Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008310.1 Hibiscus syriacus cultivar Beakdansim tig00111000_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: 3887810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 15
Found at i:3292128 original size:39 final size:39
Alignment explanation
Indices: 3292039--3292119 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
3292029 AATCAGGTAG
* *
3292039 TAATAAT-TA-ATACATATGCTTAACTAATGATAATAAT
1 TAATAATATATATACATATGCATAACTAATAATAATAAT
3292076 TAATAATATATATACATATGCATAACTAATAACTAATAAT
1 TAATAATATATATACATATGCATAACTAATAA-TAATAAT
3292116 TAAT
1 TAAT
3292120 GCTTATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
37 7 0.18
38 2 0.05
39 19 0.49
40 11 0.28
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (39 bp):
TAATAATATATATACATATGCATAACTAATAATAATAAT
Found at i:3292238 original size:2 final size:2
Alignment explanation
Indices: 3292231--3292287 Score: 73
Period size: 2 Copynumber: 29.0 Consensus size: 2
3292221 CTAACTAGTA
* *
3292231 AT AT AT AT AT AT AT AT AT GA- AA AT AC A- 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
3292272 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3292288 GTGAAAATAC
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.94
3 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3295923 original size:3 final size:3
Alignment explanation
Indices: 3295915--3295957 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
3295905 GAAAAAGGAA
3295915 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3295958 AAAAGGTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3297010 original size:39 final size:39
Alignment explanation
Indices: 3296787--3297020 Score: 202
Period size: 39 Copynumber: 6.2 Consensus size: 39
3296777 AATAATATAG
* *
3296787 TATAGTTTTT-GAAAA-C-ATTTTTGAAAAACATATAACA
1 TATAGTTTTTAAAAAATCGATTTTTG-AAAACATATAATA
* * * *
3296824 TATAATTTTTAGAAAAT-GATTTTTGAAAGCATATAATT
1 TATAGTTTTTAAAAAATCGATTTTTGAAAACATATAATA
*
3296862 TATAGTTTTTTAAAAAA-CGATTTTTGAAAATATAT-ATAA
1 TATAG-TTTTTAAAAAATCGATTTTTGAAAACATATAAT-A
* * * * *
3296901 CATGGTTTTGAAAACA-C-ATTTTTGAAAACATATAATT
1 TATAGTTTTTAAAAAATCGATTTTTGAAAACATATAATA
* * * *
3296938 TAT-GGTTTTGAAACAT--ATTTTTGAAAACGTATAATA
1 TATAGTTTTTAAAAAATCGATTTTTGAAAACATATAATA
* *
3296974 TATAGTTTTTAAAAAATCGGTTTTGGAAAACATATAATA
1 TATAGTTTTTAAAAAATCGATTTTTGAAAACATATAATA
3297013 TATAGTTT
1 TATAGTTT
3297021 GAAAACATAT
Statistics
Matches: 159, Mismatches: 27, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
36 30 0.19
37 36 0.23
38 33 0.21
39 60 0.38
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (39 bp):
TATAGTTTTTAAAAAATCGATTTTTGAAAACATATAATA
Found at i:3297024 original size:22 final size:22
Alignment explanation
Indices: 3296999--3297042 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3296989 ATCGGTTTTG
3296999 GAAAACATATAATATATAGTTT
1 GAAAACATATAATATATAGTTT
3297021 GAAAACATATAATATATAGTTT
1 GAAAACATATAATATATAGTTT
3297043 TTAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (22 bp):
GAAAACATATAATATATAGTTT
Found at i:3297150 original size:15 final size:16
Alignment explanation
Indices: 3297124--3297156 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3297114 ATTTTCAGTA
3297124 TTTTAGTTTTTTGTAT
1 TTTTAGTTTTTTGTAT
3297140 TTTTAG-TTTTTGTAT
1 TTTTAGTTTTTTGTAT
3297155 TT
1 TT
3297157 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (16 bp):
TTTTAGTTTTTTGTAT
Found at i:3298566 original size:19 final size:18
Alignment explanation
Indices: 3298517--3298570 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
3298507 ACCTCTCTTT
* *
3298517 TAATAATTTTTAATTTAA
1 TAATTATTTTTTATTTAA
* *
3298535 TCATTGTTTTTTATTTAA
1 TAATTATTTTTTATTTAA
3298553 TAATTATTTGTTTATTTA
1 TAATTATTT-TTTATTTA
3298571 TTTTTATGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (18 bp):
TAATTATTTTTTATTTAA
Found at i:3312278 original size:15 final size:16
Alignment explanation
Indices: 3312249--3312279 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3312239 ACGAGGGGAG
3312249 TCATCCCATCACTCTA
1 TCATCCCATCACTCTA
3312265 TCATCCCA-CACTCTA
1 TCATCCCATCACTCTA
3312280 GGTAAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (16 bp):
TCATCCCATCACTCTA
Found at i:3312343 original size:2 final size:2
Alignment explanation
Indices: 3312332--3312384 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
3312322 GAGTCATCCC
3312332 TA TA -A 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 TA TA
3312373 TA TA TA TA TA TA
1 TA TA TA TA TA TA
3312385 GCAAATAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3314267 original size:13 final size:13
Alignment explanation
Indices: 3314245--3314274 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3314235 GAGATGAAAG
*
3314245 AAAGTGAAAGTGA
1 AAAGTAAAAGTGA
3314258 AAAGTAAAAGTGA
1 AAAGTAAAAGTGA
3314271 AAAG
1 AAAG
3314275 AAGATAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (13 bp):
AAAGTAAAAGTGA
Found at i:3328102 original size:37 final size:36
Alignment explanation
Indices: 3328059--3328372 Score: 262
Period size: 37 Copynumber: 8.4 Consensus size: 36
3328049 AGTAATATAG
*
3328059 TATAGTTTTTGAAAATATTTTTGAAAAAAATATAATA
1 TATAGTTTTTGAAAATATTTTTG-AAAACATATAATA
* *
3328096 TATAGTTTTT-AGAAATGGTTTTTGAAAGCATATAATA
1 TATAGTTTTTGA-AAAT-ATTTTTGAAAACATATAATA
* *
3328133 TATAGTTTTTTAAAATATATTTTTTGAAAATATAT-ATA
1 TATAG-TTTTTGAAA-ATA-TTTTTGAAAACATATAATA
* * *
3328171 -ACATGGTTTTGAAAACACTTTTTGAAAACATATAATA
1 TATA-GTTTTTGAAAATA-TTTTTGAAAACATATAATA
*
3328208 TATAG-TTTTGAAAACATGTTTTTGAAAACGTATATAATA
1 TATAGTTTTTG-AAA-ATATTTTTGAAAAC--ATATAATA
* * *
3328247 TGTAATTTTTAGAAAATTGATTTTGGAAAACATATAATA
1 TATAGTTTTT-GAAAA-T-ATTTTTGAAAACATATAATA
* * *
3328286 TATA-ATTTTGAAAACACATTTTTAAAAACATATAATA
1 TATAGTTTTTG-AAA-ATATTTTTGAAAACATATAATA
* * *
3328323 TCTAGTTTTTAAAAATATTTTTGAAAACGTAT-ATAA
1 TATAGTTTTTGAAAATATTTTTGAAAACATATAAT-A
3328359 TATAGTTTTTGAAA
1 TATAGTTTTTGAAA
3328373 GTGTATTTTT
Statistics
Matches: 224, Mismatches: 32, Indels: 43
0.75 0.11 0.14
Matches are distributed among these distances:
35 2 0.01
36 50 0.22
37 82 0.37
38 31 0.14
39 40 0.18
40 8 0.04
41 11 0.05
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (36 bp):
TATAGTTTTTGAAAATATTTTTGAAAACATATAATA
Found at i:3328151 original size:17 final size:16
Alignment explanation
Indices: 3328129--3328169 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
3328119 GAAAGCATAT
*
3328129 AATATATAGTTTTTTAA
1 AATATATA-TTTTTGAA
3328146 AATATAT-TTTTTGAA
1 AATATATATTTTTGAA
3328161 AATATATAT
1 AATATATAT
3328170 AACATGGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 14 0.64
16 1 0.05
17 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
AATATATATTTTTGAA
Found at i:3328193 original size:36 final size:37
Alignment explanation
Indices: 3328153--3328372 Score: 141
Period size: 36 Copynumber: 5.9 Consensus size: 37
3328143 TAAAATATAT
* *
3328153 TTTTTGAAAATATATATAACATGGTTTTGAAAACA-C
1 TTTTTGAAAACATATATAACATAGTTTTGAAAACATC
* *
3328189 TTTTTGAAAACATATA-ATATATAGTTTTGAAAACATG
1 TTTTTGAAAACATATATA-ACATAGTTTTGAAAACATC
* * * *
3328226 TTTTTGAAAACGTATATAATATGTAATTTTTAGAAA-AT-
1 TTTTTGAAAACATATATAACA--TAGTTTTGA-AAACATC
* *
3328264 TGATTTTGGAAAACATATA-ATATATAATTTTGAAAACA-C
1 T--TTTT-GAAAACATATATA-ACATAGTTTTGAAAACATC
* * * *
3328303 ATTTTTAAAAACATATAATATC-TAGTTTTTAAAA-ATA
1 -TTTTTGAAAACATAT-ATAACATAGTTTTGAAAACATC
* *
3328340 TTTTTGAAAACGTATATAATATAGTTTTTGAAA
1 TTTTTGAAAACATATATAACATAG-TTTTGAAA
3328373 GTGTATTTTT
Statistics
Matches: 146, Mismatches: 20, Indels: 35
0.73 0.10 0.17
Matches are distributed among these distances:
35 4 0.03
36 47 0.32
37 44 0.30
38 10 0.07
39 19 0.13
40 9 0.06
41 13 0.09
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (37 bp):
TTTTTGAAAACATATATAACATAGTTTTGAAAACATC
Found at i:3328295 original size:78 final size:73
Alignment explanation
Indices: 3328075--3328362 Score: 231
Period size: 78 Copynumber: 3.8 Consensus size: 73
3328065 TTTTGAAAAT
* * * * * * *
3328075 ATTTTTGAAAAAAATATAATATATAGTTTTTAGAAATGGTTTTTGAAAGCATATAATATATAGTT
1 ATTTTT-AAAAACATATAATATCTAATTTTTAAAAAT-ATTTTTGAAAACATATAATATATA-AT
* * *
3328140 TTTTAAAATAT
63 TTTGAAAACAC
** * * * *
3328151 ATTTTTTGAAA-ATAT-ATAT-AACATGGTTTTGAAAACACTTTTTGAAAACATATAATATATAG
1 ATTTTTAAAAACATATAATATCTA-AT--TTTTAAAAATA-TTTTTGAAAACATATAATATATAA
*
3328213 TTTTGAAAACAT
62 TTTTGAAAACAC
* * * *
3328225 GTTTTTGAAAACGTATATAATATGTAATTTTTAGAAAATTGATTTTGGAAAACATATAATATATA
1 ATTTTTAAAAAC--ATATAATATCTAATTTTTA-AAAA-T-ATTTTTGAAAACATATAATATATA
3328290 ATTTTGAAAACAC
61 ATTTTGAAAACAC
*
3328303 ATTTTTAAAAACATATAATATCTAGTTTTTAAAAATATTTTTGAAAACGTATATAATATA
1 ATTTTTAAAAACATATAATATCTAATTTTTAAAAATATTTTTGAAAAC--ATATAATATA
3328363 GTTTTTGAAA
Statistics
Matches: 172, Mismatches: 26, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
72 1 0.01
73 16 0.09
74 23 0.13
75 46 0.27
76 27 0.16
77 8 0.05
78 49 0.28
79 2 0.01
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (73 bp):
ATTTTTAAAAACATATAATATCTAATTTTTAAAAATATTTTTGAAAACATATAATATATAATTTT
GAAAACAC
Found at i:3328297 original size:114 final size:113
Alignment explanation
Indices: 3328065--3328362 Score: 347
Period size: 114 Copynumber: 2.6 Consensus size: 113
3328055 ATAGTATAGT
* * * *
3328065 TTTTGAAAATA-TTTTTGAAAAAAATATAATATATAGTTTTTAGAAATGGTTTTTG-AAA-GCAT
1 TTTTGAAAACACTTTTTG-AAAACATATAATATATAGTTTTTAAAAAT-GTTTTTGAAAACGTAT
* * * * **
3328127 ATAATATATAGTTTTTTAAAATATATTTTTTGAAAATATATATAACATGG
64 ATAATATATAATTTTTGAAAATATATTTTTGGAAAACATATATAACATAA
*
3328177 TTTTGAAAACACTTTTTGAAAACATATAATATATAGTTTTGAAAACATGTTTTTGAAAACGTATA
1 TTTTGAAAACACTTTTTGAAAACATATAATATATAGTTTTTAAAA-ATGTTTTTGAAAACGTATA
* *
3328242 TAATATGTAATTTTTAGAAAAT-TGA-TTTTGGAAAACATATA-ATATATAA
65 TAATATATAATTTTT-GAAAATAT-ATTTTTGGAAAACATATATA-ACATAA
* * *
3328291 TTTTGAAAACACATTTTTAAAAACATATAATATCTAGTTTTTAAAAATATTTTTGAAAACGTATA
1 TTTTGAAAACAC-TTTTTGAAAACATATAATATATAGTTTTTAAAAATGTTTTTGAAAACGTATA
3328356 TAATATA
65 TAATATA
3328363 GTTTTTGAAA
Statistics
Matches: 160, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
112 41 0.26
113 12 0.08
114 71 0.44
115 36 0.22
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (113 bp):
TTTTGAAAACACTTTTTGAAAACATATAATATATAGTTTTTAAAAATGTTTTTGAAAACGTATAT
AATATATAATTTTTGAAAATATATTTTTGGAAAACATATATAACATAA
Found at i:3328449 original size:21 final size:21
Alignment explanation
Indices: 3328411--3328453 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3328401 TTAGTATTAG
*
3328411 TATTTTATTTTTGTTTTTATT
1 TATTTTATTTTTGCTTTTATT
3328432 TATTTTATTTATT-CTTTTATT
1 TATTTTATTT-TTGCTTTTATT
3328453 T
1 T
3328454 TTTGGTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (21 bp):
TATTTTATTTTTGCTTTTATT
Found at i:3329647 original size:19 final size:20
Alignment explanation
Indices: 3329625--3329671 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
3329615 AATTTGATCC
3329625 TTTAAATTTTATTTATTT-A
1 TTTAAATTTTATTTATTTCA
* *
3329644 TTT-ATTCTTTATTTATTTCT
1 TTTAAAT-TTTATTTATTTCA
3329664 TTTAAATT
1 TTTAAATT
3329672 AAGCATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
18 2 0.09
19 14 0.64
20 4 0.18
21 2 0.09
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTAAATTTTATTTATTTCA
Found at i:3329654 original size:11 final size:12
Alignment explanation
Indices: 3329632--3329665 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3329622 TCCTTTAAAT
*
3329632 TTTATTTATTTA
1 TTTATTTCTTTA
3329644 TTTA-TTCTTTA
1 TTTATTTCTTTA
3329655 TTTATTTCTTT
1 TTTATTTCTTT
3329666 TAAATTAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTCTTTA
Found at i:3329825 original size:19 final size:18
Alignment explanation
Indices: 3329779--3329829 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
3329769 CCTCTTTTAA
*
3329779 TATTTTTTAATTTAATCAT
1 TATTTTTT-ATTTAATAAT
*
3329798 TGTTTTTTATTTAATAAT
1 TATTTTTTATTTAATAAT
3329816 TATTTGTTTATTTA
1 TATTT-TTTATTTA
3329830 TTTTTATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
TATTTTTTATTTAATAAT
Found at i:3333018 original size:17 final size:17
Alignment explanation
Indices: 3332996--3333041 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
3332986 ATCCGAACCA
*
3332996 TTGACCGTTGATTGTCG
1 TTGACCGTTGACTGTCG
* *
3333013 TTGACCATTGGCTGTCG
1 TTGACCGTTGACTGTCG
3333030 TTGACCGTTGAC
1 TTGACCGTTGAC
3333042 GGTTAACTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (17 bp):
TTGACCGTTGACTGTCG
Found at i:3340615 original size:59 final size:59
Alignment explanation
Indices: 3340513--3340634 Score: 172
Period size: 59 Copynumber: 2.1 Consensus size: 59
3340503 CAGCAGGCTG
* ** * *
3340513 CATATTCGGGATTACACTAAAGGATACTTAGTGTATATTGTGGGCACGACCTTATGTGT
1 CATATTCGGGATTACACTAAAGGATACCTAGTACAAATAGTGGGCACGACCTTATGTGT
** *
3340572 CATATTCGGGATTGTACTTAAGGATACCTAGTACAAATAGTGGGCACGACCTTATGTGT
1 CATATTCGGGATTACACTAAAGGATACCTAGTACAAATAGTGGGCACGACCTTATGTGT
3340631 CATA
1 CATA
3340635 CACGGGTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (59 bp):
CATATTCGGGATTACACTAAAGGATACCTAGTACAAATAGTGGGCACGACCTTATGTGT
Found at i:3366335 original size:52 final size:52
Alignment explanation
Indices: 3366257--3366379 Score: 210
Period size: 52 Copynumber: 2.4 Consensus size: 52
3366247 TACTTTACGC
* * *
3366257 TGTAAGAGCATTGAGAGATCGCCTGGGGTTTTGGTAAAACATGTCTTGGTAT
1 TGTAAGAGCATCGAGAGATCACCTGGGGTTTTGGTAAAACATGTCTTGGCAT
*
3366309 TGTAAGAGCATCGAGAGATCACCTGGGGTTTTGGTAAAATATGTCTTGGCAT
1 TGTAAGAGCATCGAGAGATCACCTGGGGTTTTGGTAAAACATGTCTTGGCAT
3366361 TGTAAGAGCATCGAGAGAT
1 TGTAAGAGCATCGAGAGAT
3366380 AGCCTTTTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (52 bp):
TGTAAGAGCATCGAGAGATCACCTGGGGTTTTGGTAAAACATGTCTTGGCAT
Found at i:3367203 original size:39 final size:39
Alignment explanation
Indices: 3367152--3367320 Score: 146
Period size: 39 Copynumber: 4.3 Consensus size: 39
3367142 CATTAACCCT
* *
3367152 TTTATTGA-ACTCATCACCCTCACCTTAGGTGTTTTCT-CC
1 TTTATT-ACACTCATCATCCTCACCTTAGG-GTTTACTGCC
* ***
3367191 TTTATTACACTCAACATCCTCACCTTAGAAATTACTGCC
1 TTTATTACACTCATCATCCTCACCTTAGGGTTTACTGCC
* * *
3367230 TTTATTGCACTCACCATCCTCACCTT-GGGTATTACTGAC
1 TTTATTACACTCATCATCCTCACCTTAGGGT-TTACTGCC
* * *** *
3367269 TTTATTACACTCATCAACCTCACCCTAGAAATTATTGCC
1 TTTATTACACTCATCATCCTCACCTTAGGGTTTACTGCC
*
3367308 TTTATAACACTCA
1 TTTATTACACTCA
3367321 CCTAATAACA
Statistics
Matches: 104, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
38 6 0.06
39 97 0.93
40 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.08, T:0.36
Consensus pattern (39 bp):
TTTATTACACTCATCATCCTCACCTTAGGGTTTACTGCC
Found at i:3367251 original size:78 final size:78
Alignment explanation
Indices: 3367152--3367322 Score: 211
Period size: 78 Copynumber: 2.2 Consensus size: 78
3367142 CATTAACCCT
* * * * *
3367152 TTTATTGAACTCATCACCCTCACCTTAGGTGT-TTTCT-CCTTTATTACACTCAACATCCTCACC
1 TTTATTGCACTCACCACCCTCACCTT-GG-GTATTACTGACTTTATTACACTCAACAACCTCACC
*
3367215 TTAGAAATTACTGCC
64 CTAGAAATTACTGCC
* *
3367230 TTTATTGCACTCACCATCCTCACCTTGGGTATTACTGACTTTATTACACTCATCAACCTCACCCT
1 TTTATTGCACTCACCACCCTCACCTTGGGTATTACTGACTTTATTACACTCAACAACCTCACCCT
*
3367295 AGAAATTATTGCC
66 AGAAATTACTGCC
**
3367308 TTTATAACACTCACC
1 TTTATTGCACTCACC
3367323 TAATAACAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
76 2 0.03
77 6 0.08
78 72 0.90
ACGTcount: A:0.26, C:0.31, G:0.08, T:0.36
Consensus pattern (78 bp):
TTTATTGCACTCACCACCCTCACCTTGGGTATTACTGACTTTATTACACTCAACAACCTCACCCT
AGAAATTACTGCC
Found at i:3370993 original size:14 final size:14
Alignment explanation
Indices: 3370974--3371000 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3370964 TTGTAAGGGT
3370974 AAATGCAAATGTGA
1 AAATGCAAATGTGA
3370988 AAATGCAAATGTG
1 AAATGCAAATGTG
3371001 GGATACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (14 bp):
AAATGCAAATGTGA
Found at i:3374127 original size:11 final size:10
Alignment explanation
Indices: 3374106--3374162 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
3374096 CTCATATATT
3374106 TAAAAATCAA
1 TAAAAATCAA
3374116 TAAAAATACAA
1 TAAAAAT-CAA
*
3374127 TAAAAA-GAA
1 TAAAAATCAA
* *
3374136 TTAAAAGTGAA
1 -TAAAAATCAA
*
3374147 TAAAATTCAA
1 TAAAAATCAA
3374157 TAAAAA
1 TAAAAA
3374163 AGAATGTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 2 0.05
10 25 0.64
11 12 0.31
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (10 bp):
TAAAAATCAA
Found at i:3374149 original size:31 final size:31
Alignment explanation
Indices: 3374109--3374172 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
3374099 ATATATTTAA
3374109 AAATCAATAAAAATACAAT-AAAAAGAATTAA
1 AAATCAAT-AAAATACAATAAAAAAGAATTAA
* * *
3374140 AAGTGAATAAAATTCAATAAAAAAGAATGTAA
1 AAATCAATAAAATACAATAAAAAAGAAT-TAA
3374172 A
1 A
3374173 GCTAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 9 0.32
31 15 0.54
32 4 0.14
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.20
Consensus pattern (31 bp):
AAATCAATAAAATACAATAAAAAAGAATTAA
Found at i:3378748 original size:40 final size:41
Alignment explanation
Indices: 3378691--3378770 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
3378681 CGTTTTCTAA
* * *
3378691 CAAAAAACGCCGCAATAGGTTTTGTTATTTAGCGGTGTTTGT
1 CAAAAAAC-CCGCAATAGGTGTTGATATTTAGCGGCGTTTGT
*
3378733 CAAAAAA-CCGCAATAGGTGTTGATGTTTAGCGGCGTTT
1 CAAAAAACCCGCAATAGGTGTTGATATTTAGCGGCGTTT
3378771 TCCCTACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 27 0.79
42 7 0.21
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (41 bp):
CAAAAAACCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT
Found at i:3378796 original size:43 final size:42
Alignment explanation
Indices: 3378741--3378856 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 42
3378731 GTCAAAAAAC
* *
3378741 CGCAATAGGTGTTGATGTTTAGCGGCGTTTTCCCTACAAATGT
1 CGCAGTAGGTGTTGATGTTTAGCGGCGTTTTCCC-ACAAACGT
*
3378784 CGTAGTAGGTGTTGA-GATTTAGCGGCGTTTTTCCCACAAACGT
1 CGCAGTAGGTGTTGATG-TTTAGCGGCG-TTTTCCCACAAACGT
* * * *
3378827 CGCAGAAGGTTTTGATATTTTGCGGCGTTT
1 CGCAGTAGGTGTTGATGTTTAGCGGCGTTT
3378857 GTATCGAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
42 4 0.06
43 51 0.82
44 7 0.11
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (42 bp):
CGCAGTAGGTGTTGATGTTTAGCGGCGTTTTCCCACAAACGT
Found at i:3378895 original size:43 final size:43
Alignment explanation
Indices: 3378848--3378942 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
3378838 TTGATATTTT
* *
3378848 GCGGCGTTTGTATCGAAAATGAC-GCAATAAGTGTTAAGAATTA
1 GCGGCGTTTGTATCGAAAACG-CTACAATAAGTGTTAAGAATTA
* * * * *
3378891 GCGGCGTTTTTATTGAAAACGCTACAATAGGTGTTGAGATTTA
1 GCGGCGTTTGTATCGAAAACGCTACAATAAGTGTTAAGAATTA
3378934 GCGGCGTTT
1 GCGGCGTTT
3378943 CCATACAGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 1 0.02
43 43 0.98
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTGTATCGAAAACGCTACAATAAGTGTTAAGAATTA
Found at i:3379349 original size:21 final size:21
Alignment explanation
Indices: 3379325--3379367 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3379315 GATGATATGT
*
3379325 TGCTTCTCTCTGTGCTACTGC
1 TGCTTCTCTCTCTGCTACTGC
* *
3379346 TGCTTCTTTCTCTGCTGCTGC
1 TGCTTCTCTCTCTGCTACTGC
3379367 T
1 T
3379368 CTGGTTGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.33, G:0.19, T:0.47
Consensus pattern (21 bp):
TGCTTCTCTCTCTGCTACTGC
Found at i:3388555 original size:42 final size:42
Alignment explanation
Indices: 3388504--3388901 Score: 157
Period size: 42 Copynumber: 9.7 Consensus size: 42
3388494 ATTTATGTTA
*
3388504 AAAATGCCACTAAAGTACGTGTAATTAGCGGCGTCTGTG-TGT
1 AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTCTGTGCT-T
* * *
3388546 AAAACGCCACAAAAATACGTGTAATTAGCGGCGTTTGTGCTT
1 AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTCTGTGCTT
** * * * * * *
3388588 GCAACGCCACTAAAGTA--TG-ACCTTTAGTGACGTTTGT-ATA
1 AAAACGCCACTAAAGTACGTGTA--ATTAGCGGCGTCTGTGCTT
** * * * * * * *
3388628 AAAACGCCACTAAAGTAC-AATATTTATCGGTGTTTAT-ATA
1 AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTCTGTGCTT
* * * *
3388668 AAAATGCAACTAGAGTACGTGTAATTAGCGGCGTTTGTGCTT
1 AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTCTGTGCTT
* ** * *
3388710 AAAATGCCACTAAAGTA--TGTCCTTTAGCGGCGT-T-TGAATA
1 AAAACGCCACTAAAGTACGTGT-AATTAGCGGCGTCTGTG-CTT
* * * * * * *
3388750 AAAACACCACTAAAGTA--TAGTATTTATCGGCGTTTAT-ATA
1 AAAACGCCACTAAAGTACGT-GTAATTAGCGGCGTCTGTGCTT
* * *
3388790 AAAATGCCACTATAA-TGA-GTGTAATTAGCGGCGTTTGTGCAT
1 AAAACGCCACTA-AAGT-ACGTGTAATTAGCGGCGTCTGTGCTT
* * * *
3388832 AAAACGCCACGT-ATGTACGTGTAATTAGCGACGTTTGTGCAT
1 AAAACGCCAC-TAAAGTACGTGTAATTAGCGGCGTCTGTGCTT
* * *
3388874 AAAATGCCACGT-ATGTACATGTAATTAG
1 AAAACGCCAC-TAAAGTACGTGTAATTAG
3388902 AAAACGCCAT
Statistics
Matches: 281, Mismatches: 56, Indels: 38
0.75 0.15 0.10
Matches are distributed among these distances:
39 3 0.01
40 91 0.32
41 58 0.21
42 127 0.45
43 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (42 bp):
AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTCTGTGCTT
Found at i:3388668 original size:40 final size:40
Alignment explanation
Indices: 3388618--3388801 Score: 156
Period size: 40 Copynumber: 4.5 Consensus size: 40
3388608 CCTTTAGTGA
* * * *
3388618 CGTTTGTATAAAAACGCCACTAAAGTACAATATTTATCGG
1 CGTTTATATAAAAATGCCACTAAAGTACAGTATTTAGCGG
* * * * *
3388658 TGTTTATATAAAAATGCAACTAGAGTACGTGTAATTAGCGG
1 CGTTTATATAAAAATGCCACTAAAGTAC-AGTATTTAGCGG
* * * * *
3388699 CGTTTGTGCTTAAAATGCCACTAAAGTA-TGTCCTTTAGCGG
1 CGTTTAT-ATAAAAATGCCACTAAAGTACAGT-ATTTAGCGG
** * *
3388740 CGTTTGA-ATAAAAACACCACTAAAGTATAGTATTTATCGG
1 CGTTT-ATATAAAAATGCCACTAAAGTACAGTATTTAGCGG
3388780 CGTTTATATAAAAATGCCACTA
1 CGTTTATATAAAAATGCCACTA
3388802 TAATGAGTGT
Statistics
Matches: 111, Mismatches: 27, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
39 1 0.01
40 67 0.60
41 27 0.24
42 16 0.14
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (40 bp):
CGTTTATATAAAAATGCCACTAAAGTACAGTATTTAGCGG
Found at i:3388701 original size:122 final size:122
Alignment explanation
Indices: 3388559--3388841 Score: 415
Period size: 122 Copynumber: 2.3 Consensus size: 122
3388549 ACGCCACAAA
** *
3388559 AATACGTGTAATTAGCGGCGTTTGTGCTTGCAACGCCACTAAAGTATGACCTTTAGTGACGTTTG
1 AATACGTGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTATGACCTTTAGCGACGTTTG
* * *
3388624 TATAAAAACGCCACTAAAGTACAATATTTATCGGTGTTTATATAAAAATGCAACTAG
66 AATAAAAACACCACTAAAGTACAATATTTATCGGCGTTTATATAAAAATGCAACTAG
* * * *
3388681 AGTACGTGTAATTAGCGGCGTTTGTGCTTAAAATGCCACTAAAGTATGTCCTTTAGCGGCGTTTG
1 AATACGTGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTATGACCTTTAGCGACGTTTG
* * * *
3388746 AATAAAAACACCACTAAAGTATAGTATTTATCGGCGTTTATATAAAAATGCCACTAT
66 AATAAAAACACCACTAAAGTACAATATTTATCGGCGTTTATATAAAAATGCAACTAG
*
3388803 AATGA-GTGTAATTAGCGGCGTTTGTGCATAAAACGCCAC
1 AAT-ACGTGTAATTAGCGGCGTTTGTGCTTAAAACGCCAC
3388842 GTATGTACGT
Statistics
Matches: 143, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
122 142 0.99
123 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (122 bp):
AATACGTGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTATGACCTTTAGCGACGTTTG
AATAAAAACACCACTAAAGTACAATATTTATCGGCGTTTATATAAAAATGCAACTAG
Found at i:3388915 original size:28 final size:28
Alignment explanation
Indices: 3388874--3388929 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
3388864 GTTTGTGCAT
*
3388874 AAAATGCCACGTATGTACATGTAATTAG
1 AAAACGCCACGTATGTACATGTAATTAG
* *
3388902 AAAACGCCATGTATGTACGTGTAATTAG
1 AAAACGCCACGTATGTACATGTAATTAG
3388930 CGGCGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (28 bp):
AAAACGCCACGTATGTACATGTAATTAG
Found at i:3388957 original size:40 final size:40
Alignment explanation
Indices: 3388902--3389052 Score: 146
Period size: 40 Copynumber: 3.7 Consensus size: 40
3388892 ATGTAATTAG
*
3388902 AAAACGCCATGTATGTACGTGTAATTAGCGGCGTTTATAT
1 AAAACGCCACGTATGTACGTGTAATTAGCGGCGTTTATAT
* * *
3388942 AAAACGCCACGTATGTACAT-TATTTATCGGCGTTTATAT
1 AAAACGCCACGTATGTACGTGTAATTAGCGGCGTTTATAT
* * *
3388981 AAAAACGCCAC-TATAGTGCTTGTAATTAGCAGCGTTTATACGT
1 -AAAACGCCACGTAT-GTACGTGTAATTAGCGGCGTTTATA--T
* * *
3389024 TAAACGCCACCGCA-GTACGTGAAATTAGC
1 AAAACGCCA-CGTATGTACGTGTAATTAGC
3389053 AACGTTTGTG
Statistics
Matches: 90, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
39 20 0.22
40 32 0.36
41 15 0.17
42 20 0.22
43 2 0.02
44 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (40 bp):
AAAACGCCACGTATGTACGTGTAATTAGCGGCGTTTATAT
Found at i:3389626 original size:2 final size:2
Alignment explanation
Indices: 3389619--3389665 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3389609 TTTATTATTA
3389619 AT AT AT AT -T 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
3389660 AT AT AT
1 AT AT AT
3389666 TGAAAGAGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3395055 original size:13 final size:13
Alignment explanation
Indices: 3395037--3395062 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3395027 TTATTATTTC
3395037 AAATTAATTAAAT
1 AAATTAATTAAAT
3395050 AAATTAATTAAAT
1 AAATTAATTAAAT
3395063 CTATATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTAATTAAAT
Found at i:3403169 original size:13 final size:13
Alignment explanation
Indices: 3403151--3403181 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3403141 AATTAGTCCT
3403151 TTATCTTTTATAA
1 TTATCTTTTATAA
3403164 TTATCTTTTATAA
1 TTATCTTTTATAA
3403177 TTATC
1 TTATC
3403182 ATGAATGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATCTTTTATAA
Found at i:3403789 original size:55 final size:55
Alignment explanation
Indices: 3403730--3403838 Score: 137
Period size: 55 Copynumber: 2.0 Consensus size: 55
3403720 ACATGTGTTA
* *
3403730 CACACCCACTACCAATACGGAAATTCATAAACATATTATGAATTTCTTAGTTTTG
1 CACACACACTACCAATAAGGAAATTCATAAACATATTATGAATTTCTTAGTTTTG
* * * * * * *
3403785 CACACATATTGCCCATAAGGAATTTCGTAAACTTATTATGAATTTCTTAGTTTT
1 CACACACACTACCAATAAGGAAATTCATAAACATATTATGAATTTCTTAGTTTT
3403839 TTAACTAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (55 bp):
CACACACACTACCAATAAGGAAATTCATAAACATATTATGAATTTCTTAGTTTTG
Found at i:3404065 original size:72 final size:72
Alignment explanation
Indices: 3403989--3404126 Score: 213
Period size: 72 Copynumber: 1.9 Consensus size: 72
3403979 TTTAGTAATT
* * *
3403989 ATTCATTAATTTCATATATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTAT
1 ATTCATGAATTTCATATATGACATCCTTTCATGCCTTAATACATCCTTTCATGCATTTCATTTAT
3404054 GACATCC
66 GACATCC
* * * *
3404061 ATTCATGCATTTCATTTATGGCATCCTTTTATGCCTTAATACATCCTTTCATGCATTTCATTTAT
1 ATTCATGAATTTCATATATGACATCCTTTCATGCCTTAATACATCCTTTCATGCATTTCATTTAT
3404126 G
66 G
3404127 GAATCCTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.46
Consensus pattern (72 bp):
ATTCATGAATTTCATATATGACATCCTTTCATGCCTTAATACATCCTTTCATGCATTTCATTTAT
GACATCC
Found at i:3404066 original size:26 final size:26
Alignment explanation
Indices: 3404030--3404126 Score: 89
Period size: 26 Copynumber: 4.0 Consensus size: 26
3404020 TGCCTTAATG
* *
3404030 CATCCTTTCATGCATTTTATTTATGA
1 CATCCATTCATGCATTTCATTTATGA
*
3404056 CATCCATTCATGCATTTCATTTATGG
1 CATCCATTCATGCATTTCATTTATGA
* * *
3404082 CATCCTTTTATGC----C-TTAAT-A
1 CATCCATTCATGCATTTCATTTATGA
*
3404102 CATCCTTTCATGCATTTCATTTATG
1 CATCCATTCATGCATTTCATTTATG
3404127 GAATCCTTCC
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
20 12 0.21
21 4 0.07
22 1 0.02
24 1 0.02
25 4 0.07
26 34 0.61
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (26 bp):
CATCCATTCATGCATTTCATTTATGA
Found at i:3404105 original size:46 final size:46
Alignment explanation
Indices: 3404055--3404311 Score: 302
Period size: 46 Copynumber: 5.6 Consensus size: 46
3404045 TTTATTTATG
*
3404055 ACATCCATTCATGCATTTCATTTATGGCATCCTTTTATGCCTTAAT
1 ACATCCATTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
* * * * *
3404101 ACATCCTTTCATGCATTTCATTTATGGAATCCTTCCACGCCTTATT
1 ACATCCATTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
** * * *
3404147 GTATCCTTTCATGCACTTCATTTATGGCATCATTTCATGCCTTAAT
1 ACATCCATTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
*
3404193 ACAT-CATTTCATGCATTTCATTTATGACATCCTTTCATGCCTTAAT
1 ACATCCA-TTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
* ** ** *
3404239 GCATCTTTTCATGCATTTCATTTATGAAATCCTTTCATGCCCTAAT
1 ACATCCATTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
* *
3404285 GCAT-CATTTCATGTATTTCATTTATGG
1 ACATCCA-TTCATGCATTTCATTTATGG
3404312 ATTTGTTTTA
Statistics
Matches: 179, Mismatches: 29, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
45 1 0.01
46 178 0.99
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (46 bp):
ACATCCATTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
Found at i:3404167 original size:92 final size:93
Alignment explanation
Indices: 3404056--3404312 Score: 365
Period size: 92 Copynumber: 2.8 Consensus size: 93
3404046 TTATTTATGA
* * *
3404056 CATCCATTCATGCATTTCATTTATGGCATCCTTTTATGCCTTAATACATCCTTTCATGCATTTCA
1 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATACATCATTTCATGCATTTCA
*
3404121 TTTATGGA-ATCCTTCCACGCCTTATTG
66 TTTATGGACATCCTTCCACGCCTTAATG
* * *
3404148 TATCCTTTCATGCACTTCATTTATGGCATCATTTCATGCCTTAATACATCATTTCATGCATTTCA
1 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATACATCATTTCATGCATTTCA
* *
3404213 TTTAT-GACATCCTTTCATGCCTTAATG
66 TTTATGGACATCCTTCCACGCCTTAATG
* ** * * *
3404240 CATCTTTTCATGCATTTCATTTATGAAATCCTTTCATGCCCTAATGCATCATTTCATGTATTTCA
1 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATACATCATTTCATGCATTTCA
3404305 TTTATGGA
66 TTTATGGA
3404313 TTTGTTTTAG
Statistics
Matches: 145, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
91 2 0.01
92 141 0.97
93 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (93 bp):
CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATACATCATTTCATGCATTTCA
TTTATGGACATCCTTCCACGCCTTAATG
Found at i:3404204 original size:138 final size:138
Alignment explanation
Indices: 3404062--3404311 Score: 383
Period size: 138 Copynumber: 1.8 Consensus size: 138
3404052 ATGACATCCA
* *
3404062 TTCATGCATTTCATTTATGGCATCCTTTTATGCCTTAATACATCCTTTCATGCATTTCATTTATG
1 TTCATGCATTTCATTTATGACATCCTTTCATGCCTTAATACATCCTTTCATGCATTTCATTTATG
* * * * *
3404127 GAATCCTTCCACGCCTTATTGTATCCTTTCATGCACTTCATTTATGGCATCATTTCATGCCTTAA
66 AAATCCTTCCACGCCCTAATGCATCATTTCATGCACTTCATTTATGGCATCATTTCATGCCTTAA
3404192 TACATCAT
131 TACATCAT
* *
3404200 TTCATGCATTTCATTTATGACATCCTTTCATGCCTTAATGCATCTTTTCATGCATTTCATTTATG
1 TTCATGCATTTCATTTATGACATCCTTTCATGCCTTAATACATCCTTTCATGCATTTCATTTATG
* * * *
3404265 AAATCCTTTCATGCCCTAATGCATCATTTCATGTATTTCATTTATGG
66 AAATCCTTCCACGCCCTAATGCATCATTTCATGCACTTCATTTATGG
3404312 ATTTGTTTTA
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 99 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (138 bp):
TTCATGCATTTCATTTATGACATCCTTTCATGCCTTAATACATCCTTTCATGCATTTCATTTATG
AAATCCTTCCACGCCCTAATGCATCATTTCATGCACTTCATTTATGGCATCATTTCATGCCTTAA
TACATCAT
Found at i:3404781 original size:42 final size:41
Alignment explanation
Indices: 3404735--3404827 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 41
3404725 CCCTACCATG
* * *
3404735 GTATCGATACTTCTATACTATGGCACCGATACCTTTCTCTT-A
1 GTATCGATACTACTACACTATGGCACCGATA-CTCTCT-TTCA
*
3404777 GTATCGATACTACTACACTATGGTACCGATACTCTCTTTCA
1 GTATCGATACTACTACACTATGGCACCGATACTCTCTTTCA
3404818 GTATCGATAC
1 GTATCGATAC
3404828 CAATTTGACA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
40 2 0.04
41 16 0.35
42 28 0.61
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (41 bp):
GTATCGATACTACTACACTATGGCACCGATACTCTCTTTCA
Found at i:3407080 original size:25 final size:24
Alignment explanation
Indices: 3407052--3407099 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3407042 GAAAAATACA
3407052 AAAAGAAAAGAAAAATCAAAAAAAG
1 AAAAGAAAA-AAAAATCAAAAAAAG
* *
3407077 AAAAGAAAAAGAATTCAAAAAAA
1 AAAAGAAAAAAAAATCAAAAAAA
3407100 ATCAAGCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.79, C:0.04, G:0.10, T:0.06
Consensus pattern (24 bp):
AAAAGAAAAAAAAATCAAAAAAAG
Found at i:3407100 original size:25 final size:20
Alignment explanation
Indices: 3407033--3407086 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
3407023 ATTGGAGTGC
* *
3407033 AAAAGGAAAGAAAAAT-ACA
1 AAAAGAAAAGAAAAATCAAA
3407052 AAAAGAAAAGAAAAATCAAA
1 AAAAGAAAAGAAAAATCAAA
3407072 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
3407087 GAATTCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.04
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:3417417 original size:36 final size:36
Alignment explanation
Indices: 3417300--3417417 Score: 89
Period size: 36 Copynumber: 3.2 Consensus size: 36
3417290 GCAGACTTAG
* *
3417300 TTTGGGTTGTGTTACGTCGAGTGTGGTTGGTACTGA
1 TTTGGGTTGTGTTAAGTAGAGTGTGGTTGGTACTGA
* * * **
3417336 TTTGGGTT-CGTAAGAGTAAAGATAAGTGGAAGGTA-T-A
1 TTTGGGTTGTGTTA-AGTAGAG-T--GTGGTTGGTACTGA
* *
3417373 GTTTGGGTTGTGTTATGTTGAGTGTGGTTGGTACTGA
1 -TTTGGGTTGTGTTAAGTAGAGTGTGGTTGGTACTGA
3417410 TTTGGGTT
1 TTTGGGTT
3417418 CACAAGAGTA
Statistics
Matches: 60, Mismatches: 14, Indels: 16
0.67 0.16 0.18
Matches are distributed among these distances:
35 11 0.18
36 21 0.35
37 4 0.07
38 13 0.22
39 11 0.18
ACGTcount: A:0.18, C:0.04, G:0.37, T:0.41
Consensus pattern (36 bp):
TTTGGGTTGTGTTAAGTAGAGTGTGGTTGGTACTGA
Found at i:3417418 original size:74 final size:74
Alignment explanation
Indices: 3417297--3417444 Score: 251
Period size: 74 Copynumber: 2.0 Consensus size: 74
3417287 GGTGCAGACT
**
3417297 TAGTTTGGGTTGTGTTACGTCGAGTGTGGTTGGTACTGATTTGGGTTCGTAAGAGTAAAGATAAG
1 TAGTTTGGGTTGTGTTACGTCGAGTGTGGTTGGTACTGATTTGGGTTCACAAGAGTAAAGATAAG
*
3417362 TGGAAGGTA
66 TGAAAGGTA
* *
3417371 TAGTTTGGGTTGTGTTATGTTGAGTGTGGTTGGTACTGATTTGGGTTCACAAGAGTAAAGATAAG
1 TAGTTTGGGTTGTGTTACGTCGAGTGTGGTTGGTACTGATTTGGGTTCACAAGAGTAAAGATAAG
3417436 TGAAAGGTA
66 TGAAAGGTA
3417445 CGGTGATTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.24, C:0.05, G:0.35, T:0.36
Consensus pattern (74 bp):
TAGTTTGGGTTGTGTTACGTCGAGTGTGGTTGGTACTGATTTGGGTTCACAAGAGTAAAGATAAG
TGAAAGGTA
Found at i:3418915 original size:10 final size:10
Alignment explanation
Indices: 3418895--3418946 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
3418885 CATCCGAGTG
3418895 TTATATATATA
1 TTAT-TATATA
3418906 TTATTATATA
1 TTATTATATA
3418916 -TATTA-ATA
1 TTATTATATA
3418924 -TA-TA-A-A
1 TTATTATATA
3418930 TTATTATATA
1 TTATTATATA
3418940 TTATTAT
1 TTATTAT
3418947 TACAAATGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
6 1 0.03
7 5 0.14
8 7 0.19
9 6 0.16
10 14 0.38
11 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTATTATATA
Found at i:3418915 original size:12 final size:12
Alignment explanation
Indices: 3418898--3418948 Score: 75
Period size: 12 Copynumber: 4.2 Consensus size: 12
3418888 CCGAGTGTTA
3418898 TATATATATTAT
1 TATATATATTAT
*
3418910 TATATATATTAA
1 TATATATATTAT
*
3418922 TATATAAATTAT
1 TATATATATTAT
3418934 TATATATTATTAT
1 TATATA-TATTAT
3418947 TA
1 TA
3418949 CAAATGGAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 27 0.79
13 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATATATTAT
Found at i:3419368 original size:21 final size:21
Alignment explanation
Indices: 3419338--3419390 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
3419328 TCCGGTGACT
*
3419338 CACCAGATCTTGTTATCATTG
1 CACCAAATCTTGTTATCATTG
3419359 CACCAAATCTTGTTATCATTG
1 CACCAAATCTTGTTATCATTG
3419380 CACCAAATCTT
1 CACCAAATCTT
3419391 CAAGGCCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (21 bp):
CACCAAATCTTGTTATCATTG
Found at i:3426685 original size:22 final size:22
Alignment explanation
Indices: 3426655--3426709 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
3426645 ATGTCTACAT
3426655 TTTTTAAAGATGATAGATTCTC
1 TTTTTAAAGATGATAGATTCTC
* *
3426677 TTTTCAAAGATGGTAGATTCTC
1 TTTTTAAAGATGATAGATTCTC
3426699 TTTTTAAAGAT
1 TTTTTAAAGAT
3426710 AAAAGCTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (22 bp):
TTTTTAAAGATGATAGATTCTC
Found at i:3427935 original size:12 final size:12
Alignment explanation
Indices: 3427914--3427964 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
3427904 CCGAGTGTTA
3427914 TATATATATTAT
1 TATATATATTAT
* *
3427926 TATATTTATTAA
1 TATATATATTAT
* *
3427938 TATATAAATTAC
1 TATATATATTAT
3427950 TATATATTATTAT
1 TATATA-TATTAT
3427963 TA
1 TA
3427965 CAAATAGAGG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 25 0.81
13 6 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATATATTAT
Found at i:3427948 original size:24 final size:25
Alignment explanation
Indices: 3427913--3427961 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
3427903 TCCGAGTGTT
* *
3427913 ATATATATATTATTATAT-TTATTA
1 ATATATAAATTACTATATATTATTA
3427937 ATATATAAATTACTATATATTATTA
1 ATATATAAATTACTATATATTATTA
3427962 TTACAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
ATATATAAATTACTATATATTATTA
Found at i:3433858 original size:9 final size:9
Alignment explanation
Indices: 3433828--3433871 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 9
3433818 CTTTAGGGTA
3433828 TTTTTTCACT
1 TTTTTTC-CT
3433838 TTTTTCTCCCT
1 TTTTT-T-CCT
3433849 TTTTTTCCTT
1 TTTTTTCC-T
3433859 TTTTTTCCT
1 TTTTTTCCT
3433868 TTTT
1 TTTT
3433872 AAGAGTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 7 0.23
10 15 0.48
11 8 0.26
12 1 0.03
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:3450496 original size:14 final size:14
Alignment explanation
Indices: 3450477--3450516 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
3450467 TTGTGCACAG
3450477 TGTATCGATACATA
1 TGTATCGATACATA
*
3450491 TGTATCGATACCTA
1 TGTATCGATACATA
3450505 TGTATCGATACA
1 TGTATCGATACA
3450517 CCCTCACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (14 bp):
TGTATCGATACATA
Found at i:3454177 original size:25 final size:25
Alignment explanation
Indices: 3454148--3454252 Score: 156
Period size: 25 Copynumber: 4.2 Consensus size: 25
3454138 GTGCGCAATA
* *
3454148 TGCACTCGAAAGTGTCTCGTATAAT
1 TGCACTCAAAAGTGCCTCGTATAAT
*
3454173 TGCACTCGAAAGTGCCTCGTATAAT
1 TGCACTCAAAAGTGCCTCGTATAAT
3454198 TGCACTCAAAAGTGCCTCGTATAAT
1 TGCACTCAAAAGTGCCTCGTATAAT
** *
3454223 TAAACTCAAAAGTTCCTCGTATAAT
1 TGCACTCAAAAGTGCCTCGTATAAT
3454248 TGCAC
1 TGCAC
3454253 CATAGGTGTC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 73 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (25 bp):
TGCACTCAAAAGTGCCTCGTATAAT
Found at i:3454585 original size:63 final size:59
Alignment explanation
Indices: 3454404--3454565 Score: 143
Period size: 63 Copynumber: 2.7 Consensus size: 59
3454394 TCCATAATGC
* * * * *
3454404 TATCATATCAAAGTGTGTTGGGC-AGTTCATACCCGAAATCAT-TTAGAACCAT-TA-AAAAA
1 TATCATAT-AAA-TGTATTGGGCAAG-TCATACCCAAAATCATCAT-GAAACATATAGTAAAA
*
3454463 TATCGTATAAATGTATTGGGCAAGTCATACCCAAAATCATCCATGAAACATATAGTAAAA
1 TATCATATAAATGTATTGGGCAAGTCATACCCAAAATCAT-CATGAAACATATAGTAAAA
* * *
3454523 TATCATATAAAAATTGTATTGGGTAATTCATACCGAAAATCAT
1 TATCATAT--AAA-TGTATTGGGCAAGTCATACCCAAAATCAT
3454566 TTGAATACCA
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
57 24 0.28
58 11 0.13
59 10 0.12
60 11 0.13
62 3 0.04
63 26 0.31
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (59 bp):
TATCATATAAATGTATTGGGCAAGTCATACCCAAAATCATCATGAAACATATAGTAAAA
Found at i:3461910 original size:4 final size:4
Alignment explanation
Indices: 3461901--3462095 Score: 194
Period size: 4 Copynumber: 48.5 Consensus size: 4
3461891 TATACATAAA
* * * * *
3461901 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAC CTAC CTAC CTAC CTAC
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
* * * * *
3461949 CTAT CTAT CTAT CTAT CTAT ATAT CTAC CTAC CTAC CTAG CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
* * * * *
3461997 CTAT CTAT CTAT CTAT CTAT CTAC CTAC CTAC CTA- CTTAT CTAA CTAC
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT C-TAT CTAT CTAT
* * * *
3462045 CTAC CTAC CTAT CCTAT CTAT CTAT CTAT CCAT CTAT CCAT CTAT CTAT
1 CTAT CTAT CTAT -CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
3462094 CT
1 CT
3462096 TATGTTATAC
Statistics
Matches: 173, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
3 1 0.01
4 167 0.97
5 5 0.03
ACGTcount: A:0.26, C:0.33, G:0.01, T:0.41
Consensus pattern (4 bp):
CTAT
Found at i:3463864 original size:2 final size:2
Alignment explanation
Indices: 3463857--3463891 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3463847 TTATCATTAT
3463857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3463892 TTGATTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3464235 original size:23 final size:24
Alignment explanation
Indices: 3464195--3464239 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3464185 GGTATTAGGT
*
3464195 TTTTTTATTACTATTATTTTTTCC
1 TTTTTCATTACTATTATTTTTTCC
*
3464219 TTTTTCATTATTA-TATTTTTT
1 TTTTTCATTACTATTATTTTTT
3464240 TACCTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTCATTACTATTATTTTTTCC
Found at i:3468235 original size:22 final size:22
Alignment explanation
Indices: 3468203--3468279 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
3468193 GCTACCCCAT
*
3468203 CAAACTTTTGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGA
* *
3468225 CAAACCATTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGA
*
3468247 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGA
3468269 CAAACCTTTGA
1 CAAACCTTTGA
3468280 CCAAACACGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGA
Found at i:3469140 original size:21 final size:20
Alignment explanation
Indices: 3469114--3469153 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3469104 GCTTGAGATA
3469114 GTCTCCCTTGAAACAAGTTTT
1 GTCTCCCTTGAAAC-AGTTTT
*
3469135 GTCTCCCTTGAGACAGTTT
1 GTCTCCCTTGAAACAGTTT
3469154 CTCTTGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (20 bp):
GTCTCCCTTGAAACAGTTTT
Found at i:3470002 original size:106 final size:106
Alignment explanation
Indices: 3469880--3470197 Score: 519
Period size: 106 Copynumber: 3.0 Consensus size: 106
3469870 CGCGCCATTT
* * *
3469880 AAGACAACACAAGTTCAACTTCACGACGAAGGGATGACTGGTTGTCAACAAACAACTTCCCAATT
1 AAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAATT
3469945 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* *
3469986 AAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTATCAACAAACAATTTCCCAATT
1 AAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAATT
* * *
3470051 TTAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
*
3470092 AAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAGTT
1 AAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAATT
* * * *
3470157 CCAGAACCAATTTCAACTTCACAGCGGAGGATTTTGGACTC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
3470198 GGAACAGTAC
Statistics
Matches: 194, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 194 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
AAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAATT
TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
Found at i:3472144 original size:12 final size:12
Alignment explanation
Indices: 3472088--3472145 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
3472078 TTATGTTTTC
*
3472088 ATTAGTATATAT
1 ATTATTATATAT
*
3472100 TTTATTAT-TAT
1 ATTATTATATAT
3472111 CATTATTATATAT
1 -ATTATTATATAT
3472124 A-TATATATATAT
1 ATTAT-TATATAT
*
3472136 ATGATTATAT
1 ATTATTATAT
3472146 TTTCTATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 6 0.16
12 27 0.71
13 5 0.13
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (12 bp):
ATTATTATATAT
Found at i:3472184 original size:24 final size:22
Alignment explanation
Indices: 3472142--3472186 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
3472132 ATATATGATT
3472142 ATATTTTCTATTTTTGTTTTCC
1 ATATTTTCTATTTTTGTTTTCC
*
3472164 ATATTTCTTTATTTTTAGTTTTC
1 ATATTT-TCTATTTTT-GTTTTC
3472187 TTTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (22 bp):
ATATTTTCTATTTTTGTTTTCC
Found at i:3472475 original size:25 final size:24
Alignment explanation
Indices: 3472447--3472493 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3472437 GGTATTAGGT
*
3472447 TTTTTTATTACTATTATTTTTTTCC
1 TTTTTCATTACTA-TATTTTTTTCC
*
3472472 TTTTTCATTATTATATTTTTTT
1 TTTTTCATTACTATATTTTTTT
3472494 ACCTAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTTCATTACTATATTTTTTTCC
Found at i:3473512 original size:26 final size:26
Alignment explanation
Indices: 3473482--3473539 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
3473472 ATTGCTTCCA
3473482 AAATAGCAGACAAATCAATTTTCCCC
1 AAATAGCAGACAAATCAATTTTCCCC
*
3473508 AAATAGCAGACAAATGAATTTTCCCC
1 AAATAGCAGACAAATCAATTTTCCCC
3473534 AAATAG
1 AAATAG
3473540 TATTTGGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.22
Consensus pattern (26 bp):
AAATAGCAGACAAATCAATTTTCCCC
Found at i:3474618 original size:24 final size:24
Alignment explanation
Indices: 3474581--3474637 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
3474571 CTTTTAAAGA
* *
3474581 AATTTT-AAGATTATTTTTTATTT
1 AATTTTCAAGATTATATTTGATTT
* *
3474604 GATTTTCAAGTTTATATTTGATTT
1 AATTTTCAAGATTATATTTGATTT
3474628 AATTGTTCAA
1 AATT-TTCAA
3474638 ATATAGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 5 0.19
24 17 0.63
25 5 0.19
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.58
Consensus pattern (24 bp):
AATTTTCAAGATTATATTTGATTT
Found at i:3482591 original size:75 final size:76
Alignment explanation
Indices: 3482496--3482687 Score: 253
Period size: 75 Copynumber: 2.5 Consensus size: 76
3482486 ACAATGGGGA
* * * *
3482496 AATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAACT
1 AATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAACC
* * *
3482560 GTTTAGGGGGG
66 ATTCAGGAGGG
* * * *
3482571 AATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCAAACC
1 AATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAACC
3482635 ATTCAGGAGGG
66 ATTCAGGAGGG
*
3482646 AATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 AATCGGTTCCTCCTATGGGGGGG-ATCGGTTCCCTCCGAGCA
3482688 ATCTAGAATT
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
75 78 0.77
76 6 0.06
77 17 0.17
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (76 bp):
AATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAACC
ATTCAGGAGGG
Found at i:3485301 original size:21 final size:20
Alignment explanation
Indices: 3485276--3485334 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
3485266 CAGAACCCCA
* *
3485276 GGGGGTATCGATTCCC-CTG
1 GGGGGGATCGATTCCCTCAG
*
3485295 TGGGGGGAATCGGTTCCCTCAG
1 -GGGGGG-ATCGATTCCCTCAG
3485317 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
3485335 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 16 0.48
21 15 0.45
22 2 0.06
ACGTcount: A:0.12, C:0.25, G:0.39, T:0.24
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAG
Found at i:3489186 original size:22 final size:21
Alignment explanation
Indices: 3489144--3489183 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3489134 GAGTTTGTTT
*
3489144 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3489165 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3489184 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3489347 original size:15 final size:15
Alignment explanation
Indices: 3489327--3489365 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
3489317 TTCTTGTTCC
3489327 TCTTCATCGGAACTT
1 TCTTCATCGGAACTT
3489342 TCTTCATCGGAACTT
1 TCTTCATCGGAACTT
*
3489357 TCTTAATCG
1 TCTTCATCG
3489366 CTCCATGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.41
Consensus pattern (15 bp):
TCTTCATCGGAACTT
Found at i:3491272 original size:74 final size:74
Alignment explanation
Indices: 3491121--3491313 Score: 237
Period size: 74 Copynumber: 2.6 Consensus size: 74
3491111 GTTGTACAAT
* * * * *
3491121 GGGGGAATCGGTACCCCCT-TGGGGGGATCGGTTCCCTCCGAGCATACTGAATTCTTGGAACAAA
1 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATACTGAAATCTCGGAACAAA
** *
3491185 ACTGTTTAG
66 ACCATTCAG
* * *
3491194 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCA
1 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATACT-GAAATCTCGGAACAA
3491259 AACCATTCA-
65 AACCATTCAG
* *
3491268 GGGGGAATCGATTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCA
3491314 ATCTAGAATT
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
73 17 0.16
74 47 0.45
75 40 0.38
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.24
Consensus pattern (74 bp):
GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATACTGAAATCTCGGAACAAA
ACCATTCAG
Found at i:3492627 original size:20 final size:20
Alignment explanation
Indices: 3492590--3492632 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3492580 AATCCACCAC
*
3492590 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
3492610 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
3492630 ATG
1 ATG
3492633 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:3493210 original size:13 final size:13
Alignment explanation
Indices: 3493194--3493218 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3493184 TAATTTATAT
3493194 TTCTTTTTTTTTC
1 TTCTTTTTTTTTC
3493207 TTCTTTTTTTTT
1 TTCTTTTTTTTT
3493219 TATGCGGGGT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Found at i:3497639 original size:19 final size:19
Alignment explanation
Indices: 3497596--3497641 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
3497586 CTGCGGAATT
3497596 ATGAAGGTGTTGATGGCCTTG
1 ATGAAGGTGTTGATGG-C-TG
3497617 ATGAAGGATGTTGATGG-TG
1 ATGAAGG-TGTTGATGGCTG
3497636 ATGAAG
1 ATGAAG
3497642 TTGAAATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.33
21 7 0.29
22 9 0.38
ACGTcount: A:0.26, C:0.04, G:0.39, T:0.30
Consensus pattern (19 bp):
ATGAAGGTGTTGATGGCTG
Found at i:3500411 original size:16 final size:15
Alignment explanation
Indices: 3500382--3500418 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
3500372 CAAGCGGACC
3500382 AGTTTA-GGTAAACT
1 AGTTTAGGGTAAACT
3500396 AGTTTAGGGTTAAACT
1 AGTTTAGGG-TAAACT
3500412 AGTTTAG
1 AGTTTAG
3500419 TGGATTGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.29
15 2 0.10
16 13 0.62
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.38
Consensus pattern (15 bp):
AGTTTAGGGTAAACT
Found at i:3500511 original size:12 final size:12
Alignment explanation
Indices: 3500494--3500528 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
3500484 TTTTTGCACC
3500494 AAAAATTCCAGA
1 AAAAATTCCAGA
3500506 AAAAATTCCAGA
1 AAAAATTCCAGA
3500518 AAAAATTCCAG
1 AAAAATTCCAG
3500529 CACACGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (12 bp):
AAAAATTCCAGA
Found at i:3500807 original size:14 final size:14
Alignment explanation
Indices: 3500790--3500817 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3500780 ATGGTCTAGG
3500790 GAAAAAAAAGAAAA
1 GAAAAAAAAGAAAA
3500804 GAAAAAAAAGAAAA
1 GAAAAAAAAGAAAA
3500818 AAATAAGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAGAAAA
Found at i:3514928 original size:21 final size:21
Alignment explanation
Indices: 3514865--3514931 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
3514855 ACATTTTATT
*
3514865 TTAATAATTTAATATTAATATAC
1 TTAATAATTT-ATTTTAAT-TAC
** *
3514888 TTAA-AAAATAATTT-ATTAC
1 TTAATAATTTATTTTAATTAC
3514907 TTAATAATTTATTTTAATTAC
1 TTAATAATTTATTTTAATTAC
3514928 TTAA
1 TTAA
3514932 AAATAAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 7 0.20
20 9 0.26
21 12 0.34
22 3 0.09
23 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATAATTTATTTTAATTAC
Found at i:3517336 original size:46 final size:46
Alignment explanation
Indices: 3517265--3517506 Score: 367
Period size: 46 Copynumber: 5.3 Consensus size: 46
3517255 AAATGAATGA
* *
3517265 ATAAATGAAAATGCATAACGATGCATTATAGGCATGAAAGGATGAC
1 ATAAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCC
** *
3517311 ATAAATGAATGTGCATAATGGTGCATTATAGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCC
* *
3517357 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCC
* * *
3517403 ATAAATGAAAATGCATAATGGTGCATTATAGGCATCAAAAGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCC
* * *
3517449 ATAAATGAAAATACATAACGATGCATTATAGGCATGAAAGGATGCA
1 ATAAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCC
3517495 ATAAATGAAAAT
1 ATAAATGAAAAT
3517507 AAAGAATAAT
Statistics
Matches: 176, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 176 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCC
Found at i:3524227 original size:29 final size:29
Alignment explanation
Indices: 3524152--3524232 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 29
3524142 TATTTTTCTA
*
3524152 AAATTATATTTTAGTC-CCTAAACTTTCC
1 AAATTATAATTTAGTCACCTAAACTTTCC
*
3524180 AAAGTTTTTAATTTAGTCACC-AAACTTTACC
1 AAA--TTATAATTTAGTCACCTAAACTTT-CC
*
3524211 AAATTATAATTTGGTCA-CTAAA
1 AAATTATAATTTAGTCACCTAAA
3524233 TAAATCCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 4 0.09
29 15 0.34
30 18 0.41
31 7 0.16
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (29 bp):
AAATTATAATTTAGTCACCTAAACTTTCC
Found at i:3534025 original size:46 final size:46
Alignment explanation
Indices: 3533973--3534212 Score: 338
Period size: 46 Copynumber: 5.2 Consensus size: 46
3533963 TATAATATAG
** *
3533973 AAATGAAAATTAATAACGGTGTATTATAGGCATGAAAGGATGCCAT
1 AAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCCAT
* *
3534019 AAATGAAAATGCATAACGATGCATTATAGGCATGAAAGGATGCAAT
1 AAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCCAT
* * *
3534065 AAATGAAAATGCATAATGGTGCATTATCGACATGAAAGGATGCCAT
1 AAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCCAT
* * * * *
3534111 ACATGAAAATACATAATGGTTCATTATAGGCATGAAAGAATGCCAT
1 AAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCCAT
*
3534157 AAATGAAAATGCATAACGGTGCATTATAGGTATGAAAGGAT-CTCAT
1 AAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGC-CAT
3534203 AAATGAAAAT
1 AAATGAAAAT
3534213 AAAGAATAAT
Statistics
Matches: 171, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.01
46 170 0.99
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (46 bp):
AAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCCAT
Found at i:3535951 original size:39 final size:39
Alignment explanation
Indices: 3535891--3536049 Score: 156
Period size: 39 Copynumber: 4.1 Consensus size: 39
3535881 ACCTTACTGT
* * * *
3535891 TTACCACAGACTTCTCAGCTTTGTGCTCAGGGTAAGTCC
1 TTACCACAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCC
* **
3535930 TTACCACAGGCTCCTCGGCTTTGTGCTTAGGGTAAGTCC
1 TTACCACAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCC
* * * * * *
3535969 TTACTACAGGCACCTCTGATTTGTGCACATGATAAGACC
1 TTACCACAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCC
* ** * *
3536008 TTATCGTAGGCTTCTCTGCTTTGTGCACAGGGTAAGCCC
1 TTACCACAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCC
3536047 TTA
1 TTA
3536050 TTGGGTGTAT
Statistics
Matches: 97, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 97 1.00
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.31
Consensus pattern (39 bp):
TTACCACAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCC
Found at i:3542566 original size:11 final size:11
Alignment explanation
Indices: 3542552--3542576 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3542542 TTTATTTTCT
3542552 TTCACTTGCAC
1 TTCACTTGCAC
3542563 TTCACTTGCAC
1 TTCACTTGCAC
3542574 TTC
1 TTC
3542577 TTTTTGGTAT
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:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:3547205 original size:36 final size:37
Alignment explanation
Indices: 3547138--3547413 Score: 205
Period size: 36 Copynumber: 7.4 Consensus size: 37
3547128 TTTTTTTAGT
* * * * *
3547138 ATATATGTTATATATAG--TTTGAAATCATTTTGGAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTGAAA
* **
3547173 AT-TATATAATATATAGTTTTTAAATATTTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTGAAA
3547209 ACT-TATAT-ATATAT-GATTTTTAAAAACATTTTGAAAAA
1 A-TATATATAATATATAG-TTTTTAAAAACATTTTG--AAA
3547247 ATATATATAATATATAGTTTTTGAAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTT-AAAAACATTTTGAAA
* *
3547285 ATATATATATTATATAGATTTTGAAAAAAACATTTT-AAA
1 ATATATATAATATATAG-TTTT--TAAAAACATTTTGAAA
* **
3547324 A-ATATATACTATAGGGTTTTTGAAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTT-AAAAACATTTTGAAA
* * * * *
3547361 ACACATA-AA-ATATAG-TTTTCAACATATTTTGGAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTT-GAAA
3547396 ATATAATATATATATATA
1 ATAT-ATATA-ATATATA
3547414 TATATATATA
Statistics
Matches: 194, Mismatches: 26, Indels: 38
0.75 0.10 0.15
Matches are distributed among these distances:
34 20 0.10
35 13 0.07
36 51 0.26
37 17 0.09
38 45 0.23
39 24 0.12
40 24 0.12
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTAAAAACATTTTGAAA
Found at i:3547254 original size:38 final size:38
Alignment explanation
Indices: 3547175--3547361 Score: 158
Period size: 40 Copynumber: 4.9 Consensus size: 38
3547165 TTTTGGAAAT
* ** *
3547175 TATATA-ATATAT-AGTTTTTAAATATTTTTTG-AAAAC
1 TATATATATATATGA-TTTTTAAAAACATTTTGAAAAAA
3547211 T-TATATATATATGATTTTTAAAAACATTTTGAAAAAA
1 TATATATATATATGATTTTTAAAAACATTTTGAAAAAA
*
3547248 TATATATAATATAT-AGTTTTTGAAAAACATTTTGAAAATA
1 TATATAT-ATATATGA-TTTTT-AAAAACATTTTGAAAAAA
*
3547288 TATATAT-TATATAGATTTTGAAAAAAACATTTT--AAAAA
1 TATATATATATAT-GATTTT--TAAAAACATTTTGAAAAAA
* * *
3547326 TATATA-CTATAGGGTTTTTGAAAAACATTTTGAAAA
1 TATATATATATATGATTTTT-AAAAACATTTTGAAAA
3547362 CACATAAAAT
Statistics
Matches: 126, Mismatches: 10, Indels: 28
0.77 0.06 0.17
Matches are distributed among these distances:
35 4 0.03
36 32 0.25
37 11 0.09
38 28 0.22
39 15 0.12
40 36 0.29
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (38 bp):
TATATATATATATGATTTTTAAAAACATTTTGAAAAAA
Found at i:3547375 original size:38 final size:37
Alignment explanation
Indices: 3547155--3547375 Score: 148
Period size: 38 Copynumber: 5.9 Consensus size: 37
3547145 TTATATATAG
* * * * *
3547155 TTTG-AAATCATTTTGGAAATTATATAATATATAGTT
1 TTTGAAAAACATTTTGAAAAATATAAAATATAGAGTT
* ** * *
3547191 TTT-AAATATTTTTTGAAAACT-TATATATATATGA-TT
1 TTTGAAAAACATTTTGAAAAATATA-AAATATA-GAGTT
*
3547227 TTT-AAAAACATTTTGAAAAAATATATATAATATATAGTT
1 TTTGAAAAACATTTTG-AAAAATATA-A-AATATAGAGTT
* * * *
3547266 TTTGAAAAACATTTTGAAAATATATATATTATATAGAT
1 TTTGAAAAACATTTTGAAAA-ATATAAAATATAGAGTT
* * *
3547304 TTTGAAAAAAACATTTT-AAAAATATATACTATAGGGTT
1 TTTG--AAAAACATTTTGAAAAATATAAAATATAGAGTT
*
3547342 TTTGAAAAACATTTTGAAAACACATAAAATATAG
1 TTTGAAAAACATTTTGAAAA-ATATAAAATATAG
3547376 TTTTCAACAT
Statistics
Matches: 147, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
35 2 0.01
36 44 0.30
37 10 0.07
38 45 0.31
39 18 0.12
40 28 0.19
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (37 bp):
TTTGAAAAACATTTTGAAAAATATAAAATATAGAGTT
Found at i:3547408 original size:2 final size:2
Alignment explanation
Indices: 3547396--3547432 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3547386 ATTTTGGAAA
3547396 AT AT A- 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
3547433 TTAAAAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3547489 original size:36 final size:36
Alignment explanation
Indices: 3547449--3547553 Score: 147
Period size: 36 Copynumber: 2.8 Consensus size: 36
3547439 AAACATTTTG
*
3547449 AATATATAATATATAGTTTTTTAAATTTTTTTTGAA
1 AATATATAATATATAGTTTTTAAAATTTTTTTTGAA
*
3547485 AATATATAATATATAGTTTTTAAAACATTTTTTTTTAA
1 AATATATAATATATAGTTTTT-AAA-ATTTTTTTTGAA
* *
3547523 ATATATATATTATATAGTTTTTAAAAATTTT
1 A-ATATATAATATATAGTTTTTAAAATTTTT
3547554 GGAAAAATAT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
36 21 0.34
37 7 0.11
38 15 0.24
39 19 0.31
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (36 bp):
AATATATAATATATAGTTTTTAAAATTTTTTTTGAA
Found at i:3547515 original size:125 final size:125
Alignment explanation
Indices: 3547285--3547515 Score: 279
Period size: 125 Copynumber: 1.8 Consensus size: 125
3547275 CATTTTGAAA
3547285 ATATATATATTATATAGATTTTGAAAAAAACATTTTAAAAATATATACTATAGGGTTTTTGAAAA
1 ATATATATATTATATAGATTTTGAAAAAAACATTTTAAAAATATATACTATA-GGTTTTTGAAAA
* *
3547350 ACATTTTGAAAACACATAAAATATAGTTTTCAACATATTTTGGAAAATATAATATATATAT
65 ACATTTTGAAAACACATAAAATATAGTTTTCAAAACATTTTGGAAAATATAATATATATAT
* * * *
3547411 ATATATATATATATATATATATTT-AAAAAAACATTTTGAATATATAATA-TATA-GTTTTTTAA
1 ATATATATAT-TATATAGAT-TTTGAAAAAAACATTTTAAAAATAT-ATACTATAGGTTTTTGAA
**** * * * *
3547473 ATTTTTTTTGAAAATATATAATATATAGTTTTTAAAACATTTT
63 AAACATTTTGAAAACACATAAAATATAGTTTTCAAAACATTTT
3547516 TTTTTAAATA
Statistics
Matches: 88, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
125 41 0.47
126 10 0.11
127 31 0.35
128 6 0.07
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (125 bp):
ATATATATATTATATAGATTTTGAAAAAAACATTTTAAAAATATATACTATAGGTTTTTGAAAAA
CATTTTGAAAACACATAAAATATAGTTTTCAAAACATTTTGGAAAATATAATATATATAT
Found at i:3547529 original size:39 final size:37
Alignment explanation
Indices: 3547449--3547553 Score: 158
Period size: 39 Copynumber: 2.8 Consensus size: 37
3547439 AAACATTTTG
*
3547449 AATATATAATATATAGTTTTT-TAAATTTTTTTTGAA
1 AATATATAATATATAGTTTTTAAAAATTTTTTTTGAA
*
3547485 AATATATAATATATAGTTTTTAAAACATTTTTTTTTAA
1 AATATATAATATATAGTTTTTAAAA-ATTTTTTTTGAA
*
3547523 ATATATATATTATATAGTTTTTAAAAATTTT
1 A-ATATATAATATATAGTTTTTAAAAATTTT
3547554 GGAAAAATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
36 21 0.33
37 2 0.03
38 17 0.27
39 23 0.37
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (37 bp):
AATATATAATATATAGTTTTTAAAAATTTTTTTTGAA
Found at i:3547562 original size:37 final size:35
Alignment explanation
Indices: 3547417--3547581 Score: 126
Period size: 36 Copynumber: 4.6 Consensus size: 35
3547407 ATATATATAT
** *
3547417 ATATATATATATATA-TTTAAAAAAACATTTTG--A
1 ATATATATATATATAGTTTTTAAAAA-TTTTTGAAA
**
3547450 ATATATA-ATATATAGTTTTTTAAATTTTTTTTGAAA
1 ATATATATATATATAG-TTTTTAAA-AATTTTTGAAA
**
3547486 ATATATA-ATATATAGTTTTTAAAACATTTTTTTTTAA
1 ATATATATATATATAGTTTTTAAAA-A--TTTTTGAAA
*
3547523 ATATATATATTATATAGTTTTTAAAAATTTTGGAAA
1 ATATATATA-TATATAGTTTTTAAAAATTTTTGAAA
*
3547559 A-ATATATATTATATGATTTTTTA
1 ATATATATA-TATAT-AGTTTTTA
3547582 TATTATTCTT
Statistics
Matches: 108, Mismatches: 13, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
32 7 0.06
33 7 0.06
34 11 0.10
35 21 0.19
36 30 0.28
37 14 0.13
38 2 0.02
39 16 0.15
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (35 bp):
ATATATATATATATAGTTTTTAAAAATTTTTGAAA
Found at i:3547566 original size:39 final size:39
Alignment explanation
Indices: 3547483--3547567 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 39
3547473 ATTTTTTTTG
****
3547483 AAAATATATA-A-TATATAGTTTTTAAAACATTTTTTTT
1 AAAATATATATATTATATAGTTTTTAAAACATTTTGGAA
*
3547520 TAAATATATATATTATATAGTTTTTAAAA-ATTTTGG-A
1 AAAATATATATATTATATAGTTTTTAAAACATTTTGGAA
3547557 AAAATATATAT
1 AAAATATATAT
3547568 TATATGATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 19 0.46
38 6 0.15
39 16 0.39
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (39 bp):
AAAATATATATATTATATAGTTTTTAAAACATTTTGGAA
Found at i:3547599 original size:20 final size:20
Alignment explanation
Indices: 3547576--3547614 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3547566 ATTATATGAT
3547576 TTTTTATATT-ATTCTTTTTC
1 TTTTTATATTCATT-TTTTTC
*
3547596 TTTTTTTATTCATTTTTTT
1 TTTTTATATTCATTTTTTT
3547615 TTCAGGTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTATATTCATTTTTTTC
Found at i:3547604 original size:17 final size:17
Alignment explanation
Indices: 3547584--3547616 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3547574 ATTTTTTATA
3547584 TTATTC-TTTTTCTTTTT
1 TTATTCATTTTT-TTTTT
3547601 TTATTCATTTTTTTTT
1 TTATTCATTTTTTTTT
3547617 CAGGTCCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (17 bp):
TTATTCATTTTTTTTTT
Found at i:3552920 original size:95 final size:95
Alignment explanation
Indices: 3552803--3553065 Score: 312
Period size: 95 Copynumber: 2.7 Consensus size: 95
3552793 ACATTATAAT
* * * * *
3552803 ATTATATATATACAATAAAGCTTAAGTTGTCTCTCTAAAGCAATTGGTTAAATGCCTTGGCTTTA
1 ATTATA-ATATACAATCAAGCTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTA
* *
3552868 TGGATAAGATTCAACTAACCTGATAAAGGTG
65 TGGATAAAATTCAACTAACCTGATAAAGGCG
* *
3552899 ATTATAATATACAATCAAGCTTGAGTTGTCCCTGTAGAGCAATTGGTTAAACGCCCTGGCTTTAT
1 ATTATAATATACAATCAAGCTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTAT
* * * *
3552964 AGATAAAATTCAGCTATCCTTATAAAGGCG
66 GGATAAAATTCAACTAACCTGATAAAGGCG
* * * * *
3552994 ATTATAATAT-CTATACAATGATATTAAGCTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCT
1 ATTATAATATACAAT-CAA-G--CTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCT
3553058 TTATGGAT
62 TTATGGAT
3553066 TCAGCTAGCC
Statistics
Matches: 142, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
94 3 0.02
95 89 0.63
96 7 0.05
98 43 0.30
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (95 bp):
ATTATAATATACAATCAAGCTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTAT
GGATAAAATTCAACTAACCTGATAAAGGCG
Found at i:3554486 original size:36 final size:36
Alignment explanation
Indices: 3554398--3554549 Score: 236
Period size: 36 Copynumber: 4.2 Consensus size: 36
3554388 TAATTTACTC
3554398 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
3554435 AAAA-AAATTTTGTCTCTCTTGAGACAGTTTCT-TGT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCT-T
*
3554470 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
3554506 AAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
3554542 GAAACAAA
1 AAAACAAA
3554550 AACTTTGAAT
Statistics
Matches: 107, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
34 1 0.01
35 30 0.28
36 71 0.66
37 5 0.05
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:3554655 original size:174 final size:174
Alignment explanation
Indices: 3554442--3554840 Score: 564
Period size: 174 Copynumber: 2.3 Consensus size: 174
3554432 CTTAAAAAAA
* * * * *
3554442 TTTTGTCTCTCTTGAGACAGTTTCTTGTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTA
1 TTTTGTCTCTCTTAAGACAGTTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA
* *
3554507 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTG
66 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATATGTTTTCCTTG
* *
3554572 AAAAAAATTTTGTCTCCCTTGAGATAGCTTCTTTTGGAACTAAG
131 AAAAAAATTTTGTCTCCCTCGAGACAGCTTCTTTTGGAACTAAG
* * * * * *
3554616 TTTTGGCTCTCTTTAGACAATTTATTTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTAAGACAGTTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA
* * *
3554681 AATCAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTT
66 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATATGTTTTCCTTG
* * *
3554746 AAACAAATTTTGTCTCTCTCGAGACAGTTTCTTTTGGAACTAAG
131 AAAAAAATTTTGTCTCCCTCGAGACAGCTTCTTTTGGAACTAAG
* * ** *
3554790 TTTTATCTCTCTCAAGACAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGA
1 TTTTGTCTCTCTTAAGACAGTTTCTTTTGAAACAAATTTTGTCTCTCTTGA
3554841 AACACCAACC
Statistics
Matches: 195, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
174 195 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (174 bp):
TTTTGTCTCTCTTAAGACAGTTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATATGTTTTCCTTG
AAAAAAATTTTGTCTCCCTCGAGACAGCTTCTTTTGGAACTAAG
Found at i:3554662 original size:36 final size:36
Alignment explanation
Indices: 3554567--3554723 Score: 127
Period size: 36 Copynumber: 4.3 Consensus size: 36
3554557 AATCTGTTTT
* * * **
3554567 CCTTGAAAAAAATTTTGTCTCCCTTGAGATAGCTT-
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTA
* * * * *
3554602 CTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAATTTA
1 C-CTTGAAAC-AAATTTTGTCTCTCTTGAGACAATTTA
** * * *
3554640 TTTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTA
* * *
3554676 CCTTGAATCAAATTTTGTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTA
3554712 CCTTGAAACAAA
1 CCTTGAAACAAA
3554724 ATCTTTGAAT
Statistics
Matches: 96, Mismatches: 23, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
35 1 0.01
36 69 0.72
37 26 0.27
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
CCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTA
Found at i:3554682 original size:138 final size:137
Alignment explanation
Indices: 3554427--3554687 Score: 353
Period size: 138 Copynumber: 1.9 Consensus size: 137
3554417 CTTGAGACAG
* * *
3554427 TTTCTCTTAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTTGTAAAACAAATTTTGTCTCTCTTG
1 TTTCTCTTAAAAAAATTTTGTCTCCCTTGAGACAGCTTCTTGTAAAACAAATTTTGGCTCTCTTG
* * *
3554492 AGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAACTTTG
66 AGACAATTTATCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTG
3554557 AATCTGT
131 AATCTGT
* * ** *
3554564 TTTC-CTTGAAAAAAATTTTGTCTCCCTTGAGATAGCTTCTTTTGGAACTAAGTTTTGGCTCTCT
1 TTTCTCTT-AAAAAAATTTTGTCTCCCTTGAGACAGCTTCTTGTAAAAC-AAATTTTGGCTCTCT
* * * * *
3554628 TTAGACAATTTATTTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTGAATCAAA
64 TGAGACAATTTATCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
3554688 TTTTGTCTCT
Statistics
Matches: 106, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
136 3 0.03
137 38 0.36
138 65 0.61
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.43
Consensus pattern (137 bp):
TTTCTCTTAAAAAAATTTTGTCTCCCTTGAGACAGCTTCTTGTAAAACAAATTTTGGCTCTCTTG
AGACAATTTATCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTG
AATCTGT
Found at i:3554835 original size:36 final size:36
Alignment explanation
Indices: 3554736--3554837 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 36
3554726 CTTTGAATAT
* * * *
3554736 GTTTTCCTTTAAACAAATTTTGTCTCTCTCGAGACA
1 GTTTCCCTTGAAACAAGTTTTGTCTCTCTCAAGACA
** * *
3554772 GTTTCTTTTGGAACTAAGTTTTATCTCTCTCAAGACA
1 GTTTCCCTTGAAAC-AAGTTTTGTCTCTCTCAAGACA
3554809 GTTTCCCTTGAAACAAGTTTTGTCTCTCT
1 GTTTCCCTTGAAACAAGTTTTGTCTCTCT
3554838 TGAAACACCA
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
36 23 0.43
37 30 0.57
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.43
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAGTTTTGTCTCTCTCAAGACA
Found at i:3556722 original size:23 final size:22
Alignment explanation
Indices: 3556654--3556723 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
3556644 AATTTGGTCC
*
3556654 TTCTATTTTTATTTTATTATTA
1 TTCTACTTTTATTTTATTATTA
*
3556676 TT-T-CTTTTTATTTTATTTGTTTA
1 TTCTAC-TTTTATTTTA-TT-ATTA
3556699 TTCTACTTTTATTTTATTACTTA
1 TTCTACTTTTATTTTATTA-TTA
3556722 TT
1 TT
3556724 ACTTATTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
21 11 0.28
22 4 0.10
23 12 0.31
24 11 0.28
25 1 0.03
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.73
Consensus pattern (22 bp):
TTCTACTTTTATTTTATTATTA
Found at i:3557165 original size:17 final size:18
Alignment explanation
Indices: 3557127--3557174 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
3557117 TCTTATTTGC
*
3557127 CTTTTATTTTTTAC-TTA
1 CTTTTATTTTTTTCTTTA
3557144 CTTTTATTTTTTTCTTTA
1 CTTTTATTTTTTTCTTTA
*
3557162 -TTTT-TTTTATTCT
1 CTTTTATTTTTTTCT
3557175 ACCTTCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.29
17 17 0.61
18 3 0.11
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.77
Consensus pattern (18 bp):
CTTTTATTTTTTTCTTTA
Found at i:3557680 original size:21 final size:22
Alignment explanation
Indices: 3557651--3557701 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3557641 CAAACTACAT
* *
3557651 AATATAAATAAAT-AAATTAAA
1 AATAAAAATAAATGAAATGAAA
3557672 AATAAAAATAAATGAAATGAAA
1 AATAAAAATAAATGAAATGAAA
*
3557694 AAGAAAAA
1 AATAAAAA
3557702 GGAAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (22 bp):
AATAAAAATAAATGAAATGAAA
Found at i:3558787 original size:84 final size:83
Alignment explanation
Indices: 3558319--3559253 Score: 822
Period size: 84 Copynumber: 11.3 Consensus size: 83
3558309 TGAACTGATT
* * * * * * * *
3558319 GTAATCGAACTCGAGGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATG
* * *
3558384 ATGTGCCTTGGAGTTTAGT
65 ATGTGCCTTGGAGCTGAGC
* * * * *
3558403 GTAGTCGAACTCGAATGTATTTGGTGACAGATAACCCTTCTA-CCTTGAGTTATGCTGTAAATGA
1 GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGA
* * *
3558467 TGTGCCCTCGAAGCTGAGT
66 TGTG-CCTTGGAGCTGAGC
* * * * * *
3558486 GCAATCGAACTCG-AGTGTATTT-G-G-CAGATAGCCCTTCTCGACTTAAGTTATGTTGCAAATG
1 GTAATCGAACTCGAAG-GTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATG
* *
3558547 ATGTGCCTTGGAGCTTAAC
65 ATGTGCCTTGGAGCTGAGC
* *
3558566 GTAATCGAACTCGAAGGTCTTTAGTGACAGATAACCCTTCTAG-CTTTGAGTTATGCTGTAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGAC-TTAAGTTATGCTGTAAATG
* * * *
3558630 ATGTGCCCTCGAAACTGAGT
65 ATGTG-CCTTGGAGCTGAGC
* * * * *
3558650 GTAATCGAACTTGAGGGTCTTTGGTTGATAGATAACCCTTCTTGACTTAAGTTATGTTGTAAATG
1 GTAATCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATG
* *
3558715 ATATGCCTTGGAGCTAAGC
65 ATGTGCCTTGGAGCTGAGC
* * * * * *
3558734 GTAGTCGAACTCAAAGGTCTTTTAGTGACATATAACCCTTCTAG-CTTTGAGTTATGTTGTAAAT
1 GTAATCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGAC-TTAAGTTATGCTGTAAAT
* * * *
3558798 GATGTTCCCTCGAAGCTGAGT
64 GATG-TGCCTTGGAGCTGAGC
* * * * *
3558819 GTAATCGAACTCGAGGGTCTTTGGT---AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGA
*
3558881 TGTGCCTTGGAGCTGAAC
66 TGTGCCTTGGAGCTGAGC
* * * *
3558899 GTAGTCGAACTCAAAGGTCTTTGGTTGGA-AGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
1 GTAATCGAACTCGAAGGTCTTTGG-T-GACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAAT
* *
3558963 GATATGCCTTAGAGCTGAGC
64 GATGTGCCTTGGAGCTGAGC
* * *
3558983 GTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAG-CTTTGAGTTATACTGTAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGAC-TTAAGTTATGCTGTAAATG
* ***
3559047 ATGTTCCCTCAAAGCTGA-C
65 ATG-TGCCTTGGAGCTGAGC
* * * * **
3559066 TGTAATCGAACTCGAGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATG
1 -GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATG
*
3559128 ATGTGCCTTGGAGCTAAGC
65 ATGTGCCTTGGAGCTGAGC
* * * * * **
3559147 ATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATG
1 GTAATCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATG
* *
3559212 TTGTGCCTTTGAGCTGAGC
65 ATGTGCCTTGGAGCTGAGC
* * **
3559231 ATAGTTAAACTCGAAGGTCTTTG
1 GTAATCGAACTCGAAGGTCTTTG
3559254 TTGGAAAATA
Statistics
Matches: 692, Mismatches: 130, Indels: 58
0.79 0.15 0.07
Matches are distributed among these distances:
80 99 0.14
81 90 0.13
82 31 0.04
83 114 0.16
84 288 0.42
85 69 0.10
86 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (83 bp):
GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGA
TGTGCCTTGGAGCTGAGC
Found at i:3558878 original size:333 final size:331
Alignment explanation
Indices: 3558310--3559023 Score: 977
Period size: 333 Copynumber: 2.2 Consensus size: 331
3558300 GTTTACCTCT
* * * *
3558310 GAACTGATTGTAATCGAACTCGAGGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
1 GAACTGAGTGTAATCGAACTCGAGGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGCTATG
* * * * * * *
3558375 ATGCAAATGATGTGCCTTGGAGTTTAGTGTAGTCGAACTCGAATGTATTTGGTGACAGATAACCC
66 ATGCAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCAAAGGTATTTAGTGACAGATAACCC
*
3558440 TTCTACCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCGAACTCGAGTGTA
131 TTCTACCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCGAACTCGAGGGTA
* * *
3558505 TTTGGCAGATAGCCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCTTGGAGCTTAACGTAA
196 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAA
* * *
3558570 TCGAACTCGAAGGTCTTTAG-T-GACAGATAACCCTTCTAG-CTTTGAGTTATGCTGTAAATGAT
261 TCGAACTCAAAGGTCTTTAGTTGGA-AGATAACCCTTCTAGAC-TTAAGTTATGCTGCAAATGAT
* *
3558632 GTGCCCTC
324 ATGCCCTA
* * * *
3558640 GAAACTGAGTGTAATCGAACTTGAGGGTCTTTGGTTGATAGATAACCCTTCTTGACTTAAGTTAT
1 G-AACTGAGTGTAATCGAACTCGAGGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGCTAT
* * * *
3558705 GTTGTAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCAAAGGTCTTTTAGTGACATATAAC
65 GATGCAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCAAAGGT-ATTTAGTGACAGATAAC
* * * *
3558770 CCTTCTAGCTTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGAGG
129 CCTTCTA-CCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCGAACTCGAGG
* *
3558835 GTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACG
193 GTATTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACG
* * *
3558900 TAGTCGAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
258 TAATCGAACTCAAAGGTCTTTAGTTGGAAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
*
3558965 TATGCCTTA
323 TATGCCCTA
* * * *
3558974 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCT
1 GAACTGAGTGTAATCGAACTCGAGGGTCTTTGGTTGACAGATAACCCTTCT
3559024 AGCTTTGAGT
Statistics
Matches: 334, Mismatches: 44, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
330 1 0.00
331 94 0.28
332 37 0.11
333 159 0.48
334 40 0.12
335 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (331 bp):
GAACTGAGTGTAATCGAACTCGAGGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGCTATG
ATGCAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCAAAGGTATTTAGTGACAGATAACCC
TTCTACCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCGAACTCGAGGGTA
TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAA
TCGAACTCAAAGGTCTTTAGTTGGAAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATAT
GCCCTA
Found at i:3559077 original size:333 final size:330
Alignment explanation
Indices: 3558319--3559271 Score: 938
Period size: 333 Copynumber: 2.9 Consensus size: 330
3558309 TGAACTGATT
* * * * * * *
3558319 GTAATCGAACTCGAGGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGA-TGCAAAT
1 GTAATCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTAT-ACTGTAAAT
* * *** * * * * * * * *
3558383 GATGTGCCTTGGAGTTTAGTGTAGTCGAACTCGAATGTATTTGGTGACAGATAACCCTTCTACCT
65 GATATCCCTCAAAGCTAAGCGTAATCGAACTCAAAGGTCTTT-GTGACAGATAACCCTTCTAGCT
* * * * *
3558448 TGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCGAACTCGAGTGTATTTGGCAG
129 TGAGTTATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAG
* * *
3558513 ATAGCCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCTTGGAGCTTAACGTAATCGAACTC
194 ATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTC
* * * *
3558578 GAAGGTCTTTAG-T-GACAGATAACCCTTCTAGCTTTGAGTTATGCTGTAAATGATGTGCCCTCG
259 GAAGGTCTTT-GTTGGA-AGATAACCCTTCTAGCTTTAAGTTATGCTGCAAATGATATGCCCTAG
*
3558641 AAACTGAGT
322 AAACTGAGC
* * * * **
3558650 GTAATCGAACTTGAGGGTCTTTGGTTGATAGATAACCCTTCTTGACTTAAGTTATGTTGTAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATACTGTAAATG
* *** * *
3558715 ATATGCCTTGGAGCTAAGCGTAGTCGAACTCAAAGGTCTTTTAGTGACATATAACCCTTCTAGCT
66 ATATCCCTCAAAGCTAAGCGTAATCGAACTCAAAGGTC-TTT-GTGACAGATAACCCTTCTAGC-
*
3558780 TTGAGTTATGTTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTA
128 TTGAGTTATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTA
*
3558845 GATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACT
193 GATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACT
* * *
3558910 CAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGAC-TTAAGTTATGCTGCAAATGATATGCCTTA
258 CGAAGGTCTTT-GTTGGAAGATAACCCTTCTAG-CTTTAAGTTATGCTGCAAATGATATGCCCTA
*
3558974 G-AGCTGAGC
321 GAAACTGAGC
* *
3558983 GTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAG-CTTTGAGTTATACTGTAAAT
1 GTAATCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGAC-TTAAGTTATACTGTAAAT
* * * * * *
3559046 GATGTTCCCTCAAAGCTGA-CTGTAATCGAACTCGAGGGTCTTTG-G-CAGATAGCCCTTCTCGA
65 GAT-ATCCCTCAAAGCTAAGC-GTAATCGAACTCAAAGGTCTTTGTGACAGATAACCCTTCTAG-
* * ** * * * * ** * *
3559108 CTTAAGCTATGCTACAAATGATG-TGCCTTGGAGCTAAGCATAGTCGAACTCGAAGGTCTTTGGT
127 CTTGAGTTATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG-
* * * * * * * *
3559172 TGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGTTGTGCCTTTGAGCTGAGCATAGTT
191 T---AGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTC
* * *
3559237 AAACTCGAAGGTCTTTGTTGGAAAATAGCCCTTCT
253 GAACTCGAAGGTCTTTGTTGGAAGATAACCCTTCT
3559272 TGCCTTGAGC
Statistics
Matches: 523, Mismatches: 85, Indels: 28
0.82 0.13 0.04
Matches are distributed among these distances:
328 32 0.06
329 31 0.06
330 2 0.00
331 105 0.20
332 127 0.24
333 183 0.35
334 40 0.08
335 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (330 bp):
GTAATCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATACTGTAAATG
ATATCCCTCAAAGCTAAGCGTAATCGAACTCAAAGGTCTTTGTGACAGATAACCCTTCTAGCTTG
AGTTATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAGAT
AGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGA
AGGTCTTTGTTGGAAGATAACCCTTCTAGCTTTAAGTTATGCTGCAAATGATATGCCCTAGAAAC
TGAGC
Found at i:3559100 original size:248 final size:248
Alignment explanation
Indices: 3558258--3559253 Score: 1059
Period size: 248 Copynumber: 4.0 Consensus size: 248
3558248 AAAGTTTTAT
* * * * * * * *
3558258 TGACATATAGCCCTTCTTGCCTTGAGCTATGTTGTAAAT-TTGGTTTACCTCTGAA-CTGATTGT
1 TGACAGATAACCCTTCTAGCTTTGAGTTATGTTGTAAATGAT-G-TTCCCTC-GAAGCTGACTGT
*
3558321 AATCGAACTCGAGGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGAT
63 AATCGAACTCGAGGGTC-T---TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
* * ** * *
3558386 GTGCCTTGGAGTTTAGTGTAGTCGAACTCGAATGTATTTGG-TGACAGATAACCCTTCT--ACCT
124 GTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGA-CT
* * * * * * * * *
3558448 TGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCGAACTCG-AGTGTATTT-G
188 TAAGTTATGCTGCAAATGATATGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAG-GTCTTTGG
* * * * * * * *
3558509 -G-CAGATAGCCCTTCTCGAC-TTAAGTTATGTTGCAAATGATG-TGCCTTGGAGCTTAAC-GTA
1 TGACAGATAACCCTTCTAG-CTTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGC-TGACTGTA
* * * * * *
3558569 ATCGAACTCGAAGGTCTTTAGTGACAGATAACCCTTCTAG-CTTTGAGTTATGCTGTAAATGATG
64 ATCGAACTCGAGGGTCTTT-G-G-CAGATAGCCCTTCTCGAC-TTAAGCTATGCTGCAAATGATG
* * * ** * * * * *
3558633 TGCCCTCGAAACTGAGTGTAATCGAACTTGAGGGTCTTTGGTTGATAGATAACCCTTCTTGACTT
125 TG-CCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTT
* * * * * *
3558698 AAGTTATGTTGTAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCAAAGGTCTTTTAG
189 AAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
* *
3558759 TGACATATAACCCTTCTAGCTTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCTTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGCTGACTGTAAT
*
3558824 CGAACTCGAGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
66 CGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
*
3558889 GGAGCTGAACGTAGTCGAACTCAAAGGTCTTTGGTTGGA-AGATAACCCTTCTCGACTTAAGTTA
131 GGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTT-GACAGATAACCCTTCTCGACTTAAGTTA
3558953 TGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
195 TGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
** *
3559007 TGACAGATAACCCTTCTAGCTTTGAGTTATACTGTAAATGATGTTCCCTCAAAGCTGACTGTAAT
1 TGACAGATAACCCTTCTAGCTTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGCTGACTGTAAT
*
3559072 CGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTT
66 CGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* *
3559137 GGAGCT-AAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
131 GGAGCTGAA-CGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTA
* * * * * * **
3559201 TACTACAAATGTTGTGCCTTTGAGCTGAGCATAGTTAAACTCGAAGGTCTTTG
195 TGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
3559254 TTGGAAAATA
Statistics
Matches: 630, Mismatches: 91, Indels: 51
0.82 0.12 0.07
Matches are distributed among these distances:
243 2 0.00
244 1 0.00
245 2 0.00
246 37 0.06
247 54 0.09
248 264 0.42
249 160 0.25
250 41 0.07
251 4 0.01
252 36 0.06
253 29 0.05
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (248 bp):
TGACAGATAACCCTTCTAGCTTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGCTGACTGTAAT
CGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
GGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTAT
GCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:3559244 original size:164 final size:161
Alignment explanation
Indices: 3558323--3559253 Score: 592
Period size: 164 Copynumber: 5.6 Consensus size: 161
3558313 CTGATTGTAA
* * * *
3558323 TCGAACTCGAGGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGA-TGCAAATGATG
1 TCGAACTCGAAGGTCTTTGG-T-GCAGATAACCCTTCTCGACTTAAGTTAT-ACTGCAAATGATG
* * * * * * *
3558387 TGCCTTGGAGTTTAGTGTAGTCGAACTCGAATGTATTTGGTGACAGATAACCCTTCT--ACCTTG
63 TGCCTTAGAGCTGA-CGTAGTCGAACTCGAAGGTCTTT-G-GA-AGATAACCCTTCTCGA-CTTA
* ** * * * *
3558450 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCA-A-
123 AGCTATGCTACAAATGATATGCCTTAG-AGCT-A-AGCATAG
* * **
3558490 TCGAACTCG-AGTGTATTT-G-GCAGATAGCCCTTCTCGACTTAAGTTATGTTGCAAATGATGTG
1 TCGAACTCGAAG-GTCTTTGGTGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTG
* * * * *
3558552 CCTTGGAGCTTAACGTAATCGAACTCGAAGGTCTTTAGTGACAGATAACCCTTCTAG-CTTTGAG
65 CCTTAGAGC-TGACGTAGTCGAACTCGAAGGTCTTT-G-GA-AGATAACCCTTCTCGAC-TTAAG
* ** * * * * * ** *
3558616 TTATGCTGTAAATGATGTGCCCTCGAAACTGAGTGTAA
125 CTATGCTACAAATGATATGCCTTAG-AGCTAAGCATAG
* * * * ** * *
3558654 TCGAACTTGAGGGTCTTTGGTTGATAGATAACCCTTCTTGACTTAAGTTATGTTGTAAATGATAT
1 TCGAACTCGAAGGTCTTTGG-TG-CAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
* * * * * *
3558719 GCCTTGGAGCTAAGCGTAGTCGAACTCAAAGGTCTTTTAGTGACATATAACCCTTCTAG-CTTTG
64 GCCTTAGAGCTGA-CGTAGTCGAACTCGAAGGTC-TTT-G-GA-AGATAACCCTTCTCGAC-TTA
* * ** * * * * * ** *
3558783 AGTTATGTTGTAAATGATGTTCCCTCGAAGCTGAGTGTAA
123 AGCTATGCTACAAATGATATGCCTTAG-AGCTAAGCATAG
* * * *
3558823 TCGAACTCGAGGGTCTTTGGT--AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
1 TCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGC
* * *
3558886 CTTGGAGCTGAACGTAGTCGAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGT
66 CTTAGAGCTG-ACGTAGTCGAACTCGAAGGTC--T--TTGGAAGATAACCCTTCTCGACTTAAGC
* * *
3558951 TATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAG
126 TATGCTACAAATGATATGCCTTAGAGCTAAGCATAG
* * *
3558987 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAG-CTTTGAGTTATACTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTG-CAGATAACCCTTCTCGAC-TTAAGTTATACTGCAAATGATG-
* * * * * * *
3559051 TCCCTCAAAGCTGACTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
63 TGCCTTAGAGCTGAC-GTAGTCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTCGACTTAAGCT
* *
3559116 ATGCTACAAATGATGTGCCTTGGAGCTAAGCATAG
127 ATGCTACAAATGATATGCCTTAGAGCTAAGCATAG
* *
3559151 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGTTGT
1 TCGAACTCGAAGGTCTTTGG-T-GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
* * **
3559216 GCCTTTGAGCTGAGCATAGTTAAACTCGAAGGTCTTTG
64 GCCTTAGAGCTGA-CGTAGTCGAACTCGAAGGTCTTTG
3559254 TTGGAAAATA
Statistics
Matches: 648, Mismatches: 86, Indels: 63
0.81 0.11 0.08
Matches are distributed among these distances:
162 1 0.00
163 87 0.13
164 183 0.28
165 138 0.21
166 12 0.02
167 51 0.08
168 92 0.14
169 84 0.13
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (161 bp):
TCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGC
CTTAGAGCTGACGTAGTCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTCGACTTAAGCTATGC
TACAAATGATATGCCTTAGAGCTAAGCATAG
Found at i:3563139 original size:19 final size:18
Alignment explanation
Indices: 3563117--3563157 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
3563107 GGTAGAATAA
3563117 AAAAATAAAGGAAAAAAAT
1 AAAAAT-AAGGAAAAAAAT
*
3563136 AAAAATAAGTAAAAAAAT
1 AAAAATAAGGAAAAAAAT
3563154 AAAA
1 AAAA
3563158 GGCAAAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAAATAAGGAAAAAAAT
Found at i:3565600 original size:30 final size:31
Alignment explanation
Indices: 3565566--3565630 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
3565556 ATTCTTTAAA
*
3565566 AAATTTCAAAGACTAAATTG-AATTTTGATT
1 AAATTTCAAAGACTAAAGTGAAATTTTGATT
**
3565596 AAA-TTCAGGGACTAAAGTGAAATTTTGATT
1 AAATTTCAAAGACTAAAGTGAAATTTTGATT
3565626 AAATT
1 AAATT
3565631 CAGATCCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 13 0.43
30 16 0.53
31 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (31 bp):
AAATTTCAAAGACTAAAGTGAAATTTTGATT
Found at i:3565608 original size:29 final size:30
Alignment explanation
Indices: 3565576--3565633 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3565566 AAATTTCAAA
*
3565576 GACTAAATTG-AATTTTGATTAAATTCAGG
1 GACTAAAGTGAAATTTTGATTAAATTCAGG
3565605 GACTAAAGTGAAATTTTGATTAAATTCAG
1 GACTAAAGTGAAATTTTGATTAAATTCAG
3565634 ATCCAAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (30 bp):
GACTAAAGTGAAATTTTGATTAAATTCAGG
Found at i:3567139 original size:117 final size:116
Alignment explanation
Indices: 3566929--3567211 Score: 343
Period size: 117 Copynumber: 2.4 Consensus size: 116
3566919 CTGCTTACCG
* ** *
3566929 TAGGCTCC-TTGACTTTGTGCTAAGGGTAAGTCCTTACCGTAGGCTCCTCGGTTTTTTGCTCAAG
1 TAGGCTCCTTTG-CTTTGTGCT-AGGGTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAAG
* * * *
3566993 GTAAGTCTTTACTGCAGGCTCCTCTACTTTGTGGACATGATAAGACCTTATCA
64 GTAAGTCCTTACTGCAGGCTCCTCGACTTTGTGCACAGGATAAGACCTTATCA
* * *
3567046 TATGCTCCTTTGCTTTCTGCTCAGGGTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAGGG
1 TAGGCTCCTTTGCTTTGTGCT-AGGGTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAAGG
* * * *
3567111 TAAGTCCTTACTGCAGGCTCCTCGACTTTGTGCTCAGGGTAAGTCCTTATTA
65 TAAGTCCTTACTGCAGGCTCCTCGACTTTGTGCACAGGATAAGACCTTATCA
* * * * *
3567163 TAGGCTTCTCTGCTTTGTGCATAGGATAAGACCTTACCGCAAGCTCCTC
1 TAGGCTCCTTTGCTTTGTGC-TAGGGTAAGTCCTTACCGCAGGCTCCTC
3567212 TGCTTTCCCT
Statistics
Matches: 141, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
117 137 0.97
118 4 0.03
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (116 bp):
TAGGCTCCTTTGCTTTGTGCTAGGGTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAAGGT
AAGTCCTTACTGCAGGCTCCTCGACTTTGTGCACAGGATAAGACCTTATCA
Found at i:3567213 original size:39 final size:39
Alignment explanation
Indices: 3566922--3567217 Score: 258
Period size: 39 Copynumber: 7.6 Consensus size: 39
3566912 GACCTTACTG
* *
3566922 CTTACCGTAGGCTCCT-TGACTTTGTGCTAAGGGTAAGTC
1 CTTACCGCAGGCTCCTCTG-CTTTGTGCTCAGGGTAAGTC
* * * * *
3566961 CTTACCGTAGGCTCCTCGGTTTTTTGCTCAAGGTAAGTC
1 CTTACCGCAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTC
* * * ** * * *
3567000 TTTACTGCAGGCTCCTCTACTTTGTGGACATGATAAGAC
1 CTTACCGCAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTC
* ** * * *
3567039 CTTATCATATGCTCCTTTGCTTTCTGCTCAGGGTAAGTC
1 CTTACCGCAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTC
3567078 CTTACCGCAGGCTCCTC-GACTTTGTGCTCAGGGTAAGTC
1 CTTACCGCAGGCTCCTCTG-CTTTGTGCTCAGGGTAAGTC
*
3567117 CTTACTGCAGGCTCCTC-GACTTTGTGCTCAGGGTAAGTC
1 CTTACCGCAGGCTCCTCTG-CTTTGTGCTCAGGGTAAGTC
**** * * *
3567156 CTTATTATAGGCTTCTCTGCTTTGTGCAT-AGGATAAGAC
1 CTTACCGCAGGCTCCTCTGCTTTGTGC-TCAGGGTAAGTC
*
3567195 CTTACCGCAAGCTCCTCTGCTTT
1 CTTACCGCAGGCTCCTCTGCTTT
3567218 CCCTTACTTG
Statistics
Matches: 203, Mismatches: 50, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
38 1 0.00
39 199 0.98
40 3 0.01
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (39 bp):
CTTACCGCAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTC
Found at i:3568360 original size:13 final size:13
Alignment explanation
Indices: 3568344--3568378 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3568334 AAAAAGAATT
*
3568344 TTTAAAATTGTTG
1 TTTAAAATTGTAG
*
3568357 TTTAAAAGTGTAG
1 TTTAAAATTGTAG
3568370 TTTAAAATT
1 TTTAAAATT
3568379 TAATTATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (13 bp):
TTTAAAATTGTAG
Found at i:3575356 original size:29 final size:31
Alignment explanation
Indices: 3575318--3575385 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
3575308 AAACAAAAGT
* *
3575318 AATTCGAAAGTTTAGTGAATAAATTAA-AA-A
1 AATT-GAAAGTATAGTGAATAAAATAATAAGA
* *
3575348 AATTGAAAGTATGGTGAGTAAAATAATAAGA
1 AATTGAAAGTATAGTGAATAAAATAATAAGA
3575379 AATTGAA
1 AATTGAA
3575386 CCCATTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 18 0.56
30 6 0.19
31 8 0.25
ACGTcount: A:0.53, C:0.01, G:0.18, T:0.28
Consensus pattern (31 bp):
AATTGAAAGTATAGTGAATAAAATAATAAGA
Done.