Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002534.1 Hibiscus syriacus cultivar Beakdansim tig00005150_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: 86927
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:20614 original size:168 final size:168
Alignment explanation
Indices: 20329--20768 Score: 546
Period size: 168 Copynumber: 2.6 Consensus size: 168
20319 GCTGTTTAGG
* * ** * *
20329 ATACAACCATTTCTCTTTTTCTTGACAAGTTCAGATCAATGGGATATATATATCATATGGTTAAA
1 ATACAACCATTTCTCTTTTTCATGACAAGTTTAGATCAAT-CTATATATATATCATAT-GATCAA
* * * *
20394 AGGG-TTTTAGTACATGTAGTTTGTGGCAGGTTGAAACGGACGCATAATTTCATATGTT-AGAAG
64 AGGGTTTTTAGTATATGTCGTTTGTGGCAGGTTGAGACGGACACATAATTTCATATGTTAAG-AG
*
20457 GAACAAACTTCTAAAATTTAATAAGCAAACGAACTTATAAA
128 GAACAAACTTATAAAATTTAATAAGCAAACGAACTTATAAA
** *
20498 ATACAACCATTTCTCCCTTTCATGACAAGTTTAGATCAATCTATATATATATCACATGATCAAAG
1 ATACAACCATTTCTCTTTTTCATGACAAGTTTAGATCAATCTATATATATATCATATGATCAAAG
* * * *
20563 GGTTTTTAGCATATGTCGTTTGTGGCAGGTTGAGACGGACATATGATTTCATATGTTAAGAGGGA
66 GGTTTTTAGTATATGTCGTTTGTGGCAGGTTGAGACGGACACATAATTTCATATGTTAAGAGGAA
** * * **
20628 TGAACTTATAAAATTTGATGAGTGAACGAACTTATAAA
131 CAAACTTATAAAATTTAATAAGCAAACGAACTTATAAA
* * *
20666 ATACAACAATTTCTCTTTTTCATGACAAGTTTAGATCGATCTATATGATATAT-ATATCA-CAGG
1 ATACAACCATTTCTCTTTTTCATGACAAGTTTAGATCAATCTATAT-ATATATCATATGATCA--
*
20729 GAGGGTTTTTAGTATATGTCGTTTGTGGCAGGTTGAGACG
63 AAGGGTTTTTAGTATATGTCGTTTGTGGCAGGTTGAGACG
20769 AACGTAATTT
Statistics
Matches: 234, Mismatches: 32, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
167 10 0.04
168 142 0.61
169 82 0.35
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (168 bp):
ATACAACCATTTCTCTTTTTCATGACAAGTTTAGATCAATCTATATATATATCATATGATCAAAG
GGTTTTTAGTATATGTCGTTTGTGGCAGGTTGAGACGGACACATAATTTCATATGTTAAGAGGAA
CAAACTTATAAAATTTAATAAGCAAACGAACTTATAAA
Found at i:24979 original size:38 final size:36
Alignment explanation
Indices: 24937--25019 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 36
24927 AATTATATCG
* *
24937 AAAATTTAGTTTTTGTTTCATTTTAGTAT-TCACTGTT
1 AAAATTTAGTTTTTATTTCATTTTAATATCTCA-T-TT
24974 AAAAATTTA-TTTTTATTTCATTTTAATATCTCATTT
1 -AAAATTTAGTTTTTATTTCATTTTAATATCTCATTT
25010 AAAATTTAGT
1 AAAATTTAGT
25020 GTTAAACTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 8 0.20
36 3 0.07
37 19 0.46
38 11 0.27
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.55
Consensus pattern (36 bp):
AAAATTTAGTTTTTATTTCATTTTAATATCTCATTT
Found at i:26942 original size:2 final size:2
Alignment explanation
Indices: 26935--26974 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
26925 ACTTTTCTTT
26935 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
26975 GATTATAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27868 original size:151 final size:148
Alignment explanation
Indices: 27594--28131 Score: 579
Period size: 151 Copynumber: 3.8 Consensus size: 148
27584 TTGATGGTTT
* * * *
27594 AGCTTGAATGG-TTAGTAATTTGGTGAAGAATTCTGTAATCTTTTAGTATATTGCTGATTCTGGT
1 AGCTTGAATGGATT-GTAATTTGGTGAAGAATTCTGTGATCTTTGAGTTTATTGCTAATTCTGGT
* * * *
27658 CTTTTAGCTTGTCTTTAATGAAGTTCAATTCGTAGCTGCAAATTTCAGTATCTTTTCATGTTTAT
65 CTTTGAGCTTGTCTTTAATGAAGTTCAATTTGTAGCTGCAAATTTCAATTTCTTTTCATGTTTAT
27723 GGATTTGGTGGTTGAGCACTTG
130 GGATTTGGTGGTT--G-ACTTG
*
27745 AGCTTGAATGGATTGTAATTTGGTGAAGAATTCTGTGACCTTTGAGTTTATTGCTAATTCTGGTC
1 AGCTTGAATGGATTGTAATTTGGTGAAGAATTCTGTGATCTTTGAGTTTATTGCTAATTCTGGTC
* * *
27810 TTTGA-ATT-TCTTTAATGAATTTCAATTTTGTAGCTGCAAATTTCATTTTCTTTTTCATGTTTA
66 TTTGAGCTTGTCTTTAATGAAGTTCAA-TTTGTAGCTGCAAATTTCAATTTC-TTTTCATGTTTA
27873 TGGATTTGGTGGTT--C---
129 TGGATTTGGTGGTTGACTTG
* * *
27888 AGCTTGAATGGATTGCAA-TT--T---G------GTGATCTTTGAGCTGATTGCTAATTCTGGTC
1 AGCTTGAATGGATTGTAATTTGGTGAAGAATTCTGTGATCTTTGAGTTTATTGCTAATTCTGGTC
* * *
27941 TTTGAGTTTGTCTTCAACGAAGTTCAATTTTGTAGCTGCAAATTTCAATTTCCTTTTCATGTTTA
66 TTTGAGCTTGTCTTTAATGAAGTTCAA-TTTGTAGCTGCAAATTTCAATTT-CTTTTCATGTTTA
* *
28006 TGCA-TT--T-GATGA-TTG
129 TGGATTTGGTGGTTGACTTG
* * * * *
28021 AGCTTGAGTGGATTGTAATTTGGTGAACAATTCGGTGATCTTTGATTTTATTGCTAACTCTGGTC
1 AGCTTGAATGGATTGTAATTTGGTGAAGAATTCTGTGATCTTTGAGTTTATTGCTAATTCTGGTC
*
28086 TTTGA-CTCTGTCTTTAATGAAGTTCAATTTGTTGCTGCAAATTTCA
66 TTTGAGCT-TGTCTTTAATGAAGTTCAATTTGTAGCTGCAAATTTCA
28132 GTCCCTTGAT
Statistics
Matches: 330, Mismatches: 33, Indels: 55
0.79 0.08 0.13
Matches are distributed among these distances:
129 2 0.01
130 1 0.00
131 33 0.10
132 4 0.01
133 68 0.21
134 3 0.01
136 1 0.00
137 1 0.00
140 1 0.00
142 2 0.01
143 17 0.05
144 19 0.06
145 49 0.15
146 1 0.00
149 16 0.05
150 23 0.07
151 87 0.26
152 2 0.01
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.45
Consensus pattern (148 bp):
AGCTTGAATGGATTGTAATTTGGTGAAGAATTCTGTGATCTTTGAGTTTATTGCTAATTCTGGTC
TTTGAGCTTGTCTTTAATGAAGTTCAATTTGTAGCTGCAAATTTCAATTTCTTTTCATGTTTATG
GATTTGGTGGTTGACTTG
Found at i:28025 original size:133 final size:131
Alignment explanation
Indices: 27779--28046 Score: 383
Period size: 133 Copynumber: 2.0 Consensus size: 131
27769 GAAGAATTCT
* * * * *
27779 GTGACCTTTGAGTTTATTGCTAATTCTGGTCTTTGAATTTCTTTAATGAATTTCAATTTTGTAGC
1 GTGACCTTTGAGCTGATTGCTAATTCTGGTCTTTGAATTTCTTCAACGAAGTTCAATTTTGTAGC
* * * * *
27844 TGCAAATTTCATTTTCTTTTTCATGTTTATGGATTTGGTGGTTCAGCTTGAATGGATTGCAATTT
66 TGCAAATTTCAATTTCCTTTTCATGTTTATGCATTTGATGATTCAGCTTGAATGGATTGCAATTT
27909 G
131 G
* *
27910 GTGATCTTTGAGCTGATTGCTAATTCTGGTCTTTGAGTTTGTCTTCAACGAAGTTCAATTTTGTA
1 GTGACCTTTGAGCTGATTGCTAATTCTGGTCTTTGA-ATT-TCTTCAACGAAGTTCAATTTTGTA
* * *
27975 GCTGCAAATTTCAATTTCCTTTTCATGTTTATGCATTTGATGATTGAGCTTGAGTGGATTGTAAT
64 GCTGCAAATTTCAATTTCCTTTTCATGTTTATGCATTTGATGATTCAGCTTGAATGGATTGCAAT
28040 TTG
129 TTG
28043 GTGA
1 GTGA
28047 ACAATTCGGT
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
131 33 0.28
132 2 0.02
133 85 0.71
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (131 bp):
GTGACCTTTGAGCTGATTGCTAATTCTGGTCTTTGAATTTCTTCAACGAAGTTCAATTTTGTAGC
TGCAAATTTCAATTTCCTTTTCATGTTTATGCATTTGATGATTCAGCTTGAATGGATTGCAATTT
G
Found at i:28383 original size:96 final size:96
Alignment explanation
Indices: 28219--28477 Score: 382
Period size: 96 Copynumber: 2.7 Consensus size: 96
28209 ACCTCGATGC
* * *
28219 TGATTATCGTTATCATGCTTAATTATGAAGTTGCAAAGTGTG-CATATGAAGAACTTATCAGTTT
1 TGATTATCGTTATCATGTTTAATTATGAACTTGCAAAGTGTGTC-TATGAAGAATTTATCAGTTT
28283 GACGGCATGTATCGAACTC-GATGAGTTCT-AGT
65 GACGGCATGTATCGAACTCTG-TGAGTTCTGA-T
* *
28315 TGATTATCGTTATCATGTTTAATTATGAACTTGCAAAGTGAGTCTATGAAGAATTTATCAATTTG
1 TGATTATCGTTATCATGTTTAATTATGAACTTGCAAAGTGTGTCTATGAAGAATTTATCAGTTTG
*
28380 ACGGCATGTATCGAACTCTGTGATTTCTGAT
66 ACGGCATGTATCGAACTCTGTGAGTTCTGAT
* *
28411 TGATTATTGTTATCATGTTTAATTATGAAGC-TGCAAAGTGTGTGTATGAAGAATTTATCAGTTT
1 TGATTATCGTTATCATGTTTAATTATGAA-CTTGCAAAGTGTGTCTATGAAGAATTTATCAGTTT
28475 GAC
65 GAC
28478 TTTGTGTTTT
Statistics
Matches: 149, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
96 145 0.97
97 4 0.03
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (96 bp):
TGATTATCGTTATCATGTTTAATTATGAACTTGCAAAGTGTGTCTATGAAGAATTTATCAGTTTG
ACGGCATGTATCGAACTCTGTGAGTTCTGAT
Found at i:29524 original size:42 final size:44
Alignment explanation
Indices: 29447--29552 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 44
29437 GATTATATTG
**
29447 CTCTGCATAAGGTTTTTATGATCTTTATGATACCCG-T-TTT-T
1 CTCTGCATAAGGTTTTTATGATCGCTATGATACCCGATGTTTGT
*
29488 ACTCTGCGTAAGGTTTTTATGATCGCTATG-TCACCCGATGTTTGT
1 -CTCTGCATAAGGTTTTTATGATCGCTATGAT-ACCCGATGTTTGT
29533 C-CTGCATAAGGTTTTTATGA
1 CTCTGCATAAGGTTTTTATGA
29553 CCGGCTTCTC
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
41 1 0.02
42 31 0.55
43 19 0.34
44 4 0.07
45 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (44 bp):
CTCTGCATAAGGTTTTTATGATCGCTATGATACCCGATGTTTGT
Found at i:31031 original size:15 final size:15
Alignment explanation
Indices: 30990--31033 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
30980 ATGCTATTAG
*
30990 TTTTGTTTAATTCCC
1 TTTTGTTTAAGTCCC
*
31005 TTTTATTTTAAGTCCC
1 TTTT-GTTTAAGTCCC
31021 TTTTGTTTAAGTC
1 TTTTGTTTAAGTC
31034 ACTAATATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.59
Consensus pattern (15 bp):
TTTTGTTTAAGTCCC
Found at i:31104 original size:31 final size:31
Alignment explanation
Indices: 31050--31133 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
31040 ATAGCTAAGG
* * **
31050 GACTAAAATCGAACGGATTGATAACATTAAA
1 GACTGAAATCGGACGGACCGATAACATTAAA
*
31081 GACTGAAATCGGATGGACCGATAACATTAAA
1 GACTGAAATCGGACGGACCGATAACATTAAA
*
31112 GACTTAAATCGGACGGACCGAT
1 GACTGAAATCGGACGGACCGAT
31134 GGCGTTAGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (31 bp):
GACTGAAATCGGACGGACCGATAACATTAAA
Found at i:31740 original size:9 final size:9
Alignment explanation
Indices: 31726--31752 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
31716 ATACATATTT
31726 AAAAATATA
1 AAAAATATA
31735 AAAAATATA
1 AAAAATATA
31744 AAAAATATA
1 AAAAATATA
31753 TTTTAACCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAATATA
Found at i:33345 original size:2 final size:2
Alignment explanation
Indices: 33340--33390 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
33330 TTCACAAACA
33340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33382 AT AT AT AT A
1 AT AT AT AT A
33391 ATGAGTTGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42806 original size:21 final size:20
Alignment explanation
Indices: 42720--42877 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
42710 AAATGACCAA
**
42720 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
42739 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
42759 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
42779 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
42800 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
42821 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
42841 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
42862 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
42878 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:42906 original size:20 final size:20
Alignment explanation
Indices: 42844--43037 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
42834 CGATTTTCCA
* ** *
42844 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
42864 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
42884 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
42904 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
42924 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
42944 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
42964 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
42984 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
43004 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
43025 AAATCGCAACGCG
1 AAATCGCAACGCG
43038 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:42928 original size:60 final size:60
Alignment explanation
Indices: 42844--43037 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
42834 CGATTTTCCA
* ** * *
42844 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
42904 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
42964 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
43025 AAATCGCAACGCG
1 AAATCGCAACGCG
43038 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:43457 original size:33 final size:33
Alignment explanation
Indices: 43418--43488 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
43408 TTCACTTAGA
43418 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
43451 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
43484 TTTCA
1 TTTCA
43489 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:43612 original size:20 final size:20
Alignment explanation
Indices: 43568--43642 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
43558 TGCAGAAGAG
*
43568 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
43589 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
*
43609 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
43628 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
43643 CGCAACGCGA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.34
20 18 0.41
21 11 0.25
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:43631 original size:19 final size:19
Alignment explanation
Indices: 43568--43638 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
43558 TGCAGAAGAG
43568 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAG--AAATGAAAA
***
43589 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGA-AATGAAAA
*
43609 TCGCAACGCGAAATGAAAA
1 TCGCAACGAGAAATGAAAA
43628 TCGCAACGAGA
1 TCGCAACGAGA
43639 GAATCGCAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 16 0.39
20 15 0.37
21 10 0.24
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
TCGCAACGAGAAATGAAAA
Found at i:43651 original size:33 final size:36
Alignment explanation
Indices: 43561--43665 Score: 108
Period size: 39 Copynumber: 2.9 Consensus size: 36
43551 TTCAATTTGC
* *
43561 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAAGACTCGCAACGCG--AAATGAAAATCGCAACGAG
43599 AGAATGACTGTCGCAACGCGAAATGAAAATCGCAACGAG
1 AGAA-GAC--TCGCAACGCGAAATGAAAATCGCAACGAG
**
43638 AG-A-A-TCGCAACGCGAAACCAAAATCGCA
1 AGAAGACTCGCAACGCGAAATGAAAATCGCA
43666 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
33 22 0.37
36 1 0.02
38 5 0.08
39 23 0.38
41 9 0.15
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (36 bp):
AGAAGACTCGCAACGCGAAATGAAAATCGCAACGAG
Found at i:43702 original size:14 final size:14
Alignment explanation
Indices: 43683--43771 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
43673 TTTTATTTCG
43683 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
43697 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
43715 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
43729 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
43746 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
*
43762 TGTTGCGATT
1 CGTTGCGATT
43772 TTCATTTCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
14 27 0.43
15 4 0.06
16 5 0.08
17 8 0.13
18 11 0.17
19 8 0.13
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:43751 original size:19 final size:18
Alignment explanation
Indices: 43661--43757 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
43651 GAAACCAAAA
* * *
43661 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGA-TTTCATC
43680 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
*
43696 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATC
43712 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
43728 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
43745 TCGCGTTGCGATT
1 TCGCGTTGCGATT
43758 CTCTTGTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
14 16 0.25
15 4 0.06
16 8 0.12
17 8 0.12
18 8 0.12
19 20 0.31
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:43754 original size:33 final size:33
Alignment explanation
Indices: 43666--43779 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
43656 CAAAATCGCA
*
43666 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
43699 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* * *
43731 TTGCGATTGTCATCTCGCGTTGCGATTCTCTTG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
43764 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
43780 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
32 31 0.42
33 43 0.58
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:45635 original size:93 final size:93
Alignment explanation
Indices: 45476--45672 Score: 376
Period size: 93 Copynumber: 2.1 Consensus size: 93
45466 TAGATTGCTT
45476 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
45541 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
45569 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
45634 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45662 AGTAAATTTAT
1 AGTAAATTTAT
45673 CCATTCAAGT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 101 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:45753 original size:19 final size:19
Alignment explanation
Indices: 45713--45841 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
45703 TAGTTTACTT
* *
45713 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
*
45733 TCGCAACGTGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
45752 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
45771 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
*
45785 TCGCAACGCGAAACCATAA
1 TCGCAACGCGAAACCAAAA
*
45804 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
45818 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
45837 TCGCA
1 TCGCA
45842 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
14 18 0.21
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.52
20 12 0.14
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:45792 original size:33 final size:32
Alignment explanation
Indices: 45749--45841 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
45739 CGTGAAACCA
**
45749 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
45781 AGAATCGCAACGCGAAACCATAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
45814 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
45842 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.45, C:0.28, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:45839 original size:52 final size:52
Alignment explanation
Indices: 45713--45841 Score: 122
Period size: 52 Copynumber: 2.5 Consensus size: 52
45703 TAGTTTACTT
** *
45713 TCGCAACACGAAACTTAAAATCGCAACGTGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * * *
45765 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCATAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
45818 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
45842 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 40 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.10
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:45864 original size:19 final size:19
Alignment explanation
Indices: 45837--45971 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
45827 GAAACCAAAA
*
45837 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
45856 TCGTGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
45872 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
45889 TCGCATTGCGA--TT-ATG
1 TCGCGTTGCGATTTTCATT
45905 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
45922 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
45941 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
45961 TCGTGTTGCGA
1 TCGCGTTGCGA
45972 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 14 0.15
16 11 0.12
17 11 0.12
19 45 0.48
20 12 0.13
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45884 original size:33 final size:33
Alignment explanation
Indices: 45842--45934 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
45832 CAAAATCGCA
* *
45842 TTGCGATTTTCATTTCGTGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATTTCG
* *
45875 TTGCGATTTTCATTTCGCATTGCGATTATGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATTTCG
45908 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
45935 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTATTTCG
Found at i:47915 original size:14 final size:14
Alignment explanation
Indices: 47896--47931 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
47886 ATTGTTTAAT
47896 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
47910 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
47924 TGATTTGT
1 TGATTTGT
47932 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:48062 original size:19 final size:19
Alignment explanation
Indices: 48038--48135 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
48028 AAAATTGACT
48038 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48057 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
48076 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
48090 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48109 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
48129 ATCGCAA
1 ATCGCAA
48136 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:48167 original size:53 final size:53
Alignment explanation
Indices: 48038--48154 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
48028 AAAATTGACT
48038 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
48090 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
48143 ATCGCAATGCGA
1 ATCGCAATGCGA
48155 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:50489 original size:12 final size:12
Alignment explanation
Indices: 50472--50496 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50462 TCTTCGGGGA
50472 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50484 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50496 C
1 C
50497 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:50705 original size:24 final size:24
Alignment explanation
Indices: 50671--50717 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
50661 CTGAAACATC
50671 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
50695 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
50718 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:51426 original size:20 final size:20
Alignment explanation
Indices: 51398--51647 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
51388 AAATTTCAGT
* * *
51398 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
51418 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
51438 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
51458 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
51478 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
51498 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
51518 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
51538 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
51558 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
51578 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
51598 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
51618 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
51638 GTTGCGATTT
1 GTTGCGATTT
51648 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:51664 original size:19 final size:20
Alignment explanation
Indices: 51640--51735 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 20
51630 ATATTCGCGT
51640 TGCGATTTTGGAAAATCGC-
1 TGCGATTTTGGAAAATCGCA
51659 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
51680 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
51700 TTGCGATTTT-CAAGAATCGCGT
1 -TGCGATTTTGGAA-AATCGC-A
51722 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
51736 CTGATTTGCG
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
19 19 0.31
20 2 0.03
21 38 0.62
22 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:51878 original size:2 final size:2
Alignment explanation
Indices: 51871--51908 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
51861 CGATTTTCTC
51871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51909 TCAGAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55483 original size:8 final size:8
Alignment explanation
Indices: 55470--55567 Score: 51
Period size: 8 Copynumber: 11.6 Consensus size: 8
55460 CATAAAGTCA
55470 ATTAATAT
1 ATTAATAT
55478 ATTAATATAT
1 ATT-A-ATAT
55488 ATACTAATAT
1 AT--TAATAT
*
55498 ATTAAT-G
1 ATTAATAT
*
55505 A-T-ATGT
1 ATTAATAT
55511 ATTAATAT
1 ATTAATAT
55519 ATTAATGAT
1 ATTAAT-AT
*
55528 A-TACTAAT
1 ATTAAT-AT
55536 ATTAATAAT
1 ATTAAT-AT
*
55545 ACTAATATAT
1 A-TTA-ATAT
55555 ATTAATAT
1 ATTAATAT
55563 ATTAA
1 ATTAA
55568 CTACTTTGTT
Statistics
Matches: 71, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 2 0.03
8 31 0.44
9 13 0.18
10 17 0.24
11 3 0.04
12 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (8 bp):
ATTAATAT
Found at i:55516 original size:21 final size:21
Alignment explanation
Indices: 55470--55567 Score: 108
Period size: 21 Copynumber: 4.6 Consensus size: 21
55460 CATAAAGTCA
55470 ATTAATATATTAAT-ATATAT
1 ATTAATATATTAATGATATAT
* *
55490 ACTAATATATTAATGATATGT
1 ATTAATATATTAATGATATAT
55511 ATTAATATATTAATGATATACT
1 ATTAATATATTAATGATATA-T
* * * * *
55533 AATATTAATAATACTAATATAT
1 ATTAAT-ATATTAATGATATAT
55555 ATTAATATATTAA
1 ATTAATATATTAA
55568 CTACTTTGTT
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
20 13 0.21
21 28 0.45
22 10 0.16
23 11 0.18
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTAATATATTAATGATATAT
Found at i:55538 original size:25 final size:25
Alignment explanation
Indices: 55510--55562 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
55500 TAATGATATG
*
55510 TATTAAT-ATATTAATGATATACTAA
1 TATTAATAATACTAAT-ATATACTAA
*
55535 TATTAATAATACTAATATATATTAA
1 TATTAATAATACTAATATATACTAA
55560 TAT
1 TAT
55563 ATTAACTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (25 bp):
TATTAATAATACTAATATATACTAA
Found at i:55560 original size:44 final size:41
Alignment explanation
Indices: 55470--55567 Score: 117
Period size: 44 Copynumber: 2.3 Consensus size: 41
55460 CATAAAGTCA
* * *
55470 ATTAATATATTAATATATATACTAATATATTAATGATATGT
1 ATTAATATATTAATAGATATACTAATATATTAATAATATAT
*
55511 ATTAATATATTAAT-GATATACTAATATTAATAATACTAATATAT
1 ATTAATATATTAATAGATATACTAATA-T-AT--TAATAATATAT
55555 ATTAATATATTAA
1 ATTAATATATTAA
55568 CTACTTTGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 11 0.22
41 15 0.31
42 2 0.04
44 21 0.43
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (41 bp):
ATTAATATATTAATAGATATACTAATATATTAATAATATAT
Found at i:63078 original size:382 final size:381
Alignment explanation
Indices: 62217--65265 Score: 5173
Period size: 382 Copynumber: 8.0 Consensus size: 381
62207 GTACCTAAAT
62217 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTATTTTTTTTCAAAAAGTTACCTAAGATTTT
1 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTA-TTTTTTTCAAAAAGTTACCTAAGATTTT
* *
62282 ATTTTTATTTCATTTTAGTACCATTCGTTAAAAACTTAACGCGTTTAATATTTAAACTATCAGTT
65 ATTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTT
* *
62347 TGTGCACGTTCTAGTACTTAAGCTTTCAAAAACAAATTCCAAACATAACATTAAATTTTGAACGA
130 TGTGCACGTTCTAGTACTTAAGCTTTCAAAAA-AAATTCAAAACATAACATTAAATTTTGAACAA
*
62412 TATACTAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATAC
194 TGTACTAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATAC
*
62477 TAAAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTCTGTACTAAA
259 TAAAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAA
*
62542 CCTAAAATTAAATAAAGAAAAATATCACAATTCACATACCAAAAAAGGGCGAAATTCC
324 CCTAAAATTAAATAAAGAAAAATATCACAATTCACATACCAAAAAAGGGGGAAATTCC
* *
62600 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTATTTATTTTTAAAAAGTTACTTAAGATTTT
1 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTATTT-TTTTCAAAAAGTTACCTAAGATTTT
** * * *
62665 ATTTTTATTTCATTTTAGTATATTTCGTTAAAAACTTAACACATTTAGTATTTAGACTATCAGTT
65 ATTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTT
*
62730 TGTGCACGTTCTAGTACTTAAGCTTTCAAAAACAAATTCCAAACATAACATTAAATTTTGAACAA
130 TGTGCACGTTCTAGTACTTAAGCTTTCAAAAA-AAATTCAAAACATAACATTAAATTTTGAACAA
62795 TGTACTAAAATGAAACAAAAACTAAACTTTAGACATGA-TTTGAAAAAATTAAAAGTTTAAATAC
194 TGTACTAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATAC
62859 TAAAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAA
259 TAAAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAA
62924 CCTAAAATTAAATAAAGAAAAATATCACAATTCACATACCAAAAAAAGGGGGAAATTCC
324 CCTAAAATTAAATAAAGAAAAATATCACAATTCACATACC-AAAAAAGGGGGAAATTCC
62983 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTATTTTTTTCAAAAAGTTACCTAAGATTTTA
1 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTATTTTTTTCAAAAAGTTACCTAAGATTTTA
63048 TTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTTT
66 TTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTTT
* *
63113 TTGCACGTTATAGTACTTAAGCTTTCAAAAAAAA-TCAAAACATAACATTAAATTTTGAACAATG
131 GTGCACGTTCTAGTACTTAAGCTTTCAAAAAAAATTCAAAACATAACATTAAATTTTGAACAATG
* *
63177 ATACTAAAATGAAACAAAACCTAAACTTTAGATATGATTTTGAAAAAATTAAAAGTTTAAATACT
196 -TACTAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATACT
* * *
63242 AAAATATATAAAAGCTTATATTTTAAGTATTAAACACGTAATTTACCCAAGTTTTTGAACTAAAC
260 AAAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAAC
* *
63307 CTAAAATTAAATAAAGAAAAATATCACAATTCACATACCCAGAAAAGGGGGAAATTCA
325 CTAAAATTAAATAAAGAAAAATATCACAATTCACATA-CCAAAAAAGGGGGAAATTCC
*
63365 TATAAGTTTCGATCTGTTTTAGTACCTTAACTTTTATTTTTTTCAAAAAGTTACCTAAGATTTTA
1 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTATTTTTTTCAAAAAGTTACCTAAGATTTTA
* *
63430 TTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACATGTTTAGTATTTAAACTATCAGTTT
66 TTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTTT
* *
63495 GTGCACGTTCTAGTACTTAAGCTTTCAAAAACAAATTCCAAACATAGCATTAAATTTTGAACAAT
131 GTGCACGTTCTAGTACTTAAGCTTTCAAAAA-AAATTCAAAACATAACATTAAATTTTGAACAAT
*
63560 GTAATAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATACT
195 GTACTAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATACT
63625 AAAATAGATAAAAGCTTAT-TTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAAC
260 AAAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAAC
63689 CTAAAATTAAATAAAGAAAAATATCACAATTCACATACCCAAAAAAGGGGGAAATTCC
325 CTAAAATTAAATAAAGAAAAATATCACAATTCACATA-CCAAAAAAGGGGGAAATTCC
* *
63747 TATAAATTTTGATCTGTTTTAGTACCTTAACTTTTATTTATTTTCAAAAAGTTACTTAAGATTTT
1 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTATTT-TTTTCAAAAAGTTACCTAAGATTTT
* * *
63812 A-TTTTATTTCATTTTAGTACATTTCGTTAAAAACTTAACATGTTTAGTATTTAAACTATCAGTT
65 ATTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTT
* *
63876 TGTGCACGTTCTAGTACTTAAGCTTTCAAAAACAAATTCCAAACATAGCATTAAATTTTGAACAA
130 TGTGCACGTTCTAGTACTTAAGCTTTCAAAAA-AAATTCAAAACATAACATTAAATTTTGAACAA
*
63941 TGTAATAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATAC
194 TGTACTAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATAC
64006 TAAAATAGATAAAAGCTTAT-TTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAA
259 TAAAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAA
*
64070 CCTAAAATTAAATAAAGAAAAATATCACAATTCACATACCCAAAAA-GGGGAAATTCC
324 CCTAAAATTAAATAAAGAAAAATATCACAATTCACATACCAAAAAAGGGGGAAATTCC
* *
64127 TATAAATTTTGATCTGTTTTAGTACCTTAACTTTTATTTATTTTCAAAAAGTTACTTAAGATTTT
1 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTATTT-TTTTCAAAAAGTTACCTAAGATTTT
* *
64192 ATTTTTATTTCATTTTAGTACATTTCGTTAAAAACTTAACACGTTTAATATTTAAGCTATCAGTT
65 ATTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTT
* *
64257 TTTGCACGTTCTAATACTTAAGCTTTCAAAAAAAATTCAAAACATAACATTAAATTTTGAACAAT
130 TGTGCACGTTCTAGTACTTAAGCTTTCAAAAAAAATTCAAAACATAACATTAAATTTTGAACAAT
* *
64322 GATACTAAAATGAAACAAAACCTAAACTTTAGATATGATTTTGAAAAAATTAAAAGTTTAAATAC
195 G-TACTAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATAC
* * *
64387 TAAAATATATAAAAGCTTATATTTTAAGTATTAAACACGTAATTTACCCAAGTTTTTGAACTAAA
259 TAAAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAA
*
64452 CCTAAAATTAAATAAAGAAAAATATCACAATTCACATACCCAAAAAAGGGGGAAATTCA
324 CCTAAAATTAAATAAAGAAAAATATCACAATTCACATA-CCAAAAAAGGGGGAAATTCC
*
64511 TATAAGTTTCGATCTGTTTTAGTACCTTAACTTTTATTTTTTTCAAAAAGTTACCTAAGATTTTA
1 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTATTTTTTTCAAAAAGTTACCTAAGATTTTA
64576 TTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTTT
66 TTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTTT
* *
64641 TTGCACGTTCTAGTACTTAAGCTTTCAAAAAAAAATCAAAACATAACATTAAATTTTGAACAATA
131 GTGCACGTTCTAGTACTTAAGCTTTCAAAAAAAATTCAAAACATAACATTAAATTTTGAACAAT-
* * *
64706 ATACTAAAATGAAACAAAAACTAAACTTTAGATATGACTTTGAAAAAATTAAAAGTTTAAATACT
195 GTACTAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATACT
*
64771 AAAATAGATAAAAGCTTATATTTTAAGTATTAAACACGTAATTTACCCAAGTTTTTGTACTAAAC
260 AAAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAAC
*
64836 C-AAAATTAAATAAA-AAAAATATCACAATTCACATACTCAAAAAAGGGGAAAATTCC
325 CTAAAATTAAATAAAGAAAAATATCACAATTCACATAC-CAAAAAAGGGGGAAATTCC
* *
64892 TATAAGTTTTGATATGTTTTAGTACCTTAACTTTTATTTTTTTTCAAAAAGTTACTTAAGATTTT
1 TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTA-TTTTTTTCAAAAAGTTACCTAAGATTTT
*
64957 ATTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAGCTATCAGTT
65 ATTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTT
* * * *
65022 TTTGCACATTCTAATACTTAAGCTTTC-AAAAAAATTCAAAACATAACATTAAATTTTGAACAAA
130 TGTGCACGTTCTAGTACTTAAGCTTTCAAAAAAAATTCAAAACATAACATTAAATTTTGAACAAT
* **
65086 GATACTAAAATGAAACAAAAACTAAACTTTAGATATGATTTAAAAAAAATTAAAAGTTTAAATAC
195 G-TACTAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATAC
* * * ** * *
65151 TAAAATAGATAAAAGCTTATAGTTTAAGTATTAAATACGTAATTTACTTAAATTGTTGTACTAAA
259 TAAAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAA
*
65216 CCTAAAATTAAATAAAGAAAAATATCACAATTCACATA-AAAAAAAGGGGG
324 CCTAAAATTAAATAAAGAAAAATATCACAATTCACATACCAAAAAAGGGGG
65266 GGTTTTCCTA
Statistics
Matches: 2548, Mismatches: 99, Indels: 40
0.95 0.04 0.01
Matches are distributed among these distances:
380 139 0.05
381 451 0.18
382 1196 0.47
383 687 0.27
384 75 0.03
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (381 bp):
TATAAGTTTTGATCTGTTTTAGTACCTTAACTTTTATTTTTTTCAAAAAGTTACCTAAGATTTTA
TTTTTATTTCATTTTAGTACCTTTCGTTAAAAACTTAACACGTTTAATATTTAAACTATCAGTTT
GTGCACGTTCTAGTACTTAAGCTTTCAAAAAAAATTCAAAACATAACATTAAATTTTGAACAATG
TACTAAAATGAAACAAAAACTAAACTTTAGACATGATTTTGAAAAAATTAAAAGTTTAAATACTA
AAATAGATAAAAGCTTATATTTTAAGTATTAAACACATAATTTACCCAAGTTTTTGTACTAAACC
TAAAATTAAATAAAGAAAAATATCACAATTCACATACCAAAAAAGGGGGAAATTCC
Found at i:66535 original size:2 final size:2
Alignment explanation
Indices: 66528--66554 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
66518 TTCTTCATGA
66528 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
66555 TTCTGTGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:74783 original size:29 final size:29
Alignment explanation
Indices: 74750--74813 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
74740 TCAGACCATC
74750 ATAAAATTTTGAGGGACTAATTTAAATTT
1 ATAAAATTTTGAGGGACTAATTTAAATTT
74779 ATAAAATTTTGAGGGACTAATTTAAATTT
1 ATAAAATTTTGAGGGACTAATTTAAATTT
74808 ATAAAA
1 ATAAAA
74814 AAATTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.39
Consensus pattern (29 bp):
ATAAAATTTTGAGGGACTAATTTAAATTT
Found at i:77123 original size:19 final size:19
Alignment explanation
Indices: 77095--77204 Score: 94
Period size: 19 Copynumber: 5.4 Consensus size: 19
77085 GCTTGAGAAT
*
77095 CTTTTACACTATCGCAACA
1 CTTTTTCACTATCGCAACA
77114 CTTTTTCACTATCGCAACAACA
1 CTTTTTCACTATCG---CAACA
*
77136 CGTTTTTCAAACTCTCGCAACA
1 C-TTTTTC--ACTATCGCAACA
* *
77158 CATTTTAACTATCGCAACA
1 CTTTTTCACTATCGCAACA
* * *
77177 CATTTTAACTATCGCAACG
1 CTTTTTCACTATCGCAACA
77196 CATTTTTCA
1 C-TTTTTCA
77205 AAATCACGTT
Statistics
Matches: 76, Mismatches: 8, Indels: 13
0.78 0.08 0.13
Matches are distributed among these distances:
19 43 0.57
20 5 0.07
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (19 bp):
CTTTTTCACTATCGCAACA
Found at i:78042 original size:123 final size:124
Alignment explanation
Indices: 77838--78119 Score: 367
Period size: 123 Copynumber: 2.3 Consensus size: 124
77828 AACCTATTAG
* *
77838 TTTTGGTCCGTTTTAGTACCTAAACTTTC-ATTTTTTCCAAAATCATACCTAACGTTTAGTTTTT
1 TTTTGGTCCGTTTTAGTACCTAAACTTTCAATTTTTTCCAAAACCACACCTAACGTTTAGTTTTT
* **
77902 GTTTCATTTTAGTTACCCGCCGTTAAAAACTTAATCGCAATTAGTACGTAAACTAT-AAA
66 GTTTCATTTTAGTTACCCACCGTTAAAAACTTAA-CGCAATTAGTACCCAAACTATCAAA
77961 TTTTGGTCCGTTTTAGTACCTAAACTTTCAATTTTTT-CAAAACCACACCTAACGTTTAGTTTTT
1 TTTTGGTCCGTTTTAGTACCTAAACTTTCAATTTTTTCCAAAACCACACCTAACGTTTAGTTTTT
* * ***
78025 GTTTCATTTTTAG-TACCCACTGTTAAAACCTTAACGTGTTTAGTACCCAAACTATCAAA
66 GTTTCA-TTTTAGTTACCCACCGTTAAAAACTTAACGCAATTAGTACCCAAACTATCAAA
* * ** * *
78084 -TTCGATCCACTTTAGTACCTAAACTTTTATTTTTTT
1 TTTTGGTCCGTTTTAGTACCTAAACTTTCAATTTTTT
78120 TTCAAAACTT
Statistics
Matches: 140, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
122 46 0.33
123 81 0.58
124 13 0.09
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.43
Consensus pattern (124 bp):
TTTTGGTCCGTTTTAGTACCTAAACTTTCAATTTTTTCCAAAACCACACCTAACGTTTAGTTTTT
GTTTCATTTTAGTTACCCACCGTTAAAAACTTAACGCAATTAGTACCCAAACTATCAAA
Found at i:78942 original size:2 final size:2
Alignment explanation
Indices: 78937--78990 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
78927 AACAAAAAAC
78937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78979 AT AT AT AT AT AT
1 AT AT AT AT AT AT
78991 TTCAATACAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79697 original size:21 final size:21
Alignment explanation
Indices: 79673--79730 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
79663 TCCGAGTTAC
* *
79673 CCGCGATGGCCGCAATAGCGT
1 CCGCGACGACCGCAATAGCGT
* *
79694 CCGCGACGACCGTAATAGCGC
1 CCGCGACGACCGCAATAGCGT
*
79715 CCACGACGGA-CGCAAT
1 CCGCGAC-GACCGCAAT
79731 TACGGTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.24, C:0.36, G:0.29, T:0.10
Consensus pattern (21 bp):
CCGCGACGACCGCAATAGCGT
Done.