Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 29
Found at i:3527802 original size:21 final size:20
Alignment explanation
Indices: 3527766--3527807 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3527756 AGTGTTGTCC
* *
3527766 TATTAAAAAGCGTAAAGTAG
1 TATTAAAAAGCATAAAATAG
3527786 TATTAAAAAGCAATAAAATAG
1 TATTAAAAAGC-ATAAAATAG
3527807 T
1 T
3527808 TACCCGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.26
Consensus pattern (20 bp):
TATTAAAAAGCATAAAATAG
Found at i:3537862 original size:2 final size:2
Alignment explanation
Indices: 3537855--3537940 Score: 149
Period size: 2 Copynumber: 44.0 Consensus size: 2
3537845 CATATTAGTC
3537855 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
*
3537897 AT AT A- AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3537937 AT AT
1 AT AT
3537941 GAGTGTGTCG
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 2 0.03
2 78 0.98
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3540321 original size:3 final size:3
Alignment explanation
Indices: 3540308--3540360 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
3540298 TTTTTTATCG
3540308 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
3540352 TTA ATA TTA
1 TTA TTA TTA
3540361 CATTTTACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3540899 original size:12 final size:12
Alignment explanation
Indices: 3540882--3540923 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
3540872 AAAAAAACAG
3540882 AGGAAATCAGAA
1 AGGAAATCAGAA
3540894 AGGAAATCAGAA
1 AGGAAATCAGAA
3540906 AGGAAATCAGAA
1 AGGAAATCAGAA
3540918 AGGAAA
1 AGGAAA
3540924 AAAGGAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.60, C:0.07, G:0.26, T:0.07
Consensus pattern (12 bp):
AGGAAATCAGAA
Found at i:3542484 original size:22 final size:22
Alignment explanation
Indices: 3542459--3542502 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3542449 TCAAACGATG
*
3542459 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
3542481 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
3542503 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:3544041 original size:32 final size:32
Alignment explanation
Indices: 3544005--3544098 Score: 172
Period size: 31 Copynumber: 3.0 Consensus size: 32
3543995 ATTTTACATG
3544005 TACTAACTTATTTTTTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTTTTCTCTTTTGTTTGTGTA
3544037 TACTAACTTA-TTTTTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTTTTCTCTTTTGTTTGTGTA
*
3544068 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTTTTCTCTTTTGTTTGTGT
3544099 CATTCTGTCA
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 31 0.52
32 29 0.48
ACGTcount: A:0.15, C:0.14, G:0.10, T:0.62
Consensus pattern (32 bp):
TACTAACTTATTTTTTCTCTTTTGTTTGTGTA
Found at i:3546545 original size:26 final size:25
Alignment explanation
Indices: 3546516--3546593 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
3546506 CAATTTTGAC
3546516 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
3546542 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
* *
3546562 ATTCCCTCTCTTTGTGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
3546588 ATTCTT
1 ATTCTT
3546594 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:3546554 original size:20 final size:20
Alignment explanation
Indices: 3546531--3546605 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
3546521 ATCTCTTTGA
3546531 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
3546551 GACCTTGAAACATTCCCTCTCTTTGT
1 GACCTTGAAATA-T---TCT-TTT-C
3546577 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
3546596 CACCTTGAAA
1 GACCTTGAAA
3546606 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:3547206 original size:30 final size:31
Alignment explanation
Indices: 3547170--3547230 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
3547160 GACGCAGAGT
**
3547170 GCAAAGATCAAACCAAAG-AAAAAACAAAGA
1 GCAAAGAGAAAACCAAAGCAAAAAACAAAGA
* *
3547200 GCAAAGAGAAAATCAAAGCAAAAATCAAAGA
1 GCAAAGAGAAAACCAAAGCAAAAAACAAAGA
3547231 AAAAGCAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.66, C:0.15, G:0.15, T:0.05
Consensus pattern (31 bp):
GCAAAGAGAAAACCAAAGCAAAAAACAAAGA
Found at i:3547223 original size:12 final size:11
Alignment explanation
Indices: 3547201--3547242 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
3547191 AAACAAAGAG
3547201 CAAAGAGAAAAT
1 CAAAGA-AAAAT
3547213 CAAAGCAAAAAT
1 CAAAG-AAAAAT
*
3547225 CAAAGAAAAAG
1 CAAAGAAAAAT
3547236 CAAAGAA
1 CAAAGAA
3547243 CAAAAAGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 12 0.43
12 15 0.54
13 1 0.04
ACGTcount: A:0.69, C:0.12, G:0.14, T:0.05
Consensus pattern (11 bp):
CAAAGAAAAAT
Found at i:3548426 original size:4 final size:4
Alignment explanation
Indices: 3548417--3548475 Score: 104
Period size: 4 Copynumber: 15.2 Consensus size: 4
3548407 TCGAGAAAAG
3548417 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
3548464 -ACA TACA TACA T
1 TACA TACA TACA T
3548476 GATACATAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
4 51 0.96
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:3549068 original size:102 final size:104
Alignment explanation
Indices: 3548930--3549116 Score: 272
Period size: 102 Copynumber: 1.8 Consensus size: 104
3548920 TGAGAATTTT
* * *
3548930 AAAACAAATTGCGTCTCGCTTGAGATATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTGCG-CTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
3548994 TTAAAACAAA-TTAATCTCACCTTAGATTGTTGTTTCTTTC
65 TT-AAACAAAGTTAATCTCACCTTAGATTGTTGTTTCTTTC
* * *
3549034 AAAACAAATTGCG-TCGTTTGAGACATTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACAT
1 AAAACAAATTGCGCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACAT
*
3549098 TAAACAAAGTTGATCTCAC
66 TAAACAAAGTTAATCTCAC
3549117 TTGAGATCGT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
102 50 0.68
103 11 0.15
104 13 0.18
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.39
Consensus pattern (104 bp):
AAAACAAATTGCGCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACAT
TAAACAAAGTTAATCTCACCTTAGATTGTTGTTTCTTTC
Found at i:3549182 original size:36 final size:35
Alignment explanation
Indices: 3549111--3549230 Score: 127
Period size: 34 Copynumber: 3.4 Consensus size: 35
3549101 ACAAAGTTGA
* * *
3549111 TCTCACTTGAGATCGTTTCTC-AAAAACAAACTTTG
1 TCTCGCTTGAGA-CATTTCTCTAAAAACAAATTTTG
3549146 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCGCTTGAGAC-ATTTCTCTAAAAACAAATTTTG
** * * * *
3549182 TCTCATTTGAGAC-TATATCTAAAAGCAAATTTCG
1 TCTCGCTTGAGACATTTCTCTAAAAACAAATTTTG
3549216 TCTCGCTTGAGACAT
1 TCTCGCTTGAGACAT
3549231 CATTTTCTCT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
34 29 0.41
35 18 0.25
36 24 0.34
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (35 bp):
TCTCGCTTGAGACATTTCTCTAAAAACAAATTTTG
Found at i:3549583 original size:40 final size:40
Alignment explanation
Indices: 3549520--3549599 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
3549510 TTGTCTCTCG
*
3549520 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTGGAGATCGTTT
* * *
3549560 AGACAATTTCTTTT-AAAACTACCCACCTTGGAGATTGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACATTGGAGATCGTTT
3549600 TTATTAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTGGAGATCGTTT
Found at i:3549734 original size:46 final size:46
Alignment explanation
Indices: 3549661--3549752 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 46
3549651 TCTTCGAGTT
* * *
3549661 TTTTCACTTAAAATAAAACCATTTTTGAGTCGTTTCACTTGAAACA
1 TTTTCACTTAAAACAAAACCATCTTTGAGTCGTTTCACTGGAAACA
* * * * *
3549707 TTTTCTCTTAAAACAAGATCATCTTTGAGTTGTTTCTCTGGAAACA
1 TTTTCACTTAAAACAAAACCATCTTTGAGTCGTTTCACTGGAAACA
3549753 ATGTTTTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (46 bp):
TTTTCACTTAAAACAAAACCATCTTTGAGTCGTTTCACTGGAAACA
Found at i:3549889 original size:1 final size:1
Alignment explanation
Indices: 3549883--3549909 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3549873 ATGTCTTTTC
3549883 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
3549910 TCATTGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3550047 original size:33 final size:34
Alignment explanation
Indices: 3550006--3550069 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
3549996 ACAAAATTAC
* *
3550006 CATCTTTGA-ATCTGTTTCCCTT-GAAACAAAAAA
1 CATCTTTGAGAAC-GTTTCCCTTAAAAACAAAAAA
3550039 CATCTTTGAGAACGTTTCCCTTAAAAACAAA
1 CATCTTTGAGAACGTTTCCCTTAAAAACAAA
3550070 TTTTGTCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (34 bp):
CATCTTTGAGAACGTTTCCCTTAAAAACAAAAAA
Found at i:3550489 original size:46 final size:45
Alignment explanation
Indices: 3550332--3550749 Score: 209
Period size: 43 Copynumber: 9.6 Consensus size: 45
3550322 ATTATTCCTA
* *
3550332 AGATGGCCAGTAGTCCTCATCACATAGGAACCGTGTCATC-CC-C
1 AGATGGCCAGTAGTCCTCATCACGTAGGAACCGTGTCATCACCTT
* ** *
3550375 AGA---CCAG-ATCTCCTCATCACGTAGGAGTCGTGTCA--ACCAT
1 AGATGGCCAGTA-GTCCTCATCACGTAGGAACCGTGTCATCACCTT
* ** ** *
3550415 GGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
1 AGATGGCCAGTAGTCCTCATCACGTAGGAACCGTGTCATCACCTT
* *
3550460 AAGATGGCCAGTAGTCCTCATCACATAGGAACCGTGTCATC-CC-C
1 -AGATGGCCAGTAGTCCTCATCACGTAGGAACCGTGTCATCACCTT
** *
3550504 AGA---CCAGATA-TCCTCATCACGTAGGAGTCGTGTCA--ACCAT
1 AGATGGCCAG-TAGTCCTCATCACGTAGGAACCGTGTCATCACCTT
* ** ** *
3550544 GGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATGGCCAGTAGTCCTCATCACGTAGGAACCGTGTCATCACC-TT
* * * * * * *
3550590 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATTC-CC-C
1 AGATGGCCAGTAGTCCTCATCACGTAGGAACCGTGTCA-TCACCTT
* * *
3550634 AGA---CCAG-ATCTCCTCATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGGCCAGTA-GTCCTCATCACGTAGGAACCGTGTCATCACCTT
*** ** * *
3550674 AGATAATCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTAA
1 AGATGGCCAGTAGTCCTCATCACGTAGGAACCGTGTCATCACCT-T
* * *
3550720 AGATGGCCAAGAACTCTTCATCACGTAGGA
1 AGATGGCC-AGTAGTCCTCATCACGTAGGA
3550750 GAAGTGTCAT
Statistics
Matches: 282, Mismatches: 61, Indels: 60
0.70 0.15 0.15
Matches are distributed among these distances:
39 7 0.02
40 60 0.21
41 29 0.10
43 84 0.30
44 3 0.01
45 12 0.04
46 68 0.24
47 19 0.07
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.22
Consensus pattern (45 bp):
AGATGGCCAGTAGTCCTCATCACGTAGGAACCGTGTCATCACCTT
Found at i:3550717 original size:130 final size:129
Alignment explanation
Indices: 3550330--3550789 Score: 672
Period size: 129 Copynumber: 3.6 Consensus size: 129
3550320 CCATTATTCC
* *
3550330 TAAGATGGCCAGTAGTCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCAC
1 TAAGATGGCCAGAACTCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCAC
3550395 GTAGGAGTCGTGTCAACCATGGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCT
66 GTAGGAGTCGTGTCAACCATGGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCT
* * *
3550459 TAAGATGGCCAGTAGTCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATATCCTCATCAC
1 TAAGATGGCCAGAACTCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCAC
3550524 GTAGGAGTCGTGTCAACCATGGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCT
66 GTAGGAGTCGTGTCAACCATGGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCT
* * * * * *
3550588 TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATTCCCCAGACCAGATCTCCTCATCA
1 TAAGATGGCCAGAACTCCTCATCACATAGGAACCGTGTCA-TCCCCAGACCAGATCTCCTCATCA
* * *
3550653 CGTAGGAGCCGTGTCAACCATAGATAATCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCT
65 CGTAGGAGTCGTGTCAACCATGGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCT
* * * * * *
3550718 AAAGATGGCCAAGAACTCTTCATCACGTAGGAGA-AGTGTCATCCCTC-GATCAGATTTCCTCAT
1 TAAGATGGCC-AGAACTCCTCATCACATAGGA-ACCGTGTCATCCC-CAGACCAGATCTCCTCAT
* *
3550781 TATGTAGGA
63 CACGTAGGA
3550790 ACCTTGTCAC
Statistics
Matches: 304, Mismatches: 23, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
129 160 0.53
130 118 0.39
131 26 0.09
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (129 bp):
TAAGATGGCCAGAACTCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCAC
GTAGGAGTCGTGTCAACCATGGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCT
Found at i:3551574 original size:12 final size:12
Alignment explanation
Indices: 3551557--3551598 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
3551547 AAAAAAACAG
3551557 AGGAAATCAGAA
1 AGGAAATCAGAA
3551569 AGGAAATCAGAA
1 AGGAAATCAGAA
3551581 AGGAAATCAGAA
1 AGGAAATCAGAA
3551593 AGGAAA
1 AGGAAA
3551599 AAAAGGAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.60, C:0.07, G:0.26, T:0.07
Consensus pattern (12 bp):
AGGAAATCAGAA
Found at i:3551608 original size:24 final size:23
Alignment explanation
Indices: 3551548--3551610 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 23
3551538 AATACCAAAA
3551548 AAAAAACAGAGGAAATCAGAAAGG
1 AAAAAA-AGAGGAAATCAGAAAGG
*
3551572 AAATCAGAA-AGGAAATCAGAAAGG
1 AAA--AAAAGAGGAAATCAGAAAGG
3551596 AAAAAAAGGAGGAAA
1 AAAAAAA-GAGGAAA
3551611 CCGAAGCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 3 0.09
24 27 0.82
25 1 0.03
26 2 0.06
ACGTcount: A:0.63, C:0.06, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAAAAGAGGAAATCAGAAAGG
Found at i:3553010 original size:22 final size:22
Alignment explanation
Indices: 3552985--3553028 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3552975 TTCAACGATG
*
3552985 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
3553007 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
3553029 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:3559778 original size:32 final size:28
Alignment explanation
Indices: 3559742--3559811 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 28
3559732 AACCATCGTT
3559742 TATATTTTTAAATTTTACAAGATTTTATAGTA
1 TATATTTTTAAATTTTA-AAGA-TTTA-A-TA
* *
3559774 TATATTTTAAAATTTTAAATATTTAATA
1 TATATTTTTAAATTTTAAAGATTTAATA
3559802 TATATTTTTA
1 TATATTTTTA
3559812 TATTCCTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.31
29 1 0.03
30 4 0.11
31 3 0.09
32 16 0.46
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (28 bp):
TATATTTTTAAATTTTAAAGATTTAATA
Found at i:3560755 original size:31 final size:31
Alignment explanation
Indices: 3560695--3560776 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
3560685 GTTTTGAAAG
* *
3560695 TTACAAAATGGTCTTTGAACTATATCAAACTA
1 TTACAAAATGGTCATT-AAATATATCAAACTA
* *
3560727 TTACAAAATGGTCATTAAATTTATCAAACTG
1 TTACAAAATGGTCATTAAATATATCAAACTA
** *
3560758 TTGTAAAATGATCATTAAA
1 TTACAAAATGGTCATTAAA
3560777 CTTGTCGAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 28 0.65
32 15 0.35
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (31 bp):
TTACAAAATGGTCATTAAATATATCAAACTA
Found at i:3561974 original size:32 final size:32
Alignment explanation
Indices: 3561943--3562002 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3561933 TTATCCTAAG
*
3561943 AGAACA-A-CTTAGGGCCGTGGGGCCTACCTA
1 AGAACATATCTTAGGGCCGTAGGGCCTACCTA
*
3561973 AGAACATATCTTAGGGTCGTAGGGCCTACC
1 AGAACATATCTTAGGGCCGTAGGGCCTACC
3562003 CGAGAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 6 0.23
31 1 0.04
32 19 0.73
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (32 bp):
AGAACATATCTTAGGGCCGTAGGGCCTACCTA
Found at i:3562967 original size:30 final size:29
Alignment explanation
Indices: 3562926--3563029 Score: 117
Period size: 29 Copynumber: 3.6 Consensus size: 29
3562916 CACATTCGAA
3562926 AATTA-CAAAAATATCACCTTTTTTAAAAT
1 AATTACCAAAAATATCA-CTTTTTTAAAAT
3562955 AATTACCAAAAATATCA-TTGTTTTAAAAAT
1 AATTACCAAAAATATCACTT-TTTT-AAAAT
* *
3562985 AATTACC-AGAATATCACTGTTTTAAAAAT
1 AATTACCAAAAATATCACT-TTTTTAAAAT
*
3563014 AATT-CCTAAAATATCA
1 AATTACCAAAAATATCA
3563030 TCGGGTCGGG
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
28 4 0.06
29 34 0.52
30 27 0.41
31 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (29 bp):
AATTACCAAAAATATCACTTTTTTAAAAT
Found at i:3570348 original size:29 final size:30
Alignment explanation
Indices: 3570282--3570348 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
3570272 CATTCGAAAC
* * *
3570282 TTACAAAAATATCACTTTTTTAAAAAAATAA
1 TTACCAAAAGATCACTGTTTT-AAAAAATAA
3570313 TTACCAAAAGATCACTGTTTT-AAAAATAA
1 TTACCAAAAGATCACTGTTTTAAAAAATAA
*
3570342 TTCCCAA
1 TTACCAA
3570349 CATAACACCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.44
31 18 0.56
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (30 bp):
TTACCAAAAGATCACTGTTTTAAAAAATAA
Found at i:3570381 original size:17 final size:17
Alignment explanation
Indices: 3570359--3570392 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3570349 CATAACACCG
3570359 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
3570376 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
3570393 CCAGTCGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:3580987 original size:29 final size:28
Alignment explanation
Indices: 3580922--3580996 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
3580912 ATCTTAAATT
* *
3580922 TTAAAATTATCTTTTATTTTTTTTTAAC
1 TTAAAAATATATTTTATTTTTTTTTAAC
*
3580950 TTATTAAATATATTTTATTTTTATTTTAA-
1 TTA-AAAATATATTTTATTTTT-TTTTAAC
3580979 TGTAAAAATATATATTTA
1 T-TAAAAATATAT-TTTA
3580997 AATATCTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.08
29 24 0.62
30 12 0.31
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (28 bp):
TTAAAAATATATTTTATTTTTTTTTAAC
Found at i:3582970 original size:30 final size:30
Alignment explanation
Indices: 3582934--3582995 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3582924 CACCATCATT
3582934 ACTCTCTTCTCGAAAGACATGTATGAGTGA
1 ACTCTCTTCTCGAAAGACATGTATGAGTGA
3582964 ACTCTCTTCTCGAAAGACATGTATGAGTGA
1 ACTCTCTTCTCGAAAGACATGTATGAGTGA
3582994 AC
1 AC
3582996 GTGAATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (30 bp):
ACTCTCTTCTCGAAAGACATGTATGAGTGA
Found at i:3594268 original size:47 final size:49
Alignment explanation
Indices: 3594202--3594365 Score: 145
Period size: 47 Copynumber: 3.2 Consensus size: 49
3594192 AACTTTAATT
*
3594202 AAAATACACTAATTTAATTTGTGATGGAATAATCATTCCGTCGGAAATAA
1 AAAATATAC-AATTTAATTTGTGATGGAATAATCATTCCGTCGGAAATAA
* * * * *
3594252 AAAA-AT-CAATTTAATTTATGACAGG-ACAATAATTCCGTCGGAATTTTTTTAA
1 AAAATATACAATTTAATTTGTGA-TGGAATAATCATTCCGTCGGAA-----ATAA
**
3594304 TTAAAATATAACAATTTAATTTGTGATGGAATGGTCATTCCGTCGGAAATAA
1 --AAAATAT-ACAATTTAATTTGTGATGGAATAATCATTCCGTCGGAAATAA
3594356 AAAATATACA
1 AAAATATACA
3594366 TTCATTTCTT
Statistics
Matches: 89, Mismatches: 13, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
47 29 0.33
48 3 0.03
49 4 0.04
50 11 0.12
52 6 0.07
54 4 0.04
55 2 0.02
56 2 0.02
57 28 0.31
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (49 bp):
AAAATATACAATTTAATTTGTGATGGAATAATCATTCCGTCGGAAATAA
Found at i:3595205 original size:23 final size:23
Alignment explanation
Indices: 3595174--3595234 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
3595164 CTCATATAAA
* *
3595174 TGCAACGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
*
3595197 TGCACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
3595220 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
3595235 TATAAGATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:3595501 original size:31 final size:30
Alignment explanation
Indices: 3595457--3595516 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
3595447 TATTGTATAG
3595457 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
3595487 ACATATCATATTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
3595517 GCTTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:3598367 original size:23 final size:23
Alignment explanation
Indices: 3598323--3598367 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3598313 ATCATTATAT
*
3598323 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
3598346 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
3598368 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:3604767 original size:12 final size:12
Alignment explanation
Indices: 3604750--3604775 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3604740 ACTCTATAGA
3604750 CTCTGGTTTATG
1 CTCTGGTTTATG
3604762 CTCTGGTTTATG
1 CTCTGGTTTATG
3604774 CT
1 CT
3604776 TAGAATCGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.19, G:0.23, T:0.50
Consensus pattern (12 bp):
CTCTGGTTTATG
Found at i:3605433 original size:23 final size:23
Alignment explanation
Indices: 3605402--3605457 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
3605392 ATAAACGCAA
*
3605402 CGAAGTGCCACGTAGAATTGCAC
1 CGAAGTGCCACGTAAAATTGCAC
* *
3605425 TGAAGTGCCGCGTAAAATTGCAC
1 CGAAGTGCCACGTAAAATTGCAC
*
3605448 CGTAGTGCCA
1 CGAAGTGCCA
3605458 TATAAGATTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
CGAAGTGCCACGTAAAATTGCAC
Found at i:3605723 original size:31 final size:30
Alignment explanation
Indices: 3605679--3605738 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
3605669 TATTGTATAG
3605679 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
3605709 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
3605739 GCCTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:3606175 original size:63 final size:64
Alignment explanation
Indices: 3606081--3606236 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 64
3606071 AATGAAGGTA
** * ** *
3606081 TGCATCGATGCACCACACCATGCATCGATGCATAAAT-CCTATTCGATGTTTATA-TTTAAGGGG
1 TGCATCGATGCACTTC-CTATGCATCGATGCATAAATGCC-ATTCGATGTTTATATTTTAAAAGA
3606144 G
64 G
** * *
3606145 TGCATCGATGCAC-TCCTTATGCATCGATGCATTGATGGCATTCGATGTTTGTATTTTAAAAGAG
1 TGCATCGATGCACTTCC-TATGCATCGATGCATAAATGCCATTCGATGTTTATATTTTAAAAGAG
*
3606209 TGCATCGATGCACTTCCTGTGCATCGAT
1 TGCATCGATGCACTTCCTATGCATCGAT
3606237 ACACCTTGAA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
62 1 0.01
63 30 0.38
64 44 0.56
65 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (64 bp):
TGCATCGATGCACTTCCTATGCATCGATGCATAAATGCCATTCGATGTTTATATTTTAAAAGAG
Found at i:3613422 original size:4 final size:4
Alignment explanation
Indices: 3613413--3613441 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3613403 GTTTAAATTA
3613413 TTAG TTAG TTAG TTAG TTAG TTAG TTAG T
1 TTAG TTAG TTAG TTAG TTAG TTAG TTAG T
3613442 GGCTATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TTAG
Found at i:3616056 original size:24 final size:24
Alignment explanation
Indices: 3616026--3616181 Score: 86
Period size: 24 Copynumber: 6.1 Consensus size: 24
3616016 GTATTAAATC
*
3616026 ATTATTA-TAATTTCATTATTAGTA
1 ATTATTAGTAATATCATTATTA-TA
*
3616050 ATTATTAGTATCAAATCATTATTATA
1 ATTATTAGTA--ATATCATTATTATA
* * *
3616076 ATTTCATTATTAGTAATCATTAGTATCAAATC
1 A-TT-ATTAGTAAT-ATCATTA-T-T---ATA
*
3616108 ATTATTA-TAATTTCATTATTAGTA
1 ATTATTAGTAATATCATTATTA-TA
*
3616132 ATCATTAGTAA-ATCATTATTACTA
1 ATTATTAGTAATATCATTATTA-TA
* *
3616156 ATCATTACTAA-ATCATTATTATA
1 ATTATTAGTAATATCATTATTATA
3616179 ATT
1 ATT
3616182 TTAAATATAA
Statistics
Matches: 105, Mismatches: 14, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
23 5 0.05
24 45 0.43
25 5 0.05
26 4 0.04
27 20 0.19
28 13 0.12
29 4 0.04
30 4 0.04
31 2 0.02
32 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (24 bp):
ATTATTAGTAATATCATTATTATA
Found at i:3616056 original size:41 final size:41
Alignment explanation
Indices: 3616012--3616157 Score: 244
Period size: 41 Copynumber: 3.6 Consensus size: 41
3616002 TATTATGATT
* *
3616012 ATTAGTATTAAATCATTATTATAATTTCATTATTAGTAATT
1 ATTAGTATCAAATCATTATTATAATTTCATTATTAGTAATC
3616053 ATTAGTATCAAATCATTATTATAATTTCATTATTAGTAATC
1 ATTAGTATCAAATCATTATTATAATTTCATTATTAGTAATC
3616094 ATTAGTATCAAATCATTATTATAATTTCATTATTAGTAATC
1 ATTAGTATCAAATCATTATTATAATTTCATTATTAGTAATC
3616135 ATTAG--T-AAATCATTATTACTAAT
1 ATTAGTATCAAATCATTATTA-TAAT
3616158 CATTACTAAA
Statistics
Matches: 102, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
38 12 0.12
39 5 0.05
41 85 0.83
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (41 bp):
ATTAGTATCAAATCATTATTATAATTTCATTATTAGTAATC
Found at i:3616093 original size:27 final size:23
Alignment explanation
Indices: 3616017--3616180 Score: 123
Period size: 27 Copynumber: 6.4 Consensus size: 23
3616007 TGATTATTAG
3616017 TATTA-AATCATTATTATAATTTCAT
1 TATTATAATCATTATTA-AA--TCAT
*
3616042 TATTAGTAATTATTAGTATCAAATCAT
1 TATTA-TAATCATTA-T-T-AAATCAT
3616069 TATTATAATTTCATTATTAGTAATCAT
1 TATTATAA--TCATTATTA--AATCAT
*
3616096 TAGTATCAAATCATTATTATAATTTCAT
1 TATTAT--AATCATTATTA-AA--TCAT
*
3616124 TATTAGTAATCATTAGTAAATCAT
1 TATTA-TAATCATTATTAAATCAT
*
3616148 TATTACTAATCATTACTAAATCAT
1 TATTA-TAATCATTATTAAATCAT
3616172 TATTATAAT
1 TATTATAAT
3616181 TTTAAATATA
Statistics
Matches: 118, Mismatches: 7, Indels: 30
0.76 0.05 0.19
Matches are distributed among these distances:
23 4 0.03
24 31 0.26
25 6 0.05
26 9 0.08
27 47 0.40
28 14 0.12
29 6 0.05
30 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (23 bp):
TATTATAATCATTATTAAATCAT
Found at i:3616145 original size:11 final size:11
Alignment explanation
Indices: 3616125--3616173 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
3616115 TAATTTCATT
3616125 ATTAGT-AATC
1 ATTAGTAAATC
3616135 ATTAGTAAATC
1 ATTAGTAAATC
*
3616146 ATTATTACTAATC
1 ATTAGTA--AATC
*
3616159 ATTACTAAATC
1 ATTAGTAAATC
3616170 ATTA
1 ATTA
3616174 TTATAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 6 0.18
11 18 0.53
13 10 0.29
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (11 bp):
ATTAGTAAATC
Found at i:3616225 original size:62 final size:62
Alignment explanation
Indices: 3616103--3616232 Score: 156
Period size: 62 Copynumber: 2.1 Consensus size: 62
3616093 CATTAGTATC
* * * * * *
3616103 AAATCATTATTATAATTTCATTATTAGTAATCATTAGTAAATCATTATTACTAATCATTACT
1 AAATCATTATTATAATTTAAATATTAGAAATCATGAGTAAATCATGATTACAAATCATTACT
* *
3616165 AAATCATTATTATAATTTTAAATA-TA-AAATCATGATTAAATCATGATTACCAAATTATTACT
1 AAATCATTATTATAA-TTTAAATATTAGAAATCATGAGTAAATCATGATTA-CAAATCATTACT
3616227 AAATCA
1 AAATCA
3616233 AATCATATCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 19 0.33
62 33 0.57
63 6 0.10
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (62 bp):
AAATCATTATTATAATTTAAATATTAGAAATCATGAGTAAATCATGATTACAAATCATTACT
Found at i:3616531 original size:11 final size:10
Alignment explanation
Indices: 3616509--3616582 Score: 52
Period size: 10 Copynumber: 7.8 Consensus size: 10
3616499 TAATTTCATT
3616509 ATTACTAATC
1 ATTACTAATC
3616519 ATTACTAAATC
1 ATTACT-AATC
*
3616530 ATTAAT-ATC
1 ATTACTAATC
3616539 GATTA--AAT-
1 -ATTACTAATC
* *
3616547 ATTAATAATA
1 ATTACTAATC
*
3616557 ATT--TCATC
1 ATTACTAATC
3616565 ATTACTAATC
1 ATTACTAATC
3616575 ATTACTAA
1 ATTACTAA
3616583 ATTTTTAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
7 4 0.08
8 6 0.12
9 8 0.15
10 25 0.48
11 9 0.17
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:3616642 original size:24 final size:25
Alignment explanation
Indices: 3616615--3616686 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 25
3616605 ATATTAATAA
* *
3616615 TAAATCATTATTA-CTAATCATTAT
1 TAAATCATTAATATCAAATCATTAT
3616639 TAAATCATTAATATCAAATC---AT
1 TAAATCATTAATATCAAATCATTAT
3616661 TAAAT-ATTAATAAT-AAATCATTAT
1 TAAATCATTAAT-ATCAAATCATTAT
3616685 TA
1 TA
3616687 CTAATTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 11 0.27
22 9 0.22
24 16 0.39
25 5 0.12
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.42
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAT
Found at i:3616659 original size:14 final size:13
Alignment explanation
Indices: 3616602--3616663 Score: 60
Period size: 14 Copynumber: 4.8 Consensus size: 13
3616592 ATCAAATTAT
3616602 TAAAT-ATTAATAA
1 TAAATCATTAAT-A
*
3616615 TAAATCATTATTA
1 TAAATCATTAATA
3616628 CT-AATCATT-AT-
1 -TAAATCATTAATA
3616639 TAAATCATTAATA
1 TAAATCATTAATA
3616652 TCAAATCATTAA
1 T-AAATCATTAA
3616664 ATATTAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 1 0.02
11 7 0.17
12 3 0.07
13 14 0.34
14 16 0.39
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATCATTAATA
Found at i:3616678 original size:21 final size:22
Alignment explanation
Indices: 3616637--3616683 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
3616627 ACTAATCATT
3616637 ATTAAATCATTAATATCAAATC
1 ATTAAATCATTAATATCAAATC
3616659 ATTAAAT-ATTAATAAT-AAATC
1 ATTAAATCATTAAT-ATCAAATC
3616680 ATTA
1 ATTA
3616684 TTACTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTAAATCATTAATATCAAATC
Found at i:3616697 original size:59 final size:60
Alignment explanation
Indices: 3616484--3616722 Score: 303
Period size: 59 Copynumber: 4.1 Consensus size: 60
3616474 TTCCATAATT
* *
3616484 ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC----G
1 ATTAAATATTAATAATAATATCATTATTACTAATCATTACTAAATCATTAATATCAAATC
* * ** *
3616540 ATTAAATATTAATAATAATTTCATCATTACTAATCATTACTAAATTTTTAATATCAAATT
1 ATTAAATATTAATAATAATATCATTATTACTAATCATTACTAAATCATTAATATCAAATC
*
3616600 ATTAAATATTAATAATAA-ATCATTATTACTAATCATTATTAAATCATTAATATCAAATC
1 ATTAAATATTAATAATAATATCATTATTACTAATCATTACTAAATCATTAATATCAAATC
* * * *
3616659 ATTAAATATTAATAATAA-ATCATTATTACTAATTATTATTATAAT-TTTAAATATAAAATC
1 ATTAAATATTAATAATAATATCATTATTACTAATCATTACTA-AATCATT-AATATCAAATC
3616719 ATTA
1 ATTA
3616723 TTAAATCATG
Statistics
Matches: 164, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
56 52 0.32
59 77 0.47
60 35 0.21
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (60 bp):
ATTAAATATTAATAATAATATCATTATTACTAATCATTACTAAATCATTAATATCAAATC
Found at i:3616738 original size:14 final size:14
Alignment explanation
Indices: 3616719--3616745 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3616709 ATATAAAATC
3616719 ATTATTAAATCATG
1 ATTATTAAATCATG
3616733 ATTATTAAATCAT
1 ATTATTAAATCAT
3616746 TACTAAATCA
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:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
ATTATTAAATCATG
Found at i:3619689 original size:26 final size:26
Alignment explanation
Indices: 3619660--3619719 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
3619650 ATTATTGATC
**
3619660 TAATAATTTGA-TATTTAATGATTTAA
1 TAATAATTTGATTAAGTAATGA-TTAA
* *
3619686 TAATAATATGATTAAGTAATGATTAC
1 TAATAATTTGATTAAGTAATGATTAA
3619712 TAATAATT
1 TAATAATT
3619720 ATTTATTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (26 bp):
TAATAATTTGATTAAGTAATGATTAA
Found at i:3620064 original size:14 final size:14
Alignment explanation
Indices: 3620045--3620071 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3620035 ACACATACAC
3620045 AACAACAAAAAATG
1 AACAACAAAAAATG
3620059 AACAACAAAAAAT
1 AACAACAAAAAAT
3620072 AATAAATAAC
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:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
AACAACAAAAAATG
Found at i:3620134 original size:11 final size:10
Alignment explanation
Indices: 3620100--3620135 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3620090 TTATGCCTTC
3620100 TTCTTTTCCT
1 TTCTTTTCCT
3620110 TTCTTTTCCT
1 TTCTTTTCCT
*
3620120 TTCTTGTTTCT
1 TTCTT-TTCCT
3620131 TTCTT
1 TTCTT
3620136 CGAATCAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (10 bp):
TTCTTTTCCT
Found at i:3620493 original size:25 final size:23
Alignment explanation
Indices: 3620465--3620515 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 23
3620455 TTTATATAAT
3620465 CTAATATATATCTTAAACTAACAAA
1 CTAATATA-AT-TTAAACTAACAAA
*
3620490 CT-A-ATAATTTATACTAACAAA
1 CTAATATAATTTAAACTAACAAA
3620511 CTAAT
1 CTAAT
3620516 TAACTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
21 14 0.61
22 3 0.13
23 3 0.13
24 1 0.04
25 2 0.09
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (23 bp):
CTAATATAATTTAAACTAACAAA
Found at i:3620951 original size:29 final size:28
Alignment explanation
Indices: 3620931--3620998 Score: 109
Period size: 29 Copynumber: 2.4 Consensus size: 28
3620921 CGCATGGCGT
3620931 GCATGGCGACCAAGCATGTCGTCCGGAAG
1 GCATGGCGACCAAGCATGTCG-CCGGAAG
3620960 GCATGGCGACCAAGCATGTCGCCCGGAAG
1 GCATGGCGACCAAGCATGTCG-CCGGAAG
*
3620989 GTATGGCGAC
1 GCATGGCGAC
3620999 ATGGTATATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.24, C:0.28, G:0.35, T:0.13
Consensus pattern (28 bp):
GCATGGCGACCAAGCATGTCGCCGGAAG
Found at i:3621994 original size:160 final size:170
Alignment explanation
Indices: 3621810--3622141 Score: 560
Period size: 160 Copynumber: 2.0 Consensus size: 170
3621800 TGGTGGTTAA
3621810 TAATTTAGGATGAAATGATAATAGAACTAAATTTTAAATAATTAAAGGTTTTAAAAAAATAAAAA
1 TAATTTAGGATGAAATGATAATAGAACTAAATTTTAAATAATTAAAGGTTTTAAAAAAATAAAAA
3621875 CAA-TTAACG-A-A-ATAT-ATTTAAAAGGC-AATAA-T-TTTACTTTTTTTCTTTTAAATGATA
66 CAATTTAACGAATACATATAATTTAAAAGGCAAATAATTATTTACTTTTTTTC-TTTAAATGATA
3621932 AATTAA-TGTTCATCATCATATGA-TGATG-ATACTAGATT
130 AATTAATTGTTCATCATCATATGATTGATGAATACTAGATT
3621970 TAATTTAGGATGAAATGATAATAGAACTAAATTTTAAATAATTAAAGGTTTTAAAAAAATAAAAA
1 TAATTTAGGATGAAATGATAATAGAACTAAATTTTAAATAATTAAAGGTTTTAAAAAAATAAAAA
3622035 CAATTTAACGAAATACATATAATTTAAAAGGCAAATAATTATTTACTTTTTTTCTTTAAATGATA
66 CAATTTAACG-AATACATATAATTTAAAAGGCAAATAATTATTTACTTTTTTTCTTTAAATGATA
3622100 AATTAATTGTTCATCATCATATGATTGATGATATACTAGATT
130 AATTAATTGTTCATCATCATATGATTGATGA-ATACTAGATT
3622142 CTTTAAATAA
Statistics
Matches: 159, Mismatches: 0, Indels: 14
0.92 0.00 0.08
Matches are distributed among these distances:
160 68 0.43
161 6 0.04
163 1 0.01
164 1 0.01
165 4 0.03
166 11 0.07
167 5 0.03
168 18 0.11
169 30 0.19
170 5 0.03
172 10 0.06
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (170 bp):
TAATTTAGGATGAAATGATAATAGAACTAAATTTTAAATAATTAAAGGTTTTAAAAAAATAAAAA
CAATTTAACGAATACATATAATTTAAAAGGCAAATAATTATTTACTTTTTTTCTTTAAATGATAA
ATTAATTGTTCATCATCATATGATTGATGAATACTAGATT
Found at i:3623799 original size:318 final size:318
Alignment explanation
Indices: 3623222--3624175 Score: 1881
Period size: 318 Copynumber: 3.0 Consensus size: 318
3623212 TTTTAAATCA
3623222 GTGTAAAACAAATTTTACATTGTGTGACTGGATCTTACCTCTAAATAGGTTAAGATCCACTCACA
1 GTGTAAAACAAATTTTACATTGTGTGACTGGATCTTACCTCTAAATAGGTTAAGATCCACTCACA
*
3623287 CAAATATAAAAAACTTATAATTGTACACTGGTTTAGGCTCGTTAGATAAGTAGATATAAACTGTT
66 CAAATATAAAAAACTTATAATAGTACACTGGTTTAGGCTCGTTAGATAAGTAGATATAAACTGTT
3623352 GATTTTATCTCATTATTTTATTCTTACTCGTACAACGATTCTAAATCAATATAAAACTTTTTAGT
131 GATTTTATCTCATTATTTTATTCTTACTCGTACAACGATTCTAAATCAATATAAAACTTTTTAGT
*
3623417 TTTACGTTGTGTAACTACATCATACTTCTAAATGGGTTAGGATATACTTACACAATGTAAAAACT
196 TTTACGTTGTGTAACTACATCCTACTTCTAAATGGGTTAGGATATACTTACACAATGTAAAAACT
3623482 TTTAATTTTTCATTTATTTAGGCTCATTGGATAAGTGGATAGAGACGGTTAAGATTAT
261 TTTAATTTTTCATTTATTTAGGCTCATTGGATAAGTGGATAGAGACGGTTAAGATTAT
3623540 GTGTAAAACAAATTTTACATTGTGTGACTGGATCTTACCTCTAAATAGGTTAAGATCCACTCACA
1 GTGTAAAACAAATTTTACATTGTGTGACTGGATCTTACCTCTAAATAGGTTAAGATCCACTCACA
3623605 CAAATATAAAAAACTTATAATAGTACACTGGTTTAGGCTCGTTAGATAAGTAGATATAAACTGTT
66 CAAATATAAAAAACTTATAATAGTACACTGGTTTAGGCTCGTTAGATAAGTAGATATAAACTGTT
3623670 GATTTTATCTCATTATTTTATTCTTACTCGTACAACGATTCTAAATCAATATAAAACTTTTTAGT
131 GATTTTATCTCATTATTTTATTCTTACTCGTACAACGATTCTAAATCAATATAAAACTTTTTAGT
3623735 TTTACGTTGTGTAACTACATCCTACTTCTAAATGGGTTAGGATATACTTACACAATGTAAAAACT
196 TTTACGTTGTGTAACTACATCCTACTTCTAAATGGGTTAGGATATACTTACACAATGTAAAAACT
3623800 TTTAATTTTTCATTTATTTAGGCTCATTGGATAAGTGGATAGAGACGGTTAAGATTAT
261 TTTAATTTTTCATTTATTTAGGCTCATTGGATAAGTGGATAGAGACGGTTAAGATTAT
3623858 GTGTAAAACAAATTTTACATTGTGTGACTGGATCTTACCTCTAAATAGGTTAAGATCCACTCACA
1 GTGTAAAACAAATTTTACATTGTGTGACTGGATCTTACCTCTAAATAGGTTAAGATCCACTCACA
*
3623923 CAAATATAAAAAACTTATAATAGTACACTGGTTTAGACTCGTTAGATAAGTAGATATAAACTGTT
66 CAAATATAAAAAACTTATAATAGTACACTGGTTTAGGCTCGTTAGATAAGTAGATATAAACTGTT
3623988 GATTTTATCTCATTATTTTATTCTTACTCGTACAACGATTCTAAATCAATATAAAACTTTTTAGT
131 GATTTTATCTCATTATTTTATTCTTACTCGTACAACGATTCTAAATCAATATAAAACTTTTTAGT
3624053 TTTACGTTGTGTAACTACATCCTACTTCTAAATGGGTTAGGATATACTTACACAATGTAAAAACT
196 TTTACGTTGTGTAACTACATCCTACTTCTAAATGGGTTAGGATATACTTACACAATGTAAAAACT
3624118 TTTAATTTTTCATTTATTTAGGCTCATTGGATAAGTGGATAGAGACGGTTAAGATTAT
261 TTTAATTTTTCATTTATTTAGGCTCATTGGATAAGTGGATAGAGACGGTTAAGATTAT
3624176 CTCATTATTT
Statistics
Matches: 633, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
318 633 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (318 bp):
GTGTAAAACAAATTTTACATTGTGTGACTGGATCTTACCTCTAAATAGGTTAAGATCCACTCACA
CAAATATAAAAAACTTATAATAGTACACTGGTTTAGGCTCGTTAGATAAGTAGATATAAACTGTT
GATTTTATCTCATTATTTTATTCTTACTCGTACAACGATTCTAAATCAATATAAAACTTTTTAGT
TTTACGTTGTGTAACTACATCCTACTTCTAAATGGGTTAGGATATACTTACACAATGTAAAAACT
TTTAATTTTTCATTTATTTAGGCTCATTGGATAAGTGGATAGAGACGGTTAAGATTAT
Found at i:3628398 original size:21 final size:22
Alignment explanation
Indices: 3628368--3628410 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3628358 TTAGGATCAA
3628368 TGGGATTAGGAAT-AGGATTTGG
1 TGGGATTAGG-ATGAGGATTTGG
3628390 TGGGA-TAGGATGAGGATTTGG
1 TGGGATTAGGATGAGGATTTGG
3628411 AGGAGGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.10
21 13 0.65
22 5 0.25
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.30
Consensus pattern (22 bp):
TGGGATTAGGATGAGGATTTGG
Found at i:3628833 original size:16 final size:16
Alignment explanation
Indices: 3628812--3628850 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
3628802 TCATTATTTC
3628812 AATCTAGAACTACGTA
1 AATCTAGAACTACGTA
3628828 AATCTAGAACTACGTA
1 AATCTAGAACTACGTA
3628844 AATCTAG
1 AATCTAG
3628851 TCCTATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (16 bp):
AATCTAGAACTACGTA
Found at i:3629181 original size:22 final size:23
Alignment explanation
Indices: 3629135--3629184 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
3629125 ATTCCCCTAG
3629135 GGGGGAATCGGTTCCCATTCAAA
1 GGGGGAATCGGTTCCCATTCAAA
3629158 GGGGGAATCGGTTCCTC-TTC-AA
1 GGGGGAATCGGTTCC-CATTCAAA
3629180 GGGGG
1 GGGGG
3629185 TATTGATTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.27
23 18 0.69
24 1 0.04
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCATTCAAA
Found at i:3634673 original size:13 final size:13
Alignment explanation
Indices: 3634655--3634679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3634645 TCGAATATAC
3634655 TTAGAAAATCTTT
1 TTAGAAAATCTTT
3634668 TTAGAAAATCTT
1 TTAGAAAATCTT
3634680 AAAATTCATT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:3638440 original size:87 final size:89
Alignment explanation
Indices: 3638337--3638513 Score: 340
Period size: 87 Copynumber: 2.0 Consensus size: 89
3638327 TAATTCAATT
3638337 TTTTTAATCTATTAATAATACATACATATTCTATAAATATAATTATATTAACATGTTTTTTTTAT
1 TTTTTAATCTATTAATAATACATACATATTCTATAAATATAATTATATTAACATGTTTTTTTTAT
3638402 ATATAACATTC-C-TCTATTACAC
66 ATATAACATTCTCTTCTATTACAC
3638424 TTTTTAATCTATTAATAATACATACATATTCTATAAATATAATTATATTAACATGTTTTTTTTAT
1 TTTTTAATCTATTAATAATACATACATATTCTATAAATATAATTATATTAACATGTTTTTTTTAT
3638489 ATATAACATTCTCTTCTATTACAC
66 ATATAACATTCTCTTCTATTACAC
3638513 T
1 T
3638514 AAAACCGCTT
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
87 76 0.86
88 1 0.01
89 11 0.12
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.49
Consensus pattern (89 bp):
TTTTTAATCTATTAATAATACATACATATTCTATAAATATAATTATATTAACATGTTTTTTTTAT
ATATAACATTCTCTTCTATTACAC
Found at i:3645441 original size:64 final size:63
Alignment explanation
Indices: 3645311--3645461 Score: 216
Period size: 64 Copynumber: 2.4 Consensus size: 63
3645301 CACTCACCAT
*
3645311 ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCAATACACTCAAGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACAACCATGCATCAATACACTCAAGTTTTATGAAAAC
* * *
3645374 ATCGAATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCAGGCTTGTT-TG-AAA
1 ATCGAATGCATTTTATGCATCGATGCAC-AACCATGCATCAATACACTCAAG-TT-TTATGAAAA
3645437 C
63 C
*
3645438 ATCGAATGCATTTAATGCATCGAT
1 ATCGAATGCATTTTATGCATCGAT
3645462 TCACTCTTAG
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
63 28 0.35
64 46 0.57
65 4 0.05
66 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACAACCATGCATCAATACACTCAAGTTTTATGAAAAC
Found at i:3645476 original size:64 final size:62
Alignment explanation
Indices: 3645311--3645486 Score: 203
Period size: 64 Copynumber: 2.8 Consensus size: 62
3645301 CACTCACCAT
*
3645311 ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCAATACACTCAAGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACT-CCATGCATCGATACACTCAAGTTTTATGAAAAC
* * *
3645374 ATCGAATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCAGGCTTGTT-TG-AAA
1 ATCGAATGCATTTTATGCATCGATGCAC--TCCATGCATCGATACACTCAAG-TT-TTATGAAAA
3645437 C
62 C
* * * *
3645438 ATCGAATGCATTTAATGCATCGATTCACTCTTAGTGCATCGATTCACTC
1 ATCGAATGCATTTTATGCATCGATGCACTC-CA-TGCATCGATACACTC
3645487 TTAGTGCACT
Statistics
Matches: 98, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.01
63 29 0.30
64 62 0.63
65 4 0.04
66 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (62 bp):
ATCGAATGCATTTTATGCATCGATGCACTCCATGCATCGATACACTCAAGTTTTATGAAAAC
Found at i:3645477 original size:19 final size:19
Alignment explanation
Indices: 3645453--3645494 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
3645443 ATGCATTTAA
3645453 TGCATCGATTCACTCTTAG
1 TGCATCGATTCACTCTTAG
3645472 TGCATCGATTCACTCTTAG
1 TGCATCGATTCACTCTTAG
3645491 TGCA
1 TGCA
3645495 CTGATGCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (19 bp):
TGCATCGATTCACTCTTAG
Found at i:3645504 original size:19 final size:19
Alignment explanation
Indices: 3645453--3645504 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3645443 ATGCATTTAA
*
3645453 TGCATCGATTCACTCTTAG
1 TGCATCGATGCACTCTTAG
*
3645472 TGCATCGATTCACTCTTAG
1 TGCATCGATGCACTCTTAG
3645491 TGCA-CTGATGCACT
1 TGCATC-GATGCACT
3645505 AAGGGCCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 1 0.03
19 30 0.97
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (19 bp):
TGCATCGATGCACTCTTAG
Found at i:3649714 original size:17 final size:17
Alignment explanation
Indices: 3649689--3649730 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
3649679 TTGTTGCTCA
*
3649689 AGGGTATACTCAAGAAG
1 AGGGCATACTCAAGAAG
3649706 AGGGCATACTCAAGAAG
1 AGGGCATACTCAAGAAG
3649723 AGGGCATA
1 AGGGCATA
3649731 GACTATGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.40, C:0.14, G:0.31, T:0.14
Consensus pattern (17 bp):
AGGGCATACTCAAGAAG
Found at i:3654318 original size:169 final size:169
Alignment explanation
Indices: 3654039--3654382 Score: 679
Period size: 169 Copynumber: 2.0 Consensus size: 169
3654029 TTAATAATTG
*
3654039 TTTTCACACTTAAACGGCTCCATTGACTCCACTAATCATCCCCAACGTTCAGAATCAATTGAAGG
1 TTTTCACACTTAAACGGCTCCATTGACTCCACTAATCATCCCCAACATTCAGAATCAATTGAAGG
3654104 AGTATTTAAACAAGCTTAGAAGCCATTGATCAAAAAGAAGAAACAACAATCAACAAGAATCAAGA
66 AGTATTTAAACAAGCTTAGAAGCCATTGATCAAAAAGAAGAAACAACAATCAACAAGAATCAAGA
3654169 GAGAATCAAAGAGAAAGCATCAAACCTCAAGTTTGAGCA
131 GAGAATCAAAGAGAAAGCATCAAACCTCAAGTTTGAGCA
3654208 TTTTCACACTTAAACGGCTCCATTGACTCCACTAATCATCCCCAACATTCAGAATCAATTGAAGG
1 TTTTCACACTTAAACGGCTCCATTGACTCCACTAATCATCCCCAACATTCAGAATCAATTGAAGG
3654273 AGTATTTAAACAAGCTTAGAAGCCATTGATCAAAAAGAAGAAACAACAATCAACAAGAATCAAGA
66 AGTATTTAAACAAGCTTAGAAGCCATTGATCAAAAAGAAGAAACAACAATCAACAAGAATCAAGA
3654338 GAGAATCAAAGAGAAAGCATCAAACCTCAAGTTTGAGCA
131 GAGAATCAAAGAGAAAGCATCAAACCTCAAGTTTGAGCA
3654377 TTTTCA
1 TTTTCA
3654383 AGCCTATTTC
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 174 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (169 bp):
TTTTCACACTTAAACGGCTCCATTGACTCCACTAATCATCCCCAACATTCAGAATCAATTGAAGG
AGTATTTAAACAAGCTTAGAAGCCATTGATCAAAAAGAAGAAACAACAATCAACAAGAATCAAGA
GAGAATCAAAGAGAAAGCATCAAACCTCAAGTTTGAGCA
Found at i:3660038 original size:298 final size:301
Alignment explanation
Indices: 3659498--3660097 Score: 1161
Period size: 299 Copynumber: 2.0 Consensus size: 301
3659488 CGTTCATGCA
3659498 TATTCTCTTCACACTGTTACAGCTTTGCTTTGATTAGGGGTTCATGCAGTGGTGGATCTATAGCT
1 TATTCTCTTCACACTGTTACAGCTTTGCTTTGATTAGGGGTTCATGCAGTGGTGGATCTATAGCT
3659563 ATTCTAGGATGGGCATGAACCCATTCCGAAATCCGAATTTTATTCGATTAATTACTTATTTTACT
66 ATTCTAGGATGGGCATGAACCCATTCCGAAATCCGAATTTTATTCGATTAATTACTTATTTTACT
3659628 AATGGTACCCACCGTGAAATTTTATTTGTCCTTGTCCCAGTTATTAAAATATTTGTCTTCATCCT
131 AATGGTACCCACCGTGAAATTTTATTTGTCCTTGTCCCAGTTATTAAAATATTTGTCTTCATCCT
*
3659693 AAAATAATTTCTAAATCTGCTATTAATTCCATACTTATTTTGACTCCC-AAAACACAATGCATGC
196 AAAATAATTTCTAAATCTGCTATTAATTCCATACTTATTTTGACTCCCAAAAACACAATGAATGC
3659757 CAGCAA-TAATTTGGTGCATATTTATTAGGGTTTTACAGCT
261 CAGCAATTAATTTGGTGCATATTTATTAGGGTTTTACAGCT
3659797 TATTCTCTTCACACTGTTACAGCTTTGCTTTGATTAGGGGTTCATGCAGTGGTGGATCTATAGCT
1 TATTCTCTTCACACTGTTACAGCTTTGCTTTGATTAGGGGTTCATGCAGTGGTGGATCTATAGCT
3659862 ATTCTAGGATGGGCATGAACCCATTCCGAAATCCGAATTTTATTCGATTAATTAC-TATTTTACT
66 ATTCTAGGATGGGCATGAACCCATTCCGAAATCCGAATTTTATTCGATTAATTACTTATTTTACT
*
3659926 AATGGTACCCACCGTGAAATTTTATTTGTCCTTGTCCCAGTTATTAATATATTTGTCTTCATCCT
131 AATGGTACCCACCGTGAAATTTTATTTGTCCTTGTCCCAGTTATTAAAATATTTGTCTTCATCCT
3659991 AAAATAATTTCTAAATCTGCTATTAATTCCATACTTATTTTGACTCCCAAAAACACAATGAATGC
196 AAAATAATTTCTAAATCTGCTATTAATTCCATACTTATTTTGACTCCCAAAAACACAATGAATGC
3660056 CAGCAATTAATTTGGTGCATATTTATTAGGGTTTTACAGCT
261 CAGCAATTAATTTGGTGCATATTTATTAGGGTTTTACAGCT
3660097 T
1 T
3660098 TGATTTGTGT
Statistics
Matches: 297, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
298 121 0.41
299 141 0.47
300 35 0.12
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (301 bp):
TATTCTCTTCACACTGTTACAGCTTTGCTTTGATTAGGGGTTCATGCAGTGGTGGATCTATAGCT
ATTCTAGGATGGGCATGAACCCATTCCGAAATCCGAATTTTATTCGATTAATTACTTATTTTACT
AATGGTACCCACCGTGAAATTTTATTTGTCCTTGTCCCAGTTATTAAAATATTTGTCTTCATCCT
AAAATAATTTCTAAATCTGCTATTAATTCCATACTTATTTTGACTCCCAAAAACACAATGAATGC
CAGCAATTAATTTGGTGCATATTTATTAGGGTTTTACAGCT
Found at i:3675927 original size:20 final size:20
Alignment explanation
Indices: 3675879--3675927 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3675869 CCTTTATTTT
* *
3675879 TCTCAAACACCTAAAATACC
1 TCTCAAACCCCTAAAACACC
3675899 TCTCAAACCCCTAAAACACC
1 TCTCAAACCCCTAAAACACC
3675919 TCTCAAACC
1 TCTCAAACC
3675928 GTCGTTCGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (20 bp):
TCTCAAACCCCTAAAACACC
Found at i:3678107 original size:16 final size:16
Alignment explanation
Indices: 3678086--3678119 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3678076 ATTTAACAAA
3678086 AAGGGAGAGAAGTGTT
1 AAGGGAGAGAAGTGTT
*
3678102 AAGGGAGAGTAGTGTT
1 AAGGGAGAGAAGTGTT
3678118 AA
1 AA
3678120 AGTAAGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21
Consensus pattern (16 bp):
AAGGGAGAGAAGTGTT
Found at i:3679440 original size:199 final size:185
Alignment explanation
Indices: 3679065--3679450 Score: 646
Period size: 199 Copynumber: 2.0 Consensus size: 185
3679055 GTTTGCAAAA
3679065 TTTGTATTATTTCTTTGGGAGAGAGTGTTCTCAAATTGAGGTATATTCTTAAGAGATTTGTAAGG
1 TTTGTATTATTTCTTTGGGAGAGAGTGTTCTCAAATTGAGGTATATTCTTAAGAGATTTGTAAGG
3679130 TTATATTTATCCTCAAAAGAAAGACAAATTAGTGAGAGAAACCCTTAGTGTGGATAGTTAAAGTA
66 TTATATTTATCCTCAAAAGAAAGACAAATTAGTGAGAGAAACCCTTAGTGTGGATAGTTAAAGTA
3679195 GGACGTAAACTTTGGTTGAGAAAGTCGAACTACTCTAAATCGCTGTGCAAATATT
131 GGACGTAAACTTTGGTTGAGAAAGTCGAACTACTCTAAATCGCTGTGCAAATATT
3679250 TTTGTATTATTCTCTTTGGGAGAGAGTGTTCTCAAGAATTTGAGGTATAATTCTTAAGAGATTTG
1 TTTGTATTATT-TCTTTGGGAGAGAGTGTTCTC-A-AA-TTGAGGTAT-ATTCTTAAGAGATTTG
3679315 TAAGGTTACTATTTATCCTCAAAAGAAAGACAAATTAGTGAATTTGTAGAAAACCCTTAGTGTGG
61 TAAGGTTA-TATTTATCCTCAAAAGAAAGACAAATTAGTG-A---G-AG-AAACCCTTAGTGTGG
3679380 ATAGTTAAAGTAGTGGACGTAAACTTTGGTTGAGAAAGTCGAACTACTCTAAATCGCTGTGCAAA
119 ATAGTTAAAGTA--GGACGTAAACTTTGGTTGAGAAAGTCGAACTACTCTAAATCGCTGTGCAAA
3679445 TATT
182 TATT
3679449 TT
1 TT
3679451 CAATTTTTTG
Statistics
Matches: 187, Mismatches: 0, Indels: 14
0.93 0.00 0.07
Matches are distributed among these distances:
185 11 0.06
186 21 0.11
187 1 0.01
188 2 0.01
189 9 0.05
190 24 0.13
191 31 0.17
192 1 0.01
195 1 0.01
196 2 0.01
197 27 0.14
199 57 0.30
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (185 bp):
TTTGTATTATTTCTTTGGGAGAGAGTGTTCTCAAATTGAGGTATATTCTTAAGAGATTTGTAAGG
TTATATTTATCCTCAAAAGAAAGACAAATTAGTGAGAGAAACCCTTAGTGTGGATAGTTAAAGTA
GGACGTAAACTTTGGTTGAGAAAGTCGAACTACTCTAAATCGCTGTGCAAATATT
Found at i:3682890 original size:29 final size:30
Alignment explanation
Indices: 3682857--3682914 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
3682847 TTACTTTTTC
3682857 AGTTTAGTGCCTAACATTT-ATTCCGTTAT
1 AGTTTAGTGCCTAACATTTCATTCCGTTAT
* * * *
3682886 AGTTTGGTGTCTAACGTTTCATTCTGTTA
1 AGTTTAGTGCCTAACATTTCATTCCGTTA
3682915 CTTAAAATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (30 bp):
AGTTTAGTGCCTAACATTTCATTCCGTTAT
Found at i:3688683 original size:88 final size:88
Alignment explanation
Indices: 3688535--3688857 Score: 459
Period size: 88 Copynumber: 3.6 Consensus size: 88
3688525 GTTGAAAGAG
* ** *
3688535 TGAAAACACATTCGCCTTCATCAAAGAAAA-CCATTCGCCTTCAACCTCCTCGTATGAAAATCCT
1 TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCT
3688599 TCGCACTTTAGAGAGATTTCGTT
66 TCGCACTTTAGAGAGATTTCGTT
3688622 TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCT
1 TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCT
*
3688687 TCGCACTTTAGAGAGATTTCGTC
66 TCGCACTTTAGAGAGATTTCGTT
* * * * *
3688710 TGAAAACCCATTCGCCTTCATCGCAGAAAACTCATTCACTTTCAACCTCCTCATCTAAAAATCCT
1 TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCT
3688775 TCGCACTTTAGAGAGATTTCGAAAGATTTCGT
66 TCGCACTTTAGAGAGATTTC----G---T--T
3688807 CTGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCC
1 -TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCC
3688858 CCGTTTAACA
Statistics
Matches: 211, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
87 27 0.13
88 135 0.64
92 1 0.00
95 1 0.00
98 47 0.22
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.28
Consensus pattern (88 bp):
TGAAAACCCATTCGCCTTCATCGCAGAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCT
TCGCACTTTAGAGAGATTTCGTT
Found at i:3689398 original size:15 final size:15
Alignment explanation
Indices: 3689378--3689407 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3689368 AATGTGAGTA
3689378 CTGCATGTATATGTT
1 CTGCATGTATATGTT
3689393 CTGCATGTATATGTT
1 CTGCATGTATATGTT
3689408 GTGTATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
CTGCATGTATATGTT
Found at i:3690102 original size:24 final size:24
Alignment explanation
Indices: 3690075--3690122 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3690065 CAAGAAATTA
*
3690075 CTGAACCCGAAATTAATGAACCAG
1 CTGAACCAGAAATTAATGAACCAG
*
3690099 CTGAGCCAGAAATTAATGAACCAG
1 CTGAACCAGAAATTAATGAACCAG
3690123 AACAAGCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (24 bp):
CTGAACCAGAAATTAATGAACCAG
Found at i:3690124 original size:15 final size:15
Alignment explanation
Indices: 3690104--3690214 Score: 75
Period size: 15 Copynumber: 7.4 Consensus size: 15
3690094 ACCAGCTGAG
3690104 CCAGAAATTAATGAA
1 CCAGAAATTAATGAA
* *
3690119 CCAGAACA--AGCTGAG
1 CCAGAA-ATTA-ATGAA
*
3690134 CCATAAATTAATGAA
1 CCAGAAATTAATGAA
*
3690149 CCTGAAATTAATGAA
1 CCAGAAATTAATGAA
* ** * *
3690164 TCAG-AACCAGCTGAG
1 CCAGAAATTA-ATGAA
3690179 CCAGAAATTAATGAA
1 CCAGAAATTAATGAA
* *
3690194 CCTGAAATTGATGAA
1 CCAGAAATTAATGAA
3690209 CCAGAA
1 CCAGAA
3690215 CCTGCTGAGG
Statistics
Matches: 69, Mismatches: 21, Indels: 12
0.68 0.21 0.12
Matches are distributed among these distances:
14 5 0.07
15 59 0.86
16 5 0.07
ACGTcount: A:0.46, C:0.18, G:0.17, T:0.19
Consensus pattern (15 bp):
CCAGAAATTAATGAA
Found at i:3690133 original size:30 final size:30
Alignment explanation
Indices: 3690092--3690150 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3690082 CGAAATTAAT
*
3690092 GAACCAGCTGAGCCAGAAATTAATGAACCA
1 GAACAAGCTGAGCCAGAAATTAATGAACCA
*
3690122 GAACAAGCTGAGCCATAAATTAATGAACC
1 GAACAAGCTGAGCCAGAAATTAATGAACC
3690151 TGAAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (30 bp):
GAACAAGCTGAGCCAGAAATTAATGAACCA
Found at i:3690176 original size:45 final size:45
Alignment explanation
Indices: 3690107--3690223 Score: 189
Period size: 45 Copynumber: 2.6 Consensus size: 45
3690097 AGCTGAGCCA
* *
3690107 GAAATTAATGAACCAGAACAAGCTGAGCCATAAATTAATGAACCT
1 GAAATTAATGAACCAGAACCAGCTGAGCCAGAAATTAATGAACCT
*
3690152 GAAATTAATGAATCAGAACCAGCTGAGCCAGAAATTAATGAACCT
1 GAAATTAATGAACCAGAACCAGCTGAGCCAGAAATTAATGAACCT
* *
3690197 GAAATTGATGAACCAGAACCTGCTGAG
1 GAAATTAATGAACCAGAACCAGCTGAG
3690224 GTGAGGATAG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.20
Consensus pattern (45 bp):
GAAATTAATGAACCAGAACCAGCTGAGCCAGAAATTAATGAACCT
Found at i:3692574 original size:43 final size:42
Alignment explanation
Indices: 3692527--3692651 Score: 112
Period size: 43 Copynumber: 2.9 Consensus size: 42
3692517 AATAGGATTT
3692527 TTATTTAATATATATATAAAATATAAAAATAAGTAAATAAATA
1 TTATTTAATATATATATAAAATATAAAAATAA-TAAATAAATA
* * * * *
3692570 TTATTTATTATATATATTTATATGATACATAATAAT-AATCAATA
1 TTATTTAATATATATA-TAAAAT-ATA-AAAATAATAAATAAATA
* * *
3692614 ATAATTAA-ATATATA-AACATATAAAAATAAATAAATAA
1 TTATTTAATATATATATAAAATATAAAAAT-AATAAATAA
3692652 CGACTAAAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
39 4 0.06
40 6 0.09
41 7 0.11
43 22 0.34
44 16 0.25
45 4 0.06
46 6 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (42 bp):
TTATTTAATATATATATAAAATATAAAAATAATAAATAAATA
Found at i:3694028 original size:39 final size:38
Alignment explanation
Indices: 3693985--3694127 Score: 180
Period size: 39 Copynumber: 3.7 Consensus size: 38
3693975 AAGGCGGAAC
3693985 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTCAAGAT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTC-AGAT
* * *
3694024 AAGTTCTTCTCATTATGAACTTATTCTTCTTCTTTAGAT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTC-TCAGAT
* *
3694063 GAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCC-TC-TCAGAT
* *
3694103 GAGTTTTTCTCATTATGAAC-TCTTC
1 AAGTTCTTCTCATTATGAACTTCTTC
3694128 CACTGGGGAT
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
39 65 0.71
40 27 0.29
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.48
Consensus pattern (38 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTCAGAT
Found at i:3694555 original size:124 final size:123
Alignment explanation
Indices: 3694311--3694590 Score: 427
Period size: 124 Copynumber: 2.3 Consensus size: 123
3694301 TTAAGGCAAT
** * *
3694311 GTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCCTTCTTCTGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
** *
3694375 ACATTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCAAACAAAAG
66 ACATTTCTGGAAAAATTGATGCTGATCTATCTCCTTCTGTGATAAAGTCAAACAAAAG
3694433 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * **
3694498 ACTTTCTCTTGAAAAATTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAG
66 ACATT-TCTGGAAAAATTGATGCTGATCTATCTCCTTCTGTGATAAAGTCAAACAAAAG
*
3694557 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
1 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCT
3694591 GAAAATGTTG
Statistics
Matches: 143, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
122 30 0.21
123 34 0.24
124 79 0.55
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (123 bp):
GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACATTTCTGGAAAAATTGATGCTGATCTATCTCCTTCTGTGATAAAGTCAAACAAAAG
Found at i:3694766 original size:113 final size:113
Alignment explanation
Indices: 3694568--3695048 Score: 590
Period size: 113 Copynumber: 4.2 Consensus size: 113
3694558 TTGAACAAGC
* ** * * * * *
3694568 TCTTCTCATTATGAACTTTTTCTGAAAATGTTGATTCATCGAGTGATGAATTCGAGCAAAAGGTT
1 TCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAAGTT
* *
3694633 GAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGT
66 GAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGT
* *
3694681 TCTTCTCATTATGAACTCTACCTGGTAATGCTGATCCATCGAATGATGAATTCTAGCAAAAAGTT
1 TCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAAGTT
*
3694746 GAATAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGT
66 GAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGT
* * *
3694794 TCTTCTTATTATGAACTCTACCTGGCAATGCTAATCCATCGAATGATGAATTCGAGCAAAAAGTT
1 TCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAAGTT
3694859 GAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGT
66 GAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGT
* * *** *
3694907 TCTTCTCATTATGAACTCCT-TCTGGAAATGTTGATGCTGATCTATCTCTTTCTGCGAT-AGAGT
1 TCTTCTCATTATGAACT-CTACCTGG-AA-----ATGCTGATCCA--TC-GAAT--GATGA-ATT
* * * *
3694970 CGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTAC-TCTTCAGATGGGT
53 CGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGT
3695030 TCTTCTCATTATGAACTCT
1 TCTTCTCATTATGAACTCT
3695049 TTCTTCTTTT
Statistics
Matches: 324, Mismatches: 31, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
113 228 0.70
114 3 0.01
119 9 0.03
121 2 0.01
122 3 0.01
123 30 0.09
124 49 0.15
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (113 bp):
TCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAAGTT
GAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGT
Found at i:3695571 original size:22 final size:22
Alignment explanation
Indices: 3695493--3695569 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
3695483 AATAAAGTTT
3695493 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3695515 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3695537 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3695559 TCATCTTTGAA
1 TCATCTTTGAA
3695570 GAATGTAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3700507 original size:8 final size:8
Alignment explanation
Indices: 3700494--3700556 Score: 67
Period size: 8 Copynumber: 8.0 Consensus size: 8
3700484 CTTGATTCAA
3700494 TTTTCCTT
1 TTTTCCTT
3700502 TTTTCC-T
1 TTTTCCTT
3700509 TTTTCCTT
1 TTTTCCTT
**
3700517 TTTCTTTTT
1 TTT-TCCTT
*
3700526 TTTTCTTT
1 TTTTCCTT
*
3700534 TTTTCCCT
1 TTTTCCTT
3700542 TTTT-CTT
1 TTTTCCTT
3700549 TTTTCCTT
1 TTTTCCTT
3700557 CTTCTTTCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
7 13 0.28
8 27 0.59
9 6 0.13
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCCTT
Found at i:3700511 original size:7 final size:7
Alignment explanation
Indices: 3700494--3700556 Score: 53
Period size: 7 Copynumber: 9.1 Consensus size: 7
3700484 CTTGATTCAA
3700494 TTTTCCTT
1 TTTTCC-T
3700502 TTTTCCT
1 TTTTCCT
3700509 TTTTCCT
1 TTTTCCT
3700516 TTTT-C-
1 TTTTCCT
3700521 TTTT--T
1 TTTTCCT
*
3700526 TTTTCTTT
1 TTTTC-CT
3700534 TTTTCCCT
1 TTTT-CCT
*
3700542 TTTTCTT
1 TTTTCCT
3700549 TTTTCCT
1 TTTTCCT
3700556 T
1 T
3700557 CTTCTTTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
5 8 0.17
6 1 0.02
7 21 0.45
8 16 0.34
9 1 0.02
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTCCT
Found at i:3700564 original size:26 final size:26
Alignment explanation
Indices: 3700513--3700564 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3700503 TTTCCTTTTT
* *
3700513 CCTTTTTCTTTTTTTTTCTTTTTTTC
1 CCTTTTTCTTTTTTCTTCTTTCTTTC
3700539 CCTTTTTCTTTTTTCCTTC-TTCTTTC
1 CCTTTTTCTTTTTT-CTTCTTTCTTTC
3700565 TTTGCTGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (26 bp):
CCTTTTTCTTTTTTCTTCTTTCTTTC
Found at i:3700868 original size:2 final size:2
Alignment explanation
Indices: 3700861--3700922 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3700851 ACAACAAAGG
3700861 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
3700903 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3700923 TTAAAAGGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3703050 original size:12 final size:13
Alignment explanation
Indices: 3703026--3703054 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3703016 ATAAACGTAA
3703026 AAATGCAAAATGT
1 AAATGCAAAATGT
3703039 AAATGC-AAATGT
1 AAATGCAAAATGT
3703051 AAAT
1 AAAT
3703055 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:3703052 original size:27 final size:28
Alignment explanation
Indices: 3702998--3703053 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
3702988 GCAAAGATGC
*
3702998 AAATGCAAAAATGAAAATATAAACGTAA
1 AAATGCAAAAATGAAAATACAAACGTAA
* * *
3703026 AAATGC-AAAATGTAAATGCAAATGTAA
1 AAATGCAAAAATGAAAATACAAACGTAA
3703053 A
1 A
3703054 TATGTGAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (28 bp):
AAATGCAAAAATGAAAATACAAACGTAA
Found at i:3703125 original size:7 final size:7
Alignment explanation
Indices: 3703113--3703185 Score: 119
Period size: 7 Copynumber: 10.3 Consensus size: 7
3703103 ATAAAAGTAT
3703113 AAATGCA
1 AAATGCA
3703120 AAATGCA
1 AAATGCA
*
3703127 AAATGAA
1 AAATGCA
3703134 AAATGCA
1 AAATGCA
*
3703141 AGGATGCA
1 A-AATGCA
3703149 AAATGCA
1 AAATGCA
3703156 AAATGCA
1 AAATGCA
3703163 AAATGCA
1 AAATGCA
3703170 AAATGCA
1 AAATGCA
3703177 AAATGCA
1 AAATGCA
3703184 AA
1 AA
3703186 TGTATGTATG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
7 55 0.90
8 6 0.10
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:3704706 original size:16 final size:17
Alignment explanation
Indices: 3704677--3704711 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3704667 TTAATATCTG
3704677 AAAATAAAGTAAAAATAA
1 AAAATAAAG-AAAAATAA
3704695 AAAATAAA-AAAAATAA
1 AAAATAAAGAAAAATAA
3704711 A
1 A
3704712 GATAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAATAAAGAAAAATAA
Found at i:3706829 original size:3 final size:3
Alignment explanation
Indices: 3706823--3706879 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
3706813 ATTATTTATT
* *
3706823 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3706867 TAA TAA TAGA TAA
1 TAA TAA TA-A TAA
3706880 AACAAATGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 8 0.17
3 36 0.77
4 3 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3706845 original size:19 final size:19
Alignment explanation
Indices: 3706823--3706874 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
3706813 ATTATTTATT
* *
3706823 TAATAATAATAATATAATA
1 TAATAATAATAATAAAACA
*
3706842 TAATAATAATATTAAAACA
1 TAATAATAATAATAAAACA
*
3706861 AAATAATAATAATA
1 TAATAATAATAATA
3706875 GATAAAACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAATAATAATAAAACA
Found at i:3706848 original size:22 final size:21
Alignment explanation
Indices: 3706801--3706880 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 21
3706791 ATTGGGCCTG
* * *
3706801 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
3706823 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
* * *
3706845 TAATAATATTAAAACAAAATAA
1 TAATAATAAT-AAATAATATAA
3706867 TAATAATAGATAAA
1 TAATAATA-ATAAA
3706881 ACAAATGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 39 0.81
23 9 0.19
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:3706886 original size:22 final size:21
Alignment explanation
Indices: 3706823--3706886 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 21
3706813 ATTATTTATT
* *
3706823 TAATAATAATAATATAATATAA
1 TAATAATAATAAAACAA-ATAA
*
3706845 TAATAATATTAAAACAAAATAA
1 TAATAATAATAAAAC-AAATAA
3706867 TAATAATAGATAAAACAAAT
1 TAATAATA-ATAAAACAAAT
3706887 GAAATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 28 0.78
23 8 0.22
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (21 bp):
TAATAATAATAAAACAAATAA
Found at i:3707255 original size:13 final size:13
Alignment explanation
Indices: 3707237--3707294 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
3707227 ATATTCTTCA
3707237 TGCATATTGTTAT
1 TGCATATTGTTAT
* *
3707250 TACATATTGTTAC
1 TGCATATTGTTAT
* *
3707263 TGTATAATGTTAT
1 TGCATATTGTTAT
*
3707276 TGCATATTGTTAA
1 TGCATATTGTTAT
3707289 TGCATA
1 TGCATA
3707295 CAGTTGTTGG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (13 bp):
TGCATATTGTTAT
Found at i:3708684 original size:26 final size:26
Alignment explanation
Indices: 3708648--3708697 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3708638 ACATACATTC
3708648 CATCTTCAATTCCAACACAAGTCTTG
1 CATCTTCAATTCCAACACAAGTCTTG
* *
3708674 CATCTTCAATTCTAACACACGTCT
1 CATCTTCAATTCCAACACAAGTCT
3708698 ATTAACCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.32, G:0.06, T:0.32
Consensus pattern (26 bp):
CATCTTCAATTCCAACACAAGTCTTG
Found at i:3710734 original size:20 final size:20
Alignment explanation
Indices: 3710709--3710805 Score: 108
Period size: 20 Copynumber: 4.8 Consensus size: 20
3710699 TTCTAAACTT
*
3710709 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
3710729 AAAATCGCAACACGAAAAGG
1 AAAATCGCAACACGAAAATG
**
3710749 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
3710770 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
3710789 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
3710806 CCAAAATTGC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
19 19 0.29
20 31 0.48
21 15 0.23
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:3710811 original size:19 final size:19
Alignment explanation
Indices: 3710770--3710812 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3710760 GAGAGAAATG
**
3710770 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
3710789 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
3710808 AAAAT
1 AAAAT
3710813 TGCATTGCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:3710859 original size:20 final size:19
Alignment explanation
Indices: 3710817--3710871 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 19
3710807 CAAAATTGCA
3710817 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
3710836 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
3710856 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3710872 AACCAAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.11, C:0.22, G:0.16, T:0.51
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:3712142 original size:18 final size:18
Alignment explanation
Indices: 3712121--3712167 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
3712111 CCACTTCGAG
3712121 AGCCATCACCTCACCCAA
1 AGCCATCACCTCACCCAA
3712139 AGCCATCACCTCACCCAA
1 AGCCATCACCTCACCCAA
3712157 AGCCATCACCT
1 AGCCATCACCT
3712168 GATCGACCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.32, C:0.49, G:0.06, T:0.13
Consensus pattern (18 bp):
AGCCATCACCTCACCCAA
Found at i:3712766 original size:94 final size:93
Alignment explanation
Indices: 3712635--3712842 Score: 371
Period size: 94 Copynumber: 2.2 Consensus size: 93
3712625 GAAGTTAGTA
3712635 TTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA
1 TTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA
*
3712700 ACACTGTGAAGTTAGTATTTGTCTTTGT
66 ACACTATGAAGTTAGTATTTGTCTTTGT
* *
3712728 TTTGTCTTTTGGTTGAGAGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTGA-AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
*
3712793 AATACTATGAAGTTAGTATTTGTCTTTGT
65 AACACTATGAAGTTAGTATTTGTCTTTGT
3712822 TTTGTCTTTTGGTTGAAGTAA
1 TTTGTCTTTTGGTTGAAGTAA
3712843 TGCAATCCAT
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 21 0.19
94 89 0.81
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (93 bp):
TTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA
ACACTATGAAGTTAGTATTTGTCTTTGT
Found at i:3712960 original size:20 final size:19
Alignment explanation
Indices: 3712933--3712987 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 19
3712923 TCTTTTGGTT
3712933 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3712952 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
3712972 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3712988 AGACAAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:3713015 original size:20 final size:20
Alignment explanation
Indices: 3712992--3713029 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3712982 TCGCAAAGAC
3712992 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
3713012 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
3713030 TATAATCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.29, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:3713057 original size:19 final size:19
Alignment explanation
Indices: 3713035--3713161 Score: 111
Period size: 19 Copynumber: 6.8 Consensus size: 19
3713025 GAAACTATAA
*
3713035 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
3713054 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
3713068 TCTCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
3713087 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3713106 CTCTCGTTACGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
**
3713126 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
3713147 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
3713162 AAGTTCCAGA
Statistics
Matches: 84, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
14 9 0.11
16 2 0.02
17 2 0.02
19 40 0.48
20 17 0.20
21 14 0.17
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3713144 original size:39 final size:39
Alignment explanation
Indices: 3713064--3713144 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
3713054 TCGCATTGCG
* * **
3713064 ATTCTCTCGTTGCGATTTTTATTTCGCGTTGCGATTTTC
1 ATTCTCTCGTTACGATTTTCATTTCGCGTTGCGATAGTC
3713103 ATTCTCTCGTTACGATTTTCATTTCGCGTTGCGATAGTC
1 ATTCTCTCGTTACGATTTTCATTTCGCGTTGCGATAGTC
3713142 ATT
1 ATT
3713145 TTTCACGTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (39 bp):
ATTCTCTCGTTACGATTTTCATTTCGCGTTGCGATAGTC
Found at i:3713679 original size:21 final size:20
Alignment explanation
Indices: 3713620--3713680 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
3713610 CTCGGGAGTC
3713620 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
3713640 CCACTATCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
3713661 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
3713681 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.25, C:0.38, G:0.18, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:3715053 original size:14 final size:14
Alignment explanation
Indices: 3715034--3715067 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3715024 ATTGTTTAAT
3715034 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3715048 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3715062 TGATTT
1 TGATTT
3715068 TTTTAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3715199 original size:19 final size:19
Alignment explanation
Indices: 3715177--3715280 Score: 114
Period size: 19 Copynumber: 5.7 Consensus size: 19
3715167 AAAAATGACT
*
3715177 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
3715196 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
3715210 ATCGCAACCCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
3715229 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
3715248 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
3715267 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
3715281 CTAAATTCGC
Statistics
Matches: 76, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 59 0.78
20 1 0.01
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:3715261 original size:38 final size:38
Alignment explanation
Indices: 3715177--3715290 Score: 132
Period size: 38 Copynumber: 3.1 Consensus size: 38
3715167 AAAAATGACT
* * *
3715177 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAACTAAA
*
3715210 ATCGCAACCCGAAATGAAAATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAACTAAA
3715248 ATCGCAACGCGAAACT-AAAATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAA-TGAAAATCGCAACGCGAAACTAAA
*
3715286 TTCGC
1 ATCGC
3715291 GTTGCGATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
33 24 0.35
35 2 0.03
37 1 0.01
38 41 0.59
39 1 0.01
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.12
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAACTAAA
Found at i:3715297 original size:19 final size:19
Alignment explanation
Indices: 3715209--3715290 Score: 130
Period size: 19 Copynumber: 4.3 Consensus size: 19
3715199 GCAACGAGAG
*
3715209 AATCGCAACCCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
3715228 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
3715247 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
3715266 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
3715285 ATTCGC
1 AATCGC
3715291 GTTGCGATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 59 0.98
20 1 0.02
ACGTcount: A:0.45, C:0.27, G:0.16, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:3715308 original size:19 final size:19
Alignment explanation
Indices: 3715286--3715436 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
3715276 CGAAACTAAA
*
3715286 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
3715305 TTCGCTTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
3715321 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3715338 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
3715353 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3715371 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
* *
3715387 CTCG--TTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
**
3715404 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
*
3715423 TTCCGCGTTGCGAT
1 TT-CGCATTGCGAT
3715437 AGTCAAATGA
Statistics
Matches: 102, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 22 0.22
16 15 0.15
17 16 0.16
19 39 0.38
20 10 0.10
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:3715332 original size:33 final size:33
Alignment explanation
Indices: 3715290--3715416 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
3715280 ACTAAATTCG
* *
3715290 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
3715323 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
3715356 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
3715389 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3715417 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:3715361 original size:14 final size:14
Alignment explanation
Indices: 3715342--3715398 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3715332 TTTCATTTCG
3715342 CATTGCGATTCTCT
1 CATTGCGATTCTCT
*
3715356 CATTGCGATTTTCATTTCG
1 CATTGCGA--TTC---TCT
3715375 CATTGCGATTCTCT
1 CATTGCGATTCTCT
*
3715389 CGTTGCGATT
1 CATTGCGATT
3715399 TTTATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (14 bp):
CATTGCGATTCTCT
Found at i:3717945 original size:23 final size:24
Alignment explanation
Indices: 3717912--3717964 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
3717902 CTGAAAAATC
3717912 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3717936 -TCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3717959 ATCAAA
1 ATCAAA
3717965 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3718853 original size:20 final size:20
Alignment explanation
Indices: 3718830--3719097 Score: 131
Period size: 20 Copynumber: 13.2 Consensus size: 20
3718820 ATCTCGTTGT
3718830 GATTTACTAAATCGCAATGC
1 GATTTACTAAATCGCAATGC
3718850 GA-TTACGTAAATCG-AAGTGC
1 GATTTAC-TAAATCGCAA-TGC
* **
3718870 GAATTAGGAAAATCGCAATGC
1 GATTTA-CTAAATCGCAATGC
3718891 GA-TTACGTAAATCG-AAGTGC
1 GATTTAC-TAAATCGCAA-TGC
* **
3718911 GAATTAGGAAAATCGCAATGC
1 GATTTA-CTAAATCGCAATGC
3718932 GA-TTACGTAAATCGCAATGC
1 GATTTAC-TAAATCGCAATGC
* *
3718952 G-GTTACGTAAATCGCATTGC
1 GATTTAC-TAAATCGCAATGC
*
3718972 GATTTACGT-AATCGCATTGC
1 GATTTAC-TAAATCGCAATGC
* * * *
3718992 GATCTTCCTAATTCGTATTGC
1 GAT-TTACTAAATCGCAATGC
* *
3719013 GATTTA-TGTAATCGCATTGC
1 GATTTACT-AAATCGCAATGC
* *
3719033 GATTTACGT-ATTCGCATTGC
1 GATTTAC-TAAATCGCAATGC
* ** *
3719053 GAATTAGGAAAATCGCAACGC
1 GATTTA-CTAAATCGCAATGC
***
3719074 GAATTTGGGAAATCGCAATGC
1 G-ATTTACTAAATCGCAATGC
3719095 GAT
1 GAT
3719098 AGTCAGAATC
Statistics
Matches: 199, Mismatches: 28, Indels: 42
0.74 0.10 0.16
Matches are distributed among these distances:
19 9 0.05
20 111 0.56
21 71 0.36
22 8 0.04
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (20 bp):
GATTTACTAAATCGCAATGC
Found at i:3718884 original size:41 final size:41
Alignment explanation
Indices: 3718838--3718982 Score: 222
Period size: 41 Copynumber: 3.5 Consensus size: 41
3718828 GTGATTTACT
3718838 AAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGA
3718879 AAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGA
* * *
3718920 AAATCGCAATGCGATTACGTAAATCGCAA-TGCG-GTTACGT
1 AAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGA
*
3718960 AAATCGCATTGCGATTTACGTAA
1 AAATCGCAATGCGA-TTACGTAA
3718983 TCGCATTGCG
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
40 17 0.17
41 79 0.81
42 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (41 bp):
AAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGA
Found at i:3718902 original size:61 final size:59
Alignment explanation
Indices: 3718833--3719097 Score: 187
Period size: 61 Copynumber: 4.4 Consensus size: 59
3718823 TCGTTGTGAT
* *
3718833 TTAC-TAAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGAAAATCGCAATGCGA
1 TTACGTAAATCGCAATGCGATTACGT-AATCGAATTGCG-ATTACGAAAATCGCAATGCGA
* * * *
3718893 TTACGTAAATCG-AAGTGCGAATTAGGAAAATCGCAA-TGCGATTACGTAAATCGCAATGCGG
1 TTACGTAAATCGCAA-TGCG-ATTACG-TAATCG-AATTGCGATTACGAAAATCGCAATGCGA
* * * ** * * *
3718954 TTACGTAAATCGCATTGCGATTTACGTAATCGCATTGCGATCTTCCTAATTCGTATTGCGA
1 TTACGTAAATCGCAATGCGA-TTACGTAATCGAATTGCGAT-TACGAAAATCGCAATGCGA
* * * * * *
3719015 TTTATGT-AATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAATCGCAACGCGAA
1 -TTACGTAAATCGCAATGCGA-TTACGTAATCGAATTGCG-ATTACGAAAATCGCAATGCG-A
** *
3719077 TTTGGGAAATCGCAATGCGAT
1 TTACGTAAATCGCAATGCGAT
3719098 AGTCAGAATC
Statistics
Matches: 163, Mismatches: 29, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
59 1 0.01
60 18 0.11
61 107 0.66
62 35 0.21
63 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (59 bp):
TTACGTAAATCGCAATGCGATTACGTAATCGAATTGCGATTACGAAAATCGCAATGCGA
Found at i:3719067 original size:41 final size:41
Alignment explanation
Indices: 3718830--3719069 Score: 143
Period size: 41 Copynumber: 5.9 Consensus size: 41
3718820 ATCTCGTTGT
* * * *
3718830 GATTTAC-TAAATCGCAATGCG-ATTACGTAAATCGAAGTGC
1 GATTTACGTAATTCGCATTGCGAATTACG-AAATCGCATTGC
* * * * * * *
3718870 GAATTAGGAAAATCGCAATGCG-ATTACGTAAATCGAAGTGC
1 GATTTACGTAATTCGCATTGCGAATTACG-AAATCGCATTGC
* * * * * *
3718911 GAATTAGGAAAATCGCAATGCG-ATTACGTAAATCGCAATGC
1 GATTTACGTAATTCGCATTGCGAATTACG-AAATCGCATTGC
* * * *
3718952 G-GTTACGTAAATCGCATTGCGATTTACGTAATCGCATTGC
1 GATTTACGTAATTCGCATTGCGAATTACGAAATCGCATTGC
* * * * *
3718992 GATCTT-CCTAATTCGTATTGCGATTTATGTAATCGCATTGC
1 GAT-TTACGTAATTCGCATTGCGAATTACGAAATCGCATTGC
*
3719033 GATTTACGT-ATTCGCATTGCGAATTAGGAAAATCGCA
1 GATTTACGTAATTCGCATTGCGAATTACG-AAATCGCA
3719070 ACGCGAATTT
Statistics
Matches: 172, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
40 50 0.29
41 120 0.70
42 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (41 bp):
GATTTACGTAATTCGCATTGCGAATTACGAAATCGCATTGC
Done.