGT
3026872 ATAAGTGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (7 bp):
ATATGTG
Found at i:3027582 original size:24 final size:23
Alignment explanation
Indices: 3027521--3027582 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 23
3027511 GGGGTGTCAC
3027521 TTTTTG-TTTATTTCGTCACACT
1 TTTTTGTTTTATTTCGTCACACT
* *
3027543 TTTTT-TTCACTCTTTCGTCACACCT
1 TTTTTGTT--TTATTTCGTCACA-CT
*
3027568 TTTTTGTTTTTTTTC
1 TTTTTGTTTTATTTC
3027583 TTTGTTTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
22 6 0.19
24 16 0.52
25 7 0.23
26 2 0.06
ACGTcount: A:0.10, C:0.21, G:0.06, T:0.63
Consensus pattern (23 bp):
TTTTTGTTTTATTTCGTCACACT
Found at i:3030379 original size:98 final size:99
Alignment explanation
Indices: 3030121--3030390 Score: 348
Period size: 100 Copynumber: 2.7 Consensus size: 99
3030111 ATATAATAAT
* * * * *
3030121 ATTAT-ATATATATACAATAAAGCTTGAGTTATCCCTCTAGAACAATTGGTTAAACGCCCTGGCT
1 ATTATAATATCTATACAAGAAAG-TTGAGCTATCCATCTAGAGCAATTGGTTAAACGCCCTGGCT
* *
3030185 TTATGGATAAGATTTACCTAAACCTGATAAAGGTG
65 TTATGGATAAGATTCACCTAAACCTGATAAAGATG
* * * *
3030220 ATTATAATATCTATACAATAAAGTTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCTGACT
1 ATTATAATATCTATACAAGAAAG-TTGAGCTATCCATCTAGAGCAATTGGTTAAACGCCCTGGCT
* * *
3030285 TTATGGATAATATTCAGCT-AGCCTGATAAAGATG
65 TTATGGATAAGATTCACCTAAACCTGATAAAGATG
* *
3030319 ATTATAATATCTATACAACGATA-TTGAGCTGTCCATCTAGAGCAATTGGTTAAACGCCCTGGCT
1 ATTATAATATCTATACAA-GAAAGTTGAGCTATCCATCTAGAGCAATTGGTTAAACGCCCTGGCT
3030383 TTATGGAT
65 TTATGGAT
3030391 CCAGCTAGCC
Statistics
Matches: 154, Mismatches: 15, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
98 45 0.29
99 36 0.23
100 73 0.47
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (99 bp):
ATTATAATATCTATACAAGAAAGTTGAGCTATCCATCTAGAGCAATTGGTTAAACGCCCTGGCTT
TATGGATAAGATTCACCTAAACCTGATAAAGATG
Found at i:3031638 original size:84 final size:84
Alignment explanation
Indices: 3031507--3032037 Score: 544
Period size: 84 Copynumber: 6.3 Consensus size: 84
3031497 CTATTGGCAA
* * * * * *
3031507 CATAACTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACATTCAAGTTCAACTACGCTCAACTC
1 CATAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGATTACACTCAGCTC
*
3031571 AAAGACACATCATTTACAG
66 AAAGGCACATCATTTACAG
* * *
3031590 CATATCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGATTACACTCAGCTT
1 CATAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGATTACACTCAGC-T
* *
3031655 CGAGGGCACATCATTTACAG
65 CAAAGGCACATCATTTACAG
* * * * * *
3031675 CATAACTCAAAGCTAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACGCTCAGCTT
1 CATAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGATTACACTCAGC-T
* *
3031740 C-AAGGCATATCATTTGCAG
65 CAAAGGCACATCATTTACAG
* * * * * ** * * * *
3031759 TATAACTCGAGGCTAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTTGACTACCCTTAGCTC
1 CATAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGATTACACTCAGCTC
* *
3031824 CAAGGCATATCATTTACAG
66 AAAGGCACATCATTTACAG
* * * * * * *
3031843 CATAGCTCAAGGCAAGAAGGGCTATATGCCAAGCAAAGACATTCAAGTTCGATTACACTCAACTC
1 CATAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGATTACACTCAGCTC
*
3031908 AAAGGCACATCATTTGCAG
66 AAAGGCACATCATTTACAG
* * * ** * *
3031927 CATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGTGTTTGATTATACTCAGCTC
1 CATAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGATTACACTCAGCTC
* *
3031992 AGAGGCAAATCAAATTTACAG
66 AAAGGCACATC--ATTTACAG
* *
3032013 CATAACTCAATGCTAGAAGGGTTAT
1 CATAACTCAAGGCGAGAAGGGTTAT
3032038 TTGTCGATCA
Statistics
Matches: 368, Mismatches: 75, Indels: 7
0.82 0.17 0.02
Matches are distributed among these distances:
83 28 0.08
84 238 0.65
85 75 0.20
86 27 0.07
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (84 bp):
CATAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTACAG
Found at i:3031846 original size:168 final size:167
Alignment explanation
Indices: 3031507--3032040 Score: 649
Period size: 168 Copynumber: 3.2 Consensus size: 167
3031497 CTATTGGCAA
* * * *
3031507 CATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACATTCAAGTTCAACTACGCTCAACTCA
1 CATAACTCAAGGCTAGAAGGGTTATTTGCCAACAAAGACATTCAAGTTCGATTACGCTCAACTCA
* * * *
3031572 AAGACACATCATTTACAGCATATCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAG
66 AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* * * *
3031637 TTCGATTACACTCAGCTTCGAGGGCACATCATTTACAG
131 TTTGATTACACTCAGC-TCCAAGGCAAATCATTTACAG
* * * *
3031675 CATAACTCAAAGCTAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACGCTCAGCTT
1 CATAACTCAAGGCTAGAAGGGTTATTTGCCAAC-AAAGACATTCAAGTTCGATTACGCTCAAC-T
* * ** * * * * *
3031740 C-AAGGCATATCATTTGCAGTATAACTCGAGGCTAGAAGGGTTATCTGCTAACAAAAGACCTTTG
64 CAAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCG
* * * *
3031804 AGTTTGACTACCCTTAGCTCCAAGGCATATCATTTACAG
129 AGTTTGATTACACTCAGCTCCAAGGCAAATCATTTACAG
* * * * *
3031843 CATAGCTCAAGGCAAGAAGGGCTATATGCCAAGCAAAGACATTCAAGTTCGATTACACTCAACTC
1 CATAACTCAAGGCTAGAAGGGTTATTTGCCAA-CAAAGACATTCAAGTTCGATTACGCTCAACTC
* *
3031908 AAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGT
65 AAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGA
*
3031973 GTTTGATTATACTCAGCT-CAGAGGCAAATCAAATTTACAG
130 GTTTGATTACACTCAGCTCCA-AGGCAAATC--ATTTACAG
*
3032013 CATAACTCAATGCTAGAAGGGTTATTTG
1 CATAACTCAAGGCTAGAAGGGTTATTTG
3032041 TCGATCAAAT
Statistics
Matches: 301, Mismatches: 58, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
167 4 0.01
168 175 0.58
169 89 0.30
170 33 0.11
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (167 bp):
CATAACTCAAGGCTAGAAGGGTTATTTGCCAACAAAGACATTCAAGTTCGATTACGCTCAACTCA
AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
TTTGATTACACTCAGCTCCAAGGCAAATCATTTACAG
Found at i:3039790 original size:7 final size:7
Alignment explanation
Indices: 3039778--3039806 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3039768 GAGGGAAACT
3039778 TTTTCAC
1 TTTTCAC
3039785 TTTTCAC
1 TTTTCAC
3039792 TTTTCAC
1 TTTTCAC
3039799 TTTT-AC
1 TTTTCAC
3039805 TT
1 TT
3039807 AGGATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTCAC
Found at i:3044862 original size:17 final size:17
Alignment explanation
Indices: 3044842--3044875 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3044832 TTAATTAATA
3044842 TTATTATATAA-TATATT
1 TTATTATA-AACTATATT
3044859 TTATTATAAACTATATT
1 TTATTATAAACTATATT
3044876 ACATAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTATAAACTATATT
Found at i:3046055 original size:17 final size:17
Alignment explanation
Indices: 3046035--3046069 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3046025 TATTAATATA
3046035 TACATTTTATTTTCTTT
1 TACATTTTATTTTCTTT
*
3046052 TACATTTTTTTTTCTTT
1 TACATTTTATTTTCTTT
3046069 T
1 T
3046070 TTTCTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (17 bp):
TACATTTTATTTTCTTT
Found at i:3046437 original size:28 final size:29
Alignment explanation
Indices: 3046384--3046460 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 29
3046374 TTTTATTTAC
3046384 TTTC-TTTACTTTTATCTATTTTTATA-TT-
1 TTTCATTTA-TTTTATCT-TTTTTATAGTTA
3046412 TTT-ATTTATTTTATCTTCTTTGTATAGTTA
1 TTTCATTTATTTTATCTT-TTT-TATAGTTA
*
3046442 TTTCATTTATTTCATCTTT
1 TTTCATTTATTTTATCTTT
3046461 ACCTTTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
26 1 0.02
27 11 0.26
28 11 0.26
29 2 0.05
30 4 0.10
31 13 0.31
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.69
Consensus pattern (29 bp):
TTTCATTTATTTTATCTTTTTTATAGTTA
Found at i:3046519 original size:15 final size:13
Alignment explanation
Indices: 3046491--3046527 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 13
3046481 TCACACCTTT
3046491 TTTGTTTTTTTTC
1 TTTGTTTTTTTTC
3046504 TTTGTTTTCATTTTC
1 TTTGTTTT--TTTTC
3046519 TTTGTTTTT
1 TTTGTTTTT
3046528 ATTATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
15 13 0.59
ACGTcount: A:0.03, C:0.08, G:0.08, T:0.81
Consensus pattern (13 bp):
TTTGTTTTTTTTC
Found at i:3046548 original size:18 final size:18
Alignment explanation
Indices: 3046513--3046554 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
3046503 CTTTGTTTTC
* * *
3046513 ATTTTCTTTGTTTTTATT
1 ATTTTATTTATTTCTATT
3046531 ATTTTATTTATTTCTATT
1 ATTTTATTTATTTCTATT
3046549 -TTTTAT
1 ATTTTAT
3046555 CTAACATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (18 bp):
ATTTTATTTATTTCTATT
Found at i:3048425 original size:25 final size:25
Alignment explanation
Indices: 3048378--3048425 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3048368 TCGCCTACCT
*
3048378 TAAAATTTTATAAATTCGCCCCTCC
1 TAAAATTTTATAAATTCGACCCTCC
* *
3048403 TAAAATTTTATAAGTTTGACCCT
1 TAAAATTTTATAAATTCGACCCT
3048426 TAATTTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (25 bp):
TAAAATTTTATAAATTCGACCCTCC
Found at i:3050205 original size:5 final size:5
Alignment explanation
Indices: 3050195--3050220 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3050185 CGTTGCTCTG
3050195 CCACT CCACT CCACT CCACT CCACT C
1 CCACT CCACT CCACT CCACT CCACT C
3050221 ACATCGGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.62, G:0.00, T:0.19
Consensus pattern (5 bp):
CCACT
Found at i:3050897 original size:13 final size:13
Alignment explanation
Indices: 3050868--3050902 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3050858 ATAACTAATA
*
3050868 ATATTAAAT-ATT
1 ATATTAAATAAAT
3050880 ATATTAAATAAAT
1 ATATTAAATAAAT
3050893 ATATTAAATA
1 ATATTAAATA
3050903 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:3053916 original size:8 final size:8
Alignment explanation
Indices: 3053903--3053943 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3053893 CTCATTTTCA
3053903 GAGAATTT
1 GAGAATTT
3053911 GAGAATTT
1 GAGAATTT
*
3053919 -AGAGTTT
1 GAGAATTT
*
3053926 GGGAATTT
1 GAGAATTT
3053934 GAGAATTT
1 GAGAATTT
3053942 GA
1 GA
3053944 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:3054239 original size:128 final size:128
Alignment explanation
Indices: 3054011--3054625 Score: 1185
Period size: 128 Copynumber: 4.8 Consensus size: 128
3054001 CTATAATCGG
3054011 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
3054076 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
3054139 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
3054204 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
3054267 TTCACTATTCACATAAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
3054332 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
3054395 TTCACTATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
3054460 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
3054523 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
3054588 TATCATTGCCCTATTATGTCACTCATGTCACTCGGGGA
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
3054626 ATAACTTAAA
Statistics
Matches: 481, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 481 1.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (128 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:3055074 original size:33 final size:34
Alignment explanation
Indices: 3055013--3055112 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
3055003 AAATTTAATG
*
3055013 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
3055047 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
3055080 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
3055113 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:3055719 original size:21 final size:21
Alignment explanation
Indices: 3055631--3055724 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
3055621 TATGGTATAA
*
3055631 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
3055652 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
3055673 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
3055694 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
3055715 AACCCTGCGG
1 AACCCTGCGG
3055725 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:3055754 original size:21 final size:21
Alignment explanation
Indices: 3055728--3055775 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3055718 CCTGCGGAGA
*
3055728 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
3055749 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
3055770 GGGCAT
1 TGGCAT
3055776 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:3057542 original size:34 final size:32
Alignment explanation
Indices: 3057498--3057586 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
3057488 TTAATAATTC
3057498 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAAT-AATAATAATTATATAAATA-TA--TTAATA
* *
3057534 -AAATAATAATATTTACATAAATATATTAATA
1 TAAATAATAATAATTATATAAATATATTAATA
* * *
3057565 TAAAAAATAATAACTATTTAAA
1 TAAATAATAATAATTATATAAA
3057587 AAAATACTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
31 6 0.13
32 16 0.36
33 2 0.04
34 17 0.38
35 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAATAATAATAATTATATAAATATATTAATA
Found at i:3057563 original size:31 final size:34
Alignment explanation
Indices: 3057498--3057577 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
3057488 TTAATAATTC
*
3057498 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAAT-AATAATAATTACATAAATATTA-TTTAATA
*
3057534 -AAATAATAATATTTACATAAATA-TA-TTAATA
1 TAAATAATAATAATTACATAAATATTATTTAATA
*
3057565 TAAAAAATAATAA
1 TAAATAATAATAA
3057578 CTATTTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 6 0.15
32 10 0.26
33 2 0.05
34 17 0.44
35 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (34 bp):
TAAATAATAATAATTACATAAATATTATTTAATA
Found at i:3057583 original size:36 final size:33
Alignment explanation
Indices: 3057533--3057605 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 33
3057523 TTATTTTAAT
* * *
3057533 AAAATAATAATATTTACATAAATATATTAATATAA
1 AAAATAATAATATTTA-A-AAAAATACTAACATAA
3057568 AAAATAATAACTATTTAAAAAAATACTAACATAA
1 AAAATAATAA-TATTTAAAAAAATACTAACATAA
3057602 AAAA
1 AAAA
3057606 CTTTCTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 17 0.50
35 11 0.32
36 6 0.18
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (33 bp):
AAAATAATAATATTTAAAAAAATACTAACATAA
Found at i:3057588 original size:18 final size:18
Alignment explanation
Indices: 3057527--3057592 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
3057517 TAAATATTAT
3057527 TTTAATAAAATAATAATA
1 TTTAATAAAATAATAATA
*
3057545 TTTACATAAATATATTAATA
1 TTTA-ATAAA-ATAATAATA
3057565 --TAA-AAAATAATAACTA
1 TTTAATAAAATAATAA-TA
*
3057581 TTTAAAAAAATA
1 TTTAATAAAATA
3057593 CTAACATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
15 6 0.15
16 5 0.12
17 1 0.03
18 9 0.22
19 11 0.28
20 8 0.20
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAATAAAATAATAATA
Found at i:3059869 original size:2 final size:2
Alignment explanation
Indices: 3059858--3059889 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3059848 CCTATCCCAA
3059858 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3059890 GAAAATCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3060053 original size:15 final size:16
Alignment explanation
Indices: 3060035--3060067 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3060025 CCCTTGGATT
3060035 AAATTGAAA-AAATTA
1 AAATTGAAATAAATTA
*
3060050 AAATTTAAATAAATTA
1 AAATTGAAATAAATTA
3060066 AA
1 AA
3060068 TAACGTACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAATTGAAATAAATTA
Found at i:3060749 original size:13 final size:13
Alignment explanation
Indices: 3060731--3060755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3060721 TAAAAAAATA
3060731 TAAATTATATATT
1 TAAATTATATATT
3060744 TAAATTATATAT
1 TAAATTATATAT
3060756 AAATTTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAATTATATATT
Found at i:3063031 original size:26 final size:26
Alignment explanation
Indices: 3062983--3063033 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3062973 TAATCTAAAA
**
3062983 TAATATATTATTTATAATTTTTTAAT
1 TAATATATTATTTATAACATTTTAAT
*
3063009 TAATATATTTTTTATAACATTTTAA
1 TAATATATTATTTATAACATTTTAA
3063034 ATTATAGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TAATATATTATTTATAACATTTTAAT
Found at i:3065739 original size:21 final size:23
Alignment explanation
Indices: 3065697--3065739 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3065687 AAATAATAAT
*
3065697 ATATATATAACGTTTTCAAAAAC
1 ATATATATAACATTTTCAAAAAC
*
3065720 ATATATATAA-ATTTTTAAAA
1 ATATATATAACATTTTCAAAA
3065740 TGTTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (23 bp):
ATATATATAACATTTTCAAAAAC
Found at i:3065771 original size:37 final size:35
Alignment explanation
Indices: 3065708--3065918 Score: 164
Period size: 36 Copynumber: 5.9 Consensus size: 35
3065698 TATATATAAC
* *
3065708 GTTTTCAAAAAC-ATATATATAAATTTTTAAAATG
1 GTTTTTAAAAACTATATATATAAATTTTCAAAATG
* *
3065742 TTTTTTTAAAAAACTATATATATATATTTTCAAAATG
1 -GTTTTT-AAAAACTATATATATAAATTTTCAAAATG
* * *
3065779 GTTTTTAAAAATTATATATATAAATGTTTCATAA-C
1 GTTTTTAAAAACTATATATATAAAT-TTTCAAAATG
* * * **
3065814 G-TTTTCAAAAGTATATATATATATTTT-AAAAAC
1 GTTTTTAAAAACTATATATATAAATTTTCAAAATG
* *
3065847 GTTTTCAAAAACTACATATTATATAATTTTCAAAAAT-
1 GTTTTTAAAAACTATATA-TATA-AATTTTC-AAAATG
*
3065884 -ATTTTAAAAACTATATAATATACATATTTTCAAAA
1 GTTTTTAAAAACTATAT-ATATA-A-ATTTTCAAAA
3065919 ATGTTTTAAA
Statistics
Matches: 142, Mismatches: 23, Indels: 21
0.76 0.12 0.11
Matches are distributed among these distances:
32 3 0.02
33 5 0.04
34 32 0.23
35 26 0.18
36 45 0.32
37 27 0.19
38 4 0.03
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (35 bp):
GTTTTTAAAAACTATATATATAAATTTTCAAAATG
Found at i:3065834 original size:34 final size:33
Alignment explanation
Indices: 3065705--3065925 Score: 118
Period size: 37 Copynumber: 6.2 Consensus size: 33
3065695 ATATATATAT
** *
3065705 AACGTTTTCAAAAACATATATATAAATTTTTAA
1 AACGTTTTCAAAAGTATATATATAAATTTTAAA
* * * *
3065738 AATGTTTTTTTAAAAAACTATATATATATATTTTCAAA
1 AACG---TTTT-CAAAAGTATATATATAAATTTT-AAA
** * * * *
3065776 ATGGTTTTTAAAAATTATATATATAAATGTTTCAT
1 AACG-TTTTCAAAAGTATATATATAAAT-TTTAAA
*
3065811 AACGTTTTCAAAAGTATATATATATATTTTAAA
1 AACGTTTTCAAAAGTATATATATAAATTTTAAA
* *
3065844 AACGTTTTCAAAAACTACATATTATATAATTTTCAAA
1 AACGTTTTC-AAAAGTATATA-TATA-AATTTT-AAA
** * *
3065881 AATATTTTAAAAACTATATAATATACATATTTTCAAA
1 AACGTTTTCAAAAGTATAT-ATATA-A-ATTTT-AAA
*
3065918 AATGTTTT
1 AACGTTTT
3065926 AAACTATATA
Statistics
Matches: 148, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
33 16 0.11
34 29 0.20
35 24 0.16
36 31 0.21
37 44 0.30
38 4 0.03
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (33 bp):
AACGTTTTCAAAAGTATATATATAAATTTTAAA
Found at i:3065893 original size:36 final size:37
Alignment explanation
Indices: 3065756--3065956 Score: 167
Period size: 37 Copynumber: 5.6 Consensus size: 37
3065746 TTTAAAAAAC
3065756 TATA-TATATATATTTTC-AAAATGGTTTTTAAAAA-T-
1 TATATTATATATATTTTCAAAAAT-G-TTTTAAAAACTA
* * * * *
3065791 TATA-TATATAAATGTTTC-ATAACGTTTTCAAAA--G
1 TATATTATATATAT-TTTCAAAAATGTTTTAAAAACTA
*
3065825 TATA-TATATATATTTT-AAAAACGTTTTCAAAAACTA
1 TATATTATATATATTTTCAAAAATGTTTT-AAAAACTA
* *
3065861 CATATTATATA-ATTTTCAAAAATATTTTAAAAACTA
1 TATATTATATATATTTTCAAAAATGTTTTAAAAACTA
* *
3065897 TATAATATACATATTTTCAAAAATGTTTT--AAACTA
1 TATATTATATATATTTTCAAAAATGTTTTAAAAACTA
3065932 TATATTATATATGTATTTTCAAAAA
1 TATATTATATA--TATTTTCAAAAA
3065957 CAATTTGCAA
Statistics
Matches: 138, Mismatches: 17, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
33 12 0.09
34 24 0.17
35 28 0.20
36 31 0.22
37 43 0.31
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATTATATATATTTTCAAAAATGTTTTAAAAACTA
Found at i:3065915 original size:106 final size:103
Alignment explanation
Indices: 3065703--3065905 Score: 248
Period size: 106 Copynumber: 1.9 Consensus size: 103
3065693 TAATATATAT
* * *
3065703 ATAACGTTTTCAAAAACATATATATAAATTTTTAAAATGTTTTTTTAAAAAACTATATATATATA
1 ATAACGTTTTCAAAAACATATATATAAATTTTAAAAACG--TTTTTAAAAAACTACATATATATA
* *
3065768 TTTTCAAAATGGTTTTTAAAAATTATATATATAAATGTTTC
64 TTTTCAAAAT-GATTTTAAAAACTATATATATAAATGTTTC
** * *
3065809 ATAACGTTTTCAAAAGTATATATATATATTTTAAAAACG-TTTTCAAAAACTACATATTATATAA
1 ATAACGTTTTCAAAAACATATATATAAATTTTAAAAACGTTTTTAAAAAACTACATA-TATAT-A
3065873 TTTTCAAAAAT-ATTTTAAAAACTATATAATATA
64 TTTTC-AAAATGATTTTAAAAACTATAT-ATATA
3065906 CATATTTTCA
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
103 15 0.18
104 19 0.23
105 11 0.13
106 39 0.46
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (103 bp):
ATAACGTTTTCAAAAACATATATATAAATTTTAAAAACGTTTTTAAAAAACTACATATATATATT
TTCAAAATGATTTTAAAAACTATATATATAAATGTTTC
Found at i:3065919 original size:37 final size:37
Alignment explanation
Indices: 3065828--3065982 Score: 147
Period size: 37 Copynumber: 4.2 Consensus size: 37
3065818 TCAAAAGTAT
* *
3065828 ATATATATATTTT-AAAAACGTTTTCAAAAACTACATA
1 ATATATATATTTTCAAAAACATTTT-AAAAACTATATA
* *
3065865 TTATATA-ATTTTCAAAAATATTTTAAAAACTATATA
1 ATATATATATTTTCAAAAACATTTTAAAAACTATATA
* **
3065901 ATATACATATTTTCAAAAATGTTTT--AAACTATATA
1 ATATATATATTTTCAAAAACATTTTAAAAACTATATA
* * ** *
3065936 TTATATATGTATTTTCAAAAACAATTTGCAAACTGTATA
1 --ATATATATATTTTCAAAAACATTTTAAAAACTATATA
3065975 ATATATAT
1 ATATATAT
3065983 GTGTATATAT
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
35 10 0.10
36 21 0.21
37 58 0.59
39 9 0.09
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (37 bp):
ATATATATATTTTCAAAAACATTTTAAAAACTATATA
Found at i:3065956 original size:74 final size:71
Alignment explanation
Indices: 3065828--3065979 Score: 171
Period size: 74 Copynumber: 2.1 Consensus size: 71
3065818 TCAAAAGTAT
* * *
3065828 ATATATATATTTTAAAAACGTTTTCAAAAACTACATATTATATAATTTTCAAAAATATTTTAAAA
1 ATATACATATTTTAAAAACGTTTT--AAAACTACATATTATATAATTTTCAAAAACAATTTAAAA
3065893 ACTATATA
64 ACTATATA
* * **
3065901 ATATACATATTTTCAAAAATGTTTT-AAACTATATATTATATATGTATTTTCAAAAACAATTTGC
1 ATATACATATTTT-AAAAACGTTTTAAAACTACATATTATATA---ATTTTCAAAAACAATTTAA
*
3065965 AAACTGTATA
62 AAACTATATA
3065975 ATATA
1 ATATA
3065980 TATGTGTATA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
71 16 0.24
73 12 0.18
74 39 0.58
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (71 bp):
ATATACATATTTTAAAAACGTTTTAAAACTACATATTATATAATTTTCAAAAACAATTTAAAAAC
TATATA
Found at i:3066899 original size:81 final size:81
Alignment explanation
Indices: 3066608--3067329 Score: 686
Period size: 84 Copynumber: 8.7 Consensus size: 81
3066598 AAGTTGAATA
* * * *
3066608 TAATCGAACTCAAAGGTC-TTTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGT
1 TAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
3066672 GCCTTGGAGCTGAGCG
66 GCCTTGAAGCTGAGCG
* * * * *
3066688 GAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
1 TAATCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
3066753 TGTGCCGTTG-AGCTGAGCG
63 TGTGCC-TTGAAGCTGAGCG
* * * * * *
3066772 TAGTCGAACTCAAAAGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGA
1 TAATCGAACTCGAAGGTC--TT-TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
* *
3066837 TGTGCCCTCGAAGCTGAGTG
63 TGTG-CCTTGAAGCTGAGCG
* ** * * *
3066857 TAATCGAACTTGGGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
3066921 GCCTTGGAGCTGAGCG
66 GCCTTGAAGCTGAGCG
* * * * *
3066937 TAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGT
1 TAATCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
* *
3067002 TATGCCCTTGAAGCTGAGTG
63 TGTG-CCTTGAAGCTGAGCG
* ** * * *
3067022 TAATCGAACTTGGGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTACT-CTGCAAATGATG
1 TAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGTTA-TGCTGCAAATGATG
*
3067085 TGCCTTGGAGCTGAGCG
65 TGCCTTGAAGCTGAGCG
* * * * *
3067102 TAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGT
1 TAATCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
* *
3067167 TATGCCCTTGAAGCTGAGTG
63 TGTG-CCTTGAAGCTGAGCG
* * ** *
3067187 TAATCGAACT-TAAGGGTC-TTTGGCAGATAGCCCTTCTCTACTTAAGCTACT-CTGCAAATGAT
1 TAATCGAACTCGAA-GGTCTTTTGGCAGATAACCCTTCTAGACTTAAGTTA-TGCTGCAAATGAT
*
3067249 GTGCCTTGGAGCTGAGCG
64 GTGCCTTGAAGCTGAGCG
* * * *
3067267 TAGTCGAACTCGAAGGTCTTTTGTTAGCAGATAACCTTTCTTGACTTAAGTTATACTGCAAAT
1 TAATCGAACTCGAAGGTCTTTTG---GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAAT
3067330 AGTTTGTTAA
Statistics
Matches: 515, Mismatches: 97, Indels: 56
0.77 0.15 0.08
Matches are distributed among these distances:
80 94 0.18
81 123 0.24
82 3 0.01
83 2 0.00
84 209 0.41
85 78 0.15
86 2 0.00
87 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (81 bp):
TAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
GCCTTGAAGCTGAGCG
Found at i:3066933 original size:165 final size:165
Alignment explanation
Indices: 3066630--3067329 Score: 922
Period size: 165 Copynumber: 4.2 Consensus size: 165
3066620 AAGGTCTTTA
* * * * * * *
3066630 GCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGGAGTCG
1 GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGTGTAATCG
* * * * * * * *
3066694 AACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTA-TGCTGTAAATGATGTGC
66 AACTTGAGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGCTACT-CTGCAAATGATGTGC
* * * *
3066758 CGTT-GAGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGTTG
126 C-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* * * * *
3066798 GCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGTGTAATCG
*
3066863 AACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA-TGCTGCAAATGATGTGCCTTG
66 AACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACT-CTGCAAATGATGTGCCTTG
3066927 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
130 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* * * * *
3066963 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGTGTAATCG
*
3067028 AACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACTCTGCAAATGATGTGCCTTGG
66 AACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACTCTGCAAATGATGTGCCTTGG
3067093 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* * * * *
3067128 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGTGTAATCG
* *
3067193 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCTACTTAAGCTACTCTGCAAATGATGTGCCTTGG
66 AACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACTCTGCAAATGATGTGCCTTGG
* *
3067258 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTA
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* * *
3067293 GCAGATAACCTTTCTTGACTTAAGTTATACTGCAAAT
1 GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAAT
3067330 AGTTTGTTAA
Statistics
Matches: 484, Mismatches: 45, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
164 2 0.00
165 413 0.85
166 1 0.00
168 43 0.09
169 25 0.05
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (165 bp):
GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGTGTAATCG
AACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACTCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
Found at i:3067142 original size:249 final size:247
Alignment explanation
Indices: 3066608--3067329 Score: 748
Period size: 249 Copynumber: 2.9 Consensus size: 247
3066598 AAGTTGAATA
* * *
3066608 TAATCGAACTCAAAGGTCTTTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
*
3066673 CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
* * *
3066738 TTATGCTGTAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGTTGGCAGA
131 TTATGCTGTAAATGATATGCCCTTGAGCTGAGCGTAATCGAACTCAAAAGTC--TTGTTGGCAGA
** *
3066803 CAACCCTTCTAGACTTAAGTTGTACTGCAAATGATGTGCCCTCGAAGCTGAGTG
194 CAACCCTTCTAGACTTAAGTACTACTGCAAATGATGTGCCCTCGAAGCTGAGCG
* ** * *
3066857 TAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
3066922 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
* * ***** *
3066987 TTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTGGGGGTC-T-TTGGCAGAT
131 TTATGCTGTAAATGATATGCCCTTG-AGCTGAGCGTAATCGAACTCAAAAGTCTTGTTGGCAGAC
* * * *
3067050 AGCCCTTCTCGACTTAAGCTACT-CTGCAAATGATGTG-CCTTGGAGCTGAGCG
195 AACCCTTCTAGACTTAAG-TACTACTGCAAATGATGTGCCCTCGAAGCTGAGCG
* * * * * *
3067102 TAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGT
1 TAATCGAACTCGAAGGTC-TTTGG---CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGA
* * * * * * ***
3067167 TATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTC-TTTGG---CAGATAGCCCTTCTCTA
62 TGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTTGGTCACAGATAACCCTTCTAGC
* * * * * * *
3067227 CTTAAGCTACT-CTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
125 CTTGAGTTA-TGCTGTAAATGATATGCCCTT-GAGCTGAGCGTAATCGAACTCAAAAGTC--TTG
* * * *
3067290 TTAGCAGATAACCTTTCTTGACTTAAGTTA-TACTGCAAAT
186 TTGGCAGACAACCCTTCTAGACTTAAG-TACTACTGCAAAT
3067330 AGTTTGTTAA
Statistics
Matches: 397, Mismatches: 61, Indels: 30
0.81 0.12 0.06
Matches are distributed among these distances:
245 52 0.13
246 75 0.19
247 4 0.01
248 2 0.01
249 218 0.55
250 46 0.12
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (247 bp):
TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
TTATGCTGTAAATGATATGCCCTTGAGCTGAGCGTAATCGAACTCAAAAGTCTTGTTGGCAGACA
ACCCTTCTAGACTTAAGTACTACTGCAAATGATGTGCCCTCGAAGCTGAGCG
Found at i:3073823 original size:26 final size:25
Alignment explanation
Indices: 3073779--3073827 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
3073769 AATAATAATA
3073779 ATATATATATAAACGTTTTCAAAAAC
1 ATATATATATAAACGTTTT-AAAAAC
*
3073805 ATATAATATATAAA-TTTTTAAAA
1 ATAT-ATATATAAACGTTTTAAAA
3073828 TGTTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 8 0.38
27 9 0.43
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATATATATAAACGTTTTAAAAAC
Found at i:3073980 original size:37 final size:38
Alignment explanation
Indices: 3073789--3074055 Score: 239
Period size: 37 Copynumber: 7.1 Consensus size: 38
3073779 ATATATATAT
* * *
3073789 AAACGTTTTCAAAAAC-ATATAATATATAAATTTT-TA
1 AAACGTTTTCAAAAACTATATATTATATATATTTTCAA
* *
3073825 AAATGTTTTTTTAAAAAACTATATATTATATATATTTTCAA
1 AAACG---TTTTCAAAAACTATATATTATATATATTTTCAA
** * * *
3073866 AATGGTTTTTAAAAATTATATATTATATAAATGTTTTC-A
1 AAACGTTTTCAAAAACTATATATTATAT--ATATTTTCAA
* *
3073905 TAACGTTTTC-AAAAGTATATATTATATATATTTT-AA
1 AAACGTTTTCAAAAACTATATATTATATATATTTTCAA
*
3073941 AAACGTTTTCAAAAACTACATATTATATA-ATTTTCAA
1 AAACGTTTTCAAAAACTATATATTATATATATTTTCAA
** * *
3073978 AAATATTTT-AAAAACTATATAATATACATATTTTCAA
1 AAACGTTTTCAAAAACTATATATTATATATATTTTCAA
*
3074015 AAATGTTTT---AAACTATATATTATATATGTATTTTCAA
1 AAACGTTTTCAAAAACTATATATTATATA--TATTTTCAA
3074052 AAAC
1 AAAC
3074056 AATTTGCAAA
Statistics
Matches: 190, Mismatches: 28, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
35 15 0.08
36 41 0.22
37 53 0.28
38 37 0.19
39 17 0.09
40 23 0.12
41 4 0.02
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (38 bp):
AAACGTTTTCAAAAACTATATATTATATATATTTTCAA
Found at i:3074077 original size:37 final size:35
Alignment explanation
Indices: 3073915--3074080 Score: 111
Period size: 37 Copynumber: 4.5 Consensus size: 35
3073905 TAACGTTTTC
* * **
3073915 AAAAGTATATATTATATATATTTT-AAAAACGTTTT
1 AAAACTATATAATATATATATTTTCAAAAA-AATTT
* * *
3073950 CAAAAACTACATATTATATA-ATTTTCAAAAATATTTT
1 --AAAACTATATAATATATATATTTTCAAAAA-AATTT
* **
3073987 AAAAACTATATAATATACATATTTTCAAAAATGTTT
1 -AAAACTATATAATATATATATTTTCAAAAAAATTT
* *
3074023 TAAACTATATATTATATATGTATTTTCAAAAACAATTT
1 AAAACTATATA--ATATATATATTTTCAAAAA-AATTT
* *
3074061 GCAAACTGTATAATATATAT
1 -AAAACTATATAATATATAT
3074081 GTGTATATAT
Statistics
Matches: 106, Mismatches: 17, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
35 10 0.09
36 24 0.23
37 60 0.57
38 3 0.03
39 9 0.08
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.42
Consensus pattern (35 bp):
AAAACTATATAATATATATATTTTCAAAAAAATTT
Found at i:3089074 original size:16 final size:16
Alignment explanation
Indices: 3089053--3089085 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3089043 ACATTGTCAC
3089053 GTCATCAATTTAACGA
1 GTCATCAATTTAACGA
3089069 GTCATCAATTTAACGA
1 GTCATCAATTTAACGA
3089085 G
1 G
3089086 GTTGACGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (16 bp):
GTCATCAATTTAACGA
Found at i:3099434 original size:21 final size:20
Alignment explanation
Indices: 3099396--3099434 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3099386 GAACATTAAG
3099396 AAAATAAGGAGAAAAACAGA
1 AAAATAAGGAGAAAAACAGA
3099416 AAAATTAA-GAGAAACAACA
1 AAAA-TAAGGAGAAA-AACA
3099435 ATATATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAATAAGGAGAAAAACAGA
Found at i:3103659 original size:12 final size:12
Alignment explanation
Indices: 3103644--3103668 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3103634 TTAATAAAAA
3103644 AAATAATATTTT
1 AAATAATATTTT
3103656 AAATAATATTTT
1 AAATAATATTTT
3103668 A
1 A
3103669 CAAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:3104398 original size:2 final size:2
Alignment explanation
Indices: 3104391--3104416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3104381 GTATGTTTCA
3104391 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
3104417 AGTTACACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3109705 original size:2 final size:2
Alignment explanation
Indices: 3109698--3109735 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3109688 AAGCAGAAAT
3109698 TA TA 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 TA TA
3109736 ATAAAGAAAA
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):
TA
Found at i:3112217 original size:28 final size:28
Alignment explanation
Indices: 3112157--3112218 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
3112147 TGAGTCCCTA
* * *
3112157 ACTATTAACAGTTAAAAATAGTCCCCCG
1 ACTATTAAAAGTTAAAAATAATCCACCG
3112185 ACTATTAAAAGTTATAAAATAAT-CACCG
1 ACTATTAAAAGTTA-AAAATAATCCACCG
*
3112213 GCTATT
1 ACTATT
3112219 CATATGTTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (28 bp):
ACTATTAAAAGTTAAAAATAATCCACCG
Found at i:3120352 original size:2 final size:2
Alignment explanation
Indices: 3120347--3120385 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3120337 TTTTTGTCAA
3120347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3120386 ACAGATCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3120634 original size:2 final size:2
Alignment explanation
Indices: 3120627--3120659 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3120617 ATAATAATTC
3120627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3120660 ATTTTTGCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3123615 original size:4 final size:4
Alignment explanation
Indices: 3123606--3123630 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3123596 TATATATCTA
3123606 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
3123631 TATGTGTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:3127724 original size:29 final size:29
Alignment explanation
Indices: 3127682--3127839 Score: 246
Period size: 29 Copynumber: 5.4 Consensus size: 29
3127672 CGACCCGACC
3127682 CGGTGATATTTTGGGAATTATTTTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
3127711 CGGTGATATTTTGGGAATTATTTTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
* *
3127740 CAGTGATATTTTGAGAATTATTTTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
* *
3127769 TGGTGATATTTTGAGAATTATTTTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
*
3127798 CGGTGATATTTTGGTAATTATTTTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
*
3127827 AGGT-ACTATTTTG
1 CGGTGA-TATTTTG
3127840 TAATTTTCGA
Statistics
Matches: 120, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
28 1 0.01
29 119 0.99
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.46
Consensus pattern (29 bp):
CGGTGATATTTTGGGAATTATTTTTAAAA
Found at i:3128895 original size:25 final size:25
Alignment explanation
Indices: 3128843--3128895 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
3128833 AGGGTAATTC
*
3128843 TTTTAAGAGATTTACTGTAATATAA
1 TTTTAAGAGATTTACTGGAATATAA
* * *
3128868 TTTTATGAGATTTACTGGACTATGA
1 TTTTAAGAGATTTACTGGAATATAA
3128893 TTT
1 TTT
3128896 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (25 bp):
TTTTAAGAGATTTACTGGAATATAA
Found at i:3134950 original size:10 final size:10
Alignment explanation
Indices: 3134935--3134982 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
3134925 TTGACCGGCT
3134935 TGACCCGACC
1 TGACCCGACC
*
3134945 TGACCCG--T
1 TGACCCGACC
3134953 TGACCCGACC
1 TGACCCGACC
*
3134963 GGACCCGACC
1 TGACCCGACC
*
3134973 GGACCCGACC
1 TGACCCGACC
3134983 CGTTGACCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 7 0.21
10 26 0.79
ACGTcount: A:0.19, C:0.48, G:0.25, T:0.08
Consensus pattern (10 bp):
TGACCCGACC
Found at i:3135159 original size:29 final size:29
Alignment explanation
Indices: 3134997--3135152 Score: 258
Period size: 29 Copynumber: 5.4 Consensus size: 29
3134987 GACCCGACTT
3134997 GGTGATATTTTGGGAATTATTTTTAAAAC
1 GGTGATATTTTGGGAATTATTTTTAAAAC
3135026 GGTGATATTTTGGGAATTATTTTTAAAAC
1 GGTGATATTTTGGGAATTATTTTTAAAAC
* *
3135055 GGTGATATTTTGAGAATTATTTTTAAAAT
1 GGTGATATTTTGGGAATTATTTTTAAAAC
*
3135084 GGTGATATTTTGGGAATTATTTTTAAAAT
1 GGTGATATTTTGGGAATTATTTTTAAAAC
* *
3135113 GGTGATATTTTGGTAATTATTTTTAAAAA
1 GGTGATATTTTGGGAATTATTTTTAAAAC
*
3135142 GGTGTTATTTT
1 GGTGATATTTT
3135153 TGTAATTTTC
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 121 1.00
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.48
Consensus pattern (29 bp):
GGTGATATTTTGGGAATTATTTTTAAAAC
Found at i:3142935 original size:3 final size:3
Alignment explanation
Indices: 3142927--3142955 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3142917 AATCAAGTCT
3142927 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3142956 TTATGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3156342 original size:31 final size:33
Alignment explanation
Indices: 3156296--3156357 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
3156286 TTTAACTATG
*
3156296 AAATTTTAAATAAAATATCATTTTG-ACCCTTA
1 AAATTTTAAATAAAATATCAATTTGAACCCTTA
* *
3156328 AAATTTT-GATAAAATGTCAATTTGAACCCT
1 AAATTTTAAATAAAATATCAATTTGAACCCT
3156358 AAATTCAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (33 bp):
AAATTTTAAATAAAATATCAATTTGAACCCTTA
Found at i:3159104 original size:21 final size:21
Alignment explanation
Indices: 3159080--3159119 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3159070 TTCTCAACCT
3159080 CAATCCCTTTC-TTCTCACTCG
1 CAAT-CCTTTCATTCTCACTCG
*
3159101 CAATCTTTTCATTCTCACT
1 CAATCCTTTCATTCTCACT
3159120 TCTCAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.38, G:0.03, T:0.42
Consensus pattern (21 bp):
CAATCCTTTCATTCTCACTCG
Found at i:3163230 original size:19 final size:19
Alignment explanation
Indices: 3163198--3163249 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
3163188 TTGGACTCTC
* *
3163198 AGTGCATCGGTGCACTAAG
1 AGTGCACCGATGCACTAAG
* ***
3163217 AGTGCACCGATGCATTCTT
1 AGTGCACCGATGCACTAAG
3163236 AGTGCACCGATGCA
1 AGTGCACCGATGCA
3163250 TGAAATGCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (19 bp):
AGTGCACCGATGCACTAAG
Found at i:3163326 original size:19 final size:20
Alignment explanation
Indices: 3163281--3163334 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
3163271 AAATAGCCTG
* *
3163281 AGTGCATCGATTCATGGTCT
1 AGTGCATCGATGCATGGTAT
3163301 AGTGCATCGATGCATGGTAT
1 AGTGCATCGATGCATGGTAT
3163321 -GTGCATCGATGCAT
1 AGTGCATCGATGCAT
3163335 AAAATGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATGGTAT
Found at i:3166103 original size:44 final size:44
Alignment explanation
Indices: 3166014--3166110 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
3166004 GATCTTGTGC
* *
3166014 ATCGATGCACATTCAAGGGCGTGCATCGGTGCATCAGCTGATGT
1 ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
* *
3166058 ATCGATGCACATTCAAAGGG-ATGCATCGGTGCA-CTGTTAAGTGT
1 ATCGATGCACATTC-AAGGGCATGCATCGGTGCATCAGCTAA-TGT
3166102 ATCGATGCA
1 ATCGATGCA
3166111 TTAAGCACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
43 4 0.09
44 38 0.81
45 5 0.11
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
Found at i:3171543 original size:20 final size:20
Alignment explanation
Indices: 3171518--3171571 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
3171508 AAATAGCCTG
*
3171518 AGTGCATCGATGCATGGTCT
1 AGTGCATCGATGCATGGTAT
*
3171538 AGTGCATCGATGAATGGTAT
1 AGTGCATCGATGCATGGTAT
3171558 -GTGCATCGATGCAT
1 AGTGCATCGATGCAT
3171572 AAAATACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATGGTAT
Found at i:3172703 original size:541 final size:541
Alignment explanation
Indices: 3171681--3172763 Score: 2166
Period size: 541 Copynumber: 2.0 Consensus size: 541
3171671 TTCAAAATAC
3171681 TTTTTGAAAATTGTTTCAAAAATAGTTTAAGTATAAAACACAATTTTACACATTTAGTAAGGTTT
1 TTTTTGAAAATTGTTTCAAAAATAGTTTAAGTATAAAACACAATTTTACACATTTAGTAAGGTTT
3171746 GAAATGATCTTGAAAGACTTGGAGTAATAATTTGATATTCGATTAATTGAATCGAATATACTTTA
66 GAAATGATCTTGAAAGACTTGGAGTAATAATTTGATATTCGATTAATTGAATCGAATATACTTTA
3171811 GAAAATCATTTGTAAAATCTTAAAATTCATTTAACTTAATTTGTTATATCGAAACATCAAAATGT
131 GAAAATCATTTGTAAAATCTTAAAATTCATTTAACTTAATTTGTTATATCGAAACATCAAAATGT
3171876 TTTCAACAAGTAAACATTCCAGTGATCACATCTTAATTAAAATAAAACAAAAGTGACTATGTATT
196 TTTCAACAAGTAAACATTCCAGTGATCACATCTTAATTAAAATAAAACAAAAGTGACTATGTATT
3171941 GTGTTTTTTAATCTAGTGACCATAAGTTTATAAAACTCAAACGAAAGTGACCAACTTTGTAGTTT
261 GTGTTTTTTAATCTAGTGACCATAAGTTTATAAAACTCAAACGAAAGTGACCAACTTTGTAGTTT
3172006 ACCCAAAACATTATTGCATCTAAAAAAGCCCTAATTTTTCTAAAATTACAAAAAAATCTCTAACC
326 ACCCAAAACATTATTGCATCTAAAAAAGCCCTAATTTTTCTAAAATTACAAAAAAATCTCTAACC
3172071 TTAAATACCATCTCCAATGTCGATCACAACCACCATCGTTATCGTTGTCTTTGTCATCTCTTTTG
391 TTAAATACCATCTCCAATGTCGATCACAACCACCATCGTTATCGTTGTCTTTGTCATCTCTTTTG
3172136 TCGATCGTCGTCGGCTTTACTGCCAAAGTCATCGGGTCACGTCATCAAACTAACGGAAGTAAATG
456 TCGATCGTCGTCGGCTTTACTGCCAAAGTCATCGGGTCACGTCATCAAACTAACGGAAGTAAATG
3172201 TTTCAGTGATCACATCTTAAT
521 TTTCAGTGATCACATCTTAAT
3172222 TTTTTGAAAATTGTTTCAAAAATAGTTTAAGTATAAAACACAATTTTACACATTTAGTAAGGTTT
1 TTTTTGAAAATTGTTTCAAAAATAGTTTAAGTATAAAACACAATTTTACACATTTAGTAAGGTTT
3172287 GAAATGATCTTGAAAGACTTGGAGTAATAATTTGATATTCGATTAATTGAATCGAATATACTTTA
66 GAAATGATCTTGAAAGACTTGGAGTAATAATTTGATATTCGATTAATTGAATCGAATATACTTTA
3172352 GAAAATCATTTGTAAAATCTTAAAATTCATTTAACTTAATTTGTTATATCGAAACATCAAAATGT
131 GAAAATCATTTGTAAAATCTTAAAATTCATTTAACTTAATTTGTTATATCGAAACATCAAAATGT
3172417 TTTCAACAAGTAAACATTCCAGTGATCACATCTTAATTAAAATAAAACAAAAGTGACTATGTATT
196 TTTCAACAAGTAAACATTCCAGTGATCACATCTTAATTAAAATAAAACAAAAGTGACTATGTATT
3172482 GTGTTTTTTAATCTAGTGACCATAAGTTTATAAAACTCAAACGAAAGTGACCAACTTTGTAGTTT
261 GTGTTTTTTAATCTAGTGACCATAAGTTTATAAAACTCAAACGAAAGTGACCAACTTTGTAGTTT
3172547 ACCCAAAACATTATTGCATCTAAAAAAGCCCTAATTTTTCTAAAATTACAAAAAAATCTCTAACC
326 ACCCAAAACATTATTGCATCTAAAAAAGCCCTAATTTTTCTAAAATTACAAAAAAATCTCTAACC
3172612 TTAAATACCATCTCCAATGTCGATCACAACCACCATCGTTATCGTTGTCTTTGTCATCTCTTTTG
391 TTAAATACCATCTCCAATGTCGATCACAACCACCATCGTTATCGTTGTCTTTGTCATCTCTTTTG
3172677 TCGATCGTCGTCGGCTTTACTGCCAAAGTCATCGGGTCACGTCATCAAACTAACGGAAGTAAATG
456 TCGATCGTCGTCGGCTTTACTGCCAAAGTCATCGGGTCACGTCATCAAACTAACGGAAGTAAATG
3172742 TTTCAGTGATCACATCTTAAT
521 TTTCAGTGATCACATCTTAAT
3172763 T
1 T
3172764 AAAATAAAAC
Statistics
Matches: 542, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
541 542 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (541 bp):
TTTTTGAAAATTGTTTCAAAAATAGTTTAAGTATAAAACACAATTTTACACATTTAGTAAGGTTT
GAAATGATCTTGAAAGACTTGGAGTAATAATTTGATATTCGATTAATTGAATCGAATATACTTTA
GAAAATCATTTGTAAAATCTTAAAATTCATTTAACTTAATTTGTTATATCGAAACATCAAAATGT
TTTCAACAAGTAAACATTCCAGTGATCACATCTTAATTAAAATAAAACAAAAGTGACTATGTATT
GTGTTTTTTAATCTAGTGACCATAAGTTTATAAAACTCAAACGAAAGTGACCAACTTTGTAGTTT
ACCCAAAACATTATTGCATCTAAAAAAGCCCTAATTTTTCTAAAATTACAAAAAAATCTCTAACC
TTAAATACCATCTCCAATGTCGATCACAACCACCATCGTTATCGTTGTCTTTGTCATCTCTTTTG
TCGATCGTCGTCGGCTTTACTGCCAAAGTCATCGGGTCACGTCATCAAACTAACGGAAGTAAATG
TTTCAGTGATCACATCTTAAT
Found at i:3173731 original size:21 final size:19
Alignment explanation
Indices: 3173698--3173739 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
3173688 TTTTCATTTA
3173698 GTTATTTTCAAATACTTTTTT
1 GTTATTTTCAAAT--TTTTTT
3173719 GTTATCTTT-AAATTTTTTT
1 GTTAT-TTTCAAATTTTTTT
3173738 GT
1 GT
3173740 ACGGACGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.40
21 9 0.45
22 3 0.15
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (19 bp):
GTTATTTTCAAATTTTTTT
Found at i:3174871 original size:39 final size:39
Alignment explanation
Indices: 3174821--3174895 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
3174811 GGGTATATAT
3174821 ATTTAAATTAAATATATAAATATTATATATATATATTTA
1 ATTTAAATTAAATATATAAATATTATATATATATATTTA
* * *
3174860 ATTTAATTTAAATTTATTAATATTATATATATATAT
1 ATTTAAATTAAATATATAAATATTATATATATATAT
3174896 ATATAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (39 bp):
ATTTAAATTAAATATATAAATATTATATATATATATTTA
Found at i:3174906 original size:39 final size:39
Alignment explanation
Indices: 3174814--3174906 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
3174804 TCGGATCGGG
* *
3174814 TATATATAT-TTAAATTAAATATATAAATATTATATATA
1 TATATATATAATAATTTAAATATATAAATATTATATATA
* *
3174852 TATAT-T-TAATTTAATTTAAATTTATTAATATTATATATA
1 TATATATATAA--TAATTTAAATATATAAATATTATATATA
3174891 TATATATATAATAATT
1 TATATATATAATAATT
3174907 ATTTTTAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
36 1 0.02
37 1 0.02
38 5 0.11
39 35 0.76
40 1 0.02
41 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (39 bp):
TATATATATAATAATTTAAATATATAAATATTATATATA
Found at i:3174964 original size:20 final size:20
Alignment explanation
Indices: 3174939--3174976 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3174929 GGTAATCGGG
3174939 GCGGGGATTACTAAACCCGA
1 GCGGGGATTACTAAACCCGA
3174959 GCGGGGATTACTAAACCC
1 GCGGGGATTACTAAACCC
3174977 ATCTCCGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (20 bp):
GCGGGGATTACTAAACCCGA
Found at i:3175209 original size:54 final size:54
Alignment explanation
Indices: 3175121--3175240 Score: 174
Period size: 54 Copynumber: 2.2 Consensus size: 54
3175111 CTCATAGGGT
*
3175121 GTACCGATACCCCTATGCTAATTTTGGCATCGAGAAAAACAGAATGT-TAAATGG
1 GTACCGATACCCCTATGCTAATTTTAGCATCGAGAAAAACAGAATGTCT-AATGG
3175175 GTACCGATACCCCTATG-TCAATTTTAGC-TCCGAGAAAAACAGAATGTCTAATGG
1 GTACCGATACCCCTATGCT-AATTTTAGCAT-CGAGAAAAACAGAATGTCTAATGG
*
3175229 GTACCGGTACCC
1 GTACCGATACCC
3175241 TTAGTCATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
53 2 0.03
54 58 0.95
55 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (54 bp):
GTACCGATACCCCTATGCTAATTTTAGCATCGAGAAAAACAGAATGTCTAATGG
Found at i:3179243 original size:21 final size:21
Alignment explanation
Indices: 3179192--3179244 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3179182 ATTATGACTA
3179192 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
3179213 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
3179234 TCGCAATGCGA
1 TCGCAATGCGA
3179245 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:3179259 original size:20 final size:21
Alignment explanation
Indices: 3179234--3179285 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3179224 TTTTCCCAAT
*
3179234 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
3179254 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3179275 TCGCAATGCGA
1 TCGCAATGCGA
3179286 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3179406 original size:20 final size:20
Alignment explanation
Indices: 3179275--3179402 Score: 175
Period size: 20 Copynumber: 6.4 Consensus size: 20
3179265 ATTTGGAAAA
* * *
3179275 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATTCTGACTT
**
3179295 TCGCAACGCGAAACTGACTT
1 TCGCAACGCGATTCTGACTT
* *
3179315 TCGCAACGTGATTTTGACTT
1 TCGCAACGCGATTCTGACTT
3179335 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
3179355 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
* *
3179375 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTT
3179395 TCGCAACG
1 TCGCAACG
3179403 AGATAATACA
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 97 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:3179960 original size:20 final size:20
Alignment explanation
Indices: 3179935--3179994 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
3179925 GACATTCATT
*
3179935 TGACTATCACAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
3179955 TGACTATCGCAACGCG-AAA
1 TGACTATCGCAACGCGAAAA
* *
3179974 TGGCTATCGCAACGAGAAAA
1 TGACTATCGCAACGCGAAAA
3179994 T
1 T
3179995 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
TGACTATCGCAACGCGAAAA
Found at i:3179980 original size:19 final size:19
Alignment explanation
Indices: 3179935--3179992 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
3179925 GACATTCATT
*
3179935 TGACTATCACAACGCGAAAA
1 TGACTATCGCAACGCG-AAA
3179955 TGACTATCGCAACGCGAAA
1 TGACTATCGCAACGCGAAA
* *
3179974 TGGCTATCGCAACGAGAAA
1 TGACTATCGCAACGCGAAA
3179993 ATCGCAATGC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (19 bp):
TGACTATCGCAACGCGAAA
Found at i:3180054 original size:19 final size:19
Alignment explanation
Indices: 3180013--3180077 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
3180003 GAAATGAAAA
3180013 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
3180029 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3180046 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3180065 TCGCATTGCGATT
1 TCGCATTGCGATT
3180078 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3182116 original size:19 final size:19
Alignment explanation
Indices: 3182082--3182183 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
3182072 AAACTTACTT
***
3182082 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
3182102 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3182121 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
3182140 ACGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
3182154 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3182173 TCGCAATGCGA
1 TCGCAACGCGA
3182184 TTTGTGTTTC
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 45 0.65
20 9 0.13
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3182214 original size:14 final size:14
Alignment explanation
Indices: 3182195--3182253 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3182185 TTGTGTTTCG
3182195 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3182209 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
3182226 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
3182242 CGTTGCGATTTT
1 CGTTGCGATTTT
3182254 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3182227 original size:33 final size:33
Alignment explanation
Indices: 3182190--3182269 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
3182180 GCGATTTGTG
*
3182190 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
3182223 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
3182256 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
3182270 ATCCATTTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:3182235 original size:19 final size:19
Alignment explanation
Indices: 3182211--3182289 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
3182201 GATTTTGTCG
3182211 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3182230 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
3182244 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
3182263 TTGCGATATCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
3182283 TTGCGAT
1 TTGCGAT
3182290 AGTCATTTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 19 0.39
20 10 0.20
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3182288 original size:20 final size:18
Alignment explanation
Indices: 3182242--3182308 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 18
3182232 GCGATTTTGT
*
3182242 CGTTGCGATTTTCATTTCG
1 CGTTGCGA-TATCATTTCG
*
3182261 CATTGCGATATCCATTTCCG
1 CGTTGCGATAT-CATTT-CG
3182281 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATA-TCA-TTTCG
*
3182301 TGTTGCGA
1 CGTTGCGA
3182309 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.05
19 12 0.30
20 22 0.55
21 4 0.10
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (18 bp):
CGTTGCGATATCATTTCG
Found at i:3182866 original size:18 final size:18
Alignment explanation
Indices: 3182843--3182890 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
3182833 CGGGTCGATC
*
3182843 AGGTGATGGCTCTGGGTT
1 AGGTGATGGCTCTGGGTG
*
3182861 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
3182879 AGGTGATGGCTC
1 AGGTGATGGCTC
3182891 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.12, G:0.44, T:0.29
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:3184216 original size:20 final size:20
Alignment explanation
Indices: 3184193--3184230 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3184183 AATAGTTTCT
3184193 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
3184213 GAAAATGACAATCGCAAC
1 GAAAATGAAAATCGCAAC
3184231 GAGAGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:3184785 original size:41 final size:41
Alignment explanation
Indices: 3184740--3184817 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
3184730 CAAAAGTCAG
*
3184740 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTAT
* *
3184781 TATCGCGTTGCGATAGTCAGTATCGTATTGCGATTTT
1 TATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTT
3184818 CCCAATTCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTAT
Found at i:3184814 original size:20 final size:20
Alignment explanation
Indices: 3184720--3184805 Score: 93
Period size: 20 Copynumber: 4.2 Consensus size: 20
3184710 AATTATGTAT
* * *
3184720 TATCTCGTTGCAAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
3184740 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
3184760 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
3184781 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
3184801 TATCG
1 TATCG
3184806 TATTGCGATT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
19 3 0.05
20 37 0.66
21 14 0.25
22 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:3184833 original size:21 final size:20
Alignment explanation
Indices: 3184807--3184854 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3184797 TCAGTATCGT
*
3184807 ATTGCGATTTTCCCAATTCGC
1 ATTGCGA-TTTACCAATTCGC
**
3184828 ATTGCGATTTACTTATTCGC
1 ATTGCGATTTACCAATTCGC
3184848 ATTGCGA
1 ATTGCGA
3184855 ATTGGGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTGCGATTTACCAATTCGC
Found at i:3184833 original size:41 final size:41
Alignment explanation
Indices: 3184740--3184835 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
3184730 CAAAAGTCAG
* * ** *
3184740 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
*
3184781 TATCGCGTTGCGATAGTCAGTATCGTATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAA
*
3184823 T-TCGCATTGCGAT
1 TATCGCGTTGCGAT
3184836 TTACTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
Found at i:3184896 original size:21 final size:22
Alignment explanation
Indices: 3184844--3184896 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3184834 ATTTACTTAT
3184844 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
3184865 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
3184886 TCGCATTGCGA
1 TCGCATTGCGA
3184897 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:3185625 original size:26 final size:27
Alignment explanation
Indices: 3185591--3185642 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
3185581 AAAGCCAATG
* * *
3185591 ATATTGCCCTTCTCAGAATA-GAAAAT
1 ATATGGCCCTACTCAAAATAGGAAAAT
3185617 ATATGGCCCTACTCAAAATAGGAAAA
1 ATATGGCCCTACTCAAAATAGGAAAA
3185643 GAGGAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.25
Consensus pattern (27 bp):
ATATGGCCCTACTCAAAATAGGAAAAT
Done.