Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold293
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: 1704560
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 11 of 12
Found at i:1540658 original size:17 final size:18
Alignment explanation
Indices: 1540627--1540669 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
1540617 TAACAGAGTG
*
1540627 TAAAGAAAATCTAAAAGA
1 TAAAAAAAATCTAAAAGA
1540645 TAAAAAAAAT-TAAAAGA
1 TAAAAAAAATCTAAAAGA
1540662 TAAAAAAA
1 TAAAAAAA
1540670 GTGGAAAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (18 bp):
TAAAAAAAATCTAAAAGA
Found at i:1540677 original size:17 final size:17
Alignment explanation
Indices: 1540639--1540685 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
1540629 AAGAAAATCT
*
1540639 AAAAGATAAAAAAAATT
1 AAAAGATAAAAAAAATG
*
1540656 AAAAGATAAAAAAAGTG
1 AAAAGATAAAAAAAATG
*
1540673 GAAAGATGAAAAA
1 AAAAGAT-AAAAA
1540686 CATAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (17 bp):
AAAAGATAAAAAAAATG
Found at i:1540835 original size:16 final size:16
Alignment explanation
Indices: 1540802--1540831 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1540792 AAAATAAAAA
1540802 TATATTATTTTATTAT
1 TATATTATTTTATTAT
1540818 TATATT-TTTTATTA
1 TATATTATTTTATTA
1540832 ATTAAGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATATTATTTTATTAT
Found at i:1546499 original size:2 final size:2
Alignment explanation
Indices: 1546492--1546552 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1546482 AGTTCTCCTG
1546492 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1546534 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1546553 CCGCCGCTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1547453 original size:15 final size:14
Alignment explanation
Indices: 1547409--1547455 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
1547399 ATTTATATTT
*
1547409 AAATATATATTAAA
1 AAATAAATATTAAA
*
1547423 CAA-AAATATT-AA
1 AAATAAATATTAAA
1547435 AAATAAATATCTAAA
1 AAATAAATAT-TAAA
1547450 AAATAA
1 AAATAA
1547456 CTAAGTGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 4 0.15
13 12 0.44
14 3 0.11
15 8 0.30
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAAATATTAAA
Found at i:1548041 original size:23 final size:23
Alignment explanation
Indices: 1548011--1548125 Score: 83
Period size: 23 Copynumber: 5.0 Consensus size: 23
1548001 CACACGAAAG
*
1548011 TAAAAAATAATATAAATATGATA
1 TAAAAAATAATATGAATATGATA
*
1548034 TAAAAAAT-ATCACGAATATGATA
1 TAAAAAATAAT-ATGAATATGATA
* * * ** *
1548057 CAAAAAAATAAAATGAACAAAACA
1 -TAAAAAATAATATGAATATGATA
* * *
1548081 TAAAAATTAATATGAATATAACA
1 TAAAAAATAATATGAATATGATA
1548104 TGAAAAAA-AATAT-AATATGATA
1 T-AAAAAATAATATGAATATGATA
1548126 AATGCATTCA
Statistics
Matches: 71, Mismatches: 17, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
22 9 0.13
23 42 0.59
24 19 0.27
25 1 0.01
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.24
Consensus pattern (23 bp):
TAAAAAATAATATGAATATGATA
Found at i:1548164 original size:11 final size:11
Alignment explanation
Indices: 1548138--1548222 Score: 63
Period size: 11 Copynumber: 7.9 Consensus size: 11
1548128 TGCATTCAAT
*
1548138 TTTTTATATCA
1 TTTTTATATTA
* *
1548149 TTTTTTGTGTTA
1 -TTTTTATATTA
1548161 TTTTTATATTA
1 TTTTTATATTA
1548172 TTTTTTGATATTA
1 -TTTTT-ATATTA
*
1548185 -TATTATA-T-
1 TTTTTATATTA
1548193 TTTTT-TATTA
1 TTTTTATATTA
*
1548203 TATTTATATTA
1 TTTTTATATTA
1548214 -TTTTATATT
1 TTTTTATATT
1548223 TATATTATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
8 2 0.03
9 5 0.09
10 15 0.26
11 17 0.29
12 13 0.22
13 6 0.10
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.71
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:1548175 original size:10 final size:10
Alignment explanation
Indices: 1548162--1548222 Score: 63
Period size: 10 Copynumber: 5.9 Consensus size: 10
1548152 TTTGTGTTAT
1548162 TTTTATATTA
1 TTTTATATTA
1548172 TTTTTTGATATTA
1 --TTTT-ATATTA
*
1548185 TATTATATT-
1 TTTTATATTA
1548194 TTTT-TATTA
1 TTTTATATTA
1548203 TATTTATATTA
1 T-TTTATATTA
1548214 TTTTATATT
1 TTTTATATT
1548223 TATATTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
8 4 0.09
9 4 0.09
10 16 0.37
11 9 0.21
12 4 0.09
13 6 0.14
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTTATATTA
Found at i:1548187 original size:5 final size:5
Alignment explanation
Indices: 1548179--1548230 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
1548169 TTATTTTTTG
* *
1548179 ATATT ATATT ATATT -T-TT TTATT ATATTT ATATT ATTTT ATATTT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATA-TT ATATT ATATT ATA-TT ATATT
1548229 AT
1 AT
1548231 TTTTATGTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 26 0.65
6 10 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
ATATT
Found at i:1548187 original size:18 final size:18
Alignment explanation
Indices: 1548164--1548234 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 18
1548154 TGTGTTATTT
1548164 TTATATTAT-TTTTTGATA
1 TTATATTATATTTTT-ATA
*
1548182 TTATATTATATTTTTTTA
1 TTATATTATATTTTTATA
1548200 TTATATTTATATTATTTTATA
1 TTATA-TTATA-T-TTTTATA
1548221 TTTATATTAT-TTTT
1 -TTATATTATATTTT
1548235 ATGTCTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 19 0.41
19 11 0.24
20 1 0.02
21 10 0.22
22 5 0.11
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.70
Consensus pattern (18 bp):
TTATATTATATTTTTATA
Found at i:1548190 original size:23 final size:23
Alignment explanation
Indices: 1548141--1548219 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
1548131 ATTCAATTTT
* * *
1548141 TTATATCATTTTTTG-TGTTATTT
1 TTATATTATTTTTTGATATTA-TA
1548164 TTATATTATTTTTTGATATTATA
1 TTATATTATTTTTTGATATTATA
*
1548187 TTATATT-TTTTTATTATATTTATA
1 TTATATTATTTTT-TGATA-TTATA
*
1548211 TTATTTTAT
1 TTATATTAT
1548220 ATTTATATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
22 5 0.11
23 26 0.55
24 15 0.32
25 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (23 bp):
TTATATTATTTTTTGATATTATA
Found at i:1548230 original size:21 final size:20
Alignment explanation
Indices: 1548164--1548230 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 20
1548154 TGTGTTATTT
1548164 TTATATTATTTTTTGATATTATA
1 TTATATTA-TTTTT-AT-TTATA
1548187 TTATATT-TTTTTA-TTATA
1 TTATATTATTTTTATTTATA
1548205 TTTATATTATTTTATATTTATA
1 -TTATATTATTTT-TATTTATA
1548227 TTAT
1 TTAT
1548231 TTTTATGTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
18 5 0.12
19 7 0.17
20 5 0.12
21 11 0.28
22 5 0.12
23 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (20 bp):
TTATATTATTTTTATTTATA
Found at i:1548651 original size:22 final size:25
Alignment explanation
Indices: 1548610--1548660 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
1548600 TAAAATTATT
*
1548610 AAAATAACTCGAACACTAT-AC-CA
1 AAAATAACACGAACACTATAACACA
1548633 AAAATAACACGAACA-TATAACACA
1 AAAATAACACGAACACTATAACACA
1548657 AAAA
1 AAAA
1548661 AATAACATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 3 0.12
23 16 0.64
24 6 0.24
ACGTcount: A:0.61, C:0.22, G:0.04, T:0.14
Consensus pattern (25 bp):
AAAATAACACGAACACTATAACACA
Found at i:1548705 original size:20 final size:22
Alignment explanation
Indices: 1548678--1548727 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
1548668 TGAACGTATT
1548678 ATAAAAAATT-ACGAATATGAC
1 ATAAAAAATTAACGAATATGAC
1548699 A-AAAAAATTAACACGAATATGAC
1 ATAAAAAATT-A-ACGAATATGAC
1548722 ATAAAA
1 ATAAAA
1548728 TATTTAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.32
21 1 0.04
23 12 0.48
24 4 0.16
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.20
Consensus pattern (22 bp):
ATAAAAAATTAACGAATATGAC
Found at i:1548985 original size:22 final size:22
Alignment explanation
Indices: 1548959--1549030 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
1548949 TTTCATGATG
*
1548959 AAAAATAACATGAACATAATAA
1 AAAAATAACACGAACATAATAA
* *
1548981 AAAAATAACACGAATATAATAT
1 AAAAATAACACGAACATAATAA
* * *
1549003 AAAAATAATACGAATACAATACA
1 AAAAATAACACGAACATAATA-A
1549026 AAAAA
1 AAAAA
1549031 ATGATATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 38 0.88
23 5 0.12
ACGTcount: A:0.68, C:0.10, G:0.04, T:0.18
Consensus pattern (22 bp):
AAAAATAACACGAACATAATAA
Found at i:1549221 original size:20 final size:20
Alignment explanation
Indices: 1549161--1549221 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 20
1549151 TTTTGTACGG
*
1549161 ATTCATGTT-TTTTCAT-AT
1 ATTCATGTTATTTTTATAAT
* *
1549179 GTTTATGTTATTTTTTATATAAT
1 ATTCATGTTA--TTTT-TATAAT
1549202 ATTCATGTTATTTTTATAAT
1 ATTCATGTTATTTTTATAAT
1549222 TAAATTTGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 7 0.21
20 6 0.18
21 8 0.24
22 2 0.06
23 10 0.30
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (20 bp):
ATTCATGTTATTTTTATAAT
Found at i:1549303 original size:19 final size:20
Alignment explanation
Indices: 1549279--1549317 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1549269 ATTGCTATAA
*
1549279 ACCAAA-AATTTTAATATTT
1 ACCAAATAATTTTAAGATTT
1549298 ACCAAATAATTTTAAGATTT
1 ACCAAATAATTTTAAGATTT
1549318 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (20 bp):
ACCAAATAATTTTAAGATTT
Found at i:1549799 original size:15 final size:14
Alignment explanation
Indices: 1549779--1549825 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
1549769 TGTCATTTAG
1549779 TTATTTTTTAAATAT
1 TTATTTTTT-AATAT
1549794 TTA-TTTTTAATAT
1 TTATTTTTTAATAT
*
1549807 TTA-TATTTAATAT
1 TTATTTTTTAATAT
*
1549820 ATATTT
1 TTATTT
1549826 AAATATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 19 0.68
14 6 0.21
15 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATTTTTTAATAT
Found at i:1549800 original size:13 final size:13
Alignment explanation
Indices: 1549784--1549831 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1549774 TTTAGTTATT
1549784 TTTTAAATATTTA
1 TTTTAAATATTTA
*
1549797 TTTTTAATATTTA
1 TTTTAAATATTTA
*
1549810 TATTT-AATATATA
1 T-TTTAAATATTTA
1549823 -TTTAAATAT
1 TTTTAAATAT
1549832 AAATATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 3 0.10
12 5 0.16
13 20 0.65
14 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:1549825 original size:17 final size:16
Alignment explanation
Indices: 1549803--1549872 Score: 51
Period size: 17 Copynumber: 4.6 Consensus size: 16
1549793 TTTATTTTTA
* *
1549803 ATATTTATATTTAATAT
1 ATATTTAAATATAA-AT
1549820 ATATTTAAATATAAAT
1 ATATTTAAATATAAAT
1549836 ATA--T-AATAT-AAT
1 ATATTTAAATATAAAT
* *
1549848 -TTTTTAAATATATAAA
1 ATATTTAAATATA-AAT
1549864 ATATTTAAA
1 ATATTTAAA
1549873 AAATTAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
11 1 0.02
12 3 0.07
13 6 0.14
14 6 0.14
16 7 0.17
17 19 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTTAAATATAAAT
Found at i:1549837 original size:25 final size:27
Alignment explanation
Indices: 1549809--1549859 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1549799 TTTAATATTT
*
1549809 ATATTTAATAT-A-TATTTAAATATAA
1 ATATATAATATAATTATTTAAATATAA
*
1549834 ATATATAATATAATTTTTTAAATATA
1 ATATATAATATAATTATTTAAATATA
1549860 TAAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 1 0.05
27 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATATATAATATAATTATTTAAATATAA
Found at i:1551044 original size:7 final size:7
Alignment explanation
Indices: 1551034--1551059 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1551024 ATAATTTATA
1551034 AATTTAG
1 AATTTAG
1551041 AATTTAG
1 AATTTAG
1551048 AATTTAG
1 AATTTAG
1551055 AATTT
1 AATTT
1551060 TTAATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (7 bp):
AATTTAG
Found at i:1554387 original size:2 final size:2
Alignment explanation
Indices: 1554382--1554413 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1554372 AAATAATCTC
*
1554382 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1554414 GTTTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1554744 original size:10 final size:10
Alignment explanation
Indices: 1554719--1554748 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
1554709 TGACCACACA
1554719 AATTTTTATT
1 AATTTTTATT
1554729 ATATTTTTATT
1 A-ATTTTTATT
1554740 AATTTTTAT
1 AATTTTTAT
1554749 ATTATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
AATTTTTATT
Found at i:1555879 original size:16 final size:17
Alignment explanation
Indices: 1555847--1555892 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1555837 TCTTTATATA
*
1555847 ATATAAAT-TACATAAT
1 ATATAAATATACAAAAT
1555863 ATATAAATATA-AAAAT
1 ATATAAATATACAAAAT
1555879 A-ATAAATA-ACAAAA
1 ATATAAATATACAAAA
1555893 AAAACATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 1 0.04
15 11 0.41
16 13 0.48
17 2 0.07
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (17 bp):
ATATAAATATACAAAAT
Found at i:1557158 original size:23 final size:23
Alignment explanation
Indices: 1557132--1557183 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1557122 ATAAGATACA
*
1557132 AAAAAATAAAATAAGTAAAACAT
1 AAAAAATAAAATAAATAAAACAT
* * *
1557155 AAAAAATAACATAAATATAATAT
1 AAAAAATAAAATAAATAAAACAT
1557178 AAAAAA
1 AAAAAA
1557184 GTGAATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (23 bp):
AAAAAATAAAATAAATAAAACAT
Found at i:1557267 original size:21 final size:21
Alignment explanation
Indices: 1557229--1557268 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1557219 TATTTAAATA
* * *
1557229 TAAATATATGATATAATTTTT
1 TAAATATATAAAAAAATTTTT
1557250 TAAATATATAAAAAAATTT
1 TAAATATATAAAAAAATTT
1557269 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TAAATATATAAAAAAATTTTT
Found at i:1557847 original size:16 final size:17
Alignment explanation
Indices: 1557821--1557860 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1557811 TTTTTTAAAT
*
1557821 TATTTAT-TATT-TTTA
1 TATTTATATATTATGTA
1557836 TATTTATATATTATGTA
1 TATTTATATATTATGTA
1557853 -ATTTATAT
1 TATTTATAT
1557861 TATATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 12 0.55
17 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TATTTATATATTATGTA
Found at i:1562730 original size:24 final size:23
Alignment explanation
Indices: 1562684--1562743 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
1562674 CCTAAATAGT
1562684 AATATTAAAA-TA--AATATTAA
1 AATATTAAAATTATTAATATTAA
*
1562704 AATATTAAAATTATTAATTATTCA
1 AATATTAAAATTATTAA-TATTAA
*
1562728 AATATTAATATT-TTAA
1 AATATTAAAATTATTAA
1562744 CATCAATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 10 0.29
21 2 0.06
23 6 0.18
24 16 0.47
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AATATTAAAATTATTAATATTAA
Found at i:1562797 original size:15 final size:15
Alignment explanation
Indices: 1562777--1562866 Score: 51
Period size: 15 Copynumber: 5.9 Consensus size: 15
1562767 TTTTAGTACT
1562777 AATATTTAATAATAA
1 AATATTTAATAATAA
*
1562792 AATATTATATTAATATTA
1 AATATT-TAATAATA--A
* **
1562810 AATACTTAA-AATGT
1 AATATTTAATAATAA
* * *
1562824 ACTATTTATTATTAA
1 AATATTTAATAATAA
*
1562839 AATA-TTAATTATAAA
1 AATATTTAATAAT-AA
1562854 AATATTTAA-AATA
1 AATATTTAATAATA
1562867 TTATAATAAT
Statistics
Matches: 53, Mismatches: 16, Indels: 13
0.65 0.20 0.16
Matches are distributed among these distances:
14 12 0.23
15 19 0.36
16 14 0.26
17 2 0.04
18 6 0.11
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (15 bp):
AATATTTAATAATAA
Found at i:1562907 original size:24 final size:23
Alignment explanation
Indices: 1562829--1562907 Score: 58
Period size: 24 Copynumber: 3.4 Consensus size: 23
1562819 AATGTACTAT
*
1562829 TTATTATTAAAATATTAATTATAAAA
1 TTATTA-TAAAATATT-ATT-TAATA
*
1562855 ATATT-TAAAATATTA--TAATAA
1 TTATTATAAAATATTATTTAAT-A
*
1562876 TTA-AATAAAATATTATTTTAATA
1 TTATTATAAAATATTA-TTTAATA
1562899 TTATTATAA
1 TTATTATAA
1562908 TATTAAAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
20 3 0.07
21 13 0.31
23 5 0.12
24 17 0.40
26 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATTATAAAATATTATTTAATA
Found at i:1562911 original size:8 final size:8
Alignment explanation
Indices: 1562900--1562943 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
1562890 ATTTTAATAT
1562900 TATTATAA
1 TATTATAA
*
1562908 TATTAAAA
1 TATTATAA
* *
1562916 CATT-TAT
1 TATTATAA
1562923 TATTATAA
1 TATTATAA
1562931 TATTATAA
1 TATTATAA
1562939 TATTA
1 TATTA
1562944 CTCCAAAGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (8 bp):
TATTATAA
Found at i:1562936 original size:11 final size:11
Alignment explanation
Indices: 1562830--1562943 Score: 67
Period size: 11 Copynumber: 10.5 Consensus size: 11
1562820 ATGTACTATT
*
1562830 TATTATTAAAA
1 TATTATTATAA
1562841 TATTAATTATAA
1 TATT-ATTATAA
* *
1562853 AAATATT-TAA
1 TATTATTATAA
*
1562863 -AATATTATAA
1 TATTATTATAA
* *
1562873 TAATTAAATAAAA
1 T-ATT-ATTATAA
*
1562886 TATTATTTTAA
1 TATTATTATAA
1562897 TATTATTATAA
1 TATTATTATAA
1562908 TATTA--A-AA
1 TATTATTATAA
* *
1562916 CATTTATTATTA
1 TA-TTATTATAA
*
1562928 TAATATTATAA
1 TATTATTATAA
1562939 TATTA
1 TATTA
1562944 CTCCAAAGAA
Statistics
Matches: 78, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
8 3 0.04
9 10 0.13
10 6 0.08
11 38 0.49
12 15 0.19
13 6 0.08
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTATTATAA
Found at i:1563732 original size:24 final size:25
Alignment explanation
Indices: 1563691--1563739 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1563681 AAACGTAAAA
1563691 GTACTGTACATGCTTTTTTTGAAAG
1 GTACTGTACATGCTTTTTTTGAAAG
1563716 GTACTGTACATGC-TTTTTTGAAAG
1 GTACTGTACATGCTTTTTTTGAAAG
1563740 AATTATGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (25 bp):
GTACTGTACATGCTTTTTTTGAAAG
Found at i:1564215 original size:21 final size:20
Alignment explanation
Indices: 1564191--1564252 Score: 52
Period size: 23 Copynumber: 2.8 Consensus size: 20
1564181 TGTTATAAAT
1564191 TTTAAAATGTTAATATATATG
1 TTTAAAAT-TTAATATATATG
*
1564212 TTTAATAATATTCAAAATATATG
1 TTTAA-AAT-TT-AATATATATG
1564235 TATTGAAAATTATAATAT
1 T-TT-AAAATT-TAATAT
1564253 TAAAATAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 5 0.15
22 5 0.15
23 15 0.45
24 6 0.18
25 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (20 bp):
TTTAAAATTTAATATATATG
Found at i:1564339 original size:42 final size:40
Alignment explanation
Indices: 1564293--1564393 Score: 120
Period size: 37 Copynumber: 2.5 Consensus size: 40
1564283 AAAAATAAAT
* *
1564293 ATTTTTTA-TTAATAATTATGATATTTAAATCAAATCAAATTA
1 ATTTTTAATTTAAAAATTATG-TATTT--ATCAAATCAAATTA
*
1564335 ATTTTTAATTTAAAAACTATG---TTATCAAATCAAATTA
1 ATTTTTAATTTAAAAATTATGTATTTATCAAATCAAATTA
1564372 ATTTTTAATTTAAAAATTATGT
1 ATTTTTAATTTAAAAATTATGT
1564394 TATTAATAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
37 34 0.64
39 2 0.04
42 7 0.13
43 10 0.19
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (40 bp):
ATTTTTAATTTAAAAATTATGTATTTATCAAATCAAATTA
Found at i:1564363 original size:37 final size:37
Alignment explanation
Indices: 1564321--1564396 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
1564311 TGATATTTAA
1564321 ATCAAATCAAATTAATTTTTAATTTAAAAACTATGTT
1 ATCAAATCAAATTAATTTTTAATTTAAAAACTATGTT
*
1564358 ATCAAATCAAATTAATTTTTAATTTAAAAATTATGTT
1 ATCAAATCAAATTAATTTTTAATTTAAAAACTATGTT
1564395 AT
1 AT
1564397 TAATAGGAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
ATCAAATCAAATTAATTTTTAATTTAAAAACTATGTT
Found at i:1564860 original size:19 final size:20
Alignment explanation
Indices: 1564823--1564862 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1564813 TTCGTTATCA
1564823 TTTTAATTTTATATAGATAT
1 TTTTAATTTTATATAGATAT
*
1564843 TTTTAATTTT-TATGGATAT
1 TTTTAATTTTATATAGATAT
1564862 T
1 T
1564863 AATTATATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (20 bp):
TTTTAATTTTATATAGATAT
Found at i:1574792 original size:15 final size:15
Alignment explanation
Indices: 1574774--1574817 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
1574764 TTTTTTGTTT
1574774 TTTTTTTCTTTTTCC
1 TTTTTTTCTTTTTCC
*
1574789 TTTTTTT-TGTTTT-G
1 TTTTTTTCT-TTTTCC
1574803 TTTTTTTCTTTTTCC
1 TTTTTTTCTTTTTCC
1574818 AATTGCCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (15 bp):
TTTTTTTCTTTTTCC
Found at i:1574799 original size:27 final size:29
Alignment explanation
Indices: 1574762--1574817 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1574752 AATCTTCACT
1574762 TTTTTTTTG-TTT-TTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1574789 TTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1574818 AATTGCCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 9 0.33
28 3 0.11
29 15 0.56
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (29 bp):
TTTTTTTTGTTTTGTTTTTTTCTTTTTCC
Found at i:1584544 original size:18 final size:18
Alignment explanation
Indices: 1584521--1584558 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1584511 TATCCTGCGA
1584521 GTTTGAGCGCCTTCGGGT
1 GTTTGAGCGCCTTCGGGT
1584539 GTTTGAGCGCCTTCGGGT
1 GTTTGAGCGCCTTCGGGT
1584557 GT
1 GT
1584559 GTGGCGCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.21, G:0.39, T:0.34
Consensus pattern (18 bp):
GTTTGAGCGCCTTCGGGT
Found at i:1586222 original size:10 final size:10
Alignment explanation
Indices: 1586207--1586240 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
1586197 TTTTTCAGCC
1586207 ATACTTGGAA
1 ATACTTGGAA
1586217 ATACTTGGAA
1 ATACTTGGAA
1586227 ATACTTGGAA
1 ATACTTGGAA
1586237 ATAC
1 ATAC
1586241 GTTGATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (10 bp):
ATACTTGGAA
Found at i:1587103 original size:2 final size:2
Alignment explanation
Indices: 1587096--1587121 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1587086 AAATTGCAAC
1587096 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
1587122 CGAGTATCAT
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:1587298 original size:22 final size:21
Alignment explanation
Indices: 1587273--1587323 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
1587263 GTTATACATA
* *
1587273 TTTTAAAAAATTACCCATCCTT
1 TTTTAAAAAACTACACA-CCTT
1587295 TTTTAAAAAACTACACACCTT
1 TTTTAAAAAACTACACACCTT
*
1587316 TTATAAAA
1 TTTTAAAA
1587324 TAAACTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTTAAAAAACTACACACCTT
Found at i:1590287 original size:20 final size:20
Alignment explanation
Indices: 1590260--1590307 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1590250 TAAAAAATAA
*
1590260 TAATTTTTTA-TCAATTTAAT
1 TAATTTTTTACT-AATTAAAT
*
1590280 TGATTTTTTACTAATTAAAT
1 TAATTTTTTACTAATTAAAT
1590300 TAATTTTT
1 TAATTTTT
1590308 GATTCTATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (20 bp):
TAATTTTTTACTAATTAAAT
Found at i:1593779 original size:22 final size:21
Alignment explanation
Indices: 1593754--1593810 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
1593744 TGTTTATATG
1593754 TTTAT-TTAGATATAAATTATT
1 TTTATATTA-ATATAAATTATT
* * *
1593775 ATTTATGTTATAAAAAAATTATT
1 -TTTATATTA-ATATAAATTATT
1593798 TTTATATTAATAT
1 TTTATATTAATAT
1593811 TTATATAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.07
22 13 0.46
23 13 0.46
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTATATTAATATAAATTATT
Found at i:1593862 original size:20 final size:19
Alignment explanation
Indices: 1593830--1593869 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1593820 TTATAAATAA
1593830 ATTTAAATAAAAATATATT
1 ATTTAAATAAAAATATATT
*
1593849 ATTTTAATATAAAATATATT
1 ATTTAAATA-AAAATATATT
1593869 A
1 A
1593870 AGTAATACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAATATATT
Found at i:1593875 original size:19 final size:19
Alignment explanation
Indices: 1593835--1593876 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1593825 AATAAATTTA
**
1593835 AATAAAAATATATTATTTT
1 AATAAAAATATATTATAGT
1593854 AATATAAAATATATTA-AGT
1 AATA-AAAATATATTATAGT
1593873 AATA
1 AATA
1593877 CTACATGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AATAAAAATATATTATAGT
Found at i:1594169 original size:17 final size:17
Alignment explanation
Indices: 1594144--1594187 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1594134 TTAATATTTA
1594144 TTATATTATTAAAATAT
1 TTATATTATTAAAATAT
* **
1594161 TTATTTTATTTTAATAT
1 TTATATTATTAAAATAT
1594178 TTATA-TATTA
1 TTATATTATTA
1594188 TTATTTAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTATTAAAATAT
Found at i:1596495 original size:76 final size:76
Alignment explanation
Indices: 1596404--1596560 Score: 296
Period size: 76 Copynumber: 2.1 Consensus size: 76
1596394 TACATTTCTT
*
1596404 AAGAAACTCAAGATCAAGAGTTAAAATATGTAATTAAAGTCATGCTGAATAAAATTCTCCAAGAA
1 AAGACACTCAAGATCAAGAGTTAAAATATGTAATTAAAGTCATGCTGAATAAAATTCTCCAAGAA
1596469 GTAGTACATCG
66 GTAGTACATCG
1596480 AAGACACTCAAGATCAAGAGTTAAAATATGTAATTAAAGTCATGCTGAATAAAATTCTCCAAGAA
1 AAGACACTCAAGATCAAGAGTTAAAATATGTAATTAAAGTCATGCTGAATAAAATTCTCCAAGAA
*
1596545 GTAGTACCTCG
66 GTAGTACATCG
1596556 AAGAC
1 AAGAC
1596561 GATAGGCCAA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (76 bp):
AAGACACTCAAGATCAAGAGTTAAAATATGTAATTAAAGTCATGCTGAATAAAATTCTCCAAGAA
GTAGTACATCG
Found at i:1599554 original size:33 final size:33
Alignment explanation
Indices: 1599512--1599577 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1599502 AAACAATAAG
1599512 GAGGTAAATCTCATTGAGGAAGAAGAAAAGCTT
1 GAGGTAAATCTCATTGAGGAAGAAGAAAAGCTT
1599545 GAGGTAAATCTCATTGAGGAAGAAGAAAAGCTT
1 GAGGTAAATCTCATTGAGGAAGAAGAAAAGCTT
1599578 AAAGCATCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.21
Consensus pattern (33 bp):
GAGGTAAATCTCATTGAGGAAGAAGAAAAGCTT
Found at i:1599874 original size:22 final size:22
Alignment explanation
Indices: 1599846--1599890 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1599836 GTTTAATGAA
1599846 AAAATGTCAAATAAGAATATCT
1 AAAATGTCAAATAAGAATATCT
1599868 AAAATGTCAAATAAGAATATCT
1 AAAATGTCAAATAAGAATATCT
1599890 A
1 A
1599891 TGTACCTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.27
Consensus pattern (22 bp):
AAAATGTCAAATAAGAATATCT
Found at i:1602931 original size:21 final size:21
Alignment explanation
Indices: 1602905--1602944 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1602895 ATTAAAAAAT
1602905 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
1602926 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
1602945 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:1602992 original size:23 final size:22
Alignment explanation
Indices: 1602936--1602994 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
1602926 TATTTTATAA
1602936 TTAAATTTAAATAAAAATAACTTT
1 TTAAATTTAAATAAAAATAA--TT
*
1602960 TTAAA-ATAAATAATAAATTAA-T
1 TTAAATTTAAATAA-AAA-TAATT
1602982 TTAAATTTAAATA
1 TTAAATTTAAATA
1602995 TATTTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 6 0.20
23 13 0.43
24 8 0.27
25 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAATTTAAATAAAAATAATT
Found at i:1603023 original size:40 final size:39
Alignment explanation
Indices: 1602931--1603036 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 39
1602921 TTATATATTT
**
1602931 TATAATTAAATTTAAATAAAAATA-ACTTTTTAAAATAAA
1 TATAATTAAATTTAAATTTAAATATA-TTTTTAAAATAAA
* **
1602970 TAATAAATT-AATTTAAATTTAAATATATTTATTTATTTAAA
1 T-AT-AATTAAATTTAAATTTAAATATATTT-TTAAAATAAA
*
1603011 TATAATTAAATTTAAA-TTAAAAATAT
1 TATAATTAAATTTAAATTTAAATATAT
1603037 CAAACAACCA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
39 14 0.25
40 29 0.52
41 13 0.23
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (39 bp):
TATAATTAAATTTAAATTTAAATATATTTTTAAAATAAA
Found at i:1604068 original size:18 final size:18
Alignment explanation
Indices: 1604031--1604097 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
1604021 TAAATATAAC
* * *
1604031 ATAAAAATAAAATATTTA
1 ATAAATATAAAAAATATA
1604049 ATAAATATAAAAAATATA
1 ATAAATATAAAAAATATA
*
1604067 ATTAATATATTATAAAATATA
1 A-TAA-ATA-TAAAAAATATA
*
1604088 ATTAATATAA
1 ATAAATATAA
1604098 TATATTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 18 0.45
19 6 0.15
20 5 0.12
21 11 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAATATAAAAAATATA
Found at i:1604102 original size:16 final size:16
Alignment explanation
Indices: 1604077--1604118 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1604067 ATTAATATAT
*
1604077 TATAAAATATAATTAA
1 TATAATATATAATTAA
1604093 TATAATATATTAATTAA
1 TATAATATA-TAATTAA
1604110 TAT-ATATAT
1 TATAATATAT
1604119 TATATGTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 13 0.54
17 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATAATATATAATTAA
Found at i:1604111 original size:26 final size:21
Alignment explanation
Indices: 1604037--1604122 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 21
1604027 TAACATAAAA
*
1604037 ATAAAATAT--TTAATAAATAT
1 ATAAAATATAATTAATATAT-T
*
1604057 AAAAAATATAATTAATATATT
1 ATAAAATATAATTAATATATT
*
1604078 ATAAAATATAATTAATATAAT
1 ATAAAATATAATTAATATATT
*
1604099 ATATTAAT-TAA-TATATATATT
1 ATA-AAATATAATTA-ATATATT
1604120 ATA
1 ATA
1604123 TGTGTATTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 10 0.18
21 35 0.62
22 11 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAATATAATTAATATATT
Found at i:1604117 original size:30 final size:31
Alignment explanation
Indices: 1604036--1604122 Score: 80
Period size: 26 Copynumber: 3.0 Consensus size: 31
1604026 ATAACATAAA
* * * *
1604036 AATAAAATAT-TTAATAAATATAAAAAATAT
1 AATATAATATATTAATTAATATATATAATAT
1604066 AAT-TAATATATT-A-TAA-A-ATATAAT-T
1 AATATAATATATTAATTAATATATATAATAT
*
1604091 AATATAATATATTAATTAATATATATATTAT
1 AATATAATATATTAATTAATATATATAATAT
1604122 A
1 A
1604123 TGTGTATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
25 4 0.09
26 14 0.31
27 2 0.04
28 5 0.11
29 7 0.16
30 11 0.24
31 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AATATAATATATTAATTAATATATATAATAT
Found at i:1604337 original size:4 final size:4
Alignment explanation
Indices: 1604328--1604352 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1604318 AAAACAAAGC
1604328 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1604353 TGTTGATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1604407 original size:2 final size:2
Alignment explanation
Indices: 1604400--1604433 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1604390 TACTTTTGTT
1604400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1604434 ATAAAAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1605679 original size:15 final size:17
Alignment explanation
Indices: 1605647--1605680 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1605637 TATTCATTTC
1605647 TTTTTAATATTTATAAA
1 TTTTTAATATTTATAAA
1605664 TTTTTAAT-TTTA-AAA
1 TTTTTAATATTTATAAA
1605679 TT
1 TT
1605681 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 4 0.24
17 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTAATATTTATAAA
Found at i:1605684 original size:22 final size:23
Alignment explanation
Indices: 1605648--1605690 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1605638 ATTCATTTCT
*
1605648 TTTTAATATTTATAAATTTTTAA
1 TTTTAATAATTATAAATTTTTAA
*
1605671 TTTTAA-AATTATAATTTTTT
1 TTTTAATAATTATAAATTTTT
1605691 TATTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTAATAATTATAAATTTTTAA
Found at i:1605700 original size:22 final size:22
Alignment explanation
Indices: 1605657--1605700 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1605647 TTTTTAATAT
**
1605657 TTATAAATTTTTAATTTTAAAA
1 TTATAAATTTTTAATTAAAAAA
* *
1605679 TTATAATTTTTTTATTAAAAAA
1 TTATAAATTTTTAATTAAAAAA
1605701 ATACATGATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATAAATTTTTAATTAAAAAA
Found at i:1606338 original size:22 final size:23
Alignment explanation
Indices: 1606294--1606339 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1606284 TTACTAATTT
**
1606294 TAAATTTATATAATATACGAATA
1 TAAATTTATATAATATAAAAATA
*
1606317 TAAA-TTATATATTATAAAAATA
1 TAAATTTATATAATATAAAAATA
1606339 T
1 T
1606340 TAATAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAATTTATATAATATAAAAATA
Found at i:1606511 original size:2 final size:2
Alignment explanation
Indices: 1606504--1606528 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1606494 GCAAATAAAG
1606504 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
1606529 CACATAATGA
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:1608186 original size:19 final size:20
Alignment explanation
Indices: 1608162--1608217 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1608152 TCATGTCGCA
*
1608162 TTTATATTATTTTTCA-TAT
1 TTTATATTATTTTTAATTAT
1608181 TTTATATTATCTTTTAATTAT
1 TTTATATTAT-TTTTAATTAT
*
1608202 TTTAATATCATTTTTA
1 TTT-ATATTATTTTTA
1608218 TCATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 10 0.31
20 5 0.16
21 11 0.34
22 6 0.19
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATATTATTTTTAATTAT
Found at i:1609565 original size:20 final size:21
Alignment explanation
Indices: 1609519--1609559 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1609509 AAAATTTTTC
*
1609519 ATTTTAAATAAAAATAAAAAT
1 ATTTAAAATAAAAATAAAAAT
*
1609540 ATTTAAAATTAAAA-AAAAAT
1 ATTTAAAATAAAAATAAAAAT
1609560 GATTAACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTTAAAATAAAAATAAAAAT
Found at i:1614396 original size:23 final size:23
Alignment explanation
Indices: 1614361--1614404 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1614351 TTTTTTATTT
1614361 TATAATATATTTATATTAATAGA
1 TATAATATATTTATATTAATAGA
* * *
1614384 TATATTATTTTTATCTTAATA
1 TATAATATATTTATATTAATA
1614405 TTGATACATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TATAATATATTTATATTAATAGA
Found at i:1615333 original size:29 final size:29
Alignment explanation
Indices: 1615299--1615366 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1615289 ATTTTTTAAT
*
1615299 TAAATTAAATTTGAA-TTTATTTAAATAA
1 TAAATTAAATTTGAATTTTAATTAAATAA
* *
1615327 TATAATT-AATTTTAATTTTAATTATATAA
1 TA-AATTAAATTTGAATTTTAATTAAATAA
1615356 TAAATTTAAAT
1 TAAA-TTAAAT
1615367 AAAAATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 11 0.33
29 19 0.58
30 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
TAAATTAAATTTGAATTTTAATTAAATAA
Found at i:1615344 original size:24 final size:24
Alignment explanation
Indices: 1615317--1615362 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1615307 ATTTGAATTT
*
1615317 ATTTAAATAATATAATTAATTTTA
1 ATTTAAATAATATAATAAATTTTA
* *
1615341 ATTTTAATTATATAATAAATTT
1 ATTTAAATAATATAATAAATTT
1615363 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTAAATAATATAATAAATTTTA
Found at i:1615824 original size:15 final size:15
Alignment explanation
Indices: 1615803--1615844 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1615793 TTTTAAATTA
1615803 AAATTAAATTTATCT
1 AAATTAAATTTATCT
* *
1615818 TAATT-AATTTATGT
1 AAATTAAATTTATCT
*
1615832 AAATTAAAATTAT
1 AAATTAAATTTAT
1615845 ATTCAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
AAATTAAATTTATCT
Found at i:1618298 original size:4 final size:4
Alignment explanation
Indices: 1618289--1618315 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1618279 AGCAAGCGGC
1618289 CTGG CTGG CTGG CTGG CTGG CTGG CTG
1 CTGG CTGG CTGG CTGG CTGG CTGG CTG
1618316 AGTTTCCAAG
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:0.00, C:0.26, G:0.48, T:0.26
Consensus pattern (4 bp):
CTGG
Found at i:1619090 original size:22 final size:23
Alignment explanation
Indices: 1619056--1619100 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1619046 TTTAAAATGC
*
1619056 AAAATAAATAAATATTTA-AATA
1 AAAATAAATAAATAGTTATAATA
1619078 AAAATTAAA-AAATAGTTATAATA
1 AAAA-TAAATAAATAGTTATAATA
1619101 TAAGAACGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATAAATAAATAGTTATAATA
Found at i:1619647 original size:21 final size:22
Alignment explanation
Indices: 1619614--1619657 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1619604 TATCATACTT
1619614 TTTATTAATTTATAAAATATTA
1 TTTATTAATTTATAAAATATTA
*
1619636 TTTATT-ATTTATAAAATTTTA
1 TTTATTAATTTATAAAATATTA
1619657 T
1 T
1619658 GATTCTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATTAATTTATAAAATATTA
Found at i:1621411 original size:2 final size:2
Alignment explanation
Indices: 1621404--1621438 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1621394 GGTCAATGGT
*
1621404 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1621439 TCTTTTAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1624259 original size:27 final size:30
Alignment explanation
Indices: 1624229--1624291 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 30
1624219 ATTTTAATAA
1624229 TTTATATAATCATA-TTATTTT-ATTA-TT
1 TTTATATAATCATACTTATTTTAATTATTT
*
1624256 TTTA-A-AATTATATCTTATTTTAATTATTT
1 TTTATATAATCATA-CTTATTTTAATTATTT
1624285 TTTATAT
1 TTTATAT
1624292 GTTATGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
25 6 0.21
26 1 0.03
27 11 0.38
28 4 0.14
29 6 0.21
30 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTATATAATCATACTTATTTTAATTATTT
Found at i:1625230 original size:18 final size:18
Alignment explanation
Indices: 1625188--1625236 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1625178 ATATATAATT
*
1625188 ATTAAAAATATTTTAAAT
1 ATTAAAAATATTTTAAAA
1625206 ATATAAAAA-ATTTTAAAAA
1 AT-TAAAAATATTTT-AAAA
*
1625225 ATTAAATATATT
1 ATTAAAAATATT
1625237 CATATCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAAAAATATTTTAAAA
Found at i:1627553 original size:24 final size:23
Alignment explanation
Indices: 1627526--1627575 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
1627516 AATAATGAAA
*
1627526 TTTTCCCTCATATGGATTTTTCTC
1 TTTTCCCTCATATAGATTTTT-TC
* * *
1627550 TTTTTCGTCATATATATTTTTTC
1 TTTTCCCTCATATAGATTTTTTC
1627573 TTT
1 TTT
1627576 GAAAACTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.14, C:0.18, G:0.06, T:0.62
Consensus pattern (23 bp):
TTTTCCCTCATATAGATTTTTTC
Found at i:1629839 original size:2 final size:2
Alignment explanation
Indices: 1629832--1629878 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1629822 TACTTTATTT
*
1629832 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1629874 TC TC T
1 TC TC T
1629879 GTTCGTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1631701 original size:24 final size:24
Alignment explanation
Indices: 1631666--1631711 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1631656 GGGGAAAGTC
* *
1631666 AATCCTTCAAATTCGTTCTTGTAG
1 AATCCTTCAAATGCGTACTTGTAG
*
1631690 AATCCTTGAAATGCGTACTTGT
1 AATCCTTCAAATGCGTACTTGT
1631712 GAAATGCGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (24 bp):
AATCCTTCAAATGCGTACTTGTAG
Found at i:1633678 original size:17 final size:17
Alignment explanation
Indices: 1633652--1633692 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1633642 ATGACAAATT
* * *
1633652 TAAAATAAATCAAAGAA
1 TAAAAAAAATAAAAAAA
1633669 TAAAAAAAATAAAAAAA
1 TAAAAAAAATAAAAAAA
1633686 TAAAAAA
1 TAAAAAA
1633693 TATAGATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (17 bp):
TAAAAAAAATAAAAAAA
Found at i:1636186 original size:2 final size:2
Alignment explanation
Indices: 1636179--1636210 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1636169 TTTTTATTAC
1636179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1636211 CATTGTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1638153 original size:21 final size:21
Alignment explanation
Indices: 1638109--1638150 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1638099 TAGTTAACCC
**
1638109 TAAATTTATATCATTATTAAT
1 TAAATTTATATCACGATTAAT
1638130 TAAATTTATATC-CGATTAAT
1 TAAATTTATATCACGATTAAT
1638150 T
1 T
1638151 TAATATACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (21 bp):
TAAATTTATATCACGATTAAT
Found at i:1638772 original size:20 final size:21
Alignment explanation
Indices: 1638747--1638799 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1638737 TAATATTTAA
*
1638747 TAATTAAAAATAT-TAAATTT
1 TAATTAAAAATATATAAATAT
*
1638767 TAATT-AATATATATAAATAT
1 TAATTAAAAATATATAAATAT
1638787 TAATATAAAAATA
1 TAAT-TAAAAATA
1638800 ATTTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 6 0.22
20 15 0.56
21 1 0.04
22 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATTAAAAATATATAAATAT
Found at i:1639270 original size:29 final size:29
Alignment explanation
Indices: 1639228--1639284 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1639218 TAATATGAAC
*
1639228 ATTTCTTCCATGTATCACATTATTAGATA
1 ATTTCTTCCATGTATCACAATATTAGATA
1639257 ATTTCTTCCATGTATCACAATATTAGAT
1 ATTTCTTCCATGTATCACAATATTAGAT
1639285 GATATGATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.44
Consensus pattern (29 bp):
ATTTCTTCCATGTATCACAATATTAGATA
Found at i:1639876 original size:15 final size:14
Alignment explanation
Indices: 1639849--1639879 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
1639839 ATTATAGAAT
1639849 ATAAAAATAAAATA
1 ATAAAAATAAAATA
1639863 ATAAAAATATAAATA
1 ATAAAAATA-AAATA
1639878 AT
1 AT
1639880 TAATATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAAATAAAATA
Found at i:1639884 original size:22 final size:22
Alignment explanation
Indices: 1639846--1639898 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
1639836 ATTATTATAG
1639846 AATATAAAAATAAAATAATAA-A
1 AATATAAAAATAAAAT-ATAAGA
* *
1639868 AATATAAATAAT-TAATATAAGT
1 AATATAAA-AATAAAATATAAGA
1639890 AATATAAAA
1 AATATAAAA
1639899 GTTCATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 19 0.70
23 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AATATAAAAATAAAATATAAGA
Found at i:1641685 original size:13 final size:14
Alignment explanation
Indices: 1641669--1641706 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1641659 TTTATTATCA
1641669 AATAAATTTA-TTT
1 AATAAATTTATTTT
*
1641682 AATAAATATATTTT
1 AATAAATTTATTTT
1641696 AATAAAATTTA
1 AAT-AAATTTA
1641707 AATTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.43
14 6 0.29
15 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAAATTTATTTT
Found at i:1641902 original size:21 final size:21
Alignment explanation
Indices: 1641876--1641920 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1641866 TAAACATTAT
*
1641876 TTTTATCTATTATTTTTAAAA
1 TTTTATCTATTATTTATAAAA
* *
1641897 TTTTATTTATTATTTATAATA
1 TTTTATCTATTATTTATAAAA
1641918 TTT
1 TTT
1641921 ATTAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTATTATTTATAAAA
Found at i:1641926 original size:31 final size:30
Alignment explanation
Indices: 1641886--1641943 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
1641876 TTTTATCTAT
*
1641886 TATTTTTAAAATTTTATTTATTATTTATAA
1 TATTTTTAAAATTTTATCTATTATTTATAA
1641916 TATTTATTAAAATTTTATCTATTATTTA
1 TATTT-TTAAAATTTTATCTATTATTTA
1641944 AAAAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TATTTTTAAAATTTTATCTATTATTTATAA
Found at i:1643648 original size:50 final size:50
Alignment explanation
Indices: 1643556--1643652 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
1643546 CAAAGCATCA
** *
1643556 TATTCTAGTAGATTCTTGATCCCATCACATTAGTGACGAATCTTGGCATG
1 TATTCTAGTAGATTCTTGATCCCATCACATTAGCAACAAATCTTGGCATG
* *
1643606 TATTCTAGTAGATTCTTGATCTCATCACATTTGCAACAAATCTTGGC
1 TATTCTAGTAGATTCTTGATCCCATCACATTAGCAACAAATCTTGGC
1643653 CTAGGCGTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (50 bp):
TATTCTAGTAGATTCTTGATCCCATCACATTAGCAACAAATCTTGGCATG
Found at i:1645449 original size:71 final size:70
Alignment explanation
Indices: 1645369--1645511 Score: 189
Period size: 71 Copynumber: 2.0 Consensus size: 70
1645359 TAAATTTTGA
* * * * * *
1645369 TACGTTAAAATATTTATTTTATAGA-TTGACATGTTATTTATTGGTGTTGAATTTTTATTATTTT
1 TACGTT-AAA-ATGTATTTTATAGATTTGACAAGTCACTTATTGGTGTCGAATTTTTATTAATTT
1645433 TTCATTT
64 TTCATTT
*
1645440 TACGTTAAAATGTGTTTTATAGATTTTGACAAGTCACTTATTGGTGTCGAATTTTTATTAATTTT
1 TACGTTAAAATGTATTTTATAGA-TTTGACAAGTCACTTATTGGTGTCGAATTTTTATTAATTTT
1645505 TCATTT
65 TCATTT
1645511 T
1 T
1645512 CTGTCACATT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
69 12 0.19
70 3 0.05
71 48 0.76
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.55
Consensus pattern (70 bp):
TACGTTAAAATGTATTTTATAGATTTGACAAGTCACTTATTGGTGTCGAATTTTTATTAATTTTT
CATTT
Found at i:1649805 original size:23 final size:22
Alignment explanation
Indices: 1649745--1649806 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
1649735 CAAACTATAC
*
1649745 TATTAAATTAAATTATAAATTTT
1 TATTAAATT-AATTAAAAATTTT
*
1649768 TATTAATATTTATTAAAAATTTT
1 TATTAA-ATTAATTAAAAATTTT
*
1649791 ATTTTAAATTAATTAA
1 -TATTAAATTAATTAA
1649807 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 25 0.76
24 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTAAATTAATTAAAAATTTT
Found at i:1652981 original size:19 final size:19
Alignment explanation
Indices: 1652949--1652998 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
1652939 TAATTAATTT
* *
1652949 ATATTATATTTATTATTTAAA
1 ATATTATATAT-TTATAT-AA
1652970 ATATTATATATTTATATAA
1 ATATTATATATTTATATAA
1652989 ATATTA-ATAT
1 ATATTATATAT
1652999 AATAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 4 0.15
19 8 0.30
20 5 0.19
21 10 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTATATATTTATATAA
Found at i:1653235 original size:2 final size:2
Alignment explanation
Indices: 1653223--1653259 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1653213 AGAATTGGGT
*
1653223 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1653260 TCGCAGGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1662012 original size:3 final size:3
Alignment explanation
Indices: 1662004--1662030 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1661994 ATAATTAAAA
1662004 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1662031 GTGACTCTTA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1662248 original size:27 final size:28
Alignment explanation
Indices: 1662212--1662290 Score: 92
Period size: 27 Copynumber: 2.9 Consensus size: 28
1662202 TATTTATCAA
*
1662212 TTAAATTATTT-ATTTAATTTAAAAATT
1 TTAATTTATTTAATTTAATTTAAAAATT
*
1662239 TTAATTTATTTAAATTTAAATTTAAATATT
1 TTAATTTATTT-AATTT-AATTTAAAAATT
*
1662269 TT--TTAATTTAATTTAATTTAAA
1 TTAATTTATTTAATTTAATTTAAA
1662291 TTAATATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
26 8 0.17
27 15 0.33
28 6 0.13
29 4 0.09
30 13 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTAATTTATTTAATTTAATTTAAAAATT
Found at i:1662249 original size:23 final size:23
Alignment explanation
Indices: 1662219--1662311 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 23
1662209 CAATTAAATT
*
1662219 ATTTATTTAATTTAAAAATTTTA
1 ATTTATTTAATTTAAAAATTTAA
1662242 ATTTATTTAAATTT--AAATTTAA
1 ATTTATTT-AATTTAAAAATTTAA
* *
1662264 ATATTTTTTAATTTAATTTAATTTAA
1 AT-TTATTTAATTTAA--AAATTTAA
1662290 ATTAATATTTAATAATTAAAAA
1 ATT--TATTTAAT--TTAAAAA
1662312 ATATTTTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
22 14 0.25
23 13 0.24
24 5 0.09
25 1 0.02
26 9 0.16
27 9 0.16
29 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTATTTAATTTAAAAATTTAA
Found at i:1662276 original size:16 final size:16
Alignment explanation
Indices: 1662224--1662327 Score: 56
Period size: 16 Copynumber: 6.8 Consensus size: 16
1662214 AAATTATTTA
1662224 TTTAATTTAAA-A-AT
1 TTTAATTTAAATATAT
** *
1662238 TTTAATTTATTTAAAT
1 TTTAATTTAAATATAT
* *
1662254 TTAAATTTAAATATTT
1 TTTAATTTAAATATAT
* *
1662270 TTTAATTT-AATTTAA
1 TTTAATTTAAATATAT
*
1662285 TTTAAATT-AATAT-T
1 TTTAATTTAAATATAT
* * *
1662299 TAATAATTAAAAAATAT
1 T-TTAATTTAAATATAT
*
1662316 TTTTATTTAAAT
1 TTTAATTTAAAT
1662328 TTAATTATAA
Statistics
Matches: 63, Mismatches: 22, Indels: 8
0.68 0.24 0.09
Matches are distributed among these distances:
14 10 0.16
15 20 0.32
16 31 0.49
17 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAATTTAAATATAT
Found at i:1662278 original size:32 final size:30
Alignment explanation
Indices: 1662237--1662299 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 30
1662227 AATTTAAAAA
1662237 TTTTAATTT-ATTTAAATTTAAATTTAAATATT
1 TTTTAATTTAATTT-AATTTAAA-TT-AATATT
1662269 TTTTAATTTAATTTAATTTAAATTAATATT
1 TTTTAATTTAATTTAATTTAAATTAATATT
1662299 T
1 T
1662300 AATAATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 7 0.23
31 2 0.07
32 17 0.57
33 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTAATTTAATTTAATTTAAATTAATATT
Found at i:1662366 original size:48 final size:48
Alignment explanation
Indices: 1662261--1662371 Score: 124
Period size: 47 Copynumber: 2.3 Consensus size: 48
1662251 AATTTAAATT
* * *
1662261 TAAATATTTTTTAATTTAATTTAATTTAAATTAATATTTAATAATTAAA
1 TAAATAATTTTT-ATTTAATTTAATTTAAAATAATATTAAATAATTAAA
1662310 -AAAT-ATTTTTATTTAAATTTAATTATAAAAT-ATA-TAAAT-ATTAATA
1 TAAATAATTTTTATTT-AATTTAATT-TAAAATAATATTAAATAATTAA-A
1662356 TAAATAATTTTTATTT
1 TAAATAATTTTTATTT
1662372 TTAGTAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
45 5 0.09
46 9 0.17
47 21 0.39
48 19 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (48 bp):
TAAATAATTTTTATTTAATTTAATTTAAAATAATATTAAATAATTAAA
Found at i:1663312 original size:2 final size:2
Alignment explanation
Indices: 1663305--1663332 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1663295 TCCACAAAGG
1663305 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
1663333 TTAAATGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1664155 original size:14 final size:13
Alignment explanation
Indices: 1664130--1664164 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 13
1664120 AATATTAAAC
1664130 AAATTATAAATATTT
1 AAATT-TAAATA-TT
1664145 AAATTTAAATATT
1 AAATTTAAATATT
1664158 AAATTTA
1 AAATTTA
1664165 TTGGAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 6 0.30
15 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTTAAATATT
Found at i:1668474 original size:13 final size:11
Alignment explanation
Indices: 1668442--1668559 Score: 61
Period size: 11 Copynumber: 10.9 Consensus size: 11
1668432 TAAAATTAAA
*
1668442 TAAAAATAATT
1 TAAATATAATT
1668453 TAAATATAATT
1 TAAATATAATT
*
1668464 TAAATATATAAT
1 TAAATATA-ATT
* *
1668476 TATATTAAAATT
1 TA-AATATAATT
*
1668488 T--ATATAATA
1 TAAATATAATT
1668497 TAAATTATTAATT
1 TAAA-TA-TAATT
*
1668510 T-ATTA-AATT
1 TAAATATAATT
* *
1668519 TATATA-AATA
1 TAAATATAATT
*
1668529 TAAA-ATATTT
1 TAAATATAATT
1668539 TAAATATAA-T
1 TAAATATAATT
1668549 TATAATATAAT
1 TA-AATATAAT
1668560 AAATTATATA
Statistics
Matches: 79, Mismatches: 17, Indels: 21
0.68 0.15 0.18
Matches are distributed among these distances:
9 12 0.15
10 17 0.22
11 31 0.39
12 10 0.13
13 9 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAATATAATT
Found at i:1668501 original size:33 final size:31
Alignment explanation
Indices: 1668456--1668536 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 31
1668446 AATAATTTAA
*
1668456 ATATAATTTAAATATATAATTATATTAAAATTT
1 ATATAATATAAATATATAATT-TATT-AAATTT
1668489 ATATAATATAAAT-TATTAATTTATTAAATTT
1 ATATAATATAAATATA-TAATTTATTAAATTT
1668520 ATATAAATATAAA-ATAT
1 ATAT-AATATAAATATAT
1668537 TTTAAATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
31 11 0.25
32 16 0.36
33 17 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
ATATAATATAAATATATAATTTATTAAATTT
Found at i:1668505 original size:24 final size:24
Alignment explanation
Indices: 1668460--1668546 Score: 63
Period size: 24 Copynumber: 3.5 Consensus size: 24
1668450 ATTTAAATAT
*
1668460 AATTTAAATATATAATTATATTAA
1 AATTTAAATATATAAATATATTAA
*
1668484 AATTTATATAATATAAAT-TATTAA
1 AATTTAAAT-ATATAAATATATTAA
**
1668508 TTTATTAAATTTATATAAATATA--AA
1 AAT-TTAAA--TATATAAATATATTAA
1668533 ATATTTTAAATATA
1 A-A-TTTAAATATA
1668547 ATTATAATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
24 19 0.39
25 13 0.27
26 13 0.27
27 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTTAAATATATAAATATATTAA
Found at i:1668512 original size:22 final size:20
Alignment explanation
Indices: 1668418--1668503 Score: 61
Period size: 19 Copynumber: 4.3 Consensus size: 20
1668408 ATAAAAAAAA
* *
1668418 TAAATTAAATTTTATAAAAT
1 TAAATTAAAATTTATATAAT
* * * *
1668438 TAAA-TAAAAATAATTTAAA
1 TAAATTAAAATTTATATAAT
*
1668457 TATAATTTAAA--TATATAAT
1 TA-AATTAAAATTTATATAAT
*
1668476 TATATTAAAATTTATATAAT
1 TAAATTAAAATTTATATAAT
1668496 ATAAATTA
1 -TAAATTA
1668504 TTAATTTATT
Statistics
Matches: 48, Mismatches: 13, Indels: 9
0.69 0.19 0.13
Matches are distributed among these distances:
18 6 0.12
19 18 0.38
20 14 0.29
21 10 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATTAAAATTTATATAAT
Found at i:1669295 original size:20 final size:19
Alignment explanation
Indices: 1669258--1669299 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1669248 AAAATTATTT
* *
1669258 TTTTATTTTTTAATCTTTC
1 TTTTATTTTTCAAGCTTTC
1669277 TTTTATTTTTCAAGGCTTTC
1 TTTTATTTTTCAA-GCTTTC
1669297 TTT
1 TTT
1669300 CCATAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTATTTTTCAAGCTTTC
Found at i:1669326 original size:12 final size:12
Alignment explanation
Indices: 1669309--1669345 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1669299 TCCATAAAAT
1669309 ATTTTTTTTTAA
1 ATTTTTTTTTAA
1669321 A--TTTTTTTAA
1 ATTTTTTTTTAA
*
1669331 ATTTTTTTATAA
1 ATTTTTTTTTAA
1669343 ATT
1 ATT
1669346 AATTGCTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTTTTTTAA
Found at i:1669327 original size:10 final size:10
Alignment explanation
Indices: 1669312--1669339 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1669302 ATAAAATATT
1669312 TTTTTTTAAA
1 TTTTTTTAAA
1669322 TTTTTTTAAA
1 TTTTTTTAAA
1669332 TTTTTTTA
1 TTTTTTTA
1669340 TAAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:1670252 original size:23 final size:22
Alignment explanation
Indices: 1670206--1670252 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1670196 ATATCAACAG
*
1670206 TAAATTATTTAATATTTTAAAT
1 TAAATTATTTAAGATTTTAAAT
1670228 TAAATT-TTTAAGATTTATTAAAT
1 TAAATTATTTAAGA-TT-TTAAAT
1670251 TA
1 TA
1670253 GATCAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 8 0.36
23 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAATTATTTAAGATTTTAAAT
Found at i:1672071 original size:29 final size:29
Alignment explanation
Indices: 1672038--1672137 Score: 75
Period size: 30 Copynumber: 3.5 Consensus size: 29
1672028 TAAAAGACCT
*
1672038 TAAAATACATGAAAATATTAAAATAGTGC
1 TAAAATACATGAAAATATTAAAATAGTCC
**
1672067 TAAAAT--AT-AAAA-ATTACATAATAGTTT
1 TAAAATACATGAAAATATTA-A-AATAGTCC
* *
1672094 TTAAA-ACATCGAAAATGATTAAAATAATCC
1 TAAAATACAT-GAAAAT-ATTAAAATAGTCC
*
1672124 TAAAATATATGAAA
1 TAAAATACATGAAA
1672138 TTGCATAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
25 4 0.07
26 5 0.09
27 12 0.22
28 2 0.04
29 6 0.11
30 17 0.31
31 4 0.07
32 4 0.07
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (29 bp):
TAAAATACATGAAAATATTAAAATAGTCC
Found at i:1672441 original size:58 final size:57
Alignment explanation
Indices: 1672394--1672507 Score: 135
Period size: 58 Copynumber: 2.0 Consensus size: 57
1672384 TAAAATTTAT
* *
1672394 TAAAATGACATTAAAGTGCATAAAATGACATAAAAG-TTCTTAGATCA-TAGCAAATGAC
1 TAAAATGACATTAAAATGCATAAAATAACA-AAAAGTTTC-TAGATCATTA-CAAATGAC
* *
1672452 TAAAATGCCATTAAAATGCATAAGATAACAAAAAGTTTCTAGATCA-TAGCAAATGA
1 TAAAATGACATTAAAATGCATAAAATAACAAAAAGTTTCTAGATCATTA-CAAATGA
1672508 TTTTAATATC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 22 0.43
58 29 0.57
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.25
Consensus pattern (57 bp):
TAAAATGACATTAAAATGCATAAAATAACAAAAAGTTTCTAGATCATTACAAATGAC
Found at i:1672504 original size:57 final size:58
Alignment explanation
Indices: 1672394--1672589 Score: 172
Period size: 57 Copynumber: 3.4 Consensus size: 58
1672384 TAAAATTTAT
* *
1672394 TAAAATGACATTAAAGTGCATAAAATGACATAAAAGTTCTTAGATCATAGCAAATGAC
1 TAAAATGACATTAAAATGCATAAAATAACATAAAAGTTCTTAGATCATAGCAAATGAC
* * *
1672452 TAAAATGCCATTAAAATGCATAAGATAACA-AAAAGTT-TCTAGATCATAGCAAATGAT
1 TAAAATGACATTAAAATGCATAAAATAACATAAAAGTTCT-TAGATCATAGCAAATGAC
** * * * * *
1672509 TTTAAT-ATC-TCTAAAATACATAAAATAACATAATAA-TTCCTAAATTATAGAAAATGAC
1 TAAAATGA-CAT-TAAAATGCATAAAATAACATAA-AAGTTCTTAGATCATAGCAAATGAC
* *
1672567 TTAAATGTAC-TT-AAATACATAAA
1 TAAAATG-ACATTAAAATGCATAAA
1672590 TAGTAATCTT
Statistics
Matches: 114, Mismatches: 16, Indels: 17
0.78 0.11 0.12
Matches are distributed among these distances:
56 2 0.02
57 57 0.50
58 50 0.44
59 4 0.04
60 1 0.01
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (58 bp):
TAAAATGACATTAAAATGCATAAAATAACATAAAAGTTCTTAGATCATAGCAAATGAC
Found at i:1678993 original size:30 final size:30
Alignment explanation
Indices: 1678957--1679017 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
1678947 TAAAATATAT
*
1678957 TTTAAAATAATTTAAAT-TTTAAATTTAAAA
1 TTTAAAATAATTTAAATAATT-AATTTAAAA
*
1678987 TTTAAAATAATTTAGATAATTAATTTAAAA
1 TTTAAAATAATTTAAATAATTAATTTAAAA
1679017 T
1 T
1679018 GATTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (30 bp):
TTTAAAATAATTTAAATAATTAATTTAAAA
Found at i:1679438 original size:3 final size:3
Alignment explanation
Indices: 1679432--1679476 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1679422 AATTGATTCG
1679432 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1679477 AAGTTGATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1679543 original size:20 final size:20
Alignment explanation
Indices: 1679520--1679600 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
1679510 TTATTAAAAA
1679520 AAATTTAAAATTTTTATATT
1 AAATTTAAAATTTTTATATT
** **
1679540 AAATTTATTATTTTTATAAA
1 AAATTTAAAATTTTTATATT
* *
1679560 AAATATAATAATTATTTTATTTT
1 AAATTTAA-AA-T-TTTTATATT
*
1679583 AATTTTAAAATTTTTATA
1 AAATTTAAAATTTTTATA
1679601 AGTAGCTTAT
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
20 28 0.62
21 2 0.04
22 3 0.07
23 12 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATTTAAAATTTTTATATT
Found at i:1679700 original size:20 final size:20
Alignment explanation
Indices: 1679659--1679710 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1679649 GTGATGCTTA
*
1679659 TAAATATTTTT-TTATTTTT
1 TAAATATTTTTATTATTTAT
1679678 TAAATATTTTTATT-TTTAAT
1 TAAATATTTTTATTATTT-AT
*
1679698 TAATTATTTTTAT
1 TAAATATTTTTAT
1679711 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TAAATATTTTTATTATTTAT
Found at i:1680040 original size:17 final size:16
Alignment explanation
Indices: 1680008--1680040 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1679998 TAAAAATTTA
1680008 ATTATAAATATATATT
1 ATTATAAATATATATT
1680024 ATTATAAA-ATA-ATT
1 ATTATAAATATATATT
1680038 ATT
1 ATT
1680041 TTATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 3 0.18
16 8 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATAAATATATATT
Done.