Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 39
Found at i:2729988 original size:21 final size:21
Alignment explanation
Indices: 2729962--2730001 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2729952 ATGGAATGTG
2729962 GATCCTGAACGATAGGAGGTA
1 GATCCTGAACGATAGGAGGTA
*
2729983 GATCCTGAACGATGGGAGG
1 GATCCTGAACGATAGGAGG
2730002 GGCCTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.38, T:0.17
Consensus pattern (21 bp):
GATCCTGAACGATAGGAGGTA
Found at i:2730033 original size:21 final size:21
Alignment explanation
Indices: 2729963--2730033 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
2729953 TGGAATGTGG
2729963 ATCCTGAACGAT-AGGAGGT-A
1 ATCCTGAACGATGA-GAGGTGA
* * *
2729983 GATCCTGAACGATGGGAGGGGC
1 -ATCCTGAACGATGAGAGGTGA
* **
2730005 CTTTTGAACGATGAGAGGTGA
1 ATCCTGAACGATGAGAGGTGA
2730026 ATCCTGAA
1 ATCCTGAA
2730034 TAATGGGAGG
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (21 bp):
ATCCTGAACGATGAGAGGTGA
Found at i:2730390 original size:21 final size:20
Alignment explanation
Indices: 2730366--2730442 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 20
2730356 GAGCACCGAC
*
2730366 CTCATCACGTAAAGCATCTAT
1 CTCACCACGTAAAGCA-CTAT
* *
2730387 CTCACCACTTAAAGCACCATT
1 CTCACCACGTAAAGCACTA-T
* * * *
2730408 TTCATCACGTAAAACAACTAC
1 CTCACCACGTAAAGC-ACTAT
2730429 CTCACCACGTAAAG
1 CTCACCACGTAAAG
2730443 ACCCTACCTC
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 2 0.05
21 37 0.88
22 3 0.07
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.23
Consensus pattern (20 bp):
CTCACCACGTAAAGCACTAT
Found at i:2730467 original size:63 final size:63
Alignment explanation
Indices: 2730362--2730518 Score: 172
Period size: 63 Copynumber: 2.5 Consensus size: 63
2730352 CGTAGAGCAC
* * * * * ** * *
2730362 CGACCTCATCACGTAAAGCATCTATCTCACCACTTAAAGCACCATTTTCATCACGTAAAACAA
1 CGACCTCACCACATAAAGCACCTAACTCATCACTCCATGCACCATTGTCATCACGTAAAACAA
* * * *
2730425 CTACCTCACCACGTAAAG-ACCCTACCTCATCACTCCATGCACCATTGTCATCACGTAAAACAC
1 CGACCTCACCACATAAAGCA-CCTAACTCATCACTCCATGCACCATTGTCATCACGTAAAACAA
*
2730488 CGACCTCATCACATAAAGCACCTAACTCATC
1 CGACCTCACCACATAAAGCACCTAACTCATC
2730519 CCATGGAGGT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
62 1 0.01
63 76 0.97
64 1 0.01
ACGTcount: A:0.34, C:0.36, G:0.08, T:0.22
Consensus pattern (63 bp):
CGACCTCACCACATAAAGCACCTAACTCATCACTCCATGCACCATTGTCATCACGTAAAACAA
Found at i:2730496 original size:21 final size:21
Alignment explanation
Indices: 2730472--2730518 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2730462 TGCACCATTG
* *
2730472 TCATCACGTAAAACACCGACC
1 TCATCACGTAAAGCACCTACC
* *
2730493 TCATCACATAAAGCACCTAAC
1 TCATCACGTAAAGCACCTACC
2730514 TCATC
1 TCATC
2730519 CCATGGAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.36, G:0.06, T:0.19
Consensus pattern (21 bp):
TCATCACGTAAAGCACCTACC
Found at i:2730518 original size:42 final size:42
Alignment explanation
Indices: 2730349--2730518 Score: 114
Period size: 42 Copynumber: 4.0 Consensus size: 42
2730339 CGAAACAATT
* * *
2730349 TCACGTAGAGCACCGACCTCATCACGTAAAGCATCTATCTCA
1 TCACGTAAAACACCGACCTCATCACGTAAAGCACCTATCTCA
* * * ** * * *
2730391 CCACTTAAAGCACC-ATTTTCATCACGTAAAACAACTACCTCA
1 TCACGTAAAACACCGA-CCTCATCACGTAAAGCACCTATCTCA
* * * * *
2730433 CCACGTAAAGAC-CCTACCTCATCAC-TCCATGCACC-ATTGTCA
1 TCACGTAAA-ACACCGACCTCATCACGT-AAAGCACCTA-TCTCA
* *
2730475 TCACGTAAAACACCGACCTCATCACATAAAGCACCTAACTCA
1 TCACGTAAAACACCGACCTCATCACGTAAAGCACCTATCTCA
2730517 TC
1 TC
2730519 CCATGGAGGT
Statistics
Matches: 96, Mismatches: 24, Indels: 16
0.71 0.18 0.12
Matches are distributed among these distances:
41 5 0.05
42 87 0.91
43 4 0.04
ACGTcount: A:0.34, C:0.36, G:0.09, T:0.21
Consensus pattern (42 bp):
TCACGTAAAACACCGACCTCATCACGTAAAGCACCTATCTCA
Found at i:2730711 original size:42 final size:42
Alignment explanation
Indices: 2730665--2730744 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
2730655 TAATCAGGTC
*
2730665 ATGGATCTCGGTGTT-GAAG-TGGAGAATCGACTCGATGAGGAG
1 ATGGATCTCGGT-TTCG-AGCTGAAGAATCGACTCGATGAGGAG
*
2730707 ATGGATCTTGGTTTCGAGCTGAAGAATCGACTCGATGA
1 ATGGATCTCGGTTTCGAGCTGAAGAATCGACTCGATGA
2730745 AAAAGTGGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 4 0.12
42 30 0.88
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.26
Consensus pattern (42 bp):
ATGGATCTCGGTTTCGAGCTGAAGAATCGACTCGATGAGGAG
Found at i:2732317 original size:34 final size:34
Alignment explanation
Indices: 2732253--2732318 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
2732243 CTTGAAACTT
* **
2732253 AAATTCGCAACATGAAAATCGAAATTCGAAAATG
1 AAATTCGCAACACGAAAATCGAAACGCGAAAATG
*
2732287 AAATTCGCAACACGAAAATCGCAACGCGAAAA
1 AAATTCGCAACACGAAAATCGAAACGCGAAAA
2732319 CTAAAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (34 bp):
AAATTCGCAACACGAAAATCGAAACGCGAAAATG
Found at i:2732366 original size:20 final size:20
Alignment explanation
Indices: 2732329--2732366 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2732319 CTAAAATCGC
* *
2732329 GTTGCGAATTTCATTTTCGT
1 GTTGCGAATTTAAGTTTCGT
2732349 GTTGCGAATTTAAGTTTC
1 GTTGCGAATTTAAGTTTC
2732367 AAAAACTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.47
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCGT
Found at i:2732725 original size:22 final size:22
Alignment explanation
Indices: 2732699--2732749 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2732689 ATGGAGGGGG
* *
2732699 GTCGTCGGATATGGGGACGGAT
1 GTCGTCGGAGATGGGAACGGAT
*
2732721 TTCGTCGGAGATGGGAACGGAT
1 GTCGTCGGAGATGGGAACGGAT
2732743 GTCGTCG
1 GTCGTCG
2732750 TAGAGAGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.43, T:0.24
Consensus pattern (22 bp):
GTCGTCGGAGATGGGAACGGAT
Found at i:2733058 original size:19 final size:20
Alignment explanation
Indices: 2732976--2733066 Score: 96
Period size: 20 Copynumber: 4.6 Consensus size: 20
2732966 AGAAATTCGA
*
2732976 GTTGCGAATTTGAAAACTGA
1 GTTGCGAATTTGAAAACTGT
2732996 GTTGCGAATTTGAAAACTGT
1 GTTGCGAATTTGAAAACTGT
* * **
2733016 GTTGCGAAATTG-GAGTTCGT
1 GTTGCGAATTTGAAAACT-GT
* *
2733036 GTTGCGAATTTGAAATC-GC
1 GTTGCGAATTTGAAAACTGT
2733055 GTTGCGAATTTG
1 GTTGCGAATTTG
2733067 TTGGGTTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
19 15 0.25
20 43 0.73
21 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAAACTGT
Found at i:2736849 original size:16 final size:16
Alignment explanation
Indices: 2736828--2736862 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2736818 ATTACCGACT
2736828 TGTTTTCAACCTGACC
1 TGTTTTCAACCTGACC
*
2736844 TGTTTTTAACCTGACC
1 TGTTTTCAACCTGACC
2736860 TGT
1 TGT
2736863 AAATGATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (16 bp):
TGTTTTCAACCTGACC
Found at i:2737990 original size:21 final size:21
Alignment explanation
Indices: 2737947--2737991 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2737937 TCCATTTATA
*
2737947 TTAGGGTTTGTGGTTTAGGAT
1 TTAGGGTTTGTGGTTTAAGAT
*
2737968 TTAGGGTTTAGT-GTTTAATAT
1 TTAGGGTTT-GTGGTTTAAGAT
2737989 TTA
1 TTA
2737992 AAGTTTAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (21 bp):
TTAGGGTTTGTGGTTTAAGAT
Found at i:2737997 original size:21 final size:20
Alignment explanation
Indices: 2737958--2738021 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
2737948 TAGGGTTTGT
* **
2737958 GGTTTAGGATTTAGGGTTTA
1 GGTTTATGATTTAAAGTTTA
2737978 GTGTTTAAT-ATTTAAAGTTTAA
1 G-GTTT-ATGATTTAAAGTTT-A
2738000 GGTTTATGATTTAAAGTTTA
1 GGTTTATGATTTAAAGTTTA
2738020 GG
1 GG
2738022 GCTTAGGGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 6 0.16
21 28 0.76
22 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (20 bp):
GGTTTATGATTTAAAGTTTA
Found at i:2738033 original size:21 final size:21
Alignment explanation
Indices: 2737987--2738033 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2737977 AGTGTTTAAT
* *
2737987 ATTTAAAGTTTAAGGTTTATG
1 ATTTAAAGTTTAAGGCTTAGG
*
2738008 ATTTAAAGTTTAGGGCTTAGG
1 ATTTAAAGTTTAAGGCTTAGG
*
2738029 GTTTA
1 ATTTA
2738034 TGATTTAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (21 bp):
ATTTAAAGTTTAAGGCTTAGG
Found at i:2738147 original size:21 final size:22
Alignment explanation
Indices: 2738121--2738163 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
2738111 TAATTTACTT
2738121 TATATAGTTTATATATA-TATA
1 TATATAGTTTATATATACTATA
2738142 TATATAGTTTATATATACTATA
1 TATATAGTTTATATATACTATA
2738164 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (22 bp):
TATATAGTTTATATATACTATA
Found at i:2738706 original size:19 final size:18
Alignment explanation
Indices: 2738682--2738725 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2738672 AAAATTTTCT
*
2738682 ATTTCCTCAAAATTTCCCA
1 ATTTCCTCAAAA-TTCACA
*
2738701 ATTTCCCTCTAAATTCACA
1 ATTT-CCTCAAAATTCACA
2738720 ATTTCC
1 ATTTCC
2738726 CCATATTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 13 0.59
20 7 0.32
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTCCTCAAAATTCACA
Found at i:2738846 original size:4 final size:4
Alignment explanation
Indices: 2738839--2738913 Score: 64
Period size: 4 Copynumber: 18.8 Consensus size: 4
2738829 ACTTTGAATA
* *
2738839 ATAT ATAT ATAT ATAT ATA- AGTAT ATAC ATAA ATAT ATAT ATAT ATA-
1 ATAT ATAT ATAT ATAT ATAT A-TAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
2738886 AGTAT ATAC ATAA ATCT ATAT ATGT ATA
1 A-TAT ATAT ATAT ATAT ATAT ATAT ATA
2738914 ATTAAACATA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
3 2 0.04
4 53 0.93
5 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:2738883 original size:28 final size:28
Alignment explanation
Indices: 2738843--2738914 Score: 126
Period size: 28 Copynumber: 2.6 Consensus size: 28
2738833 TGAATAATAT
2738843 ATATATATATATATAAGTATATACATAA
1 ATATATATATATATAAGTATATACATAA
2738871 ATATATATATATATAAGTATATACATAA
1 ATATATATATATATAAGTATATACATAA
* *
2738899 ATCTATATATGTATAA
1 ATATATATATATATAA
2738915 TTAAACATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (28 bp):
ATATATATATATATAAGTATATACATAA
Found at i:2739437 original size:2 final size:2
Alignment explanation
Indices: 2739430--2739579 Score: 109
Period size: 2 Copynumber: 76.5 Consensus size: 2
2739420 AGATATAATT
*
2739430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
2739473 CA TA TA TA GTG TA TA TA TA TA GT- TCA TA TA AA CA TA -A TT TA
1 TA TA TA TA -TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA
** *
2739514 TA TA TA TA TA TA TA TA GC T- TA TA -A TA -A T- TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
2739553 TA -A TA TA AA TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2739580 TAGTTGTTTT
Statistics
Matches: 117, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
1 8 0.07
2 104 0.89
3 5 0.04
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2739479 original size:13 final size:13
Alignment explanation
Indices: 2739461--2739496 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2739451 ATATATATAT
2739461 ATATATAGTTTAC
1 ATATATAGTTTAC
* *
2739474 ATATATAGTGTAT
1 ATATATAGTTTAC
2739487 ATATATAGTT
1 ATATATAGTT
2739497 CATATAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (13 bp):
ATATATAGTTTAC
Found at i:2739501 original size:11 final size:12
Alignment explanation
Indices: 2739461--2739502 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
2739451 ATATATATAT
2739461 ATATATAGTTTAC
1 ATATATAG-TTAC
*
2739474 ATATATAGTGTAT
1 ATATATAGT-TAC
2739487 ATATATAGTT-C
1 ATATATAGTTAC
2739498 ATATA
1 ATATA
2739503 AACATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 5 0.19
12 2 0.08
13 19 0.73
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (12 bp):
ATATATAGTTAC
Found at i:2740270 original size:216 final size:214
Alignment explanation
Indices: 2739665--2740372 Score: 1119
Period size: 216 Copynumber: 3.3 Consensus size: 214
2739655 TCCCTTCGTA
2739665 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
* *
2739730 ATTTGCATCTAAAATTGACCTATACTTATTACTTATTTCTATTTTTTAATTGGCTCATAACTTTT
66 ATTTGCATCT-AAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* *
2739795 TAAATGGGTACAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAGTTATTTCGATT
130 TAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATT
* *
2739860 TTATCCCTCATCAATGTGTT
195 TGATCCCTCATCAATGTGTG
* *
2739880 TTGTTT-ATTTATTTAAATTTTTATTTGTAATTACATATTTGTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
* * *
2739944 ATTTGCATCTGAAATTGA-CC---C--A-TACTTGTTTCTATTTTTAAATTGGCCCATAACTTGT
66 ATTTGCATCT-AAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* *
2740002 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAAACTCACAATTTAAAACTATTTCGAT
130 TAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
2740067 TTGATCCCTCATCAATGTGTG
194 TTGATCCCTCATCAATGTGTG
* *
2740088 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCACATTTATTCAATTTAGTCCTCTAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
*
2740153 ATTTGCATCTAAAGTTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAAATTTT
66 ATTTGCATCTAAA-TTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
*
2740218 TAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGAT
130 TAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
2740283 TTGATCCCTCATCAATGTGTG
194 TTGATCCCTCATCAATGTGTG
* * *
2740304 TTGTTTAATTTATTTAAATTTTTATTTGTAATTCCATATTTGTTCAATTTAATTCT-TAAATTTG
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTT-
2740368 TATTT
65 TATTT
2740373 TTCATAAAAT
Statistics
Matches: 451, Mismatches: 31, Indels: 21
0.90 0.06 0.04
Matches are distributed among these distances:
207 52 0.12
208 69 0.15
209 68 0.15
210 3 0.01
213 2 0.00
214 73 0.16
215 14 0.03
216 170 0.38
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (214 bp):
TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
ATTTGCATCTAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTTT
AAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTT
GATCCCTCATCAATGTGTG
Found at i:2742056 original size:18 final size:17
Alignment explanation
Indices: 2742002--2742050 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2741992 TTGGACCCTT
* *
2742002 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
2742020 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
2742038 AGTGCATTCGATG
1 AGTGCA-TCGATG
2742051 TTTCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:2742071 original size:65 final size:63
Alignment explanation
Indices: 2742021--2742182 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 63
2742011 GTGCACTAAG
* *
2742021 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAAATAGCCAGAGTGCATCGATGCATGGG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAT--CCACAGTGCATCGATGCAT-GG
2742085 T
63 T
* *
2742086 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGT
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCACAGTGCATCGATGCATGGT
* *
2742150 ATGTGCATCGATGCTTGAAATGCATTCGATGTT
1 A-GTGCATCGATGCATCAAATGCATTCGATGTT
2742183 CAATTTAATT
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 5 0.06
65 72 0.83
66 5 0.06
67 5 0.06
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (63 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCACAGTGCATCGATGCATGGT
Found at i:2742221 original size:65 final size:63
Alignment explanation
Indices: 2742022--2742223 Score: 216
Period size: 65 Copynumber: 3.1 Consensus size: 63
2742012 TGCACTAAGA
* *
2742022 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAAATAGC-CAGAGTGCATCGATGCATGGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAT--CTC--AGTGCATCGATGCATGGT
2742085 TG
62 TG
2742087 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
2742152 -
63 G
* * **
2742152 GTGCATCGATGCTTGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
2742215 TG
62 TG
2742217 GTGCATC
1 GTGCATC
2742224 ACTATGAAAA
Statistics
Matches: 121, Mismatches: 7, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 22 0.18
65 80 0.66
66 7 0.06
67 6 0.05
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:2744845 original size:23 final size:22
Alignment explanation
Indices: 2744815--2744894 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
2744805 GCATGGCCTT
2744815 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
2744837 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
2744859 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
2744881 ATGCATCGATGCAC
1 GTGCATCGATGCAC
2744895 GGTTAGGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.32
22 16 0.34
23 16 0.34
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:2744869 original size:44 final size:42
Alignment explanation
Indices: 2744793--2744913 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 42
2744783 AAAACCCGAT
* *
2744793 GGATGCATCGATGCATGGCCTT--GTGCATCGATGCACATTCAA
1 GGATGCATCGATGCA-CG-CTTAGGTGTATCGATGCACATTCAA
* *
2744835 GGCGTGCATCGGTGCAC-CTTCATGGTGTATCGATGCACATTCAA
1 GG-ATGCATCGATGCACGCTT-A-GGTGTATCGATGCACATTCAA
*
2744879 GGATGCATCGATGCACGGTTAGGTGTATCGATGCA
1 GGATGCATCGATGCACGCTTAGGTGTATCGATGCA
2744914 TTAAGCACAA
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
40 3 0.05
42 16 0.24
43 24 0.36
44 23 0.35
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.26
Consensus pattern (42 bp):
GGATGCATCGATGCACGCTTAGGTGTATCGATGCACATTCAA
Found at i:2744871 original size:21 final size:20
Alignment explanation
Indices: 2744815--2744913 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 20
2744805 GCATGGCCTT
2744815 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTC-A-G
* *
2744837 CGTGCATCGGTGCACCTTCATG
1 -GTGCATCGATGCACATTCA-G
*
2744859 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTC-AG
*
2744880 GATGCATCGATGCACGGTT-AG
1 G-TGCATCGATGCAC-ATTCAG
*
2744901 GTGTATCGATGCA
1 GTGCATCGATGCA
2744914 TTAAGCACAA
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.17
21 20 0.31
22 15 0.23
23 18 0.28
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (20 bp):
GTGCATCGATGCACATTCAG
Found at i:2750657 original size:19 final size:19
Alignment explanation
Indices: 2750633--2750685 Score: 97
Period size: 19 Copynumber: 2.7 Consensus size: 19
2750623 TTAGACCCTT
2750633 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
2750652 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
2750671 AGTGCATCAGGTGCA
1 AGTGCATC-GGTGCA
2750686 TTCGATGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 27 0.82
20 6 0.18
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:2750863 original size:65 final size:63
Alignment explanation
Indices: 2750673--2750866 Score: 200
Period size: 65 Copynumber: 3.0 Consensus size: 63
2750663 GCACTAAGAG
** * *
2750673 TGCATCAGGTGCATTCGATGTTTCA-AAAATAGC-CAGAGTACATCGATGCATGGTTGCTGCATC
1 TGCATCAAATGCATTCGATGTTTCATAAAAT--CTC--AGTGCATCGATGCATGGTTGGTGCATC
2750736 GA
62 GA
2750738 TGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT-GTGCATCG
1 TGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-TGGTGCATCG
2750802 A
63 A
* *
2750803 TGCATGAAATGCATTCGATG-TTCAATATAAT-TCATGGTGCATCGATGCATGGATTGGTGCATC
1 TGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGGTGCATC
2750866 G
62 G
2750867 TGGATTGGTG
Statistics
Matches: 113, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 23 0.20
65 71 0.63
66 7 0.06
67 6 0.05
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (63 bp):
TGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTGCATCGA
Found at i:2750870 original size:15 final size:15
Alignment explanation
Indices: 2750852--2750881 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2750842 CATCGATGCA
2750852 TGGATTGGTGCATCG
1 TGGATTGGTGCATCG
2750867 TGGATTGGTGCATCG
1 TGGATTGGTGCATCG
2750882 GTGCATCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.40, T:0.33
Consensus pattern (15 bp):
TGGATTGGTGCATCG
Found at i:2752395 original size:28 final size:28
Alignment explanation
Indices: 2752363--2752418 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2752353 TTGGTTTCTA
2752363 TTTGCTCCGATGAACCCGACTTCGATGG
1 TTTGCTCCGATGAACCCGACTTCGATGG
2752391 TTTGCTCCGATGAACCCGACTTCGATGG
1 TTTGCTCCGATGAACCCGACTTCGATGG
2752419 GAAGCTCCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.29
Consensus pattern (28 bp):
TTTGCTCCGATGAACCCGACTTCGATGG
Found at i:2752425 original size:28 final size:28
Alignment explanation
Indices: 2752366--2752431 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
2752356 GTTTCTATTT
***
2752366 GCTCCGATGAACCCGACTTCGATGGTTT
1 GCTCCGATGAACCCGACTTCGATGGGAA
2752394 GCTCCGATGAACCCGACTTCGATGGGAA
1 GCTCCGATGAACCCGACTTCGATGGGAA
2752422 GCTCCGATGA
1 GCTCCGATGA
2752432 CTCACAAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.21, C:0.29, G:0.27, T:0.23
Consensus pattern (28 bp):
GCTCCGATGAACCCGACTTCGATGGGAA
Found at i:2756289 original size:122 final size:121
Alignment explanation
Indices: 2756140--2756392 Score: 447
Period size: 122 Copynumber: 2.1 Consensus size: 121
2756130 CCCAAATCTT
*
2756140 TTTTTATTAATGTAATGTATTTTTTTTAAAATCAATTAAATTTTTTATAGATAATTAATTAATAG
1 TTTTTATTAATATAATGTATTTTTTTTAAAATCAATTAAATTTTTTATAGATAATTAATTAATAG
2756205 TTGTATAATTAAGAAATAAGAGAAAAAAACGTTGATGGCTTGTTTTAATTGTATGC
66 TTGTATAATTAAGAAATAAGAGAAAAAAACGTTGATGGCTTGTTTTAATTGTATGC
* *
2756261 TTCTTTATTAATATAAAT-TATTTTTTTTAAAATCAATTAGATTTTTTATATATAATTAATTAAT
1 TT-TTTATTAATAT-AATGTATTTTTTTTAAAATCAATTAAATTTTTTATAGATAATTAATTAAT
2756325 AGTTGTATAATTAAGAAATAAGAGAAAAAAACGTTGATGGCTTGTTTTAATTGTATGC
64 AGTTGTATAATTAAGAAATAAGAGAAAAAAACGTTGATGGCTTGTTTTAATTGTATGC
2756383 TTTTT-TTAAT
1 TTTTTATTAAT
2756393 CTTAATTTAT
Statistics
Matches: 127, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
120 5 0.04
121 5 0.04
122 114 0.90
123 3 0.02
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (121 bp):
TTTTTATTAATATAATGTATTTTTTTTAAAATCAATTAAATTTTTTATAGATAATTAATTAATAG
TTGTATAATTAAGAAATAAGAGAAAAAAACGTTGATGGCTTGTTTTAATTGTATGC
Found at i:2756290 original size:19 final size:19
Alignment explanation
Indices: 2756268--2756315 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2756258 TGCTTCTTTA
**
2756268 TTAATATAAATTATTTTTT
1 TTAATATAAATTAGATTTT
* *
2756287 TTAAAATCAATTAGATTTT
1 TTAATATAAATTAGATTTT
2756306 TTATATATAA
1 TTA-ATATAA
2756316 TTAATTAATA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TTAATATAAATTAGATTTT
Found at i:2757478 original size:2 final size:2
Alignment explanation
Indices: 2757471--2757496 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2757461 GCTCTGTATG
2757471 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
2757497 GGGAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2758939 original size:6 final size:6
Alignment explanation
Indices: 2758928--2759026 Score: 125
Period size: 6 Copynumber: 17.2 Consensus size: 6
2758918 CCTAAGAGGA
** *
2758928 CCCTCT CCCTCT TTCTCT CCCTCT CCCTCT CCCTCT CTCTCT CCCTCT
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT
* *
2758976 CCCTCT -CC-CT CCCTCT CTCTCT CCCTCT CCCTCT --CTCT CTCTCT
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT
2759020 CCCTCT C
1 CCCTCT C
2759027 TTCTCTTGTT
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
4 6 0.08
5 4 0.05
6 70 0.88
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
CCCTCT
Found at i:2767079 original size:22 final size:23
Alignment explanation
Indices: 2767046--2767097 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2767036 ATTTTAGGAG
2767046 ATAAAAACAAATTATC-AAAAGAA
1 ATAAAAACAAA-TATCTAAAAGAA
* *
2767069 ATAAAAA-AAATATCTAAAATAT
1 ATAAAAACAAATATCTAAAAGAA
2767091 ATAAAAA
1 ATAAAAA
2767098 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 15 0.58
23 7 0.27
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (23 bp):
ATAAAAACAAATATCTAAAAGAA
Found at i:2767297 original size:3 final size:3
Alignment explanation
Indices: 2767289--2767323 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2767279 CCAAAGCAAA
2767289 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2767324 AGGCAGTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2770394 original size:9 final size:10
Alignment explanation
Indices: 2770369--2770393 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2770359 CTTTATTTTT
2770369 ATTTTTATTA
1 ATTTTTATTA
2770379 ATTTTTATTA
1 ATTTTTATTA
2770389 ATTTT
1 ATTTT
2770394 ACTTTTACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:2771825 original size:56 final size:55
Alignment explanation
Indices: 2771639--2771834 Score: 200
Period size: 56 Copynumber: 3.5 Consensus size: 55
2771629 TATCTTTTAG
* * * *
2771639 ATATATTCGATTTTG-GAGTCTCTATTTTTATACTTTTTAATGACAATAACTGATAA
1 ATATATTCGATTTCGAGA-CCTTTATTTTTATA-TTTTTAATGACAATAATTGATAA
* * * *
2771695 ATATATTCGATTTC-AGGACCCTTATTTTTATGTTTCTTAATGGCAACAATTGATAA
1 ATATATTCGATTTCGA-GACCTTTATTTTTATATTT-TTAATGACAATAATTGATAA
* * *
2771751 ATATATTCGATTTTGAGACCTTTATTTTTATATTTATTAATAACAATAATTGATAG
1 ATATATTCGATTTCGAGACCTTTATTTTTATATTT-TTAATGACAATAATTGATAA
* *
2771807 CTATATTCAATTTCGAGA-CTCTTATTTT
1 ATATATTCGATTTCGAGACCT-TTATTTT
2771835 ATAGAGATCT
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
55 5 0.04
56 108 0.93
57 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (55 bp):
ATATATTCGATTTCGAGACCTTTATTTTTATATTTTTAATGACAATAATTGATAA
Found at i:2777941 original size:15 final size:15
Alignment explanation
Indices: 2777908--2777956 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
2777898 TAATCTTAAT
2777908 AATGAAAAACA-AAAGA
1 AATG-AAAACAGAAA-A
* *
2777924 AATGAAAAGAGACAA
1 AATGAAAACAGAAAA
2777939 AATGAAAACAGAAAA
1 AATGAAAACAGAAAA
2777954 AAT
1 AAT
2777957 ATGTATAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.71, C:0.06, G:0.14, T:0.08
Consensus pattern (15 bp):
AATGAAAACAGAAAA
Found at i:2781601 original size:16 final size:16
Alignment explanation
Indices: 2781573--2781628 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
2781563 TCAAAAAATT
*
2781573 AATAAAAATATATA-A
1 AATAAATATATATATA
2781588 AATACAATATATATATA
1 AATA-AATATATATATA
* *
2781605 AATAAATAAATACATA
1 AATAAATATATATATA
*
2781621 ATTAAATA
1 AATAAATA
2781629 ATCTTCATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.11
16 26 0.74
17 5 0.14
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAATATATATATA
Found at i:2783354 original size:35 final size:35
Alignment explanation
Indices: 2783308--2783378 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
2783298 GGTTGTTAAG
*
2783308 ACATATTTTTAATACGTTCGTCTGCGTATCATTTT
1 ACATATCTTTAATACGTTCGTCTGCGTATCATTTT
2783343 ACATATCTTTAATACGTTCGTCTGCGTATCATTTT
1 ACATATCTTTAATACGTTCGTCTGCGTATCATTTT
2783378 A
1 A
2783379 GGCTTCACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.46
Consensus pattern (35 bp):
ACATATCTTTAATACGTTCGTCTGCGTATCATTTT
Found at i:2783992 original size:23 final size:23
Alignment explanation
Indices: 2783938--2784001 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2783928 AAAAAAAAGA
* *
2783938 AGAAAAACATGTCATAAAGGTAG
1 AGAAAAACGTGTCACAAAGGTAG
2783961 AGAAAAACGTGTCACAAAGGTAG
1 AGAAAAACGTGTCACAAAGGTAG
* *
2783984 AGAAAAACGGGCCACAAA
1 AGAAAAACGTGTCACAAA
2784002 TGCAGAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.52, C:0.14, G:0.23, T:0.11
Consensus pattern (23 bp):
AGAAAAACGTGTCACAAAGGTAG
Found at i:2784837 original size:6 final size:6
Alignment explanation
Indices: 2784828--2784894 Score: 50
Period size: 6 Copynumber: 10.7 Consensus size: 6
2784818 ATATATATAT
*
2784828 TAAAGA TAAAAA TAAAAA T-AAAA TAAAAA TAGAATGAGA T-AAAA T-AAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA-AA--A-A TAAAAA TAAAAA
2784877 TAATAAGA TAAAAA TAAA
1 TAA-AA-A TAAAAA TAAA
2784895 GCAAAAAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 16
0.75 0.01 0.23
Matches are distributed among these distances:
5 12 0.23
6 25 0.48
7 6 0.12
8 6 0.12
9 1 0.02
10 2 0.04
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:2785688 original size:35 final size:34
Alignment explanation
Indices: 2785627--2785707 Score: 119
Period size: 35 Copynumber: 2.4 Consensus size: 34
2785617 TTAGTTTGTG
*
2785627 CAATAAAAT-AAAATGTTAGTAAGTTAGTAAGAA
1 CAATAAAATAAAAAAGTTAGTAAGTTAGTAAGAA
* *
2785660 CAATAAAAATAAAAAAGTTAGTATGTTAGTATGAA
1 CAAT-AAAATAAAAAAGTTAGTAAGTTAGTAAGAA
2785695 CAATAAAATAAAA
1 CAATAAAATAAAA
2785708 GGTAGAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 4 0.09
34 14 0.33
35 25 0.58
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.26
Consensus pattern (34 bp):
CAATAAAATAAAAAAGTTAGTAAGTTAGTAAGAA
Found at i:2785721 original size:32 final size:32
Alignment explanation
Indices: 2785627--2785785 Score: 162
Period size: 32 Copynumber: 4.8 Consensus size: 32
2785617 TTAGTTTGTG
**
2785627 CAATAAAATAAAATGTTAGTAA-GTTAGTAAGAA
1 CAATAAAATAAAA-GTTAG-AATGTTAGTTCGAA
*
2785660 CAATAAAAATAAAAAAGTTAGTATGTTAGTAT-GAA
1 CAAT-AAAAT--AAAAGTTAGAATGTTAGT-TCGAA
* *
2785695 CAATAAAATAAAAGGTAGAATATTAGTTCGAA
1 CAATAAAATAAAAGTTAGAATGTTAGTTCGAA
*
2785727 -AGATAAAATAAATGTTAGAATGTTAGTTCGAA
1 CA-ATAAAATAAAAGTTAGAATGTTAGTTCGAA
* *
2785759 CAATAAAATAAAGGTTAAAATGTTAGT
1 CAATAAAATAAAAGTTAGAATGTTAGT
2785786 AAGTTAGTGA
Statistics
Matches: 108, Mismatches: 10, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
31 2 0.02
32 68 0.63
33 5 0.05
34 11 0.10
35 18 0.17
36 4 0.04
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.28
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGAATGTTAGTTCGAA
Found at i:2785909 original size:19 final size:18
Alignment explanation
Indices: 2785880--2785920 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 18
2785870 AATTGAAAGT
2785880 AATGAAAATAAAGTGACAAA
1 AATGAAAATAAA-TGA-AAA
2785900 AATG-AAATAAATGAAAA
1 AATGAAAATAAATGAAAA
2785917 AATG
1 AATG
2785921 TAGAGATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 3 0.14
19 7 0.33
20 4 0.19
ACGTcount: A:0.66, C:0.02, G:0.15, T:0.17
Consensus pattern (18 bp):
AATGAAAATAAATGAAAA
Found at i:2787403 original size:31 final size:31
Alignment explanation
Indices: 2787368--2787437 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
2787358 CTAGTCCATC
*
2787368 TGATGTGGCATGCACATGTGGTTATCGATGA
1 TGATGTGGCATGCACATGTGGTCATCGATGA
*
2787399 TGATGTGGCATGCACATGTGGTCATTGATGA
1 TGATGTGGCATGCACATGTGGTCATCGATGA
2787430 TGATGTGG
1 TGATGTGG
2787438 TATTTCCACG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.11, G:0.34, T:0.33
Consensus pattern (31 bp):
TGATGTGGCATGCACATGTGGTCATCGATGA
Found at i:2790897 original size:20 final size:21
Alignment explanation
Indices: 2790843--2790899 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
2790833 CACTGGGAGT
2790843 GAAAAAA-AGAAAAG-GAGAA
1 GAAAAAAGAGAAAAGAGAGAA
* **
2790862 GAAAGAAGAGTCAAGAG-GAA
1 GAAAAAAGAGAAAAGAGAGAA
2790882 GAAAAAAGAGAAAAGAGA
1 GAAAAAAGAGAAAAGAGA
2790900 AATAAACAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 6 0.21
20 22 0.76
21 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.02
Consensus pattern (21 bp):
GAAAAAAGAGAAAAGAGAGAA
Found at i:2791593 original size:21 final size:20
Alignment explanation
Indices: 2791560--2791611 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2791550 AGCGATGGTG
*
2791560 TTATTATTATTTAATAAATAA
1 TTATAATTATTTAATAAAT-A
* *
2791581 TTATAATTTTTTATTAAATA
1 TTATAATTATTTAATAAATA
*
2791601 TTATAAATATT
1 TTATAATTATT
2791612 AATGTTTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATAATTATTTAATAAATA
Found at i:2792220 original size:20 final size:20
Alignment explanation
Indices: 2792197--2792247 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
2792187 ACTCAGTTTC
2792197 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
*
2792217 CAAATTCGCAACACAGTAGT
1 CAAATTCGCAACACAGAAGT
2792237 CAAATTCGCAA
1 CAAATTCGCAA
2792248 AGCGCGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:2792225 original size:40 final size:40
Alignment explanation
Indices: 2792157--2792247 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
2792147 AAATGACCAA
* * * *
2792157 CAAATTCGCAACGCGAACTCCAATTTCGCAACTCAGT-TT
1 CAAATTCGCAACACGAACTCCAAATTCGCAACACAGTAGT
*
2792196 CCAAATTCGCAACACAGAAGT-CAAATTCGCAACACAGTAGT
1 -CAAATTCGCAACAC-GAACTCCAAATTCGCAACACAGTAGT
2792237 CAAATTCGCAA
1 CAAATTCGCAA
2792248 AGCGCGTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
40 39 0.89
41 5 0.11
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (40 bp):
CAAATTCGCAACACGAACTCCAAATTCGCAACACAGTAGT
Found at i:2792409 original size:22 final size:22
Alignment explanation
Indices: 2792394--2792439 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2792384 ACGACATCTG
*
2792394 TCCCCATCTCTGACGAAATCCA
1 TCCCCATCTCCGACGAAATCCA
2792416 TCCCCATCTCCGACGAAATCCA
1 TCCCCATCTCCGACGAAATCCA
2792438 TC
1 TC
2792440 TATTTCCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.43, G:0.09, T:0.22
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCCA
Found at i:2793874 original size:198 final size:201
Alignment explanation
Indices: 2793488--2793884 Score: 682
Period size: 198 Copynumber: 2.0 Consensus size: 201
2793478 AGAGGACCTA
2793488 AATGCATGGAACCTATTTCCGTGGGGTTCATATCTATGGAAAACTACCTGGAAAAAGTTGTCGTC
1 AATGCATGGAA-CTATTTCCGTGGGGTTCATATCTATGGAAAACTACCTGGAAAAAGTTGTCGTC
2793553 TGCCTTTGAGGACCGAAAAAGTTTGCGTGGCCATGTTTCCAAATATACTTTGGCAGGCTTTATTT
65 TGCCTTTGAGGACCGAAAAAGTTTGCGTGGCCATGTTTCCAAATATACTTTGGCAGGCTTTATTT
*
2793618 GGGCCTTTAAGGTAAGAATTTCTATAATGTTTCCAAATATAATTAATTATTTACAATTACTAATG
130 GGGCCTTTAAGGTAAGAATTTCTATAATGTTTCCAAATATAATTAATTATTAACAATTACTAATG
2793683 TTTGGAT
195 TTTGGAT
*
2793690 AATGCATGGAA-TATTTCCTTGGGGTTCA-ATCTAT-GAAAACTACCTGGAAAAAGTTGTCGT-T
1 AATGCATGGAACTATTTCCGTGGGGTTCATATCTATGGAAAACTACCTGGAAAAAGTTGTCGTCT
2793751 GCCTTTGAGGACCGAAAAAGTTTGCGTGGCCATGTTTCC-AATATACTTTGGCA-GCTTTATTTG
66 GCCTTTGAGGACCGAAAAAGTTTGCGTGGCCATGTTTCCAAATATACTTTGGCAGGCTTTATTTG
2793814 GGCCTTTAAGGTAAG-ATTTCTATATAATGTTTCCAAAATTATAATTAATTATTAACAATTACTA
131 GGCCTTTAAGGTAAGAATTTC--TATAATGTTTCC-AAA-TATAATTAATTATTAACAATTACTA
2793878 ATGTTTG
192 ATGTTTG
2793885 TGTATTATAT
Statistics
Matches: 189, Mismatches: 2, Indels: 12
0.93 0.01 0.06
Matches are distributed among these distances:
194 5 0.03
195 25 0.13
196 26 0.14
197 43 0.23
198 57 0.30
199 6 0.03
200 16 0.08
202 11 0.06
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (201 bp):
AATGCATGGAACTATTTCCGTGGGGTTCATATCTATGGAAAACTACCTGGAAAAAGTTGTCGTCT
GCCTTTGAGGACCGAAAAAGTTTGCGTGGCCATGTTTCCAAATATACTTTGGCAGGCTTTATTTG
GGCCTTTAAGGTAAGAATTTCTATAATGTTTCCAAATATAATTAATTATTAACAATTACTAATGT
TTGGAT
Found at i:2794867 original size:21 final size:21
Alignment explanation
Indices: 2794843--2794929 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
2794833 GCCCGATTCA
*
2794843 CCTATCATCATTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
*
2794864 CCTATCATCCTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
** * *
2794885 CCTCCCACCGTTCAAGAGGTC
1 CCTATCATCGTTCAAGAGGCC
* * *
2794906 TCTGTCATCGTTCAAGAGGTC
1 CCTATCATCGTTCAAGAGGCC
2794927 CCT
1 CCT
2794930 CCCACCTTTC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (21 bp):
CCTATCATCGTTCAAGAGGCC
Found at i:2794914 original size:42 final size:42
Alignment explanation
Indices: 2794853--2794944 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
2794843 CCTATCATCA
2794853 TTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACCG
* * * * * *
2794895 TTCAAGAGGTCTCTGTCATCGTTCAAGAGGTCCCTCCCACCT
1 TTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACCG
*
2794937 TTCGAGAG
1 TTCAAGAG
2794945 CCCGATTCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.24
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACCG
Found at i:2794944 original size:21 final size:21
Alignment explanation
Indices: 2794874--2794944 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
2794864 CCTATCATCC
*
2794874 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGTCCCTCCCACCG
* ** *
2794895 TTCAAGAGGTCTCTGTCATCG
1 TTCAAGAGGTCCCTCCCACCG
*
2794916 TTCAAGAGGTCCCTCCCACCT
1 TTCAAGAGGTCCCTCCCACCG
*
2794937 TTCGAGAG
1 TTCAAGAG
2794945 CCCGATTCAC
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.20, C:0.35, G:0.21, T:0.24
Consensus pattern (21 bp):
TTCAAGAGGTCCCTCCCACCG
Found at i:2796371 original size:64 final size:62
Alignment explanation
Indices: 2796234--2796380 Score: 240
Period size: 64 Copynumber: 2.3 Consensus size: 62
2796224 AAATTGATGT
2796234 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGAAATAAGAATTATTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGAAATAAGAATTATTTTTGCTTGTTTAATTG
* ***
2796296 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAG-AAATAAGAATTA-TTTTTGCTTGTTTAATTG
2796360 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
2796381 GTTTTAAATT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
62 31 0.39
63 9 0.11
64 39 0.49
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (62 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGAAATAAGAATTATTTTTGCTTGTTTAATTG
Found at i:2796493 original size:74 final size:74
Alignment explanation
Indices: 2796372--2796515 Score: 279
Period size: 74 Copynumber: 1.9 Consensus size: 74
2796362 TTGTAAAAGT
*
2796372 TGATTTGTTGTTTTAAATTTCAATCTGCATTATGTTGAAGGCAAAAAAGACCTGTTGAAAGTACA
1 TGATTTGTTGTTTTAAATTTCAATATGCATTATGTTGAAGGCAAAAAAGACCTGTTGAAAGTACA
2796437 CTTTCGCAA
66 CTTTCGCAA
2796446 TGATTTGTTGTTTTAAATTTCAATATGCATTATGTTGAAGGCAAAAAAGACCTGTTGAAAGTACA
1 TGATTTGTTGTTTTAAATTTCAATATGCATTATGTTGAAGGCAAAAAAGACCTGTTGAAAGTACA
2796511 CTTTC
66 CTTTC
2796516 TTAACGCAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (74 bp):
TGATTTGTTGTTTTAAATTTCAATATGCATTATGTTGAAGGCAAAAAAGACCTGTTGAAAGTACA
CTTTCGCAA
Found at i:2796564 original size:20 final size:20
Alignment explanation
Indices: 2796518--2796557 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2796508 ACACTTTCTT
*
2796518 AACGCAAAAGTCAAATTCGC
1 AACGCGAAAGTCAAATTCGC
2796538 AACGCGAAAGTCAAATTCGC
1 AACGCGAAAGTCAAATTCGC
2796558 GTTGCGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (20 bp):
AACGCGAAAGTCAAATTCGC
Found at i:2796602 original size:20 final size:20
Alignment explanation
Indices: 2796579--2796642 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
2796569 CACGTTACGA
* *
2796579 TTTCACGTTTCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
***
2796599 TTTCGCAACGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
2796619 TTTCGCGTTGCGAATTGGAC
1 TTTCGCGTTGCGAATTTGAC
2796639 TTTC
1 TTTC
2796643 TCAACAATTG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:2798033 original size:18 final size:18
Alignment explanation
Indices: 2798010--2798046 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2798000 CGAAATTTAT
2798010 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2798028 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2798046 A
1 A
2798047 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2798461 original size:25 final size:25
Alignment explanation
Indices: 2798429--2798478 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2798419 CATTATTTTC
*
2798429 CAAATAATATACCCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
*
2798454 CAAATAATGTACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
2798479 TAATTGATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:2798574 original size:20 final size:20
Alignment explanation
Indices: 2798549--2798593 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2798539 AAGGTACACT
*
2798549 TTCGCAACGCGAAAGTCAAA
1 TTCGCAAAGCGAAAGTCAAA
*
2798569 TTCGCAAATCGAAAGTCAAA
1 TTCGCAAAGCGAAAGTCAAA
2798589 TTCGC
1 TTCGC
2798594 GTTACGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
TTCGCAAAGCGAAAGTCAAA
Found at i:2801422 original size:12 final size:12
Alignment explanation
Indices: 2801401--2801434 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2801391 GGTTTTGGGT
*
2801401 TTTGAGATTGTG
1 TTTGATATTGTG
2801413 TTTGATATTGTG
1 TTTGATATTGTG
*
2801425 TTTGGTATTG
1 TTTGATATTG
2801435 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2802309 original size:20 final size:20
Alignment explanation
Indices: 2802284--2802374 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
2802274 AAATTCAGTG
*
2802284 TTGCGAATTTGTAAATCGCA
1 TTGCGAATTTGGAAATCGCA
** * *
2802304 TTGCGAATTTTTAAATCACG
1 TTGCGAATTTGGAAATCGCA
2802324 TTGCGAATTTGGAAATCGCA
1 TTGCGAATTTGGAAATCGCA
*
2802344 TTGCGAATTTGGAAATCGCG
1 TTGCGAATTTGGAAATCGCA
*
2802364 TTGTGAATTTG
1 TTGCGAATTTG
2802375 ACTTATGTGT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGAATTTGGAAATCGCA
Found at i:2802340 original size:40 final size:40
Alignment explanation
Indices: 2802266--2802374 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
2802256 AATCGAGTTA
* *
2802266 CGAATTT-GAAATTCAGTGTTGCGAATTTGTAAATCGCATTG
1 CGAATTTGGAAA-TCA-CGTTGCGAATTTGGAAATCGCATTG
**
2802307 CGAATTTTTAAATCACGTTGCGAATTTGGAAATCGCATTG
1 CGAATTTGGAAATCACGTTGCGAATTTGGAAATCGCATTG
* *
2802347 CGAATTTGGAAATCGCGTTGTGAATTTG
1 CGAATTTGGAAATCACGTTGCGAATTTG
2802375 ACTTATGTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 47 0.78
41 10 0.17
42 3 0.05
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (40 bp):
CGAATTTGGAAATCACGTTGCGAATTTGGAAATCGCATTG
Found at i:2802408 original size:20 final size:20
Alignment explanation
Indices: 2802383--2802429 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2802373 TGACTTATGT
2802383 GTTGCGATTTACAGATTCAC
1 GTTGCGATTTACAGATTCAC
2802403 GTTGCGATTTACAGATTCAC
1 GTTGCGATTTACAGATTCAC
*
2802423 TTTGCGA
1 GTTGCGA
2802430 ATTTGGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCAC
Found at i:2806735 original size:2 final size:2
Alignment explanation
Indices: 2806728--2806754 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2806718 AAGCATTGTC
2806728 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2806755 TAAAGGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2808389 original size:37 final size:37
Alignment explanation
Indices: 2808339--2808418 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
2808329 ATCTTCTTTA
* *
2808339 CAATTGCTTCTGCTTCCTGTATCAATTTTCTGAATTG
1 CAATTGATTCTGCTCCCTGTATCAATTTTCTGAATTG
2808376 CAATTGATTCTGCTCCCTGTATCAATTTTCTGAATTG
1 CAATTGATTCTGCTCCCTGTATCAATTTTCTGAATTG
2808413 CAATTG
1 CAATTG
2808419 CCTCGATTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (37 bp):
CAATTGATTCTGCTCCCTGTATCAATTTTCTGAATTG
Found at i:2809103 original size:39 final size:42
Alignment explanation
Indices: 2809060--2809150 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
2809050 ATGGAGGGGG
*
2809060 ATGCGTCTTC-ATGGGG-AAC-GGTAAGACGCTTGGACTCCA
1 ATGCGTCTTCAAGGGGGTAACGGGTAAGACGCTTGGACTCCA
* ** *
2809099 ATGCGTTTTCAAGGGGGTTTCGGGTAAGTCGCTTGGACTCCA
1 ATGCGTCTTCAAGGGGGTAACGGGTAAGACGCTTGGACTCCA
*
2809141 ATGCATCTTC
1 ATGCGTCTTC
2809151 GGGGTTCACT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
39 9 0.21
40 5 0.12
41 1 0.02
42 27 0.64
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.29
Consensus pattern (42 bp):
ATGCGTCTTCAAGGGGGTAACGGGTAAGACGCTTGGACTCCA
Found at i:2811496 original size:17 final size:16
Alignment explanation
Indices: 2811476--2811520 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
2811466 TTTTCAATAA
2811476 AAAATATAAAAAATTCT
1 AAAATATAAAAAATT-T
2811493 AAAATATATAAAAATTT
1 AAAATATA-AAAAATTT
*
2811510 AAAATTTAAAA
1 AAAATATAAAA
2811521 TTTTTATTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 3 0.12
17 16 0.62
18 7 0.27
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATATAAAAAATTT
Found at i:2813552 original size:18 final size:17
Alignment explanation
Indices: 2813529--2813563 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2813519 TGATATTTAA
*
2813529 TTATTATTTATCATTATT
1 TTATTATCTAT-ATTATT
2813547 TTATTATCTATATTATT
1 TTATTATCTATATTATT
2813564 CTCAAACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTATCTATATTATT
Found at i:2815938 original size:2 final size:2
Alignment explanation
Indices: 2815931--2815955 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2815921 TTCTCTAATC
2815931 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2815956 ATGGGATAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2816915 original size:21 final size:23
Alignment explanation
Indices: 2816860--2816915 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
2816850 TTTAATCAAT
2816860 TAATTTAATAAAATAACATATTA
1 TAATTTAATAAAATAACATATTA
*
2816883 -AATTT-ATTAAATAA-A-ATTA
1 TAATTTAATAAAATAACATATTA
*
2816902 TAATTTAAAAAAAT
1 TAATTTAATAAAAT
2816916 TCAATATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.14
20 6 0.21
21 13 0.46
22 5 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATTTAATAAAATAACATATTA
Found at i:2818056 original size:21 final size:20
Alignment explanation
Indices: 2818032--2818091 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
2818022 AACTGCAAAA
2818032 AAAATAATTAAATAAAATAC
1 AAAATAATTAAATAAAATAC
*
2818052 TAAAAAAATTAAAT--AATAC
1 -AAAATAATTAAATAAAATAC
2818071 --AATAATTAAATAAAATAC
1 AAAATAATTAAATAAAATAC
2818089 AAA
1 AAA
2818092 CAAAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
16 10 0.30
18 5 0.15
19 5 0.15
20 1 0.03
21 12 0.36
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAATAATTAAATAAAATAC
Found at i:2819624 original size:18 final size:18
Alignment explanation
Indices: 2819601--2819635 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2819591 GTATTATTTG
2819601 TAATAATAATAATATAAA
1 TAATAATAATAATATAAA
*
2819619 TAATAATAGTAATATAA
1 TAATAATAATAATATAA
2819636 TATTTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TAATAATAATAATATAAA
Found at i:2827832 original size:19 final size:19
Alignment explanation
Indices: 2827804--2827840 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2827794 CCTTTTGCCT
* *
2827804 TGTTTTTTTTTTCTATTTC
1 TGTTTCTTTTTTCCATTTC
2827823 TGTTTCTTTTTTCCATTT
1 TGTTTCTTTTTTCCATTT
2827841 GCAAAACCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.76
Consensus pattern (19 bp):
TGTTTCTTTTTTCCATTTC
Found at i:2828801 original size:31 final size:31
Alignment explanation
Indices: 2828740--2828801 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
2828730 AGAAAGTATT
* *
2828740 AATTTGAATCGAAAAGTCAAATTCAGATATC
1 AATTTGAATCGAAAAATCAAATTCAAATATC
* *
2828771 AATTTGAA-CGATAAAATCAATTTTAAATATC
1 AATTTGAATCGA-AAAATCAAATTCAAATATC
2828802 TTACAAGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (31 bp):
AATTTGAATCGAAAAATCAAATTCAAATATC
Found at i:2829587 original size:36 final size:36
Alignment explanation
Indices: 2829540--2829610 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
2829530 AATATCTCCT
*
2829540 TGTTCTTGCTTTTGGAGGTTTCTCCCAACTCTTTCA
1 TGTTCTTGCTTTTGGAGGTCTCTCCCAACTCTTTCA
*
2829576 TGTTCTTGCTTTTGGAGGTCTCTCTCAACTCTTTC
1 TGTTCTTGCTTTTGGAGGTCTCTCCCAACTCTTTC
2829611 GCTAATCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.10, C:0.25, G:0.17, T:0.48
Consensus pattern (36 bp):
TGTTCTTGCTTTTGGAGGTCTCTCCCAACTCTTTCA
Found at i:2832012 original size:13 final size:13
Alignment explanation
Indices: 2831994--2832019 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2831984 TAAATTTTAA
2831994 AAAAATTTAAAAT
1 AAAAATTTAAAAT
2832007 AAAAATTTAAAAT
1 AAAAATTTAAAAT
2832020 TACAATAAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTTAAAAT
Found at i:2832114 original size:28 final size:30
Alignment explanation
Indices: 2832072--2832174 Score: 124
Period size: 30 Copynumber: 3.5 Consensus size: 30
2832062 AAAAATAATA
* * *
2832072 TTTTGATATATTAC-AATAAAGACCAAAAC
1 TTTTTATAAATTACAAAAAAAGACCAAAAC
*
2832101 -TTTTATAAATTACAAACAAATG-CC-AAAC
1 TTTTTATAAATTACAAA-AAAAGACCAAAAC
*
2832129 TTTTTATAAATTACAAAAAAATACCAAAAC
1 TTTTTATAAATTACAAAAAAAGACCAAAAC
2832159 TTTTTATAAATTACAA
1 TTTTTATAAATTACAA
2832175 CAAATGCCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
28 18 0.29
29 22 0.35
30 23 0.37
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (30 bp):
TTTTTATAAATTACAAAAAAAGACCAAAAC
Found at i:2832126 original size:29 final size:30
Alignment explanation
Indices: 2832094--2832186 Score: 147
Period size: 29 Copynumber: 3.2 Consensus size: 30
2832084 ACAATAAAGA
2832094 CCAAAAC-TTTTATAAATTACAAACAAATG
1 CCAAAACTTTTTATAAATTACAAACAAATG
* *
2832123 CC-AAACTTTTTATAAATTACAAAAAAATA
1 CCAAAACTTTTTATAAATTACAAACAAATG
2832152 CCAAAACTTTTTATAAATTAC-AACAAATG
1 CCAAAACTTTTTATAAATTACAAACAAATG
2832181 CCAAAA
1 CCAAAA
2832187 AAATTAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 4 0.07
29 36 0.62
30 18 0.31
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (30 bp):
CCAAAACTTTTTATAAATTACAAACAAATG
Found at i:2837636 original size:15 final size:16
Alignment explanation
Indices: 2837616--2837645 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2837606 TGATGACTGG
2837616 AAACCCTAG-GGTTTC
1 AAACCCTAGTGGTTTC
2837631 AAACCCTAGTGGTTT
1 AAACCCTAGTGGTTT
2837646 TGGGTTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (16 bp):
AAACCCTAGTGGTTTC
Found at i:2840233 original size:24 final size:24
Alignment explanation
Indices: 2840206--2840258 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2840196 AGGTGGATAT
2840206 TCAGGGGTCTCAGAACGGTGC-GTA
1 TCAGGGGTCTCAGAACGGTGCTG-A
*
2840230 TCAGGTGTCTCAGAACGGTGCTGA
1 TCAGGGGTCTCAGAACGGTGCTGA
2840254 TCAGG
1 TCAGG
2840259 AGTCGGGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.23
Consensus pattern (24 bp):
TCAGGGGTCTCAGAACGGTGCTGA
Found at i:2841521 original size:21 final size:20
Alignment explanation
Indices: 2841472--2841528 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2841462 GATGAGGAAA
* *
2841472 TAAAA-GAAAAAGTAAAAGT
1 TAAAATGAAAGAGAAAAAGT
*
2841491 TAAAATGAAATAGAAAAAGT
1 TAAAATGAAAGAGAAAAAGT
*
2841511 TAAGGATGAAAGAGAAAA
1 TAA-AATGAAAGAGAAAA
2841529 TAAAAAGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.16
20 15 0.47
21 12 0.38
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (20 bp):
TAAAATGAAAGAGAAAAAGT
Found at i:2841822 original size:22 final size:23
Alignment explanation
Indices: 2841794--2841837 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2841784 ACTGTGGTCC
*
2841794 CTAC-AAATCAAATAAAAATTAT
1 CTACAAAATAAAATAAAAATTAT
2841816 CTACAAAATAAAATAAAAATTA
1 CTACAAAATAAAATAAAAATTA
2841838 AAGAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (23 bp):
CTACAAAATAAAATAAAAATTAT
Found at i:2851682 original size:967 final size:967
Alignment explanation
Indices: 2849808--2851742 Score: 3645
Period size: 967 Copynumber: 2.0 Consensus size: 967
2849798 AGAACCATTA
*
2849808 TCAAAGGAAGAAACGAAAGATGAAGAAACTCATGATCCTCTCGAGAATCCAACCATTGAAGAAAG
1 TCAAAGGAAGAAACGAAAGATGAAGAAACTCATGATCATCTCGAGAATCCAACCATTGAAGAAAG
2849873 GGAAGTATCTTATCCAAGAGAGTACAACTATGTCAAGGATGGTGAGATTATAGGTGATCCATCCA
66 GGAAGTATCTTATCCAAGAGAGTACAACTATGTCAAGGATGGTGAGATTATAGGTGATCCATCCA
*
2849938 AAGGGGTAACAACTCGATCTTCTCTTAGAAATATTTGTAATTATATTGCATTTATCTCATGCATA
131 AAGGGGTAACAACTCGATATTCTCTTAGAAATATTTGTAATTATATTGCATTTATCTCATGCATA
* *
2850003 GAGCCTAAGAATATTAAAGAAATATTAAATGATGAACATTGGATTATGGCTATGTAAGAAGAGTT
196 GAGCCTAAGAATATTAAAGAAACATTAAATGATGAACATTGGATTATGGCTATGCAAGAAGAGTT
2850068 AAATCAATTTGAGAGAAGTAAAGTATTGACATTAGTTGAAAGGCCTAATAATAAATCTATTGTAG
261 AAATCAATTTGAGAGAAGTAAAGTATTGACATTAGTTGAAAGGCCTAATAATAAATCTATTGTAG
2850133 GTACTAGATGGGTATTTAGGAATAAGCTTGATGAGAGTGGTAATATAGTGAGAAACAAGGCTAGA
326 GTACTAGATGGGTATTTAGGAATAAGCTTGATGAGAGTGGTAATATAGTGAGAAACAAGGCTAGA
*
2850198 CTTGTTGCTCAAGGGTATACTCAAGAAGAGGGCATAGACTATAATGAAACATACGCTCCCGTAGC
391 CTTGTTGCTCAAGGGTATACTCAAGAAAAGGGCATAGACTATAATGAAACATACGCTCCCGTAGC
2850263 AAGGATGAAAGCAATTAGAATGTTATTACCATTTGCATGTTTTCATGAATTTAAATTATATCAAA
456 AAGGATGAAAGCAATTAGAATGTTATTACCATTTGCATGTTTTCATGAATTTAAATTATATCAAA
* *
2850328 TGGAAGTTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAGTGTTTGTGGAACAACCTCCT
521 TGGAAGTTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAGTGTATGTGGAAAAACCTCCT
* **
2850393 AGTTTTGAAGATTTAAAATTTTTGAATCATGTTCTTAAATTGACAAAAGCGCTTTATGGTTTAAA
586 AATTTTGAAGATTTAAAATTTCCGAATCATGTTCTTAAATTGACAAAAGCGCTTTATGGTTTAAA
2850458 ACAAGATCCTAGAGCTTGGTATGAAAGATTGTCAAACTTTTTAATTGAAAAAGGTTTTCCAAAGG
651 ACAAGATCCTAGAGCTTGGTATGAAAGATTGTCAAACTTTTTAATTGAAAAAGGTTTTCCAAAGG
*
2850523 GAAGGTTGACACTACATTGTTTTTAAAGTATAAAGGTAAAGATTTATTAGTAGCTCAAATTTATG
716 GAAGGTTGACACTACATTGTTTTTAAACTATAAAGGTAAAGATTTATTAGTAGCTCAAATTTATG
*
2850588 TTGGTGATATAATATTTGGTTATACTAATGATGTTCTTTGCCAAGAATTTTCTAAGCTAATGCAA
781 TTGGTGATATAATATTTGGTTATACTAAAGATGTTCTTTGCCAAGAATTTTCTAAGCTAATGCAA
2850653 AGTGAATTAGAGATGAGCATGATGGGGGAGCTCTCATTTTTCTTGGGACTCCAAATCAAGAAAAG
846 AGTGAATTAGAGATGAGCATGATGGGGGAGCTCTCATTTTTCTTGGGACTCCAAATCAAGAAAAG
2850718 AAAAGATGGCATCTTCATCAATCAAGCTAAGTACGTCAAAGATATGCTCAAGAAGTT
911 AAAAGATGGCATCTTCATCAATCAAGCTAAGTACGTCAAAGATATGCTCAAGAAGTT
2850775 TCAAAGGAAGAAACGAAAGATGAAGAAACTCATGATCATCTCGAGAATCCAACCATTGAAGAAAG
1 TCAAAGGAAGAAACGAAAGATGAAGAAACTCATGATCATCTCGAGAATCCAACCATTGAAGAAAG
2850840 GGAAGTATCTTATCCAAGAGAGTACAACTATGTCAAGGATGGTGAGATTATAGGTGATCCATCCA
66 GGAAGTATCTTATCCAAGAGAGTACAACTATGTCAAGGATGGTGAGATTATAGGTGATCCATCCA
* *
2850905 AAGGGGTAACAACTCGATATTCTCTTAGAAATATTTGTAATTATGTTGTATTTATCTCATGCATA
131 AAGGGGTAACAACTCGATATTCTCTTAGAAATATTTGTAATTATATTGCATTTATCTCATGCATA
* *
2850970 GAGCCTAAGATTATTAAAGAAGCATTAAATGATGAACATTGGATTATGGCTATGCAAGAAGAGTT
196 GAGCCTAAGAATATTAAAGAAACATTAAATGATGAACATTGGATTATGGCTATGCAAGAAGAGTT
2851035 AAATCAATTTGAGAGAAGTAAAGTATTGACATTAGTTGAAAGGCCTAATAATAAATCTATTGTAG
261 AAATCAATTTGAGAGAAGTAAAGTATTGACATTAGTTGAAAGGCCTAATAATAAATCTATTGTAG
2851100 GTACTAGATGGGTATTTAGGAATAAGCTTGATGAGAGTGGTAATATAGTGAGAAACAAGGCTAGA
326 GTACTAGATGGGTATTTAGGAATAAGCTTGATGAGAGTGGTAATATAGTGAGAAACAAGGCTAGA
* *
2851165 CTTGTTGCTCAAGGGTATACTCAAGAAAAGGGCATAGACTATGATGAAACATATGCTCCCGTAGC
391 CTTGTTGCTCAAGGGTATACTCAAGAAAAGGGCATAGACTATAATGAAACATACGCTCCCGTAGC
* *
2851230 TAGGATGGAAGCAATTAGAATGTTATTACCATTTGCATGTTTTCATGAATTTAAATTATATCAAA
456 AAGGATGAAAGCAATTAGAATGTTATTACCATTTGCATGTTTTCATGAATTTAAATTATATCAAA
*
2851295 TGGATGTTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAGTGTATGTGGAAAAACCTCCT
521 TGGAAGTTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAGTGTATGTGGAAAAACCTCCT
2851360 AATTTTGAAGATTTAAAATTTCCGAATCATGTTCTTAAATTGACAAAAGCGCTTTATGGTTTAAA
586 AATTTTGAAGATTTAAAATTTCCGAATCATGTTCTTAAATTGACAAAAGCGCTTTATGGTTTAAA
* *
2851425 ACAAGATCCTAGAGCTTGTTATGAAAGATTGTCAAACTTTTTAATTGAAAAAGGTTTTCCAAATG
651 ACAAGATCCTAGAGCTTGGTATGAAAGATTGTCAAACTTTTTAATTGAAAAAGGTTTTCCAAAGG
2851490 GAAGGTTGACACTACATTGTTTTTAAACTATAAAGGTAAAGATTTATTAGTAGCTCAAATTTATG
716 GAAGGTTGACACTACATTGTTTTTAAACTATAAAGGTAAAGATTTATTAGTAGCTCAAATTTATG
2851555 TTGGTGATATAATATTTGGTTATACTAAAGATGTTCTTTGCCAAGAATTTTCTAAGCTAATGCAA
781 TTGGTGATATAATATTTGGTTATACTAAAGATGTTCTTTGCCAAGAATTTTCTAAGCTAATGCAA
* *
2851620 AGTGAATTCGAGATGAGCATGATGGGGGTGCTCTCATTTTTCTTGGGACTCCAAATCAAGAAAAG
846 AGTGAATTAGAGATGAGCATGATGGGGGAGCTCTCATTTTTCTTGGGACTCCAAATCAAGAAAAG
2851685 AAAAGATGGCATCTTCATCAATCAAGCTAAGTACGTCAAAGATATGCTCAAGAAGTT
911 AAAAGATGGCATCTTCATCAATCAAGCTAAGTACGTCAAAGATATGCTCAAGAAGTT
2851742 T
1 T
2851743 GGACTGGAAA
Statistics
Matches: 943, Mismatches: 25, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
967 943 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (967 bp):
TCAAAGGAAGAAACGAAAGATGAAGAAACTCATGATCATCTCGAGAATCCAACCATTGAAGAAAG
GGAAGTATCTTATCCAAGAGAGTACAACTATGTCAAGGATGGTGAGATTATAGGTGATCCATCCA
AAGGGGTAACAACTCGATATTCTCTTAGAAATATTTGTAATTATATTGCATTTATCTCATGCATA
GAGCCTAAGAATATTAAAGAAACATTAAATGATGAACATTGGATTATGGCTATGCAAGAAGAGTT
AAATCAATTTGAGAGAAGTAAAGTATTGACATTAGTTGAAAGGCCTAATAATAAATCTATTGTAG
GTACTAGATGGGTATTTAGGAATAAGCTTGATGAGAGTGGTAATATAGTGAGAAACAAGGCTAGA
CTTGTTGCTCAAGGGTATACTCAAGAAAAGGGCATAGACTATAATGAAACATACGCTCCCGTAGC
AAGGATGAAAGCAATTAGAATGTTATTACCATTTGCATGTTTTCATGAATTTAAATTATATCAAA
TGGAAGTTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAGTGTATGTGGAAAAACCTCCT
AATTTTGAAGATTTAAAATTTCCGAATCATGTTCTTAAATTGACAAAAGCGCTTTATGGTTTAAA
ACAAGATCCTAGAGCTTGGTATGAAAGATTGTCAAACTTTTTAATTGAAAAAGGTTTTCCAAAGG
GAAGGTTGACACTACATTGTTTTTAAACTATAAAGGTAAAGATTTATTAGTAGCTCAAATTTATG
TTGGTGATATAATATTTGGTTATACTAAAGATGTTCTTTGCCAAGAATTTTCTAAGCTAATGCAA
AGTGAATTAGAGATGAGCATGATGGGGGAGCTCTCATTTTTCTTGGGACTCCAAATCAAGAAAAG
AAAAGATGGCATCTTCATCAATCAAGCTAAGTACGTCAAAGATATGCTCAAGAAGTT
Found at i:2852626 original size:23 final size:23
Alignment explanation
Indices: 2852600--2852654 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
2852590 GTAGTTTAAG
2852600 GATTAATTTGATTGATTGAACAT
1 GATTAATTTGATTGATTGAACAT
2852623 GATTAATTTGATTGATTGAACAT
1 GATTAATTTGATTGATTGAACAT
2852646 GATTAATTT
1 GATTAATTT
2852655 TCAATATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (23 bp):
GATTAATTTGATTGATTGAACAT
Found at i:2855180 original size:14 final size:13
Alignment explanation
Indices: 2855148--2855181 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2855138 AAGGGGAGTA
2855148 ATTTC-AAACTTG
1 ATTTCAAAACTTG
2855160 ATTTCAAAACTTG
1 ATTTCAAAACTTG
2855173 ATTTTCAAA
1 A-TTTCAAA
2855182 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 8 0.40
14 7 0.35
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTCAAAACTTG
Found at i:2855596 original size:64 final size:64
Alignment explanation
Indices: 2855480--2855622 Score: 184
Period size: 64 Copynumber: 2.2 Consensus size: 64
2855470 TTTCAAAGGG
* *
2855480 ATGCACCGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTGAACATCGAATGCATTTT
1 ATGCATCGATGCA-CAATCCATGCATCGATGCACCATGGAATAAATTGAACATCGAATGCATTTC
* **
2855545 ATGCATCGATGCAC-ATACCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATT
1 ATGCATCGATGCACAAT-CCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
2855607 TC
63 TC
2855609 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2855623 TCTTAGTGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
63 7 0.10
64 49 0.70
65 14 0.20
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACAATCCATGCATCGATGCACCATGGAATAAATTGAACATCGAATGCATTTC
Found at i:2855734 original size:21 final size:21
Alignment explanation
Indices: 2855681--2855736 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
2855671 TTTACACTTG
* *
2855681 ATGCACCGATACACCTTGTGC
1 ATGCATCGATGCACCTTGTGC
*
2855702 ATGCATCAATGCACCTTGTGC
1 ATGCATCGATGCACCTTGTGC
2855723 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2855737 TGACGTTCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (21 bp):
ATGCATCGATGCACCTTGTGC
Found at i:2861857 original size:8 final size:8
Alignment explanation
Indices: 2861838--2861914 Score: 74
Period size: 9 Copynumber: 9.8 Consensus size: 8
2861828 CTTAAAGATA
2861838 AAAAAATG
1 AAAAAATG
2861846 -AAAAATG
1 AAAAAATG
2861853 AAAAAAATG
1 -AAAAAATG
2861862 AAAAAAATG
1 -AAAAAATG
2861871 AAAAAATG
1 AAAAAATG
*
2861879 -AAATA-G
1 AAAAAATG
2861885 -AAAAATAG
1 AAAAAAT-G
2861893 AAAAAATGG
1 AAAAAAT-G
2861902 AAAAAAT-
1 AAAAAATG
2861909 AAAAAA
1 AAAAAA
2861915 AAGAAGAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
6 5 0.08
7 17 0.28
8 9 0.15
9 30 0.49
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:2861858 original size:9 final size:9
Alignment explanation
Indices: 2861837--2861925 Score: 71
Period size: 9 Copynumber: 9.8 Consensus size: 9
2861827 GCTTAAAGAT
2861837 AAAAAAATG
1 AAAAAAATG
2861846 --AAAAATG
1 AAAAAAATG
2861853 AAAAAAATG
1 AAAAAAATG
2861862 AAAAAAATG
1 AAAAAAATG
2861871 -AAAAAATG
1 AAAAAAATG
2861879 AAATAGAAAAAT-
1 --A-A-AAAAATG
2861891 AGAAAAAATG
1 A-AAAAAATG
*
2861901 GAAAAAAT-
1 AAAAAAATG
*
2861909 AAAAAAAAG
1 AAAAAAATG
2861918 AAGAAAAA
1 AA-AAAAA
2861926 AAGAAGATGA
Statistics
Matches: 66, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
7 7 0.11
8 14 0.21
9 31 0.47
10 7 0.11
12 1 0.02
13 6 0.09
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:2861882 original size:22 final size:22
Alignment explanation
Indices: 2861857--2861900 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2861847 AAAATGAAAA
2861857 AAATGAAAAAAAT-GAAAAAATG
1 AAAT-AAAAAAATAGAAAAAATG
*
2861879 AAATAGAAAAATAGAAAAAATG
1 AAATAAAAAAATAGAAAAAATG
2861901 GAAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (22 bp):
AAATAAAAAAATAGAAAAAATG
Found at i:2861888 original size:39 final size:38
Alignment explanation
Indices: 2861841--2861915 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 38
2861831 AAAGATAAAA
*
2861841 AAATGAAAAAT-GAAAAAAATGAAAAAAATGAAAAAATG
1 AAATGAAAAATAG-AAAAAATGAAAAAAATAAAAAAATG
*
2861879 AAATAGAAAAATAGAAAAAATGGAAAAAATAAAAAAA
1 AAAT-GAAAAATAGAAAAAATGAAAAAAATAAAAAAA
2861916 AGAAGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 4 0.12
39 28 0.85
40 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (38 bp):
AAATGAAAAATAGAAAAAATGAAAAAAATAAAAAAATG
Found at i:2861926 original size:14 final size:14
Alignment explanation
Indices: 2861909--2861943 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2861899 TGGAAAAAAT
2861909 AAAAAAAAGAAGAA
1 AAAAAAAAGAAGAA
* *
2861923 AAAAAGAAGATGAA
1 AAAAAAAAGAAGAA
2861937 AAAAAAA
1 AAAAAAA
2861944 CAAAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (14 bp):
AAAAAAAAGAAGAA
Found at i:2861930 original size:8 final size:8
Alignment explanation
Indices: 2861837--2861925 Score: 51
Period size: 8 Copynumber: 10.9 Consensus size: 8
2861827 GCTTAAAGAT
2861837 AAAAAAATG
1 AAAAAAA-G
*
2861846 -AAAAATG
1 AAAAAAAG
2861853 AAAAAAATG
1 AAAAAAA-G
2861862 AAAAAAATG
1 AAAAAAA-G
*
2861871 AAAAAATG
1 AAAAAAAG
*
2861879 --AAATAG
1 AAAAAAAG
*
2861885 AAAAATAG
1 AAAAAAAG
*
2861893 AAAAAATGG
1 AAAAAA-AG
2861902 AAAAAATA-
1 AAAAAA-AG
2861910 AAAAAAAG
1 AAAAAAAG
2861918 AAGAAAAA
1 AA-AAAAA
2861926 AAGAAGATGA
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
6 4 0.06
7 2 0.03
8 30 0.46
9 29 0.45
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2863195 original size:55 final size:55
Alignment explanation
Indices: 2863111--2863390 Score: 465
Period size: 55 Copynumber: 5.1 Consensus size: 55
2863101 TGAAGCAAAA
2863111 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * * *
2863166 GAAGATTATTTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
2863221 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
2863274 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
2863329 GAAGATTGTTTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
2863384 GGAGATT
1 GAAGATT
2863391 ATTGTTCGAG
Statistics
Matches: 208, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
53 47 0.23
54 6 0.03
55 155 0.75
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:2863314 original size:108 final size:110
Alignment explanation
Indices: 2863111--2863393 Score: 489
Period size: 108 Copynumber: 2.6 Consensus size: 110
2863101 TGAAGCAAAA
2863111 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
*
2863176 TGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
2863221 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
* *
2863284 CGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
2863329 GAAGATTGTTTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
2863394 GTTCGAGTTC
Statistics
Matches: 163, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
108 100 0.61
109 6 0.04
110 57 0.35
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
Found at i:2863446 original size:52 final size:52
Alignment explanation
Indices: 2863386--2864146 Score: 1243
Period size: 52 Copynumber: 14.6 Consensus size: 52
2863376 CGATCGTTGG
*
2863386 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTCGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
2863438 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
2863490 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
2863542 AGATTATTGTTCGAGTTCTAGTCCTTGAATAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* ** * * *
2863594 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGATAGTCTCATAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
2863646 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
2863698 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
2863750 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAAGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
2863802 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
2863854 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
2863906 AGATTATTCTTCGAGTTCTAGTCCTTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * * * *
2863958 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTCGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
2864010 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
2864062 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
2864114 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
2864147 TAGAGAGCGA
Statistics
Matches: 667, Mismatches: 42, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 667 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Found at i:2863468 original size:28 final size:28
Alignment explanation
Indices: 2863436--2863520 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 28
2863426 AGACCCGTAG
2863436 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGATTATTGTTCGAGTTCTAGTCCCT
** ** * **
2863464 GAAGAAAATTGGGC-AG-TCTCGT--AG
1 GAAGATTATTGTTCGAGTTCTAGTCCCT
2863488 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGATTATTGTTCGAGTTCTAGTCCCT
2863516 GAAGA
1 GAAGA
2863521 AAATTGGGCA
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 10 0.26
25 2 0.05
26 10 0.26
27 2 0.05
28 15 0.38
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (28 bp):
GAAGATTATTGTTCGAGTTCTAGTCCCT
Found at i:2864040 original size:28 final size:28
Alignment explanation
Indices: 2864008--2864092 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 28
2863998 AGTCTCGTAG
2864008 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGATTATTGTTCGAGTTCTAGTCCCT
** ** * **
2864036 GAAGAAAATTGGGC-AG-TCTCGT--AG
1 GAAGATTATTGTTCGAGTTCTAGTCCCT
2864060 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGATTATTGTTCGAGTTCTAGTCCCT
2864088 GAAGA
1 GAAGA
2864093 AAATTGGGCA
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 10 0.26
25 2 0.05
26 10 0.26
27 2 0.05
28 15 0.38
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (28 bp):
GAAGATTATTGTTCGAGTTCTAGTCCCT
Found at i:2864063 original size:24 final size:24
Alignment explanation
Indices: 2864036--2864116 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
2864026 TCTAGTCCCT
2864036 GAAGAAAATTGGGCAGTCTCGTAG
1 GAAGAAAATTGGGCAGTCTCGTAG
** ** * **
2864060 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGAAAATTGGGC-AG-TCTCGT--AG
2864088 GAAGAAAATTGGGCAGTCTCGTAG
1 GAAGAAAATTGGGCAGTCTCGTAG
2864112 GAAGA
1 GAAGA
2864117 TTATCGTTCG
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 15 0.38
25 2 0.05
26 10 0.26
27 2 0.05
28 10 0.26
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.26
Consensus pattern (24 bp):
GAAGAAAATTGGGCAGTCTCGTAG
Found at i:2864412 original size:3 final size:3
Alignment explanation
Indices: 2864404--2864435 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2864394 GGATACTATC
2864404 ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2864436 ATAATAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2871885 original size:3 final size:3
Alignment explanation
Indices: 2871877--2871908 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
2871867 CTTTAGTATT
2871877 GAA GAA GAA GAA GAA GAA GAA GAA GATA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA G
2871909 GCATTGGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:2873045 original size:8 final size:8
Alignment explanation
Indices: 2873032--2873099 Score: 63
Period size: 9 Copynumber: 8.5 Consensus size: 8
2873022 TAAAGATAAA
2873032 AAAAAATG
1 AAAAAATG
2873040 AAAAAAATG
1 -AAAAAATG
2873049 AAAAAAATG
1 -AAAAAATG
2873058 AAAAAATG
1 AAAAAATG
*
2873066 -AAATA-G
1 AAAAAATG
2873072 -AAAAATAG
1 AAAAAAT-G
2873080 AAAAAATGG
1 AAAAAAT-G
2873089 AAAAAAT-
1 AAAAAATG
2873096 AAAA
1 AAAA
2873100 GGGGGGTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
6 5 0.09
7 8 0.15
8 9 0.17
9 31 0.58
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:2873045 original size:9 final size:9
Alignment explanation
Indices: 2873031--2873068 Score: 69
Period size: 9 Copynumber: 4.3 Consensus size: 9
2873021 TTAAAGATAA
2873031 AAAAAAATG
1 AAAAAAATG
2873040 AAAAAAATG
1 AAAAAAATG
2873049 AAAAAAATG
1 AAAAAAATG
2873058 -AAAAAATG
1 AAAAAAATG
2873066 AAA
1 AAA
2873069 TAGAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAAAATG
Found at i:2873069 original size:22 final size:22
Alignment explanation
Indices: 2873044--2873087 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2873034 AAAATGAAAA
2873044 AAATGAAAAAAAT-GAAAAAATG
1 AAAT-AAAAAAATAGAAAAAATG
*
2873066 AAATAGAAAAATAGAAAAAATG
1 AAATAAAAAAATAGAAAAAATG
2873088 GAAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (22 bp):
AAATAAAAAAATAGAAAAAATG
Found at i:2874336 original size:55 final size:55
Alignment explanation
Indices: 2874252--2874531 Score: 483
Period size: 55 Copynumber: 5.1 Consensus size: 55
2874242 TGAAGCAAAA
2874252 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
2874307 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
2874362 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
2874415 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
2874470 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
2874525 GGAGATT
1 GAAGATT
2874532 ATTGTTCGAG
Statistics
Matches: 210, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
53 47 0.22
54 6 0.03
55 157 0.75
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:2874455 original size:108 final size:110
Alignment explanation
Indices: 2874252--2874534 Score: 507
Period size: 108 Copynumber: 2.6 Consensus size: 110
2874242 TGAAGCAAAA
2874252 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
2874317 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
2874362 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
* *
2874425 CGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
*
2874470 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
2874535 GTTCGAGTTC
Statistics
Matches: 164, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
108 101 0.62
109 6 0.04
110 57 0.35
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
Found at i:2874587 original size:52 final size:52
Alignment explanation
Indices: 2874527--2875339 Score: 1401
Period size: 52 Copynumber: 15.6 Consensus size: 52
2874517 CGATCGTTGG
* *
2874527 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
*
2874579 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTAGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
2874631 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
2874683 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* * *
2874735 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
2874787 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
2874839 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* * *
2874891 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
2874943 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
2874995 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
2875047 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* * * *
2875099 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
2875151 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
2875203 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
2875255 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
2875307 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
2875340 TAGAGAGCGA
Statistics
Matches: 729, Mismatches: 32, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 729 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
Found at i:2875256 original size:24 final size:24
Alignment explanation
Indices: 2875229--2875309 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
2875219 TCTAGTCCCT
2875229 GAAGAAAATTGGGCAGTCTCGTAG
1 GAAGAAAATTGGGCAGTCTCGTAG
** ** * **
2875253 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGAAAATTGGGC-AG-TCTCGT--AG
2875281 GAAGAAAATTGGGCAGTCTCGTAG
1 GAAGAAAATTGGGCAGTCTCGTAG
2875305 GAAGA
1 GAAGA
2875310 TTATCGTTCG
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 15 0.38
25 2 0.05
26 10 0.26
27 2 0.05
28 10 0.26
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.26
Consensus pattern (24 bp):
GAAGAAAATTGGGCAGTCTCGTAG
Found at i:2875601 original size:3 final size:3
Alignment explanation
Indices: 2875593--2875628 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2875583 TCCGGGATAC
2875593 TAT TAT TAT TAT TAT TAT TA- TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2875629 ATAATAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2876702 original size:146 final size:146
Alignment explanation
Indices: 2876444--2876706 Score: 348
Period size: 146 Copynumber: 1.8 Consensus size: 146
2876434 TCGGGAACTC
* * *
2876444 CGATCAACATTCCGAACGGTGAAAAGTTGCGGAAGGTCATCACGAACAACATATTGAAAATTCAA
1 CGATCAACATTCCGAACGGTGAAAAGTTGCGGAAGGCCAACACGAACAACATATTGAAAAATCAA
* ** * * *
2876509 GACGATCGGACGGTGGACGGTGACGGATCAGAGAAAACATATCCGGACGGTTTTTAGCCTCTTGC
66 GACGATCGGACAGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTTTTAGCCTCTTGC
2876574 TGGTGATCGGAATCTT
131 TGGTGATCGGAATCTT
* * * *
2876590 CGATCAATATTCCGAACGGTGAAAAGTTGTGTG-ATGCCAACACGAACAACCTATTGAAAAATCA
1 CGATCAACATTCCGAACGGTGAAAAGTTGCG-GAAGGCCAACACGAACAACATATTGAAAAATCA
* * * * *
2876654 GGACGATCGGACAGTGGATGACGGCAGATCAAAGAAAATACATTCGGACGGTT
65 AGACGATCGGACAGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTT
2876707 ATCTTTGTAT
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
146 97 0.99
147 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (146 bp):
CGATCAACATTCCGAACGGTGAAAAGTTGCGGAAGGCCAACACGAACAACATATTGAAAAATCAA
GACGATCGGACAGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTTTTAGCCTCTTGC
TGGTGATCGGAATCTT
Found at i:2878393 original size:21 final size:21
Alignment explanation
Indices: 2878340--2878395 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
2878330 TTTACACTTG
* *
2878340 ATGCACCGATACACCTTGTGC
1 ATGCATCGATGCACCTTGTGC
*
2878361 ATGCATCAATGCACCTTGTGC
1 ATGCATCGATGCACCTTGTGC
2878382 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2878396 TGACGTTCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (21 bp):
ATGCATCGATGCACCTTGTGC
Found at i:2882883 original size:42 final size:41
Alignment explanation
Indices: 2882786--2882887 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
2882776 AAGGTCTTAT
*
2882786 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGAC
1 AGATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
* * * * *
2882827 AGATGACTCAAAGGATTTAATCATCATGCTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTGAC
*
2882869 TGATGGCCCGAAGGACTTA
1 AGATGGCCCGAAGGACTTA
2882888 CCAATTTTGG
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 15 0.31
42 34 0.69
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
Done.