Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 12 of 21
Found at i:1242785 original size:33 final size:34
Alignment explanation
Indices: 1242719--1242783 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1242709 TTTATTGTAT
*
1242719 TTTTTATTTAAATTATTATTTAATTATAAAAATA
1 TTTTTATTTAAATTATAATTTAATTATAAAAATA
1242753 TTTTTATTATGAAATTATAATTT-A-TATAAAA
1 TTTTTATT-T-AAATTATAATTTAATTATAAAA
1242784 TAATTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 15 0.54
35 2 0.07
36 11 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (34 bp):
TTTTTATTTAAATTATAATTTAATTATAAAAATA
Found at i:1242812 original size:26 final size:29
Alignment explanation
Indices: 1242783--1242847 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 29
1242773 TTTATATAAA
* *
1242783 ATAATTTAAATTTA-TAA-A-AATTTATT
1 ATAATTAAAATTTATTAAGACAATTAATT
*
1242809 ATAAATAAAATTTATTAAGACAATTAATT
1 ATAATTAAAATTTATTAAGACAATTAATT
1242838 ATAA-TAAAAT
1 ATAATTAAAAT
1242848 AATTTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 12 0.36
27 3 0.09
28 7 0.21
29 11 0.33
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (29 bp):
ATAATTAAAATTTATTAAGACAATTAATT
Found at i:1242838 original size:29 final size:25
Alignment explanation
Indices: 1242790--1242847 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 25
1242780 AAAATAATTT
*
1242790 AAATTTATAAAAATTTATTATAAATA
1 AAATTTATAAAAATTAATTAT-AATA
1242816 AAATTTATTAAGACAATTAATTATAATA
1 AAATTTA-TAA-A-AATTAATTATAATA
1242844 AAAT
1 AAAT
1242848 AATTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.25
27 3 0.11
28 9 0.32
29 9 0.32
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
AAATTTATAAAAATTAATTATAATA
Found at i:1243891 original size:2 final size:2
Alignment explanation
Indices: 1243884--1243910 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1243874 TGGGAAACAA
1243884 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 A
1243911 AACATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1244805 original size:2 final size:2
Alignment explanation
Indices: 1244798--1244831 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1244788 AAAACTAGTT
1244798 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1244832 TATTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1245016 original size:22 final size:22
Alignment explanation
Indices: 1244973--1245017 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1244963 GAAAGTAAAA
*
1244973 TAATTTTGTTGTATTATGTTAT
1 TAATTTTGTTGTATTATATTAT
*
1244995 TAATTTT-TTGTTATTGTATTAT
1 TAATTTTGTTG-TATTATATTAT
1245017 T
1 T
1245018 CATATTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (22 bp):
TAATTTTGTTGTATTATATTAT
Found at i:1245872 original size:15 final size:15
Alignment explanation
Indices: 1245827--1245889 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
1245817 ATGGTGGCTA
* *
1245827 ATATATTGAATTAGAT
1 ATATATTTAA-TATAT
*
1245843 ATATATTTAAAATAT
1 ATATATTTAATATAT
* *
1245858 TTATATTTGATATAT
1 ATATATTTAATATAT
*
1245873 ATGTATTTAATATAT
1 ATATATTTAATATAT
1245888 AT
1 AT
1245890 TTAGATATAT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
15 29 0.76
16 9 0.24
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (15 bp):
ATATATTTAATATAT
Found at i:1251433 original size:14 final size:15
Alignment explanation
Indices: 1251405--1251447 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1251395 TTTATAAATG
1251405 AAAAAAATTACTATT
1 AAAAAAATTACTATT
*
1251420 AAAAAAATTTTATTATT
1 AAAAAAA--TTACTATT
1251437 AAAATAAATTA
1 AAAA-AAATTA
1251448 ATTCAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.29
16 3 0.12
17 11 0.46
18 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAAAATTACTATT
Found at i:1252230 original size:15 final size:15
Alignment explanation
Indices: 1252210--1252257 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
1252200 TATGAAATAA
*
1252210 TTATTATTTTCTTTT
1 TTATTATTTTATTTT
1252225 TTATTATTTTATTTT
1 TTATTATTTTATTTT
*
1252240 TT-TATCTTTTATTTT
1 TTAT-TATTTTATTTT
1252255 TTA
1 TTA
1252258 CTAATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 1 0.03
15 28 0.97
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTATTTTATTTT
Found at i:1252236 original size:8 final size:7
Alignment explanation
Indices: 1252210--1252257 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
1252200 TATGAAATAA
1252210 TTATTATT
1 TTATT-TT
*
1252218 TTCTTTT
1 TTATTTT
1252225 TTATTATT
1 TTATT-TT
1252233 TTATTTTT
1 TTA-TTTT
*
1252241 TTATCTT
1 TTATTTT
1252248 TTATTTT
1 TTATTTT
1252255 TTA
1 TTA
1252258 CTAATTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
7 18 0.53
8 14 0.41
9 2 0.06
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (7 bp):
TTATTTT
Found at i:1252451 original size:2 final size:2
Alignment explanation
Indices: 1252438--1252502 Score: 76
Period size: 2 Copynumber: 32.5 Consensus size: 2
1252428 TATTTGTATG
* * * * * *
1252438 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TG TA TG TG TG TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1252480 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1252503 TGCTTTGGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1253010 original size:2 final size:2
Alignment explanation
Indices: 1252960--1252992 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1252950 TAAGCCACAA
1252960 AT AT 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 AT AT A
1252993 ATTCCAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1253086 original size:75 final size:76
Alignment explanation
Indices: 1252965--1253108 Score: 204
Period size: 75 Copynumber: 1.9 Consensus size: 76
1252955 CACAAATATA
* * *
1252965 TATATATATATATATATATATATATATAATTCCAAAATAGATATATTTAAAAAAATTATATTTTA
1 TATATATATATATATATATATATATATAATTCAAAAATAGATATATTTAAAAAAATAAAATTTTA
1253030 AATATTTAATT
66 AATATTTAATT
* *
1253041 TATATATATCATATATATATATATATA-AATGTTAAAAATA-A-ATATTTTAAAAAATAAAATTT
1 TATATATAT-ATATATATATATATATATAAT-TCAAAAATAGATATATTTAAAAAAATAAAATTT
1253103 TAAATA
64 TAAATA
1253109 ATATAGTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
75 24 0.39
76 13 0.21
77 24 0.39
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (76 bp):
TATATATATATATATATATATATATATAATTCAAAAATAGATATATTTAAAAAAATAAAATTTTA
AATATTTAATT
Found at i:1253092 original size:15 final size:14
Alignment explanation
Indices: 1253067--1253111 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
1253057 ATATATATAT
*
1253067 AAATGTTAAAAATA
1 AAATTTTAAAAATA
1253081 AATATTTTAAAAAATA
1 AA-ATTTT-AAAAATA
1253097 AAATTTTAAATAATA
1 AAATTTTAAA-AATA
1253112 TAGTTTCGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.19
15 13 0.48
16 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AAATTTTAAAAATA
Found at i:1253095 original size:16 final size:15
Alignment explanation
Indices: 1253074--1253111 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1253064 TATAAATGTT
1253074 AAAAATAAATATTTTA
1 AAAAATAAA-ATTTTA
1253090 AAAAATAAAATTTTA
1 AAAAATAAAATTTTA
*
1253105 AATAATA
1 AAAAATA
1253112 TAGTTTCGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATAAAATTTTA
Found at i:1255694 original size:19 final size:20
Alignment explanation
Indices: 1255654--1255699 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1255644 TATAAATATT
*
1255654 TTTTATATTTATTGTAATAA
1 TTTTATATTTATTGTAAAAA
1255674 TTTTA-ATTTATT-TAAAAAA
1 TTTTATATTTATTGT-AAAAA
1255693 TTTTATA
1 TTTTATA
1255700 ATTAAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTATATTTATTGTAAAAA
Found at i:1257102 original size:26 final size:25
Alignment explanation
Indices: 1257079--1257167 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
1257069 ATCATATTCA
* *
1257079 AATTATATTTTAATATTTTATATTAT
1 AATTATA-ATTAAAATTTTATATTAT
*
1257105 AATTTTAATTAAAATTTTATATTAT
1 AATTATAATTAAAATTTTATATTAT
* * * *
1257130 -A-TAT-ATTCATATTATATATTTT
1 AATTATAATTAAAATTTTATATTAT
1257152 AATTAT-ATATAAAATT
1 AATTATAAT-TAAAATT
1257168 ATCAAATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
22 14 0.28
23 3 0.06
24 6 0.12
25 21 0.42
26 6 0.12
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (25 bp):
AATTATAATTAAAATTTTATATTAT
Found at i:1257111 original size:13 final size:14
Alignment explanation
Indices: 1257081--1257161 Score: 89
Period size: 15 Copynumber: 5.9 Consensus size: 14
1257071 CATATTCAAA
*
1257081 TTATATTTTAATATT
1 TTATATTAT-ATATT
1257096 TTATATTATA-ATT
1 TTATATTATATATT
*
1257109 TTA-ATTA-AAATT
1 TTATATTATATATT
1257121 TTATATTATATATAT
1 TTATATTATATAT-T
*
1257136 TCATATTATATATT
1 TTATATTATATATT
1257150 TTA-ATTATATAT
1 TTATATTATATAT
1257162 AAAATTATCA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
11 1 0.02
12 10 0.17
13 19 0.33
14 7 0.12
15 21 0.36
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATTATATATT
Found at i:1257120 original size:12 final size:13
Alignment explanation
Indices: 1257042--1257128 Score: 63
Period size: 13 Copynumber: 6.8 Consensus size: 13
1257032 TTAATAATTT
1257042 ATTTTATA-T-AA
1 ATTTTATATTAAA
* *
1257053 ATTTTAAAATAAAA
1 ATTTT-ATATTAAA
* * *
1257067 ATATCATATTCAA
1 ATTTTATATTAAA
* * *
1257080 ATTATATTTTAAT
1 ATTTTATATTAAA
*
1257093 ATTTTATATTATA
1 ATTTTATATTAAA
1257106 ATTTTA-ATTAAA
1 ATTTTATATTAAA
1257118 ATTTTATATTA
1 ATTTTATATTA
1257129 TATATATTCA
Statistics
Matches: 54, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
11 5 0.09
12 13 0.24
13 31 0.57
14 5 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATATTAAA
Found at i:1258771 original size:11 final size:10
Alignment explanation
Indices: 1258754--1258791 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
1258744 TTTTATATAA
1258754 ATAAAATTAT
1 ATAAAATTAT
1258764 ATTAAAATTAT
1 A-TAAAATTAT
1258775 A-AAAA-TAT
1 ATAAAATTAT
1258783 ATAAAATTA
1 ATAAAATTA
1258792 AATTAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.16
9 8 0.32
10 3 0.12
11 10 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAAAATTAT
Found at i:1258778 original size:19 final size:18
Alignment explanation
Indices: 1258754--1258791 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1258744 TTTTATATAA
*
1258754 ATAAAATTATATTAAAATT
1 ATAAAAATATA-TAAAATT
1258773 ATAAAAATATATAAAATT
1 ATAAAAATATATAAAATT
1258791 A
1 A
1258792 AATTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAAATATATAAAATT
Found at i:1259012 original size:15 final size:16
Alignment explanation
Indices: 1258994--1259026 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1258984 GTTATTATAT
1258994 ATTTAATTAT-TTTTA
1 ATTTAATTATATTTTA
*
1259009 ATTTTATTATATTTTA
1 ATTTAATTATATTTTA
1259025 AT
1 AT
1259027 ATATATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTAATTATATTTTA
Found at i:1259022 original size:10 final size:10
Alignment explanation
Indices: 1258985--1259052 Score: 56
Period size: 10 Copynumber: 6.9 Consensus size: 10
1258975 AATTAAAAAG
1258985 TTATTATATAT
1 TTATTATAT-T
*
1258996 TTAAT-TA-T
1 TTATTATATT
1259004 TT-TTA-ATT
1 TTATTATATT
1259012 TTATTATATT
1 TTATTATATT
1259022 TTAATATATATT
1 TT-AT-TATATT
1259034 TTATTA-ATT
1 TTATTATATT
1259043 TTATTTATAT
1 TTA-TTATAT
1259053 AGTTTAATAG
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
7 2 0.04
8 6 0.13
9 9 0.19
10 12 0.26
11 10 0.21
12 8 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTATATT
Found at i:1259051 original size:22 final size:22
Alignment explanation
Indices: 1259000--1259067 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
1258990 ATATATTTAA
*
1259000 TTATTTTTA-ATTTTATTATATT
1 TTATTTATATATTTTATTA-ATT
*
1259022 TTA-ATATATATTTTATTAATT
1 TTATTTATATATTTTATTAATT
* * *
1259043 TTATTTATATAGTTTAATAGTT
1 TTATTTATATATTTTATTAATT
1259065 TTA
1 TTA
1259068 GTAGAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
21 9 0.24
22 29 0.76
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (22 bp):
TTATTTATATATTTTATTAATT
Found at i:1260074 original size:2 final size:2
Alignment explanation
Indices: 1260067--1260103 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1260057 AATATGAGGA
1260067 AT AT AT AT 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 AT AT AT AT A
1260104 CTGAAGCAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1260562 original size:33 final size:33
Alignment explanation
Indices: 1260491--1260589 Score: 107
Period size: 33 Copynumber: 3.0 Consensus size: 33
1260481 AATTATAAAG
**
1260491 TAAATATTAAATAT-A-AAAT-TTTAATTTTAAA
1 TAAATATTAAATATAATAAATATTTAA-TAAAAA
1260522 TAAATATTAAATATAATAAATATTTAATAAAAA
1 TAAATATTAAATATAATAAATATTTAATAAAAA
* *
1260555 TATATATTTAACT-TAATAAATATTTAATAGAAAA
1 TAAATA-TTAAATATAATAAATATTTAATA-AAAA
1260589 T
1 T
1260590 TCACAATTGA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
31 14 0.24
32 1 0.02
33 29 0.49
34 15 0.25
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (33 bp):
TAAATATTAAATATAATAAATATTTAATAAAAA
Found at i:1260628 original size:2 final size:2
Alignment explanation
Indices: 1260621--1260649 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1260611 AGGCATGTTT
1260621 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 T
1260650 GTATGTACGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1261025 original size:22 final size:22
Alignment explanation
Indices: 1260984--1261026 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1260974 TATAAAATTT
* *
1260984 TTTTCTATTTGTCTCGTTTTTA
1 TTTTATATTTGTCTCATTTTTA
*
1261006 TTTTATATTTGTCTTATTTTT
1 TTTTATATTTGTCTCATTTTT
1261027 CTATTTGTCT
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:0.12, C:0.09, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTATATTTGTCTCATTTTTA
Found at i:1261031 original size:17 final size:17
Alignment explanation
Indices: 1261006--1261042 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1260996 CTCGTTTTTA
*
1261006 TTTTATATTTGTCTTAT
1 TTTTATATTTGTCTCAT
*
1261023 TTTTCTATTTGTCTCAT
1 TTTTATATTTGTCTCAT
1261040 TTT
1 TTT
1261043 GCTACTTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTTATATTTGTCTCAT
Found at i:1261288 original size:2 final size:2
Alignment explanation
Indices: 1261281--1261310 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1261271 GTTGTAAAAG
1261281 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
1261311 GGGATTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1261653 original size:9 final size:9
Alignment explanation
Indices: 1261612--1261679 Score: 56
Period size: 9 Copynumber: 8.1 Consensus size: 9
1261602 TATTAAATGA
*
1261612 ATTATATTA
1 ATTATATTT
1261621 ATTATATTT
1 ATTATATTT
*
1261630 A--A-ATAT
1 ATTATATTT
*
1261636 ATCATATTT
1 ATTATATTT
1261645 ATTATATTT
1 ATTATATTT
1261654 -TT-TATTT
1 ATTATATTT
* *
1261661 ATTAAATAT
1 ATTATATTT
1261670 ATTATATTT
1 ATTATATTT
1261679 A
1 A
1261680 CTCATATTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
6 4 0.09
7 6 0.13
8 5 0.11
9 31 0.67
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTATATTT
Found at i:1261674 original size:16 final size:16
Alignment explanation
Indices: 1261614--1261674 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
1261604 TTAAATGAAT
1261614 TATATTAATTATATTTAAA
1 TATATT-ATT-TA-TTAAA
*
1261633 TATATCATATTTATTATA
1 TATAT--TATTTATTAAA
* *
1261651 TTTTTTATTTATTAAA
1 TATATTATTTATTAAA
1261667 TATATTAT
1 TATATTAT
1261675 ATTTACTCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
16 16 0.47
18 7 0.21
19 7 0.21
20 3 0.09
21 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTATTTATTAAA
Found at i:1263412 original size:20 final size:20
Alignment explanation
Indices: 1263387--1263426 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1263377 CGATAATCGA
1263387 ATTAAATAAATAT-TAAACAT
1 ATTAAA-AAATATATAAACAT
*
1263407 ATTAAAAATTATATAAACAT
1 ATTAAAAAATATATAAACAT
1263427 GTAAAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTAAAAAATATATAAACAT
Found at i:1263679 original size:24 final size:24
Alignment explanation
Indices: 1263652--1263701 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1263642 TATTTCGTAT
*
1263652 TTTATATTATATTTTCATATAGTA
1 TTTATATTATATTTTCATATAATA
* * *
1263676 TTTATGTTATCTTTTTATATAATA
1 TTTATATTATATTTTCATATAATA
1263700 TT
1 TT
1263702 ATAATTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTATATTATATTTTCATATAATA
Found at i:1263908 original size:21 final size:19
Alignment explanation
Indices: 1263884--1263941 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
1263874 GAAAAAAAAT
*
1263884 AAAAAATTCATTTGTTTTTGC
1 AAAAAATTAATTT-TTTTT-C
* *
1263905 AAAAAATGAATTTATTTTTT
1 AAAAAATTAATTT-TTTTTC
1263925 AAAAAATTAATTTTTTT
1 AAAAAATTAATTTTTTT
1263942 ACTATTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 4 0.12
20 12 0.38
21 16 0.50
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
AAAAAATTAATTTTTTTTC
Found at i:1263922 original size:20 final size:19
Alignment explanation
Indices: 1263898--1263941 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1263888 AATTCATTTG
1263898 TTTTTGCAAAAAATGAATT
1 TTTTTGCAAAAAATGAATT
** *
1263917 TATTTTTTAAAAAATTAATT
1 T-TTTTGCAAAAAATGAATT
1263937 TTTTT
1 TTTTT
1263942 ACTATTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTTGCAAAAAATGAATT
Found at i:1264235 original size:2 final size:2
Alignment explanation
Indices: 1264228--1264269 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1264218 ACCAAGTAAT
*
1264228 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1264270 CTTGATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1264385 original size:46 final size:46
Alignment explanation
Indices: 1264319--1264430 Score: 111
Period size: 46 Copynumber: 2.4 Consensus size: 46
1264309 TAGAATAGTA
* * * ** *
1264319 ATTTAAAAATTTTTAAAATTTATTATTTATATTTAATTT-TAATTT-T
1 ATTTATAAATTTATATAATTTATTA-AAATATTTATTTTAT-ATTTAT
* *
1264365 ATTTATAAATTTATTTAATTTTTTAAAATATTTATTTTATATTTAT
1 ATTTATAAATTTATATAATTTATTAAAATATTTATTTTATATTTAT
*
1264411 ATTTATATATTTATATAATT
1 ATTTATAAATTTATATAATT
1264431 AAATAAAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
45 14 0.26
46 40 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (46 bp):
ATTTATAAATTTATATAATTTATTAAAATATTTATTTTATATTTAT
Found at i:1264419 original size:14 final size:13
Alignment explanation
Indices: 1264397--1264426 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1264387 TTAAAATATT
1264397 TATTTTATATTTA
1 TATTTTATATTTA
1264410 TATTTATATATTTA
1 TATTT-TATATTTA
1264424 TAT
1 TAT
1264427 AATTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTATATTTA
Found at i:1264438 original size:46 final size:45
Alignment explanation
Indices: 1264347--1264442 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 45
1264337 TTTATTATTT
* ***
1264347 ATATTTAATTTTAATTTTATTTATAAATTTATTTAATTTTTTAAA
1 ATATTTAATTTTAATTTTATTTATAAATTTATATAATTAAATAAA
*
1264392 ATATTT-ATTTTATATTTATATTTATATATTTATATAATTAAATAAA
1 ATATTTAATTTTA-ATTT-TATTTATAAATTTATATAATTAAATAAA
1264438 A-ATTT
1 ATATTT
1264443 TATTAATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
44 6 0.14
45 14 0.32
46 24 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (45 bp):
ATATTTAATTTTAATTTTATTTATAAATTTATATAATTAAATAAA
Found at i:1264442 original size:20 final size:21
Alignment explanation
Indices: 1264419--1264475 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
1264409 ATATTTATAT
1264419 ATTTATA-TAATTAAATAAAA
1 ATTTATATTAATTAAATAAAA
*
1264439 ATTT-TATTAATTAAATAATA
1 ATTTATATTAATTAAATAAAA
*
1264459 ATTTAAATTAAATTAAA
1 ATTTATATT-AATTAAA
1264476 ATTGTTGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 20 0.62
21 3 0.09
22 7 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTATATTAATTAAATAAAA
Found at i:1265463 original size:3 final size:3
Alignment explanation
Indices: 1265455--1265502 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
1265445 CCTCTTGTTT
* * * * *
1265455 ATC ATC ATC ATC ATC TTC ATC ATT ATC ACC ATC ACC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1265503 CTCGACCTCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:1274089 original size:23 final size:24
Alignment explanation
Indices: 1274043--1274095 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1274033 TTTTATTTTT
* *
1274043 TATTTAATTTTTAATATAAATAAA
1 TATTTTATTTTAAATATAAATAAA
*
1274067 TATTTTATTTTAAAT-TAATTAAA
1 TATTTTATTTTAAATATAAATAAA
*
1274090 TTTTTT
1 TATTTT
1274096 TAAAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TATTTTATTTTAAATATAAATAAA
Found at i:1277164 original size:18 final size:18
Alignment explanation
Indices: 1277130--1277164 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1277120 GACAAGGACG
* *
1277130 AGGAGGTGGAGGTGCTGC
1 AGGAGGTGAAGGAGCTGC
1277148 AGGAGGTGAAGGAGCTG
1 AGGAGGTGAAGGAGCTG
1277165 ATCACCCTGG
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:0.23, C:0.09, G:0.54, T:0.14
Consensus pattern (18 bp):
AGGAGGTGAAGGAGCTGC
Found at i:1277953 original size:21 final size:21
Alignment explanation
Indices: 1277927--1277968 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1277917 TGAGCCTATG
1277927 TGTTGATTTGATACACTAACC
1 TGTTGATTTGATACACTAACC
1277948 TGTTGATTTGATACACTAACC
1 TGTTGATTTGATACACTAACC
1277969 AGATATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
TGTTGATTTGATACACTAACC
Found at i:1279944 original size:14 final size:14
Alignment explanation
Indices: 1279927--1279984 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 14
1279917 ATCTATTAAA
*
1279927 AATATATAATTATT
1 AATATATTATTATT
*
1279941 AATAT-TTATTTTT
1 AATATATTATTATT
*
1279954 AAAATA-TATTAATT
1 AATATATTATT-ATT
1279968 AA-ATATTATTATAT
1 AATATATTATTAT-T
1279982 AAT
1 AAT
1279985 CCATCGATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
13 19 0.54
14 16 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATATATTATTATT
Found at i:1281752 original size:65 final size:63
Alignment explanation
Indices: 1281645--1281835 Score: 265
Period size: 65 Copynumber: 2.9 Consensus size: 63
1281635 GATAAGTATC
* * *
1281645 AATAACCCATAAAAGCAAACATTGTGTTAAGACAATGCATTATTCCTAGCAACTTGCAGATCTTT
1 AATAACCCATAAAAGC-AACATTATGTTAAGATAATGTATTATTCCT-GCAACTTGCAGATC-TT
1281710 T
63 T
* * * *
1281711 AATAATCCATAAAGGCAACATTTTGTTAAGATAATGTATTATTCCTGACAACTTGCAGTTCTTT
1 AATAACCCATAAAAGCAACATTATGTTAAGATAATGTATTATTCCTG-CAACTTGCAGATCTTT
1281775 AATAACCCATAAAAGCAACATTATGTTAAAGATAATGTATTATTCCTGGCAACTTGCAGAT
1 AATAACCCATAAAAGCAACATTATGTT-AAGATAATGTATTATTCCT-GCAACTTGCAGAT
1281836 GTAGGAAAGA
Statistics
Matches: 112, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
64 28 0.25
65 69 0.62
66 15 0.13
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (63 bp):
AATAACCCATAAAAGCAACATTATGTTAAGATAATGTATTATTCCTGCAACTTGCAGATCTTT
Found at i:1282897 original size:11 final size:11
Alignment explanation
Indices: 1282883--1282917 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1282873 AACTATAATT
1282883 ATAATATATAA
1 ATAATATATAA
1282894 AT-A-ATATAA
1 ATAATATATAA
1282903 ATAATATATAA
1 ATAATATATAA
1282914 ATAA
1 ATAA
1282918 ATAAATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 8 0.36
10 2 0.09
11 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATAATATATAA
Found at i:1282906 original size:20 final size:19
Alignment explanation
Indices: 1282883--1282923 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
1282873 AACTATAATT
1282883 ATAATATATAAATAATATAA
1 ATAATATATAAATAA-ATAA
1282903 ATAATATATAAATAAATAA
1 ATAATATATAAATAAATAA
1282922 AT
1 AT
1282924 TATAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAATATATAAATAAATAA
Found at i:1282975 original size:19 final size:18
Alignment explanation
Indices: 1282931--1282977 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1282921 AATTATAATT
*
1282931 TATTTATTTATTTTTACC
1 TATTAATTTATTTTTACC
*
1282949 TATTAATTTATTTATTATC
1 TATTAATTTATTT-TTACC
*
1282968 TTTTAATTTA
1 TATTAATTTA
1282978 ATAAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTAATTTATTTTTACC
Found at i:1283985 original size:13 final size:13
Alignment explanation
Indices: 1283967--1283991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1283957 GGATATATCT
1283967 AATTTTTTTATAA
1 AATTTTTTTATAA
1283980 AATTTTTTTATA
1 AATTTTTTTATA
1283992 TTTTTAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTTTTTATAA
Found at i:1286371 original size:25 final size:26
Alignment explanation
Indices: 1286348--1286399 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1286338 ATTTTATTAA
*
1286348 ATTAATTTATATATTTAAAAATTATAT
1 ATTAATAT-TATATTTAAAAATTATAT
*
1286375 TTTAATATTATATTTAAAAA-TATAT
1 ATTAATATTATATTTAAAAATTATAT
1286400 TAAACATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 12 0.52
27 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTAATATTATATTTAAAAATTATAT
Found at i:1286382 original size:21 final size:22
Alignment explanation
Indices: 1286329--1286383 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
1286319 TCTGATATAA
*
1286329 ATATATTTAAT-TTTATTAAATT
1 ATAT-TTTAATATTTATAAAATT
1286351 A-A-TTTATATATTTA-AAAATT
1 ATATTTTA-ATATTTATAAAATT
1286371 ATATTTTAATATT
1 ATATTTTAATATT
1286384 ATATTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
19 4 0.14
20 8 0.29
21 11 0.39
22 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTTTAATATTTATAAAATT
Found at i:1286412 original size:25 final size:26
Alignment explanation
Indices: 1286358--1286413 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1286348 ATTAATTTAT
** *
1286358 ATATTTAAAAATTATATTTTAATATT
1 ATATTTAAAAATTATATTAAAATATA
1286384 ATATTTAAAAA-TATATTAAACATA-A
1 ATATTTAAAAATTATATTAAA-ATATA
1286409 ATATT
1 ATATT
1286414 AAATATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTTAAAAATTATATTAAAATATA
Found at i:1286414 original size:13 final size:13
Alignment explanation
Indices: 1286388--1286438 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
1286378 AATATTATAT
1286388 TTAAAAAT--ATA
1 TTAAAAATAAATA
*
1286399 TTAAACATAAATA
1 TTAAAAATAAATA
*
1286412 TTAAATATAAATA
1 TTAAAAATAAATA
1286425 CTTAAAAATAAATA
1 -TTAAAAATAAATA
1286439 AATAATCTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 7 0.21
13 15 0.44
14 12 0.35
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAAAAATAAATA
Found at i:1287617 original size:15 final size:16
Alignment explanation
Indices: 1287586--1287627 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1287576 TCATGTTTTA
1287586 TTTCTTATT-AATAAT
1 TTTCTTATTCAATAAT
1287601 TTAT-TTATTCAAT-AT
1 TT-TCTTATTCAATAAT
1287616 TTTCTTATTCAA
1 TTTCTTATTCAA
1287628 CAATATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 1 0.04
15 19 0.79
16 4 0.17
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTCTTATTCAATAAT
Found at i:1288041 original size:20 final size:21
Alignment explanation
Indices: 1288008--1288059 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
1287998 ATAATTTTTT
*
1288008 TAAATATAATTATAATA-TAAA
1 TAAATA-AAATATAATATTAAA
1288029 -AAATACAAATATAATATTAAA
1 TAAATA-AAATATAATATTAAA
1288050 TAAATAAAAT
1 TAAATAAAAT
1288060 TTTTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 14 0.52
21 8 0.30
22 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATAAAATATAATATTAAA
Found at i:1296063 original size:2 final size:2
Alignment explanation
Indices: 1296056--1296107 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
1296046 TTTTGAATTT
* * * * *
1296056 TA TA TA TA TA TA TA CA CA CA TA CA TA CA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1296097 TA TA TA TA TA T
1 TA TA TA TA TA T
1296108 GATTACATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (2 bp):
TA
Found at i:1296325 original size:15 final size:15
Alignment explanation
Indices: 1296282--1296327 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1296272 AACATACTCT
1296282 TATAAAA-AATCTAAA
1 TATAAAATAAT-TAAA
* *
1296297 AATAATAT-ATTAAA
1 TATAAAATAATTAAA
1296311 TATAAAATAATTAAA
1 TATAAAATAATTAAA
1296326 TA
1 TA
1296328 ATTTTTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TATAAAATAATTAAA
Found at i:1296627 original size:22 final size:25
Alignment explanation
Indices: 1296584--1296662 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 25
1296574 TTTTAAATTT
1296584 ATATTAAA-A-ATT-ATA-TTATTA
1 ATATTAAATATATTAATATTTATTA
1296605 A-ATTAAATATA-TAAT-TTTATTA
1 ATATTAAATATATTAATATTTATTA
*
1296627 ATTATTAATTATATTAATATTTATTTA
1 A-TATTAAATATATTAATATTTA-TTA
*
1296654 ACATTAAAT
1 ATATTAAAT
1296663 TTAACAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
20 6 0.13
21 3 0.07
22 10 0.22
24 9 0.20
25 4 0.09
26 10 0.22
27 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATTAAATATATTAATATTTATTA
Found at i:1296641 original size:16 final size:16
Alignment explanation
Indices: 1296597--1296644 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1296587 TTAAAAATTA
* *
1296597 TATT-ATTAAATTAAA
1 TATTAATTATATTAAT
*
1296612 TATATAATTTTATTAAT
1 TAT-TAATTATATTAAT
1296629 TATTAATTATATTAAT
1 TATTAATTATATTAAT
1296645 ATTTATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 3 0.11
16 13 0.48
17 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTAATTATATTAAT
Found at i:1296659 original size:26 final size:22
Alignment explanation
Indices: 1296599--1296662 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 22
1296589 AAAAATTATA
1296599 TTATTAAATTAAATATATAATT
1 TTATTAAATTAAATATATAATT
*
1296621 TTATTAATTATTAATTATATTAATAT
1 TTATTAA--ATTAAATATA-TAAT-T
1296647 TTATTTAACATTAAAT
1 TTA-TTAA-ATTAAAT
1296663 TTAACAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 7 0.21
24 9 0.26
25 4 0.12
26 10 0.29
27 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATTAAATTAAATATATAATT
Found at i:1300169 original size:89 final size:90
Alignment explanation
Indices: 1300017--1300281 Score: 363
Period size: 89 Copynumber: 3.0 Consensus size: 90
1300007 TTACACAAAC
* * * * * *
1300017 ACGTACAACATTCTCTTTCAAGAATCGTAATTGCAGCTCTGTGAATTATCTGCATGATATCCAAA
1 ACGTACAACATTCTCTTTCAAGCATCATAGTTGTAGCTTTGTGAATTATCTGCATGATGTCCAAA
* *
1300082 GTTGCTGTTTAATGTAATTTTAAAT
66 GATGCTGTTCAATGTAATTTTAAAT
**
1300107 ACGTACAACATTCT-TTTCAAGCATCATAGTTGTAGCTTTGCAAATTATCTGCATGATGTCCAAA
1 ACGTACAACATTCTCTTTCAAGCATCATAGTTGTAGCTTTGTGAATTATCTGCATGATGTCCAAA
* *
1300171 GATGGTGTTCAATATAATTTTAAAT
66 GATGCTGTTCAATGTAATTTTAAAT
** *
1300196 ATATACAACATTCTCTTTCAAGCATCATAGTTGTAGCTTTGTGCATTAT-TGCATGATGTCCAAA
1 ACGTACAACATTCTCTTTCAAGCATCATAGTTGTAGCTTTGTGAATTATCTGCATGATGTCCAAA
*
1300260 GATGCTATTCAATGTATATTTT
66 GATGCTGTTCAATGTA-ATTTT
1300282 TTTCCGGGAG
Statistics
Matches: 153, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
89 103 0.67
90 50 0.33
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (90 bp):
ACGTACAACATTCTCTTTCAAGCATCATAGTTGTAGCTTTGTGAATTATCTGCATGATGTCCAAA
GATGCTGTTCAATGTAATTTTAAAT
Found at i:1301697 original size:18 final size:18
Alignment explanation
Indices: 1301676--1301715 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1301666 TTAATGAATA
*
1301676 ATATGAAT-TTTATATGAT
1 ATATGAATATGTATAT-AT
1301694 ATATGAATATGTATATAT
1 ATATGAATATGTATATAT
1301712 ATAT
1 ATAT
1301716 ATATATGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (18 bp):
ATATGAATATGTATATAT
Found at i:1307027 original size:26 final size:27
Alignment explanation
Indices: 1306992--1307047 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
1306982 TATTAATATA
1306992 TATATAAATATTTATCAAT-A-TATTTT
1 TATATAAATATTT-TCAATAATTATTTT
* *
1307018 TATATTAATATTTTTAATAATTATTTT
1 TATATAAATATTTTCAATAATTATTTT
1307045 TAT
1 TAT
1307048 CTTTACATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 13 0.50
27 9 0.35
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TATATAAATATTTTCAATAATTATTTT
Found at i:1307042 original size:13 final size:14
Alignment explanation
Indices: 1307011--1307047 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1307001 ATTTATCAAT
1307011 ATATTTTTATATTA
1 ATATTTTTATATTA
1307025 ATATTTTTA-A-TA
1 ATATTTTTATATTA
1307037 ATTATTTTTAT
1 A-TATTTTTAT
1307048 CTTTACATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 9 0.43
14 9 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATATTTTTATATTA
Found at i:1307131 original size:20 final size:21
Alignment explanation
Indices: 1307098--1307183 Score: 95
Period size: 21 Copynumber: 4.2 Consensus size: 21
1307088 ATCTAATCAT
*
1307098 TAAT-TTTAATTTTATTATTA
1 TAATATTTAATTTTACTATTA
* * *
1307118 TAATATTTAA-TTTAATCTCA
1 TAATATTTAATTTTACTATTA
* *
1307138 TAATAATTAATTTTACTATAA
1 TAATATTTAATTTTACTATTA
*
1307159 TAATATTTATTTTTACTATTA
1 TAATATTTAATTTTACTATTA
1307180 TAAT
1 TAAT
1307184 CATTAACTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 20 0.37
21 34 0.63
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATATTTAATTTTACTATTA
Found at i:1307196 original size:24 final size:21
Alignment explanation
Indices: 1307137--1307195 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
1307127 ATTTAATCTC
1307137 ATAATAATTAA-TTTTACTATA
1 ATAAT-ATTAATTTTTACTATA
* *
1307158 ATAATATTTATTTTTACTATT
1 ATAATATTAATTTTTACTATA
1307179 ATAATCATTAACTTTTT
1 ATAAT-ATTAA-TTTTT
1307196 TTTTACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.12
21 19 0.59
22 4 0.12
23 5 0.16
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (21 bp):
ATAATATTAATTTTTACTATA
Found at i:1307385 original size:14 final size:14
Alignment explanation
Indices: 1307368--1307419 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
1307358 TTTTTTTTAA
1307368 TAAAATTTTATAAT
1 TAAAATTTTATAAT
1307382 TAAATATTTTA-AAT
1 TAAA-ATTTTATAAT
* * **
1307396 AAAAAATTTATTGT
1 TAAAATTTTATAAT
1307410 TAAAATTTTA
1 TAAAATTTTA
1307420 ACTTTACAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
13 5 0.17
14 19 0.63
15 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TAAAATTTTATAAT
Found at i:1310806 original size:61 final size:61
Alignment explanation
Indices: 1310711--1310832 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
1310701 CCTGGAGGGC
1310711 AAGGCTTTGGTGGCAAGATGTTAGGCATTAACAACTATCATAAACATTGTGATTTCCTTTT
1 AAGGCTTTGGTGGCAAGATGTTAGGCATTAACAACTATCATAAACATTGTGATTTCCTTTT
1310772 AAGGCTTTGGTGGCAAGATGTTAGGCATTAACAACTATCATAAACATTGTGATTTCCTTTT
1 AAGGCTTTGGTGGCAAGATGTTAGGCATTAACAACTATCATAAACATTGTGATTTCCTTTT
1310833 GTTTTTTTCT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (61 bp):
AAGGCTTTGGTGGCAAGATGTTAGGCATTAACAACTATCATAAACATTGTGATTTCCTTTT
Found at i:1321390 original size:134 final size:134
Alignment explanation
Indices: 1321196--1321457 Score: 400
Period size: 134 Copynumber: 2.0 Consensus size: 134
1321186 TCTAGCTTTC
* * ** ** *
1321196 ACAACAAAATATGGGAACATAAACAAATTATCTCGGACAGGAGTATGAAAGTAAGGCAAGATGTA
1 ACAACAAAATATGGCAACATAAACAAATTATCTCGGACAAGAGTACAAAAGTAAAACAAGATGCA
* *
1321261 TGGCTTAAAACAGAGCACATGTAT-CTATATATGTACAATATTTATTGGATCCATCGACCAATAT
66 TGGCCTAAAACAGAGCACATGTATGC-ATATATGTACAATATTTATTGGATCCATCAACCAATAT
1321325 ATTTG
130 ATTTG
* *
1321330 ACAACAAAATATGGCAACATAAACGAATTATCTCGGACAAGATTACAAAAGTAAAACAAGATGCA
1 ACAACAAAATATGGCAACATAAACAAATTATCTCGGACAAGAGTACAAAAGTAAAACAAGATGCA
*
1321395 TGGCCTAAAATAGAGCACATGTATGCATATATGTACAATATTTATTGGATCCATCAACCAATA
66 TGGCCTAAAACAGAGCACATGTATGCATATATGTACAATATTTATTGGATCCATCAACCAATA
1321458 AATTGTTTAC
Statistics
Matches: 115, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
134 114 0.99
135 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (134 bp):
ACAACAAAATATGGCAACATAAACAAATTATCTCGGACAAGAGTACAAAAGTAAAACAAGATGCA
TGGCCTAAAACAGAGCACATGTATGCATATATGTACAATATTTATTGGATCCATCAACCAATATA
TTTG
Found at i:1321799 original size:142 final size:144
Alignment explanation
Indices: 1321575--1321861 Score: 388
Period size: 142 Copynumber: 2.0 Consensus size: 144
1321565 AAATCAATCA
*
1321575 AAACTCTGATTATTTGACCAAAATACTGATTGTAGGTGTCTAGGTGATAAGCGGGAGCACATAGA
1 AAACTCTGATTATTTGACCAAAATACTGATTGTAGGTGTCTAGGTGATAAGCGGGACCACATAGA
** *
1321640 CATAGCCATAGCAAATGCTACCAAAATCCCAAGGCAACTCCCAAAACACATTTAACACAAAACAT
66 CATAGAAATAGCAAATGCTACCAAAATCCCAAGGCAACTCCCAAAACACATTAAACACAAAACAT
1321705 ATT-TTAATATACAT
131 ATTGTT-ATATACAT
* *
1321719 AAACTCTGATTATTTGACC-AGATCACT-ATT-TAGGTGTCTAGGTGATAAGCGGGACCACGT-G
1 AAACTCTGATTATTTGACCAAAAT-ACTGATTGTAGGTGTCTAGGTGATAAGCGGGACCACATAG
* * * ** *
1321780 ACATATAAATTCAG-GAATGCTACCAAAATTCCAAGGCAACTCTTAAACCACATTAAACACAAAA
65 ACATAGAAA-T-AGCAAATGCTACCAAAATCCCAAGGCAACTCCCAAAACACATTAAACACAAAA
1321844 CATATTGTTATATACAT
128 CATATTGTTATATACAT
1321861 A
1 A
1321862 CCTAATGGTT
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
141 7 0.06
142 88 0.69
143 10 0.08
144 22 0.17
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (144 bp):
AAACTCTGATTATTTGACCAAAATACTGATTGTAGGTGTCTAGGTGATAAGCGGGACCACATAGA
CATAGAAATAGCAAATGCTACCAAAATCCCAAGGCAACTCCCAAAACACATTAAACACAAAACAT
ATTGTTATATACAT
Found at i:1326383 original size:30 final size:32
Alignment explanation
Indices: 1326333--1326399 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 32
1326323 ATGTATATAT
* *
1326333 ATAATAAATTATTAAAATTATATTAATATTAA
1 ATAATAAATTATTAAAATTATATAAACATTAA
*
1326365 ATAATAAATT-TT-AAATTATATAAACGTTAA
1 ATAATAAATTATTAAAATTATATAAACATTAA
1326395 ATAAT
1 ATAAT
1326400 TTTTATCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 20 0.62
31 2 0.06
32 10 0.31
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (32 bp):
ATAATAAATTATTAAAATTATATAAACATTAA
Found at i:1326441 original size:18 final size:18
Alignment explanation
Indices: 1326415--1326465 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 18
1326405 TCAAAAATAT
*
1326415 TTATATTAAATAATAAAA
1 TTATGTTAAATAATAAAA
* *
1326433 TTATGTTAAA-AATATAC
1 TTATGTTAAATAATAAAA
* *
1326450 TTTTGCTAAATAATAA
1 TTATGTTAAATAATAA
1326466 TATATAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (18 bp):
TTATGTTAAATAATAAAA
Found at i:1330150 original size:34 final size:34
Alignment explanation
Indices: 1330095--1330160 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1330085 GCATCATGTT
*
1330095 AATATAAATAGATCAAGTTTAATCGTGTCGTATA
1 AATATAAATAAATCAAGTTTAATCGTGTCGTATA
* *
1330129 AATATTAATAAATC-AGTTTTAATTGTGTCGTA
1 AATATAAATAAATCAAG-TTTAATCGTGTCGTA
1330161 ATAATGTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (34 bp):
AATATAAATAAATCAAGTTTAATCGTGTCGTATA
Found at i:1331021 original size:23 final size:25
Alignment explanation
Indices: 1330994--1331042 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1330984 TAAAATTTAA
*
1330994 ATTTA-ATTATAA-AATATATAAAT
1 ATTTATATTAAAATAATATATAAAT
*
1331017 ATTTATATTAAAATAATATTTAAAT
1 ATTTATATTAAAATAATATATAAAT
1331042 A
1 A
1331043 ATAAAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 6 0.27
25 11 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTATATTAAAATAATATATAAAT
Found at i:1331715 original size:2 final size:2
Alignment explanation
Indices: 1331708--1331736 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1331698 AAAGGTAGAT
1331708 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 T
1331737 TCCTTTTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1333930 original size:2 final size:2
Alignment explanation
Indices: 1333923--1333948 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1333913 GCTTTCCTTG
1333923 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
1333949 TTTTATATTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1336453 original size:23 final size:23
Alignment explanation
Indices: 1336423--1336469 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1336413 TTTTAGCTTC
1336423 TATATATTACTTACACTCAAGTG
1 TATATATTACTTACACTCAAGTG
1336446 TATATATTACTTACACTCAAGTG
1 TATATATTACTTACACTCAAGTG
1336469 T
1 T
1336470 GACTGTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (23 bp):
TATATATTACTTACACTCAAGTG
Found at i:1338555 original size:22 final size:22
Alignment explanation
Indices: 1338511--1338556 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1338501 TAATAATTTT
* *
1338511 TATATAAATTTAATTTATTAAA
1 TATATAAATTTAATATATAAAA
1338533 TATATAAATATTAATATA-AAAA
1 TATATAAAT-TTAATATATAAAA
1338555 TA
1 TA
1338557 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATAAATTTAATATATAAAA
Found at i:1339034 original size:3 final size:3
Alignment explanation
Indices: 1339026--1339055 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1339016 TTTTAGATTG
1339026 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1339056 GGGACTTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1339387 original size:25 final size:26
Alignment explanation
Indices: 1339335--1339392 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
1339325 AAAATTTAAT
*
1339335 TTAAATTTAAATTTTATTATAAATAA
1 TTAAATTTAAATTATATTATAAATAA
1339361 TTAAATTTAAAATTATA-TATAAA-AA
1 TTAAATTT-AAATTATATTATAAATAA
1339386 TTAAATT
1 TTAAATT
1339393 ATTTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 9 0.30
26 14 0.47
27 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAAATTTAAATTATATTATAAATAA
Found at i:1343844 original size:17 final size:17
Alignment explanation
Indices: 1343819--1343852 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1343809 TATGATATAT
*
1343819 TTAAAATAATTAATAAA
1 TTAAAATAATAAATAAA
*
1343836 TTAATATAATAAATAAA
1 TTAAAATAATAAATAAA
1343853 ATGAAATGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAATAATAAATAAA
Found at i:1343951 original size:2 final size:2
Alignment explanation
Indices: 1343944--1343974 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1343934 TGTAAGCCTG
1343944 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 T
1343975 TTAAGAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1344179 original size:15 final size:15
Alignment explanation
Indices: 1344150--1344178 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1344140 AACATATATC
1344150 AAATTGATTAATTTT
1 AAATTGATTAATTTT
1344165 AAATT-ATTAATTTT
1 AAATTGATTAATTTT
1344179 TTATTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
AAATTGATTAATTTT
Found at i:1344191 original size:5 final size:5
Alignment explanation
Indices: 1344181--1344236 Score: 60
Period size: 5 Copynumber: 11.2 Consensus size: 5
1344171 TTAATTTTTT
* * * *
1344181 ATTAA ATTAA ATTAA ATTAA AATAA ATTAA ATAAA ATT-T TTTAA ATTTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A-TTAA
1344231 ATTAA A
1 ATTAA A
1344237 ATTGACAGCT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
4 2 0.05
5 34 0.83
6 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:1344670 original size:16 final size:16
Alignment explanation
Indices: 1344625--1344672 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1344615 TATTATATAT
1344625 TTATATAAATTTT-AA
1 TTATATAAATTTTAAA
*
1344640 -TATATTAATAATTTAAA
1 TTATA-TAA-ATTTTAAA
1344657 TTATATAAATTTTAAA
1 TTATATAAATTTTAAA
1344673 ATATTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 4 0.15
15 3 0.11
16 11 0.41
17 5 0.19
18 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATATAAATTTTAAA
Found at i:1344681 original size:27 final size:27
Alignment explanation
Indices: 1344589--1344681 Score: 62
Period size: 27 Copynumber: 3.2 Consensus size: 27
1344579 ATTCTTATAT
* * *
1344589 TTTTTATATTATAATTATTTTTAAAATA
1 TTTTTAAATTAT-ATAAATTTTAAAATA
* *
1344617 -TTATATATTTATATAAATTTTAATATATTAA
1 TTTTTA-AATTATATAAATTTTAA-A-A-T-A
*
1344648 TAATTTAAATTATATAAATTTTAAAATA
1 T-TTTTAAATTATATAAATTTTAAAATA
1344676 TTTTTA
1 TTTTTA
1344682 TGTTAATATA
Statistics
Matches: 49, Mismatches: 9, Indels: 15
0.67 0.12 0.21
Matches are distributed among these distances:
27 17 0.35
28 7 0.14
29 2 0.04
30 2 0.04
31 2 0.04
32 16 0.33
33 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTTAAATTATATAAATTTTAAAATA
Found at i:1344701 original size:6 final size:6
Alignment explanation
Indices: 1344690--1344768 Score: 66
Period size: 5 Copynumber: 14.5 Consensus size: 6
1344680 TATGTTAATA
*
1344690 TATATT TATA-T TATATT TATATT TAT-TT TAT-TT TATATT T-TAAT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
* * *
1344734 TA-ATT T-TAAT T-TATT TATTTT TAAATT TAT-TT TAT
1 TATATT TATATT TATATT TATATT TATATT TATATT TAT
1344769 TCTATATATG
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
5 34 0.57
6 26 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:1344706 original size:11 final size:11
Alignment explanation
Indices: 1344690--1344729 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1344680 TATGTTAATA
1344690 TATATTTATAT
1 TATATTTATAT
1344701 TATATTTATAT
1 TATATTTATAT
*
1344712 T-TATTTTATTT
1 TATA-TTTATAT
1344723 TATATTT
1 TATATTT
1344730 TAATTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 2 0.08
11 22 0.85
12 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1344716 original size:10 final size:10
Alignment explanation
Indices: 1344687--1344795 Score: 52
Period size: 10 Copynumber: 11.1 Consensus size: 10
1344677 TTTTATGTTA
*
1344687 ATATATATTT
1 ATATTTATTT
1344697 ATATTATATTT
1 ATATT-TATTT
1344708 ATATTTATTT
1 ATATTTATTT
*
1344718 -TATTT-TAT
1 ATATTTATTT
*
1344726 AT-TTTAATT
1 ATATTTATTT
1344735 A-ATTTTAATTT
1 ATA-TTT-ATTT
*
1344746 AT-TTATTTTT
1 ATATT-TATTT
*
1344756 AAATTTATTT
1 ATATTTATTT
*
1344766 -TATTCTATAT
1 ATATT-TATTT
*
1344776 ATGTTTA-TT
1 ATATTTATTT
*
1344785 AAATTTATTT
1 ATATTTATTT
1344795 A
1 A
1344796 AAGTAGTATT
Statistics
Matches: 73, Mismatches: 14, Indels: 24
0.66 0.13 0.22
Matches are distributed among these distances:
8 5 0.07
9 17 0.23
10 31 0.42
11 20 0.27
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (10 bp):
ATATTTATTT
Found at i:1344725 original size:22 final size:22
Alignment explanation
Indices: 1344677--1344775 Score: 67
Period size: 22 Copynumber: 4.4 Consensus size: 22
1344667 TTTAAAATAT
* * *
1344677 TTTTATGTTAATATATA-TTTA
1 TTTTATATTTATATTTATTTTA
*
1344698 TATTATATTTATATTTATTTTA
1 TTTTATATTTATATTTATTTTA
*
1344720 TTTTATATTT-TAATTAATTTTAA
1 TTTTATATTTAT-ATTTATTTT-A
* *
1344743 TTTATTTATTTTTAAATTTATTTTA
1 --T-TTTATATTTATATTTATTTTA
*
1344768 TTCTATAT
1 TTTTATAT
1344776 ATGTTTATTA
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
21 14 0.23
22 26 0.43
23 2 0.03
25 2 0.03
26 16 0.27
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (22 bp):
TTTTATATTTATATTTATTTTA
Found at i:1346535 original size:172 final size:174
Alignment explanation
Indices: 1346280--1346594 Score: 535
Period size: 172 Copynumber: 1.8 Consensus size: 174
1346270 TAACGTCTTA
1346280 TGATTTTGGCTTGAATGGTAAATTTTGGGTACGCGGTATGCCTTTTTCAAACCATTGATGCACTT
1 TGATTTTGGCTTGAATGGTAAATTTTGGGTACGCGGTATGCCTTTTTCAAACCATTGATGCACTT
* * * *
1346345 TTTCGATTGTTTC-TT-TATACATAGTGATGTAGTAAGAACCTTAAATTCGATCATCTTGATACG
66 TTTCGATTGTTTCTTTATATACATAGTAATGTAGGAAGAACCTTAAATTAGATAATCTTGATACG
1346408 AAAATAATTAAGTAATATGGGTTTGTTATAACGCATATGACTAG
131 AAAATAATTAAGTAATATGGGTTTGTTATAACGCATATGACTAG
*
1346452 TGATTTTGGCTTGAATGGTAAATTTTGGGTATGCGGTATGCCTTTTTCAAACCATTGATGCACTT
1 TGATTTTGGCTTGAATGGTAAATTTTGGGTACGCGGTATGCCTTTTTCAAACCATTGATGCACTT
* * * *
1346517 TTTCGTTTGTTTCTTTATATATATAGTAATGTAGGAAGAACCTTAACTTAGATAATCTTGATATG
66 TTTCGATTGTTTCTTTATATACATAGTAATGTAGGAAGAACCTTAAATTAGATAATCTTGATACG
1346582 AAAATAATTAAGT
131 AAAATAATTAAGT
1346595 GCATTCAGTT
Statistics
Matches: 132, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
172 76 0.58
173 2 0.02
174 54 0.41
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (174 bp):
TGATTTTGGCTTGAATGGTAAATTTTGGGTACGCGGTATGCCTTTTTCAAACCATTGATGCACTT
TTTCGATTGTTTCTTTATATACATAGTAATGTAGGAAGAACCTTAAATTAGATAATCTTGATACG
AAAATAATTAAGTAATATGGGTTTGTTATAACGCATATGACTAG
Found at i:1348166 original size:18 final size:18
Alignment explanation
Indices: 1348133--1348172 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1348123 CGAAATCGTG
* *
1348133 TATATATATCTGTGTATA
1 TATATATATATATGTATA
*
1348151 TATATATATATATGTATG
1 TATATATATATATGTATA
1348169 TATA
1 TATA
1348173 ATTTGTGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (18 bp):
TATATATATATATGTATA
Found at i:1353545 original size:17 final size:17
Alignment explanation
Indices: 1353523--1353556 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1353513 ACATATTTAA
1353523 ATGTTGATATGAATTAC
1 ATGTTGATATGAATTAC
1353540 ATGTTGATATGAATTAC
1 ATGTTGATATGAATTAC
1353557 GATCCTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (17 bp):
ATGTTGATATGAATTAC
Found at i:1353780 original size:8 final size:8
Alignment explanation
Indices: 1353763--1353823 Score: 53
Period size: 7 Copynumber: 8.4 Consensus size: 8
1353753 AAATCTGTTT
1353763 TTAT-TTA
1 TTATATTA
1353770 TTATATTA
1 TTATATTA
* *
1353778 TTAAAATA
1 TTATATTA
1353786 TTAT-TTA
1 TTATATTA
1353793 TTATATTA
1 TTATATTA
*
1353801 ATAT-TTA
1 TTATATTA
1353808 -TATATT-
1 TTATATTA
1353814 TT-TATTA
1 TTATATTA
1353821 TTA
1 TTA
1353824 AATAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
6 7 0.16
7 18 0.42
8 18 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATATTA
Found at i:1353793 original size:20 final size:22
Alignment explanation
Indices: 1353770--1353827 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
1353760 TTTTTATTTA
1353770 TTATATTATTAAA-ATAT-TAT
1 TTATATTATTAAATATATATAT
*
1353790 TTAT-TATATTAATATTTATATAT
1 TTATAT-TATTAA-ATATATATAT
*
1353813 TTTTATTATTAAATA
1 TTATATTATTAAATA
1353828 ATAATTGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
19 1 0.03
20 10 0.33
21 1 0.03
22 5 0.17
23 12 0.40
24 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATTATTAAATATATATAT
Found at i:1353819 original size:14 final size:15
Alignment explanation
Indices: 1353763--1353823 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
1353753 AAATCTGTTT
1353763 TTAT-TTATTATATTA
1 TTATATTATTAT-TTA
* *
1353778 TTAAAATATTATTTA
1 TTATATTATTATTTA
*
1353793 TTATATTAATATTTA
1 TTATATTATTATTTA
*
1353808 -TATATTTTTA-TTA
1 TTATATTATTATTTA
1353821 TTA
1 TTA
1353824 AATAATAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
13 3 0.08
14 10 0.27
15 18 0.49
16 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATATTATTATTTA
Found at i:1355135 original size:20 final size:19
Alignment explanation
Indices: 1355110--1355148 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1355100 GATTTAATTT
*
1355110 AAATAATTATTTATTTAATA
1 AAATAATAATTT-TTTAATA
1355130 AAATAATAATTTTTTAATA
1 AAATAATAATTTTTTAATA
1355149 TTTTCAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATAATAATTTTTTAATA
Found at i:1355191 original size:22 final size:21
Alignment explanation
Indices: 1355166--1355206 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1355156 ACACTAATTC
1355166 AAATTTATAAATCAAGCAAACT
1 AAATTT-TAAATCAAGCAAACT
* *
1355188 AAATTTTAACTTAAGCAAA
1 AAATTTTAAATCAAGCAAA
1355207 GAGTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (21 bp):
AAATTTTAAATCAAGCAAACT
Found at i:1355322 original size:19 final size:19
Alignment explanation
Indices: 1355285--1355322 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1355275 TATTAATTTC
*
1355285 AAATAATTAAAATACATAA
1 AAATAATTAAAATAAATAA
1355304 AAATAATATAAAA-AAATAA
1 AAATAAT-TAAAATAAATAA
1355323 TTAAAATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAATTAAAATAAATAA
Found at i:1358346 original size:3 final size:3
Alignment explanation
Indices: 1358338--1358365 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1358328 GATCCCTGAA
1358338 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1358366 CGTACATAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:1358543 original size:20 final size:20
Alignment explanation
Indices: 1358509--1358549 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1358499 AAAAAAAAAA
** *
1358509 AAACCAAAATTTAAAGTAAT
1 AAACCAAAAAATAAAATAAT
1358529 AAACCAAAAAATAAAATAAT
1 AAACCAAAAAATAAAATAAT
1358549 A
1 A
1358550 TTTTTACCTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.10, G:0.02, T:0.20
Consensus pattern (20 bp):
AAACCAAAAAATAAAATAAT
Found at i:1360958 original size:3 final size:3
Alignment explanation
Indices: 1360950--1360979 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1360940 TATTTTTATC
1360950 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1360980 CAGTGTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1361760 original size:3 final size:3
Alignment explanation
Indices: 1361747--1361777 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1361737 GCAAAACAAT
*
1361747 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1361778 AAGTTAAAAA
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:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1363568 original size:16 final size:16
Alignment explanation
Indices: 1363543--1363584 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1363533 CGTTTTCTTC
1363543 TTTC-CTTCCCTTTCT
1 TTTCTCTTCCCTTTCT
1363558 TTTCTCTTCCCTTTCT
1 TTTCTCTTCCCTTTCT
1363574 TCTTCTTCTTC
1 T-TTC-TCTTC
1363585 TTCCACAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.17
16 12 0.50
17 3 0.12
18 5 0.21
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTCTCTTCCCTTTCT
Found at i:1365896 original size:21 final size:21
Alignment explanation
Indices: 1365871--1365913 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1365861 TTTTCTTCTG
1365871 GCATTCTGATTACTGGCTAAT
1 GCATTCTGATTACTGGCTAAT
1365892 GCATTCTGATTACTGGCTAAT
1 GCATTCTGATTACTGGCTAAT
1365913 G
1 G
1365914 TGTGTCCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (21 bp):
GCATTCTGATTACTGGCTAAT
Found at i:1374237 original size:43 final size:43
Alignment explanation
Indices: 1374185--1374272 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
1374175 TTTTTTTTTC
1374185 TTTTCTTTTTCAACAATGACCGCCACCGAAAGCTATTTTAACT
1 TTTTCTTTTTCAACAATGACCGCCACCGAAAGCTATTTTAACT
1374228 TTTTCTTTTTCAACAATGACCGCCACCGAAAGCTATTTTAACT
1 TTTTCTTTTTCAACAATGACCGCCACCGAAAGCTATTTTAACT
1374271 TT
1 TT
1374273 GGCCGGAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (43 bp):
TTTTCTTTTTCAACAATGACCGCCACCGAAAGCTATTTTAACT
Found at i:1385763 original size:7 final size:7
Alignment explanation
Indices: 1385751--1385799 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
1385741 ACTTTACTGC
1385751 CTTAAGT
1 CTTAAGT
1385758 CTTAAGT
1 CTTAAGT
1385765 CTTAAGT
1 CTTAAGT
*
1385772 C-T--GA
1 CTTAAGT
*
1385776 CTTAAGA
1 CTTAAGT
1385783 CTTAAGT
1 CTTAAGT
1385790 CTTAAGT
1 CTTAAGT
1385797 CTT
1 CTT
1385800 CACACACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 2 0.05
5 1 0.03
6 1 0.03
7 33 0.89
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (7 bp):
CTTAAGT
Found at i:1385786 original size:25 final size:25
Alignment explanation
Indices: 1385751--1385798 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1385741 ACTTTACTGC
*
1385751 CTTAAGTCTTAAGTCTTAAGTCTGA
1 CTTAAGACTTAAGTCTTAAGTCTGA
1385776 CTTAAGACTTAAGTCTTAAGTCT
1 CTTAAGACTTAAGTCTTAAGTCT
1385799 TCACACACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (25 bp):
CTTAAGACTTAAGTCTTAAGTCTGA
Found at i:1390789 original size:9 final size:9
Alignment explanation
Indices: 1390777--1390801 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1390767 TCATTCTACC
1390777 TATTCCACG
1 TATTCCACG
1390786 TATTCCACG
1 TATTCCACG
1390795 TATTCCA
1 TATTCCA
1390802 TTTCATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (9 bp):
TATTCCACG
Found at i:1391977 original size:2 final size:2
Alignment explanation
Indices: 1391970--1392045 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
1391960 TGGGAGGTAA
1391970 TC TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC TC
1392012 TC TC TC TC 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 TC TC TC TC
1392046 CTATTGCATG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1400054 original size:24 final size:26
Alignment explanation
Indices: 1400019--1400084 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 26
1400009 TCAATCATAA
1400019 AATTATTAATTTTTTAAAAAA-T-ATT
1 AATTA-TAATTTTTTAAAAAACTCATT
*
1400044 AATTATAA--TTTAAAAAAACTCATT
1 AATTATAATTTTTTAAAAAACTCATT
* *
1400068 AATCATATTTTTTTAAA
1 AATTATAATTTTTTAAA
1400085 CCTAATTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
22 9 0.27
23 1 0.03
24 12 0.36
25 5 0.15
26 6 0.18
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (26 bp):
AATTATAATTTTTTAAAAAACTCATT
Found at i:1400278 original size:19 final size:21
Alignment explanation
Indices: 1400256--1400294 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1400246 TAAAATTATT
*
1400256 TACTTATA-TTAA-AAAAAAC
1 TACTCATAGTTAATAAAAAAC
1400275 TACTCATAGTTAATAAAAAA
1 TACTCATAGTTAATAAAAAA
1400295 TTATTTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (21 bp):
TACTCATAGTTAATAAAAAAC
Found at i:1400816 original size:25 final size:26
Alignment explanation
Indices: 1400768--1400817 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1400758 TCTATTTATA
1400768 TTTAAATATAAATATAAAATATAAATT
1 TTTAAATAT-AATATAAAATATAAATT
1400795 TTTAAATAT-ATA-AAAATAATAAA
1 TTTAAATATAATATAAAAT-ATAAA
1400818 AATTCAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 8 0.36
27 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TTTAAATATAATATAAAATATAAATT
Found at i:1406423 original size:9 final size:11
Alignment explanation
Indices: 1406395--1406427 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1406385 AAAGAGAATG
1406395 AAATATTTTAT
1 AAATATTTTAT
1406406 AAATATTTTA-
1 AAATATTTTAT
1406416 AAAT-TTTTAT
1 AAATATTTTAT
1406426 AA
1 AA
1406428 TATAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.24
10 6 0.29
11 10 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AAATATTTTAT
Found at i:1406448 original size:15 final size:15
Alignment explanation
Indices: 1406416--1406465 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1406406 AAATATTTTA
1406416 AAATTTTTATAATAT
1 AAATTTTTATAATAT
*
1406431 AAATTATTTATTAT-T
1 AAATT-TTTATAATAT
*
1406446 AAATTTATATAAATAT
1 AAATTTTTAT-AATAT
1406462 AAAT
1 AAAT
1406466 ATTAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 4 0.14
15 13 0.45
16 12 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATTTTTATAATAT
Found at i:1406479 original size:31 final size:31
Alignment explanation
Indices: 1406402--1406480 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 31
1406392 ATGAAATATT
* *
1406402 TTATAAATATTTTAAAATTTTTATAATATAAA
1 TTATTAATATTTT-AAATTTATATAATATAAA
1406434 TTATT--TATTATTAAATTTATATAAATATAAA
1 TTATTAATATT-TTAAATTTATAT-AATATAAA
1406465 -TATTAATATTTTAAAT
1 TTATTAATATTTTAAAT
1406481 ATAATTATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
30 17 0.41
31 16 0.39
32 8 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TTATTAATATTTTAAATTTATATAATATAAA
Found at i:1407668 original size:3 final size:3
Alignment explanation
Indices: 1407660--1407686 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1407650 CCGGTAAACT
1407660 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1407687 AATTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1407699 original size:18 final size:18
Alignment explanation
Indices: 1407659--1407709 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1407649 ACCGGTAAAC
**
1407659 TTAATAATAATAATAATAA
1 TTAATAATAA-AATTTTAA
1407678 -TAATAATAAAATTTTAA
1 TTAATAATAAAATTTTAA
* *
1407695 TTAATGATAATATTT
1 TTAATAATAAAATTT
1407710 ATAAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TTAATAATAAAATTTTAA
Done.