Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007924.1 Hibiscus syriacus cultivar Beakdansim tig00110330_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: 1741266
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 7 of 7
Found at i:1499123 original size:30 final size:29
Alignment explanation
Indices: 1499020--1499124 Score: 113
Period size: 28 Copynumber: 3.6 Consensus size: 29
1499010 AAAATATTTG
* * *
1499020 AATAGTTTAGGTACCTATTTTGAC-ATAA
1 AATACTTTAGGTACTTATTTTGACAAAAA
* *
1499048 AATACTTTAGGTATTTATGTTGACAAAAA
1 AATACTTTAGGTACTTATTTTGACAAAAA
* *
1499077 AGATAACTTTATGTACTTATTTTTATCAAAAA
1 A-AT-ACTTTAGGTACTTATTTTGA-CAAAAA
1499109 AATACTTTAGGTACTT
1 AATACTTTAGGTACTT
1499125 CAATAAAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
28 20 0.32
29 4 0.06
30 14 0.22
31 18 0.29
32 7 0.11
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (29 bp):
AATACTTTAGGTACTTATTTTGACAAAAA
Found at i:1503455 original size:20 final size:21
Alignment explanation
Indices: 1503414--1503455 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1503404 AAGTTAAAAT
*
1503414 ATCGATACTTATGATATGTTG
1 ATCGATACTTATGATATATTG
*
1503435 ATCGATACTT-TTATATATTG
1 ATCGATACTTATGATATATTG
1503455 A
1 A
1503456 GAAAGTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (21 bp):
ATCGATACTTATGATATATTG
Found at i:1510009 original size:3 final size:3
Alignment explanation
Indices: 1510001--1510034 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
1509991 AATAGGAAAT
1510001 ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
1510035 TATATAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1510042 original size:16 final size:16
Alignment explanation
Indices: 1510001--1510034 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1509991 AATAGGAAAT
1510001 ATAATAAT-AATAATA
1 ATAATAATAAATAATA
1510016 ATAATAATAAATAATA
1 ATAATAATAAATAATA
1510032 ATA
1 ATA
1510035 TATATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATAATAAATAATA
Found at i:1510060 original size:25 final size:25
Alignment explanation
Indices: 1510032--1510079 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1510022 ATAAATAATA
1510032 ATAT-ATATAAAAAGTTTTCAAAAAC
1 ATATCATATAAAAA-TTTTCAAAAAC
*
1510057 ATATCATATATAAATTTTCAAAA
1 ATATCATATAAAAATTTTCAAAA
1510080 TGCTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.35
Consensus pattern (25 bp):
ATATCATATAAAAATTTTCAAAAAC
Found at i:1510099 original size:13 final size:12
Alignment explanation
Indices: 1510077--1510103 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1510067 TAAATTTTCA
1510077 AAATGCTTTTTT
1 AAATGCTTTTTT
1510089 AAATGCTTTTTT
1 AAATGCTTTTTT
1510101 AAA
1 AAA
1510104 AAACTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (12 bp):
AAATGCTTTTTT
Found at i:1510220 original size:40 final size:40
Alignment explanation
Indices: 1510095--1510240 Score: 147
Period size: 42 Copynumber: 3.6 Consensus size: 40
1510085 TTTTAAATGC
* ** *
1510095 TTTTTTAAAAAACTATATATTATACGTATTTTCAAAAACG
1 TTTTTTAAAAAACTATATAATATATATATATTCAAAAACG
* **
1510135 --TTTTAAAAAATTATATAATATATATA-ACTTCAAAAATATT
1 TTTTTTAAAAAACTATATAATATATATATA-TTC-AAAA-ACG
* *
1510175 TTTTTTAAAAAATTATATATTATATATATATTC-AAAACG
1 TTTTTTAAAAAACTATATAATATATATATATTCAAAAACG
1510214 TCTTTTTAAAAAACTATATAATATATA
1 T-TTTTTAAAAAACTATATAATATATA
1510241 AATGTTTTCA
Statistics
Matches: 87, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
38 25 0.29
39 6 0.07
40 27 0.31
42 28 0.32
43 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (40 bp):
TTTTTTAAAAAACTATATAATATATATATATTCAAAAACG
Found at i:1510289 original size:35 final size:34
Alignment explanation
Indices: 1510240--1510463 Score: 151
Period size: 35 Copynumber: 6.4 Consensus size: 34
1510230 TATAATATAT
*
1510240 AAATGTTTTCAAAACTATATACTATATAATTTTCA
1 AAATGTTTTAAAAACTATATA-TATATAATTTTCA
1510275 AAATGTTTTAAAAACTATATATTATATATATTTTTCA
1 AAATGTTTTAAAAACTATATA-TATATA-A-TTTTCA
1510312 AAATGACTTTTAAAAACTATATA-ATAT-A---T--
1 AAATG--TTTTAAAAACTATATATATATAATTTTCA
** * *
1510341 AAATGTTTTCGAAACTATATATTATATATTTTTAA
1 AAATGTTTTAAAAACTATATA-TATATAATTTTCA
* * *
1510376 AAATGTTTTCAAAATTATACA-ATATATATTTTCGA
1 AAATGTTTTAAAAACTATATATATATA-ATTTTC-A
* * *
1510411 AAACCGTTTTCTGAAAACTATATAT-TATACTTTGTCAA
1 AAA-TG-TTT-TAAAAACTATATATATATAATTT-TC-A
1510449 AAATGTTTTGAAAAA
1 AAATGTTTT-AAAAA
1510464 AAAACTATAT
Statistics
Matches: 151, Mismatches: 18, Indels: 39
0.73 0.09 0.19
Matches are distributed among these distances:
27 14 0.09
29 9 0.06
31 1 0.01
33 6 0.04
34 4 0.03
35 50 0.33
36 9 0.06
37 22 0.15
38 20 0.13
39 16 0.11
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (34 bp):
AAATGTTTTAAAAACTATATATATATAATTTTCA
Found at i:1510356 original size:66 final size:62
Alignment explanation
Indices: 1510275--1510403 Score: 168
Period size: 62 Copynumber: 2.0 Consensus size: 62
1510265 ATAATTTTCA
* *
1510275 AAATGTTTTAAAAACTATATATTATATATATTTTTCAAAATGACTTTTAAAAACTATATAATATA
1 AAATGTTTTAAAAACTATATA-T-TATATATTTTTAAAAATG--TTTTAAAAACTATACAATATA
1510340 T
62 T
** * *
1510341 AAATGTTTTCGAAACTATATATTATATATTTTTAAAAATGTTTTCAAAATTATACAATATAT
1 AAATGTTTTAAAAACTATATATTATATATTTTTAAAAATGTTTTAAAAACTATACAATATAT
1510403 A
1 A
1510404 TTTTCGAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
62 20 0.35
64 17 0.30
65 1 0.02
66 19 0.33
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (62 bp):
AAATGTTTTAAAAACTATATATTATATATTTTTAAAAATGTTTTAAAAACTATACAATATAT
Found at i:1510359 original size:101 final size:102
Alignment explanation
Indices: 1510177--1510407 Score: 317
Period size: 101 Copynumber: 2.3 Consensus size: 102
1510167 AAAATATTTT
* *
1510177 TTTTAAAAAATTATATATTATATATA-TATTCAAAACGTCTTTTTAAAAAACTATATAATATATA
1 TTTT-AAAAA-TATATATTATATATATTTTTCAAAACGACTTTTTAAAAAACTATATAATATATA
*
1510241 AATGTTTTCAAAACTATATACTATATAATTTTCAAAATG
64 AATGTTTTCAAAACTATATACTATATAATTTTAAAAATG
*
1510280 TTTTAAAAACTATATATTATATATATTTTTCAAAATGAC-TTTT-AAAAACTATATAATATATAA
1 TTTTAAAAA-TATATATTATATATATTTTTCAAAACGACTTTTTAAAAAACTATATAATATATAA
* * *
1510343 ATGTTTTCGAAACTATATATTATATATTTTTAAAAATG
65 ATGTTTTCAAAACTATATACTATATAATTTTAAAAATG
* **
1510381 TTTTCAAAAT-TATACAATATATATTTT
1 TTTTAAAAATATATATTATATATATTTT
1510408 CGAAAACCGT
Statistics
Matches: 116, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
99 15 0.13
100 1 0.01
101 62 0.53
102 24 0.21
103 14 0.12
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (102 bp):
TTTTAAAAATATATATTATATATATTTTTCAAAACGACTTTTTAAAAAACTATATAATATATAAA
TGTTTTCAAAACTATATACTATATAATTTTAAAAATG
Found at i:1511520 original size:9 final size:9
Alignment explanation
Indices: 1511508--1511539 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
1511498 TTGATATTTT
1511508 ATTAAAAAA
1 ATTAAAAAA
1511517 ATTAAAAAAA
1 ATT-AAAAAA
1511527 ATTAAAAAA
1 ATTAAAAAA
1511536 ATTA
1 ATTA
1511540 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:1511526 original size:10 final size:10
Alignment explanation
Indices: 1511511--1511536 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1511501 ATATTTTATT
1511511 AAAAAAATTA
1 AAAAAAATTA
1511521 AAAAAAATTA
1 AAAAAAATTA
1511531 AAAAAA
1 AAAAAA
1511537 TTATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:1512634 original size:5 final size:5
Alignment explanation
Indices: 1512624--1512655 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1512614 TTCTATAACT
1512624 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1512656 AAAGAAGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1513821 original size:39 final size:39
Alignment explanation
Indices: 1513743--1513837 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
1513733 AAGACTCTAC
* * * * *
1513743 TGGCATCTTCAGGAAAATGAAGAAAACCTCACGATTGCA
1 TGGCATCTTCAAGCAAATGAAGAAAACCCCAAGAGTGCA
*
1513782 TGGCATCTTCAAGCAAAT-ATAGAATACCCCAAGAGTGCA
1 TGGCATCTTCAAGCAAATGA-AGAAAACCCCAAGAGTGCA
*
1513821 TGGTATCTTCAGAGCAA
1 TGGCATCTTCA-AGCAA
1513838 TAAGAAGCTC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.02
39 41 0.87
40 5 0.11
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (39 bp):
TGGCATCTTCAAGCAAATGAAGAAAACCCCAAGAGTGCA
Found at i:1513942 original size:3 final size:3
Alignment explanation
Indices: 1513936--1513972 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1513926 AAAAGGTGTA
1513936 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1513973 TTGGATTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1514593 original size:40 final size:35
Alignment explanation
Indices: 1514502--1514623 Score: 154
Period size: 35 Copynumber: 3.4 Consensus size: 35
1514492 TAAAACTTGT
*
1514502 AAAATAATCCTCAATTTCATTCTAAACCCCAATTTCC
1 AAAATAAT--TCAATTTCATTCTAAACCCCAAATTCC
* *
1514539 AAAGTAATTCAATTTCATTCTAAACCCTAAATTCC
1 AAAATAATTCAATTTCATTCTAAACCCCAAATTCC
** * *
1514574 AAAATAATTCAATTAAATTTTAAACCCCAAATTCT
1 AAAATAATTCAATTTCATTCTAAACCCCAAATTCC
*
1514609 AAAATACTTCAATTT
1 AAAATAATTCAATTT
1514624 AAGGTTTAGA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 67 0.91
37 7 0.09
ACGTcount: A:0.43, C:0.22, G:0.01, T:0.34
Consensus pattern (35 bp):
AAAATAATTCAATTTCATTCTAAACCCCAAATTCC
Found at i:1514687 original size:35 final size:35
Alignment explanation
Indices: 1514619--1514693 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
1514609 AAAATACTTC
* * *
1514619 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
1514654 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
1514689 AATTT
1 AATTT
1514694 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:1516165 original size:29 final size:27
Alignment explanation
Indices: 1516092--1516214 Score: 93
Period size: 29 Copynumber: 4.3 Consensus size: 27
1516082 TATTATCAAA
* * *
1516092 AATATATTCTTTAACTATTAAAAATAT
1 AATATATTATTTAAATATTTAAAATAT
* *
1516119 ACAAATATTATTTTAATAGTTTAAAATAT
1 A-ATATATTATTTAAATA-TTTAAAATAT
** *
1516148 AATATATTATTATAAATATATTACTATAA
1 AATATATTATT-TAAATAT-TTAAAATAT
* *
1516177 AATATACTATTTTAATTATTTTAAAATATT
1 AATATATTA-TTTAAATA-TTTAAAATA-T
1516207 AATATATT
1 AATATATT
1516215 TGGATCGAAT
Statistics
Matches: 73, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
27 1 0.01
28 22 0.30
29 40 0.55
30 10 0.14
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (27 bp):
AATATATTATTTAAATATTTAAAATAT
Found at i:1516184 original size:12 final size:14
Alignment explanation
Indices: 1516148--1516186 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1516138 TTTAAAATAT
*
1516148 AATATATTATTATA
1 AATATATTACTATA
1516162 AATATATTACTATA
1 AATATATTACTATA
1516176 AA-ATA-TACTAT
1 AATATATTACTAT
1516187 TTTAATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 6 0.25
13 3 0.12
14 15 0.62
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATATTACTATA
Found at i:1535547 original size:40 final size:41
Alignment explanation
Indices: 1535503--1535590 Score: 97
Period size: 43 Copynumber: 2.1 Consensus size: 41
1535493 ACGCATGAGT
* * **
1535503 CGTGTCATCCTTCG-ACCAGATTTCCTCATCACATAGGAAC
1 CGTGTCACCCTTAGAACCAGACGTCCTCATCACATAGGAAC
* *
1535543 CGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAAC
1 CGTGTCACCCTTAG--AACCAGACGTCCTCATCACATAGGAAC
1535586 CGTGT
1 CGTGT
1535591 TATCACCTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
40 12 0.31
43 27 0.69
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (41 bp):
CGTGTCACCCTTAGAACCAGACGTCCTCATCACATAGGAAC
Found at i:1535676 original size:130 final size:133
Alignment explanation
Indices: 1535411--1535767 Score: 373
Period size: 130 Copynumber: 2.7 Consensus size: 133
1535401 TAGGAGCAAC
* * *
1535411 GTCAACATTAGATAACCAGCCATCCTCATCGCGTAGGAACCAAGTTATCACCCTTCCTAAAGATG
1 GTCAACCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCACCCTT-CT-AAGATG
** * **
1535476 GCCAAGAACTCTTCATCACGCATGAGTCGTGTCATCCTTCGACCAGATTTCCTCATCACATAGGA
64 GCCAAGAACTCTTCATCACGCATGAGTAATGTCATCCATCGACCAGAACTCCTCATCACATAGGA
1535541 ACCGT
129 ACCGT
* **
1535546 GTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA-CCTT-T-AGATGGC
1 GTCAACCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCACCCTTCTAAGATGGC
* * * * * *
1535608 CAAGAACTCTTCATCATGTATGAGTAATGTCATCCCAT-GACCAGAACTCTTCATCACGTATGAG
66 CAAGAACTCTTCATCACGCATGAGTAATGTCAT-CCATCGACCAGAACTCCTCATCACATAGGAA
1535672 CCGT
130 CCGT
* * * * * * *
1535676 GTCAACCTCAGATAACCAGCCGTCCCCAGCAGAGT-GGAACCATGTTATCATCTTTCCTAAAGAT
1 GTCAACCTTAGATAACCAGCCGTCCTCATCA-CGTAGGAACCAAGTTATCACCCTT-CT-AAGAT
* * *
1535740 GGCCAAGATTCTCTTCATCGCGGATGAG
63 GGCCAAGA-ACTCTTCATCACGCATGAG
1535768 CAGTGTCGTC
Statistics
Matches: 186, Mismatches: 28, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
130 101 0.54
131 8 0.04
132 1 0.01
133 1 0.01
134 4 0.02
135 56 0.30
136 15 0.08
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (133 bp):
GTCAACCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCACCCTTCTAAGATGGC
CAAGAACTCTTCATCACGCATGAGTAATGTCATCCATCGACCAGAACTCCTCATCACATAGGAAC
CGT
Found at i:1537972 original size:2 final size:2
Alignment explanation
Indices: 1537967--1538002 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1537957 GGTTATGACA
1537967 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
1538003 GAGCCAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1542858 original size:6 final size:6
Alignment explanation
Indices: 1542833--1542859 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1542823 TAATATTAAT
1542833 AAATTA AAATTA AAATTA AAATTA AAA
1 AAATTA AAATTA AAATTA AAATTA AAA
1542860 AATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:1542886 original size:17 final size:17
Alignment explanation
Indices: 1542862--1542907 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
1542852 AATTAAAAAA
1542862 TATATATATATATAATAT
1 TATATATATATATAAT-T
1542880 T-TATATAT-T-TAATT
1 TATATATATATATAATT
*
1542894 TAAATATATATATA
1 TATATATATATATA
1542908 CCCGACCCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
14 2 0.08
15 10 0.42
16 2 0.08
17 9 0.38
18 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATATATAATT
Found at i:1543722 original size:20 final size:21
Alignment explanation
Indices: 1543685--1543723 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1543675 TATTTTTTAG
*
1543685 AATTTATTTTTCATAAATTGT
1 AATTCATTTTTCATAAATTGT
1543706 AATTCATTTTTCA-AAATT
1 AATTCATTTTTCATAAATT
1543724 CATTTTCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (21 bp):
AATTCATTTTTCATAAATTGT
Found at i:1562402 original size:29 final size:30
Alignment explanation
Indices: 1562316--1562403 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 30
1562306 TCGAGTGATC
* *
1562316 ATTTTATAACTTTTAATAATTAAGAGATTTA
1 ATTTTATAATTTTTAATAATAAAGAGA-TTA
** * *
1562347 ACATAACAATTTTT-ATAATTAAA-AGATT-
1 ATTTTATAATTTTTAATAA-TAAAGAGATTA
1562375 ATTTTATAATTTTTAATAATAAAGAGATT
1 ATTTTATAATTTTTAATAATAAAGAGATT
1562404 CAATAGAATA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
28 14 0.32
29 11 0.25
30 7 0.16
31 12 0.27
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (30 bp):
ATTTTATAATTTTTAATAATAAAGAGATTA
Found at i:1566389 original size:45 final size:45
Alignment explanation
Indices: 1566319--1566469 Score: 230
Period size: 45 Copynumber: 3.3 Consensus size: 45
1566309 TTTATTTTTG
* *
1566319 TTTTTCGAATAAATGCATGCAAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTTGAAT-AA-GCATGCGAACTAGATATCATGCGGTTAGGTTTA
*
1566366 TTTTTTGAATAAGCATGCGAACTAGATGTCATGCGGTTAGGTTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
*
1566411 TTTTTTGAATAAGCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1566457 TTTTTGTGAATAA
1 TTTTT-TGAATAA
1566470 CAAAGCATGG
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
45 70 0.72
46 11 0.11
47 16 0.16
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (45 bp):
TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
Found at i:1576142 original size:15 final size:14
Alignment explanation
Indices: 1576117--1576204 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
1576107 AAGAAGAAAT
1576117 AAAAGAGAAAATGAA
1 AAAAGA-AAAATGAA
1576132 AAAATGAAAAA--AA
1 AAAA-GAAAAATGAA
*
1576145 TAATAATAAAAATGAGA
1 -AA-AAGAAAAATGA-A
*
1576162 AGAAGAAAAA-GAA
1 AAAAGAAAAATGAA
1576175 GAAAAGAAAAATGAGAA
1 -AAAAGAAAAAT--GAA
1576192 AAAAGAAAAATGA
1 AAAAGAAAAATGA
1576205 TGGAAAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 21
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.05
14 20 0.34
15 17 0.29
16 15 0.25
17 4 0.07
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAAGAAAAATGAA
Found at i:1576146 original size:29 final size:27
Alignment explanation
Indices: 1576113--1576287 Score: 99
Period size: 29 Copynumber: 6.1 Consensus size: 27
1576103 CTTGAAGAAG
1576113 AAATAAAAGAGAAAATGAAAAAATGAAAA
1 AAATAAAAGA-AAAATG-AAAAATGAAAA
*
1576142 AAATAATAATAAAAATGAGAAGAA-GAAAA
1 AAATAA-AAGAAAAATGA-AA-AATGAAAA
*
1576171 AGAAGAAAAGAAAAATGAGAAAA--AAGAA
1 A-AATAAAAGAAAAATGA-AAAATGAA-AA
* ** *
1576199 AAATGATGGAAAAAATG-AAAAGGAAAA
1 AAATAAAAG-AAAAATGAAAAATGAAAA
*
1576226 AAA-AAGAAGAAAAAATGGAAAATGGAAGAAA
1 AAATAA-AAG-AAAAATGAAAAAT-G-A-AAA
* *
1576257 AAATGAAAGAGAAAATGAAAAATAAAAA
1 AAATAAAAGA-AAAATGAAAAATGAAAA
1576285 AAA
1 AAA
1576288 GAAATAAAAG
Statistics
Matches: 117, Mismatches: 14, Indels: 31
0.72 0.09 0.19
Matches are distributed among these distances:
26 5 0.04
27 20 0.17
28 25 0.21
29 35 0.30
30 11 0.09
31 20 0.17
32 1 0.01
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (27 bp):
AAATAAAAGAAAAATGAAAAATGAAAA
Found at i:1576197 original size:16 final size:16
Alignment explanation
Indices: 1576152--1576219 Score: 70
Period size: 16 Copynumber: 4.2 Consensus size: 16
1576142 AAATAATAAT
*
1576152 AAAAATGAG-AAGAAG
1 AAAAATGAGAAAAAAG
*
1576167 AAAAA-GA-AGAAAAG
1 AAAAATGAGAAAAAAG
1576181 AAAAATGAGAAAAAAG
1 AAAAATGAGAAAAAAG
1576197 AAAAATGATGGAAAAAATG
1 AAAAATGA--GAAAAAA-G
1576216 AAAA
1 AAAA
1576220 GGAAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
14 11 0.25
15 7 0.16
16 14 0.32
18 7 0.16
19 5 0.11
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (16 bp):
AAAAATGAGAAAAAAG
Found at i:1576230 original size:45 final size:46
Alignment explanation
Indices: 1576169--1576291 Score: 130
Period size: 46 Copynumber: 2.7 Consensus size: 46
1576159 AGAAGAAGAA
*
1576169 AAAGAAGAAAAGAAAAATGAGAAAAAAGAAAAAT-GATGGAAAAAATG
1 AAAG-AGAAAAGAAAAATGAGAAAAAAGAAAAATGGA-AGAAAAAATG
*
1576216 AAA-AGGAAAA-AAAAA-GAAGAAAAAATGGAAAATGGAAGAAAAAATG
1 AAAGA-GAAAAGAAAAATG-AGAAAAAA-GAAAAATGGAAGAAAAAATG
*
1576262 AAAGAGAAAATGAAAAAT-AAAAAAAAGAAA
1 AAAGAGAAAA-GAAAAATGAGAAAAAAGAAA
1576292 TAAAAGGAGG
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
44 1 0.02
45 14 0.22
46 31 0.48
47 13 0.20
48 5 0.08
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (46 bp):
AAAGAGAAAAGAAAAATGAGAAAAAAGAAAAATGGAAGAAAAAATG
Found at i:1576247 original size:19 final size:19
Alignment explanation
Indices: 1576225--1576261 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1576215 GAAAAGGAAA
1576225 AAAAAAGAAGAAAAAATGG
1 AAAAAAGAAGAAAAAATGG
**
1576244 AAAATGGAAGAAAAAATG
1 AAAAAAGAAGAAAAAATG
1576262 AAAGAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.08
Consensus pattern (19 bp):
AAAAAAGAAGAAAAAATGG
Found at i:1577624 original size:37 final size:37
Alignment explanation
Indices: 1577574--1577680 Score: 205
Period size: 37 Copynumber: 2.9 Consensus size: 37
1577564 TCAAAATAGT
1577574 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAG
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAG
1577611 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAG
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAG
*
1577648 TCAATCTTAAGCTTTCACGGAAGAGTAGTGAAG
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAG
1577681 AAAACTTATT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAG
Found at i:1577837 original size:110 final size:110
Alignment explanation
Indices: 1577700--1578176 Score: 733
Period size: 110 Copynumber: 4.3 Consensus size: 110
1577690 TTCATGAAGA
* *
1577700 TCGAGTTATATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTATGAAGATTATTCGAGTTCTA
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTATTCGAGTTCTA
* **
1577765 TACTCCCTGAACGGATAGGGTGCATACCCGTTTGTTGAAGATTGT
66 TACTCCCTGAACGGATAGGGAGCGGACCCGTTTGTTGAAGATTGT
1577810 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTATTCGAGTTCTA
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTATTCGAGTTCTA
* *
1577875 TACTCCGTGAACAGATAGGGAGCGGACCCGTTTGTTGAAGATTGT
66 TACTCCCTGAACGGATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* *
1577920 TCGAGTTCTATACTCTTTGAAGGAATAGAGAGCGGACCCG-TTTATTGAAGATTGTTCGAGTTCT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTATTCGAGTTCT
* *
1577984 ATACTCCCTGAACGGGTAGGGAGCGGACCCGTTTATTGAAGATTGT
65 ATACTCCCTGAACGGATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * *
1578030 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGGTTTATGAAGATTGTTCAAGTTCTA
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTATTCGAGTTCTA
* *
1578095 TACTCCCTGAACGGATAGGGAGCGGACTCATTT-TATGAAGATTGT
66 TACTCCCTGAACGGATAGGGAGCGGACCCGTTTGT-TGAAGATTGT
* * * * *
1578140 TCGAGTTTTATACTCCCTGAAGAAATAGGGAGTGGAC
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1578177 TTATCATTTG
Statistics
Matches: 341, Mismatches: 23, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
109 5 0.01
110 332 0.97
111 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (110 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTATTCGAGTTCTA
TACTCCCTGAACGGATAGGGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:1578177 original size:55 final size:55
Alignment explanation
Indices: 1577700--1578176 Score: 592
Period size: 55 Copynumber: 8.7 Consensus size: 55
1577690 TTCATGAAGA
* * * * *
1577700 TCGAGTTATATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTATGAAGATTAT
1 TCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTTATGAAGATTGT
* **
1577755 TCGAGTTCTATACTCCCTGAACGG-ATAGGGTGCATACCCGTTTGT-TGAAGATTGT
1 TCGAGTTCTATACTCCCTGAA-GGAATAGGGAGCGGACCCGTTT-TATGAAGATTGT
* * *
1577810 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTAT
1 TCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTTATGAAGATTGT
* *
1577865 TCGAGTTCTATACTCCGTGAA-CAGATAGGGAGCGGACCCGTTTGT-TGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAGGA-ATAGGGAGCGGACCCGTTT-TATGAAGATTGT
** *
1577920 TCGAGTTCTATACTCTTTGAAGGAATAGAGAGCGGACCCG-TTTATTGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTTA-TGAAGATTGT
*
1577975 TCGAGTTCTATACTCCCTGAACGG-GTAGGGAGCGGACCCG-TTTATTGAAGATTGT
1 TCGAGTTCTATACTCCCTGAA-GGAATAGGGAGCGGACCCGTTTTA-TGAAGATTGT
* * *
1578030 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGGTTTATGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTTATGAAGATTGT
* * *
1578085 TCAAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACTCATTTTATGAAGATTGT
1 TCGAGTTCTATACTCCCTGAA-GGAATAGGGAGCGGACCCGTTTTATGAAGATTGT
* * *
1578140 TCGAGTTTTATACTCCCTGAAGAAATAGGGAGTGGAC
1 TCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGAC
1578177 TTATCATTTG
Statistics
Matches: 369, Mismatches: 39, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
53 1 0.00
54 9 0.02
55 346 0.94
56 13 0.04
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (55 bp):
TCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTTATGAAGATTGT
Found at i:1588969 original size:27 final size:23
Alignment explanation
Indices: 1588910--1588965 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1588900 TACACACAAG
* *
1588910 CATACAACAATACCTATAGGCCA
1 CATACATCAACACCTATAGGCCA
1588933 CATACATCAACACCTATAGGCCA
1 CATACATCAACACCTATAGGCCA
1588956 CATACATCAA
1 CATACATCAA
1588966 TCAATACCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.32, G:0.07, T:0.18
Consensus pattern (23 bp):
CATACATCAACACCTATAGGCCA
Found at i:1601388 original size:186 final size:187
Alignment explanation
Indices: 1601069--1601461 Score: 664
Period size: 186 Copynumber: 2.1 Consensus size: 187
1601059 ATAAAATTTT
1601069 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
*
1601134 TTTAAGATCCAATAACTTTTAAACCTAAATAAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATACAATAACTTTTAAACCTAAATAAATATTAATTAATTAAAAAATTTATATAAAATTT
* *
1601199 TTATTTTATAATTATATATTATTTAAATTAATTGTAAATTGTTTTTCTGAATTA-AA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTCTGAATTATAA
* *
1601255 AAATATTAAATATATTATATATAACATATGGGTTCAGCCCAAACTATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
* * * *
1601320 TTTAAGATATAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTTTATATAAATTTT
66 TTTAAGATACAATAACTTTTAAACCTAAATAAATATTAATTAATTAAAAAATTTATATAAAATTT
*
1601385 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTATAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTCTGAATTATAA
* *
1601442 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1601462 AATTAGAAAA
Statistics
Matches: 194, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
186 182 0.94
187 12 0.06
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (187 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATACAATAACTTTTAAACCTAAATAAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTCTGAATTATAA
Found at i:1604992 original size:30 final size:31
Alignment explanation
Indices: 1604948--1605016 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
1604938 ATACACTTTT
* * *
1604948 GGTCAATTATGTTATTGTTTTATTAAGTTTG
1 GGTCACTTACGTTATCGTTTTATTAAGTTTG
*
1604979 GGT-ACTTACGTTATCGTTTTATTAAGTTTT
1 GGTCACTTACGTTATCGTTTTATTAAGTTTG
1605009 GGTCACTT
1 GGTCACTT
1605017 GAACGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.20, C:0.09, G:0.19, T:0.52
Consensus pattern (31 bp):
GGTCACTTACGTTATCGTTTTATTAAGTTTG
Found at i:1605887 original size:18 final size:18
Alignment explanation
Indices: 1605864--1605912 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
1605854 TAAAAATGTC
1605864 AGCAAACCATTAAAGGTT
1 AGCAAACCATTAAAGGTT
1605882 AGCAAACCATTAAAGGTT
1 AGCAAACCATTAAAGGTT
*
1605900 AACAAACCATTAA
1 AGCAAACCATTAA
1605913 CCTTCAGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.20
Consensus pattern (18 bp):
AGCAAACCATTAAAGGTT
Found at i:1611861 original size:54 final size:54
Alignment explanation
Indices: 1611779--1611886 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
1611769 ACCCATTTGA
* *
1611779 CACGGTGCCTTCAAGTTCTAGGGGGAGGCATTCAACTGCGAGCTTCTTCGACCT
1 CACGGTGCCTTCAAGTTCCAGGGAGAGGCATTCAACTGCGAGCTTCTTCGACCT
* *
1611833 CACGGTGCCTTCAAGTTCCAGGGAGAGGCATTCAACTGTGAGCTTCTTTGACCT
1 CACGGTGCCTTCAAGTTCCAGGGAGAGGCATTCAACTGCGAGCTTCTTCGACCT
1611887 TAATGTGGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (54 bp):
CACGGTGCCTTCAAGTTCCAGGGAGAGGCATTCAACTGCGAGCTTCTTCGACCT
Found at i:1617250 original size:3 final size:3
Alignment explanation
Indices: 1617242--1617304 Score: 63
Period size: 3 Copynumber: 20.0 Consensus size: 3
1617232 AATTTAGTAG
* * **
1617242 ATA ATA ATA ATA ATA TATA ATTA TTA ATA ATA ACA ATA CCA ATA ATA
1 ATA ATA ATA ATA ATA -ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
1617289 ATA ATA ATA ATCA ATA
1 ATA ATA ATA AT-A ATA
1617305 TTAAAGGGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
3 41 0.84
4 8 0.16
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1617556 original size:41 final size:36
Alignment explanation
Indices: 1617520--1617591 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
1617510 TTCAATTAAA
1617520 AAAATAATTACCGTTTTCGTAACATTTTAAGTTCAA-T
1 AAAA-AATTA-CGTTTTCGTAACATTTTAAGTTCAATT
* * *
1617557 CAAACATTAGGTTTTCGTAACATTTTAAGTTCAAT
1 AAAAAATTACGTTTTCGTAACATTTTAAGTTCAAT
1617592 CAAACATTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 24 0.77
36 4 0.13
37 3 0.10
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (36 bp):
AAAAAATTACGTTTTCGTAACATTTTAAGTTCAATT
Found at i:1617564 original size:19 final size:19
Alignment explanation
Indices: 1617540--1617599 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1617530 CCGTTTTCGT
1617540 AACATTTTAAGTTCAATCA
1 AACATTTTAAGTTCAATCA
* * *
1617559 AACA--TTAGGTT--TTCGT
1 AACATTTTAAGTTCAATC-A
1617575 AACATTTTAAGTTCAATCA
1 AACATTTTAAGTTCAATCA
1617594 AACATT
1 AACATT
1617600 AGGTTATCGT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
15 2 0.07
16 4 0.13
17 6 0.20
18 6 0.20
19 10 0.33
20 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (19 bp):
AACATTTTAAGTTCAATCA
Found at i:1617572 original size:35 final size:35
Alignment explanation
Indices: 1617532--1617610 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
1617522 AATAATTACC
1617532 GTTTTCGTAACATTTTAAGTTCAATCAAACATTAG
1 GTTTTCGTAACATTTTAAGTTCAATCAAACATTAG
1617567 GTTTTCGTAACATTTTAAGTTCAATCAAACATTAG
1 GTTTTCGTAACATTTTAAGTTCAATCAAACATTAG
*
1617602 GTTATCGTA
1 GTTTTCGTA
1617611 CCGTTTTTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (35 bp):
GTTTTCGTAACATTTTAAGTTCAATCAAACATTAG
Found at i:1619543 original size:2 final size:2
Alignment explanation
Indices: 1619531--1619565 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1619521 ATAAACTAAC
* *
1619531 GA GA GA AA GA GA GA GA GA GA GA GA GA AA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1619566 GAAAATACAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1619546 original size:10 final size:10
Alignment explanation
Indices: 1619531--1619565 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
1619521 ATAAACTAAC
1619531 GAGAGAAAGA
1 GAGAGAAAGA
*
1619541 GAGAGAGAGA
1 GAGAGAAAGA
1619551 GAGAGAAAGA
1 GAGAGAAAGA
1619561 GAGAG
1 GAGAG
1619566 GAAAATACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (10 bp):
GAGAGAAAGA
Found at i:1620393 original size:25 final size:24
Alignment explanation
Indices: 1620333--1620394 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
1620323 GTTTAATTTT
*
1620333 TTAAAAAATAAAAATTATTTTAAA
1 TTAAAAAATAAAAATTATTTAAAA
*
1620357 TTATAAATATAAAAA-TATTTAAATA
1 TTA-AAAAATAAAAATTATTTAAA-A
1620382 TTCAAAAAATAAA
1 TT-AAAAAATAAA
1620395 TATAAAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 10 0.31
25 21 0.66
26 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
TTAAAAAATAAAAATTATTTAAAA
Found at i:1620410 original size:21 final size:21
Alignment explanation
Indices: 1620386--1620433 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1620376 TAAATATTCA
* *
1620386 AAAAATAAATATAAAAATGCT
1 AAAAATAAAAATAAAAATACT
* *
1620407 AAAAATAAAAATTAAATTACT
1 AAAAATAAAAATAAAAATACT
1620428 AAAAAT
1 AAAAAT
1620434 TGAATCTACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (21 bp):
AAAAATAAAAATAAAAATACT
Found at i:1621278 original size:29 final size:30
Alignment explanation
Indices: 1621205--1621278 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 30
1621195 AAAAATAAAT
1621205 TTTTGTAATAGTTTTAGTATATTTAATAGGTA
1 TTTT-TAATA-TTTTAGTATATTTAATAGGTA
* ***
1621237 TATTTAACT-TTTTAGTA-ATTTAATTTTTA
1 TTTTTAA-TATTTTAGTATATTTAATAGGTA
1621266 TTTTTAATATTTT
1 TTTTTAATATTTT
1621279 TATATGTAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
28 1 0.03
29 19 0.54
30 8 0.23
31 3 0.09
32 4 0.11
ACGTcount: A:0.30, C:0.01, G:0.08, T:0.61
Consensus pattern (30 bp):
TTTTTAATATTTTAGTATATTTAATAGGTA
Found at i:1621326 original size:23 final size:24
Alignment explanation
Indices: 1621290--1621354 Score: 60
Period size: 26 Copynumber: 2.7 Consensus size: 24
1621280 ATATGTAACT
* *
1621290 TTTTG-AATATTTTAATAATTTTG
1 TTTTGAAAAATTTAAATAATTTTG
*
1621313 TTTTGAAAAATTTAAAATAATTTTTA
1 TTTTGAAAAATTT-AAATAA-TTTTG
**
1621339 TTTTTTAAAATTTAAA
1 TTTTGAAAAATTTAAA
1621355 CAAGTCATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.15
24 6 0.18
25 8 0.24
26 15 0.44
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (24 bp):
TTTTGAAAAATTTAAATAATTTTG
Found at i:1626936 original size:26 final size:25
Alignment explanation
Indices: 1626886--1626941 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1626876 TGTTAACGGT
*
1626886 ATAAAATTTTAAAAAAATAGCATAA
1 ATAAAATTTTAAAAAAATAACATAA
*
1626911 ATAAAATTTTAGAGAAAAA-AATATAA
1 ATAAAATTTTA-A-AAAAATAACATAA
1626937 ATAAA
1 ATAAA
1626942 TATGTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 11 0.41
26 11 0.41
27 5 0.19
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (25 bp):
ATAAAATTTTAAAAAAATAACATAA
Found at i:1627258 original size:24 final size:24
Alignment explanation
Indices: 1627226--1627277 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1627216 AATCATATTC
*
1627226 TGAAACTAAATAAGGAATGAGTGA
1 TGAAACTAAATAAAGAATGAGTGA
1627250 TGAAACTAAATAAAGAATGAGTGA
1 TGAAACTAAATAAAGAATGAGTGA
1627274 TGAA
1 TGAA
1627278 TACCATGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.23, T:0.21
Consensus pattern (24 bp):
TGAAACTAAATAAAGAATGAGTGA
Found at i:1633665 original size:15 final size:15
Alignment explanation
Indices: 1633645--1633679 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1633635 CCGTAGGACC
*
1633645 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGA
1633660 ACTACGTCCCGAAGA
1 ACTACGTCCCGAAGA
1633675 ACTAC
1 ACTAC
1633680 AGAACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.34, G:0.20, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGA
Found at i:1640479 original size:15 final size:15
Alignment explanation
Indices: 1640459--1640493 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1640449 CCGTAGGACC
1640459 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1640474 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1640489 ACTAC
1 ACTAC
1640494 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:1643806 original size:27 final size:27
Alignment explanation
Indices: 1643766--1643818 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1643756 ATTTCCCCTC
* *
1643766 CCCTTCTCCGGTGCTCTCCCCATCATT
1 CCCTTCGCCGGTGCTATCCCCATCATT
*
1643793 CCCTTCGCCTGTGCTATCCCCATCAT
1 CCCTTCGCCGGTGCTATCCCCATCAT
1643819 CCCCACTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.09, C:0.47, G:0.11, T:0.32
Consensus pattern (27 bp):
CCCTTCGCCGGTGCTATCCCCATCATT
Found at i:1645076 original size:31 final size:31
Alignment explanation
Indices: 1645023--1645083 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1645013 CAACGTCCAA
*
1645023 GCACCTAAAAAGGTAATAGAGAAAACGTTAC
1 GCACCTAAAAAGGTAACAGAGAAAACGTTAC
* *
1645054 GCACCTAAAATA-GTAACGGAGAAAGCGTTA
1 GCACCTAAAA-AGGTAACAGAGAAAACGTTA
1645084 AACATCGGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.16
Consensus pattern (31 bp):
GCACCTAAAAAGGTAACAGAGAAAACGTTAC
Found at i:1653256 original size:14 final size:14
Alignment explanation
Indices: 1653237--1653285 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
1653227 CGTTAAAATG
1653237 ATAAACGAACACAA
1 ATAAACGAACACAA
1653251 ATAAAC-AA-AC--
1 ATAAACGAACACAA
*
1653261 ATAAACGAACAAAA
1 ATAAACGAACACAA
*
1653275 ATAAATGAACA
1 ATAAACGAACA
1653286 TAAAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 6 0.21
11 2 0.07
12 3 0.10
13 2 0.07
14 16 0.55
ACGTcount: A:0.67, C:0.16, G:0.06, T:0.10
Consensus pattern (14 bp):
ATAAACGAACACAA
Found at i:1653264 original size:24 final size:24
Alignment explanation
Indices: 1653237--1653289 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1653227 CGTTAAAATG
*
1653237 ATAAACGAACACAAATAAACAAAC
1 ATAAACGAACAAAAATAAACAAAC
**
1653261 ATAAACGAACAAAAATAAATGAAC
1 ATAAACGAACAAAAATAAACAAAC
1653285 ATAAA
1 ATAAA
1653290 ATTAATTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.68, C:0.15, G:0.06, T:0.11
Consensus pattern (24 bp):
ATAAACGAACAAAAATAAACAAAC
Found at i:1656001 original size:22 final size:22
Alignment explanation
Indices: 1655973--1656047 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
1655963 CAGTAGTAGG
1655973 TGATTGAGCATTCATTATCATA
1 TGATTGAGCATTCATTATCATA
* * *
1655995 TGATTGA-AAAT-ATTTAGTAATA
1 TGATTGAGCATTCA-TTA-TCATA
*
1656017 GGTGATTGAGCATTCATTATCAGA
1 --TGATTGAGCATTCATTATCATA
1656041 TGATTGA
1 TGATTGA
1656048 AAATATTTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 1 0.03
21 5 0.12
22 18 0.45
24 10 0.25
25 5 0.12
26 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.39
Consensus pattern (22 bp):
TGATTGAGCATTCATTATCATA
Found at i:1656030 original size:46 final size:46
Alignment explanation
Indices: 1655964--1656057 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
1655954 CAACGACTAC
* *
1655964 AGTAGTAGGTGATTGAGCATTCATTATCATATGATTGAAAATATTT
1 AGTAATAGGTGATTGAGCATTCATTATCAGATGATTGAAAATATTT
1656010 AGTAATAGGTGATTGAGCATTCATTATCAGATGATTGAAAATATTT
1 AGTAATAGGTGATTGAGCATTCATTATCAGATGATTGAAAATATTT
1656056 AG
1 AG
1656058 AACATATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.37
Consensus pattern (46 bp):
AGTAATAGGTGATTGAGCATTCATTATCAGATGATTGAAAATATTT
Found at i:1659715 original size:18 final size:18
Alignment explanation
Indices: 1659673--1659716 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1659663 CGGTCACAAC
1659673 CCGACCCGACCCGTTGAT
1 CCGACCCGACCCGTTGAT
* *
1659691 CCTACCCGACCTGTTGAAT
1 CCGACCCGACCCGTTG-AT
1659710 -CGACCCG
1 CCGACCCG
1659717 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.18, C:0.43, G:0.20, T:0.18
Consensus pattern (18 bp):
CCGACCCGACCCGTTGAT
Found at i:1660455 original size:24 final size:24
Alignment explanation
Indices: 1660428--1660535 Score: 96
Period size: 24 Copynumber: 4.5 Consensus size: 24
1660418 AATTATTTTA
1660428 TCTGATTTCTGACTTGAATTCTGT
1 TCTGATTTCTGACTTGAATTCTGT
* * * *
1660452 TCTGA-TACATTACCTAAATTCTGT
1 TCTGATTTC-TGACTTGAATTCTGT
1660476 TCTGATTTCTGATCTTG-ATTCTGT
1 TCTGATTTCTGA-CTTGAATTCTGT
* * *
1660500 TATGATATCTG-TTCTGAATTCTGT
1 TCTGATTTCTGACT-TGAATTCTGT
*
1660524 TTTGATTTCTGA
1 TCTGATTTCTGA
1660536 TATCTCCGTT
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
22 1 0.02
23 4 0.06
24 56 0.86
25 4 0.06
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGACTTGAATTCTGT
Found at i:1660520 original size:48 final size:49
Alignment explanation
Indices: 1660428--1660536 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 49
1660418 AATTATTTTA
*
1660428 TCTGATTTCTGA-CTTGAATTCTGTTCTGATACATTACCTAAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTATGATACATTACCTAAATTCTGT
* *
1660476 TCTGATTTCTGATCTTG-ATTCTGTTATGATATC-TGT-TCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTATGATA-CAT-TACCTAAATTCTGT
*
1660524 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1660537 ATCTCCGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
48 48 0.89
49 6 0.11
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.50
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTGTTATGATACATTACCTAAATTCTGT
Found at i:1662620 original size:13 final size:13
Alignment explanation
Indices: 1662586--1662628 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1662576 AACCCGACCC
1662586 GACCCGACCTGTT
1 GACCCGACCTGTT
* * *
1662599 GAACTGACCCGTT
1 GACCCGACCTGTT
1662612 GACCCGACCTGTT
1 GACCCGACCTGTT
1662625 GACC
1 GACC
1662629 GTTGACCGGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.19, C:0.37, G:0.23, T:0.21
Consensus pattern (13 bp):
GACCCGACCTGTT
Found at i:1668775 original size:22 final size:22
Alignment explanation
Indices: 1668747--1668831 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
1668737 TTTTGGTGCA
*
1668747 GAGGGAATCGATCCCCCCTCAT
1 GAGGGAACCGATCCCCCCTCAT
* *
1668769 GAGGGAACCGATTCCCCCT-TT
1 GAGGGAACCGATCCCCCCTCAT
* *
1668790 GAAGGGGAACCGATTCCCCCACA-
1 G-A-GGGAACCGATCCCCCCTCAT
*
1668813 G-GGGAATCGATACCCCCCT
1 GAGGGAACCGAT-CCCCCCT
1668832 GGGGTTCTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
20 9 0.18
21 7 0.14
22 18 0.35
23 17 0.33
ACGTcount: A:0.24, C:0.35, G:0.25, T:0.16
Consensus pattern (22 bp):
GAGGGAACCGATCCCCCCTCAT
Found at i:1668835 original size:19 final size:20
Alignment explanation
Indices: 1668792--1668829 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1668782 CCCCCTTTGA
*
1668792 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
1668812 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
1668830 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:1672106 original size:17 final size:19
Alignment explanation
Indices: 1672084--1672124 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
1672074 TTTTACATAC
1672084 ATATTGATCTG-ATAA-AA
1 ATATTGATCTGCATAAGAA
*
1672101 ATATTGATGTGCATAAGAA
1 ATATTGATCTGCATAAGAA
1672120 ATATT
1 ATATT
1672125 AGTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 4 0.19
19 7 0.33
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (19 bp):
ATATTGATCTGCATAAGAA
Found at i:1673767 original size:12 final size:12
Alignment explanation
Indices: 1673752--1673821 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1673742 GATACATGAC
1673752 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1673764 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
1673776 ATGGATTCTGTT
1 CTGAATTCTGTT
1673788 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
1673800 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1673812 TTGATTTCTG
1 CTGAATTCTG
1673822 ATATCTCTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1673769 original size:48 final size:48
Alignment explanation
Indices: 1673715--1673825 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
1673705 AATTATTTTA
1673715 TCTGATTTCCGACT-TGAACTCTGTTCTGATA-CATGACCTGAATTCTGT
1 TCTGATTTCCGA-TATGAACTCTGTTCTGATATC-TGACCTGAATTCTGT
* * * **
1673763 TCTGATTTCTGATATGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCCGATATGAACTCTGTTCTGATATCTGACCTGAATTCTGT
* *
1673811 TTTGATTTCTGATAT
1 TCTGATTTCCGATAT
1673826 CTCTGTTCTG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 1 0.02
48 53 0.96
49 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (48 bp):
TCTGATTTCCGATATGAACTCTGTTCTGATATCTGACCTGAATTCTGT
Found at i:1673783 original size:24 final size:24
Alignment explanation
Indices: 1673753--1673825 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
1673743 ATACATGACC
1673753 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * * *
1673777 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATTTCTGATA
*
1673801 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
1673825 T
1 T
1673826 CTCTGTTCTG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:1673801 original size:17 final size:18
Alignment explanation
Indices: 1673758--1673809 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
1673748 TGACCTGAAT
1673758 TCTGTTCTGATTTCTGATA
1 TCTGTTCTGA-TTCTGATA
*
1673777 T-GGATTCTG-TTCTGATA
1 TCTG-TTCTGATTCTGATA
1673794 TCTGTTCTGAATTCTG
1 TCTGTTCTG-ATTCTG
1673810 TTTTGATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 11 0.41
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.50
Consensus pattern (18 bp):
TCTGTTCTGATTCTGATA
Found at i:1677101 original size:21 final size:18
Alignment explanation
Indices: 1677058--1677103 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 18
1677048 GAAGGAAAAA
1677058 ATTTGATTTGTTTATGAT
1 ATTTGATTTGTTTATGAT
1677076 ATTTGATGTTGATTTACTGAT
1 ATTTGAT-TTG-TTTA-TGAT
*
1677097 TTTTGAT
1 ATTTGAT
1677104 AAAATCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 3 0.12
20 4 0.17
21 10 0.42
ACGTcount: A:0.22, C:0.02, G:0.17, T:0.59
Consensus pattern (18 bp):
ATTTGATTTGTTTATGAT
Found at i:1682871 original size:29 final size:29
Alignment explanation
Indices: 1682799--1682857 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1682789 CAAGGCACCT
* *
1682799 AGTAGCGACAGTATTGATACTGTAAGAAC
1 AGTAGTGACAATATTGATACTGTAAGAAC
1682828 AGTAGTGACAATATTGATACTGTAAGAAC
1 AGTAGTGACAATATTGATACTGTAAGAAC
1682857 A
1 A
1682858 TTATCGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (29 bp):
AGTAGTGACAATATTGATACTGTAAGAAC
Found at i:1683924 original size:13 final size:14
Alignment explanation
Indices: 1683893--1683928 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1683883 GTCGTAACTT
*
1683893 TATTTGGTATTTGG
1 TATTTTGTATTTGG
1683907 TATTTTGTATTT-G
1 TATTTTGTATTTGG
1683920 TATTTTGTA
1 TATTTTGTA
1683929 GATATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.17, C:0.00, G:0.19, T:0.64
Consensus pattern (14 bp):
TATTTTGTATTTGG
Found at i:1688749 original size:16 final size:17
Alignment explanation
Indices: 1688718--1688751 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1688708 AAAATATTAT
1688718 TTTAAAAAAGAAAAAAA
1 TTTAAAAAAGAAAAAAA
*
1688735 TTTAGAAAA-AAAAAAA
1 TTTAAAAAAGAAAAAAA
1688751 T
1 T
1688752 CAACCCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
TTTAAAAAAGAAAAAAA
Found at i:1691055 original size:72 final size:73
Alignment explanation
Indices: 1690917--1691062 Score: 240
Period size: 72 Copynumber: 2.0 Consensus size: 73
1690907 GCTGCCCCAA
*
1690917 CGTCAGGTTGAGAGCAACTTCTGTGGAAGACCTCCGGTTATGAATTGCCCTCAGTGAGACTCGAT
1 CGTCAGGTTGAGAGCAACTTCCGTGGAAGACCTCCGGTTATGAATTGCCCTCAGTGAGACTCGAT
1690982 CCCACGAC
66 CCCACGAC
* * * *
1690990 CGTCAGGTTGAGAGCAGCTTCCGTGGAAGACTTCC-GTTATGAATTGCCCTCAGTGGGACTTGAT
1 CGTCAGGTTGAGAGCAACTTCCGTGGAAGACCTCCGGTTATGAATTGCCCTCAGTGAGACTCGAT
1691054 CCCACGAC
66 CCCACGAC
1691062 C
1 C
1691063 ACAAGGTTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
72 36 0.53
73 32 0.47
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (73 bp):
CGTCAGGTTGAGAGCAACTTCCGTGGAAGACCTCCGGTTATGAATTGCCCTCAGTGAGACTCGAT
CCCACGAC
Found at i:1693812 original size:24 final size:24
Alignment explanation
Indices: 1693780--1693829 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1693770 TTGGGATATA
1693780 AGACTTGGTCGAACACCAAAATTT
1 AGACTTGGTCGAACACCAAAATTT
1693804 AGACTTGGTCGAACACCAAAATTT
1 AGACTTGGTCGAACACCAAAATTT
1693828 AG
1 AG
1693830 GCAGAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (24 bp):
AGACTTGGTCGAACACCAAAATTT
Found at i:1698177 original size:27 final size:27
Alignment explanation
Indices: 1698147--1698198 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1698137 CATAGGGATA
*
1698147 ATGGGGAGAGCACAGGCGAAGGGGACG
1 ATGGGGAGAGAACAGGCGAAGGGGACG
* *
1698174 ATGGGGAGAGAACCGGCTAAGGGGA
1 ATGGGGAGAGAACAGGCGAAGGGGA
1698199 GGGGGAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.50, T:0.06
Consensus pattern (27 bp):
ATGGGGAGAGAACAGGCGAAGGGGACG
Found at i:1698382 original size:31 final size:31
Alignment explanation
Indices: 1698344--1698440 Score: 149
Period size: 31 Copynumber: 3.1 Consensus size: 31
1698334 TAACGCCCTA
* * *
1698344 ACACCTAAAATGTTAATGAAGAAAACGTTAG
1 ACACCTAAAATGGTAACGGAGAAAACGTTAG
*
1698375 ACACCTAAAATGGTAACGGAGAAAACGTTAA
1 ACACCTAAAATGGTAACGGAGAAAACGTTAG
*
1698406 ACACCTAAAATGGTAACGGAGAAAATGTTAG
1 ACACCTAAAATGGTAACGGAGAAAACGTTAG
1698437 ACAC
1 ACAC
1698441 TAGGATTAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (31 bp):
ACACCTAAAATGGTAACGGAGAAAACGTTAG
Found at i:1701032 original size:24 final size:22
Alignment explanation
Indices: 1701005--1701058 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 22
1700995 TGTGAATGTT
*
1701005 TTTATTTTTATTTTTTAGTATTA
1 TTTATTTTTAATTTTTA-TATTA
1701028 GTTTATATTTTAATTTTTATATTA
1 -TTTAT-TTTTAATTTTTATATTA
1701052 TTTATTT
1 TTTATTT
1701059 AATTAGGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 5 0.18
24 10 0.36
25 11 0.39
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTATTTTTAATTTTTATATTA
Found at i:1701059 original size:27 final size:26
Alignment explanation
Indices: 1701002--1701056 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1700992 TATTGTGAAT
* *
1701002 GTTTTTATTTTTATTTTTTAGTATTA
1 GTTTATATTTTAATTTTTTAGTATTA
1701028 GTTTATATTTTAA-TTTTTA-TATTA
1 GTTTATATTTTAATTTTTTAGTATTA
1701052 -TTTAT
1 GTTTAT
1701057 TTAATTAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 6 0.22
26 11 0.41
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (26 bp):
GTTTATATTTTAATTTTTTAGTATTA
Found at i:1715466 original size:14 final size:14
Alignment explanation
Indices: 1715437--1715483 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
1715427 TATACTTTAT
*
1715437 CTCTAACTTA-AAA
1 CTCTAAATTATAAA
1715450 CTCTAAATTATAAA
1 CTCTAAATTATAAA
1715464 CTCTAAATTATAAA
1 CTCTAAATTATAAA
*
1715478 CACTAA
1 CTCTAA
1715484 GGTTATTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
CTCTAAATTATAAA
Found at i:1716508 original size:29 final size:31
Alignment explanation
Indices: 1716476--1716542 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
1716466 TGAATTCCTA
** *
1716476 AAAATTTTGTGGGTC-AAATTA-AATTTTTT
1 AAAATTTTAAGGGTCAAAATTATAATTTTTC
**
1716505 AAAACATTAAGGGTCAAAATTATAATTTTTC
1 AAAATTTTAAGGGTCAAAATTATAATTTTTC
1716536 AAAATTT
1 AAAATTT
1716543 GGGGAACCAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
29 11 0.38
30 6 0.21
31 12 0.41
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (31 bp):
AAAATTTTAAGGGTCAAAATTATAATTTTTC
Found at i:1729320 original size:22 final size:21
Alignment explanation
Indices: 1729285--1729325 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1729275 AATATTAAAT
1729285 TAAAAATAAAATATTTAAAAG
1 TAAAAATAAAATATTTAAAAG
*
1729306 TAAAGAATAATATATTTAAA
1 TAAA-AATAAAATATTTAAA
1729326 TTTGTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
TAAAAATAAAATATTTAAAAG
Found at i:1730738 original size:20 final size:19
Alignment explanation
Indices: 1730713--1730778 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
1730703 TAATAGTATC
1730713 TAATTAATATACTTTTAATA
1 TAATTAATATACTTTT-ATA
* * *
1730733 TAATT-ATTTAATCTTTTGTT
1 TAATTAATAT-A-CTTTTATA
*
1730753 TAATTAATATATTTTTCATA
1 TAATTAATATACTTTT-ATA
1730773 TAATTA
1 TAATTA
1730779 TAATATTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 7 0.20
20 20 0.57
21 8 0.23
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (19 bp):
TAATTAATATACTTTTATA
Found at i:1739852 original size:23 final size:23
Alignment explanation
Indices: 1739822--1739867 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1739812 AGAGACCTAT
1739822 CTTAAAATTTT-ATTGGTGTCCAC
1 CTTAAAATTTTGATT-GTGTCCAC
1739845 CTTAAAATTTTGATTGTGTCCAC
1 CTTAAAATTTTGATTGTGTCCAC
1739868 TCATTGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (23 bp):
CTTAAAATTTTGATTGTGTCCAC
Done.