Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006206.1 Hibiscus syriacus cultivar Beakdansim tig00014773_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: 480835
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 3
Found at i:198801 original size:32 final size:31
Alignment explanation
Indices: 198765--198840 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
198755 CGGGGCCGTG
*
198765 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
198797 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
198828 GAGCCTACCTAAG
1 GGGCCTACCTAAG
198841 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:198824 original size:63 final size:63
Alignment explanation
Indices: 198718--198840 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
198708 ACCTAAGGGA
* * ** *
198718 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
198781 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
198841 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:201673 original size:17 final size:16
Alignment explanation
Indices: 201651--201697 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
201641 TTTTGGTCAA
201651 CAACGGTCAACGTGGGT
1 CAACGGTCAACG-GGGT
201668 CAACGGTCAAC-GGGT
1 CAACGGTCAACGGGGT
201683 CAACGGGTCAACGGG
1 CAAC-GGTCAACGGG
201698 TCGGGTCGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 13 0.46
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (16 bp):
CAACGGTCAACGGGGT
Found at i:201685 original size:8 final size:8
Alignment explanation
Indices: 201651--201699 Score: 66
Period size: 8 Copynumber: 6.1 Consensus size: 8
201641 TTTTGGTCAA
201651 CAAC-GGT
1 CAACGGGT
201658 CAACGTGGGT
1 CAAC--GGGT
201668 CAAC-GGT
1 CAACGGGT
201675 CAACGGGT
1 CAACGGGT
201683 CAACGGGT
1 CAACGGGT
201691 CAACGGGT
1 CAACGGGT
201699 C
1 C
201700 GGGTCGGGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
7 11 0.29
8 20 0.53
10 7 0.18
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.14
Consensus pattern (8 bp):
CAACGGGT
Found at i:201704 original size:5 final size:5
Alignment explanation
Indices: 201694--201719 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
201684 AACGGGTCAA
201694 CGGGT CGGGT CGGGT CGGGT CGGGT C
1 CGGGT CGGGT CGGGT CGGGT CGGGT C
201720 AACTGGTTAG
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:0.00, C:0.23, G:0.58, T:0.19
Consensus pattern (5 bp):
CGGGT
Found at i:201704 original size:13 final size:13
Alignment explanation
Indices: 201672--201758 Score: 66
Period size: 13 Copynumber: 6.3 Consensus size: 13
201662 GTGGGTCAAC
201672 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
201688 GGTCAACGGGTCG
1 GGTCAACGGGTCG
**
201701 GGTCGGGTCGGGTCG
1 GGTC--AACGGGTCG
* **
201716 GGTCAACTGGTTA
1 GGTCAACGGGTCG
*
201729 GGTAAACGGGTCG
1 GGTCAACGGGTCG
*
201742 GGTAAACGGGTCG
1 GGTCAACGGGTCG
201755 GGTC
1 GGTC
201759 GGGTCGGGTT
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
13 35 0.61
15 11 0.19
16 11 0.19
ACGTcount: A:0.17, C:0.20, G:0.45, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:205979 original size:3 final size:3
Alignment explanation
Indices: 205961--206019 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
205951 TTGGTTTTAA
* * **
205961 ATT ATT TTT AATT ATT ATT ACT ATT ATT ATT ATT ATT ATT GCT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
206007 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
206020 ATTTACATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 45 0.96
4 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:213739 original size:17 final size:17
Alignment explanation
Indices: 213705--213756 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
213695 ACCATACAAA
* *
213705 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
213722 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
213739 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
213754 TTT
1 TTT
213757 TTACTGTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:224606 original size:16 final size:16
Alignment explanation
Indices: 224587--224617 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
224577 CCTTTCAAAC
224587 GACCCCATTTTCTAAG
1 GACCCCATTTTCTAAG
224603 GACCCCATTTTCTAA
1 GACCCCATTTTCTAA
224618 ATGAGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.32
Consensus pattern (16 bp):
GACCCCATTTTCTAAG
Found at i:226260 original size:2 final size:2
Alignment explanation
Indices: 226253--226292 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
226243 CCATGCAATA
226253 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
226293 TCAAAAGGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228791 original size:2 final size:2
Alignment explanation
Indices: 228784--228815 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
228774 TACAACAATG
228784 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
228816 AACTAGGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:230945 original size:11 final size:11
Alignment explanation
Indices: 230929--230953 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
230919 ATTTAATAGT
230929 TTATTATTTAA
1 TTATTATTTAA
230940 TTATTATTTAA
1 TTATTATTTAA
230951 TTA
1 TTA
230954 ACTAATTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATTATTTAA
Found at i:231126 original size:24 final size:24
Alignment explanation
Indices: 231086--231136 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
231076 ATTGTGAATG
*
231086 TTTTATTTATTTA-TTTTAGTATTA
1 TTTTATATATTTATTTTTA-TATTA
231110 TTTTATAT-TTTATTTTTTATATTA
1 TTTTATATATTTA-TTTTTATATTA
231134 TTT
1 TTT
231137 ATTTAATTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 15 0.62
25 5 0.21
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTATATATTTATTTTTATATTA
Found at i:231139 original size:16 final size:16
Alignment explanation
Indices: 231087--231140 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
231077 TTGTGAATGT
*
231087 TTTATTTATTTATTTTA
1 TTTATTT-TTTATATTA
*
231104 -GTATTATTTTATA-T-
1 TTTATT-TTTTATATTA
231118 TTTATTTTTTATATTA
1 TTTATTTTTTATATTA
231134 TTTATTT
1 TTTATTT
231141 AATTAGGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
14 7 0.23
15 6 0.20
16 16 0.53
17 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTATTTTTTATATTA
Found at i:231145 original size:12 final size:12
Alignment explanation
Indices: 231086--231145 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
231076 ATTGTGAATG
231086 TTTTAT-TTATTT
1 TTTTATATTA-TT
231098 ATTTTAGTATTATT
1 -TTTTA-TATTATT
* *
231112 TTATATTTTATT
1 TTTTATATTATT
231124 TTTTATATTATT
1 TTTTATATTATT
231136 TATTTA-ATTA
1 T-TTTATATTA
231146 GGGGAATGAC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 21 0.52
13 13 0.32
14 3 0.08
15 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTATATTATT
Found at i:232834 original size:21 final size:21
Alignment explanation
Indices: 232801--232841 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
232791 TACATGGGTA
*
232801 CACCGCAGCCATTTCAGATGG
1 CACCACAGCCATTTCAGATGG
* *
232822 CACCACAGTCATTTTAGATG
1 CACCACAGCCATTTCAGATG
232842 CCACTGCAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
CACCACAGCCATTTCAGATGG
Found at i:233433 original size:14 final size:14
Alignment explanation
Indices: 233374--233435 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
233364 TTTCTTAATG
*
233374 TTGTTATTATTTAA
1 TTGTTTTTATTTAA
**
233388 TTGTTTGAATTGTAA
1 TTGTTTTTATT-TAA
*
233403 -TGTTTGTATTT-A
1 TTGTTTTTATTTAA
233415 TTGTTTTTATTTAA
1 TTGTTTTTATTTAA
233429 TTGTTTT
1 TTGTTTT
233436 AATTGTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 11 0.28
14 25 0.62
15 3 0.08
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (14 bp):
TTGTTTTTATTTAA
Found at i:233440 original size:23 final size:23
Alignment explanation
Indices: 233406--233476 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
233396 ATTGTAATGT
233406 TTGTATTT-ATTGTTTTTATTTAA
1 TTGT-TTTAATTGTTTTTATTTAA
* *
233429 TTGTTTTAATTGTTTTTA-CTAT
1 TTGTTTTAATTGTTTTTATTTAA
233451 TTAGTTTGTAA-TGTTTTTATTTAA
1 TT-GTTT-TAATTGTTTTTATTTAA
233475 TT
1 TT
233477 TTCACTTGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.17
23 26 0.65
24 7 0.17
ACGTcount: A:0.21, C:0.01, G:0.10, T:0.68
Consensus pattern (23 bp):
TTGTTTTAATTGTTTTTATTTAA
Found at i:234975 original size:31 final size:32
Alignment explanation
Indices: 234934--235001 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
234924 TTTTTAAAAG
*
234934 TTATAAAATAATTATT-AATTTTATCAAACTA
1 TTATAAAATAAATATTGAATTTTATCAAACTA
* * *
234965 TTATGAAATAAATATTGAATTTTATCGAACTG
1 TTATAAAATAAATATTGAATTTTATCAAACTA
234997 TTATA
1 TTATA
235002 TAATGATCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (32 bp):
TTATAAAATAAATATTGAATTTTATCAAACTA
Found at i:245022 original size:2 final size:2
Alignment explanation
Indices: 245017--245070 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
245007 TCTCTCTCTC
* * *
245017 TA TA TA TA TA TA TA TA TG TA TG TA TG 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 TA TA
245059 TA TA TA TA TA TA
1 TA TA TA TA TA TA
245071 CCATCTCCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:249262 original size:24 final size:24
Alignment explanation
Indices: 249231--249282 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
249221 AATTCCACAA
* *
249231 ACTG-GACTCCGGCTCCTGCTTCT
1 ACTGCGACTCCGGCTCCGGCTCCT
* *
249254 ACTGCGACTTCTGCTCCGGCTCCT
1 ACTGCGACTCCGGCTCCGGCTCCT
249278 ACTGC
1 ACTGC
249283 TTCTGAGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.10, C:0.40, G:0.21, T:0.29
Consensus pattern (24 bp):
ACTGCGACTCCGGCTCCGGCTCCT
Found at i:272002 original size:392 final size:392
Alignment explanation
Indices: 271273--272061 Score: 1524
Period size: 392 Copynumber: 2.0 Consensus size: 392
271263 TACGGCCGCT
*
271273 TGCACCGTCTTGTAACACTCTATATGATCTTTACACACCGTTATGTCCACCTTCAAGTTCGTGGG
1 TGCAACGTCTTGTAACACTCTATATGATCTTTACACACCGTTATGTCCACCTTCAAGTTCGTGGG
271338 AACCCCCCCTTCAAATCTCAACTCCGATTTCTGACCCGGTCGGTCCTCGTAAAACCCGTCCCGTT
66 AACCCCCCCTTCAAATCTCAACTCCGATTTCTGACCCGGTCGGTCCTCGTAAAACCCGTCCCGTT
*
271403 CCGTTTTGGGAGGGGTCCATGATAGAGTGTCCTCCCCGTTATTATCATAGGCCACCATCATGCTC
131 CCGTTTTGGGAGGGGTCCATGAGAGAGTGTCCTCCCCGTTATTATCATAGGCCACCATCATGCTC
*
271468 AACGCATTGCTGCTGAGACGAGTCAACTCGTCCAGAGACGTCATCACGTGGGCGATAGACATGGT
196 AACGCATTGCTGCTGAGACGAGTCAACTCCTCCAGAGACGTCATCACGTGGGCGATAGACATGGT
271533 GTCATTGATGCGCTTGAGGGCGCCCCAACTTCCTTTTTGGTAGGCAAGAGCGGCACTCATCCATG
261 GTCATTGATGCGCTTGAGGGCGCCCCAACTTCCTTTTTGGTAGGCAAGAGCGGCACTCATCCATG
271598 CACGTGCATCTTTTACCTTCCCTTGTGTTAACGCGTGGCTGGCAGATTCCATGCGGTGGTCTGAG
326 CACGTGCATCTTTTACCTTCCCTTGTGTTAACGCGTGGCTGGCAGATTCCATGCGGTGGTCTGAG
271663 TA
391 TA
271665 TGCAACGTCTTGTAACACTCTATATGATCTTTACACACCGTTATGTCCACCTTCAAGTTCGTGGG
1 TGCAACGTCTTGTAACACTCTATATGATCTTTACACACCGTTATGTCCACCTTCAAGTTCGTGGG
271730 AACCCCCCCTTCAAATCTCAACTCCGATTTCTGACCCGGTCGGTCCTCGTAAAACCCGTCCCGTT
66 AACCCCCCCTTCAAATCTCAACTCCGATTTCTGACCCGGTCGGTCCTCGTAAAACCCGTCCCGTT
271795 CCGTTTTGGGAGGGGTCCATGAGAGAGTGTCCTCCCCGTTATTATCATAGGCCACCATCATGCTC
131 CCGTTTTGGGAGGGGTCCATGAGAGAGTGTCCTCCCCGTTATTATCATAGGCCACCATCATGCTC
271860 AACGCATTGCTGCTGAGACGAGTCAACTCCTCCAGAGACGTCATCACGTGGGCGATAGACATGGT
196 AACGCATTGCTGCTGAGACGAGTCAACTCCTCCAGAGACGTCATCACGTGGGCGATAGACATGGT
* **
271925 GTCATTGATGCGCTTGATGTTGCCCCAACTTCCTTTTTGGTAGGCAAGAGCGGCACTCATCCATG
261 GTCATTGATGCGCTTGAGGGCGCCCCAACTTCCTTTTTGGTAGGCAAGAGCGGCACTCATCCATG
271990 CACGTGCATCTTTTACCTTCCCTTGTGTTAACGCGTGGCTGGCAGATTCCATGCGGTGGTCTGAG
326 CACGTGCATCTTTTACCTTCCCTTGTGTTAACGCGTGGCTGGCAGATTCCATGCGGTGGTCTGAG
272055 TA
391 TA
272057 TGCAA
1 TGCAA
272062 GGATCTCCAA
Statistics
Matches: 391, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
392 391 1.00
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (392 bp):
TGCAACGTCTTGTAACACTCTATATGATCTTTACACACCGTTATGTCCACCTTCAAGTTCGTGGG
AACCCCCCCTTCAAATCTCAACTCCGATTTCTGACCCGGTCGGTCCTCGTAAAACCCGTCCCGTT
CCGTTTTGGGAGGGGTCCATGAGAGAGTGTCCTCCCCGTTATTATCATAGGCCACCATCATGCTC
AACGCATTGCTGCTGAGACGAGTCAACTCCTCCAGAGACGTCATCACGTGGGCGATAGACATGGT
GTCATTGATGCGCTTGAGGGCGCCCCAACTTCCTTTTTGGTAGGCAAGAGCGGCACTCATCCATG
CACGTGCATCTTTTACCTTCCCTTGTGTTAACGCGTGGCTGGCAGATTCCATGCGGTGGTCTGAG
TA
Found at i:275367 original size:21 final size:21
Alignment explanation
Indices: 275341--275391 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
275331 TGGGTAGAGA
275341 GTATCGATACTTGCT-CATATG
1 GTATCGATACTTGCTCCA-ATG
* *
275362 GTATCGATA-TTGTTCCACTG
1 GTATCGATACTTGCTCCAATG
275382 GTATCGATAC
1 GTATCGATAC
275392 CATAGGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (21 bp):
GTATCGATACTTGCTCCAATG
Found at i:276584 original size:34 final size:32
Alignment explanation
Indices: 276531--276600 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
276521 CCTTACAAAC
*
276531 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
**
276563 TCCCTAGCTTTTACACGGGCTACGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
276597 TCCC
1 TCCC
276601 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:276910 original size:21 final size:21
Alignment explanation
Indices: 276884--276925 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
276874 CCAGAATGGG
276884 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
276905 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
276926 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:277071 original size:19 final size:19
Alignment explanation
Indices: 277031--277077 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
277021 GAGCCTCGGG
* *
277031 TACTGTTCAAACAGTGATT
1 TACTGTTCAAACAGTAAAT
*
277050 TACTGTTCAAATAGTAAAT
1 TACTGTTCAAACAGTAAAT
*
277069 TACTATTCA
1 TACTGTTCA
277078 CAAATACATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TACTGTTCAAACAGTAAAT
Found at i:277174 original size:29 final size:31
Alignment explanation
Indices: 277142--277201 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
277132 AAATTTTGAA
*
277142 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
277171 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
277202 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:278496 original size:19 final size:20
Alignment explanation
Indices: 278453--278500 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
278443 TCTAAATCCT
*
278453 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
278473 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
278492 TTTTCAAAA
1 TTTTCAAAA
278501 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:279413 original size:34 final size:32
Alignment explanation
Indices: 279360--279429 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
279350 CCTTACAAAC
*
279360 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
**
279392 TCCCTAGCTTTTACACGGGCTACGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
279426 TCCC
1 TCCC
279430 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:279739 original size:21 final size:21
Alignment explanation
Indices: 279713--279754 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
279703 CCAGAATGGG
279713 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
279734 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
279755 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:279900 original size:19 final size:19
Alignment explanation
Indices: 279860--279906 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
279850 GAGCCTCGGG
* *
279860 TACTGTTCAAACAGTGATT
1 TACTGTTCAAACAGTAAAT
*
279879 TACTGTTCAAATAGTAAAT
1 TACTGTTCAAACAGTAAAT
*
279898 TACTATTCA
1 TACTGTTCA
279907 CAAATACATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TACTGTTCAAACAGTAAAT
Found at i:280003 original size:29 final size:31
Alignment explanation
Indices: 279971--280030 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
279961 AAATTTTGAA
*
279971 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
280000 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
280031 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:281320 original size:19 final size:20
Alignment explanation
Indices: 281277--281324 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
281267 TCTAAATCCT
*
281277 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
281297 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
281316 TTTTCAAAA
1 TTTTCAAAA
281325 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:282234 original size:34 final size:32
Alignment explanation
Indices: 282181--282250 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
282171 CCTTACAAAC
*
282181 TCCCTAGTTTTTCCGGGCTAAACTAGAACCCT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCCT
* *
282213 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCCT
282247 TCCC
1 TCCC
282251 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCCT
Found at i:282559 original size:20 final size:21
Alignment explanation
Indices: 282534--282574 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
282524 CCAGAATGGG
282534 GGGAATCG-TACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
282554 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
282575 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:282718 original size:19 final size:19
Alignment explanation
Indices: 282678--282724 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
282668 GAGCCTCGGG
* *
282678 TACTGTTCAAACAGTGATT
1 TACTGTTCAAACAGTAAAT
*
282697 TACTGTTCAAATAGTAAAT
1 TACTGTTCAAACAGTAAAT
*
282716 TACTATTCA
1 TACTGTTCA
282725 CAAATACATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TACTGTTCAAACAGTAAAT
Found at i:284531 original size:20 final size:21
Alignment explanation
Indices: 284490--284531 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
284480 CCAGAATGGG
*
284490 GGAATCGGTACCCCTATTCATA
1 GGAATCGATACCCC-ATTCATA
284512 GGAATCGATACCCC-TTCATA
1 GGAATCGATACCCCATTCATA
284532 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (21 bp):
GGAATCGATACCCCATTCATA
Found at i:284777 original size:29 final size:31
Alignment explanation
Indices: 284745--284804 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
284735 AAATTTTGAA
*
284745 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
284774 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
284805 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:286995 original size:21 final size:21
Alignment explanation
Indices: 286969--287034 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
286959 TAAAAGATTT
286969 GATCCCTTCTCTCGAAGGATC
1 GATCCCTTCTCTCGAAGGATC
286990 GATCCC-T-TCTCGAAGGATC
1 GATCCCTTCTCTCGAAGGATC
* *
287009 GATCCCTTCTCTCGAAAGAAC
1 GATCCCTTCTCTCGAAGGATC
287030 GATCC
1 GATCC
287035 TTTGGTTGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.44
20 2 0.05
21 21 0.51
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (21 bp):
GATCCCTTCTCTCGAAGGATC
Found at i:287002 original size:19 final size:19
Alignment explanation
Indices: 286978--287019 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
286968 TGATCCCTTC
286978 TCTCGAAGGATCGATCCCT
1 TCTCGAAGGATCGATCCCT
286997 TCTCGAAGGATCGATCCCT
1 TCTCGAAGGATCGATCCCT
287016 TCTC
1 TCTC
287020 TCGAAAGAAC
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:0.33, G:0.19, T:0.29
Consensus pattern (19 bp):
TCTCGAAGGATCGATCCCT
Found at i:288388 original size:20 final size:21
Alignment explanation
Indices: 288350--288389 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
288340 TCAAGGTTTG
288350 AATATCGATATTGGGATGAAC
1 AATATCGATATTGGGATGAAC
288371 AATATCGATATT-GGATGAA
1 AATATCGATATTGGGATGAA
288390 TTGGGGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (21 bp):
AATATCGATATTGGGATGAAC
Found at i:291026 original size:26 final size:26
Alignment explanation
Indices: 290997--291047 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
290987 TCAAAATAGA
290997 AAATAGGTCTTAACTATGAAAATCAT
1 AAATAGGTCTTAACTATGAAAATCAT
291023 AAATAGGTCTTAACTATGAAAATCA
1 AAATAGGTCTTAACTATGAAAATCA
291048 GATCAACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (26 bp):
AAATAGGTCTTAACTATGAAAATCAT
Found at i:294087 original size:24 final size:24
Alignment explanation
Indices: 294032--294088 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
294022 ATAATAGTAG
* *
294032 AATAATATTAGTTTATTTATGATT
1 AATATTATTAGTTTAGTTATGATT
* * *
294056 AATGTTATTATTTTAGTTATTATT
1 AATATTATTAGTTTAGTTATGATT
*
294080 ATTATTATT
1 AATATTATT
294089 TTACTTACTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (24 bp):
AATATTATTAGTTTAGTTATGATT
Found at i:296210 original size:17 final size:17
Alignment explanation
Indices: 296188--296231 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
296178 ATGTAAAACT
296188 AAATATTTAAATTT-TAA
1 AAATATTTAAATTTAT-A
* *
296205 AAATATATAAATTTATT
1 AAATATTTAAATTTATA
296222 AAATATTTAA
1 AAATATTTAA
296232 TTAAATATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:297630 original size:27 final size:27
Alignment explanation
Indices: 297596--297649 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
297586 TTTTAGGAGC
297596 AACTAGGTACAAATGATATAATTCAGG
1 AACTAGGTACAAATGATATAATTCAGG
297623 AACTAGGTACAAATGATATAATTCAGG
1 AACTAGGTACAAATGATATAATTCAGG
297650 TGGCAATGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (27 bp):
AACTAGGTACAAATGATATAATTCAGG
Found at i:301196 original size:64 final size:63
Alignment explanation
Indices: 301111--301271 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
301101 TTGTTTAAGG
* * * *
301111 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * *
301175 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACTTCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
301239 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
301272 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:302477 original size:31 final size:31
Alignment explanation
Indices: 302439--302543 Score: 140
Period size: 31 Copynumber: 3.4 Consensus size: 31
302429 TCGAGGGTTT
**
302439 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAACGA-ACATATGGACAGTA
*
302470 TACCTATGTTCTAAGGAACATATGGACAGTA
1 TACCTATGTTCTAACGAACATATGGACAGTA
* *
302501 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAACGAACATATGGACAGTA
*
302532 TACCTAGGTTCT
1 TACCTATGTTCT
302544 TCGGGACCTA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
31 63 0.93
32 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGACAGTA
Found at i:302556 original size:31 final size:31
Alignment explanation
Indices: 302456--302562 Score: 151
Period size: 31 Copynumber: 3.5 Consensus size: 31
302446 GTCTTTCGAG
*
302456 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGTTTACCTATGTTCTAAGGA
*
302487 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGTTTACCTATGTTCTAAGGA
* ** *
302518 ACATATGGACAGTTTACCTAGGTTCTTCGGG
1 ACATATGGACAGTTTACCTATGTTCTAAGGA
*
302549 ACCTATGGACAGTT
1 ACATATGGACAGTT
302563 ACCGAGGATC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (31 bp):
ACATATGGACAGTTTACCTATGTTCTAAGGA
Found at i:305895 original size:64 final size:63
Alignment explanation
Indices: 305810--305970 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
305800 TTGTTTAAGG
* * * *
305810 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
305874 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
305938 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
305971 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:306467 original size:2 final size:2
Alignment explanation
Indices: 306460--306492 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
306450 CATGAGTTAG
*
306460 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
306493 AGAATTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:307273 original size:31 final size:31
Alignment explanation
Indices: 307167--307254 Score: 158
Period size: 31 Copynumber: 2.8 Consensus size: 31
307157 GTCTTTCGAG
307167 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGTATACCTATGTTCTAAGGA
307198 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGTATACCTATGTTCTAAGGA
* *
307229 ACATATGGACAGTTTACCTAGGTTCT
1 ACATATGGACAGTATACCTATGTTCT
307255 TCGGGATCTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (31 bp):
ACATATGGACAGTATACCTATGTTCTAAGGA
Found at i:307304 original size:30 final size:30
Alignment explanation
Indices: 307265--307331 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
307255 TCGGGATCTA
*
307265 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
307295 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
307325 TGGATAG
1 TGGATAG
307332 GTCCTTTGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:308163 original size:21 final size:21
Alignment explanation
Indices: 308138--308185 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
308128 CCTAATATTG
308138 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
308159 CAATGTCAACATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
308180 TAATGT
1 CAATGT
308186 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:311114 original size:29 final size:29
Alignment explanation
Indices: 311081--311168 Score: 167
Period size: 29 Copynumber: 3.0 Consensus size: 29
311071 CAATATATGG
311081 ATGGAATTATAGTGAAAACATCCCATTAA
1 ATGGAATTATAGTGAAAACATCCCATTAA
311110 ATGGAATTATAGTGAAAACATCCCATTAA
1 ATGGAATTATAGTGAAAACATCCCATTAA
*
311139 ATGGTATTATAGTGAAAACATCCCATTAA
1 ATGGAATTATAGTGAAAACATCCCATTAA
311168 A
1 A
311169 GCCTAAAGAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (29 bp):
ATGGAATTATAGTGAAAACATCCCATTAA
Found at i:312143 original size:21 final size:21
Alignment explanation
Indices: 312117--312173 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
312107 ATTTACCGTG
*
312117 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGACGCT
*
312138 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
312159 ATTGCGGCCGTCGCG
1 ATTGCGGCCGTCGCG
312174 TGTAACTCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.07, C:0.32, G:0.40, T:0.21
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:313456 original size:120 final size:120
Alignment explanation
Indices: 313199--313507 Score: 359
Period size: 120 Copynumber: 2.5 Consensus size: 120
313189 TGCACATCCC
* *
313199 CTCTCCTCTTCTTTCCATTTTGTTCGCTAAAATTGTCCACTTCCTTCAAAAGCTTTTTTCCTCTG
1 CTCTCCTCTTCTTTCCATTTTGTTTGC----ATT-TCC-CTTCCTTCAAAAGC--TTTTCCTTTG
* * **
313264 CTCTCCTCTTCTTTCCATTTTGTTTGCTTACATTTTCTGCTTCCTTCAAAAGCTTTTCCTCTG
58 CTCTCATCTTCTTTCCATTTTGTTTGCTGACATTTTCCCCTTCCTTCAAAAGCTTTTCCTCTG
* *
313327 CTTTTCTCTTCTTTCCATTTTGTTTGC-TTTCCCTTTCCTTCAAAAGCTTTTCCTTTGCTCTCAT
1 CTCTCCTCTTCTTTCCATTTTGTTTGCATTTCCC-TTCCTTCAAAAGCTTTTCCTTTGCTCTCAT
* * *
313391 CTTTTTTCCATTTTGTTTGCTGACGTTTTCCCCTTCCTTCAAAAGCTTTTCCTTTG
65 CTTCTTTCCATTTTGTTTGCTGACATTTTCCCCTTCCTTCAAAAGCTTTTCCTCTG
* *
313447 CTCTCCTCTTCTTTCCATTCTGTTTACTAATATTTTCCCCTTCCTTCAAAAGCTTTTCCTT
1 CTCTCCTCTTCTTTCCATTTTGTTTGC----A-TTT-CCCTTCCTTCAAAAGCTTTTCCTT
313508 ACTACAACCC
Statistics
Matches: 158, Mismatches: 15, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
120 88 0.56
121 1 0.01
122 16 0.10
123 2 0.01
126 24 0.15
127 3 0.02
128 24 0.15
ACGTcount: A:0.12, C:0.30, G:0.07, T:0.50
Consensus pattern (120 bp):
CTCTCCTCTTCTTTCCATTTTGTTTGCATTTCCCTTCCTTCAAAAGCTTTTCCTTTGCTCTCATC
TTCTTTCCATTTTGTTTGCTGACATTTTCCCCTTCCTTCAAAAGCTTTTCCTCTG
Found at i:313507 original size:63 final size:63
Alignment explanation
Indices: 313199--313507 Score: 387
Period size: 63 Copynumber: 5.0 Consensus size: 63
313189 TGCACATCCC
* * * * *
313199 CTCTCCTCTTCTTTCCATTTTGTTCGCTAAAATTGTCCACTTCCTTCAAAAGCTTTTTTCCTCTG
1 CTCTCCTCTTCTTTCCATTTTGTTTGCTAACATTTTCCCCTTCCTTCAAAAGC--TTTTCCTTTG
* ** *
313264 CTCTCCTCTTCTTTCCATTTTGTTTGCTTACATTTTCTGCTTCCTTCAAAAGCTTTTCCTCTG
1 CTCTCCTCTTCTTTCCATTTTGTTTGCTAACATTTTCCCCTTCCTTCAAAAGCTTTTCCTTTG
* * *
313327 CTTTTCTCTTCTTTCCATTTTGTTTG----C--TTTCCCTTTCCTTCAAAAGCTTTTCCTTTG
1 CTCTCCTCTTCTTTCCATTTTGTTTGCTAACATTTTCCCCTTCCTTCAAAAGCTTTTCCTTTG
* * * *
313384 CTCTCATCTTTTTTCCATTTTGTTTGCTGACGTTTTCCCCTTCCTTCAAAAGCTTTTCCTTTG
1 CTCTCCTCTTCTTTCCATTTTGTTTGCTAACATTTTCCCCTTCCTTCAAAAGCTTTTCCTTTG
* * *
313447 CTCTCCTCTTCTTTCCATTCTGTTTACTAATATTTTCCCCTTCCTTCAAAAGCTTTTCCTT
1 CTCTCCTCTTCTTTCCATTTTGTTTGCTAACATTTTCCCCTTCCTTCAAAAGCTTTTCCTT
313508 ACTACAACCC
Statistics
Matches: 214, Mismatches: 24, Indels: 14
0.85 0.10 0.06
Matches are distributed among these distances:
57 48 0.22
59 1 0.00
61 1 0.00
63 117 0.55
65 47 0.22
ACGTcount: A:0.12, C:0.30, G:0.07, T:0.50
Consensus pattern (63 bp):
CTCTCCTCTTCTTTCCATTTTGTTTGCTAACATTTTCCCCTTCCTTCAAAAGCTTTTCCTTTG
Found at i:314579 original size:63 final size:63
Alignment explanation
Indices: 314475--314628 Score: 240
Period size: 63 Copynumber: 2.4 Consensus size: 63
314465 GGTTTGTAGT
* * * *
314475 AAGGGAAAGCTTTTGAAGG-AAGGGAAAAATGTTAGCAAACAGAATGGAAAGAAGAGGAGAGCA
1 AAGGAAAAGCCTTTGAAGGAAAGGG-AAAACGTTAACAAACAGAATGGAAAGAAGAGGAGAGCA
314538 AAGGAAAAGCCTTTGAAGGAAAGGGAAAACGTTAACAAACAGAATGGAAAGAAGAGGAGAGCA
1 AAGGAAAAGCCTTTGAAGGAAAGGGAAAACGTTAACAAACAGAATGGAAAGAAGAGGAGAGCA
314601 AAGGAAAAG-CTATTGAAGGAAAGGGAAA
1 AAGGAAAAGCCT-TTGAAGGAAAGGGAAA
314629 GCAAACAGAA
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
62 2 0.02
63 78 0.92
64 5 0.06
ACGTcount: A:0.50, C:0.07, G:0.32, T:0.11
Consensus pattern (63 bp):
AAGGAAAAGCCTTTGAAGGAAAGGGAAAACGTTAACAAACAGAATGGAAAGAAGAGGAGAGCA
Found at i:314649 original size:57 final size:58
Alignment explanation
Indices: 314508--314652 Score: 213
Period size: 63 Copynumber: 2.4 Consensus size: 58
314498 GAAAAATGTT
314508 AGCAAACAGAATGGAAAGAAGAGGAGAGCAAAGGAAAAGCCTTTGAAGGAAAGGGAAA
1 AGCAAACAGAATGGAAAGAAGAGGAGAGCAAAGGAAAAGCCTTTGAAGGAAAGGGAAA
314566 ACGTTAACAAACAGAATGGAAAGAAGAGGAGAGCAAAGGAAAAG-CTATTGAAGGAAAGGG-AA
1 A-G----CAAACAGAATGGAAAGAAGAGGAGAGCAAAGGAAAAGCCT-TTGAAGGAAAGGGAAA
*
314628 AGCAAACAGAACGGAAAGAAGAGGA
1 AGCAAACAGAATGGAAAGAAGAGGA
314653 AAAGCTTTTG
Statistics
Matches: 80, Mismatches: 1, Indels: 13
0.85 0.01 0.14
Matches are distributed among these distances:
57 22 0.28
58 1 0.01
59 1 0.01
61 1 0.01
62 5 0.06
63 50 0.62
ACGTcount: A:0.52, C:0.09, G:0.32, T:0.07
Consensus pattern (58 bp):
AGCAAACAGAATGGAAAGAAGAGGAGAGCAAAGGAAAAGCCTTTGAAGGAAAGGGAAA
Found at i:316397 original size:4 final size:4
Alignment explanation
Indices: 316388--316419 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
316378 TTTCTAAACG
316388 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
316420 TGTAATATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:319904 original size:4 final size:4
Alignment explanation
Indices: 319895--319923 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
319885 TGGCATTCAT
319895 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
319924 GGTTTAACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:321300 original size:6 final size:6
Alignment explanation
Indices: 321289--321313 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
321279 CCGAAAGCAC
321289 CAAAAG CAAAAG CAAAAG CAAAAG C
1 CAAAAG CAAAAG CAAAAG CAAAAG C
321314 GAGCTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.20, G:0.16, T:0.00
Consensus pattern (6 bp):
CAAAAG
Found at i:323500 original size:25 final size:25
Alignment explanation
Indices: 323466--323518 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
323456 GGCTTAGGTC
323466 ATCCAGGGTTTAATTTTCAAGTAAA
1 ATCCAGGGTTTAATTTTCAAGTAAA
323491 ATCCAGGGTTTAATTTTCAAGTAAA
1 ATCCAGGGTTTAATTTTCAAGTAAA
323516 ATC
1 ATC
323519 AGTTTAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (25 bp):
ATCCAGGGTTTAATTTTCAAGTAAA
Found at i:326019 original size:2 final size:2
Alignment explanation
Indices: 326012--326040 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
326002 CCATATAAAT
326012 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
326041 TAAAAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:326344 original size:13 final size:13
Alignment explanation
Indices: 326326--326368 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
326316 TTAATATAAT
326326 TTAATTCATATCA
1 TTAATTCATATCA
326339 TTAATT-ATA--A
1 TTAATTCATATCA
326349 TTTAATTCATATCA
1 -TTAATTCATATCA
326363 TTAATT
1 TTAATT
326369 ATTCGTGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 1 0.04
11 6 0.23
12 6 0.23
13 12 0.46
14 1 0.04
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAATTCATATCA
Found at i:326348 original size:24 final size:24
Alignment explanation
Indices: 326316--326370 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
326306 AAGTTTTTAT
326316 TTAA-TATAATTTAATTCATATCA
1 TTAATTATAATTTAATTCATATCA
326339 TTAATTATAATTTAATTCATATCA
1 TTAATTATAATTTAATTCATATCA
326363 TTAATTAT
1 TTAATTAT
326371 TCGTGTAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.13
24 27 0.87
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAATTATAATTTAATTCATATCA
Found at i:327078 original size:18 final size:17
Alignment explanation
Indices: 327057--327090 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
327047 AAAAACGCAA
327057 AGAAAACAAATAAAAATG
1 AGAAAA-AAATAAAAATG
*
327075 AGAAAAATATAAAAAT
1 AGAAAAAAATAAAAAT
327091 ATAAAAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.15
Consensus pattern (17 bp):
AGAAAAAAATAAAAATG
Found at i:337021 original size:25 final size:25
Alignment explanation
Indices: 336993--337050 Score: 62
Period size: 29 Copynumber: 2.2 Consensus size: 25
336983 ATCTTAGGGG
*
336993 TAAGTCTTTGTTTTCTCTTGTCCTT
1 TAAGTCTTTGCTTTCTCTTGTCCTT
*
337018 TAAGGGTGTGTTTGCTTTCTCTTGTCCTT
1 TAA----GTCTTTGCTTTCTCTTGTCCTT
337047 TAAG
1 TAAG
337051 GGTGTGTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
25 4 0.15
29 23 0.85
ACGTcount: A:0.10, C:0.17, G:0.19, T:0.53
Consensus pattern (25 bp):
TAAGTCTTTGCTTTCTCTTGTCCTT
Found at i:337041 original size:29 final size:29
Alignment explanation
Indices: 336999--337060 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
336989 GGGGTAAGTC
*
336999 TTTGTTTTCTCTTGTCCTTTAAGGGTGTG
1 TTTGCTTTCTCTTGTCCTTTAAGGGTGTG
337028 TTTGCTTTCTCTTGTCCTTTAAGGGTGTG
1 TTTGCTTTCTCTTGTCCTTTAAGGGTGTG
337057 TTTG
1 TTTG
337061 GTTGGGGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.06, C:0.15, G:0.24, T:0.55
Consensus pattern (29 bp):
TTTGCTTTCTCTTGTCCTTTAAGGGTGTG
Found at i:338031 original size:21 final size:21
Alignment explanation
Indices: 338007--338075 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
337997 ATTGACAAGT
338007 TGAAAGATCGTGGAGAATGAA
1 TGAAAGATCGTGGAGAATGAA
* ** * * *
338028 TGAATGATTATTGACAA--AT
1 TGAAAGATCGTGGAGAATGAA
*
338047 TGAAAGATCGTGGGGAATGAA
1 TGAAAGATCGTGGAGAATGAA
338068 TGAAAGAT
1 TGAAAGAT
338076 GTACAATGAA
Statistics
Matches: 33, Mismatches: 13, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
19 12 0.36
21 21 0.64
ACGTcount: A:0.42, C:0.04, G:0.29, T:0.25
Consensus pattern (21 bp):
TGAAAGATCGTGGAGAATGAA
Found at i:338050 original size:40 final size:40
Alignment explanation
Indices: 337995--338071 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
337985 GTTTAGATGG
*
337995 TTATTGACAAGTTGAAAGATCGTGGAGAATGAATGAATGA
1 TTATTGACAAATTGAAAGATCGTGGAGAATGAATGAATGA
*
338035 TTATTGACAAATTGAAAGATCGTGGGGAATGAATGAA
1 TTATTGACAAATTGAAAGATCGTGGAGAATGAATGAA
338072 AGATGTACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.40, C:0.05, G:0.27, T:0.27
Consensus pattern (40 bp):
TTATTGACAAATTGAAAGATCGTGGAGAATGAATGAATGA
Found at i:354078 original size:17 final size:19
Alignment explanation
Indices: 354070--354114 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
354060 TCAACGGTCG
354070 GGTCGGGTCGGGTC-A-AC
1 GGTCGGGTCGGGTCGATAC
* *
354087 GGTCGCGTCGGGTCGATAG
1 GGTCGGGTCGGGTCGATAC
354106 GGTCGGGTC
1 GGTCGGGTC
354115 AGACCGGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 13 0.57
18 1 0.04
19 9 0.39
ACGTcount: A:0.09, C:0.22, G:0.49, T:0.20
Consensus pattern (19 bp):
GGTCGGGTCGGGTCGATAC
Found at i:354083 original size:22 final size:22
Alignment explanation
Indices: 354058--354101 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
354048 GGAAGTCAAC
*
354058 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGCGTCGGGTCG
354080 GGTCAACGGTCGCGTCGGGTCG
1 GGTCAACGGTCGCGTCGGGTCG
354102 ATAGGGTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGCGTCGGGTCG
Found at i:354148 original size:10 final size:9
Alignment explanation
Indices: 354111--354160 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
354101 GATAGGGTCG
*
354111 GGTCAGACC
1 GGTCAAACC
354120 GGTCAAACC
1 GGTCAAACC
*
354129 GGTTCGAACC
1 GG-TCAAACC
*
354139 GGTAGAAACC
1 GGT-CAAACC
354149 GGTCAAACC
1 GGTCAAACC
354158 GGT
1 GGT
354161 TTCCAGCCCT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:361442 original size:17 final size:17
Alignment explanation
Indices: 361420--361457 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
361410 AACGGTCAAC
361420 GGTCAACGGTCGCGTCG
1 GGTCAACGGTCGCGTCG
361437 GGTCAACGGTCGCGTCG
1 GGTCAACGGTCGCGTCG
361454 GGTC
1 GGTC
361458 TGTAGGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.29, G:0.42, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGCGTCG
Found at i:371919 original size:20 final size:21
Alignment explanation
Indices: 371894--371986 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
371884 TTTTCCCAAT
*
371894 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
371914 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
371935 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
371955 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
371976 TCGCAATGCGA
1 TCGCAATGCGA
371987 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:371939 original size:41 final size:41
Alignment explanation
Indices: 371894--371986 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
371884 TTTTCCCAAT
371894 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
371935 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
371976 TCGCAATGCGA
1 TCGCAATGCGA
371987 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:371999 original size:41 final size:41
Alignment explanation
Indices: 371913--372047 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
371903 GAATAAGTAA
* *
371913 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
371954 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
371995 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
372036 TTCGCAACGCGA
1 ATCGCAACGCGA
372048 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:372000 original size:20 final size:20
Alignment explanation
Indices: 371975--372089 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
371965 AATTGGGAAA
*
371975 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
371995 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
372016 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
372036 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
372056 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
372076 TTCGCAACGCGATA
1 ATCGCAACGCGATA
372090 ATACATAATC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 65 0.82
21 14 0.18
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:372048 original size:41 final size:41
Alignment explanation
Indices: 371972--372109 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
371962 GCGAATTGGG
* * *
371972 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* * * *
372013 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACT-G
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
*** * *
372053 ACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* *
372094 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
372110 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
Found at i:372305 original size:22 final size:22
Alignment explanation
Indices: 372277--372320 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
372267 CACTCTCTCA
372277 CCCATCTCCGACAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
372299 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
372321 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.45, G:0.11, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:372621 original size:20 final size:20
Alignment explanation
Indices: 372598--372640 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
372588 GATAGTCGAA
372598 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
372618 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
372638 TTC
1 TTC
372641 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:373979 original size:18 final size:18
Alignment explanation
Indices: 373958--374002 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
373948 TCCACTTCGG
*
373958 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
373976 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
373994 GAGCCATCA
1 GAGCCATCA
374003 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:374552 original size:14 final size:14
Alignment explanation
Indices: 374533--374590 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
374523 ATGTGAAATG
374533 AAAATCGCAACGAA
1 AAAATCGCAACGAA
374547 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAA
*
374563 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAA
374579 AAAATCGCAACG
1 AAAATCGCAACG
374591 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:374574 original size:32 final size:33
Alignment explanation
Indices: 374517--374607 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
374507 GGAAATGGAT
* *
374517 ATCGTAATGTGAAATGAAAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
374550 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
374582 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
374608 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.57
33 23 0.43
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:374601 original size:19 final size:19
Alignment explanation
Indices: 374478--374612 Score: 76
Period size: 19 Copynumber: 7.6 Consensus size: 19
374468 TAGTTTACTT
* **
374478 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
* *
374498 TCGCAACGCGGAAATGGATA
1 TCGCAACGC-GAAATGAAAA
* * *
374518 TCGTAATGTGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
374537 TCGCAA--CG-AA--AAAA
1 TCGCAACGCGAAATGAAAA
*
374551 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
374569 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
374583 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
374602 TCGCAATGCGA
1 TCGCAACGCGA
374613 TTTGTGTTTC
Statistics
Matches: 90, Mismatches: 13, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
14 20 0.22
16 8 0.09
17 3 0.03
18 10 0.11
19 27 0.30
20 21 0.23
21 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:374643 original size:14 final size:14
Alignment explanation
Indices: 374624--374681 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
374614 TTGTGTTTCG
374624 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
374638 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
374654 CACGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
374670 CGTTGCGATTTT
1 CGTTGCGATTTT
374682 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:374663 original size:32 final size:33
Alignment explanation
Indices: 374619--374697 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
374609 GCGATTTGTG
374619 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
374651 TTTCACGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
374684 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
374698 AGCCATTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 26 0.60
33 17 0.40
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:374696 original size:19 final size:19
Alignment explanation
Indices: 374670--374736 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
374660 GCGATTTTGT
**
374670 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
374689 CATTGCGATAGCCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
374709 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
374728 CGTTGCGAT
1 CGTTGCGAT
374737 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:374709 original size:20 final size:19
Alignment explanation
Indices: 374682--374736 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
374672 TTGCGATTTT
*
374682 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
374701 CATTTTCGCGTTGCGATAGT
1 CA-TTTCGCGTTGCGATAGC
374721 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
374737 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:376627 original size:14 final size:14
Alignment explanation
Indices: 376608--376643 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
376598 ATTGTTTAAT
376608 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
376622 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
376636 TGATTTGT
1 TGATTTGT
376644 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:376782 original size:19 final size:19
Alignment explanation
Indices: 376760--376804 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
376750 ATCGCAACGA
*
376760 GAAAATCATAATGCGAAAT
1 GAAAATCACAATGCGAAAT
*
376779 GAAAATCGCAATGCGAAAT
1 GAAAATCACAATGCGAAAT
*
376798 AAAAATC
1 GAAAATC
376805 GCAACGAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (19 bp):
GAAAATCACAATGCGAAAT
Found at i:376805 original size:19 final size:19
Alignment explanation
Indices: 376769--376808 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
376759 AGAAAATCAT
*
376769 AATGCGAAATGAAAATCGC
1 AATGCGAAATAAAAATCGC
376788 AATGCGAAATAAAAATCGC
1 AATGCGAAATAAAAATCGC
376807 AA
1 AA
376809 CGAGAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.15, G:0.17, T:0.15
Consensus pattern (19 bp):
AATGCGAAATAAAAATCGC
Found at i:376815 original size:19 final size:19
Alignment explanation
Indices: 376774--376815 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
376764 ATCATAATGC
* * *
376774 GAAATGAAAATCGCAATGC
1 GAAATAAAAATCGCAACGA
376793 GAAATAAAAATCGCAACGA
1 GAAATAAAAATCGCAACGA
376812 GAAA
1 GAAA
376816 ATCGCAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.14, G:0.19, T:0.12
Consensus pattern (19 bp):
GAAATAAAAATCGCAACGA
Found at i:376871 original size:20 final size:20
Alignment explanation
Indices: 376846--376903 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
376836 TCGCATTGCG
* *
376846 ATTTTCTCGTTGTGATAGCC
1 ATTTTCGCGTTGCGATAGCC
376866 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
376886 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
376904 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:378011 original size:24 final size:24
Alignment explanation
Indices: 377955--378013 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
377945 AGTCAGTATT
* *
377955 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
377979 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
378003 CGAATTTTGAT
1 CGAAATTTGAT
378014 GATGTTTCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:378205 original size:12 final size:12
Alignment explanation
Indices: 378188--378212 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
378178 ATATAATCCT
378188 GAAGAAGAAAAA
1 GAAGAAGAAAAA
378200 GAAGAAGAAAAA
1 GAAGAAGAAAAA
378212 G
1 G
378213 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:380525 original size:19 final size:19
Alignment explanation
Indices: 380503--380633 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
380493 GGAAATTACT
380503 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
380522 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
380536 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
380555 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
380569 TTCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
380588 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
380602 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
380621 ATCGCAACGCGAA
1 ATCGCAATGCGAA
380634 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 5 0.06
17 5 0.06
18 3 0.04
19 39 0.48
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:380545 original size:33 final size:33
Alignment explanation
Indices: 380503--380629 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
380493 GGAAATTACT
380503 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
380536 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
380568 TTTCGCAATGCAAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
380602 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
380630 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:380610 original size:66 final size:66
Alignment explanation
Indices: 380504--380636 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
380494 GAAATTACTA
* *
380504 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
380569 T
66 T
*
380570 TCGCAATGCAAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
380635 T
66 T
380636 T
1 T
380637 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:380811 original size:14 final size:14
Alignment explanation
Indices: 380792--380828 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
380782 CATCAATTAA
380792 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
380806 ACAAATCACCTTTT
1 ACAAATCAACTTTT
380820 ACAAATCAA
1 ACAAATCAA
380829 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:384384 original size:33 final size:33
Alignment explanation
Indices: 384327--384425 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
384317 ACGAGATAAT
* *
384327 GAGAATCACAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
384361 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
384394 GATAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
384426 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:384419 original size:19 final size:19
Alignment explanation
Indices: 384302--384481 Score: 155
Period size: 19 Copynumber: 9.8 Consensus size: 19
384292 TCTTTTGGTT
*
384302 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
384321 GATAATGAGAATCACAACGC
1 GA-AATGAAAATCGCAACGC
**
384341 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
384359 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
384375 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
384393 ---A-GATAATCGCAACGC
1 GAAATGAAAATCGCAACGC
384408 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
384428 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
384447 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
384466 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
384482 TGCAATTTTT
Statistics
Matches: 130, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 18 0.14
15 3 0.02
16 2 0.02
17 1 0.01
18 4 0.03
19 57 0.44
20 43 0.33
21 2 0.02
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:384440 original size:39 final size:38
Alignment explanation
Indices: 384397--384481 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 38
384387 GCGACCAGAT
384397 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
384436 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
384474 AATCGCAA
1 AATCGCAA
384482 TGCAATTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 19 0.41
39 27 0.59
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:384509 original size:19 final size:19
Alignment explanation
Indices: 384487--384523 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
384477 CGCAATGCAA
*
384487 TTTTTGTTTCGCGTTGCGT
1 TTTTTATTTCGCGTTGCGT
384506 TTTTTATTTCGCGTTGCG
1 TTTTTATTTCGCGTTGCG
384524 ATTATCTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.24, T:0.57
Consensus pattern (19 bp):
TTTTTATTTCGCGTTGCGT
Found at i:385150 original size:20 final size:20
Alignment explanation
Indices: 385125--385174 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
385115 TTGTATTATT
385125 GCATTGCGATAGTAAGTATC
1 GCATTGCGATAGTAAGTATC
*
385145 GCATTGCGATAGTCAGTATC
1 GCATTGCGATAGTAAGTATC
385165 GCATTGCGAT
1 GCATTGCGAT
385175 TTTCCCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (20 bp):
GCATTGCGATAGTAAGTATC
Found at i:385658 original size:21 final size:19
Alignment explanation
Indices: 385624--385662 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
385614 ATTGAATTTA
385624 TTCAAAAAATTTCAAAGTT
1 TTCAAAAAATTTCAAAGTT
385643 TTCAAAAAATAATTCAAAGT
1 TTCAAAAAAT--TTCAAAGT
385663 CCATTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
TTCAAAAAATTTCAAAGTT
Found at i:386044 original size:21 final size:19
Alignment explanation
Indices: 386014--386058 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
386004 TATTTTGCAG
*
386014 AGAAAACATCCCCAAACGGCT
1 AGAAAACAT-CCC-AACAGCT
*
386035 AGAAATCATCCCAACAGCT
1 AGAAAACATCCCAACAGCT
386054 AGAAA
1 AGAAA
386059 CAACCACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 3 0.14
21 8 0.36
ACGTcount: A:0.47, C:0.29, G:0.13, T:0.11
Consensus pattern (19 bp):
AGAAAACATCCCAACAGCT
Found at i:387390 original size:20 final size:20
Alignment explanation
Indices: 387351--387390 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
387341 GTCATCCTAT
**
387351 TCACTGATAATCTTTTATTC
1 TCACTGATAATCTTACATTC
*
387371 TCACTGGTAATCTTACATTC
1 TCACTGATAATCTTACATTC
387391 CGTGAACCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (20 bp):
TCACTGATAATCTTACATTC
Found at i:395293 original size:37 final size:37
Alignment explanation
Indices: 395238--395309 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
395228 GAGATAATTT
*
395238 AGAATATTACGAAAATTAAGCTCTAGAAAACAGATGC
1 AGAATATTACGAAAATTAAGATCTAGAAAACAGATGC
* *
395275 AGAATATTACTAATATTAAGATCTAGAAAACAGAT
1 AGAATATTACGAAAATTAAGATCTAGAAAACAGAT
395310 CTGCACAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (37 bp):
AGAATATTACGAAAATTAAGATCTAGAAAACAGATGC
Found at i:395795 original size:75 final size:75
Alignment explanation
Indices: 395695--395843 Score: 235
Period size: 75 Copynumber: 2.0 Consensus size: 75
395685 GTCAATGTCA
* * * * *
395695 CGCTCCCTCTCTTGCTCGCGCTCACTCTCGTGCCTCCTCAACCTACTACTGCTTCTCTCTCTCCT
1 CGCTCCCTCTCTAGCTCACGATCACTCTCATGCCTCCTCAACCTACTACTGCTTCTCTCCCTCCT
395760 ATCTCTCTCC
66 ATCTCTCTCC
* *
395770 CGCTCCCTCTCTAGCTCACGATCACTCTCATGCCTCCTCGACCTACTGCTGCTTCTCTCCCTCCT
1 CGCTCCCTCTCTAGCTCACGATCACTCTCATGCCTCCTCAACCTACTACTGCTTCTCTCCCTCCT
395835 ATCTCTCTC
66 ATCTCTCTC
395844 AATCTCACGA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.09, C:0.48, G:0.09, T:0.34
Consensus pattern (75 bp):
CGCTCCCTCTCTAGCTCACGATCACTCTCATGCCTCCTCAACCTACTACTGCTTCTCTCCCTCCT
ATCTCTCTCC
Found at i:395906 original size:63 final size:63
Alignment explanation
Indices: 395761--395906 Score: 186
Period size: 63 Copynumber: 2.3 Consensus size: 63
395751 CTCTCTCCTA
* * *
395761 TCTCTCTCCCGCTCCCTCTCTAGCTCACGATCACTCTCATGCCTCCTCGACCTACTGCTGCTTC
1 TCTCTCTCCC-TTCCCTCTCAAGCTCACGATCACTCTCATGCCTCCTCGACCTACTGCTACTTC
* * * * * *
395825 TCTCCCT-CCTATCTCTCTCAATCTCACGATCACTTTCGTGCCTTCTCGACCTACTGCTACTTC
1 TCTCTCTCCCT-TCCCTCTCAAGCTCACGATCACTCTCATGCCTCCTCGACCTACTGCTACTTC
395888 TCTCTCTCCCTTCCCTCTC
1 TCTCTCTCCCTTCCCTCTC
395907 TTTCTCCTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 60 0.87
64 9 0.13
ACGTcount: A:0.11, C:0.46, G:0.08, T:0.35
Consensus pattern (63 bp):
TCTCTCTCCCTTCCCTCTCAAGCTCACGATCACTCTCATGCCTCCTCGACCTACTGCTACTTC
Found at i:396196 original size:3 final size:3
Alignment explanation
Indices: 396190--396222 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
396180 TCCTCCGTCT
396190 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
396223 GAATCTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:397292 original size:22 final size:22
Alignment explanation
Indices: 397262--397304 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
397252 CACACATGCA
* *
397262 TTAATGAAGAAATTTTCAATTT
1 TTAAAGAAGAAAATTTCAATTT
*
397284 TTAAAGAAGAAAATTTGAATT
1 TTAAAGAAGAAAATTTCAATT
397305 CCATAATATT
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:0.47, C:0.02, G:0.12, T:0.40
Consensus pattern (22 bp):
TTAAAGAAGAAAATTTCAATTT
Found at i:398943 original size:27 final size:27
Alignment explanation
Indices: 398913--398966 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
398903 AGTTGAGCAG
398913 CTGCTTCCTGGTGTGCATGAAAGATGA
1 CTGCTTCCTGGTGTGCATGAAAGATGA
398940 CTGCTTCCTGGTGTGCATGAAAGATGA
1 CTGCTTCCTGGTGTGCATGAAAGATGA
398967 TAGTATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (27 bp):
CTGCTTCCTGGTGTGCATGAAAGATGA
Found at i:402301 original size:33 final size:33
Alignment explanation
Indices: 402233--402331 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
402223 CCCATCTGCA
* * **
402233 AAGTTGGCTACCTACCAAAGATGAATTTTTTAAT
1 AAGTTGGCCACCAACC-AAGATGAATTTTCCAAT
*
402267 AAGTTGGCCACCAACCAAGATGAAATTTCCAAT
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
*
402300 AAGTTGGCCACCAACTAAGATGAATTTTCCAA
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
402332 CTTACCAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
Found at i:410293 original size:2 final size:2
Alignment explanation
Indices: 410286--410321 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
410276 AGCCAAAATA
410286 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
410322 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:411404 original size:20 final size:21
Alignment explanation
Indices: 411364--411405 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
411354 TGTTGGTATG
411364 TATCGATACCATTAAAATATA
1 TATCGATACCATTAAAATATA
411385 TATCGATA-CA-TAATAATATA
1 TATCGATACCATTAA-AATATA
411405 T
1 T
411406 CAGGTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.15
20 9 0.45
21 8 0.40
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.36
Consensus pattern (21 bp):
TATCGATACCATTAAAATATA
Found at i:417791 original size:20 final size:20
Alignment explanation
Indices: 417766--417816 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
417756 TTCCTTGAAT
417766 GTGTATCGATACACTCAGGA
1 GTGTATCGATACACTCAGGA
417786 GTGTATCGATACACTCAGGA
1 GTGTATCGATACACTCAGGA
* *
417806 CTGTACCGATA
1 GTGTATCGATA
417817 TACCCGTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (20 bp):
GTGTATCGATACACTCAGGA
Found at i:420096 original size:45 final size:45
Alignment explanation
Indices: 420047--420143 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 45
420037 AAAAAGGGAG
* *
420047 AAAAT-AAAAT-AAACTAAGGGGGAGTAATTTTCAAAAATGATTTCA
1 AAAATGAAAATCAAAATAAGGGGGAATAATTTTC--AAATGATTTCA
*** *
420092 AAAATGATTTTCAAAATAAGGGGGAATAATTTTCAATTGATTTCA
1 AAAATGAAAATCAAAATAAGGGGGAATAATTTTCAAATGATTTCA
420137 AAAATGA
1 AAAATGA
420144 TTTTCAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
45 22 0.50
46 2 0.05
47 20 0.45
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.30
Consensus pattern (45 bp):
AAAATGAAAATCAAAATAAGGGGGAATAATTTTCAAATGATTTCA
Done.