Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 19 of 77
Found at i:3463713 original size:29 final size:29
Alignment explanation
Indices: 3463672--3463736 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
3463662 AGTAAATTAT
* *
3463672 TTTTAAATCATTTAATTTTGATAT-TTTAA
1 TTTTAAATAATTTAATTAT-ATATATTTAA
* *
3463701 TTTTATATAATTTAATTATATTTATTTAA
1 TTTTAAATAATTTAATTATATATATTTAA
3463730 TTTTAAA
1 TTTTAAA
3463737 AGTAAACGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTTAAATAATTTAATTATATATATTTAA
Found at i:3463716 original size:15 final size:14
Alignment explanation
Indices: 3463681--3463734 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
3463671 TTTTTAAATC
3463681 ATTTAATTTTGATAT
1 ATTTAATTTT-ATAT
3463696 -TTTAATTTTATAT
1 ATTTAATTTTATAT
* *
3463709 AATTTAATTATATTT
1 -ATTTAATTTTATAT
3463724 ATTTAATTTTA
1 ATTTAATTTTA
3463735 AAAGTAAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 4 0.12
14 19 0.56
15 11 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
ATTTAATTTTATAT
Found at i:3463862 original size:16 final size:15
Alignment explanation
Indices: 3463832--3463870 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
3463822 TACATACTCA
*
3463832 AAATTATTCAAATTT
1 AAATTAATCAAATTT
3463847 AAATTAATCTAAATTT
1 AAATTAATC-AAATTT
3463863 AAATTAAT
1 AAATTAAT
3463871 TTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTAATCAAATTT
Found at i:3473969 original size:13 final size:14
Alignment explanation
Indices: 3473937--3473971 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
3473927 AATGATAACT
3473937 CAAAAATGTTTTAA
1 CAAAAATGTTTTAA
3473951 CAAAAATGTTTTAA
1 CAAAAATGTTTTAA
3473965 CAAAAAT
1 CAAAAAT
3473972 ATGGTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (14 bp):
CAAAAATGTTTTAA
Found at i:3473970 original size:15 final size:15
Alignment explanation
Indices: 3473938--3473985 Score: 62
Period size: 14 Copynumber: 3.1 Consensus size: 15
3473928 ATGATAACTC
3473938 AAAAATGTTTTAAC-
1 AAAAATGTTTTAACA
3473952 AAAAATGTTTTAACA
1 AAAAATGTTTTAACA
3473967 AAAATATGGTTTTTAACA
1 AAAA-AT-G-TTTTAACA
3473985 A
1 A
3473986 TAGCTTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.47
15 4 0.13
16 2 0.07
17 1 0.03
18 9 0.30
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.35
Consensus pattern (15 bp):
AAAAATGTTTTAACA
Found at i:3474744 original size:16 final size:17
Alignment explanation
Indices: 3474715--3474747 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3474705 ATATATATAA
3474715 TTAAATTTATTATTTAT
1 TTAAATTTATTATTTAT
*
3474732 TTAATTTTA-TATTTAT
1 TTAAATTTATTATTTAT
3474748 ATATATGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTAAATTTATTATTTAT
Found at i:3482515 original size:12 final size:11
Alignment explanation
Indices: 3482496--3482546 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
3482486 TTTTGCAAAA
3482496 GTTTTTTTTTT
1 GTTTTTTTTTT
* * *
3482507 CTTTGTTTTGT
1 GTTTTTTTTTT
3482518 -TTTTTTTTTT
1 GTTTTTTTTTT
*
3482528 GTTTTGTTTTT
1 GTTTTTTTTTT
3482539 GTATTTTT
1 GT-TTTTT
3482547 CTCTTATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
10 8 0.26
11 19 0.61
12 4 0.13
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:3482520 original size:17 final size:17
Alignment explanation
Indices: 3482500--3482538 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3482490 GCAAAAGTTT
3482500 TTTTTTTCTTTGTTTTG
1 TTTTTTTCTTTGTTTTG
*
3482517 TTTTTTTTTTTGTTTTG
1 TTTTTTTCTTTGTTTTG
3482534 TTTTT
1 TTTTT
3482539 GTATTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (17 bp):
TTTTTTTCTTTGTTTTG
Found at i:3482847 original size:50 final size:49
Alignment explanation
Indices: 3482764--3482969 Score: 178
Period size: 50 Copynumber: 4.3 Consensus size: 49
3482754 AAAGGCCTTA
* *
3482764 AAACTTT-AAAA--TTTTGGAAAATGACTTCC-CATAAATAAAAGCTTTG
1 AAACTTTAAAAATCTTTTTGAAAATGGC-TCCTCATAAATAAAAGCTTTG
* * * *
3482810 AAATTTTAAAAATCTTATTTGAAAATAGCTCCTCATAAATAAAGGTTTTG
1 AAACTTTAAAAATCTT-TTTGAAAATGGCTCCTCATAAATAAAAGCTTTG
*
3482860 AAACTTTAAAAATC---TTGAGAAATGGCTCCACATAAATAGAGAA--TTTG
1 AAACTTTAAAAATCTTTTTGA-AAATGGCTCCTCATAAATA-A-AAGCTTTG
* * * * *
3482907 GAACTTTAAAGATCTTGTTTGAAAATGGCTCTTCATAAATAGAGGCTTTG
1 AAACTTTAAAAATCTT-TTTGAAAATGGCTCCTCATAAATAAAAGCTTTG
*
3482957 AAACTTTACAAAT
1 AAACTTTAAAAAT
3482970 TTAAAATATT
Statistics
Matches: 127, Mismatches: 19, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
46 10 0.08
47 37 0.29
48 2 0.02
49 6 0.05
50 68 0.54
51 4 0.03
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (49 bp):
AAACTTTAAAAATCTTTTTGAAAATGGCTCCTCATAAATAAAAGCTTTG
Found at i:3482895 original size:97 final size:97
Alignment explanation
Indices: 3482733--3482969 Score: 263
Period size: 97 Copynumber: 2.5 Consensus size: 97
3482723 TTTTTTAAAT
* * * *
3482733 TTTGAAAA-AGCTCTTC-TAAACAAAGGCCTTAAAACTTT-AAAATTTTGGAAAATGACTTCCCA
1 TTTGAAAATAGCTCTTCATAAATAAAGGCTTTGAAACTTTAAAAATCTTGGAAAATGACTTCCCA
*
3482795 TAAATA-A-AAGCTTTGAAATTTTAAAAATCTTA
66 TAAATAGAGAA--TTTGAAACTTTAAAAATCTTA
* * *
3482827 TTTGAAAATAGCTCCTCATAAATAAAGGTTTTGAAACTTTAAAAATCTT-GAGAAATGGC-TCCA
1 TTTGAAAATAGCTCTTCATAAATAAAGGCTTTGAAACTTTAAAAATCTTGGA-AAATGACTTCC-
* * *
3482890 CATAAATAGAGAATTTGGAACTTTAAAGATCTTG
64 CATAAATAGAGAATTTGAAACTTTAAAAATCTTA
* * *
3482924 TTTGAAAATGGCTCTTCATAAATAGAGGCTTTGAAACTTTACAAAT
1 TTTGAAAATAGCTCTTCATAAATAAAGGCTTTGAAACTTTAAAAAT
3482970 TTAAAATATT
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
94 8 0.07
95 7 0.06
96 23 0.19
97 79 0.66
98 1 0.01
99 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (97 bp):
TTTGAAAATAGCTCTTCATAAATAAAGGCTTTGAAACTTTAAAAATCTTGGAAAATGACTTCCCA
TAAATAGAGAATTTGAAACTTTAAAAATCTTA
Found at i:3482912 original size:47 final size:47
Alignment explanation
Indices: 3482828--3482969 Score: 151
Period size: 47 Copynumber: 3.0 Consensus size: 47
3482818 AAAATCTTAT
* * *
3482828 TTGA-AAATAGCTCCTCATAAATAAAGGTTTTGAAACTTTAAAAATC
1 TTGAGAAATGGCTCCTCATAAATAGAGGATTTGAAACTTTAAAAATC
* * * *
3482874 TTGAGAAATGGCTCCACATAAATAGAGAATTTGGAACTTTAAAGATC
1 TTGAGAAATGGCTCCTCATAAATAGAGGATTTGAAACTTTAAAAATC
* * * *
3482921 TTGTTTGAAAATGGCTCTTCATAAATAGAGGCTTTGAAACTTTACAAAT
1 TTG--AG-AAATGGCTCCTCATAAATAGAGGATTTGAAACTTTAAAAAT
3482970 TTAAAATATT
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
46 4 0.05
47 38 0.49
49 1 0.01
50 34 0.44
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (47 bp):
TTGAGAAATGGCTCCTCATAAATAGAGGATTTGAAACTTTAAAAATC
Found at i:3483146 original size:40 final size:39
Alignment explanation
Indices: 3483011--3483158 Score: 152
Period size: 40 Copynumber: 3.6 Consensus size: 39
3483001 ATTTCGAATC
*
3483011 TTTGCTCAAAAGTCTTTGGGAAATCATTTAAAAATTTAAAGT
1 TTTG-TCAAAAGTCTTT--GAAATCATTTAAAAATTTAAAAT
* *
3483053 TTTGCCTAAAAGTCTTTGAAATCGTTTAAAAATTTAAAAT
1 TTTGTC-AAAAGTCTTTGAAATCATTTAAAAATTTAAAAT
** * *
3483093 TTTGTTCGGAGGTCTTTGAAATCATTTAAAAATCTAAAAT
1 TTTG-TCAAAAGTCTTTGAAATCATTTAAAAATTTAAAAT
* * *
3483133 TTCGATCAAAGGTCTTTGAGATCATT
1 TTTG-TCAAAAGTCTTTGAAATCATT
3483159 CGAAGATTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 74 0.82
41 2 0.02
42 14 0.16
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (39 bp):
TTTGTCAAAAGTCTTTGAAATCATTTAAAAATTTAAAAT
Found at i:3483655 original size:23 final size:23
Alignment explanation
Indices: 3483625--3483671 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3483615 CTTAAAATCT
* *
3483625 AGGTGCCAGCTAATTTGGGCTTA
1 AGGTGCCAACTAATCTGGGCTTA
*
3483648 AGGTGCCAACTAATCTGGGTTTA
1 AGGTGCCAACTAATCTGGGCTTA
3483671 A
1 A
3483672 AATCTAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (23 bp):
AGGTGCCAACTAATCTGGGCTTA
Found at i:3483937 original size:11 final size:11
Alignment explanation
Indices: 3483923--3483961 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3483913 TCTTTCCTTC
3483923 TTTTTGCTTTT
1 TTTTTGCTTTT
*
3483934 TTTTTTCTTTT
1 TTTTTGCTTTT
**
3483945 TTTTTTTTTTT
1 TTTTTGCTTTT
3483956 TTTTTG
1 TTTTTG
3483962 AACTTTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.90
Consensus pattern (11 bp):
TTTTTGCTTTT
Found at i:3483943 original size:18 final size:17
Alignment explanation
Indices: 3483920--3483961 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
3483910 TCTTCTTTCC
3483920 TTCTTTTTGCTTTTTTTT
1 TTCTTTTTG-TTTTTTTT
3483938 TTCTTTTT-TTTTTTTT
1 TTCTTTTTGTTTTTTTT
3483954 TT-TTTTTG
1 TTCTTTTTG
3483962 AACTTTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
18 8 0.35
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (17 bp):
TTCTTTTTGTTTTTTTT
Found at i:3483978 original size:1 final size:1
Alignment explanation
Indices: 3483930--3483960 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
3483920 TTCTTTTTGC
*
3483930 TTTTTTTTTTCTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3483961 GAACTTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:3489415 original size:3 final size:3
Alignment explanation
Indices: 3489400--3489430 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3489390 TTTTGTCTTC
*
3489400 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3489431 AACAAGACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3491194 original size:62 final size:62
Alignment explanation
Indices: 3491073--3491194 Score: 138
Period size: 62 Copynumber: 1.9 Consensus size: 62
3491063 ACATACTATT
* * *
3491073 GGAATTGGAGATAAAAGACAAATATACAATTAGTCTATAGAAATTGATCACTGCTATTCTCTAA
1 GGAATTGGAGAT--AAGACAAATATACAATTAGTCTATAGAAATTAAGCACTGCCATTCTCTAA
* * * * *
3491137 GGAATTGGAGAT-AGACGAAATATACAATTATTTTATGGAATTTAAGCATTGCCATTCT
1 GGAATTGGAGATAAGAC-AAATATACAATTAGTCTATAGAAATTAAGCACTGCCATTCT
3491195 TTTAGTTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
61 4 0.08
62 33 0.67
64 12 0.24
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.32
Consensus pattern (62 bp):
GGAATTGGAGATAAGACAAATATACAATTAGTCTATAGAAATTAAGCACTGCCATTCTCTAA
Found at i:3500672 original size:29 final size:29
Alignment explanation
Indices: 3500636--3500695 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
3500626 AAAAGATTGT
3500636 TTTTGATAAAAATGAATGGCATACAAATA
1 TTTTGATAAAAATGAATGGCATACAAATA
3500665 TTTTGATAAAAATGAATGGCATACAAATA
1 TTTTGATAAAAATGAATGGCATACAAATA
3500694 TT
1 TT
3500696 CAAAACTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (29 bp):
TTTTGATAAAAATGAATGGCATACAAATA
Found at i:3501204 original size:22 final size:21
Alignment explanation
Indices: 3501165--3501224 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
3501155 AATTGTCTAA
* * *
3501165 TAAATGTACTTATGGTTATAAG
1 TAAATATACATATAGTTAT-AG
*
3501187 TAAATTTACATATAGTTATAG
1 TAAATATACATATAGTTATAG
3501208 TAATATATACATATAGT
1 TAA-ATATACATATAGT
3501225 CGTAGTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (21 bp):
TAAATATACATATAGTTATAG
Found at i:3501230 original size:22 final size:21
Alignment explanation
Indices: 3501185--3501230 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3501175 TATGGTTATA
* *
3501185 AGTAAATTTACATATAGTTAT
1 AGTAAATATACATATAGTCAT
*
3501206 AGTAATATATACATATAGTCGT
1 AGTAA-ATATACATATAGTCAT
3501228 AGT
1 AGT
3501231 TTCATGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (21 bp):
AGTAAATATACATATAGTCAT
Found at i:3503846 original size:33 final size:35
Alignment explanation
Indices: 3503804--3503871 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
3503794 TTATTTGATA
3503804 TAATAAATAAA-ATT-TATTATATAATGAATTAAT
1 TAATAAATAAATATTATATTATATAATGAATTAAT
*
3503837 TAATAAATAAATATTAGTATTATATTATGAATTAA
1 TAATAAATAAATATTA-TATTATATAATGAATTAA
3503872 AAATATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 11 0.35
34 3 0.10
36 17 0.55
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (35 bp):
TAATAAATAAATATTATATTATATAATGAATTAAT
Found at i:3503935 original size:19 final size:20
Alignment explanation
Indices: 3503897--3503935 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3503887 ATAAATTTTA
3503897 TTATTATATCATAATATATT
1 TTATTATATCATAATATATT
* *
3503917 TTATT-TATTATATTATATT
1 TTATTATATCATAATATATT
3503936 AATGAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTATATCATAATATATT
Found at i:3513792 original size:30 final size:30
Alignment explanation
Indices: 3513695--3513823 Score: 104
Period size: 30 Copynumber: 4.3 Consensus size: 30
3513685 AGAGCCAAAG
* * *
3513695 CAGTAGCCACACCACCTAGAGTGATCATAG
1 CAGTAGCCACACCACCTAAAGTGACCATAA
*
3513725 CAGTAGCCACACCACCTACAA-TGACTA-AA
1 CAGTAGCCACACCACCTA-AAGTGACCATAA
* * *
3513754 GCAATAGTCACACTACCTAAAGTGACCATAA
1 -CAGTAGCCACACCACCTAAAGTGACCATAA
* *
3513785 CAGTAGTCA-AGCCATCTATAA-TGACCATAA
1 CAGTAGCCACA-CCACCTA-AAGTGACCATAA
*
3513815 CAATAGCCA
1 CAGTAGCCA
3513824 AGCCACCCAC
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
29 4 0.05
30 71 0.89
31 5 0.06
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.18
Consensus pattern (30 bp):
CAGTAGCCACACCACCTAAAGTGACCATAA
Found at i:3513819 original size:60 final size:60
Alignment explanation
Indices: 3513689--3513820 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
3513679 ATAACCAGAG
* * * * *
3513689 CCAAAGCAGTAGCCACACCACCTAGAGTGATCATAGCAGTAGCCACACCACCTACAATGA
1 CCAAAGCAATAGTCACACCACCTAAAGTGACCATAACAGTAGCCACACCACCTACAATGA
* * * * *
3513749 CTAAAGCAATAGTCACACTACCTAAAGTGACCATAACAGTAGTCA-AGCCATCTATAATGA
1 CCAAAGCAATAGTCACACCACCTAAAGTGACCATAACAGTAGCCACA-CCACCTACAATGA
3513809 CCATAA-CAATAG
1 CCA-AAGCAATAG
3513821 CCAAGCCACC
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 1 0.02
60 56 0.95
61 2 0.03
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.17
Consensus pattern (60 bp):
CCAAAGCAATAGTCACACCACCTAAAGTGACCATAACAGTAGCCACACCACCTACAATGA
Found at i:3513838 original size:30 final size:30
Alignment explanation
Indices: 3513776--3513841 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
3513766 CTACCTAAAG
* * * * *
3513776 TGACCATAACAGTAGTCAAGCCATCTATAA
1 TGACCATAACAATAGCCAAGCCACCCACAA
3513806 TGACCATAACAATAGCCAAGCCACCCACAA
1 TGACCATAACAATAGCCAAGCCACCCACAA
3513836 TGACCA
1 TGACCA
3513842 CTATAGTTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.30, G:0.12, T:0.17
Consensus pattern (30 bp):
TGACCATAACAATAGCCAAGCCACCCACAA
Found at i:3513921 original size:27 final size:27
Alignment explanation
Indices: 3513870--3513922 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3513860 CCATACGCTC
* *
3513870 TACAACACCCATAATATCCACATAAAG
1 TACAACACCCACAATATCAACATAAAG
* *
3513897 TACAACACCCACACTATCAAGATAAA
1 TACAACACCCACAATATCAACATAAA
3513923 CTATAGCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.49, C:0.30, G:0.04, T:0.17
Consensus pattern (27 bp):
TACAACACCCACAATATCAACATAAAG
Found at i:3522433 original size:21 final size:21
Alignment explanation
Indices: 3522394--3522433 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3522384 TTTATTTTAT
*
3522394 TAAAAAAACTAAATAAAAAGC
1 TAAAAAAACTAAAAAAAAAGC
3522415 TAAAAAAA-TAAAAATAAAA
1 TAAAAAAACTAAAAA-AAAA
3522434 TTAAGACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (21 bp):
TAAAAAAACTAAAAAAAAAGC
Found at i:3522472 original size:13 final size:13
Alignment explanation
Indices: 3522450--3522487 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3522440 CAACAAAATG
3522450 AATAAAATCAAAA
1 AATAAAATCAAAA
*
3522463 AATCAAATCAAAA
1 AATAAAATCAAAA
3522476 AATAAAAT-AAAA
1 AATAAAATCAAAA
3522488 TGAAAATGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
AATAAAATCAAAA
Found at i:3523364 original size:3 final size:3
Alignment explanation
Indices: 3523344--3523450 Score: 112
Period size: 3 Copynumber: 36.7 Consensus size: 3
3523334 GGAAAAAGAA
* * * *
3523344 AAT AAA AAT AAA AAT AAT AAT AAT GAT AAT AAT AAT AA- CAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * *
3523391 ACT AAT ACG AAT AAT AAT ACT -AT AAT GAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3523437 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
3523451 CAGTATACCA
Statistics
Matches: 83, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
2 4 0.05
3 79 0.95
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3523390 original size:23 final size:23
Alignment explanation
Indices: 3523360--3523452 Score: 88
Period size: 23 Copynumber: 4.0 Consensus size: 23
3523350 AATAAAAATA
3523360 ATAATAATGATAATAATAATAAC
1 ATAATAATGATAATAATAATAAC
*
3523383 ATAATAAT-ACTAATACGAATAATAAT
1 ATAATAATGA-TAAT---AATAATAAC
3523409 ACT-ATAATGATAATAATAAT-A-
1 A-TAATAATGATAATAATAATAAC
*
3523430 ATAA-AATAATAATAATAATAAC
1 ATAATAATGATAATAATAATAAC
3523452 A
1 A
3523453 GTATACCATT
Statistics
Matches: 59, Mismatches: 2, Indels: 19
0.74 0.03 0.24
Matches are distributed among these distances:
20 15 0.25
21 3 0.05
22 3 0.05
23 18 0.31
26 18 0.31
27 2 0.03
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.30
Consensus pattern (23 bp):
ATAATAATGATAATAATAATAAC
Found at i:3523403 original size:26 final size:25
Alignment explanation
Indices: 3523354--3523450 Score: 88
Period size: 26 Copynumber: 3.7 Consensus size: 25
3523344 AATAAAAATA
* *
3523354 AAAATAATAATAATGATAATAATAAT
1 AAAATAATAAT-ATAATAAGAATAAT
* *
3523380 AACATAATAATACTAATACGAATAAT
1 AAAATAATAATA-TAATAAGAATAAT
* *
3523406 AATACT-ATAATGATAATAATAATAAT
1 AA-AATAATAAT-ATAATAAGAATAAT
3523432 AAAATAATAATAATAATAA
1 AAAATAATAAT-ATAATAA
3523451 CAGTATACCA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
25 3 0.05
26 52 0.91
27 2 0.04
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (25 bp):
AAAATAATAATATAATAAGAATAAT
Found at i:3524019 original size:115 final size:117
Alignment explanation
Indices: 3523737--3524045 Score: 313
Period size: 115 Copynumber: 2.6 Consensus size: 117
3523727 AGTCAAAAGG
* * * ** * * *
3523737 TGATCTAGACTGAGCCAAGATCAAGTGA-CTGGGATGAAACCACGAGTCAAAATGAAGTGACCAA
1 TGATCTAGACTGAACTAAGATCAAATGATC-AAGACGAAACCATGAGTCAAAATGAGGTGACCAA
* * * **
3523801 AATCGAGTCAAGGTAAAAAATAAATGACCAGGACAAAACCATGAATCATATAAGG
65 GATCGAGTCAAGGT--AAAATAAATGACCAGGACAAAACCACGAATCATAAAAAA
* * * * *
3523856 TGATTTAGACTGAACTAAGATCAGATGATCAAGATGAAACCATTAGTCAAAATGAGGCGACCAAG
1 TGATCTAGACTGAACTAAGATCAAATGATCAAGACGAAACCATGAGTCAAAATGAGGTGACCAAG
* *
3523921 ATCGAGTCAAGGT-AAA-AAATGA-CTGGCACAAAATCACGAATCATAAAAAA
66 ATCGAGTCAAGGTAAAATAAATGACCAGG-ACAAAACCACGAATCATAAAAAA
* * * **
3523971 TGATCTGGATTGAGCTAAGATCAAATGATCGAA-ACGAAATTATGAGTCAAAATGAGGTGACCAA
1 TGATCTAGACTGAACTAAGATCAAATGATC-AAGACGAAACCATGAGTCAAAATGAGGTGACCAA
3524035 GATCGAGTCAA
65 GATCGAGTCAA
3524046 TGCCAAAAAT
Statistics
Matches: 159, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
114 3 0.02
115 86 0.54
116 5 0.03
119 64 0.40
120 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (117 bp):
TGATCTAGACTGAACTAAGATCAAATGATCAAGACGAAACCATGAGTCAAAATGAGGTGACCAAG
ATCGAGTCAAGGTAAAATAAATGACCAGGACAAAACCACGAATCATAAAAAA
Found at i:3524883 original size:44 final size:45
Alignment explanation
Indices: 3524786--3524923 Score: 136
Period size: 48 Copynumber: 3.0 Consensus size: 45
3524776 GCCCAAACTA
* * * **
3524786 CCCTTTTGAATTTTCAACTTGAATTTTCTTTTTTTTGGGTTCAAGTTG
1 CCCTTTTGGATTTTCAACTTGAA-TCT-TTTTTTTTAGG-TCAAGCCG
3524834 CCCTTTTGGATTTTCAACTTGAA-CTTTTTTTTTAGGTCAAGCCG
1 CCCTTTTGGATTTTCAACTTGAATCTTTTTTTTTAGGTCAAGCCG
* *
3524878 TCCTTTCAGG-TTTTCAACTTGAACTGTCTTTTTTTTTAGGTCAAGC
1 CCCTTT-TGGATTTTCAACTTGAA---TCTTTTTTTTTAGGTCAAGC
3524924 AAAGTACTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
44 24 0.31
45 12 0.15
46 1 0.01
48 41 0.53
ACGTcount: A:0.17, C:0.18, G:0.15, T:0.49
Consensus pattern (45 bp):
CCCTTTTGGATTTTCAACTTGAATCTTTTTTTTTAGGTCAAGCCG
Found at i:3535557 original size:13 final size:13
Alignment explanation
Indices: 3535529--3535567 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
3535519 CAACAAAATG
3535529 AATAAAATCAAAAA
1 AATAAAATC-AAAA
*
3535543 AATCAAATCAAAA
1 AATAAAATCAAAA
3535556 AATAAAAT-AAAA
1 AATAAAATCAAAA
3535568 TAAAAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAAATCAAAA
Found at i:3536444 original size:3 final size:3
Alignment explanation
Indices: 3536436--3536474 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
3536426 AAATATAAAC
*
3536436 AAT AAT AAT -AT AAT AA- AAT AAT AAT AAT AAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3536475 GCCGAACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3538290 original size:14 final size:14
Alignment explanation
Indices: 3538273--3538316 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3538263 AAAAAAAGGA
3538273 AAAAAGAAAAATTG
1 AAAAAGAAAAATTG
*
3538287 AAAAAGTAAAATT-
1 AAAAAGAAAAATTG
3538300 AAAAA-AAAAA-TG
1 AAAAAGAAAAATTG
3538312 AAAAA
1 AAAAA
3538317 AATGTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 9 0.33
13 5 0.19
14 12 0.44
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (14 bp):
AAAAAGAAAAATTG
Found at i:3538317 original size:14 final size:13
Alignment explanation
Indices: 3538262--3538318 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
3538252 ATTAAAAACT
*
3538262 AAAAAAAAGGAAA
1 AAAAAAAATGAAA
3538275 AAAGAAAAATTGAAA
1 AAA-AAAAA-TGAAA
** *
3538290 AAGTAAAAT-TAA
1 AAAAAAAATGAAA
3538302 AAAAAAAATGAAA
1 AAAAAAAATGAAA
3538315 AAAA
1 AAAA
3538319 TGTTCATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
12 9 0.26
13 10 0.29
14 9 0.26
15 6 0.18
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (13 bp):
AAAAAAAATGAAA
Found at i:3538532 original size:26 final size:25
Alignment explanation
Indices: 3538477--3538535 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
3538467 TTAATTTTTA
3538477 AAATTAA-AGTATTAAATAATAATT
1 AAATTAATAGTATTAAATAATAATT
**
3538501 TTATTAATA-TATATAAATATATAATT
1 AAATTAATAGTAT-TAAATA-ATAATT
3538527 AAATTAATA
1 AAATTAATA
3538536 ATAAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 8 0.29
25 7 0.25
26 13 0.46
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATTAATAGTATTAAATAATAATT
Found at i:3538544 original size:26 final size:26
Alignment explanation
Indices: 3538490--3538546 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
3538480 TTAAAGTATT
** *
3538490 AAATA-ATAATTTTATTAATATATAT
1 AAATATATAATTAAATTAATATATAA
3538515 AAATATATAATTAAATTAATA-ATAA
1 AAATATATAATTAAATTAATATATAA
3538540 AAA-ATAT
1 AAATATAT
3538547 TATATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 11 0.39
26 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATATATAATTAAATTAATATATAA
Found at i:3539339 original size:17 final size:17
Alignment explanation
Indices: 3539298--3539339 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
3539288 GCTCATTTTG
*
3539298 TTTTAAAATTTATTTAA
1 TTTTAAAATTTATCTAA
**
3539315 TTAAAAAATTTATCTAA
1 TTTTAAAATTTATCTAA
3539332 TTTTAAAA
1 TTTTAAAA
3539340 AAATTAAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAAATTTATCTAA
Found at i:3539991 original size:18 final size:17
Alignment explanation
Indices: 3539970--3540008 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
3539960 AAAAAATGAA
*
3539970 AAAAGAAAAGTAAAAAGT
1 AAAAGAAAAATAAAAA-T
3539988 AAAAGAAAAATAAAAAT
1 AAAAGAAAAATAAAAAT
3540005 AAAA
1 AAAA
3540009 AAGAGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAGAAAAATAAAAAT
Found at i:3540296 original size:14 final size:15
Alignment explanation
Indices: 3540277--3540332 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 15
3540267 CTGAAATTAA
3540277 TAAAATAT-TATTTT
1 TAAAATATATATTTT
* *
3540291 TAAAATATAAATATT
1 TAAAATATATATTTT
* *
3540306 T-AAATATATAATTA
1 TAAAATATATATTTT
3540320 TATAAATATATAT
1 TA-AAATATATAT
3540333 AAATAAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
14 18 0.56
15 5 0.16
16 9 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAAATATATATTTT
Found at i:3540311 original size:8 final size:8
Alignment explanation
Indices: 3540291--3540331 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3540281 ATATTATTTT
3540291 TAAA-ATA
1 TAAATATA
*
3540298 TAAATATT
1 TAAATATA
3540306 TAAATATA
1 TAAATATA
*
3540314 TAATTATA
1 TAAATATA
3540322 TAAATATA
1 TAAATATA
3540330 TA
1 TA
3540332 TAAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAATATA
Found at i:3540337 original size:26 final size:24
Alignment explanation
Indices: 3540295--3540346 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
3540285 TATTTTTAAA
* *
3540295 ATATAAATATTTAAATATATAATT
1 ATATAAATATTTAAATAAAAAATT
3540319 ATATAAATATATATAAATAAAAAATT
1 ATATAAATAT-T-TAAATAAAAAATT
3540345 AT
1 AT
3540347 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
25 1 0.04
26 13 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATAAATATTTAAATAAAAAATT
Found at i:3540894 original size:16 final size:15
Alignment explanation
Indices: 3540873--3540905 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
3540863 TTAATGCTAT
3540873 AATTATATAAATATAC
1 AATTATATAAATA-AC
3540889 AATTATATAAATAAC
1 AATTATATAAATAAC
3540904 AA
1 AA
3540906 AAAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTATATAAATAAC
Found at i:3541705 original size:18 final size:18
Alignment explanation
Indices: 3541677--3541722 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3541667 TTTTTAATAA
* *
3541677 AAAACAAAAAAGGAATGAC
1 AAAA-AAAAAAGAAAAGAC
*
3541696 AAAAAAAAAAGAAAAGAT
1 AAAAAAAAAAGAAAAGAC
3541714 AAAAAAAAA
1 AAAAAAAAA
3541723 TCAAATGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.04
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAGAC
Found at i:3543714 original size:2 final size:2
Alignment explanation
Indices: 3543707--3543738 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3543697 ATCAATAGTT
3543707 TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3543739 TTAAGCTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3544688 original size:21 final size:22
Alignment explanation
Indices: 3544639--3544682 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3544629 TCATCAAATT
3544639 TTAATTTTTATATTATTTTAAA
1 TTAATTTTTATATTATTTTAAA
3544661 TTAATTTTTA-A-TATATTTAAA
1 TTAATTTTTATATTAT-TTTAAA
3544682 T
1 T
3544683 AGATTTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAATTTTTATATTATTTTAAA
Found at i:3548100 original size:22 final size:22
Alignment explanation
Indices: 3548059--3548101 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3548049 TAGTATTATT
* *
3548059 ATAAATGAACAGCAATCGAACA
1 ATAAATGAACAACAAACGAACA
*
3548081 ATAAATGAACAATAAACGAAC
1 ATAAATGAACAACAAACGAAC
3548102 GAGTTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.16, G:0.12, T:0.14
Consensus pattern (22 bp):
ATAAATGAACAACAAACGAACA
Found at i:3554948 original size:22 final size:22
Alignment explanation
Indices: 3554908--3554949 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3554898 TGTATATTTA
* *
3554908 TATTTGTATATCTAGAATTAAG
1 TATTTGTATACCTAAAATTAAG
*
3554930 TATTTGTATCCCTAAAATTA
1 TATTTGTATACCTAAAATTA
3554950 GGATAGACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATACCTAAAATTAAG
Found at i:3558889 original size:22 final size:22
Alignment explanation
Indices: 3558863--3558904 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3558853 TGTATATTTA
* *
3558863 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
3558885 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
3558905 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:3559145 original size:3 final size:3
Alignment explanation
Indices: 3559137--3559181 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3559127 GCAAGGGCTA
3559137 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3559182 GAACCGATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3568339 original size:16 final size:15
Alignment explanation
Indices: 3568318--3568350 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
3568308 GCAAAAAAAG
3568318 AAGATAAAAAAGATAA
1 AAGATAAAAAA-ATAA
3568334 AAGATAAAAAAATAA
1 AAGATAAAAAAATAA
3568349 AA
1 AA
3568351 TAAAAGCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAGATAAAAAAATAA
Found at i:3571231 original size:20 final size:18
Alignment explanation
Indices: 3571206--3571259 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
3571196 TTCAGTTTCA
3571206 TTCAAGTTAATTTAAATT
1 TTCAAGTTAATTTAAATT
*
3571224 TATGCAAGTTTAATTTTAAGTT
1 T-T-CAAG-TTAA-TTTAAATT
3571246 TTCAAG-TAATTTAA
1 TTCAAGTTAATTTAA
3571260 GTTCAAGCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
17 5 0.16
18 4 0.13
19 1 0.03
20 8 0.26
21 5 0.16
22 8 0.26
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (18 bp):
TTCAAGTTAATTTAAATT
Found at i:3572300 original size:29 final size:30
Alignment explanation
Indices: 3572266--3572324 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
3572256 AGAACAAATC
3572266 AATTTTT-GA-AAAAATAAAACAT-TTTTAA
1 AATTTTTGGATAAAAATAAAA-ATATTTTAA
*
3572294 AATTTTTGGATCAAAATAAAAATATTTTAA
1 AATTTTTGGATAAAAATAAAAATATTTTAA
3572324 A
1 A
3572325 TATTGAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 7 0.26
29 4 0.15
30 16 0.59
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (30 bp):
AATTTTTGGATAAAAATAAAAATATTTTAA
Found at i:3572812 original size:14 final size:15
Alignment explanation
Indices: 3572776--3572825 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
3572766 TGGGAATTTA
* *
3572776 GGGTTTCAAATTTTT
1 GGGTTTCAAAGTTTG
*
3572791 GAGTTTC-AAGTTTG
1 GGGTTTCAAAGTTTG
*
3572805 GGGTTTCAAATTTTG
1 GGGTTTCAAAGTTTG
3572820 GGGTTT
1 GGGTTT
3572826 TATGAAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.18, C:0.06, G:0.28, T:0.48
Consensus pattern (15 bp):
GGGTTTCAAAGTTTG
Found at i:3573620 original size:61 final size:63
Alignment explanation
Indices: 3573547--3573663 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
3573537 TATCAACTAA
* * *
3573547 AATGCCTTGAATAAT-CCTTTAT-AAAAAAT-TAGAGTGATTACTGAAGGCATTTTTGACAGAC
1 AATGCCTTGAATAATCCCCTCATAAAAAAATATAG-GCGATTACTGAAGGCATTTTTGACAGAC
*
3573608 AATGCCTTGAATAATCCCCTCATAAAAAAATATAGGCGATTATTGAAGGCATTTTT
1 AATGCCTTGAATAATCCCCTCATAAAAAAATATAGGCGATTACTGAAGGCATTTTT
3573664 TGTAAGAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
61 15 0.31
62 5 0.10
63 26 0.53
64 3 0.06
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (63 bp):
AATGCCTTGAATAATCCCCTCATAAAAAAATATAGGCGATTACTGAAGGCATTTTTGACAGAC
Found at i:3573678 original size:63 final size:61
Alignment explanation
Indices: 3573550--3573685 Score: 152
Period size: 63 Copynumber: 2.2 Consensus size: 61
3573540 CAACTAAAAT
* * * *
3573550 GCCTTGAATAATCCTTTATAAAAAATTAGAGTGATTACTGAAGGCATTTTTGACAGACAAT
1 GCCTTGAATAATCCCTCATAAAAAATTAGAGCGATTACTGAAGGCATTTTTGACAGACAAC
*
3573611 GCCTTGAATAATCCCCTCATAAAAAAATATAG-GCGATTATTGAAGGCATTTTTTGTA-AGA-AA
1 GCCTTGAATAAT-CCCTCAT-AAAAAAT-TAGAGCGATTACTGAAGGCA-TTTTTG-ACAGACAA
3573673 C
61 C
*
3573674 GCCTTTAATAAT
1 GCCTTGAATAAT
3573686 TTCGCTAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
61 12 0.19
62 5 0.08
63 34 0.53
64 12 0.19
65 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (61 bp):
GCCTTGAATAATCCCTCATAAAAAATTAGAGCGATTACTGAAGGCATTTTTGACAGACAAC
Found at i:3574000 original size:63 final size:63
Alignment explanation
Indices: 3573856--3574000 Score: 159
Period size: 65 Copynumber: 2.3 Consensus size: 63
3573846 TGTAAGGAAT
* * ** *
3573856 TATTCAAGGCATTTTTTGGGCAAAAAGGCCTTCACTAATCCATTTAAAAAATTTTGAAGAGAGAA
1 TATTGAAGGCA-TTTTT-GGCAAAAAGGCCTTCAATAATCCATAGAAAAAATTTAGAAGAGAGAA
* * *
3573921 TATTGAAGGCATTTTTGGCAAATAAATGCCTTCAATAATCCATAGAAAAAATTTAGAA-TG-GAT
1 TATTGAAGGCATTTTTGGC-AA-AAAGGCCTTCAATAATCCATAGAAAAAATTTAGAAGAGAGAA
*
3573984 TCTTGAAGGCATTTTTG
1 TATTGAAGGCATTTTTG
3574001 ACCAAAAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
63 21 0.30
64 8 0.12
65 40 0.58
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (63 bp):
TATTGAAGGCATTTTTGGCAAAAAGGCCTTCAATAATCCATAGAAAAAATTTAGAAGAGAGAA
Found at i:3574171 original size:61 final size:62
Alignment explanation
Indices: 3573854--3574177 Score: 226
Period size: 63 Copynumber: 5.2 Consensus size: 62
3573844 TTTGTAAGGA
* * ** * *
3573854 ATTATTCAAGGCATTTTTTGGGCAAAAAGGCCTTCACTAATCCATTTAAAAAATTTTGA-AGAGA
1 ATTATTGAAGGCA-TTTTTGGCCAAAAACACCTTCAATAATCCA-TTAAAAAATTTT-ATA-ATA
3573918 G
62 G
* * ** * * *
3573919 AATATTGAAGGCATTTTTGGCAAATAAATGCCTTCAATAATCCA-TAGAAAAAATTTAGAATGG
1 ATTATTGAAGGCATTTTTGGCCAA-AAACACCTTCAATAATCCATTA-AAAAATTTTATAATAG
* * * * ** * * **
3573982 ATTCTTGAAGGCATTTTTGACCAAAAATACCTTTAATAATAAATCAATAAATTTTTATAAGGG
1 ATTATTGAAGGCATTTTTGGCCAAAAACACCTTCAATAATCCATTAA-AAAATTTTATAATAG
* * * * * **
3574045 ATTATTGAAGG-AGATTTTGGTCAAAAACACCTTTAATAATCCATATAAAAAAGTTGA-AACGG
1 ATTATTGAAGGCA-TTTTTGGCCAAAAACACCTTCAATAATCCAT-TAAAAAATTTTATAATAG
* * * *
3574107 ATTATTGAAGGCA-TTTTGGCCCAAAACACCTTCAATAATCCATTTATAAATTTTATATTAG
1 ATTATTGAAGGCATTTTTGGCCAAAAACACCTTCAATAATCCATTAAAAAATTTTATAATAG
3574168 ATTATTGAAG
1 ATTATTGAAG
3574178 ATGATTTTGA
Statistics
Matches: 206, Mismatches: 44, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
60 8 0.04
61 39 0.19
62 32 0.16
63 79 0.38
64 20 0.10
65 28 0.14
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (62 bp):
ATTATTGAAGGCATTTTTGGCCAAAAACACCTTCAATAATCCATTAAAAAATTTTATAATAG
Found at i:3574356 original size:35 final size:35
Alignment explanation
Indices: 3574300--3574369 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
3574290 TATATATGTA
*
3574300 AAGTTAGTTATAGGTTTATGCCCAGAAAACATTTG
1 AAGTCAGTTATAGGTTTATGCCCAGAAAACATTTG
* * *
3574335 AAGTCAGTTGTAGGTTTATGCCTAGAAAATATTTG
1 AAGTCAGTTATAGGTTTATGCCCAGAAAACATTTG
3574370 GTTTATATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (35 bp):
AAGTCAGTTATAGGTTTATGCCCAGAAAACATTTG
Found at i:3577608 original size:25 final size:25
Alignment explanation
Indices: 3577539--3577620 Score: 94
Period size: 25 Copynumber: 3.2 Consensus size: 25
3577529 CAATGTGTTT
* *
3577539 AAAAATACCATTCAGTAAACCATTT
1 AAAAACACCATTCAGTAAACCATTC
* *
3577564 AAAAGCACCATTCAGGAAACCATTC
1 AAAAACACCATTCAGTAAACCATTC
*
3577589 AAAAACACCATT-TGATAAACCATTC
1 AAAAACACCATTCAG-TAAACCATTC
3577614 AATAAAC
1 AA-AAAC
3577621 CAATATCATA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
24 1 0.02
25 43 0.90
26 4 0.08
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.22
Consensus pattern (25 bp):
AAAAACACCATTCAGTAAACCATTC
Found at i:3577640 original size:28 final size:28
Alignment explanation
Indices: 3577621--3577684 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 28
3577611 TTCAATAAAC
3577621 CAATATCATACAATACCATTAAGCAAAA
1 CAATATCATACAATACCATTAAGCAAAA
*
3577649 CAATATCATACAATAGCATTAAGCAAACCA
1 CAATATCATACAATACCATTAAGCAAA--A
3577679 CAATAT
1 CAATAT
3577685 TTAAACCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 26 0.79
30 7 0.21
ACGTcount: A:0.52, C:0.22, G:0.05, T:0.22
Consensus pattern (28 bp):
CAATATCATACAATACCATTAAGCAAAA
Found at i:3579173 original size:187 final size:186
Alignment explanation
Indices: 3578924--3579303 Score: 541
Period size: 186 Copynumber: 2.0 Consensus size: 186
3578914 GAAGGGATTG
* *
3578924 TTGAAGGCTTATTATGCAAAAAATGTCTTCAATAAATTTCTTCAAAAGACTTGAGAGAATTAGCA
1 TTGAAGGCGTATTATGCAAAAAATGTCTTAAATAAATTTCTTCAAAAGACTTGAGAGAATTAGCA
* *
3578989 AAGGC-GTTGTAGTAAAAAATCCCTTCAATAATT-GCTTAAAATTTTACTATGAGATTATTGAAG
66 AAGGCAGTTGTAGTAAAAAATCCCTTCAATAATTCACTTAAAA-TTTACTACGAGATTATTGAAG
* * *
3579052 GTGTTTTTTTTACTAAAAGACACTTTTAATAATCCTAAAAAACTTTTAAAAGGAATTTA
130 ATG--TTTTTTACTAAAAGACACCTTTAATAATCCTAAAAAACTTTTAAAAAGAATTTA
* * * * *
3579111 TTGAAGGCGTATTATGTAAAAAATGTCTTAAATAAATTCTTTTTAAAA-ACTTGAGGGAATTAGT
1 TTGAAGGCGTATTATGCAAAAAATGTCTTAAATAAATT-TCTTCAAAAGACTTGAGAGAATTAGC
* **
3579175 AAAGGCATTTGTAGTAAAAAATGTCTTCAATAATTCACTTAAAATTTACTACGAGATTATTGAAG
65 AAAGGCAGTTGTAGTAAAAAATCCCTTCAATAATTCACTTAAAATTTACTACGAGATTATTGAAG
** *
3579240 ATGTTTTTTACTAAAAGATGCCTTTAATAATCTTAAAAAACTTTTAAAAAGAATTTA
130 ATGTTTTTTACTAAAAGACACCTTTAATAATCCTAAAAAACTTTTAAAAAGAATTTA
3579297 TTGAAGG
1 TTGAAGG
3579304 TATTTTCTAA
Statistics
Matches: 172, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
186 56 0.33
187 55 0.32
188 54 0.31
189 7 0.04
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (186 bp):
TTGAAGGCGTATTATGCAAAAAATGTCTTAAATAAATTTCTTCAAAAGACTTGAGAGAATTAGCA
AAGGCAGTTGTAGTAAAAAATCCCTTCAATAATTCACTTAAAATTTACTACGAGATTATTGAAGA
TGTTTTTTACTAAAAGACACCTTTAATAATCCTAAAAAACTTTTAAAAAGAATTTA
Found at i:3585904 original size:161 final size:158
Alignment explanation
Indices: 3585558--3585996 Score: 442
Period size: 161 Copynumber: 2.7 Consensus size: 158
3585548 AAATGAATGA
* * ** * * *
3585558 ACTTTTTATGCCGTTAAAAGGTAAAAATGCAAATTAACAGTTATTGTTCTGTTTTAATAGTTTTG
1 ACTTTTTGT-CCGTTAATAGGTAAAAATATAAATTAA-ACTTATTATTCT-TTTTAATAGTTTGG
* * * *
3585623 ATAGTTTCAATACATGATATTAAACTTATCCAAA-GTATTGAACTTAGTTTCCACAGTTGATATG
63 ATAGCTTCAATACATGATATTAAACTTGTTCAAATG-ATTGAACTTGGTTTCCACAGTTGATATG
*
3585687 TATGAAAAAGTTATTGTTTATCTCTATTTAGG
127 TATGAAAAAGTTATCGTTTATCTCTATTTAGG
*
3585719 ACTTTTTGTGCCGTTAATAGGTAAAAATATAAAATTATTA-TTATTATTCTATTTTAATAGTTTG
1 ACTTTTTGT-CCGTTAATAGGTAAAAATAT-AAATTA-AACTTATTATTCT-TTTTAATAGTTTG
* * *
3585783 GATAGCTTCAATACATGATATTAAACTTGTTCGAATGATTGAACTTGGTTTCGATAGTTGATATG
62 GATAGCTTCAATACATGATATTAAACTTGTTCAAATGATTGAACTTGGTTTCCACAGTTGATATG
* * *
3585848 TGTGAAAAAGTTGTCGTTTATGTCTATTT-GAG
127 TATGAAAAAGTTATCGTTTATCTCTATTTAG-G
* * *
3585880 ACCATTTTTGT-CTTCTAA-AGGTAAAAATATAAGTTAAACTT-TTGGATGGC-TTTTAATAGTT
1 A-C-TTTTTGTCCGT-TAATAGGTAAAAATATAAATTAAACTTATT--AT-TCTTTTTAATAGTT
* * * * * *
3585941 TGGATGGCTTCAATCCATGCTATTAAACTTGTCCAAATAATTGAATTTGGTTTCCA
60 TGGATAGCTTCAATACATGATATTAAACTTGTTCAAATGATTGAACTTGGTTTCCA
3585997 TGATCGATAT
Statistics
Matches: 236, Mismatches: 31, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
159 3 0.01
160 67 0.28
161 146 0.62
162 13 0.06
163 7 0.03
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (158 bp):
ACTTTTTGTCCGTTAATAGGTAAAAATATAAATTAAACTTATTATTCTTTTTAATAGTTTGGATA
GCTTCAATACATGATATTAAACTTGTTCAAATGATTGAACTTGGTTTCCACAGTTGATATGTATG
AAAAAGTTATCGTTTATCTCTATTTAGG
Found at i:3587478 original size:33 final size:33
Alignment explanation
Indices: 3587397--3587499 Score: 102
Period size: 33 Copynumber: 3.1 Consensus size: 33
3587387 TTAGTAGTGT
* **
3587397 TTTTATGATACAAACGTTGCTAATTTAGTGGCA
1 TTTTATGATACAAATGCCGCTAATTTAGTGGCA
**
3587430 -TTTATCTTGACAAATGCCGCTAATTTAGTGGCA
1 TTTTATGAT-ACAAATGCCGCTAATTTAGTGGCA
* * *
3587463 TTTTATGATATAAATGCCAC-CATATTAGTGGCA
1 TTTTATGATACAAATGCCGCTAAT-TTAGTGGCA
3587496 TTTT
1 TTTT
3587500 TTGGGTATAA
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
32 8 0.14
33 43 0.75
34 6 0.11
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (33 bp):
TTTTATGATACAAATGCCGCTAATTTAGTGGCA
Found at i:3587521 original size:33 final size:33
Alignment explanation
Indices: 3587454--3587522 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
3587444 TGCCGCTAAT
*
3587454 TTAGTGGCATTTTATGATATAAATGCCACCATA
1 TTAGTGGCATTTTATGATATAAACGCCACCATA
* * *
3587487 TTAGTGGCATTTTTTGGGTATAAACG-CACTATA
1 TTAGTGGCATTTTAT-GATATAAACGCCACCATA
3587520 TTA
1 TTA
3587523 TTAATGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 23 0.74
34 8 0.26
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (33 bp):
TTAGTGGCATTTTATGATATAAACGCCACCATA
Found at i:3599477 original size:19 final size:19
Alignment explanation
Indices: 3599439--3599479 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3599429 TTTAAATTGC
**
3599439 AAATAATTAAAGTGTTTGA
1 AAATAATTAAAGTGCATGA
*
3599458 AAATATTTAAAGTGCATGA
1 AAATAATTAAAGTGCATGA
3599477 AAA
1 AAA
3599480 ATAAATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (19 bp):
AAATAATTAAAGTGCATGA
Found at i:3602523 original size:32 final size:32
Alignment explanation
Indices: 3602486--3602557 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
3602476 TTAAATACTC
*
3602486 GATATTTAAGCCAAGATACTAAGTGAAGAAAG
1 GATATTAAAGCCAAGATACTAAGTGAAGAAAG
* *
3602518 GATATTAAAGCCAAGATACTGAGTGAGGAAAG
1 GATATTAAAGCCAAGATACTAAGTGAAGAAAG
3602550 GATATTAA
1 GATATTAA
3602558 TTATACACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.46, C:0.08, G:0.24, T:0.22
Consensus pattern (32 bp):
GATATTAAAGCCAAGATACTAAGTGAAGAAAG
Found at i:3604181 original size:19 final size:19
Alignment explanation
Indices: 3604153--3604194 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3604143 GATATTGGCA
*
3604153 TCTCATTTTTTTTATTCTC
1 TCTCAATTTTTTTATTCTC
*
3604172 TCTCAATTTTTTTATTTTC
1 TCTCAATTTTTTTATTCTC
3604191 TCTC
1 TCTC
3604195 TCTTTCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (19 bp):
TCTCAATTTTTTTATTCTC
Found at i:3605399 original size:21 final size:19
Alignment explanation
Indices: 3605362--3605417 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
3605352 ATATTAGAAG
*
3605362 AAAAATTAAAAAAAATCTTA
1 AAAAATTACAAAAAATC-TA
*
3605382 AAAAATTCACAAATAATCTA
1 AAAAATT-ACAAAAAATCTA
3605402 AAAATATTTACAAAAA
1 AAAA-A-TTACAAAAA
3605418 TATGAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 13 0.43
21 15 0.50
22 2 0.07
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAATTACAAAAAATCTA
Found at i:3605471 original size:24 final size:24
Alignment explanation
Indices: 3605453--3605505 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3605443 AGAAATTTGG
3605453 AAAAAT-TAAAAATGTGAAAATTT
1 AAAAATCTAAAAATGTGAAAATTT
* *
3605476 AAAAATCTAAAAATCTAAAAATTT
1 AAAAATCTAAAAATGTGAAAATTT
3605500 CAAAAA
1 -AAAAA
3605506 ATCCCAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 6 0.23
24 15 0.58
25 5 0.19
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAAATCTAAAAATGTGAAAATTT
Found at i:3605504 original size:16 final size:16
Alignment explanation
Indices: 3605454--3605523 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
3605444 GAAATTTGGA
* *
3605454 AAAAT-TAAAAATGTG
1 AAAATCTAAAAATTTC
* * *
3605469 AAAATTTAAAAATCTA
1 AAAATCTAAAAATTTC
3605485 AAAATCTAAAAATTTC
1 AAAATCTAAAAATTTC
*
3605501 AAAAAATCCCAAAAATTTC
1 --AAAAT-CTAAAAATTTC
3605520 AAAA
1 AAAA
3605524 CAATCTAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 5 0.11
16 21 0.47
17 4 0.09
18 5 0.11
19 10 0.22
ACGTcount: A:0.61, C:0.10, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAATCTAAAAATTTC
Found at i:3605505 original size:9 final size:8
Alignment explanation
Indices: 3605453--3605497 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
3605443 AGAAATTTGG
3605453 AAAAAT-T
1 AAAAATCT
*
3605460 AAAAATGT
1 AAAAATCT
* *
3605468 GAAAATTT
1 AAAAATCT
3605476 AAAAATCT
1 AAAAATCT
3605484 AAAAATCT
1 AAAAATCT
3605492 AAAAAT
1 AAAAAT
3605498 TTCAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (8 bp):
AAAAATCT
Found at i:3605612 original size:23 final size:22
Alignment explanation
Indices: 3605586--3605631 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
3605576 AACAAATTCT
*
3605586 AAAAGACTAAAAAATTATAAAAA
1 AAAAAACTAAAAAATTA-AAAAA
*
3605609 AAAAAACTAAAGAATTAAAAAA
1 AAAAAACTAAAAAATTAAAAAA
3605631 A
1 A
3605632 TTTGCTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (22 bp):
AAAAAACTAAAAAATTAAAAAA
Found at i:3605769 original size:18 final size:16
Alignment explanation
Indices: 3605734--3605782 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
3605724 GAAGATTTTT
3605734 TGAAAATTTAAATAAATAA
1 TGAAAA-TTAAA-AAAT-A
3605753 TGAAAATTAAAACAATA
1 TGAAAATTAAAA-AATA
*
3605770 TAAAAATTAAAAA
1 TGAAAATTAAAAA
3605783 CATTCCCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
18 8 0.29
19 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
TGAAAATTAAAAAATA
Found at i:3606027 original size:18 final size:17
Alignment explanation
Indices: 3605986--3606028 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3605976 AGTTTTTAAA
*
3605986 CATTTTTTAGATTTTTTT
1 CATTTTTTAGA-GTTTTT
* *
3606004 AATTTTTGAGAGTTTTT
1 CATTTTTTAGAGTTTTT
3606021 CATTTTTT
1 CATTTTTT
3606029 TTAATTTTCT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.19, C:0.05, G:0.09, T:0.67
Consensus pattern (17 bp):
CATTTTTTAGAGTTTTT
Found at i:3606672 original size:18 final size:18
Alignment explanation
Indices: 3606649--3606692 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
3606639 TGCCACATCA
**
3606649 ATGTAAATTTTTTTGCAC
1 ATGTAAATTTTTTAACAC
3606667 ATGTAATAATTTTTTAACAC
1 ATGT-A-AATTTTTTAACAC
3606687 ATGTAA
1 ATGTAA
3606693 TTGTTGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.23
19 2 0.09
20 15 0.68
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (18 bp):
ATGTAAATTTTTTAACAC
Found at i:3606679 original size:20 final size:20
Alignment explanation
Indices: 3606654--3606693 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3606644 CATCAATGTA
**
3606654 AATTTTTTTGCACATGTAAT
1 AATTTTTTAACACATGTAAT
3606674 AATTTTTTAACACATGTAAT
1 AATTTTTTAACACATGTAAT
3606694 TGTTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (20 bp):
AATTTTTTAACACATGTAAT
Found at i:3617250 original size:2 final size:2
Alignment explanation
Indices: 3617243--3617268 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3617233 TGTACTCAAG
3617243 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
3617269 CTTATTGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3618664 original size:3 final size:3
Alignment explanation
Indices: 3618656--3618694 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3618646 CAGGCCACCG
3618656 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3618695 AATAAATCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3618930 original size:28 final size:29
Alignment explanation
Indices: 3618872--3618948 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
3618862 TTTTCCATGG
* *
3618872 AAATA-AAAATTTATTTAAATATAAATCA
1 AAATATAAAACTTATTTAAATATAAATAA
*
3618900 AAATATAAAACTTATTTAAATA-CAATAA
1 AAATATAAAACTTATTTAAATATAAATAA
*
3618928 AAATATAAAATCTTACTTAAA
1 AAATATAAAA-CTTATTTAAA
3618949 ATTTAATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 19 0.44
29 24 0.56
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (29 bp):
AAATATAAAACTTATTTAAATATAAATAA
Found at i:3621302 original size:2 final size:2
Alignment explanation
Indices: 3621295--3621323 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3621285 ACATACATAC
3621295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3621324 CACACACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3623533 original size:13 final size:13
Alignment explanation
Indices: 3623517--3623551 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3623507 TTTTTGTGTT
*
3623517 ATTTATTTAATTA
1 ATTTAATTAATTA
3623530 ATTTAATTAATTA
1 ATTTAATTAATTA
*
3623543 ATTTTATTA
1 ATTTAATTA
3623552 TTTATCTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTAATTAATTA
Found at i:3626626 original size:2 final size:2
Alignment explanation
Indices: 3626619--3626655 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3626609 TAGTTATGTT
3626619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3626656 GAAAAGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3628804 original size:20 final size:20
Alignment explanation
Indices: 3628766--3628841 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 20
3628756 TTTATATTTT
3628766 TAATAATTA-TATATGAATA
1 TAATAATTATTATATGAATA
*
3628785 GTAATAATTATTTTAT-AATA
1 -TAATAATTATTATATGAATA
*
3628805 -AATAATTATAATTATGCAAATA
1 TAATAATTATTA-TATG--AATA
3628827 TAAATAAATTATTAT
1 T-AAT-AATTATTAT
3628842 TTATAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 9 0.20
19 3 0.07
20 13 0.30
21 4 0.09
22 4 0.09
24 4 0.09
25 7 0.16
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (20 bp):
TAATAATTATTATATGAATA
Found at i:3628858 original size:18 final size:18
Alignment explanation
Indices: 3628825--3628859 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3628815 ATTATGCAAA
*
3628825 TATAAATAAATTATTATT
1 TATAAATAAATGATTATT
*
3628843 TATAAATATATGATTAT
1 TATAAATAAATGATTAT
3628860 ATAAAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TATAAATAAATGATTATT
Found at i:3629087 original size:174 final size:172
Alignment explanation
Indices: 3628898--3629245 Score: 606
Period size: 174 Copynumber: 2.0 Consensus size: 172
3628888 ATATATATAT
*
3628898 ATATTTATTTATTATAAATAATTCATTCAATATAATTATTTTTACTACTTCAAATTAAAAAATTT
1 ATATTTATTTATTATAAATAATTCATTCAATATAATTATTTTCACTACTTCAAATTAAAAAATTT
* * *
3628963 GAAATTTTGTTGTATTTTAAAAATATAGTTATTTTTAAAAAAATATTCTTAATATATCAAAGCCA
66 GAAATTTTATTGTATTTTAAAAACATAATTATTTTTAAAAAAATATTCTTAATATATCAAAGCCA
3629028 AATTTCTTTTATTATTTATTTATTTTTTTAATAATTTAAAGGAA
131 AATTT-TTTT-TTATTTATTTATTTTTTTAATAATTTAAAGGAA
*
3629072 ATATTTATTTATTATAAATAATTCATTCAGTATAATTATTTTCACTACTTCAAATTAAAAAATTT
1 ATATTTATTTATTATAAATAATTCATTCAATATAATTATTTTCACTACTTCAAATTAAAAAATTT
** *
3629137 GAGGTTTTATTGTATTTTAAAAGCATAATTATTTTTAAAAAAATATTCTTAATATATCAAAGCCA
66 GAAATTTTATTGTATTTTAAAAACATAATTATTTTTAAAAAAATATTCTTAATATATCAAAGCCA
3629202 AATTTTTTTTTATTTATTTATTTTTTTAATAATTTAAAGGAA
131 AATTTTTTTTTATTTATTTATTTTTTTAATAATTTAAAGGAA
3629244 AT
1 AT
3629246 TATAAGAAAG
Statistics
Matches: 166, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
172 35 0.21
173 4 0.02
174 127 0.77
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (172 bp):
ATATTTATTTATTATAAATAATTCATTCAATATAATTATTTTCACTACTTCAAATTAAAAAATTT
GAAATTTTATTGTATTTTAAAAACATAATTATTTTTAAAAAAATATTCTTAATATATCAAAGCCA
AATTTTTTTTTATTTATTTATTTTTTTAATAATTTAAAGGAA
Found at i:3633819 original size:17 final size:17
Alignment explanation
Indices: 3633774--3633812 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
3633764 CTTGAATGAA
*
3633774 AAAAAAATATAATTTTAT
1 AAAAAAAT-TAATTTAAT
3633792 AAAAAAATTAATTTAAT
1 AAAAAAATTAATTTAAT
3633809 AAAA
1 AAAA
3633813 TATTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAAAATTAATTTAAT
Found at i:3634613 original size:8 final size:8
Alignment explanation
Indices: 3634592--3634637 Score: 74
Period size: 8 Copynumber: 5.5 Consensus size: 8
3634582 AACCAAAAAT
3634592 AAAAATTA
1 AAAAATTA
3634600 GAAAAATTA
1 -AAAAATTA
3634609 GAAAAATTA
1 -AAAAATTA
3634618 AAAAATTA
1 AAAAATTA
3634626 AAAAATTA
1 AAAAATTA
3634634 AAAA
1 AAAA
3634638 CGAAAAACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 20 0.54
9 17 0.46
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (8 bp):
AAAAATTA
Found at i:3634723 original size:20 final size:21
Alignment explanation
Indices: 3634700--3634743 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3634690 TAAAAAAAGG
*
3634700 AAATTGAAAGAATC-AAATAA
1 AAATGGAAAGAATCAAAATAA
*
3634720 AAATGGAAGGAATCAAAATAA
1 AAATGGAAAGAATCAAAATAA
3634741 AAA
1 AAA
3634744 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.66, C:0.05, G:0.14, T:0.16
Consensus pattern (21 bp):
AAATGGAAAGAATCAAAATAA
Found at i:3640786 original size:14 final size:15
Alignment explanation
Indices: 3640767--3640799 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3640757 AAGACATATA
3640767 TTTTTTTAA-TGTTT
1 TTTTTTTAATTGTTT
3640781 TTTTTTTAATTGTTT
1 TTTTTTTAATTGTTT
3640796 TTTT
1 TTTT
3640800 AGGGATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTTTTAATTGTTT
Found at i:3645996 original size:35 final size:33
Alignment explanation
Indices: 3645956--3646035 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 33
3645946 ATTATAATAA
3645956 GATAATACATGCATTGCATCCCATCCACATCAATG
1 GATAATACATGCA-T-CATCCCATCCACATCAATG
*
3645991 GATAATACAT--A-CATCCCATTCACATCAATG
1 GATAATACATGCATCATCCCATCCACATCAATG
* *
3646021 GATAGTATATGCATC
1 GATAATACATGCATC
3646036 CCATTTTCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 26 0.67
32 1 0.03
33 2 0.05
35 10 0.26
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (33 bp):
GATAATACATGCATCATCCCATCCACATCAATG
Found at i:3646040 original size:30 final size:30
Alignment explanation
Indices: 3645970--3646040 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
3645960 ATACATGCAT
*
3645970 TGCATCCCATCCACATCAATGGATAATACA
1 TGCATCCCATTCACATCAATGGATAATACA
* * *
3646000 TACATCCCATTCACATCAATGGATAGTATA
1 TGCATCCCATTCACATCAATGGATAATACA
3646030 TGCATCCCATT
1 TGCATCCCATT
3646041 TTCTACACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (30 bp):
TGCATCCCATTCACATCAATGGATAATACA
Found at i:3650019 original size:34 final size:34
Alignment explanation
Indices: 3649975--3650164 Score: 149
Period size: 34 Copynumber: 5.7 Consensus size: 34
3649965 ATTCTCAGGC
* *
3649975 ATGTAGGCCCAATTTAGCTGTCCTTCAAAGAAAG
1 ATGTAAGCCCAATTTAGCTGGCCTTCAAAGAAAG
* *
3650009 ATGTAAGCCCAGTTTAGCTGGCCTTCAAAAAAAG
1 ATGTAAGCCCAATTTAGCTGGCCTTCAAAGAAAG
* * * *
3650043 ATTTAAACCCAGA-TTAGCTAG-CTTC-AA-TAA-
1 ATGTAAGCCCA-ATTTAGCTGGCCTTCAAAGAAAG
* * *
3650073 ATGTAAGCCCAATTTAACTGACTTTCAAAGAAAG
1 ATGTAAGCCCAATTTAGCTGGCCTTCAAAGAAAG
* * * * *
3650107 ATTTAAGCCTAAATTAGTTGGCCTTTAAAGAAAG
1 ATGTAAGCCCAATTTAGCTGGCCTTCAAAGAAAG
* * *
3650141 ATTTAAACCC-ATATTAGCTAGCCT
1 ATGTAAGCCCAAT-TTAGCTGGCCT
3650165 CTAATGAATA
Statistics
Matches: 120, Mismatches: 29, Indels: 14
0.74 0.18 0.09
Matches are distributed among these distances:
29 1 0.01
30 14 0.12
31 5 0.04
32 4 0.03
33 7 0.06
34 89 0.74
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (34 bp):
ATGTAAGCCCAATTTAGCTGGCCTTCAAAGAAAG
Found at i:3650144 original size:98 final size:99
Alignment explanation
Indices: 3649975--3650224 Score: 297
Period size: 98 Copynumber: 2.5 Consensus size: 99
3649965 ATTCTCAGGC
* * * * * * *
3649975 ATGTAGGCCCAATTTAGCTGTCCTTCAAAGAAAGATGTAAGCCCAGTTTAGCTGGCCTTCAAAAA
1 ATGTAAGCCCAATTTAACTGACTTTCAAAGAAAGATTTAAGCCTAGATTAGCTGGCCTTCAAAAA
*
3650040 AAGATTTAAACCCAGATTAGCTAGCTTC-AATAA
66 AAGATTTAAACCCAGATTAGCTAGCCTCTAATAA
* * * *
3650073 ATGTAAGCCCAATTTAACTGACTTTCAAAGAAAGATTTAAGCCTAAATTAGTTGGCCTTTAAAGA
1 ATGTAAGCCCAATTTAACTGACTTTCAAAGAAAGATTTAAGCCTAGATTAGCTGGCCTTCAAAAA
* *
3650138 AAGATTTAAACCCATATTAGCTAGCCTCTAATGA
66 AAGATTTAAACCCAGATTAGCTAGCCTCTAATAA
* * ** * *
3650172 ATATAAGCCCAGTTTGGTCGGCCTTT-AAAGAAAGATTTAAGCCTAGATTAGCT
1 ATGTAAGCCCAATTT-AACTGACTTTCAAAGAAAGATTTAAGCCTAGATTAGCT
3650225 AGCCCCCTCA
Statistics
Matches: 128, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
98 80 0.62
99 42 0.33
100 6 0.05
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (99 bp):
ATGTAAGCCCAATTTAACTGACTTTCAAAGAAAGATTTAAGCCTAGATTAGCTGGCCTTCAAAAA
AAGATTTAAACCCAGATTAGCTAGCCTCTAATAA
Found at i:3650478 original size:14 final size:14
Alignment explanation
Indices: 3650459--3650515 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
3650449 AGAAATTTGT
*
3650459 ATTTACATCATGGC
1 ATTTACATCATAGC
*
3650473 ATTTACAT--TCGC
1 ATTTACATCATAGC
3650485 ATTTACATCATAGC
1 ATTTACATCATAGC
3650499 ATTTACATCA-AGC
1 ATTTACATCATAGC
3650512 ATTT
1 ATTT
3650516 GCATTCGCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
12 11 0.28
13 7 0.18
14 21 0.54
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.39
Consensus pattern (14 bp):
ATTTACATCATAGC
Found at i:3650834 original size:22 final size:22
Alignment explanation
Indices: 3650809--3650916 Score: 117
Period size: 22 Copynumber: 4.9 Consensus size: 22
3650799 AGACCTTCGG
3650809 GCATAATTTTTAAGACCTCTAA
1 GCATAATTTTTAAGACCTCTAA
* * ** *
3650831 GCATAATCTTTAAAATTTCTGA
1 GCATAATTTTTAAGACCTCTAA
* *
3650853 GCATAATCTTTAAGACCTCTAT
1 GCATAATTTTTAAGACCTCTAA
* * *
3650875 GCATAATTTGTAAGATCTCTAG
1 GCATAATTTTTAAGACCTCTAA
*
3650897 GCATAATTTTCAAGACCTCT
1 GCATAATTTTTAAGACCTCT
3650917 GGGGGAACAT
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 69 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (22 bp):
GCATAATTTTTAAGACCTCTAA
Found at i:3650859 original size:44 final size:44
Alignment explanation
Indices: 3650808--3650916 Score: 141
Period size: 44 Copynumber: 2.5 Consensus size: 44
3650798 AAGACCTTCG
*
3650808 GGCATAATTTTTAAGACCTCTAAGCATAATCTT-TAAAATTTCT-
1 GGCATAATTTTTAAGACCTCTAAGCATAAT-TTGTAAAATCTCTA
* * *
3650851 GAGCATAATCTTTAAGACCTCTATGCATAATTTGTAAGATCTCTA
1 G-GCATAATTTTTAAGACCTCTAAGCATAATTTGTAAAATCTCTA
*
3650896 GGCATAATTTTCAAGACCTCT
1 GGCATAATTTTTAAGACCTCT
3650917 GGGGGAACAT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
43 3 0.05
44 53 0.93
45 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (44 bp):
GGCATAATTTTTAAGACCTCTAAGCATAATTTGTAAAATCTCTA
Found at i:3652440 original size:24 final size:23
Alignment explanation
Indices: 3652387--3652440 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
3652377 AGTTCTTTTT
* * *
3652387 TAAAAAAAAAGAGAGAACGAAAA
1 TAAAAAAAAAAAGAAAACAAAAA
*
3652410 CACAAAAAAAAAAGAAAAGCAAAAA
1 TA-AAAAAAAAAAGAAAA-CAAAAA
3652435 TAAAAA
1 TAAAAA
3652441 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 1 0.04
24 17 0.71
25 6 0.25
ACGTcount: A:0.78, C:0.07, G:0.11, T:0.04
Consensus pattern (23 bp):
TAAAAAAAAAAAGAAAACAAAAA
Found at i:3654202 original size:24 final size:23
Alignment explanation
Indices: 3654154--3654202 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
3654144 TCGATAATGG
*
3654154 GATTCTAAGGAAGTCCAGGTAGA
1 GATTCTAAGAAAGTCCAGGTAGA
*
3654177 GATTCCTAAGAAATTCCTAGGT-GA
1 GATT-CTAAGAAAGTCC-AGGTAGA
3654201 GA
1 GA
3654203 AAATTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 4 0.18
24 14 0.64
25 4 0.18
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (23 bp):
GATTCTAAGAAAGTCCAGGTAGA
Found at i:3655126 original size:26 final size:26
Alignment explanation
Indices: 3655074--3655126 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
3655064 CAAGTTTACT
* * **
3655074 AAAATAATAAAAATATGTTTTTAAAA
1 AAAATAATAAAAATATATATACAAAA
*
3655100 AAAATAATAAAAATATATATACGAAA
1 AAAATAATAAAAATATATATACAAAA
3655126 A
1 A
3655127 TTAATTTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (26 bp):
AAAATAATAAAAATATATATACAAAA
Found at i:3660876 original size:18 final size:18
Alignment explanation
Indices: 3660853--3660887 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3660843 TGCCACTTCA
3660853 GCCCGTAGCTTTGTTGTG
1 GCCCGTAGCTTTGTTGTG
3660871 GCCCGTAGCTTTGTTGT
1 GCCCGTAGCTTTGTTGT
3660888 TGTTGTACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.23, G:0.31, T:0.40
Consensus pattern (18 bp):
GCCCGTAGCTTTGTTGTG
Found at i:3666486 original size:19 final size:19
Alignment explanation
Indices: 3666462--3666525 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
3666452 TAATAAGGTT
3666462 TATATAATTGTTTATATTA
1 TATATAATTGTTTATATTA
3666481 TATATAA----TTAT-TTA
1 TATATAATTGTTTATATTA
*
3666495 T-T-T-ATTGTTTAAATTA
1 TATATAATTGTTTATATTA
3666511 TATATAATTGTTTAT
1 TATATAATTGTTTAT
3666526 TGTTTGGCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 16
0.66 0.04 0.30
Matches are distributed among these distances:
11 1 0.03
12 1 0.03
13 1 0.03
14 4 0.11
15 7 0.20
16 4 0.11
17 1 0.03
18 1 0.03
19 15 0.43
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TATATAATTGTTTATATTA
Found at i:3666502 original size:30 final size:30
Alignment explanation
Indices: 3666468--3666526 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3666458 GGTTTATATA
*
3666468 ATTGTTTATATTATATATAATTATTTATTT
1 ATTGTTTAAATTATATATAATTATTTATTT
*
3666498 ATTGTTTAAATTATATATAATTGTTTATT
1 ATTGTTTAAATTATATATAATTATTTATT
3666527 GTTTGGCTTT
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:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (30 bp):
ATTGTTTAAATTATATATAATTATTTATTT
Found at i:3666670 original size:19 final size:19
Alignment explanation
Indices: 3666646--3666712 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
3666636 TAAGGTTTAG
3666646 ATAATTGTTTAGATTATAT
1 ATAATTGTTTAGATTATAT
3666665 ATAATTGTTTATTG-TT-TAT
1 ATAATTGTTTA--GATTATAT
* *
3666684 AT-ATTTTTTATATTATAT
1 ATAATTGTTTAGATTATAT
3666702 ATAATTGTTTA
1 ATAATTGTTTA
3666713 TTATTTAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.05
18 12 0.30
19 23 0.57
20 2 0.05
21 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
ATAATTGTTTAGATTATAT
Found at i:3666754 original size:188 final size:181
Alignment explanation
Indices: 3666440--3666804 Score: 534
Period size: 188 Copynumber: 2.0 Consensus size: 181
3666430 TATAATAAAA
* * *
3666440 CATTTGGCAACATAATAAGGTTTATATAATTGTTTATATTATATATAATTATTTATTTATTGTTT
1 CATTTGGCAACATAATAAGGTTTAGATAATTGTTTAGATTATATATAATTATTTATATATTGTTT
* **
3666505 AAATTATATATAATTGTTTATTGTTTGGCTTTTTCAATTAAATATATATAATAAAAATATATAAT
66 AAATTATATATAATTGTTTATTATTTAACTTTTTCAATTAAATATATATAATAAAAATATATAAT
* * *
3666570 TGTTTATATGGTGGT-AGGATTTGTAATCAAATATTATACATATGGTGCTAG
131 TGTTTACATGGTGGTGA-CATTTGTAATCAAATACTATACATATGGTGCTAG
*
3666621 CATTTGGCAGCATAATAAGGTTTAGATAATTGTTTAGATTATATATAATTGTTTATTGTTTATAT
1 CATTTGGCAACATAATAAGGTTTAGATAATTGTTTAGATTATATATAA----TTA---TTTATAT
* *
3666686 ATTTTTTATATTATATATAATTGTTTATTATTTAACTTTTTCAATTAAATATATATAATAAAAAT
59 ATTGTTTAAATTATATATAATTGTTTATTATTTAACTTTTTCAATTAAATATATATAATAAAAAT
*
3666751 ATATAATTGTTTACATGGTGGTGACATTTGTAATCAAATACTATATATATGGTG
124 ATATAATTGTTTACATGGTGGTGACATTTGTAATCAAATACTATACATATGGTG
3666805 GTTATATAAT
Statistics
Matches: 163, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
181 45 0.28
185 3 0.02
188 114 0.70
189 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (181 bp):
CATTTGGCAACATAATAAGGTTTAGATAATTGTTTAGATTATATATAATTATTTATATATTGTTT
AAATTATATATAATTGTTTATTATTTAACTTTTTCAATTAAATATATATAATAAAAATATATAAT
TGTTTACATGGTGGTGACATTTGTAATCAAATACTATACATATGGTGCTAG
Found at i:3669774 original size:55 final size:55
Alignment explanation
Indices: 3669711--3669844 Score: 162
Period size: 55 Copynumber: 2.4 Consensus size: 55
3669701 ATATAATAAA
3669711 AAAATTAAAACATATAAGTCTATACTAACAATCTCTAA-CTATTAGTAAACGTAAG
1 AAAATTAAAACATATAAGTCTATACTAACAATCTCTAATC-ATTAGTAAACGTAAG
* * * * * * * * *
3669766 AAAATTAAAGCATATAATTCTATACTGACATTTTCTAATCGTTGGTATAGGTAAG
1 AAAATTAAAACATATAAGTCTATACTAACAATCTCTAATCATTAGTAAACGTAAG
*
3669821 AAAATTAAAAAATATAAGTCTATA
1 AAAATTAAAACATATAAGTCTATA
3669845 TTGACGGATG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 65 0.98
56 1 0.02
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (55 bp):
AAAATTAAAACATATAAGTCTATACTAACAATCTCTAATCATTAGTAAACGTAAG
Found at i:3673559 original size:66 final size:66
Alignment explanation
Indices: 3673439--3673570 Score: 176
Period size: 66 Copynumber: 2.0 Consensus size: 66
3673429 GTCTAGGATC
* * * * * *
3673439 ATTCATTGTTGAGCTTTCAAGGTAAGAATGATAAAGCTTATCTAAGGAACCACCCCTAAACTTAA
1 ATTCATTATTGAGCTCTCAAGGTAAGAATGATAAAACCTATCTAAAGAACCACCCCCAAACTTAA
3673504 T
66 T
* *
3673505 ATTCATTATTGAGCTCTCAAGGTAAGAAT-AGTAAAACCTATTTAAAGAATCACCCCCAAACTTA
1 ATTCATTATTGAGCTCTCAAGGTAAGAATGA-TAAAACCTATCTAAAGAACCACCCCCAAACTTA
3673569 AT
65 AT
3673571 TTTTGCTTAC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 1 0.02
66 56 0.98
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (66 bp):
ATTCATTATTGAGCTCTCAAGGTAAGAATGATAAAACCTATCTAAAGAACCACCCCCAAACTTAA
T
Found at i:3673652 original size:18 final size:18
Alignment explanation
Indices: 3673626--3673660 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3673616 ACCATTTTGT
*
3673626 TTTTGTTTTGTTTTCTTC
1 TTTTCTTTTGTTTTCTTC
*
3673644 TTTTCTTTTTTTTTCTT
1 TTTTCTTTTGTTTTCTT
3673661 TTGCAATCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTTCTTTTGTTTTCTTC
Found at i:3676944 original size:12 final size:13
Alignment explanation
Indices: 3676917--3676949 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
3676907 CCCATGAAAT
3676917 CCTAAACCTTAAAC
1 CCTAAACC-TAAAC
3676931 CCTAAACC-AAAC
1 CCTAAACCTAAAC
3676943 CCTAAAC
1 CCTAAAC
3676950 TAGACCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
14 8 0.42
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.15
Consensus pattern (13 bp):
CCTAAACCTAAAC
Found at i:3676956 original size:12 final size:12
Alignment explanation
Indices: 3676926--3676964 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3676916 TCCTAAACCT
3676926 TAAACCCTAAAC
1 TAAACCCTAAAC
*
3676938 CAAACCCTAAAC
1 TAAACCCTAAAC
* *
3676950 TAGACCCCAAAC
1 TAAACCCTAAAC
3676962 TAA
1 TAA
3676965 CACAACCCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.49, C:0.36, G:0.03, T:0.13
Consensus pattern (12 bp):
TAAACCCTAAAC
Found at i:3683856 original size:27 final size:28
Alignment explanation
Indices: 3683818--3683873 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
3683808 TCATAAACCC
3683818 ATGCAATGTTATTTGAATTTGTT-GAAA
1 ATGCAATGTTATTTGAATTTGTTGGAAA
3683845 ATGCAATGTTATTTGAATTTGTTGGAAA
1 ATGCAATGTTATTTGAATTTGTTGGAAA
3683873 A
1 A
3683874 GTAAGTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.43
Consensus pattern (28 bp):
ATGCAATGTTATTTGAATTTGTTGGAAA
Found at i:3684063 original size:77 final size:77
Alignment explanation
Indices: 3683966--3684112 Score: 174
Period size: 77 Copynumber: 1.9 Consensus size: 77
3683956 ATTTTTTTGT
* * *
3683966 AATAATTTAGGTATTGATTTAGGGT-TTGATTTATGATAATT-ATTGTCAATAAATAATGTATGT
1 AATAATTTAGGTATTGATTTA-GGTAATAATTTAGGATAATTAATT-TCAATAAATAATGTATGT
3684029 TATTTGGTTAGAAA
64 TATTTGGTTAGAAA
* * * * *
3684043 AATAATTTTGGTAATT-ATTTATGTAATAATTTAGGTTTATTAATTTCAATAAATAATTTATGTT
1 AATAATTTAGGT-ATTGATTTAGGTAATAATTTAGGATAATTAATTTCAATAAATAATGTATGTT
3684107 ATTTGG
65 ATTTGG
3684113 CTGAAAACAA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
76 2 0.03
77 51 0.86
78 6 0.10
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.48
Consensus pattern (77 bp):
AATAATTTAGGTATTGATTTAGGTAATAATTTAGGATAATTAATTTCAATAAATAATGTATGTTA
TTTGGTTAGAAA
Found at i:3691625 original size:35 final size:35
Alignment explanation
Indices: 3691513--3691625 Score: 106
Period size: 35 Copynumber: 3.1 Consensus size: 35
3691503 GTAGTTCAAA
3691513 ATTTCTCTGCACATTTGTTCTTGTTTATGAATATC
1 ATTTCTCTGCACATTTGTTCTTGTTTATGAATATC
* ** * *
3691548 ATTTCT-AGCTAGGGTTTG--CTTGAGAATTCTGGAATATC
1 ATTTCTCTGC-A-CATTTGTTCTT--G-TTTAT-GAATATC
3691586 ATTTCTCTGCACATTTGTTCTTGTTTATGAATATC
1 ATTTCTCTGCACATTTGTTCTTGTTTATGAATATC
3691621 ATTTC
1 ATTTC
3691626 GATATATATT
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
34 5 0.08
35 19 0.32
36 8 0.14
37 8 0.14
38 14 0.24
39 5 0.08
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.48
Consensus pattern (35 bp):
ATTTCTCTGCACATTTGTTCTTGTTTATGAATATC
Found at i:3691742 original size:2 final size:2
Alignment explanation
Indices: 3691731--3691784 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
3691721 TCACACACGC
* *
3691731 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3691773 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3691785 TATGTACTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3693390 original size:22 final size:22
Alignment explanation
Indices: 3693365--3693407 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3693355 TATTAGCTTT
*
3693365 TTTATTATTTATAAATATATTA
1 TTTATTATTCATAAATATATTA
* *
3693387 TTTATTGTTCATGAATATATT
1 TTTATTATTCATAAATATATT
3693408 CATTAGTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTATTATTCATAAATATATTA
Found at i:3693979 original size:30 final size:30
Alignment explanation
Indices: 3693888--3693979 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 30
3693878 GATTTATATT
3693888 AGGAGTTTATTTAG-TACAAATTAAAGGTTA
1 AGGA-TTTATTTAGATACAAATTAAAGGTTA
* * *
3693918 AAGATTTATTTGGATACAAATTAAAGTTTA
1 AGGATTTATTTAGATACAAATTAAAGGTTA
* * *
3693948 AGGATTTATTTAGATGCAAATCAATGGTTA
1 AGGATTTATTTAGATACAAATTAAAGGTTA
3693978 AG
1 AG
3693980 AACTTATATG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.15
30 44 0.85
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.37
Consensus pattern (30 bp):
AGGATTTATTTAGATACAAATTAAAGGTTA
Found at i:3695715 original size:2 final size:2
Alignment explanation
Indices: 3695694--3695734 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
3695684 GAGATGTTGA
* * *
3695694 AT AT TT AT AT AT GT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3695735 AGGAGAGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Done.