Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007918.1 Hibiscus syriacus cultivar Beakdansim tig00110321_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: 2302251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1424559 original size:36 final size:35
Alignment explanation
Indices: 1424504--1424641 Score: 143
Period size: 36 Copynumber: 3.9 Consensus size: 35
1424494 TTTTGAGAAT
*
1424504 TTTAAAACAAATTTTTGTCTCGTTTGAGACAATTTC
1 TTTAAAACAAA-TTTTGTCTCGCTTGAGACAATTTC
* * *
1424540 TTTCAAAGCAAATTTTGTCTCGCTTGAAACAGCTTTC
1 TTT-AAAACAAATTTTGTCTCGCTTGAGACA-ATTTC
* * *
1424577 -TAAAAACAAATTTTGTCTCGTTTGAGACAAATTC
1 TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
* * *
1424611 TCTTGAAACAAACTTCGTCTCGCTTGAGACA
1 T-TTAAAACAAATTTTGTCTCGCTTGAGACA
1424642 TTTTTCCTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
34 3 0.04
35 24 0.29
36 45 0.54
37 11 0.13
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (35 bp):
TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
Found at i:1424735 original size:105 final size:102
Alignment explanation
Indices: 1424616--1424853 Score: 277
Period size: 105 Copynumber: 2.3 Consensus size: 102
1424606 AATTCTCTTG
* * *
1424616 AAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-T
1 AAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACAT
*
1424680 AAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-A
66 -AAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCAA
* * *
1424721 AAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACAT
1 AAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACAT
* * * *
1424786 TAAACAAAGTTGATTTCACTTGAGATCGTTTTCTCAA
66 AAAACAAAATTAATCTCACTTGAGATCGTTTTCTCAA
*
1424823 AAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAACAAA-TTTCGTCTCGCTTGAGACATTTTC
1424854 TCTAAAAACA
Statistics
Matches: 116, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 26 0.22
103 7 0.06
104 4 0.03
105 76 0.66
106 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (102 bp):
AAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACAT
AAAACAAAATTAATCTCACTTGAGATCGTTTTCTCAA
Found at i:1424844 original size:36 final size:36
Alignment explanation
Indices: 1424815--1424918 Score: 117
Period size: 36 Copynumber: 3.0 Consensus size: 36
1424805 TTGAGATCGT
1424815 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
* ** *
1424850 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
* *
1424886 TATCT-T-AAAGCAAA-TTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAACTTT-GTCTCGCTTGAGACA
1424919 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
33 3 0.05
34 19 0.33
35 7 0.12
36 29 0.50
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
Found at i:1425240 original size:30 final size:28
Alignment explanation
Indices: 1425160--1425258 Score: 103
Period size: 29 Copynumber: 3.5 Consensus size: 28
1425150 TCTTGAGACA
*
1425160 GTTTCTCTTGAAAAA-ATCTTTGAGTTT
1 GTTTCTCTTAAAAAATATCTTTGAGTTT
* * *
1425187 GTTCCTTTTGAATAAATATCTTTGAGTTT
1 GTTTCTCTT-AAAAAATATCTTTGAGTTT
*
1425216 GTTTCTCTTAACAAAATCATCTTTGAGTCT
1 GTTTCTCTTAA-AAAAT-ATCTTTGAGTTT
*
1425246 ATTTCT-TTAAAAA
1 GTTTCTCTTAAAAA
1425259 CAAATGTTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
27 7 0.12
28 9 0.15
29 27 0.46
30 16 0.27
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.47
Consensus pattern (28 bp):
GTTTCTCTTAAAAAATATCTTTGAGTTT
Found at i:1425381 original size:120 final size:119
Alignment explanation
Indices: 1425232--1425456 Score: 269
Period size: 120 Copynumber: 1.9 Consensus size: 119
1425222 CTTAACAAAA
* * * *
1425232 TCATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAA
1 TCATCTTTGAGTATATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAA
1425295 AACTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGTGAT
64 AA--AATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGAT
* ** **
1425352 TCATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 TCATCTTTGAGTATATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAA
* * *
1425417 AATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
1425457 TCGAGACAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
118 23 0.26
119 19 0.21
120 43 0.48
121 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (119 bp):
TCATCTTTGAGTATATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAA
AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGAT
Found at i:1425433 original size:64 final size:63
Alignment explanation
Indices: 1425354--1425478 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
1425344 GATGTGATTC
* *
1425354 ATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
1425418 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
1425479 TACCAACCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:1425658 original size:15 final size:15
Alignment explanation
Indices: 1425635--1425693 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
1425625 TTTTGAGTCG
*
1425635 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
1425650 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
1425665 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
1425680 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
1425694 AGATCATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:1425962 original size:35 final size:34
Alignment explanation
Indices: 1425923--1426022 Score: 95
Period size: 35 Copynumber: 3.0 Consensus size: 34
1425913 TTGAGATCAA
1425923 TTCCCTTTAAACGAATTTTGTCTCATTGAGACAGT
1 TTCCCTTTAAACGAATTTTGTCTC-TTGAGACAGT
* *
1425958 TTCCCTTTAAACG----TCGTCT-TTGAGTC-GT
1 TTCCCTTTAAACGAATTTTGTCTCTTGAGACAGT
* *
1425986 TTCCCTTAAAACAAATTTTGTCTCTTTTGAGACAGT
1 TTCCCTTTAAACGAATTTTGTCTC--TTGAGACAGT
1426022 T
1 T
1426023 GCTTTTAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
28 13 0.25
29 6 0.12
31 5 0.10
32 5 0.10
35 19 0.37
36 3 0.06
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (34 bp):
TTCCCTTTAAACGAATTTTGTCTCTTGAGACAGT
Found at i:1426173 original size:40 final size:40
Alignment explanation
Indices: 1426115--1426305 Score: 152
Period size: 40 Copynumber: 4.5 Consensus size: 40
1426105 CCAGTCGTCC
* * *
1426115 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCT
* ** * *
1426155 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCCAG---ACCAGATC-TCT
* * * * *
1426198 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--CAGA---CCAGATCTCT
1426244 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCT
1426284 TCATCACGTATGAGCCGTGTCA
1 TCATCACGTATGAGCCGTGTCA
1426306 CCCTAGATAA
Statistics
Matches: 119, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
40 54 0.45
42 1 0.01
43 30 0.25
44 1 0.01
46 30 0.25
47 3 0.03
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (40 bp):
TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCT
Found at i:1426258 original size:89 final size:83
Alignment explanation
Indices: 1426105--1426265 Score: 223
Period size: 83 Copynumber: 1.9 Consensus size: 83
1426095 CTAAAGATGG
* * *
1426105 CCAGTCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGC
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
1426170 CGTGTCAACCATAGATAA
66 CGTGTCAACCATAGATAA
* *
1426188 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGAACTCTTCATCACGT
1426253 ATGAGCCGTGTCA
60 ATGAGCCGTGTCA
1426266 TTCCCCGACC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 31 0.46
84 2 0.03
86 3 0.04
89 31 0.46
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (83 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
CGTGTCAACCATAGATAA
Found at i:1426439 original size:91 final size:93
Alignment explanation
Indices: 1426274--1426441 Score: 234
Period size: 91 Copynumber: 1.8 Consensus size: 93
1426264 CATTCCCCGA
* * * * *
1426274 CCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAACCAGCTGTCCTCATCACGTAGGA
1 CCAGAACTCTTCATCACGTACGAGCCATGTCACCCTAGACAACCAGCTATCCTCATCACGTAGGA
*
1426339 ACCGTGTTATCACCCTTCCTAAAGATGG
66 ACCGAGTTATCACCCTTCCTAAAGATGG
* *
1426367 CCAGAACTCTTCATCACGTACGAGCCATGTCATCC-A-CCAACCAG-TCATCCTCATCACGTAGG
1 CCAGAACTCTTCATCACGTACGAGCCATGTCACCCTAGACAACCAGCT-ATCCTCATCACGTAGG
1426429 AACCGAGTTATCA
65 AACCGAGTTATCA
1426442 TCCACCCTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.02
91 33 0.50
92 1 0.02
93 31 0.47
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.24
Consensus pattern (93 bp):
CCAGAACTCTTCATCACGTACGAGCCATGTCACCCTAGACAACCAGCTATCCTCATCACGTAGGA
ACCGAGTTATCACCCTTCCTAAAGATGG
Found at i:1426647 original size:3 final size:3
Alignment explanation
Indices: 1426634--1426706 Score: 80
Period size: 3 Copynumber: 24.3 Consensus size: 3
1426624 GTCCGGGTCT
*
1426634 TTA TTA TTTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTT TTA -TA
1 TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
1426680 TT- TATA TTA TTA TT- TTA TTA ATA TTA T
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA T
1426707 ATTTTTACAT
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 5 0.08
3 48 0.80
4 7 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1426658 original size:19 final size:19
Alignment explanation
Indices: 1426634--1426706 Score: 91
Period size: 19 Copynumber: 4.1 Consensus size: 19
1426624 GTCCGGGTCT
1426634 TTATTATTTATTATTATTA
1 TTATTATTTATTATTATTA
1426653 TTATTATTTATTATTATTA
1 TTATTATTTATTATTATTA
* *
1426672 TTTTTATAT-TTA-TATTA
1 TTATTATTTATTATTATTA
*
1426689 TTA-T-TTTATTAATATTA
1 TTATTATTTATTATTATTA
1426706 T
1 T
1426707 ATTTTTACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.04
16 4 0.08
17 13 0.27
18 3 0.06
19 26 0.54
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATTTATTATTATTA
Found at i:1426687 original size:14 final size:13
Alignment explanation
Indices: 1426634--1426697 Score: 64
Period size: 13 Copynumber: 4.9 Consensus size: 13
1426624 GTCCGGGTCT
1426634 TTATTA-TTTATTA
1 TTATTATTTTA-TA
1426647 TTATTATTATTAT-
1 TTATTATT-TTATA
1426660 TTATTATTATTAT-
1 TTATTATT-TTATA
1426673 TT-TTATATTTATA
1 TTATTAT-TTTATA
1426686 TTATTATTTTAT
1 TTATTATTTTAT
1426698 TAATATTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.17
13 29 0.63
14 6 0.13
15 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTATTTTATA
Found at i:1426687 original size:17 final size:17
Alignment explanation
Indices: 1426648--1426711 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
1426638 TATTTATTAT
* *
1426648 TATTATTATTATTTATTA
1 TATTATTTTTATAT-TTA
1426666 TTATTATTTTTATATTTA
1 -TATTATTTTTATATTTA
*
1426684 TATTATTATTT-TATTAA
1 TATTATT-TTTATATTTA
1426701 TATTATATTTT
1 TATTAT-TTTT
1426712 TACATATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 21 0.52
18 7 0.17
19 12 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATTTTTATATTTA
Found at i:1428770 original size:22 final size:22
Alignment explanation
Indices: 1428745--1428788 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1428735 TCAAACGATG
*
1428745 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
1428767 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
1428789 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:1460332 original size:32 final size:32
Alignment explanation
Indices: 1460296--1460365 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
1460286 TTATAATATA
* *
1460296 AAAATTTAATTCGAACATAACATTAAATATCC
1 AAAATTTAATTCAAACACAACATTAAATATCC
* * *
1460328 AAAATTTAATTTAAATACAACTTTAAATATCC
1 AAAATTTAATTCAAACACAACATTAAATATCC
*
1460360 TAAATT
1 AAAATT
1460366 AATATAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.36
Consensus pattern (32 bp):
AAAATTTAATTCAAACACAACATTAAATATCC
Found at i:1460933 original size:13 final size:13
Alignment explanation
Indices: 1460915--1460939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1460905 AAAAATAAGA
1460915 AAAAATAAAAAAT
1 AAAAATAAAAAAT
1460928 AAAAATAAAAAA
1 AAAAATAAAAAA
1460940 GCCTCTAAAT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:1461542 original size:23 final size:21
Alignment explanation
Indices: 1461504--1461546 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1461494 TTAATTATTT
1461504 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
1461525 AAAAACATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
1461546 A
1 A
1461547 TTTTTATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:1463697 original size:3 final size:3
Alignment explanation
Indices: 1463689--1463715 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1463679 CACTAATCCC
1463689 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1463716 GTTTGGGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1473214 original size:21 final size:20
Alignment explanation
Indices: 1473188--1473226 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1473178 AACAAAATGG
1473188 TAACAATTGATATCATTTTGT
1 TAACAATTGATATC-TTTTGT
1473209 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
1473227 CATTAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (20 bp):
TAACAATTGATATCTTTTGT
Found at i:1473232 original size:21 final size:21
Alignment explanation
Indices: 1473188--1473232 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1473178 AACAAAATGG
*
1473188 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTAT
1473209 TAACAATTGATATC-TTTTCAT
1 TAACAATTGATATCATTTT-AT
1473230 TAA
1 TAA
1473233 ACATTTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (21 bp):
TAACAATTGATATCATTTTAT
Found at i:1476867 original size:23 final size:22
Alignment explanation
Indices: 1476840--1476882 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1476830 ATATCATTCC
1476840 ATAATAGTTTAATAAATTTAACA
1 ATAATAGTTTAA-AAATTTAACA
* *
1476863 ATAATTGTTTAAAATTTTAA
1 ATAATAGTTTAAAAATTTAA
1476883 TTATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATAATAGTTTAAAAATTTAACA
Found at i:1480681 original size:114 final size:115
Alignment explanation
Indices: 1480490--1480712 Score: 387
Period size: 114 Copynumber: 1.9 Consensus size: 115
1480480 ATTTTGTTTC
* *
1480490 TTTTTTTTACCCACCATTAAAAAATTTACGGTGATGATGATGTTGCATTTTTTAAATTATTTTTT
1 TTTTTTTTACCCACCATTAAAAAATTAACGGCGATGATGATGTTGCATTTTTTAAATTATTTTTT
1480555 CACTTCACACTTAATTATTATTTTATTATTTTTTGACAAGATGGTTTCTT
66 CACTTCACACTTAATTATTATTTTATTATTTTTTGACAAGATGGTTTCTT
*
1480605 TTTTTTTTACCCACCATTAAAAAATTAACGGCGATGTTGATG-TG-ATATTTTTAAATTATTTTT
1 TTTTTTTTACCCACCATTAAAAAATTAACGGCGATGATGATGTTGCAT-TTTTTAAATTATTTTT
*
1480668 TCACTTCACACTTAATTATTCTTTTATTATTTTTTGACAAGATGG
65 TCACTTCACACTTAATTATTATTTTATTATTTTTTGACAAGATGG
1480713 ATAAGGTTAA
Statistics
Matches: 103, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
113 2 0.02
114 62 0.60
115 39 0.38
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.50
Consensus pattern (115 bp):
TTTTTTTTACCCACCATTAAAAAATTAACGGCGATGATGATGTTGCATTTTTTAAATTATTTTTT
CACTTCACACTTAATTATTATTTTATTATTTTTTGACAAGATGGTTTCTT
Found at i:1483784 original size:47 final size:49
Alignment explanation
Indices: 1483691--1483786 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 49
1483681 AGGATTAGAT
*
1483691 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAACAATATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGGTAGAGTTAAAACAATA-TTTTAGTTA
*
1483741 TTATTATTTTATTAGGAATT-AGAGTAGAGTTAAGAC-ATA-TTTAGTT
1 TTATTATTTTATTAGGAATTAAG-GTAGAGTTAAAACAATATTTTAGTT
1483787 TGTTATTGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
47 7 0.16
49 5 0.12
50 31 0.72
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (49 bp):
TTATTATTTTATTAGGAATTAAGGTAGAGTTAAAACAATATTTTAGTTA
Found at i:1484039 original size:50 final size:52
Alignment explanation
Indices: 1483971--1484108 Score: 154
Period size: 59 Copynumber: 2.6 Consensus size: 52
1483961 CACACTCCAA
* * *
1483971 TTTGCCTTTTTATCGCGACGAGGAGGGTT-GG-TTAGAGTCATATTATCGAG
1 TTTGCCTTTTCATTGCGACTAGGAGGGTTAGGATTAGAGTCATATTATCGAG
*
1484021 TTTGTCTTTTCATTGCGACTAGGAGGGTTCGATAGGACATTTAGAGTCATATTATCGAG
1 TTTGCCTTTTCATTGCGACTAGGAGGG-T---TAGG--A-TTAGAGTCATATTATCGAG
*
1484080 TTTGCCTTTTCATTGCGACTTGGAGGGTT
1 TTTGCCTTTTCATTGCGACTAGGAGGGTT
1484109 CAATAGGACA
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
50 23 0.32
51 1 0.01
54 1 0.01
55 3 0.04
58 1 0.01
59 44 0.60
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (52 bp):
TTTGCCTTTTCATTGCGACTAGGAGGGTTAGGATTAGAGTCATATTATCGAG
Found at i:1484094 original size:59 final size:59
Alignment explanation
Indices: 1484002--1484118 Score: 207
Period size: 59 Copynumber: 2.0 Consensus size: 59
1483992 GGAGGGTTGG
* *
1484002 TTAGAGTCATATTATCGAGTTTGTCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAT
1 TTAGAGTCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGGACAT
*
1484061 TTAGAGTCATATTATCGAGTTTGCCTTTTCATTGCGACTTGGAGGGTTCAATAGGACA
1 TTAGAGTCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGGACA
1484119 CTTATCCATC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.37
Consensus pattern (59 bp):
TTAGAGTCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGGACAT
Found at i:1485819 original size:26 final size:26
Alignment explanation
Indices: 1485759--1485820 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
1485749 AAAGTTGATG
* *
1485759 GAAGAAAAAGAAATGGGTTTATGGAA
1 GAAGAAGAAGAAACGGGTTTATGGAA
* *
1485785 GAAGAAGAAGAAACGTGTTTATGGGA
1 GAAGAAGAAGAAACGGGTTTATGGAA
*
1485811 GAAGTAGAAG
1 GAAGAAGAAG
1485821 GGTTCTGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.47, C:0.02, G:0.34, T:0.18
Consensus pattern (26 bp):
GAAGAAGAAGAAACGGGTTTATGGAA
Found at i:1500226 original size:35 final size:36
Alignment explanation
Indices: 1500180--1500258 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
1500170 TTTAAATTTT
1500180 AAGACTAATATTATATAT-AAAAAATAAGTAGTACA
1 AAGACTAATATTATATATAAAAAAATAAGTAGTACA
*
1500215 AAGACTAATATTATATATAAAAAAATAAGTGGTACA
1 AAGACTAATATTATATATAAAAAAATAAGTAGTACA
1500251 AAGACTAA
1 AAGACTAA
1500259 ATCTGATACT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 18 0.43
36 24 0.57
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (36 bp):
AAGACTAATATTATATATAAAAAAATAAGTAGTACA
Found at i:1501792 original size:26 final size:26
Alignment explanation
Indices: 1501763--1501820 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1501753 TAAACCTTTT
*
1501763 TATATTTTTAATTTTGTAAAAAAAAA
1 TATATATTTAATTTTGTAAAAAAAAA
* * * *
1501789 TATAAATTTAATTTTTTTAAAGAAAA
1 TATATATTTAATTTTGTAAAAAAAAA
1501815 TATATA
1 TATATA
1501821 AATATTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (26 bp):
TATATATTTAATTTTGTAAAAAAAAA
Found at i:1501797 original size:28 final size:30
Alignment explanation
Indices: 1501766--1501828 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
1501756 ACCTTTTTAT
1501766 ATTTTTAA-TTTTGTAAA-AAAAAATATAA
1 ATTTTTAATTTTTGTAAAGAAAAAATATAA
* *
1501794 A--TTTAATTTTTTTAAAGAAAATATATAA
1 ATTTTTAATTTTTGTAAAGAAAAAATATAA
1501822 ATATTTT
1 AT-TTTT
1501829 TTAACTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
26 5 0.18
27 8 0.29
28 12 0.43
31 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
ATTTTTAATTTTTGTAAAGAAAAAATATAA
Found at i:1502894 original size:2 final size:2
Alignment explanation
Indices: 1502887--1502914 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1502877 GTATATGTGT
1502887 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
1502915 GCCATTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1529078 original size:88 final size:88
Alignment explanation
Indices: 1528928--1529104 Score: 318
Period size: 88 Copynumber: 2.0 Consensus size: 88
1528918 GTCTGTTGAT
* *
1528928 GTATGTGGTGTATTTTCTTTATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCGATGTCCG
1 GTATGAGGTGTATTTTCTTTATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCG
*
1528993 TTGAGGTACTTATGTACAGCGAC
66 CTGAGGTACTTATGTACAGCGAC
1529016 GTATGAGGTGTATTTTCTTTATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCG
1 GTATGAGGTGTATTTTCTTTATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCG
*
1529081 CTGAGGTACTTATGTACAGTGAC
66 CTGAGGTACTTATGTACAGCGAC
1529104 G
1 G
1529105 AGTATGAAGG
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.40
Consensus pattern (88 bp):
GTATGAGGTGTATTTTCTTTATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCG
CTGAGGTACTTATGTACAGCGAC
Found at i:1529137 original size:88 final size:87
Alignment explanation
Indices: 1528948--1529127 Score: 236
Period size: 88 Copynumber: 2.0 Consensus size: 87
1528938 TATTTTCTTT
* *
1528948 ATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCGATGTCCGTTGAGGTACTTATGTACAGC
1 ATGGAAT-AAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCGCTGAGGTACTTATGTACAGC
* ** *
1529013 GACGTATGAGGTGTATTTTCTTT
65 GACGTATGAGGGGTATTTTAATG
*
1529036 ATGGAATAAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCGCTGAGGTACTTATGTACAGT
1 ATGGAAT-AAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCGCTGAGGTACTTATGTACAGC
1529101 GACGAGTATGAAGGGGGT-TTTTAATG
65 GAC--GTATG-A-GGGGTATTTTAATG
1529127 A
1 A
1529128 GGCCTAATTT
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
88 65 0.80
90 5 0.06
91 7 0.09
92 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (87 bp):
ATGGAATAAATTTTTAGGCACTCTTTTCCTCCTTCCAATGTCCGCTGAGGTACTTATGTACAGCG
ACGTATGAGGGGTATTTTAATG
Found at i:1535754 original size:352 final size:353
Alignment explanation
Indices: 1535109--1535814 Score: 1387
Period size: 352 Copynumber: 2.0 Consensus size: 353
1535099 ACGGATCATG
1535109 ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
1 ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
1535174 AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
66 AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
1535239 AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
131 AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
1535304 TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
196 TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
1535369 GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
261 GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
1535434 GAATTTTGATCAAAATATCCAATCAGAT
326 GAATTTTGATCAAAATATCCAATCAGAT
1535462 ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGAT-AACTACTCTAACA
1 ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
1535526 AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
66 AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
*
1535591 AGATCAGGGCAAAACACCACAGGAGTTAATGAAATATCCATTCCGTTTAATCTGAAAGTGACAAG
131 AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
1535656 TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
196 TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
1535721 GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
261 GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
*
1535786 GATTTTTGATCAAAATATCCAATCAGAT
326 GAATTTTGATCAAAATATCCAATCAGAT
1535814 A
1 A
1535815 ACAAACAGAA
Statistics
Matches: 351, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
352 300 0.85
353 51 0.15
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (353 bp):
ATTGCATAAGCTTATGAAATGAACAGAGCCGTGCAGTTAACAGTGAATGATAAACTACTCTAACA
AATGGAACTTTCTGCTACAAACACTACGGGAAGATGAGGGAAAGTTCAAAAAAGAAGGGTCCTTC
AGATCAGGGCAAAACACCACAGGAGTTAATGAAATAACCATTCCGTTTAATCTGAAAGTGACAAG
TCACCTCCAAGCCTCATTGGATTAATGACGCTGTAAACAATCCCAGAACAAAAATTAAATTGGCA
GTACAGGAAAGGAAAACATGCACTCTGACAACATTCAACTGTTGAGAAAGGCGTACCTAAATCTT
GAATTTTGATCAAAATATCCAATCAGAT
Found at i:1542312 original size:25 final size:25
Alignment explanation
Indices: 1542284--1542335 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1542274 AGAATAGGAC
* *
1542284 TTGTTTTGTAATGTCTTAGTTGTTA
1 TTGTCTTGTAATGTCTTAGTTCTTA
1542309 TTGTCTTGTAATGTCTTAGTTCTTA
1 TTGTCTTGTAATGTCTTAGTTCTTA
1542334 TT
1 TT
1542336 TTCGATTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.15, C:0.08, G:0.17, T:0.60
Consensus pattern (25 bp):
TTGTCTTGTAATGTCTTAGTTCTTA
Found at i:1547046 original size:6 final size:6
Alignment explanation
Indices: 1547035--1547095 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
1547025 AATTTAACTA
* * * * *
1547035 AGATAG AGATAG AGATAG AGATAG ATATAG ATATAG ATATAA ATATAG
1 AGATAG AGATAG AGATAG AGATAG AGATAG AGATAG AGATAG AGATAG
*
1547083 AGATAA AGATAG A
1 AGATAG AGATAG A
1547096 AGTCCTATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (6 bp):
AGATAG
Found at i:1547058 original size:18 final size:18
Alignment explanation
Indices: 1547035--1547095 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
1547025 AATTTAACTA
*
1547035 AGATAGAGATAGAGATAG
1 AGATAGATATAGAGATAG
*
1547053 AGATAGATATAGATATAG
1 AGATAGATATAGAGATAG
* * *
1547071 ATATAAATATAGAGATAA
1 AGATAGATATAGAGATAG
1547089 AGATAGA
1 AGATAGA
1547096 AGTCCTATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (18 bp):
AGATAGATATAGAGATAG
Found at i:1547173 original size:18 final size:19
Alignment explanation
Indices: 1547152--1547192 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1547142 ATTTTAAAAT
*
1547152 TAAAATAAATAA-ATAATA
1 TAAAATAAACAATATAATA
1547170 TAAAATAAACAATATAATA
1 TAAAATAAACAATATAATA
1547189 -AAAA
1 TAAAA
1547193 ACTAATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAATAAACAATATAATA
Found at i:1551938 original size:43 final size:43
Alignment explanation
Indices: 1551877--1551967 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
1551867 TAGGCGAGAC
* * *
1551877 ATACTTTTTATATTAAAATGTTGTGTTGTAATATATCTAGTAG
1 ATACTTTTTATACTAAAATGTTATGTTATAATATATCTAGTAG
* * *
1551920 ATACTTTTTATACTAAAATGTTATTTTATAATATATCTATTAT
1 ATACTTTTTATACTAAAATGTTATGTTATAATATATCTAGTAG
1551963 ATACT
1 ATACT
1551968 GGTTCACTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.07, G:0.08, T:0.51
Consensus pattern (43 bp):
ATACTTTTTATACTAAAATGTTATGTTATAATATATCTAGTAG
Found at i:1557604 original size:74 final size:74
Alignment explanation
Indices: 1557515--1557666 Score: 304
Period size: 74 Copynumber: 2.1 Consensus size: 74
1557505 ACTAGTTCCT
1557515 AGGTTCTCTTTCTTATTATTTGTGATTGACTTGACAGGATACTGGATAACCTCCCCCTTGTTGTT
1 AGGTTCTCTTTCTTATTATTTGTGATTGACTTGACAGGATACTGGATAACCTCCCCCTTGTTGTT
1557580 CCCATTAGA
66 CCCATTAGA
1557589 AGGTTCTCTTTCTTATTATTTGTGATTGACTTGACAGGATACTGGATAACCTCCCCCTTGTTGTT
1 AGGTTCTCTTTCTTATTATTTGTGATTGACTTGACAGGATACTGGATAACCTCCCCCTTGTTGTT
1557654 CCCATTAGA
66 CCCATTAGA
1557663 AGGT
1 AGGT
1557667 CAGATCAGGA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.40
Consensus pattern (74 bp):
AGGTTCTCTTTCTTATTATTTGTGATTGACTTGACAGGATACTGGATAACCTCCCCCTTGTTGTT
CCCATTAGA
Found at i:1575151 original size:39 final size:39
Alignment explanation
Indices: 1575097--1575182 Score: 172
Period size: 39 Copynumber: 2.2 Consensus size: 39
1575087 CTTCGTCTCA
1575097 TTAAACTTATCTCCTTCGGACTTTTTAAAAATCAAAATT
1 TTAAACTTATCTCCTTCGGACTTTTTAAAAATCAAAATT
1575136 TTAAACTTATCTCCTTCGGACTTTTTAAAAATCAAAATT
1 TTAAACTTATCTCCTTCGGACTTTTTAAAAATCAAAATT
1575175 TTAAACTT
1 TTAAACTT
1575183 TGACTATGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (39 bp):
TTAAACTTATCTCCTTCGGACTTTTTAAAAATCAAAATT
Found at i:1577595 original size:130 final size:132
Alignment explanation
Indices: 1577352--1577602 Score: 330
Period size: 130 Copynumber: 1.9 Consensus size: 132
1577342 ATATCAAACT
* * *
1577352 AAAAGGACTTTTGCACCCACAAACTACTCTATAATACACCAAAATGCAACCCTCCTAGCACAGAA
1 AAAAGGACTCTGGAACCCACAAACTACTCTATAATACACCAAAATGCAACCCTCCTAGCACAGAA
* * * * **
1577417 AACTCCGTTCAAACCTCCTAATCAAAAATTGAAAACTTGTCCTATACAAGATCACAGTAGCATAA
66 AACTCAGATCAAACCTCCAAATAAAAAATCAAAAACTTGTCCTATACAAGATCACAGTAGCATAA
1577482 TA
131 TA
* * * * *
1577484 AAAAGGACTCTGGAACCCACAGAGTACTCT-TAATACACCACAATGCAACCCTCCTAGCTTC-GC
1 AAAAGGACTCTGGAACCCACAAACTACTCTATAATACACCAAAATGCAACCCTCCTAGC-ACAGA
1577547 AAA-TCAGATCAAACCTCCAAATAAAAAATCAAAAACTTGTCC-ACTACAAGATCACA
65 AAACTCAGATCAAACCTCCAAATAAAAAATCAAAAACTTGTCCTA-TACAAGATCACA
1577603 AATATCATAC
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
129 1 0.01
130 45 0.44
131 31 0.30
132 26 0.25
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (132 bp):
AAAAGGACTCTGGAACCCACAAACTACTCTATAATACACCAAAATGCAACCCTCCTAGCACAGAA
AACTCAGATCAAACCTCCAAATAAAAAATCAAAAACTTGTCCTATACAAGATCACAGTAGCATAA
TA
Found at i:1580453 original size:3 final size:3
Alignment explanation
Indices: 1580445--1580494 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
1580435 ATATTTATAT
1580445 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1580491 TTA T
1 TTA T
1580495 AGGCCCAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1582232 original size:115 final size:113
Alignment explanation
Indices: 1582075--1582283 Score: 292
Period size: 115 Copynumber: 1.8 Consensus size: 113
1582065 AATAATCATA
* * * * **
1582075 TTTTAATATTTATTTATTTTTAATATCGAAAAAAGAGCTGTCTTAAGGTACCTAGAAGCTTTTTT
1 TTTTAATATTTATATATTTTTAATATCAAAAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTT
* * *
1582140 CTGATATTTTTGAATAAATAAATATCTTACTATATTAAAATAAAATGT
66 ATGATATTTCTAAATAAATAAATATCTTACTATATTAAAATAAAATGT
* *
1582188 TTTTGATATTTATATATTTTTTAATATCAAAGAAAAGAGTTGTCTTAAAGCACCTAGAAGCCCTT
1 TTTTAATATTTATATA-TTTTTAATATCAAA-AAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTT
*
1582253 TTATGATATTTCTAAATAAGTAAATATCTTA
64 TTATGATATTTCTAAATAAATAAATATCTTA
1582284 TTTATATATA
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
113 14 0.17
114 13 0.16
115 55 0.67
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (113 bp):
TTTTAATATTTATATATTTTTAATATCAAAAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTT
ATGATATTTCTAAATAAATAAATATCTTACTATATTAAAATAAAATGT
Found at i:1584455 original size:14 final size:14
Alignment explanation
Indices: 1584417--1584455 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1584407 ATTTTAAATA
*
1584417 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
1584431 TTTTACATTTGCAT
1 ATTTACATTTGCAT
1584445 ATTTACATTTG
1 ATTTACATTTG
1584456 GCATCTCTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:1588067 original size:19 final size:19
Alignment explanation
Indices: 1588045--1588106 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
1588035 AAAATCCAGC
*
1588045 AAAGAAAGAAAAAAAGAAA
1 AAAGAAAGAAAAAAGGAAA
*
1588064 AAAG-ATG-AAAAAGGAAA
1 AAAGAAAGAAAAAAGGAAA
*
1588081 AATGAGAA-AAAAAAGGAAA
1 AAAGA-AAGAAAAAAGGAAA
*
1588100 GAAGAAA
1 AAAGAAA
1588107 AAAGGGGAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
17 12 0.35
18 4 0.12
19 18 0.53
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (19 bp):
AAAGAAAGAAAAAAGGAAA
Found at i:1588080 original size:17 final size:16
Alignment explanation
Indices: 1588049--1588110 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
1588039 TCCAGCAAAG
1588049 AAAGA-AAAAAAGAAA
1 AAAGAGAAAAAAGAAA
*
1588064 AAAGATGAAAAAGGAAA
1 AAAGA-GAAAAAAGAAA
* *
1588081 AATGAGAAAAAA-AAGG
1 AAAGAGAAAAAAGAA-A
1588097 AAAGAAGAAAAAAG
1 AAAG-AGAAAAAAG
1588111 GGGAGAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 7 0.19
16 9 0.24
17 21 0.57
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AAAGAGAAAAAAGAAA
Found at i:1588082 original size:26 final size:26
Alignment explanation
Indices: 1588045--1588109 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
1588035 AAAATCCAGC
* *
1588045 AAAGAA-AGAAAAAAAGAAAAAAGATG
1 AAAGAAGA-AAAAAAAGAAAAAAAAGG
**
1588071 AAA-AAGGAAAAATGAGAAAAAAAAGG
1 AAAGAA-GAAAAAAAAGAAAAAAAAGG
1588097 AAAGAAGAAAAAA
1 AAAGAAGAAAAAA
1588110 GGGGAGAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 2 0.06
26 26 0.84
27 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (26 bp):
AAAGAAGAAAAAAAAGAAAAAAAAGG
Found at i:1590486 original size:113 final size:113
Alignment explanation
Indices: 1590288--1590491 Score: 354
Period size: 113 Copynumber: 1.8 Consensus size: 113
1590278 GATAAGGAGG
* * *
1590288 CCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATTTGATTTGGTATGAACCCCAAAAC
1 CCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAAAAC
*
1590353 CAATCATTTGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAAAGA
66 CAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAAAGA
* *
1590401 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCCCAAAAC
1 CCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAAAAC
1590466 CAATCATTGGATTTGAAAGATGAATT
66 CAATCATTGGATTTGAAAGATGAATT
1590492 GCATAATCGT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 85 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (113 bp):
CCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAAAAC
CAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAAAGA
Found at i:1592638 original size:54 final size:53
Alignment explanation
Indices: 1592556--1592713 Score: 198
Period size: 54 Copynumber: 3.0 Consensus size: 53
1592546 TAATTGAGAA
* *
1592556 ATCTGAGCAGACGCCACAGAAAATGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACAGAAAA-GATGAATGTGTTGTCAAATGTTTTACGAAC
* * *
1592610 ATCTGAGCAGAAGCCACAGAAAAGGATGAAGGTGTTGTCAAGTGTTTTAC-ATC
1 ATCTGAGCAGAAGCCACAGAAAA-GATGAATGTGTTGTCAAATGTTTTACGAAC
* *
1592663 -TC-GA-CAGAAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACA-GAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
1592714 CAGTGATTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
50 33 0.36
51 9 0.10
52 2 0.02
53 2 0.02
54 45 0.49
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (53 bp):
ATCTGAGCAGAAGCCACAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:1593113 original size:22 final size:22
Alignment explanation
Indices: 1593082--1593136 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1593072 ATCTACACTC
*
1593082 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
1593104 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
1593126 TTCAAAGATGA
1 TTCAAAGATGA
1593137 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:1593945 original size:113 final size:113
Alignment explanation
Indices: 1593805--1594565 Score: 872
Period size: 113 Copynumber: 6.7 Consensus size: 113
1593795 ATTTCAAGTT
* *
1593805 AAAGTTCATAAT--G-AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGA
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *
1593867 TCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAG
66 TCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAG
* * * *
1593915 AAATTTCATAATGAGAAGAACTCATATGAAGAAGAAATAAGAAGTTCATAATGAGAAGAACTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
** ** * * ** * **
1593980 TCAATTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTT
66 TCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAG
* * * * *
1594028 AGAGTTCATAATGAGAAGAATTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
*
1594093 TCAACCTTTTGCTTAAATTCATCACTTGATGGATCAAATTTTCCAGAG
66 TCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAG
* *
1594141 AAAGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * *
1594206 TGAACCTTTTGCAT-AATTCTATCACAGAATGAGATAGATCAGCATCAACTTTTCCAAAT
66 TCAACCTTTTGCTTAAATTC-ATCAC----T----T-GAT--GGATCAACTTTTCCAGAG
*
1594265 AAAGTTCATAATAAGAAGAACTCATCTGAAG-A--AAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * *
1594327 TCAA-CTTTTCGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGG
66 TCAACCTTTT-GCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAG
** * * * *
1594375 CGAGTTCATAATGAGAAAAACTCATCTGAAGAAAGAAGAAAAAAGTTCATAATGAGAAGAATTTG
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AAGAAGTTCATAATGAGAAGAACTTG
* ** *
1594440 TTCAACTTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAG
65 TTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAG
*
1594489 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
*
1594554 TCAATCTTTTGC
66 TCAACCTTTTGC
1594566 ATGATTCTAT
Statistics
Matches: 546, Mismatches: 83, Indels: 41
0.81 0.12 0.06
Matches are distributed among these distances:
110 50 0.09
111 1 0.00
112 9 0.02
113 287 0.53
114 96 0.18
115 4 0.01
117 2 0.00
120 5 0.01
121 40 0.07
122 8 0.01
123 1 0.00
124 43 0.08
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAG
Found at i:1594084 original size:24 final size:23
Alignment explanation
Indices: 1594041--1594087 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1594031 GTTCATAATG
*
1594041 AGAAGAATTCATCTGAAGAAGAA
1 AGAAGAATTCATATGAAGAAGAA
1594064 AGAAGAAATTCATAATG-AGAAGAA
1 AGAAG-AATTCAT-ATGAAGAAGAA
1594088 TTTGTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 14 0.67
25 2 0.10
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.17
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGAA
Found at i:1594359 original size:234 final size:230
Alignment explanation
Indices: 1593571--1594565 Score: 996
Period size: 234 Copynumber: 4.3 Consensus size: 230
1593561 ATTACCAGAG
* *
1593571 AAAGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAGAAAGTTCATAATGAGAAGAACTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-A-AG-AAGTTCATAATGAGAAGAACTTGT
* * *** *
1593636 TCAACCTTTTGCTCGAATTCATCATTCGATGGATCAGCGTTGCC--AGAAGGTTCATAATGAGAA
63 TCAACCTTTTGCTCAAATTCATCATTTGATGGATCAAATTTGCCAGAGAAAGTTCATAATGAGAA
* * * *
1593699 GAACTTATCTAAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTT-GA
128 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAA
* * * * *
1593762 CTCTATCACATAAGAAGATAGATCATCATTAACATTT-CAAGTT
193 TTC-ATCACAT--G-AGATAGATCA-GATCAACTTTTCCAA-AT
* *
1593805 AAAGTTCATAAT--G-AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGA
1 AAAGTTCATAATGAGAAGAACTCATCTGAAG-A--AAGAAGAAGTTCATAATGAGAAGAACTTGT
* ** * *
1593867 TCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAATTTCATAATGAGAA
63 TCAACCTTTTGCTCAAATTCATCATTTGATGGATCAAATTTGCCAGAGAAAGTTCATAATGAGAA
* * * **
1593932 GAACTCATATGAAGAAGAAATAAGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTTGCTTAAA
128 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAA
** * * * **
1593997 TTCATCACCCG-G-TGGATCAG--C-A--GTGCCAGTT
193 TTCATCACATGAGATAGATCAGATCAACTTTTCCAAAT
* * * *
1594028 AGAGTTCATAATGAGAAGAATTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCT---GAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
1594093 TCAACCTTTTGCTTAAATTCATCACTTGATGGATCAAATTTTCCAGAGAAAGTTCATAATGAGAA
63 TCAACCTTTTGCTCAAATTCATCATTTGATGGATCAAATTTGCCAGAGAAAGTTCATAATGAGAA
* * * *
1594158 GAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTGAACCTTTTGCAT-AA
128 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAA
1594222 TTCTATCACAGAATGAGATAGATCAGCATCAACTTTTCCAAAT
193 TTC-ATCAC---ATGAGATAGATCAG-ATCAACTTTTCCAAAT
*
1594265 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
** * ** *
1594330 A-CTTTTCGCTTGAATTCATCATTTGATGGATCAACA-TTGCCAGGGCGAGTTCATAATGAGAAA
66 ACCTTTT-GCTCAAATTCATCATTTGATGGATCAA-ATTTGCCAGAGAAAGTTCATAATGAGAAG
* * * * **
1594393 AACTCATCTGAAGAAAGAAGAAAAAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCGAA
129 AACTCATCTGAAGAAGGAAG-AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAA
* * *
1594458 TTCATCAC-T-CGAT-G----GATCAACTTTTCCAGAG
193 TTCATCACATGAGATAGATCAGATCAACTTTTCCAAAT
*
1594489 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAG-A--AAGAAGAAGTTCATAATGAGAAGAACTTGT
*
1594554 TCAATCTTTTGC
63 TCAACCTTTTGC
1594566 ATGATTCTAT
Statistics
Matches: 644, Mismatches: 83, Indels: 75
0.80 0.10 0.09
Matches are distributed among these distances:
223 14 0.02
224 45 0.07
225 9 0.01
226 153 0.24
227 36 0.06
228 6 0.01
229 12 0.02
230 5 0.01
231 83 0.13
232 5 0.01
233 34 0.05
234 164 0.25
235 44 0.07
236 5 0.01
237 29 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (230 bp):
AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTCAAATTCATCATTTGATGGATCAAATTTGCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTC
ATCACATGAGATAGATCAGATCAACTTTTCCAAAT
Found at i:1594494 original size:114 final size:112
Alignment explanation
Indices: 1594249--1594563 Score: 445
Period size: 114 Copynumber: 2.8 Consensus size: 112
1594239 ATAGATCAGC
* * * *
1594249 ATCAACTTTTCCAAATAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAG--AAGTTCATA
1 ATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAAAGTTCATA
* * *
1594312 ATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTTGATGG
66 ATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTCGATGG
* * * * *
1594359 ATCAACATTGCCAGGGCGAGTTCATAATGAGAAAAACTCATCTGAAGAAAGAAGAAAAAAGTTCA
1 ATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG--AAAAGTTCA
* *
1594424 TAATGAGAAGAATTTGTTCAACTTTTTGCTCGAATTCATCACTCGATGG
64 TAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTCGATGG
*
1594473 ATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAA-AAGTTCAT
1594538 AATGAGAAGAACTTGTTCAATCTTTT
65 AATGAGAAGAACTTGTTCAA-CTTTT
1594564 GCATGATTCT
Statistics
Matches: 178, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
110 45 0.25
112 2 0.01
113 27 0.15
114 104 0.58
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (112 bp):
ATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAAAGTTCATA
ATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTCGATGG
Found at i:1594507 original size:348 final size:346
Alignment explanation
Indices: 1593569--1594601 Score: 1199
Period size: 348 Copynumber: 3.0 Consensus size: 346
1593559 GCATTACCAG
* *
1593569 AGAAAGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAGAAAGTTCATAATGAGAAGAACTT
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-A-AG-AAGTTCATAATGAGAAGAACTT
* *
1593634 GTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCAGCGTTGCCA-GAAG-GTTCATAATGAG
63 GTTCAA-CTTTTGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGAAGAGTTCATAATGAG
* * * * **
1593697 AAGAACTTATCTAAAGAGGAAG-AAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTG
127 AAGAACTCATCTGAAGAAGAAGAAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
* * * *
1593761 -ACTCTATCACATAAGAAGATAGATCATCATTAACATTTCA-AGTTAAAGTTCATAAT--G-AGA
192 AATTC-ATCAC-T----AGATGGATCAAC-TT----TTCCAGAG--AAAGTTCATAATGAGAAGA
*
1593821 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGATCAACCTTTTGC-TCAA--
244 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCAT-AATT
* * * * * *
1593883 --ATC-C---ATCA-TTTGAT--GGATCAGCTTTTCCAG
308 CTATCACAGAATGAGATAGATCAGCATCAACTTTTCCAA
* * *
1593913 AGAAATTTCATAATGAGAAGAACTCATATGAAGAAGAAATAAGAAGTTCATAATGAGAAGAACTT
1 AGAAAGTTCATAATGAGAAGAACTCATCT---GAAGAAAGAAGAAGTTCATAATGAGAAGAACTT
* * ** * * **
1593978 GTTCAATTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAG
63 GTTCAA-CTTTTGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGAAGAGTTCATAATGAG
* *
1594043 AAGAATTCATCTGAAGAAGAAAGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
127 AAGAACTCATCTGAAGAAG-AAGAAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * *
1594107 AAATTCATCACTTGATGGATCAAATTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAT
191 GAATTCATCACTAGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
1594172 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTGAACCTTTTGCATAATTCTATCACAGAATG
256 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAATG
1594237 AGATAGATCAGCATCAACTTTTCCAA
321 AGATAGATCAGCATCAACTTTTCCAA
* *
1594263 ATAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * ** *
1594328 CAACTTTTCGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGGCGAGTTCATAATGAGAAA
66 CAACTTTT-GCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGAAGAGTTCATAATGAGAAG
* *
1594393 AACTCATCTGAAGAAAGAAGAAAAAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCGAA
130 AACTCATCTGAAG-AAGAAGAAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAA
* *
1594458 TTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
194 TTCATCACTAGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* * * *
1594523 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCATGATTCTATCACAGAAAGAGA
259 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAATGAGA
*
1594588 TAGATCAACATCAA
324 TAGATCAGCATCAA
1594602 TATTTCTAGA
Statistics
Matches: 590, Mismatches: 72, Indels: 50
0.83 0.10 0.07
Matches are distributed among these distances:
336 12 0.02
337 4 0.01
338 3 0.01
339 60 0.10
340 1 0.00
341 2 0.00
342 8 0.01
343 3 0.01
344 88 0.15
345 4 0.01
346 33 0.06
347 152 0.26
348 182 0.31
350 38 0.06
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (346 bp):
AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGAAGAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGAAGAAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
CATCACTAGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAATGAGATA
GATCAGCATCAACTTTTCCAA
Found at i:1594841 original size:3 final size:3
Alignment explanation
Indices: 1594835--1594904 Score: 88
Period size: 3 Copynumber: 22.3 Consensus size: 3
1594825 TTTTTTATAT
1594835 TTA TTA TTA TTA -TA TTTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
1594881 ATA TTA TTA TTTA TTA TATA TTA T
1 TTA TTA TTA -TTA TTA T-TA TTA T
1594905 AGGCCCAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
2 2 0.03
3 47 0.78
4 11 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1594863 original size:28 final size:29
Alignment explanation
Indices: 1594832--1594905 Score: 116
Period size: 28 Copynumber: 2.6 Consensus size: 29
1594822 TGTTTTTTTA
*
1594832 TATTTATTATTATTATAT-TTATTATTAT
1 TATTTATTATTATTATATATTAATATTAT
1594860 TATTTATTATTATTAT-TATTAATATTAT
1 TATTTATTATTATTATATATTAATATTAT
1594888 TATTTATTATATATTATA
1 TATTTATTAT-TATTATA
1594906 GGCCCAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 1 0.02
28 35 0.83
29 6 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TATTTATTATTATTATATATTAATATTAT
Found at i:1596432 original size:8 final size:9
Alignment explanation
Indices: 1596421--1596452 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
1596411 ATATATATAA
1596421 TATTTATT-
1 TATTTATTC
1596429 TATTTATTC
1 TATTTATTC
1596438 TATTT-TTC
1 TATTTATTC
1596446 TATTTAT
1 TATTTAT
1596453 AAATTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (9 bp):
TATTTATTC
Found at i:1596647 original size:115 final size:114
Alignment explanation
Indices: 1596494--1596703 Score: 330
Period size: 115 Copynumber: 1.8 Consensus size: 114
1596484 AATAATCATA
* * * * *
1596494 TTTTGATATTTATTTATTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGTACCTATAAGCTCTTT
1 TTTTGATATTTATTTATTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTT
* *
1596559 TCTGATATTTTTGAATAAATAAATATCTTACTATATTAAAATAAAATGT
66 TCTGATATTTCTAAATAAATAAATATCTTACTATATTAAAATAAAATGT
1596608 TTTTGATATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTT
1 TTTTGATATTTATTTA-TTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTT
* *
1596673 TTTTGATATTTCTAAATAAGTAAATATCTTA
65 TTCTGATATTTCTAAATAAATAAATATCTTA
1596704 TTTATGTATA
Statistics
Matches: 86, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
114 16 0.19
115 70 0.81
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (114 bp):
TTTTGATATTTATTTATTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTT
TCTGATATTTCTAAATAAATAAATATCTTACTATATTAAAATAAAATGT
Found at i:1596726 original size:115 final size:114
Alignment explanation
Indices: 1596482--1596726 Score: 323
Period size: 115 Copynumber: 2.1 Consensus size: 114
1596472 ACTTTTAAGA
* * *
1596482 AAAATAATCATA-TTTTGATATTTATTTATTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGTAC
1 AAAATAAT-ATATTTTTGATATTTATTTATTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCAC
* * * *
1596546 CTATAAGCTCTTTTCTGATATTTTTGAATAAATAAATATCTTACTATATT
65 CTAGAAGCCCTTTTCTGATATTTCTAAATAAATAAATATCTTACTATATT
* *
1596596 AAAATAAAATGTTTTTGATATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCAC
1 AAAATAATATATTTTTGATATTTATTTA-TTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCAC
* * *
1596661 CTAGAAGCCCTTTTTTGATATTTCTAAATAAGTAAATATCTTA-TTTATGT
65 CTAGAAGCCCTTTTCTGATATTTCTAAATAAATAAATATCTTACTATAT-T
* *
1596711 ATATTAATATATTTTT
1 AAAATAATATATTTTT
1596727 CTTAAAATTA
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
113 2 0.02
114 27 0.24
115 83 0.74
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (114 bp):
AAAATAATATATTTTTGATATTTATTTATTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACC
TAGAAGCCCTTTTCTGATATTTCTAAATAAATAAATATCTTACTATATT
Found at i:1601289 original size:26 final size:26
Alignment explanation
Indices: 1601242--1601291 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1601232 AATATTTAAA
*
1601242 TTATAATCAAATAATATCATAAACAT
1 TTATAATCAAATAAAATCATAAACAT
*
1601268 TTATAATTAAATTAAAAT-ATAAAC
1 TTATAATCAAA-TAAAATCATAAAC
1601292 TCGAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (26 bp):
TTATAATCAAATAAAATCATAAACAT
Found at i:1604160 original size:27 final size:28
Alignment explanation
Indices: 1604130--1604191 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
1604120 CTTTAGATAG
1604130 AGAAAAAAAGAACTTGGAT-AA-ATAGGA
1 AGAAAAAAA-AACTTGGATGAAGATAGGA
* *
1604157 AG-AAAGAAAACTTGGATGAAGATAGGT
1 AGAAAAAAAAACTTGGATGAAGATAGGA
1604184 A-AAAAAAA
1 AGAAAAAAA
1604192 TTATATGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 9 0.31
26 7 0.24
27 13 0.45
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (28 bp):
AGAAAAAAAAACTTGGATGAAGATAGGA
Found at i:1604191 original size:25 final size:24
Alignment explanation
Indices: 1604124--1604191 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 24
1604114 AAGAGACTTT
1604124 AGATAGAGAAAAAAAGAACTTGGATA
1 AGATAG-GAAAAAAA-AACTTGGATA
1604150 A-ATAGGAAGAAAGAAAACTTGGATGA
1 AGATAGGAA-AAA-AAAACTTGGAT-A
*
1604176 AGATAGGTAAAAAAAA
1 AGATAGGAAAAAAAAA
1604192 TTATATGTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
24 3 0.08
25 20 0.54
26 8 0.22
27 6 0.16
ACGTcount: A:0.59, C:0.03, G:0.24, T:0.15
Consensus pattern (24 bp):
AGATAGGAAAAAAAAACTTGGATA
Found at i:1606276 original size:14 final size:14
Alignment explanation
Indices: 1606257--1606312 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
1606247 CGTTCGTGAA
1606257 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
1606271 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
1606284 --TT-GTTTATGTT
1 CGTTCGATTATGTT
*
1606295 TGTTCGATTATGTT
1 CGTTCGATTATGTT
1606309 CGTT
1 CGTT
1606313 TATGTTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
13 3 0.09
14 22 0.65
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.55
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:1606291 original size:24 final size:24
Alignment explanation
Indices: 1606264--1606333 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
1606254 GAACGTTCGA
*
1606264 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
* *
1606288 TTATGTTTGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
1606312 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
1606334 AACTCAATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 1 0.03
24 38 0.97
ACGTcount: A:0.13, C:0.09, G:0.19, T:0.60
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:1607082 original size:16 final size:16
Alignment explanation
Indices: 1607059--1607135 Score: 145
Period size: 16 Copynumber: 4.8 Consensus size: 16
1607049 GGGTCTCCAA
1607059 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
1607075 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
1607091 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
1607107 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
1607123 CGTTTATGTTCGT
1 CGTTTATGTTCGT
1607136 TTATTTATTA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:1607100 original size:10 final size:10
Alignment explanation
Indices: 1607087--1607139 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
1607077 TTTATGTTCG
1607087 TGTTCGTTTA
1 TGTTCGTTTA
1607097 TGTTCG----
1 TGTTCGTTTA
1607103 TGTTCGTTTA
1 TGTTCGTTTA
1607113 TGTTCG----
1 TGTTCGTTTA
1607119 TGTTCGTTTA
1 TGTTCGTTTA
1607129 TGTTCGTTTA
1 TGTTCGTTTA
1607139 T
1 T
1607140 TTATTAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
6 12 0.34
10 23 0.66
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1607227 original size:16 final size:16
Alignment explanation
Indices: 1607206--1607238 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1607196 AAAAAAAATT
1607206 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1607222 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1607238 T
1 T
1607239 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1608006 original size:229 final size:223
Alignment explanation
Indices: 1607605--1608086 Score: 820
Period size: 229 Copynumber: 2.1 Consensus size: 223
1607595 GTAAATTATC
* *
1607605 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATTTATTATTATCTTTAGTTA
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATTTATTATTATATTTAGTTA
* *
1607670 ATATTGTTAAATTTAAAATCTTAATAATATTTTATAAATATCAAACAATCAAATAATTTTTTGTG
66 ATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAACAATCAAATAATATTTTGTG
1607735 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
131 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
1607800 ATAAATTACATAACTTTCAAAAAAGTATA
196 AT-AATTACATAACTTTCAAAAAAGTATA
* *
1607829 TATCATTTTTATAAAAGTGTCCATACTTATTTCATTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TG-AAA-ATATTTATTATTATATTTAG
*
1607894 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
63 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTAT-AAATATC-AAACAATCAAATAATATT
* *
1607959 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
126 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
*
1608024 GAAACATAATTACATAACTTTCAAAGAAGTATA
191 GAAACATAATTACATAACTTTCAAAAAAGTATA
1608057 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
1608087 AAAAGTAGGT
Statistics
Matches: 243, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
224 35 0.14
225 2 0.01
226 3 0.01
227 54 0.22
228 62 0.26
229 87 0.36
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (223 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATTTATTATTATATTTAGTTA
ATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAACAATCAAATAATATTTTGTG
TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
ATAATTACATAACTTTCAAAAAAGTATA
Found at i:1608386 original size:20 final size:19
Alignment explanation
Indices: 1608363--1608409 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
1608353 CGATATACCA
1608363 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1608383 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1608403 GGTAAAA
1 GGTAAAA
1608410 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1608456 original size:181 final size:182
Alignment explanation
Indices: 1608152--1608623 Score: 682
Period size: 181 Copynumber: 2.6 Consensus size: 182
1608142 GATCCAAATT
* * * *
1608152 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGA-CAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * * *
1608215 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAAGATCGACACTT
* * *
1608280 CGTGAATTTAAAAGAGAAGCAGTTTTA-AATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAGAA-CATATAAAGTGTCGATACTTTAA
*
1608333 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
1608398 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAAGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAAGATCGACACTTC
* *
1608462 GTGAATTTAAAAGAGAAGCAGTTATAGCACATATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAGAACATATAAAGTGTCGATACTTTAA
* * *
1608514 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
1608579 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
1608624 CGTAAGTACG
Statistics
Matches: 263, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
181 206 0.78
182 57 0.22
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAAGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAGAACATATAAAGTGTCGATACTTTAA
Found at i:1608567 original size:20 final size:19
Alignment explanation
Indices: 1608544--1608590 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1608534 CGATATAACA
1608544 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1608564 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1608584 GGTAAAA
1 GGTAAAA
1608591 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1608592 original size:17 final size:19
Alignment explanation
Indices: 1608553--1608595 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1608543 AGGTAAAAAT
1608553 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1608573 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1608590 ATGATA
1 ATGATA
1608596 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1612691 original size:17 final size:17
Alignment explanation
Indices: 1612669--1612701 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1612659 CACAATCAAA
1612669 AACGAAGACAGGAGATG
1 AACGAAGACAGGAGATG
1612686 AACGAAGACAGGAGAT
1 AACGAAGACAGGAGAT
1612702 AACAAAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.33, T:0.06
Consensus pattern (17 bp):
AACGAAGACAGGAGATG
Found at i:1613414 original size:199 final size:199
Alignment explanation
Indices: 1612914--1614063 Score: 2036
Period size: 197 Copynumber: 5.8 Consensus size: 199
1612904 GGCAAATTTA
* * *
1612914 CCATAAAGTGTCGATCC--ATATAAAAAGTGTCAATCCCAAAAACATCGAAAACC-AAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
*
1612976 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGAGAATATGTCTAA
65 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
*
1613041 ATAATGTGTCGACACTAATATA-TTTGTGTCGAT-TTTTTTTTCCAGAATGAATGG-AAACATGG
130 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
1613103 TGCAC
195 TGCAC
* *
1613108 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
*
1613173 TGTAATATGTAA-TTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGAGAATATGTCTAA
65 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
1613237 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
130 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
1613302 TGCAC
195 TGCAC
1613307 CCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
1613371 GTAATATGTAATTTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAA
66 GTAATATGTAA-TTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
1613436 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
130 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
1613501 TGCAC
195 TGCAC
1613506 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
1613571 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
1613636 TAATGTGTCGACACT-ATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1613699 GCAC
196 GCAC
1613703 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1613768 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
1613833 TAATGTGTCGACACTAATATA-TTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1613897 GCAC
196 GCAC
1613901 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1613965 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATATCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
*
1614030 TAATGTGTCGACACGAATATAGTTTGTGTCGATA
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
1614064 CTAATTTAAA
Statistics
Matches: 931, Mismatches: 13, Indels: 20
0.97 0.01 0.02
Matches are distributed among these distances:
194 17 0.02
196 109 0.12
197 355 0.38
198 153 0.16
199 245 0.26
200 52 0.06
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (199 bp):
CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
GCAC
Found at i:1615534 original size:12 final size:12
Alignment explanation
Indices: 1615517--1615603 Score: 75
Period size: 12 Copynumber: 6.9 Consensus size: 12
1615507 GGTCGCAGAA
*
1615517 GATGAAGCTGAC
1 GATGAAGATGAC
*
1615529 GATGAAGATGAT
1 GATGAAGATGAC
*
1615541 GATGATGATGAC
1 GATGAAGATGAC
* *
1615553 GATGAAGCTGGC
1 GATGAAGATGAC
1615565 GATGAAGATGATGAC
1 GATG-A-A-GATGAC
* *
1615580 GATGATGATGAT
1 GATGAAGATGAC
1615592 GATGAGAGATGA
1 GATGA-AGATGA
1615604 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
12 43 0.73
13 6 0.10
14 2 0.03
15 8 0.14
ACGTcount: A:0.36, C:0.07, G:0.36, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1615535 original size:18 final size:18
Alignment explanation
Indices: 1615514--1615575 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
1615504 AGCGGTCGCA
1615514 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
1615532 GAAGATGATGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
1615550 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
1615568 GAAGATGA
1 GAAGATGA
1615576 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:1615538 original size:6 final size:6
Alignment explanation
Indices: 1615514--1615603 Score: 54
Period size: 6 Copynumber: 14.3 Consensus size: 6
1615504 AGCGGTCGCA
* * * * * *
1615514 GAAGAT GAAGCT GACGAT GAAGAT GATGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * *
1615562 GGCGAT GAAGAT GATGACGAT GATGAT GATGAT GAGAGAT GA
1 GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GA-AGAT GA
1615604 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
6 54 0.83
7 5 0.08
8 1 0.02
9 5 0.08
ACGTcount: A:0.37, C:0.07, G:0.36, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:1615543 original size:3 final size:3
Alignment explanation
Indices: 1615529--1615607 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
1615519 TGAAGCTGAC
* * * * ** *
1615529 GAT GAA GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
1615577 GAC GAT GAT GAT GAT GAT GA- GA- GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1615608 CCAAACAAGT
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
2 4 0.07
3 56 0.93
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:1615568 original size:36 final size:36
Alignment explanation
Indices: 1615517--1615593 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
1615507 GGTCGCAGAA
*
1615517 GATGAAGCTGACGATGAAGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGACGATGATGAC
* *
1615553 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGATGACGATGATGAC
1615589 GATGA
1 GATGA
1615594 TGAGAGATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGATGACGATGATGAC
Found at i:1617371 original size:181 final size:182
Alignment explanation
Indices: 1617065--1617546 Score: 824
Period size: 181 Copynumber: 2.6 Consensus size: 182
1617055 TTCAACATAT
* *
1617065 TAAATATACCGGTTTTTTGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGTGTC
1 TAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTC
* *
1617130 GGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACATTTAC
66 GGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTATCGACATTTAC
*
1617195 ACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTA
130 ACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTA
1617248 TAAATATACCGGTTTTATGCGCGAATAGGTCTACAA-CTATATCGACACTTTTTAATATTGTGTC
1 TAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTC
* *
1617312 -GTACTTTATGTCCATATTGGAAGAAAAATATGTCGATACGATTTAAAAAAGTATCGACATTTAC
66 GGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTATCGACATTTAC
*
1617376 ACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTA
130 ACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTA
* *
1617429 TAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTC
1 TAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTC
*
1617494 TGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGT
66 GGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGT
1617547 GTCGGTAATT
Statistics
Matches: 283, Mismatches: 12, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
181 142 0.50
182 57 0.20
183 83 0.29
184 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (182 bp):
TAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTC
GGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTATCGACATTTACA
CATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTA
Found at i:1620027 original size:25 final size:25
Alignment explanation
Indices: 1619999--1620063 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1619989 TTATCATTAA
1619999 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
1620024 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
1620049 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
1620064 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:1620435 original size:23 final size:23
Alignment explanation
Indices: 1620404--1620476 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1620394 ATAGGTAAAC
*
1620404 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1620427 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1620450 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1620473 ATAT
1 ATAT
1620477 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1620920 original size:18 final size:18
Alignment explanation
Indices: 1620899--1620935 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1620889 GTAATTGGAG
1620899 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1620917 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1620935 T
1 T
1620936 ATATATTTCG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1620943 original size:24 final size:24
Alignment explanation
Indices: 1620891--1620937 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1620881 TTTCATATGT
* *
1620891 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
1620915 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
1620938 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:1621236 original size:39 final size:39
Alignment explanation
Indices: 1621193--1621279 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
1621183 TCCGATGCTC
*
1621193 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* * *
1621232 ATCAAAATTCAAATCTCATATGATGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
1621271 ATCAAAATC
1 ATCAAAATC
1621280 TACAACTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:1621677 original size:21 final size:22
Alignment explanation
Indices: 1621631--1621677 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1621621 AAATTACCTA
1621631 ACTTTTAAAAAAAGTATCGATC
1 ACTTTTAAAAAAAGTATCGATC
* * *
1621653 -CTTTTTATAAAAGTATGGA-C
1 ACTTTTAAAAAAAGTATCGATC
1621673 ACTTT
1 ACTTT
1621678 CAATAATAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
ACTTTTAAAAAAAGTATCGATC
Found at i:1621719 original size:23 final size:23
Alignment explanation
Indices: 1621693--1621765 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1621683 ATAGGTAAAC
*
1621693 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1621716 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1621739 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1621762 ATAT
1 ATAT
1621766 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1627154 original size:20 final size:20
Alignment explanation
Indices: 1627129--1627169 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1627119 TCGTCCTTCT
1627129 TCCCACTCTCGCAATTTGCG
1 TCCCACTCTCGCAATTTGCG
1627149 TCCCACTCTCGCAATTTGCG
1 TCCCACTCTCGCAATTTGCG
1627169 T
1 T
1627170 ATTACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.39, G:0.15, T:0.32
Consensus pattern (20 bp):
TCCCACTCTCGCAATTTGCG
Found at i:1633626 original size:3 final size:3
Alignment explanation
Indices: 1633618--1633646 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1633608 TTTCTTACAA
1633618 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1633647 GATGCCAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1636992 original size:16 final size:17
Alignment explanation
Indices: 1636971--1637003 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1636961 ACGTAGATTT
1636971 TATTAT-TTAAAAAATA
1 TATTATATTAAAAAATA
1636987 TATTATATTAAAAAATA
1 TATTATATTAAAAAATA
1637004 AAAAAATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTATATTAAAAAATA
Found at i:1645043 original size:121 final size:122
Alignment explanation
Indices: 1644818--1645052 Score: 454
Period size: 121 Copynumber: 1.9 Consensus size: 122
1644808 ATGTTAATAC
1644818 ATGCTTCTGTTGTAGTTCTACATTATTATATTTGGTTACATACTTGAATTTTTTTGGTGCAACAG
1 ATGCTTCTGTTGTAGTTCTACATTATTATATTTGGTTACATACTTGAATTTTTTTGGTGCAACAG
1644883 AGAGAGAACTTATGTTCGTGTTAATGGACACTTGCAAAGTTATCAAGGCGTTATTAT
66 AGAGAGAACTTATGTTCGTGTTAATGGACACTTGCAAAGTTATCAAGGCGTTATTAT
*
1644940 ATGCTTCTGTTGTAGTTCTACGTTATTATATTTGGTTACATACTTGAATTTTTTT-GTGCAACAG
1 ATGCTTCTGTTGTAGTTCTACATTATTATATTTGGTTACATACTTGAATTTTTTTGGTGCAACAG
1645004 AGAGAGAACTTATGTTCGTGTTAATGGACACTTGCAAAGTTATCAAGGC
66 AGAGAGAACTTATGTTCGTGTTAATGGACACTTGCAAAGTTATCAAGGC
1645053 AAGAAGCAAT
Statistics
Matches: 112, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
121 58 0.52
122 54 0.48
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (122 bp):
ATGCTTCTGTTGTAGTTCTACATTATTATATTTGGTTACATACTTGAATTTTTTTGGTGCAACAG
AGAGAGAACTTATGTTCGTGTTAATGGACACTTGCAAAGTTATCAAGGCGTTATTAT
Found at i:1647072 original size:19 final size:19
Alignment explanation
Indices: 1647048--1647092 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1647038 GATTCAATTT
**
1647048 ATCATTTTTTTCTTTATCC
1 ATCATTTTCGTCTTTATCC
1647067 ATCATTTTCGTCTTTAT-C
1 ATCATTTTCGTCTTTATCC
1647085 AT-ATTTTC
1 ATCATTTTC
1647093 ATATTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.25
18 3 0.12
19 15 0.62
ACGTcount: A:0.18, C:0.20, G:0.02, T:0.60
Consensus pattern (19 bp):
ATCATTTTCGTCTTTATCC
Found at i:1647577 original size:33 final size:32
Alignment explanation
Indices: 1647539--1647608 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
1647529 ATTATTTGAA
* *
1647539 TATTATTTTATTTATAAATTAGAA-TATATATTT
1 TATTATCTTAATTATAAATTA-AAGTATAT-TTT
1647572 TATTATCTTAATTATAAATTAAAGTATATTTT
1 TATTATCTTAATTATAAATTAAAGTATATTTT
1647604 TATTA
1 TATTA
1647609 CGTTGAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 10 0.29
33 24 0.71
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (32 bp):
TATTATCTTAATTATAAATTAAAGTATATTTT
Found at i:1655288 original size:16 final size:17
Alignment explanation
Indices: 1655267--1655299 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1655257 TTCTTACTTA
*
1655267 AGTCCA-TATAGTTCAT
1 AGTCCACTAAAGTTCAT
1655283 AGTCCACTAAAGTTCAT
1 AGTCCACTAAAGTTCAT
1655300 TGGATCGGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (17 bp):
AGTCCACTAAAGTTCAT
Found at i:1655364 original size:3 final size:3
Alignment explanation
Indices: 1655356--1655405 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
1655346 CAATATTTCG
*
1655356 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT TTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1655403 ATT
1 ATT
1655406 TAAAGTAGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:1689946 original size:15 final size:15
Alignment explanation
Indices: 1689926--1689964 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1689916 GAATATATAT
1689926 TGTTGTTGAATGAAA
1 TGTTGTTGAATGAAA
1689941 TGTTGTTGAATGAAA
1 TGTTGTTGAATGAAA
*
1689956 TGTTATTGA
1 TGTTGTTGA
1689965 TTTATGTATT
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:0.31, C:0.00, G:0.26, T:0.44
Consensus pattern (15 bp):
TGTTGTTGAATGAAA
Found at i:1699672 original size:15 final size:15
Alignment explanation
Indices: 1699652--1699682 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1699642 TCGTCGGAGC
1699652 GTGAGGGGAGAGAAG
1 GTGAGGGGAGAGAAG
1699667 GTGAGGGGAGAGAAG
1 GTGAGGGGAGAGAAG
1699682 G
1 G
1699683 GTTTATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.61, T:0.06
Consensus pattern (15 bp):
GTGAGGGGAGAGAAG
Found at i:1702324 original size:15 final size:15
Alignment explanation
Indices: 1702301--1702336 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1702291 TAATTATATG
*
1702301 TTTAGTATTTTATAA
1 TTTAATATTTTATAA
1702316 TTTAATATTTTATAA
1 TTTAATATTTTATAA
*
1702331 ATTAAT
1 TTTAAT
1702337 TTAATGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTAATATTTTATAA
Found at i:1702358 original size:16 final size:16
Alignment explanation
Indices: 1702337--1702372 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1702327 ATAAATTAAT
1702337 TTAATGGTACTAATCG
1 TTAATGGTACTAATCG
* *
1702353 TTAATGGTGCTCATCG
1 TTAATGGTACTAATCG
1702369 TTAA
1 TTAA
1702373 CGCTCGACGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (16 bp):
TTAATGGTACTAATCG
Found at i:1703752 original size:14 final size:13
Alignment explanation
Indices: 1703732--1703769 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
1703722 TTGAATTCGG
1703732 ATTTTTTTACCGA
1 ATTTTTTTACCGA
1703745 ATTTTTTTACCGA
1 ATTTTTTTACCGA
1703758 ATTTTTTCTACC
1 ATTTTTT-TACC
1703770 TTTCTATCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (13 bp):
ATTTTTTTACCGA
Found at i:1703956 original size:57 final size:56
Alignment explanation
Indices: 1703839--1703960 Score: 190
Period size: 57 Copynumber: 2.2 Consensus size: 56
1703829 GAAATTCTCG
* *
1703839 TTGCGAAAATAAAATTCGCGTTGCGATAGTGTGTTTACCTATGTCGGTAATTAGCA
1 TTGCGAAAACAAAATTCGCGTTGCGATAGTGTGTTTACCTATATCGGTAATTAGCA
* * *
1703895 TTGCGAAAACGAAATTCGCTTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCT
1 TTGCGAAAACAAAATTCGCGTTGCGATAG-TGTGTTTACCTATATCGGTAATTAGCA
1703952 TTGCGAAAA
1 TTGCGAAAA
1703961 TTTTCATGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
56 26 0.43
57 34 0.57
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (56 bp):
TTGCGAAAACAAAATTCGCGTTGCGATAGTGTGTTTACCTATATCGGTAATTAGCA
Found at i:1704208 original size:14 final size:14
Alignment explanation
Indices: 1704189--1704215 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1704179 AATGAAAAAT
1704189 AAAAAATAATATTA
1 AAAAAATAATATTA
1704203 AAAAAATAATATT
1 AAAAAATAATATT
1704216 TATATGAAAA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAAATAATATTA
Found at i:1720783 original size:43 final size:44
Alignment explanation
Indices: 1720702--1720784 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
1720692 TTTTAATATT
*
1720702 TATTATTATAGGTTTATATTTTCCTAATATTTATTATTAGGGCA
1 TATTATTATAGGTTTATATTTTCCTAATATTTAGTATTAGGGCA
* *
1720746 TATTCTTATA-GTTTATTTTTTTCCTAATATTT-GTATTAG
1 TATTATTATAGGTTTA-TATTTTCCTAATATTTAGTATTAG
1720785 TGTCTACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 11 0.31
44 24 0.69
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.57
Consensus pattern (44 bp):
TATTATTATAGGTTTATATTTTCCTAATATTTAGTATTAGGGCA
Found at i:1720859 original size:29 final size:31
Alignment explanation
Indices: 1720806--1720890 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 31
1720796 TTAGCAATAT
* *
1720806 TTTTTTTAACATTTATTATTAA-GGGTCCAG
1 TTTTTTTAATATTTATTATTAAGGGGTCCAA
1720836 TTTTTTTAATATTTATTATT-AGGGGTCCAA
1 TTTTTTTAATATTTATTATTAAGGGGTCCAA
* * * *
1720866 TTTATTCAATATTTTTTAGTAAGGG
1 TTTTTTTAATATTTATTATTAAGGG
1720891 AATACTTCTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.02
30 42 0.89
31 4 0.09
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.52
Consensus pattern (31 bp):
TTTTTTTAATATTTATTATTAAGGGGTCCAA
Found at i:1722670 original size:35 final size:34
Alignment explanation
Indices: 1722615--1722711 Score: 140
Period size: 35 Copynumber: 2.8 Consensus size: 34
1722605 TGGCAACCAA
*
1722615 CTTTGAAAATGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAATGTTTTCAAAGTTTGGTAAACATTT
*
1722649 CTTTGAAAATGGTTTTCAAAGTTTGGTAAACGTTT
1 CTTTGAAAAT-GTTTTCAAAGTTTGGTAAACATTT
* *
1722684 CTTTGAAAAATATTTTTAAAGTTTGGTA
1 CTTTG-AAAATGTTTTCAAAGTTTGGTA
1722712 GATGTTTGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
34 10 0.18
35 42 0.74
36 5 0.09
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.45
Consensus pattern (34 bp):
CTTTGAAAATGTTTTCAAAGTTTGGTAAACATTT
Found at i:1727233 original size:35 final size:35
Alignment explanation
Indices: 1727194--1727263 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1727184 TGTCAACCAA
1727194 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1727229 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1727264 TTCAAAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.46
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1727259 original size:21 final size:21
Alignment explanation
Indices: 1727235--1727279 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1727225 GTTTCTTTGA
1727235 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1727256 AAATGTTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1727277 AAA
1 AAA
1727280 GTTTGGTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.42
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1727280 original size:10 final size:10
Alignment explanation
Indices: 1727246--1727287 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
1727236 AATGGTTTTC
1727246 AAAGTTTGGT
1 AAAGTTTGGT
*
1727256 AAATGTTT-TT
1 AAA-GTTTGGT
1727266 CAAAGTTTGGT
1 -AAAGTTTGGT
1727277 AAAGTTTGGT
1 AAAGTTTGGT
1727287 A
1 A
1727288 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.43
Consensus pattern (10 bp):
AAAGTTTGGT
Found at i:1728646 original size:2 final size:2
Alignment explanation
Indices: 1728641--1728698 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
1728631 AACATTGGGA
**
1728641 AT AT AT AT GC 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
1728683 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1728699 TTGTCCACGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1731841 original size:45 final size:45
Alignment explanation
Indices: 1731774--1731860 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
1731764 GTTTCCAGAT
*
1731774 TCGCAACGCGATTTTGACTATCGCAACGCGATTTTCCAAATTAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATTTTCCAAATTAAA
* * * *
1731819 TCGCAATGTGATTCTGATTATCGCAATGCGATTTTCCAAATT
1 TCGCAACGCGATTCTGACTATCGCAACGCGATTTTCCAAATT
1731861 TACGTTAGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (45 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATTTTCCAAATTAAA
Found at i:1731911 original size:19 final size:19
Alignment explanation
Indices: 1731866--1731904 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1731856 AAATTTACGT
1731866 TAGTCCAAATTCGTTGCGA
1 TAGTCCAAATTCGTTGCGA
*
1731885 TAGTCCAAGTTCGTTGCGA
1 TAGTCCAAATTCGTTGCGA
1731904 T
1 T
1731905 TTTCCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (19 bp):
TAGTCCAAATTCGTTGCGA
Found at i:1737899 original size:27 final size:28
Alignment explanation
Indices: 1737866--1737960 Score: 104
Period size: 30 Copynumber: 3.3 Consensus size: 28
1737856 ATTGTTTAAC
1737866 TTATTTTAATTTA-AAATTAAATAATAT
1 TTATTTTAATTTATAAATTAAATAATAT
1737893 TTATTTTAATTTAATATAATTAAATAATTAT
1 TTATTTTAATTT-ATA-AATTAAATAA-TAT
* * * *
1737924 TTA-TATATTTTATAAAATAAATATTAGT
1 TTATTTTAATTTATAAATTAAATAATA-T
1737952 TTATTTTAA
1 TTATTTTAA
1737961 AAACTATATG
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
27 14 0.25
28 13 0.23
29 7 0.12
30 16 0.29
31 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
TTATTTTAATTTATAAATTAAATAATAT
Found at i:1741792 original size:213 final size:213
Alignment explanation
Indices: 1741425--1741855 Score: 862
Period size: 213 Copynumber: 2.0 Consensus size: 213
1741415 TATGAGTACC
1741425 TGCTTAAGTTATATGGGTTGATATATGAACATAAGAGAATAAATGATAAGTTATATGATGCAAGC
1 TGCTTAAGTTATATGGGTTGATATATGAACATAAGAGAATAAATGATAAGTTATATGATGCAAGC
1741490 TATGTGATTACATGTATATATTAATATATCTTGCTTGCATTACATGTTATGTGATATGAACATAT
66 TATGTGATTACATGTATATATTAATATATCTTGCTTGCATTACATGTTATGTGATATGAACATAT
1741555 ATGATATGTGTTATATGACAATTATTTATGAGACCATACAAGGATGTTACATGAGCTACGTGATA
131 ATGATATGTGTTATATGACAATTATTTATGAGACCATACAAGGATGTTACATGAGCTACGTGATA
1741620 ATAAGATATAAGATTACA
196 ATAAGATATAAGATTACA
1741638 TGCTTAAGTTATATGGGTTGATATATGAACATAAGAGAATAAATGATAAGTTATATGATGCAAGC
1 TGCTTAAGTTATATGGGTTGATATATGAACATAAGAGAATAAATGATAAGTTATATGATGCAAGC
1741703 TATGTGATTACATGTATATATTAATATATCTTGCTTGCATTACATGTTATGTGATATGAACATAT
66 TATGTGATTACATGTATATATTAATATATCTTGCTTGCATTACATGTTATGTGATATGAACATAT
1741768 ATGATATGTGTTATATGACAATTATTTATGAGACCATACAAGGATGTTACATGAGCTACGTGATA
131 ATGATATGTGTTATATGACAATTATTTATGAGACCATACAAGGATGTTACATGAGCTACGTGATA
1741833 ATAAGATATAAGATTACA
196 ATAAGATATAAGATTACA
1741851 TGCTT
1 TGCTT
1741856 GTACGATATA
Statistics
Matches: 218, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 218 1.00
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (213 bp):
TGCTTAAGTTATATGGGTTGATATATGAACATAAGAGAATAAATGATAAGTTATATGATGCAAGC
TATGTGATTACATGTATATATTAATATATCTTGCTTGCATTACATGTTATGTGATATGAACATAT
ATGATATGTGTTATATGACAATTATTTATGAGACCATACAAGGATGTTACATGAGCTACGTGATA
ATAAGATATAAGATTACA
Found at i:1741977 original size:21 final size:21
Alignment explanation
Indices: 1741951--1742036 Score: 109
Period size: 21 Copynumber: 4.1 Consensus size: 21
1741941 GAGTCGAGGG
*
1741951 ATATATGCGGTCCTTCGGGAC
1 ATATATGCGGTCCTTCGAGAC
* * *
1741972 ATATATGTGGTCTTTCGGGAC
1 ATATATGCGGTCCTTCGAGAC
* *
1741993 ATCTATGCGGTCATTCGAGAC
1 ATATATGCGGTCCTTCGAGAC
*
1742014 ATATATGTGGTCCTTCGAGAC
1 ATATATGCGGTCCTTCGAGAC
1742035 AT
1 AT
1742037 TTTTACGTGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (21 bp):
ATATATGCGGTCCTTCGAGAC
Found at i:1742001 original size:42 final size:42
Alignment explanation
Indices: 1741954--1742036 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
1741944 TCGAGGGATA
* * * *
1741954 TATGCGGTCCTTCGGGACATATATGTGGTCTTTCGGGACATC
1 TATGCGGTCATTCGAGACATATATGTGGTCCTTCGAGACATC
1741996 TATGCGGTCATTCGAGACATATATGTGGTCCTTCGAGACAT
1 TATGCGGTCATTCGAGACATATATGTGGTCCTTCGAGACAT
1742037 TTTTACGTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (42 bp):
TATGCGGTCATTCGAGACATATATGTGGTCCTTCGAGACATC
Found at i:1743255 original size:211 final size:212
Alignment explanation
Indices: 1742891--1743313 Score: 839
Period size: 211 Copynumber: 2.0 Consensus size: 212
1742881 AAACTTGCAT
1742891 GTATGGAGAAATGTTTGGGCAAAAAACCTAACAGTTTTTGTAAATTTGCTTTTTAGCCCCTGGTG
1 GTATGGAGAAATGTTTGGGCAAAAAACCTAACAGTTTTTGTAAATTTGCTTTTTAGCCCCTGGTG
1742956 GGTTGTTGTTTGGTTGTTGGAAAAATGAAGAAATGTAAAATTCTAACCATGATTTTTGTTTGCAG
66 GGTTGTTGTTTGGTTGTTGGAAAAATGAAGAAATGTAAAATTCTAACCATGATTTTTGTTTGCAG
1743021 CAAAAGGGTTATGATTTTCTTCTTAAATTGTAGTTTTGTTTGCTTTAGAGTAATTTTGTTTTTAA
131 CAAAAGGGTTATGATTTTCTTCTTAAATTGTAGTTTTGTTTGCTTTAGAGTAATTTTGTTTTTAA
1743086 GCTGGAAATA-TTCGTC
196 GCTGGAAATATTTCGTC
1743102 GTATGGAGAAATGTTTGGGCAAAAAACCTAACAGTTTTTGTAAATTTGCTTTTTAGCCCCTGGTG
1 GTATGGAGAAATGTTTGGGCAAAAAACCTAACAGTTTTTGTAAATTTGCTTTTTAGCCCCTGGTG
1743167 GGTTGTTGTTTGGTTGTTGGAAAAATGAAGAAATGTAAAATTCTAACCATGATTTTTGTTTGCAG
66 GGTTGTTGTTTGGTTGTTGGAAAAATGAAGAAATGTAAAATTCTAACCATGATTTTTGTTTGCAG
1743232 CAAAAGGGTTATGATTTTCTTCTTAAATTGTAGTTTTGTTTGCTTTAGAGTAATTTTGTTTTTAA
131 CAAAAGGGTTATGATTTTCTTCTTAAATTGTAGTTTTGTTTGCTTTAGAGTAATTTTGTTTTTAA
1743297 GCTGGAAATATTTCGTC
196 GCTGGAAATATTTCGTC
1743314 TTATACGGTC
Statistics
Matches: 211, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
211 205 0.97
212 6 0.03
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (212 bp):
GTATGGAGAAATGTTTGGGCAAAAAACCTAACAGTTTTTGTAAATTTGCTTTTTAGCCCCTGGTG
GGTTGTTGTTTGGTTGTTGGAAAAATGAAGAAATGTAAAATTCTAACCATGATTTTTGTTTGCAG
CAAAAGGGTTATGATTTTCTTCTTAAATTGTAGTTTTGTTTGCTTTAGAGTAATTTTGTTTTTAA
GCTGGAAATATTTCGTC
Found at i:1743341 original size:55 final size:55
Alignment explanation
Indices: 1743270--1743380 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
1743260 TGTAGTTTTG
1743270 TTTGCTTTAGAGTAATTTTGTTTTTAAGCTGGAAATATTTCGTCTTATACGGTCT
1 TTTGCTTTAGAGTAATTTTGTTTTTAAGCTGGAAATATTTCGTCTTATACGGTCT
1743325 TTTGCTTTAGAGTAATTTTGTTTTTAAGCTGGAAATATTTCGTCTTATACGGTCT
1 TTTGCTTTAGAGTAATTTTGTTTTTAAGCTGGAAATATTTCGTCTTATACGGTCT
1743380 T
1 T
1743381 CGGAGTGAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.50
Consensus pattern (55 bp):
TTTGCTTTAGAGTAATTTTGTTTTTAAGCTGGAAATATTTCGTCTTATACGGTCT
Done.