Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 8 of 189
Found at i:2694993 original size:32 final size:31
Alignment explanation
Indices: 2694955--2695027 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 31
2694945 TATAGTTAAG
*
2694955 ATATATACATAAGATAACATGTAAAAATATAT
1 ATATATAAATAAGATAACAT-TAAAAATATAT
* * *
2694987 ATATATAAATAATATAATATTAAAGATATAT
1 ATATATAAATAAGATAACATTAAAAATATAT
*
2695018 ACATA-AAATA
1 ATATATAAATA
2695028 GTATAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 5 0.14
31 14 0.39
32 17 0.47
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (31 bp):
ATATATAAATAAGATAACATTAAAAATATAT
Found at i:2695010 original size:15 final size:16
Alignment explanation
Indices: 2694976--2695018 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2694966 AGATAACATG
2694976 TAAAAATATATATATA
1 TAAAAATATATATATA
2694992 TAAATAATATA-ATAT-
1 TAAA-AATATATATATA
*
2695007 TAAAGATATATA
1 TAAAAATATATA
2695019 CATAAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 5 0.21
15 5 0.21
16 8 0.33
17 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAAAATATATATATA
Found at i:2695015 original size:23 final size:24
Alignment explanation
Indices: 2694987--2695120 Score: 82
Period size: 25 Copynumber: 5.5 Consensus size: 24
2694977 AAAAATATAT
2694987 ATATATAAATAATATAATATTAAAG
1 ATATAT-AATAATATAATATTAAAG
* * * *
2695012 ATATATACATAAAATAGTATAAAAT
1 ATATATA-ATAATATAATATTAAAG
*
2695037 ATATATATACGTAATATAAAATTTAAA-
1 ATATATA-A--TAATATAATA-TTAAAG
** *
2695064 ATATA-CCTAATAT-AT-TAAAAG
1 ATATATAATAATATAATATTAAAG
2695085 A-ATATATATAATATAATATT-AAG
1 ATATATA-ATAATATAATATTAAAG
*
2695108 AAATATAATAATA
1 ATATATAATAATA
2695121 ACAAAAAAAG
Statistics
Matches: 83, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
20 7 0.08
21 1 0.01
22 7 0.08
23 18 0.22
24 7 0.08
25 27 0.33
27 12 0.14
28 4 0.05
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATATAATAATATAATATTAAAG
Found at i:2695023 original size:25 final size:25
Alignment explanation
Indices: 2694987--2695120 Score: 93
Period size: 23 Copynumber: 5.6 Consensus size: 25
2694977 AAAAATATAT
*
2694987 ATATATAAATAATATAATATTAAAG
1 ATATATACATAATATAATATTAAAG
* * * *
2695012 ATATATACATAAAATAGTATAAAATAT
1 ATATATACATAATATAATAT-TAA-AG
* * *
2695039 ATATATACGTAATATAAAATTTAA-
1 ATATATACATAATATAATATTAAAG
* *
2695063 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATACATAATATAATATTAAAG
*
2695085 A-ATATATATAATATAATATT-AAG
1 ATATATACATAATATAATATTAAAG
*
2695108 AAATATA-ATAATA
1 ATATATACATAATA
2695121 ACAAAAAAAG
Statistics
Matches: 85, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
21 3 0.04
22 13 0.15
23 24 0.28
24 7 0.08
25 18 0.21
26 3 0.04
27 17 0.20
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATACATAATATAATATTAAAG
Found at i:2695638 original size:30 final size:30
Alignment explanation
Indices: 2695602--2695716 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
2695592 TAGGTACAAG
* *
2695602 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
2695632 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
2695662 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
2695692 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
2695717 TGAGAAAAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.22, C:0.03, G:0.50, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:2703940 original size:21 final size:21
Alignment explanation
Indices: 2703914--2703955 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2703904 AGAAAGAAAG
2703914 AACATTCTTGAGTTTTCTTAT
1 AACATTCTTGAGTTTTCTTAT
2703935 AACATTCTTGAGTTTTCTTAT
1 AACATTCTTGAGTTTTCTTAT
2703956 CCTTCATAAC
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:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (21 bp):
AACATTCTTGAGTTTTCTTAT
Found at i:2704782 original size:4 final size:4
Alignment explanation
Indices: 2704773--2704799 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2704763 AAGTTGCATA
2704773 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
2704800 ACCTCCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2705681 original size:120 final size:121
Alignment explanation
Indices: 2705426--2705669 Score: 472
Period size: 121 Copynumber: 2.0 Consensus size: 121
2705416 TAAGAGAAAA
*
2705426 TTACACTCTTTTTTTTAATAATTTCGAAAGCCTTCCTTTTCCTTGAATTATTTAGTTTTTATTTA
1 TTACACTCTTTTTTTAAATAATTTCGAAAGCCTTCCTTTTCCTTGAATTATTTAGTTTTTATTTA
2705491 CCGGAGAAGCTATGGACAAAAAAGTAGGGTTTATTTTAAAATGTAAATTAACATTT
66 CCGGAGAAGCTATGGACAAAAAAGTAGGGTTTATTTTAAAATGTAAATTAACATTT
2705547 TTACACTCTTTTTTTAAATAATTTCGAAAGCCTTCCTTTTCCTTGAATTATTTAGTTTTTATTTA
1 TTACACTCTTTTTTTAAATAATTTCGAAAGCCTTCCTTTTCCTTGAATTATTTAGTTTTTATTTA
2705612 CCGGAGAAGCTATGGACAAAAAAGTA-GGTTTATTTTAAAATGTAAATTAACATTT
66 CCGGAGAAGCTATGGACAAAAAAGTAGGGTTTATTTTAAAATGTAAATTAACATTT
2705667 TTA
1 TTA
2705670 TCTTCTTTTT
Statistics
Matches: 122, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
120 32 0.26
121 90 0.74
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (121 bp):
TTACACTCTTTTTTTAAATAATTTCGAAAGCCTTCCTTTTCCTTGAATTATTTAGTTTTTATTTA
CCGGAGAAGCTATGGACAAAAAAGTAGGGTTTATTTTAAAATGTAAATTAACATTT
Found at i:2708967 original size:14 final size:15
Alignment explanation
Indices: 2708938--2708970 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2708928 AAAAAGGTGT
2708938 TTTTATAATTACGTA
1 TTTTATAATTACGTA
*
2708953 TTTTA-AATTATGTA
1 TTTTATAATTACGTA
2708967 TTTT
1 TTTT
2708971 GATTATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTATAATTACGTA
Found at i:2709213 original size:20 final size:18
Alignment explanation
Indices: 2709171--2709210 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2709161 TATGAATATC
* *
2709171 AAATATATATACAACATA
1 AAATATATATAAAAAATA
2709189 AAATATATATGAAAAAATA
1 AAATATATAT-AAAAAATA
2709208 AAA
1 AAA
2709211 ATAAATGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (18 bp):
AAATATATATAAAAAATA
Found at i:2716683 original size:29 final size:29
Alignment explanation
Indices: 2716651--2716739 Score: 67
Period size: 29 Copynumber: 3.0 Consensus size: 29
2716641 ACTTTATGAT
2716651 TTAATTTAAAAAATTATTAAAATTATTAA
1 TTAATTTAAAAAATTATTAAAATTATTAA
** ** *
2716680 TTAA-ACATCGAAATTATTAACA-TATTAA
1 TTAATTTA-AAAAATTATTAAAATTATTAA
2716708 -TATATTTAAACCAAATTATTAATAATTATTAA
1 TTA-ATTTAAA--AAATTATTAA-AATTATTAA
2716740 ACACCAATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 11
0.67 0.16 0.17
Matches are distributed among these distances:
27 2 0.05
28 8 0.19
29 16 0.37
30 10 0.23
31 1 0.02
32 6 0.14
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.42
Consensus pattern (29 bp):
TTAATTTAAAAAATTATTAAAATTATTAA
Found at i:2721013 original size:29 final size:30
Alignment explanation
Indices: 2720981--2721043 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
2720971 ATTCTAATTT
*
2720981 AAAAAAAGT-ATAAATTATAAA-AATTATA
1 AAAAAAAGTAAAAAATTATAAATAATTATA
* *
2721009 AAAAAAATTAAAAAATTATAAATTATTATA
1 AAAAAAAGTAAAAAATTATAAATAATTATA
2721039 AAAAA
1 AAAAA
2721044 TTAAAAGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 8 0.27
29 11 0.37
30 11 0.37
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAAAAGTAAAAAATTATAAATAATTATA
Found at i:2721020 original size:10 final size:10
Alignment explanation
Indices: 2720992--2721046 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
2720982 AAAAAAGTAT
2720992 AAATTAT-AA
1 AAATTATAAA
2721001 AAATTATAAA
1 AAATTATAAA
*
2721011 AAA-AATTAAA
1 AAATTA-TAAA
2721021 AAATTATAAA
1 AAATTATAAA
**
2721031 TTATTATAAA
1 AAATTATAAA
2721041 AAATTA
1 AAATTA
2721047 AAAGATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
9 8 0.22
10 28 0.76
11 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAATTATAAA
Found at i:2721024 original size:20 final size:21
Alignment explanation
Indices: 2720992--2721030 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2720982 AAAAAAGTAT
2720992 AAATTATAAAAATTATAAAAA
1 AAATTATAAAAATTATAAAAA
2721013 AAATTA-AAAAATTATAAA
1 AAATTATAAAAATTATAAA
2721031 TTATTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATTATAAAAATTATAAAAA
Found at i:2721057 original size:19 final size:20
Alignment explanation
Indices: 2720994--2721059 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
2720984 AAAAGTATAA
2720994 ATTAT-AAAAATTATAAAA-
1 ATTATAAAAAATTATAAAAT
** *
2721012 AAAATTAAAAAATTATAAATT
1 ATTA-TAAAAAATTATAAAAT
2721033 ATTATAAAAAATTA-AAAGAT
1 ATTATAAAAAATTATAAA-AT
2721053 A-TATAAA
1 ATTATAAA
2721060 TTTATTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
18 2 0.05
19 10 0.26
20 24 0.63
21 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
ATTATAAAAAATTATAAAAT
Found at i:2721078 original size:19 final size:19
Alignment explanation
Indices: 2721056--2721136 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
2721046 AAAAGATATA
2721056 TAAAT-TTATTAAAATTATT
1 TAAATATTA-TAAAATTATT
2721075 TAAATATTATAAAATTATAGATAT
1 TAAATATTATAAAA-T-T--AT-T
2721099 GTAAAT-TTATTAAAATTATT
1 -TAAATATTA-TAAAATTATT
2721119 TAAATATTATAAAATTAT
1 TAAATATTATAAAATTAT
2721137 AAAATTTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
19 24 0.45
20 8 0.15
21 3 0.06
23 3 0.06
24 5 0.09
25 10 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAATATTATAAAATTATT
Found at i:2721091 original size:25 final size:25
Alignment explanation
Indices: 2721063--2721135 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
2721053 ATATAAATTT
2721063 ATTAAAATTATTTAAATATTATAAA
1 ATTAAAATTATTTAAATATTATAAA
* *
2721088 ATTATAGA-TATGT-AA-ATT-T---
1 ATTA-AAATTATTTAAATATTATAAA
2721107 ATTAAAATTATTTAAATATTATAAA
1 ATTAAAATTATTTAAATATTATAAA
2721132 ATTA
1 ATTA
2721136 TAAAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 2 0.06
19 8 0.22
20 2 0.06
21 3 0.08
22 2 0.06
23 3 0.08
24 2 0.06
25 12 0.33
26 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
ATTAAAATTATTTAAATATTATAAA
Found at i:2721104 original size:44 final size:44
Alignment explanation
Indices: 2721040--2721137 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
2721030 ATTATTATAA
*
2721040 AAAATTAAAAGATATATAAATTTATTAAAATTATTTAAATATTAT
1 AAAATT-ATAGATATATAAATTTATTAAAATTATTTAAATATTAT
*
2721085 AAAATTATAGATATGTAAATTTATTAAAATTATTTAAATATTAT
1 AAAATTATAGATATATAAATTTATTAAAATTATTTAAATATTAT
2721129 AAAATTATA
1 AAAATTATA
2721138 AAATTTAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 45 0.88
45 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (44 bp):
AAAATTATAGATATATAAATTTATTAAAATTATTTAAATATTAT
Found at i:2722974 original size:5 final size:6
Alignment explanation
Indices: 2722957--2722981 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2722947 TTATATATAG
2722957 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
2722982 AGACTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:2731165 original size:29 final size:30
Alignment explanation
Indices: 2731119--2731189 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
2731109 AATAAACACC
2731119 AAAAAGTTATTTTAAAAATAAAAAATAAAAA
1 AAAAAG-TATTTTAAAAATAAAAAATAAAAA
2731150 AAAAAGTATTTTAAAAATAAAAAATAAAAA
1 AAAAAGTATTTTAAAAATAAAAAATAAAAA
*
2731180 ATAAA-TATTT
1 AAAAAGTATTT
2731190 ATTATATTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 5 0.13
30 28 0.72
31 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (30 bp):
AAAAAGTATTTTAAAAATAAAAAATAAAAA
Found at i:2731178 original size:6 final size:7
Alignment explanation
Indices: 2731132--2731184 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
2731122 AAGTTATTTT
2731132 AAAAATA
1 AAAAATA
2731139 AAAAATA
1 AAAAATA
2731146 AAAAA-A
1 AAAAATA
* *
2731152 AAAGTATTTT
1 AAA--A-ATA
2731162 AAAAATA
1 AAAAATA
2731169 AAAAATA
1 AAAAATA
2731176 AAAAATA
1 AAAAATA
2731183 AA
1 AA
2731185 TATTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 4 0.11
7 29 0.76
8 2 0.05
10 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (7 bp):
AAAAATA
Found at i:2734680 original size:23 final size:23
Alignment explanation
Indices: 2734654--2734751 Score: 133
Period size: 23 Copynumber: 4.3 Consensus size: 23
2734644 GTGTTATTGA
*
2734654 TCAGTGGTAGCTTTGACTACATT
1 TCAGTGGTAGCTTCGACTACATT
* *
2734677 TCAGCGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGACTACATT
*
2734700 TCAGTGGTAGCTACGACTACATT
1 TCAGTGGTAGCTTCGACTACATT
* * *
2734723 TCAGTGGTAGCTTTGGCTACATA
1 TCAGTGGTAGCTTCGACTACATT
2734746 TCAGTG
1 TCAGTG
2734752 TGGCACTTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGACTACATT
Found at i:2734707 original size:46 final size:46
Alignment explanation
Indices: 2734653--2734751 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 46
2734643 AGTGTTATTG
**
2734653 ATCAGTGGTAGCTTTGACTACATTTCAGCGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGACTACATTTCAGCGGTAGCTTCGGCTACAT
* * *
2734699 TTCAGTGGTAGCTACGACTACATTTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTACGACTACATTTCAGCGGTAGCTTCGGCTACAT
2734745 ATCAGTG
1 ATCAGTG
2734752 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTACGACTACATTTCAGCGGTAGCTTCGGCTACAT
Found at i:2737326 original size:9 final size:9
Alignment explanation
Indices: 2737312--2737355 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
2737302 ATATTTATTC
*
2737312 AATTAATTT
1 AATTAATTA
2737321 AATTAATTA
1 AATTAATTA
*
2737330 AACTAATTA
1 AATTAATTA
*
2737339 AATTAACTA
1 AATTAATTA
2737348 AATTAATT
1 AATTAATT
2737356 TCTCAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (9 bp):
AATTAATTA
Found at i:2742663 original size:24 final size:23
Alignment explanation
Indices: 2742636--2742682 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2742626 TTTTGGAGTA
* *
2742636 TATTCGTTTTTTCTTTTTCATACT
1 TATT-GTTTTTTCATTTTAATACT
*
2742660 TATTTTTTTTTCATTTTAATACT
1 TATTGTTTTTTCATTTTAATACT
2742683 AAAAATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.68
Consensus pattern (23 bp):
TATTGTTTTTTCATTTTAATACT
Found at i:2745569 original size:15 final size:16
Alignment explanation
Indices: 2745549--2745583 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2745539 AATAATTTAT
*
2745549 TAAAAATATT-TAAAA
1 TAAAAATATTAGAAAA
2745564 TAAAAATATTAGAAAA
1 TAAAAATATTAGAAAA
2745580 TAAA
1 TAAA
2745584 GAAAACCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAATATTAGAAAA
Found at i:2750012 original size:16 final size:18
Alignment explanation
Indices: 2749980--2750012 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2749970 CAATAAACAC
2749980 TATTTTATTACTTTAAAT
1 TATTTTATTACTTTAAAT
2749998 TATTTT-TTA-TTTAAA
1 TATTTTATTACTTTAAA
2750013 ACCAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTATTACTTTAAAT
Found at i:2750037 original size:23 final size:22
Alignment explanation
Indices: 2749996--2750041 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
2749986 ATTACTTTAA
2749996 ATTATTTTTTATTTAAAACCAAT
1 ATTATTTTTTATTTAAAA-CAAT
*
2750019 ATTA-TTTTTATTATGAAACAAT
1 ATTATTTTTTATT-TAAAACAAT
2750041 A
1 A
2750042 AAAACACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATTTTTTATTTAAAACAAT
Found at i:2752167 original size:17 final size:18
Alignment explanation
Indices: 2752130--2752174 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2752120 TTTATTTTTT
2752130 ATATATAAATATTTAAAC
1 ATATATAAATATTTAAAC
*
2752148 ATA-ATAAA-ATTTAATGC
1 ATATATAAATATTTAA-AC
2752165 ATATATAAAT
1 ATATATAAAT
2752175 TACACAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 6 0.26
17 9 0.39
18 8 0.35
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATATAAATATTTAAAC
Found at i:2752392 original size:15 final size:16
Alignment explanation
Indices: 2752360--2752393 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2752350 TATGTATTTA
2752360 TTATTTTATTTATAAT
1 TTATTTTATTTATAAT
*
2752376 TTATTTT-TTTTTAAT
1 TTATTTTATTTATAAT
2752391 TTA
1 TTA
2752394 AGAAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTATTTATAAT
Found at i:2754187 original size:3 final size:3
Alignment explanation
Indices: 2754179--2754208 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2754169 GAAACATAAA
2754179 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
2754209 AATACAAGCT
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:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:2757645 original size:21 final size:21
Alignment explanation
Indices: 2757621--2757664 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2757611 TACAGACCTG
* *
2757621 AAGTTGAGTGCACGTTTGAGC
1 AAGTGGAGTGCAAGTTTGAGC
*
2757642 AAGTGGAGTGTAAGTTTGAGC
1 AAGTGGAGTGCAAGTTTGAGC
2757663 AA
1 AA
2757665 CACGTGTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.34, T:0.27
Consensus pattern (21 bp):
AAGTGGAGTGCAAGTTTGAGC
Found at i:2763210 original size:4 final size:4
Alignment explanation
Indices: 2763201--2763229 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2763191 TCCATGCATC
2763201 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
2763230 TTGTTACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:2763832 original size:14 final size:13
Alignment explanation
Indices: 2763815--2763852 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2763805 TTATAAATAA
2763815 AAAGAAGAAGAAAG
1 AAAGAAGAA-AAAG
2763829 AAAGAACGAAAAAG
1 AAAGAA-GAAAAAG
2763843 AAA-AAGAAAA
1 AAAGAAGAAAA
2763853 TTTATACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.22
13 2 0.09
14 13 0.57
15 3 0.13
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAG
Found at i:2773226 original size:24 final size:24
Alignment explanation
Indices: 2773199--2773250 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2773189 TTAGTAAGTC
*
2773199 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2773223 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2773247 AAAT
1 AAAT
2773251 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2783722 original size:33 final size:33
Alignment explanation
Indices: 2783654--2783727 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
2783644 TTGAACCCTT
* *
2783654 AACCTAAACCTTGATCCCTGAACCCAAAGCACA
1 AACCCAAACCTTGAACCCTGAACCCAAAGCACA
* * *
2783687 AACCCAAACC-TGAACCCTGAACCTTAAATCTCA
1 AACCCAAACCTTGAACCCTGAACC-CAAAGCACA
2783720 AACCCAAA
1 AACCCAAA
2783728 TCATAAATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 12 0.34
33 23 0.66
ACGTcount: A:0.42, C:0.36, G:0.07, T:0.15
Consensus pattern (33 bp):
AACCCAAACCTTGAACCCTGAACCCAAAGCACA
Found at i:2790104 original size:17 final size:16
Alignment explanation
Indices: 2790073--2790110 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2790063 CGATACAAAT
*
2790073 AATTTTAAATTTTTTA
1 AATTTTAAATATTTTA
2790089 AATTTATAAATATTTT-
1 AATTT-TAAATATTTTA
2790105 AATTTT
1 AATTTT
2790111 GGATGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 10 0.50
17 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTTAAATATTTTA
Found at i:2791316 original size:24 final size:23
Alignment explanation
Indices: 2791289--2791342 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
2791279 GTTAACATCG
*
2791289 TTTTAAAATTTATCACTAG-TATTA
1 TTTTAAAATTTAACA-T-GTTATTA
*
2791313 TTTTAAGATTTAACATGTTATTA
1 TTTTAAAATTTAACATGTTATTA
2791336 TTTTAAA
1 TTTTAAA
2791343 TTATTATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 12 0.46
24 13 0.50
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (23 bp):
TTTTAAAATTTAACATGTTATTA
Found at i:2791905 original size:17 final size:18
Alignment explanation
Indices: 2791883--2791919 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2791873 ATTCAATCGC
2791883 ATTACATTGT-TTAAAAT
1 ATTACATTGTATTAAAAT
*
2791900 ATTACATTTTATTAAAAT
1 ATTACATTGTATTAAAAT
2791918 AT
1 AT
2791920 CGAAATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTACATTGTATTAAAAT
Found at i:2792202 original size:21 final size:21
Alignment explanation
Indices: 2792176--2792219 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2792166 CTATGTTTGG
2792176 AATTTTGAGAAATTGTGCCCT
1 AATTTTGAGAAATTGTGCCCT
*
2792197 AATTTTGAGAAATTGTGCTCT
1 AATTTTGAGAAATTGTGCCCT
2792218 AA
1 AA
2792220 CAATTGAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (21 bp):
AATTTTGAGAAATTGTGCCCT
Found at i:2792912 original size:34 final size:35
Alignment explanation
Indices: 2792874--2792941 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
2792864 CCAGTAAAAT
2792874 ATTTTCCGTAAAATGATTT-CGGGAAAATATTTTA
1 ATTTTCCGTAAAATGATTTACGGGAAAATATTTTA
* *
2792908 ATTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 ATTTTCCGTAAAATGATTTACGGGAAAATATTTT
2792942 CGGCAGTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (35 bp):
ATTTTCCGTAAAATGATTTACGGGAAAATATTTTA
Found at i:2799947 original size:53 final size:53
Alignment explanation
Indices: 2799884--2800096 Score: 390
Period size: 53 Copynumber: 4.0 Consensus size: 53
2799874 CAATTAGATA
2799884 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
2799937 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
2799990 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
* * * *
2800043 TGCCATGAGCATTGATAACAATACATGGTAACAGTGTGACCATGTCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
2800096 T
1 T
2800097 ATGTAATCAA
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
53 156 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (53 bp):
TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
Found at i:2802389 original size:8 final size:8
Alignment explanation
Indices: 2802376--2802411 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
2802366 ATAACATACT
2802376 TTTTTATA
1 TTTTTATA
2802384 TTTTTATA
1 TTTTTATA
2802392 TTTTTTATA
1 -TTTTTATA
2802401 TTTTTA-A
1 TTTTTATA
2802408 TTTT
1 TTTT
2802412 ATTAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 5 0.19
8 14 0.52
9 8 0.30
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTATA
Found at i:2802396 original size:9 final size:9
Alignment explanation
Indices: 2802375--2802405 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2802365 AATAACATAC
2802375 TTTTTTATA
1 TTTTTTATA
2802384 -TTTTTATA
1 TTTTTTATA
2802392 TTTTTTATA
1 TTTTTTATA
2802401 TTTTT
1 TTTTT
2802406 AATTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTATA
Found at i:2802397 original size:17 final size:16
Alignment explanation
Indices: 2802375--2802430 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
2802365 AATAACATAC
2802375 TTTTTTATATTTTTATA
1 TTTTTTATATTTTTA-A
2802392 TTTTTTATATTTTTAA
1 TTTTTTATATTTTTAA
* *
2802408 TTTTATTAAATATTTAA
1 TTTT-TTATATTTTTAA
2802425 TTTTTT
1 TTTTTT
2802431 TTTTAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
16 7 0.19
17 29 0.81
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTATATTTTTAA
Found at i:2806378 original size:19 final size:19
Alignment explanation
Indices: 2806351--2806388 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2806341 TTAAGGTCCG
* *
2806351 TAATTTTTAATTTTCTTCT
1 TAATCTTTAATTTTATTCT
2806370 TAATCTTTAATTTTATTCT
1 TAATCTTTAATTTTATTCT
2806389 CAAATAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATCTTTAATTTTATTCT
Found at i:2807737 original size:109 final size:108
Alignment explanation
Indices: 2807547--2807761 Score: 340
Period size: 109 Copynumber: 2.0 Consensus size: 108
2807537 ATTACAATTG
* * *
2807547 TTTCGGTAGCTAAAAGCTAATAAAGTTAAAAATAAAAGGAGTTAACTAATGAGAAAGTGTCACGT
1 TTTCGGTAGCTAAAAACTAATAAAGTTAAAAATAAAAGGAGTTAACCAATGAGAAAGCGTCACGT
2807612 CATCAATGACATGGCATATTGACCAACGACATGGTATGTTATA
66 CATCAATGACATGGCATATTGACCAACGACATGGTATGTTATA
* * * * *
2807655 TTTCGGTAGCTAAAAAATTAATTACGTTAAAACTAAAAGGAGTTAACCAATGAGAACGCGTCACG
1 TTTCGGTAGCT-AAAAACTAATAAAGTTAAAAATAAAAGGAGTTAACCAATGAGAAAGCGTCACG
*
2807720 TCATCAATGACATGGCATATTGACCAACGGCATGGTATGTTA
65 TCATCAATGACATGGCATATTGACCAACGACATGGTATGTTA
2807762 ACGATCATTG
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
108 11 0.11
109 86 0.89
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (108 bp):
TTTCGGTAGCTAAAAACTAATAAAGTTAAAAATAAAAGGAGTTAACCAATGAGAAAGCGTCACGT
CATCAATGACATGGCATATTGACCAACGACATGGTATGTTATA
Found at i:2807865 original size:21 final size:19
Alignment explanation
Indices: 2807841--2807903 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 19
2807831 AAAAAATCAT
*
2807841 TAAAAGTTATCTAAAAATTTG
1 TAAAAATTAT-TAAAAA-TTG
*
2807862 TAAAAATTATTGAAAATTG
1 TAAAAATTATTAAAAATTG
*
2807881 TAAAAATTA--AAAAAATG
1 TAAAAATTATTAAAAATTG
2807898 TAAAAA
1 TAAAAA
2807904 AAAAGTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 12 0.32
19 12 0.32
20 5 0.13
21 9 0.24
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.32
Consensus pattern (19 bp):
TAAAAATTATTAAAAATTG
Found at i:2808623 original size:2 final size:2
Alignment explanation
Indices: 2808616--2808641 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2808606 TCAAAAGGAA
2808616 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
2808642 GTGATTTTTA
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:2808702 original size:20 final size:21
Alignment explanation
Indices: 2808666--2808705 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2808656 TTGTTTAATA
*
2808666 TTTTAAATAATTTTTTACAAT
1 TTTTAAATAATATTTTACAAT
2808687 TTTTAAATAA-ATTTTACAA
1 TTTTAAATAATATTTTACAA
2808706 GTTCTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTAAATAATATTTTACAAT
Found at i:2809243 original size:125 final size:124
Alignment explanation
Indices: 2809020--2809287 Score: 401
Period size: 125 Copynumber: 2.2 Consensus size: 124
2809010 CAATTTCTAG
* * * * * *
2809020 GACCTACTGTAGCAAAAGCGCGTCCACGAGAGCGCGATTTCACAAATTCTTCTCAAATAGCATCC
1 GACCTACTGTAGCAAAAGCGCGTCCACAAAACCGCGATTTCACAAATTCTTATCAAACAACATCC
*
2809085 TGCTAGAAGCGATTTTATACTATTTCCTTAGAAACGTCAACTCGAAATTATTTCTTCCAA
66 TGCTAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAACTCGAAATTATTT-TTCCAA
* * *
2809145 GACCTACTATAGCAAAAGTGCGTCCACAAAACCTCGATTTCACAAATTCTTATCAAACAACATCC
1 GACCTACTGTAGCAAAAGCGCGTCCACAAAACCGCGATTTCACAAATTCTTATCAAACAACATCC
* * * *
2809210 TGCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTTGAAATTATTTTTTCAG
66 TGCTAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAACTCGAAATTATTTTTCCAA
2809269 GACCTACTGTAGCAAAAGC
1 GACCTACTGTAGCAAAAGC
2809288 ACGTAAACGT
Statistics
Matches: 127, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
124 21 0.17
125 106 0.83
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (124 bp):
GACCTACTGTAGCAAAAGCGCGTCCACAAAACCGCGATTTCACAAATTCTTATCAAACAACATCC
TGCTAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAACTCGAAATTATTTTTCCAA
Found at i:2809366 original size:22 final size:23
Alignment explanation
Indices: 2809330--2809376 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2809320 TTTTTATACA
* *
2809330 AAACCCTAAAAATCCTAAACCCT
1 AAACCCTAAAAATCCAAAAACCT
2809353 AAACCCT-AAAATCCAAAAACCT
1 AAACCCTAAAAATCCAAAAACCT
2809375 AA
1 AA
2809377 CGTGGGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (23 bp):
AAACCCTAAAAATCCAAAAACCT
Found at i:2809774 original size:20 final size:20
Alignment explanation
Indices: 2809751--2809788 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2809741 GTCAATCTAG
2809751 CACGTCATCAGTCAACATTT
1 CACGTCATCAGTCAACATTT
**
2809771 CACGTCATTGGTCAACAT
1 CACGTCATCAGTCAACAT
2809789 GCCTATTCAT
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:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (20 bp):
CACGTCATCAGTCAACATTT
Found at i:2810338 original size:60 final size:59
Alignment explanation
Indices: 2810264--2810377 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 59
2810254 AAGACAATTG
*
2810264 AATAGTTGAGTGACCATTTTGTAACTTTTCATAGTTGAGTGACCAAAAAAGAAAATTACT
1 AATAGTTGAGTGACCATTTTGTAACATTTCATA-TTGAGTGACCAAAAAAGAAAATTACT
*
2810324 AATAGTTGTA-TGACCATTTTGTAACATTTCATATTGGGTGACCAAAAAAGAAAA
1 AATAGTTG-AGTGACCATTTTGTAACATTTCATATTGAGTGACCAAAAAAGAAAA
2810378 GAAAAAACCA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
59 20 0.39
60 30 0.59
61 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.32
Consensus pattern (59 bp):
AATAGTTGAGTGACCATTTTGTAACATTTCATATTGAGTGACCAAAAAAGAAAATTACT
Found at i:2811399 original size:169 final size:169
Alignment explanation
Indices: 2811120--2811458 Score: 678
Period size: 169 Copynumber: 2.0 Consensus size: 169
2811110 CACCGTTGGA
2811120 TCGAATTGCTAAAAGATTATGATTGTGTGATTGGTTACCATCAGGGCAAAGCTATTGTTGTTACT
1 TCGAATTGCTAAAAGATTATGATTGTGTGATTGGTTACCATCAGGGCAAAGCTATTGTTGTTACT
2811185 GATGCTTTGACCCATAAGTCGGCAATTGAATTGAGAGCAATGTTTGCTCAGCTTAGCATTTGTGA
66 GATGCTTTGACCCATAAGTCGGCAATTGAATTGAGAGCAATGTTTGCTCAGCTTAGCATTTGTGA
2811250 TGAGTAGCCTTTTGGCTGAGTTGAAAGTTAAACCCGTAT
131 TGAGTAGCCTTTTGGCTGAGTTGAAAGTTAAACCCGTAT
2811289 TCGAATTGCTAAAAGATTATGATTGTGTGATTGGTTACCATCAGGGCAAAGCTATTGTTGTTACT
1 TCGAATTGCTAAAAGATTATGATTGTGTGATTGGTTACCATCAGGGCAAAGCTATTGTTGTTACT
2811354 GATGCTTTGACCCATAAGTCGGCAATTGAATTGAGAGCAATGTTTGCTCAGCTTAGCATTTGTGA
66 GATGCTTTGACCCATAAGTCGGCAATTGAATTGAGAGCAATGTTTGCTCAGCTTAGCATTTGTGA
2811419 TGAGTAGCCTTTTGGCTGAGTTGAAAGTTAAACCCGTAT
131 TGAGTAGCCTTTTGGCTGAGTTGAAAGTTAAACCCGTAT
2811458 T
1 T
2811459 GCTTGATCAA
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 170 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (169 bp):
TCGAATTGCTAAAAGATTATGATTGTGTGATTGGTTACCATCAGGGCAAAGCTATTGTTGTTACT
GATGCTTTGACCCATAAGTCGGCAATTGAATTGAGAGCAATGTTTGCTCAGCTTAGCATTTGTGA
TGAGTAGCCTTTTGGCTGAGTTGAAAGTTAAACCCGTAT
Found at i:2822141 original size:18 final size:18
Alignment explanation
Indices: 2822113--2822151 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2822103 GGCTAATTGG
*
2822113 ATTTTTTTTATCT-TAAA
1 ATTTTTTTTATATGTAAA
2822130 ATTTTTTATTATATGTAAA
1 ATTTTTT-TTATATGTAAA
2822149 ATT
1 ATT
2822152 GAATTAGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTTTTTTATATGTAAA
Found at i:2826786 original size:11 final size:11
Alignment explanation
Indices: 2826770--2826800 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2826760 GTGAAATATG
*
2826770 AAAATTAAATT
1 AAAATTAAATC
2826781 AAAATTAAATC
1 AAAATTAAATC
2826792 AAAATTAAA
1 AAAATTAAA
2826801 GTTTGATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATTAAATC
Found at i:2827779 original size:2 final size:2
Alignment explanation
Indices: 2827772--2827796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2827762 TAGTAAATTA
2827772 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 A
2827797 ACATTATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2828989 original size:150 final size:149
Alignment explanation
Indices: 2828116--2829201 Score: 1478
Period size: 152 Copynumber: 7.2 Consensus size: 149
2828106 TTTTTTATTG
* * **
2828116 AAAGTAATAAAATCCGGTAAAAAAATACGAACAAA-GGCCGAAATAAGTTTTTTTTTAAATTTAT
1 AAAGTAATAAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTT-AATTTAT
*
2828180 TTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
65 TT-AAAAA-ACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
*
2828245 TTAGAAAATATTATATTTTTTA
128 TTAGAAAATAGTATATTTTTTA
* *
2828267 AAAGTAATAAAATCTGGGGGAAAAAATACGAACAAAGGGCCGAAATAATGATTTTTTTAAAATTT
1 AAAGTAATAAAATCT-GGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTT--AATTT
* *
2828332 ATTTAAAAAACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAA
63 ATTTAAAAAACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
*
2828397 -TACGAAAATAATATATTTTTATTA
128 TTA-GAAAATAGTATA-TTTT-TTA
* * *
2828421 AAAGTAATAAAATC---CAAAAAAATACGAATAAAGGGCCGAAATAAGAAATTTTTTTTAATTTA
1 AAAGTAATAAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAATAAG-GA-TTTTTTTAATTTA
* * *
2828483 TTTAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATTAGAAAA
64 TTTAAAAA-ACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
2828548 TTAGAAAATAGTAT-TTTTTT-
128 TTAGAAAATAGTATATTTTTTA
*
2828568 -AAGTAATAAAATCTAGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAAATTTAT
1 AAAGTAATAAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTT-AATTTAT
*
2828632 TTAAAAAACACAGTAAATTAATACATTTCAAAAATAATGTACTAAAATAATGTAAAATAATAAAA
65 TTAAAAAACAC--TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
* *
2828697 TTAGAAAATATTATATTTTTTT
128 TTAGAAAATAGTATATTTTTTA
*
2828719 AAAGTAATAAAATCCGGG-AAAAAATACGAACAAAGGGCCGAAATAATGG-TTTTTTTAATTTAT
1 AAAGTAATAAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAATAA-GGATTTTTTTAATTTAT
* * *
2828782 TTAAAAAA-ATTAAATTAATATATTTCAAATATAATGTACTAAAATAATGTAAAATAATAAAATT
65 TTAAAAAACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATT
2828846 AGAAAATAGTATATTTTTTA
130 AGAAAATAGTATATTTTTTA
* * * *
2828866 AAAGTCATAAACTCTGGGGGAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTAATTTAT
1 AAAGTAATAAAATCT-GGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAATTTAT
* *
2828931 TTAAAAAACACTAAATTAATACATTTCAAACTTGATGTACTAAAATAATGTAAAATAATAAAATT
65 TTAAAAAACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATT
*
2828996 AGAAAATAGTATATTTTTATTG
130 AGAAAATAGTATA-TTTT-TTA
* * * * *
2829018 AAAGTAATAAAAT-TCGGAAAAAAATACGAATAAATGGCCGAAATAAAGATTTTTTTATTTTATT
1 AAAGTAATAAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAATTTATT
* * * *
2829082 TAAAAAACACACTAAATTAATACATTTAAAATATAATGTAATAAAATAATGTAAAATAAAAAAAA
66 T-AAAAA-ACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT-AATAAAA
* * *
2829147 TTATAAAAAATTATATTTTTTA
128 TTAGAAAATAGTATATTTTTTA
2829169 AAAGTAATAAAAT-TCGGGAAAAAAATACGAACA
1 AAAGTAATAAAATCT-GGGAAAAAAATACGAACA
2829202 GATGGCCAAA
Statistics
Matches: 839, Mismatches: 66, Indels: 59
0.87 0.07 0.06
Matches are distributed among these distances:
146 13 0.02
147 93 0.11
148 22 0.03
149 145 0.17
150 170 0.20
151 139 0.17
152 185 0.22
153 45 0.05
154 27 0.03
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (149 bp):
AAAGTAATAAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAATTTATT
TAAAAAACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTA
GAAAATAGTATATTTTTTA
Found at i:2829353 original size:20 final size:21
Alignment explanation
Indices: 2829325--2829364 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2829315 AAAAAATTTA
2829325 TATTATTTTG-ATATTTTTTT
1 TATTATTTTGAATATTTTTTT
*
2829345 TATTTTTTTGTAATATTTTT
1 TATTATTTTG-AATATTTTT
2829365 GTAAAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (21 bp):
TATTATTTTGAATATTTTTTT
Found at i:2829509 original size:8 final size:8
Alignment explanation
Indices: 2829492--2829534 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
2829482 CTTAATTGTC
2829492 TTTTACTAT
1 TTTTA-TAT
*
2829501 TTTTTTAT
1 TTTTATAT
*
2829509 TTTTTTAT
1 TTTTATAT
*
2829517 TTTTACAT
1 TTTTATAT
2829525 TTTTATAT
1 TTTTATAT
2829533 TT
1 TT
2829535 GGTTTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
8 26 0.87
9 4 0.13
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTATAT
Found at i:2829543 original size:24 final size:25
Alignment explanation
Indices: 2829492--2829556 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 25
2829482 CTTAATTGTC
* *
2829492 TTTTACTATTTTTTTATTTTTTTAT
1 TTTTACTATTTTTATATTTGTTTAT
*
2829517 TTTTAC-ATTTTTATATTTGGTT-T
1 TTTTACTATTTTTATATTTGTTTAT
*
2829540 TTTTA-TA-TTATATATTT
1 TTTTACTATTTTTATATTT
2829557 TAAAAGTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.26
23 7 0.20
24 13 0.37
25 6 0.17
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (25 bp):
TTTTACTATTTTTATATTTGTTTAT
Found at i:2829568 original size:13 final size:13
Alignment explanation
Indices: 2829550--2829574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2829540 TTTTATATTA
2829550 TATATTTTAAAAG
1 TATATTTTAAAAG
2829563 TATATTTTAAAA
1 TATATTTTAAAA
2829575 TTTCTTGAAA
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TATATTTTAAAAG
Found at i:2836459 original size:53 final size:53
Alignment explanation
Indices: 2836279--2836459 Score: 167
Period size: 53 Copynumber: 3.4 Consensus size: 53
2836269 ATTTGATCCG
*
2836279 TATGAAACAAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCC
1 TATGAACCAAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCC
* ** * * *
2836332 TATGAACCAAACCAACTAAA-CTGAATGATAGTCATAGCCTGACTTTTTGACT-AGGT---
1 TATGAACCAAACCAACTAAATC-G---GAT-G-CATATCCCCA-GTTTAGGCTCA-GTCCC
* *
2836388 TATTAA-GAAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCC
1 TATGAACCAAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCC
2836440 TATGAACCAAACCAACTAAA
1 TATGAACCAAACCAACTAAA
2836460 CTGAATGATA
Statistics
Matches: 97, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
49 8 0.08
50 8 0.08
51 1 0.01
52 9 0.09
53 32 0.33
55 13 0.13
56 9 0.09
57 1 0.01
58 8 0.08
59 8 0.08
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (53 bp):
TATGAACCAAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCC
Found at i:2836476 original size:108 final size:108
Alignment explanation
Indices: 2836287--2836507 Score: 442
Period size: 108 Copynumber: 2.0 Consensus size: 108
2836277 CGTATGAAAC
2836287 AAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCCTATGAACCAAACCAACTAAA
1 AAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCCTATGAACCAAACCAACTAAA
2836352 CTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAG
66 CTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAG
2836395 AAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCCTATGAACCAAACCAACTAAA
1 AAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCCTATGAACCAAACCAACTAAA
2836460 CTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAG
66 CTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAG
2836503 AAACC
1 AAACC
2836508 CAAGATTTGA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 113 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (108 bp):
AAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCCTATGAACCAAACCAACTAAA
CTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAG
Found at i:2836637 original size:135 final size:135
Alignment explanation
Indices: 2836395--2836644 Score: 500
Period size: 135 Copynumber: 1.9 Consensus size: 135
2836385 GGTTATTAAG
2836395 AAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCCTATGAACCAAACCAACTAAA
1 AAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCCTATGAACCAAACCAACTAAA
2836460 CTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAGAAACCCAAGATTTGATCCGTAT
66 CTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAGAAACCCAAGATTTGATCCGTAT
2836525 GAAAC
131 GAAAC
2836530 AAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCCTATGAACCAAACCAACTAAA
1 AAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCCTATGAACCAAACCAACTAAA
2836595 CTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAGAAACCCA
66 CTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAGAAACCCA
2836645 TTGTTTTTAG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 115 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (135 bp):
AAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTCCCTATGAACCAAACCAACTAAA
CTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAGAAACCCAAGATTTGATCCGTAT
GAAAC
Found at i:2837533 original size:39 final size:39
Alignment explanation
Indices: 2837490--2837651 Score: 211
Period size: 39 Copynumber: 4.2 Consensus size: 39
2837480 TGCCATACAC
*
2837490 TTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCAT
1 TTGCTGAGGATACATTGAACCCATCTGGCCAGCTGGCAT
* * *
2837529 TTGCTGAGGATACATTGAACCCATCTGGGCC-CCCGGCAC
1 TTGCTGAGGATACATTGAACCCATCT-GGCCAGCTGGCAT
* *
2837568 TTGCTGAGGATACATTGAACCCATCTGGCCCGTTGGCAT
1 TTGCTGAGGATACATTGAACCCATCTGGCCAGCTGGCAT
* * *
2837607 TTGCTGAGGATACATGGAACTCATCTGGCCCA-CAGGCAT
1 TTGCTGAGGATACATTGAACCCATCTGG-CCAGCTGGCAT
2837646 TTGCTG
1 TTGCTG
2837652 TGGAAGCATG
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
38 4 0.04
39 97 0.91
40 6 0.06
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.25
Consensus pattern (39 bp):
TTGCTGAGGATACATTGAACCCATCTGGCCAGCTGGCAT
Found at i:2837574 original size:78 final size:78
Alignment explanation
Indices: 2837487--2837651 Score: 251
Period size: 78 Copynumber: 2.1 Consensus size: 78
2837477 GGTTGCCATA
*
2837487 CACTTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGCTGAGGATACATTGAACCCA
1 CACTTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGCTGAGGATACATGGAACCCA
*
2837552 TCTGGGCCC-CCGG
66 TCT-GGCCCACAGG
* * * *
2837565 CACTTGCTGAGGATACATTGAACCCATCTGGCCCGTTGGCATTTGCTGAGGATACATGGAACTCA
1 CACTTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGCTGAGGATACATGGAACCCA
2837630 TCTGGCCCACAGG
66 TCTGGCCCACAGG
*
2837643 CATTTGCTG
1 CACTTGCTG
2837652 TGGAAGCATG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
77 5 0.06
78 74 0.94
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.24
Consensus pattern (78 bp):
CACTTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGCTGAGGATACATGGAACCCA
TCTGGCCCACAGG
Found at i:2840371 original size:205 final size:205
Alignment explanation
Indices: 2839912--2840527 Score: 1151
Period size: 205 Copynumber: 3.0 Consensus size: 205
2839902 AATATGCAAG
*
2839912 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGGGGATTTAGCAGCGTGA
1 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
* *
2839977 AACTTCATAAACTTTCGAAAAGACTTTTCATTTTGAGAGCTGGAAAAACACAAGTTTACACAAAA
66 AACTTCATAAACTTTCGAAAAGACTTTTCATTATGAGAGCTGGAAAAACATAAGTTTACAC-AAA
*
2840042 AAAACGGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAACGCCAGTTA
130 AAAACTGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAACGCCAGTTA
2840107 TATTAAGACTT
195 TATTAAGACTT
2840118 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
1 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
2840183 AACTTCATAAACTTTCGAAAAGACTTTTCATTATGAGAGCTGGAAAAACATAAGTTTACACAAAA
66 AACTTCATAAACTTTCGAAAAGACTTTTCATTATGAGAGCTGGAAAAACATAAGTTTACACAAAA
*
2840248 AAACTGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAATGCCAGTTAT
131 AAACTGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAACGCCAGTTAT
2840313 ATTAAGACTT
196 ATTAAGACTT
2840323 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
1 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
*
2840388 AACTTCATAAACTTTCGAAAAGAATTTTCATTATGAGAGCTGGAAAAACATAAGTTTACACAAAA
66 AACTTCATAAACTTTCGAAAAGACTTTTCATTATGAGAGCTGGAAAAACATAAGTTTACACAAAA
* *
2840453 AAACTGGTTCACCATCCAATGAATTTGAGCATTCCCAACCAGATTTTTTTGCAAACGCCAGTTAT
131 AAACTGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAACGCCAGTTAT
2840518 ATTAAGACTT
196 ATTAAGACTT
2840528 AGGTAGTCAC
Statistics
Matches: 401, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
205 278 0.69
206 123 0.31
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (205 bp):
TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
AACTTCATAAACTTTCGAAAAGACTTTTCATTATGAGAGCTGGAAAAACATAAGTTTACACAAAA
AAACTGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAACGCCAGTTAT
ATTAAGACTT
Found at i:2846089 original size:25 final size:25
Alignment explanation
Indices: 2846061--2846134 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
2846051 CCAATATTTG
2846061 GCTCGCAAGAGCTTCCCGTTATACA
1 GCTCGCAAGAGCTTCCCGTTATACA
* * ** **
2846086 GCTCACATGAGCTTCTTGTTATATG
1 GCTCGCAAGAGCTTCCCGTTATACA
*
2846111 GCTCGGAAGAGCTTCCCGTT-TACA
1 GCTCGCAAGAGCTTCCCGTTATACA
2846135 TGTTTGTATA
Statistics
Matches: 36, Mismatches: 13, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
24 2 0.06
25 34 0.94
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30
Consensus pattern (25 bp):
GCTCGCAAGAGCTTCCCGTTATACA
Found at i:2847907 original size:17 final size:18
Alignment explanation
Indices: 2847885--2847924 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2847875 GTTTAGAAAT
*
2847885 TATTTTTATTAT-AGTAA
1 TATTTTTATAATAAGTAA
*
2847902 TATTTTTATAATAATTAA
1 TATTTTTATAATAAGTAA
2847920 TATTT
1 TATTT
2847925 AGAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TATTTTTATAATAAGTAA
Found at i:2848842 original size:17 final size:17
Alignment explanation
Indices: 2848820--2848855 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2848810 TCTTTAGTGA
2848820 TATCAAAAAATAACTAT
1 TATCAAAAAATAACTAT
*
2848837 TATCAAAGAATAACTAT
1 TATCAAAAAATAACTAT
2848854 TA
1 TA
2848856 CATGCAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.31
Consensus pattern (17 bp):
TATCAAAAAATAACTAT
Found at i:2851037 original size:18 final size:17
Alignment explanation
Indices: 2851004--2851042 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2850994 TTGTATAAAT
2851004 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2851022 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2851039 TGTG
1 TGTG
2851043 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2851295 original size:23 final size:23
Alignment explanation
Indices: 2851268--2851340 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
2851258 AGTGTTATTG
2851268 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
2851291 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2851314 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2851337 ATCA
1 ATCA
2851341 ATGTGGCTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2853092 original size:49 final size:49
Alignment explanation
Indices: 2853017--2853118 Score: 186
Period size: 49 Copynumber: 2.1 Consensus size: 49
2853007 AATCATATTT
*
2853017 TAAATATTGAAAATTTGAAATTGAACCACCGAAATGAACATCAATAATA
1 TAAATATTGAAAATTTGAAATCGAACCACCGAAATGAACATCAATAATA
*
2853066 TAAATATTGAAAATTTGAAATCGAACCTCCGAAATGAACATCAATAATA
1 TAAATATTGAAAATTTGAAATCGAACCACCGAAATGAACATCAATAATA
2853115 TAAA
1 TAAA
2853119 CATCAATAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (49 bp):
TAAATATTGAAAATTTGAAATCGAACCACCGAAATGAACATCAATAATA
Found at i:2859536 original size:105 final size:105
Alignment explanation
Indices: 2859277--2859648 Score: 585
Period size: 104 Copynumber: 3.6 Consensus size: 105
2859267 AACCGTTATT
* * *
2859277 GGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATCACGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
* *
2859342 ATCAGCACATAGCAACCCCCTTTT-TCATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAAATAC
2859381 GGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATCA-CGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
2859445 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAAATAT
65 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAAATAC
*
2859486 GGTGGATCACGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATCACGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
2859551 ATCAGCACATAGCAACCCCC-TTTCACATTT-AAAAATAC
66 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAAATAC
**
2859589 GGTGGACTCA-GCACTTAGCAACCACCAAT-AAGTAGGGGAATCAGCACTTAGCAACCCCTC
1 GGTGGA-TCACGCACTTAGC-ACCACCAATGAA-CCGGGGAATCAGCACTTAGCAACCCCTC
2859649 TATATGTAAT
Statistics
Matches: 251, Mismatches: 11, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
103 23 0.09
104 133 0.53
105 94 0.37
106 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (105 bp):
GGTGGATCACGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAAATAC
Found at i:2860011 original size:31 final size:30
Alignment explanation
Indices: 2859980--2860037 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2859970 CCACTCAACT
2859980 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
2860010 TTTTGCATAATTACATTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
2860038 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:2860912 original size:42 final size:42
Alignment explanation
Indices: 2860852--2860953 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
2860842 GGCTGTTACA
* *
2860852 CATAAGGGTTAAACTGAAGCTTAAAAGAGCTGAATGAAAACC
1 CATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACGAAAACC
* *
2860894 CATAAGGGTTAAATTGAAGCTCAAAAGAGCTGAACGGAAACC
1 CATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACGAAAACC
*
2860936 CATAAAGGTTAAACTGAA
1 CATAAGGGTTAAACTGAA
2860954 ACTCGTATGA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.19
Consensus pattern (42 bp):
CATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACGAAAACC
Found at i:2860954 original size:21 final size:21
Alignment explanation
Indices: 2860889--2860955 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2860879 AGCTGAATGA
* *
2860889 AAACCCATAAGGGTTAAATTG
1 AAACCCATAAAGGTTAAACTG
* * * * *
2860910 AAGCTCA-AAAGAGCTGAACGG
1 AAACCCATAAAG-GTTAAACTG
2860931 AAACCCATAAAGGTTAAACTG
1 AAACCCATAAAGGTTAAACTG
2860952 AAAC
1 AAAC
2860956 TCGTATGAGT
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 3 0.09
21 25 0.78
22 4 0.12
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.16
Consensus pattern (21 bp):
AAACCCATAAAGGTTAAACTG
Found at i:2861077 original size:24 final size:24
Alignment explanation
Indices: 2861045--2861092 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2861035 TACTTGGGTA
2861045 ATTTGCCGTCAATTCATCCTTTGC
1 ATTTGCCGTCAATTCATCCTTTGC
2861069 ATTTGCCGTCAATTCATCCTTTGC
1 ATTTGCCGTCAATTCATCCTTTGC
2861093 CACAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.42
Consensus pattern (24 bp):
ATTTGCCGTCAATTCATCCTTTGC
Found at i:2861236 original size:45 final size:46
Alignment explanation
Indices: 2861151--2861238 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
2861141 TTTTCAATTC
* * * *
2861151 ATAATTTAACAATATTTCATTTTTTTAACAATATGCTAAATACATA
1 ATAATTTAACAACATTCCATTTTTTCAACAATATACTAAATACATA
*
2861197 ATAATTTAACAACATTCCA-TTTTTCAACAATATATTAAATAC
1 ATAATTTAACAACATTCCATTTTTTCAACAATATACTAAATAC
2861239 GTAACATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 20 0.54
46 17 0.46
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (46 bp):
ATAATTTAACAACATTCCATTTTTTCAACAATATACTAAATACATA
Found at i:2863054 original size:29 final size:28
Alignment explanation
Indices: 2863010--2863088 Score: 81
Period size: 32 Copynumber: 2.8 Consensus size: 28
2863000 TTTCTTTCCT
*
2863010 TATATA-CTAAATAAAATAATAAAATAA
1 TATATATCTAATTAAAATAATAAAATAA
*
2863037 TAATATATCTCATTAAAATATTAATAAAATAA
1 T-ATATATCTAATT-AAA-A-TAATAAAATAA
*
2863069 TATTTATCTAATT-AAATAAT
1 TATATATCTAATTAAAATAAT
2863089 TATAAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 5 0.12
28 6 0.14
29 6 0.14
30 3 0.07
31 11 0.26
32 12 0.28
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (28 bp):
TATATATCTAATTAAAATAATAAAATAA
Found at i:2863083 original size:31 final size:32
Alignment explanation
Indices: 2863017--2863097 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
2863007 CCTTATATAC
* *
2863017 TAAATAAAATAATAAAATAATAATATATCTCAT
1 TAAAT-AATTAATAAAATAATAATATATCTAAT
*
2863050 TAAA-ATATTAATAAAATAAT-ATTTATCTAAT
1 TAAATA-ATTAATAAAATAATAATATATCTAAT
2863081 TAAATAATT-ATAAAATA
1 TAAATAATTAATAAAATA
2863098 TCATCAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 8 0.19
31 17 0.40
32 14 0.33
33 4 0.09
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAATAATTAATAAAATAATAATATATCTAAT
Found at i:2867598 original size:11 final size:11
Alignment explanation
Indices: 2867562--2867605 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
2867552 TCTGGAAAGT
2867562 AAATAACAAAT-
1 AAATAA-AAATA
2867573 AAATAAAAATAA
1 AAATAAAAAT-A
2867585 AAATAAAAATA
1 AAATAAAAATA
*
2867596 AAACAAAAAT
1 AAATAAAAAT
2867606 GAAGTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 4 0.13
11 16 0.53
12 10 0.33
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:2867604 original size:6 final size:6
Alignment explanation
Indices: 2867573--2867598 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2867563 AATAACAAAT
2867573 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
2867599 CAAAAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:2874331 original size:91 final size:92
Alignment explanation
Indices: 2874154--2874321 Score: 207
Period size: 91 Copynumber: 1.8 Consensus size: 92
2874144 ATATAATGTG
* * * *
2874154 TTTGATTGAATTGATGTCACGAGTTAACCTAATATCAAGTTGATCAAAGAAATTATTCATAAGTT
1 TTTGATTGAATTGATGTCACGAGTTAACCTAATATAAACTTGATCAAAGAAATAATTCAAAAGTT
* *
2874219 TTTTTTTAATAAGTAATTGAATGAGTA
66 ATTTATTAATAAGTAATTGAATGAGTA
* * * *
2874246 TTTGATTGAATTGGTGTCAC-AGTTAA-CTCGATATAAACTTGATCAGATAAATAACTT-AAAAG
1 TTTGATTGAATTGATGTCACGAGTTAACCT-AATATAAACTTGATCAAAGAAATAA-TTCAAAAG
2874308 TTATTTATTAATAA
64 TTATTTATTAATAA
2874322 AGGATTGAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
90 2 0.03
91 41 0.64
92 21 0.33
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (92 bp):
TTTGATTGAATTGATGTCACGAGTTAACCTAATATAAACTTGATCAAAGAAATAATTCAAAAGTT
ATTTATTAATAAGTAATTGAATGAGTA
Found at i:2877351 original size:2 final size:2
Alignment explanation
Indices: 2877344--2877368 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2877334 ATTTTGTCAA
2877344 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2877369 AGAAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2885883 original size:34 final size:34
Alignment explanation
Indices: 2885840--2885906 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
2885830 AAACACTGAT
2885840 AACACAGCCAAAGCAATAAGGTTTACAGAAAGGA
1 AACACAGCCAAAGCAATAAGGTTTACAGAAAGGA
*
2885874 AACACAGCCAAAGCAATAAGGTTTACAGGAAGG
1 AACACAGCCAAAGCAATAAGGTTTACAGAAAGG
2885907 TATTATCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (34 bp):
AACACAGCCAAAGCAATAAGGTTTACAGAAAGGA
Found at i:2887782 original size:27 final size:29
Alignment explanation
Indices: 2887752--2887819 Score: 97
Period size: 27 Copynumber: 2.4 Consensus size: 29
2887742 AACTTAGGTG
2887752 CCAAATTGGAACAAAAAAAAT-CAAG-TA
1 CCAAATTGGAACAAAAAAAATACAAGATA
* *
2887779 CCAAAGTGGAACAAAAAAAATACTAGATA
1 CCAAATTGGAACAAAAAAAATACAAGATA
2887808 CCAAATT-GAACA
1 CCAAATTGGAACA
2887820 TTAAAACTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.56
28 8 0.22
29 8 0.22
ACGTcount: A:0.57, C:0.16, G:0.12, T:0.15
Consensus pattern (29 bp):
CCAAATTGGAACAAAAAAAATACAAGATA
Found at i:2889540 original size:30 final size:30
Alignment explanation
Indices: 2889504--2889564 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2889494 CTAGTGACTT
* *
2889504 TAATGAGATATTCTCATTTTTTGTAGGGGG
1 TAATGAGATATTCCCATTTTATGTAGGGGG
2889534 TAATGAGATATTCCCATTTTATGTAGGGGG
1 TAATGAGATATTCCCATTTTATGTAGGGGG
2889564 T
1 T
2889565 GCTCTTTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (30 bp):
TAATGAGATATTCCCATTTTATGTAGGGGG
Found at i:2893440 original size:10 final size:10
Alignment explanation
Indices: 2893411--2893449 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2893401 AACAAAGTAT
2893411 ATAAATTTTA
1 ATAAATTTTA
2893421 GATAAATTTTA
1 -ATAAATTTTA
*
2893432 ATAATTTTTA
1 ATAAATTTTA
*
2893442 AAAAATTT
1 ATAAATTT
2893450 CAAATAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (10 bp):
ATAAATTTTA
Found at i:2893569 original size:11 final size:11
Alignment explanation
Indices: 2893553--2893585 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
2893543 ATTTTTAAAA
2893553 AATATTTTTTT
1 AATATTTTTTT
2893564 AATA-TTTTTT
1 AATATTTTTTT
2893574 AATATATTTTTT
1 AATAT-TTTTTT
2893586 CCTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
AATATTTTTTT
Found at i:2896985 original size:36 final size:38
Alignment explanation
Indices: 2896945--2897023 Score: 90
Period size: 36 Copynumber: 2.1 Consensus size: 38
2896935 AATTAACTAG
*
2896945 TAATTAAATAATTAAAATTTGAAGAAAA-AA-TTAATT
1 TAATTAAATAATTAAAATTTCAAGAAAATAAGTTAATT
* * * *
2896981 TAATTAAGTCATTATAATTTCATGAAAATAAGTTAATT
1 TAATTAAATAATTAAAATTTCAAGAAAATAAGTTAATT
*
2897019 AAATT
1 TAATT
2897024 TATTTCTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 23 0.66
37 2 0.06
38 10 0.29
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (38 bp):
TAATTAAATAATTAAAATTTCAAGAAAATAAGTTAATT
Found at i:2898017 original size:22 final size:21
Alignment explanation
Indices: 2897989--2898048 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
2897979 ATAACTGAAT
*
2897989 TAAATATAGATTTAAAATTATA
1 TAAATATAAATTTAAAA-TATA
*
2898011 TAAATATAAATTTAAAATATT
1 TAAATATAAATTTAAAATATA
*
2898032 TAAAT-TTAA-TTAAAATA
1 TAAATATAAATTTAAAATA
2898049 AAATATAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.23
20 3 0.09
21 8 0.23
22 16 0.46
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAATATAAATTTAAAATATA
Found at i:2900256 original size:21 final size:21
Alignment explanation
Indices: 2900232--2900374 Score: 80
Period size: 21 Copynumber: 6.9 Consensus size: 21
2900222 CGTGTTTGCT
*
2900232 TTCAGTTTAGCTCTTATGAGC
1 TTCAGTTTAACTCTTATGAGC
* *
2900253 TTCA-ATTAACT-TATATGAGT
1 TTCAGTTTAACTCT-TATGAGC
* * *
2900273 TTCAGTTTAACCCTTTTGAGT
1 TTCAGTTTAACTCTTATGAGC
* * * *
2900294 TTTAATTTAGCTCTTTTGAGC
1 TTCAGTTTAACTCTTATGAGC
* *
2900315 TTTAGTTTAACTCTTAT-AGGTT
1 TTCAGTTTAACTCTTATGA-G-C
* *
2900337 TTC-GTTCAGCTCTTATGAGC
1 TTCAGTTTAACTCTTATGAGC
*
2900357 TTCCA-TTTAACCCTTATG
1 TT-CAGTTTAACTCTTATG
2900375 GGTTTTCATT
Statistics
Matches: 92, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
19 1 0.01
20 18 0.20
21 69 0.75
22 4 0.04
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (21 bp):
TTCAGTTTAACTCTTATGAGC
Found at i:2900338 original size:42 final size:42
Alignment explanation
Indices: 2900278--2900401 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 42
2900268 TGAGTTTCAG
* * * *
2900278 TTTAACCCTT-TTGAGTTTTAATTTAGCTCTTTTGAGCTT-TA
1 TTTAACCCTTATAG-GTTTTCATTTAGCTCTTATGAGCTTCCA
* * *
2900319 GTTTAACTCTTATAGGTTTTCGTTCAGCTCTTATGAGCTTCCA
1 -TTTAACCCTTATAGGTTTTCATTTAGCTCTTATGAGCTTCCA
* * *
2900362 TTTAACCCTTATGGGTTTTCATTTAGCACTTATGTGCTTC
1 TTTAACCCTTATAGGTTTTCATTTAGCTCTTATGAGCTTC
2900402 TGTGCAACCT
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
42 64 0.96
43 3 0.04
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (42 bp):
TTTAACCCTTATAGGTTTTCATTTAGCTCTTATGAGCTTCCA
Found at i:2908214 original size:11 final size:11
Alignment explanation
Indices: 2908200--2908237 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2908190 GAAATAATAA
2908200 AGAAACAGAGG
1 AGAAACAGAGG
*
2908211 AGAAAGAGAGG
1 AGAAACAGAGG
2908222 AGAAACATG-GG
1 AGAAACA-GAGG
2908233 AGAAA
1 AGAAA
2908238 GAAAGAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 23 0.96
12 1 0.04
ACGTcount: A:0.55, C:0.05, G:0.37, T:0.03
Consensus pattern (11 bp):
AGAAACAGAGG
Found at i:2908904 original size:13 final size:14
Alignment explanation
Indices: 2908886--2908914 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2908876 GTACTACAAG
2908886 ATTATTTT-TTTAA
1 ATTATTTTATTTAA
2908899 ATTATTTTATTTAA
1 ATTATTTTATTTAA
2908913 AT
1 AT
2908915 GTCTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTTTATTTAA
Found at i:2908950 original size:5 final size:5
Alignment explanation
Indices: 2908942--2908972 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2908932 GAGTTATTTA
*
2908942 AAAAT AAAAT AAAAT AAAGT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
2908973 TTATGGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2909296 original size:25 final size:25
Alignment explanation
Indices: 2909260--2909364 Score: 158
Period size: 25 Copynumber: 4.2 Consensus size: 25
2909250 ACTTTAGCTC
* *
2909260 GCTCTCTAATTATTAGCGCGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
2909285 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
2909310 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
**
2909335 GCTCTCTGA-TATTTAGCACGTCAGT
1 GCTCTCTGATTA-TTAGCACGTTGGT
2909360 GCTCT
1 GCTCT
2909365 TTGTTTAGCA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
24 2 0.03
25 73 0.97
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:2909374 original size:22 final size:22
Alignment explanation
Indices: 2909346--2909391 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2909336 CTCTCTGATA
* *
2909346 TTTAGCACGTCAGTGCTCTTTG
1 TTTAGCACATCAGTGCTCTCTG
*
2909368 TTTAGCACATCTGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
2909390 TT
1 TT
2909392 CATTAGTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (22 bp):
TTTAGCACATCAGTGCTCTCTG
Found at i:2910116 original size:175 final size:175
Alignment explanation
Indices: 2909825--2910175 Score: 648
Period size: 175 Copynumber: 2.0 Consensus size: 175
2909815 ACTTGAAATA
* *
2909825 TTTTGGTATATATATGAAATGAATTAATGGAACTATACGTATGTTTGCAAATATGGTTGGTAAGT
1 TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAAT
2909890 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCGTTTTGACACCAAATG
66 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCGTTTTGACACCAAATG
*
2909955 TAATAGTCTTATACCGGGTCTGTACGATTAGACCAGGTATATGGT
131 TAATAGTCTTATACCGGGTCTGTACGATTAGACCAGGTATAGGGT
*
2910000 TTTTGGTATATATATGAAATGAATTAATGAAACTATATGTATGTTTGCAAATATGGTTGGTAAAT
1 TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAAT
2910065 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCGTTTTGACACCAAATG
66 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCGTTTTGACACCAAATG
* *
2910130 TAATAGTCTTATACTGGGTTTGTACGATTAGACCAGGTATAGGGT
131 TAATAGTCTTATACCGGGTCTGTACGATTAGACCAGGTATAGGGT
2910175 T
1 T
2910176 GTTACAGGTC
Statistics
Matches: 170, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 170 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (175 bp):
TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAAT
TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCGTTTTGACACCAAATG
TAATAGTCTTATACCGGGTCTGTACGATTAGACCAGGTATAGGGT
Found at i:2910761 original size:25 final size:26
Alignment explanation
Indices: 2910715--2910764 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
2910705 TAGAAATTTA
2910715 GTTAAAAAGATTAAGTAATTTTTTTGT
1 GTTAAAAAGA-TAAGTAATTTTTTTGT
**
2910742 GTTAAAAAG-TAAGTTTTTTTTTT
1 GTTAAAAAGATAAGTAATTTTTTT
2910765 TGAGAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
27 9 0.43
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (26 bp):
GTTAAAAAGATAAGTAATTTTTTTGT
Found at i:2924002 original size:24 final size:21
Alignment explanation
Indices: 2923969--2924011 Score: 59
Period size: 24 Copynumber: 1.9 Consensus size: 21
2923959 TGTCATGTCA
2923969 TTTTTAATTAATATCTTAAATGT
1 TTTTTAATTAA-AT-TTAAATGT
2923992 TTTTATAATTAAATTTAAAT
1 TTTT-TAATTAAATTTAAAT
2924012 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTAATTAAATTTAAATGT
Found at i:2939493 original size:2 final size:2
Alignment explanation
Indices: 2939486--2939512 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2939476 ATTTAATCAC
2939486 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2939513 TGGGAAGAAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2955903 original size:13 final size:13
Alignment explanation
Indices: 2955887--2955917 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2955877 CACATTAAAC
2955887 TAAAATTCATGTA
1 TAAAATTCATGTA
2955900 TAAAATTCATGTA
1 TAAAATTCATGTA
2955913 -AAAAT
1 TAAAAT
2955918 ATCGATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (13 bp):
TAAAATTCATGTA
Found at i:2959347 original size:52 final size:52
Alignment explanation
Indices: 2959256--2959355 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
2959246 ATGTCATAAT
* *
2959256 TATTACTTATCTCTTAATTAATTTAAATATTAAGCGATAAATAATAAAAATA
1 TATTACTTATCTCTTAATTAATTTAAATAATAAGAGATAAATAATAAAAATA
* * *
2959308 TATTA-TTATTTCTTGAATTAA-TTAAATTAATATGAGATAAATAGTAAA
1 TATTACTTATCTCTT-AATTAATTTAAA-TAATAAGAGATAAATAATAAA
2959356 TATAAAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 13 0.32
52 28 0.68
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (52 bp):
TATTACTTATCTCTTAATTAATTTAAATAATAAGAGATAAATAATAAAAATA
Found at i:2959378 original size:20 final size:20
Alignment explanation
Indices: 2959353--2959392 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2959343 GATAAATAGT
2959353 AAATAT-AAAAGAAGCTTTTG
1 AAATATGAAAAGAAG-TTTTG
*
2959373 AAATATGAAGAGAAGTTTTG
1 AAATATGAAAAGAAGTTTTG
2959393 GTACTTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (20 bp):
AAATATGAAAAGAAGTTTTG
Found at i:2964130 original size:14 final size:15
Alignment explanation
Indices: 2964091--2964130 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2964081 ATCAACAAAT
*
2964091 AATTTAAAAATTATA
1 AATTCAAAAATTATA
2964106 AATTCAAAAAATTA-A
1 AATTC-AAAAATTATA
2964121 AATTCAAAAA
1 AATTCAAAAA
2964131 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 10 0.43
16 8 0.35
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTCAAAAATTATA
Found at i:2964131 original size:15 final size:16
Alignment explanation
Indices: 2964096--2964132 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
2964086 CAAATAATTT
2964096 AAAAATTATAAATTCA
1 AAAAATTATAAATTCA
2964112 AAAAATTA-AAATTCA
1 AAAAATTATAAATTCA
2964127 AAAAAT
1 AAAAAT
2964133 ATTAAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATTATAAATTCA
Found at i:2978391 original size:21 final size:21
Alignment explanation
Indices: 2978365--2978405 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2978355 AGACGAGCAA
* *
2978365 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2978386 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2978406 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2988891 original size:26 final size:25
Alignment explanation
Indices: 2988815--2988894 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
2988805 ATTATTATTG
*
2988815 TTAAATTATATTTAATAATAATTTTA
1 TTAAATTATATTT-ATAATAATCTTA
* *
2988841 TTAAAATATGA-TTA-AAT-TTCTTA
1 TTAAATTAT-ATTTATAATAATCTTA
*
2988864 TTAAATTATATTTAGTAATAATCCTA
1 TTAAATTATATTTA-TAATAATCTTA
2988890 TTAAA
1 TTAAA
2988895 ATTTAATAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
22 1 0.02
23 15 0.35
24 3 0.07
25 4 0.09
26 19 0.44
27 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (25 bp):
TTAAATTATATTTATAATAATCTTA
Found at i:2989098 original size:16 final size:16
Alignment explanation
Indices: 2989079--2989123 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2989069 ATTATAACTT
2989079 TATTTCATTACAGCTC
1 TATTTCATTACAGCTC
* *
2989095 TATTCCGTTACAGCTC
1 TATTTCATTACAGCTC
2989111 TA-TTCTATTACAG
1 TATTTC-ATTACAG
2989124 TGAACTAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (16 bp):
TATTTCATTACAGCTC
Found at i:2989466 original size:17 final size:18
Alignment explanation
Indices: 2989438--2989471 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2989428 AAAACATAAA
2989438 AAAATATTAAAAAATATT
1 AAAATATTAAAAAATATT
*
2989456 AAAAT-TTAAAATATAT
1 AAAATATTAAAAAATAT
2989472 ATATAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATATTAAAAAATATT
Found at i:2996154 original size:94 final size:95
Alignment explanation
Indices: 2996045--2996233 Score: 299
Period size: 94 Copynumber: 2.0 Consensus size: 95
2996035 TTATAATAAT
*
2996045 TGAGAAAAAAAGTACCTGCTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGG
1 TGAGAAAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGG
* *
2996110 AAGCGCACAGAGGGAATGAAAGAGGAAGCA
66 AAGCACACAGAGGCAATGAAAGAGGAAGCA
* ** *
2996140 TGAG-AAAAAGGTACCTACTGCAAGAATGGTATTGCCAGCTCTAGAACTTCAAAAACAAAAAGGG
1 TGAGAAAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGG
*
2996204 AAGCACGCAGAGGCAATGAAAGAGGAAGCA
66 AAGCACACAGAGGCAATGAAAGAGGAAGCA
2996234 CTCAGGCTAA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 82 0.95
95 4 0.05
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (95 bp):
TGAGAAAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGG
AAGCACACAGAGGCAATGAAAGAGGAAGCA
Found at i:2999623 original size:22 final size:21
Alignment explanation
Indices: 2999605--2999647 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2999595 AGGATAAAAT
2999605 TGAAAAGATAAAAAAATAAAGA
1 TGAAAA-ATAAAAAAATAAAGA
* *
2999627 TGATAAATAATAAAATAAAGA
1 TGAAAAATAAAAAAATAAAGA
2999648 AAATATCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.19
Consensus pattern (21 bp):
TGAAAAATAAAAAAATAAAGA
Found at i:3002195 original size:199 final size:199
Alignment explanation
Indices: 3001828--3002235 Score: 548
Period size: 199 Copynumber: 2.1 Consensus size: 199
3001818 TACATGGGAG
* * *
3001828 TGTGATTTGGTCGTGTGTCCTCTGTATCTTTAAAATTGCAAAACAAAATGCTCAAGTATTTTCAC
1 TGTGGTTTGGTCGTCTGTCCCCTGTATCTTTAAAATTGCAAAACAAAATGCTCAAGTATTTTCAC
* * * *
3001893 ACGAGCAGGCACACAGACGTCTGTCTCAGTCGTATATGGCACACAACCTGGTACACGGGCGTGTG
66 ACGAGCAGGCACACAGACGTCTGTCTCAGTCGTATATGGCACACAACCTGGCACACGAGCATATG
* * * *
3001958 ACTTGACCGTGTGGCCCCTGCACCTAATTAATGTAAATTAAATTATTCACACAACTTAGCACACG
131 ACTTGACCATGTGGCCCCTACACCTAATTAAAGTAAATTAAAATATTCACACAACTTAGCACACG
*
3002023 GGCA
196 AGCA
* * * *
3002027 TGTGGTTTGGTTGTCTGTCCCCTGTATCTTTAAAATTGCAAAACAGAATGTTCAGGTATTTTCAC
1 TGTGGTTTGGTCGTCTGTCCCCTGTATCTTTAAAATTGCAAAACAAAATGCTCAAGTATTTTCAC
* * * * **
3002092 ATG-GACAGGCACACGGACGTCTGTCTCAGTCGTATGTGGCACGCGGCCTGGCACACGAGCATAT
66 ACGAG-CAGGCACACAGACGTCTGTCTCAGTCGTATATGGCACACAACCTGGCACACGAGCATAT
* * * * *
3002156 GACTTGACCATGTGGCTCTTACACCTAATTAAAGTAAATTAAAATGTTCACACAGCTTAGCATAC
130 GACTTGACCATGTGGCCCCTACACCTAATTAAAGTAAATTAAAATATTCACACAACTTAGCACAC
*
3002221 TAGCA
195 GAGCA
3002226 TGTGGTTTGG
1 TGTGGTTTGG
3002236 CCGTGTGACC
Statistics
Matches: 180, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
198 1 0.01
199 179 0.99
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (199 bp):
TGTGGTTTGGTCGTCTGTCCCCTGTATCTTTAAAATTGCAAAACAAAATGCTCAAGTATTTTCAC
ACGAGCAGGCACACAGACGTCTGTCTCAGTCGTATATGGCACACAACCTGGCACACGAGCATATG
ACTTGACCATGTGGCCCCTACACCTAATTAAAGTAAATTAAAATATTCACACAACTTAGCACACG
AGCA
Found at i:3007423 original size:26 final size:26
Alignment explanation
Indices: 3007386--3007435 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
3007376 TGGATAATCA
3007386 TTAATCAGGAAGCTCACAAAGAGCAT
1 TTAATCAGGAAGCTCACAAAGAGCAT
*
3007412 TTAATC-GAGAAGCTCACTAAGAGC
1 TTAATCAG-GAAGCTCACAAAGAGC
3007436 CATATATCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (26 bp):
TTAATCAGGAAGCTCACAAAGAGCAT
Found at i:3007551 original size:25 final size:25
Alignment explanation
Indices: 3007520--3007577 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
3007510 GGAGAGCTAT
*
3007520 TAACGGGAAGCTCGCAAGAACCATA
1 TAACGGGAAGCTCGAAAGAACCATA
*
3007545 TAACGGGAAGCTCGAAAGAGCCATA
1 TAACGGGAAGCTCGAAAGAACCATA
*
3007570 TATCGGGA
1 TAACGGGA
3007578 TGTTTATGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.38, C:0.21, G:0.28, T:0.14
Consensus pattern (25 bp):
TAACGGGAAGCTCGAAAGAACCATA
Found at i:3007927 original size:10 final size:10
Alignment explanation
Indices: 3007902--3007968 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
3007892 TATACAAATG
*
3007902 AATTTAACATC
1 AATTTAATA-C
3007913 AATTTAATAC
1 AATTTAATAC
*
3007923 AATTTACATTC
1 AATTTA-ATAC
3007934 AATTTAATAC
1 AATTTAATAC
* *
3007944 AAGTTACATTC
1 AATTTA-ATAC
* *
3007955 AATTCAATCC
1 AATTTAATAC
3007965 AATT
1 AATT
3007969 CACATCTTAG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
10 22 0.48
11 24 0.52
ACGTcount: A:0.43, C:0.16, G:0.01, T:0.39
Consensus pattern (10 bp):
AATTTAATAC
Done.