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 9 of 12
Found at i:1239193 original size:2 final size:2
Alignment explanation
Indices: 1239188--1239219 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1239178 AAGTCACAAA
*
1239188 AT AT AT AT AC 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
1239220 TATCTTTCTG
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:1239621 original size:14 final size:16
Alignment explanation
Indices: 1239591--1239622 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1239581 GGATAAAAGT
1239591 AAATTTATAAATGTTA
1 AAATTTATAAATGTTA
1239607 AAATTTA-AAAT-TTA
1 AAATTTATAAATGTTA
1239621 AA
1 AA
1239623 CTTATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 4 0.25
16 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AAATTTATAAATGTTA
Found at i:1244663 original size:22 final size:21
Alignment explanation
Indices: 1244637--1244687 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
1244627 TATTTATAAA
1244637 ATATAAAATCAAATTCACATAT
1 ATATAAAATCAAATT-ACATAT
* *
1244659 ATATAATATCAAATTATATAT
1 ATATAAAATCAAATTACATAT
1244680 AT-TAAAAT
1 ATATAAAAT
1244688 TATGTTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 5 0.19
21 7 0.27
22 14 0.54
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATAAAATCAAATTACATAT
Found at i:1244749 original size:3 final size:3
Alignment explanation
Indices: 1244741--1244781 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1244731 TAATTTAGAG
1244741 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1244782 ATTCTGTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1246240 original size:2 final size:2
Alignment explanation
Indices: 1246181--1246222 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1246171 GGATATTCAG
*
1246181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1246223 AAGAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1246811 original size:2 final size:2
Alignment explanation
Indices: 1246806--1246853 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1246796 TGATTTTTTG
1246806 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1246848 CT CT CT
1 CT CT CT
1246854 TTATTTTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1249667 original size:22 final size:19
Alignment explanation
Indices: 1249589--1249659 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 19
1249579 ATATATTTTA
*
1249589 ATATATTAATAATATAT-T
1 ATATATTAATATTATATAT
* * * *
1249607 TTATATAAATTTTA-AAAT
1 ATATATTAATATTATATAT
*
1249625 ATATATTAATATTTTAT-T
1 ATATATTAATATTATATAT
1249643 ATATATTTAATATTATA
1 ATATA-TTAATATTATA
1249660 CTCATATAAT
Statistics
Matches: 39, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
17 1 0.03
18 27 0.69
19 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATATTAATATTATATAT
Found at i:1250106 original size:3 final size:3
Alignment explanation
Indices: 1250100--1250125 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1250090 TAACATCATC
1250100 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1250126 TTAATATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1250153 original size:2 final size:2
Alignment explanation
Indices: 1250137--1250175 Score: 53
Period size: 2 Copynumber: 19.0 Consensus size: 2
1250127 TAATATTCAC
1250137 AT AT A- AT ACT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1250176 TATGACATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 29 0.85
3 4 0.12
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1251754 original size:8 final size:8
Alignment explanation
Indices: 1251741--1251820 Score: 53
Period size: 8 Copynumber: 9.9 Consensus size: 8
1251731 TATAAATTAT
1251741 TTATTAAA
1 TTATTAAA
1251749 TTATTAAA
1 TTATTAAA
1251757 -TATTAAA
1 TTATTAAA
1251764 -TATTGAATA
1 TTATT-AA-A
* *
1251773 TAATTATA
1 TTATTAAA
1251781 TTACTTGATAA
1 TTA-TT-A-AA
1251792 TT-TTAAA
1 TTATTAAA
1251799 -TATTAAA
1 TTATTAAA
1251806 TT-TTAAAA
1 TTATT-AAA
1251814 TTATTAA
1 TTATTAA
1251821 TTTTAATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
6 1 0.02
7 20 0.34
8 22 0.38
9 8 0.14
10 4 0.07
11 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (8 bp):
TTATTAAA
Found at i:1251772 original size:14 final size:15
Alignment explanation
Indices: 1251742--1251820 Score: 54
Period size: 15 Copynumber: 4.9 Consensus size: 15
1251732 ATAAATTATT
1251742 TATTAAATTATTAAA
1 TATTAAATTATTAAA
1251757 TATTAAA-TATTGAATA
1 TATTAAATTATT-AA-A
*
1251773 TAATTATATTACTTGATAA
1 T-ATTAAATTA-TT-A-AA
*
1251792 TTTTAAA-TATTAAA
1 TATTAAATTATTAAA
*
1251806 TTTTAAAATTATTAA
1 TATT-AAATTATTAA
1251821 TTTTAATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
14 10 0.19
15 13 0.25
16 10 0.19
17 7 0.13
18 6 0.11
19 6 0.11
20 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (15 bp):
TATTAAATTATTAAA
Found at i:1252273 original size:12 final size:12
Alignment explanation
Indices: 1252256--1252282 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1252246 ATTAAAATTA
1252256 AAAAAGAAGAAG
1 AAAAAGAAGAAG
1252268 AAAAAGAAGAAG
1 AAAAAGAAGAAG
1252280 AAA
1 AAA
1252283 TGCTTACGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:1255970 original size:2 final size:2
Alignment explanation
Indices: 1255963--1255992 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1255953 ATACAGTGTA
*
1255963 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1255993 CAAGAGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1257686 original size:5 final size:5
Alignment explanation
Indices: 1257670--1257723 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
1257660 ATGTTATTAC
* *
1257670 ATAAT ATAAAT ATAAT ATAAT ATAA- ATAAT -TAAA ATAAT ATAAAA ATAAT
1 ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT
1257720 ATAA
1 ATAA
1257724 AACGTGTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 7 0.17
5 25 0.61
6 9 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
ATAAT
Found at i:1257705 original size:9 final size:10
Alignment explanation
Indices: 1257678--1257725 Score: 64
Period size: 9 Copynumber: 4.9 Consensus size: 10
1257668 ACATAATATA
*
1257678 AATATAATAT
1 AATATAAAAT
1257688 AATAT-AAAT
1 AATATAAAAT
1257697 AAT-TAAAAT
1 AATATAAAAT
1257706 AATATAAAAAT
1 AATAT-AAAAT
1257717 AATATAAAA
1 AATATAAAA
1257726 CGTGTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
8 1 0.03
9 13 0.38
10 10 0.29
11 10 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATATAAAAT
Found at i:1257706 original size:20 final size:21
Alignment explanation
Indices: 1257670--1257725 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 21
1257660 ATGTTATTAC
1257670 ATAATATAAATATAATATAATATAA
1 ATAATATAAA-ATAATAT-A-A-AA
1257695 ATAAT-TAAAATAATATAAAA
1 ATAATATAAAATAATATAAAA
1257715 ATAATATAAAA
1 ATAATATAAAA
1257726 CGTGTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 1 0.03
23 7 0.23
24 4 0.13
25 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAATATAAAATAATATAAAA
Found at i:1257725 original size:11 final size:11
Alignment explanation
Indices: 1257670--1257725 Score: 62
Period size: 11 Copynumber: 5.0 Consensus size: 11
1257660 ATGTTATTAC
*
1257670 ATAATATAAAT
1 ATAATATAAAA
1257681 ATAATATAATATAA
1 ATAATAT-A-A-AA
1257695 ATAAT-T-AAA
1 ATAATATAAAA
1257704 ATAATATAAAA
1 ATAATATAAAA
1257715 ATAATATAAAA
1 ATAATATAAAA
1257726 CGTGTTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
9 7 0.18
10 2 0.05
11 21 0.54
12 1 0.03
13 2 0.05
14 6 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:1258246 original size:2 final size:2
Alignment explanation
Indices: 1258241--1258265 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1258231 GAAACATGAC
1258241 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
1258266 AATTTTCAAA
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:1259314 original size:2 final size:2
Alignment explanation
Indices: 1259307--1259337 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1259297 TGCTAAATAA
1259307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1259338 AGGTTAGATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1265113 original size:27 final size:24
Alignment explanation
Indices: 1265083--1265144 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 24
1265073 TTATATTATT
1265083 TAAAAAATATTTTATAATTAATATAAA
1 TAAAAAATATTTT-T-ATTAA-ATAAA
*
1265110 TAAAAATTTTATTTTTATTAAATAAA
1 TAAAAA--ATATTTTTATTAAATAAA
*
1265136 TAATAAATA
1 TAAAAAATA
1265145 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
24 2 0.07
26 10 0.33
27 11 0.37
28 1 0.03
29 6 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAAAATATTTTTATTAAATAAA
Found at i:1266035 original size:5 final size:5
Alignment explanation
Indices: 1266021--1266064 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
1266011 ACAATTTGCG
* *
1266021 TTTTA TTTTA ATTTA TTTTA ATTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1266065 CACTCTGAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:1266143 original size:14 final size:15
Alignment explanation
Indices: 1266124--1266161 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1266114 TATTTAAAGC
*
1266124 TTTATTTT-TTGAAT
1 TTTATTTTGTTAAAT
1266138 TTTATTTTGTTAAAT
1 TTTATTTTGTTAAAT
1266153 TTTGATTTT
1 TTT-ATTTT
1266162 AAATAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 8 0.38
16 5 0.24
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (15 bp):
TTTATTTTGTTAAAT
Found at i:1266582 original size:38 final size:36
Alignment explanation
Indices: 1266530--1266604 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 36
1266520 ATTTTATATT
*
1266530 AATATTAATATTTTTTATAATTAT-ATTTTAAATAAA
1 AATATTAATATTTTTTA-AATAATAATTTTAAATAAA
*
1266566 AATATTATATTATTTTTTAAATAATAATTTTAATTAAA
1 AATATTA-A-TATTTTTTAAATAATAATTTTAAATAAA
1266604 A
1 A
1266605 TAATTTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 7 0.21
37 6 0.18
38 21 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
AATATTAATATTTTTTAAATAATAATTTTAAATAAA
Found at i:1266606 original size:15 final size:16
Alignment explanation
Indices: 1266588--1266621 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1266578 TTTTTTAAAT
*
1266588 AATAATTTTAATTA-A
1 AATAATTTAAATTATA
1266603 AATAATTTAAATTATA
1 AATAATTTAAATTATA
1266619 AAT
1 AAT
1266622 TATTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAATTTAAATTATA
Found at i:1273604 original size:35 final size:35
Alignment explanation
Indices: 1273560--1273630 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
1273550 TGGGTTTAGC
* *
1273560 AGCAATTAAATTAAAGTCGCTGCTGAGTTAGTGTT
1 AGCAATTAAATTAAAGTCGCTGCTGAATTACTGTT
* * *
1273595 AGCAATTAAATTATATTTGCTGCTGAATTACTGTT
1 AGCAATTAAATTAAAGTCGCTGCTGAATTACTGTT
1273630 A
1 A
1273631 CATATGCAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (35 bp):
AGCAATTAAATTAAAGTCGCTGCTGAATTACTGTT
Found at i:1277320 original size:3 final size:3
Alignment explanation
Indices: 1277312--1277337 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1277302 AAATATATTT
1277312 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
1277338 TTAATATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1278579 original size:16 final size:16
Alignment explanation
Indices: 1278560--1278602 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1278550 TTTCCTTAGT
1278560 ATTTCTTTTCTTTAAA
1 ATTTCTTTTCTTTAAA
* * **
1278576 ATTTTTTTTCCTTAGT
1 ATTTCTTTTCTTTAAA
1278592 ATTTCTTTTCT
1 ATTTCTTTTCT
1278603 ATTTTAAATT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.02, T:0.67
Consensus pattern (16 bp):
ATTTCTTTTCTTTAAA
Found at i:1278586 original size:32 final size:33
Alignment explanation
Indices: 1278550--1278616 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 33
1278540 TGATAAAGGA
1278550 TTTCCTTAGTATTTCTTTTC-TTTAAAATTTTT
1 TTTCCTTAGTATTTCTTTTCATTTAAAATTTTT
*
1278582 TTTCCTTAGTATTTCTTTTCTATTTTAAATTTTT
1 TTTCCTTAGTATTTCTTTTC-ATTTAAAATTTTT
1278616 T
1 T
1278617 CCCTGATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 20 0.62
34 12 0.38
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (33 bp):
TTTCCTTAGTATTTCTTTTCATTTAAAATTTTT
Found at i:1285127 original size:26 final size:26
Alignment explanation
Indices: 1285080--1285130 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1285070 ATATTTTTAA
*
1285080 TAAATATAAAAATAATATAATATATT
1 TAAATATAAAAATAATAAAATATATT
*
1285106 TAAATATAATTAAT-ATAAAATATAT
1 TAAATATAA-AAATAATAAAATATAT
1285131 AATATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TAAATATAAAAATAATAAAATATATT
Found at i:1285189 original size:6 final size:6
Alignment explanation
Indices: 1285132--1285196 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
1285122 AAAATATATA
* * *
1285132 ATATTT ATA-TC ATATTT ACATTT AAATTT -TA-TT ATATTT AATAATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT -AT-ATTT
*
1285179 TTATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT
1285197 TAAACAATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 2 0.04
5 7 0.15
6 31 0.66
7 3 0.06
8 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (6 bp):
ATATTT
Found at i:1285351 original size:41 final size:41
Alignment explanation
Indices: 1285305--1285429 Score: 104
Period size: 43 Copynumber: 3.1 Consensus size: 41
1285295 AAAATAATAT
1285305 TAAAAATTATTTTTATATTAATATTTATAATTAAATTTAAA
1 TAAAAATTATTTTTATATTAATATTTATAATTAAATTTAAA
* * *
1285346 TAAAAATTTAATTTTT-TATTATAAATATAATAATTCAAA-TAAAA
1 TAAAAA-TT-ATTTTTATATTA-ATAT-TTATAATT-AAATTTAAA
*
1285390 T-AAAA-TAATTTTA-ATT--TATTTA-AATTAAATTTAATA
1 TAAAAATTATTTTTATATTAATATTTATAATTAAATTTAA-A
1285426 TAAA
1 TAAA
1285430 TTAAATAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
34 3 0.04
35 7 0.10
36 4 0.06
37 4 0.06
40 8 0.12
41 7 0.10
42 7 0.10
43 13 0.19
44 12 0.18
45 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (41 bp):
TAAAAATTATTTTTATATTAATATTTATAATTAAATTTAAA
Found at i:1285438 original size:20 final size:20
Alignment explanation
Indices: 1285383--1285440 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
1285373 TAATAATTCA
* *
1285383 AATA-AAATAAAATAATTTT
1 AATATAAATTAAATAAATTT
* *
1285402 AAT-TTATTTAAATTAAATTT
1 AATATAAATTAAA-TAAATTT
1285422 AATATAAATTAAATAAATT
1 AATATAAATTAAATAAATT
1285441 ATCCAGACTT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 8 0.27
20 15 0.50
21 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATATAAATTAAATAAATTT
Found at i:1285772 original size:2 final size:2
Alignment explanation
Indices: 1285765--1285818 Score: 76
Period size: 2 Copynumber: 27.0 Consensus size: 2
1285755 AGGTTTAGTT
1285765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
1285807 TA TCA TA T- TA TA
1 TA T-A TA TA TA TA
1285819 AATTTGTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.04
2 42 0.88
3 4 0.08
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1286014 original size:15 final size:14
Alignment explanation
Indices: 1285995--1286042 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 14
1285985 AAAAATATTT
1285995 TAATAAATTAATAA
1 TAATAAATTAATAA
*
1286009 TTAATAAAATAAATAA
1 -TAAT-AAATTAATAA
1286025 TAAT-AA-TAATAA
1 TAATAAATTAATAA
1286037 TAATAA
1 TAATAA
1286043 TTATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 9 0.31
13 3 0.10
15 8 0.28
16 9 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATAAATTAATAA
Found at i:1286026 original size:3 final size:3
Alignment explanation
Indices: 1286003--1286043 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
1285993 TTTAATAAAT
1286003 TAA TAA TTAA TAA -AA TAAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA -TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T
1286044 TATTATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 27 0.77
4 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1286218 original size:32 final size:29
Alignment explanation
Indices: 1286178--1286236 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 29
1286168 AAATAAATTT
1286178 TATTTTTATTCAAATTTATATTTTAAATATAA
1 TATTTTTATTCAAA--T-TATTTTAAATATAA
*
1286210 TATTTTTATTTAAATTATTTTAAATAT
1 TATTTTTATTCAAATTATTTTAAATAT
1286237 CAAATAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.46
30 1 0.04
32 13 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
TATTTTTATTCAAATTATTTTAAATATAA
Found at i:1287073 original size:270 final size:267
Alignment explanation
Indices: 1286575--1287122 Score: 863
Period size: 270 Copynumber: 2.0 Consensus size: 267
1286565 CTAATAAGCA
*
1286575 ATAAATTTAGGCATGACCCCTGGTAGTTTACTTGTTCCTATATTGAAATTTGGTTACATTGTTTT
1 ATAAATTTAGGCATGACCCCTGGTAGTTTACTTGTTCCTATATTAAAATTTGGTTACATTGTTTT
* *
1286640 TAATTGAATTTATTGCTTTTAAATTGTAATAAAAATATATGCTTTCAAAATTTGTAATAACTTCT
66 TAATTAAATTTATTGCTTTTAAATTGTAATAAAAATATATGCTTTCAAAATTTATAATAACTTCT
* *
1286705 AAATTTTATTTATTATTTATTTATTTAAAGTACTAACATGACATTTAATTATGACACGATATTAT
131 AAATTTTATTTATTATTTATTTATTTAAAGTACTAACATCACATTCAATTATGACACGATATTAT
* *
1286770 ATTAATATGGTGATACAAAATTTTTTTAAAAAATAGAAAATCAGTATGGTATAATATGACAATAA
196 ATTAATA--GTGATA-AAAATTTTTTAAAAAAATAGAAAATCAGTATGGTATAATATCACAATAA
1286835 AAAAAGAAAT
258 AAAAAGAAAT
*
1286845 ATAAATTTAGGTATGACCCCTGGTAGTTTACTTGTTCCTATATTAAAATTTGGTTACATTGTTTT
1 ATAAATTTAGGCATGACCCCTGGTAGTTTACTTGTTCCTATATTAAAATTTGGTTACATTGTTTT
*
1286910 TAATTAAATTTATTGCTTTTAAATTGTAATAAAAATATATGCTTTCAAAATTTATAGTAACTTCT
66 TAATTAAATTTATTGCTTTTAAATTGTAATAAAAATATATGCTTTCAAAATTTATAATAACTTCT
*
1286975 AAATTTTATTTATTATTTATTATTTATTTATTTAAAGTACTAATATCACATTCAATTATGACACG
131 -AA----A-TT-TTATTTATTATTTATTTATTTAAAGTACTAACATCACATTCAATTATGACACG
*
1287040 ATATTATATT-A-A-T-AT-AATATTTTTTAAAAAAAATAGAAAATCAGTATGGTATAATATCAC
189 ATATTATATTAATAGTGATAAAAATTTTTT-AAAAAAATAGAAAATCAGTATGGTATAATATCAC
1287100 AATAAAAAAAGAAAT
253 AATAAAAAAAGAAAT
1287115 ATAAATTT
1 ATAAATTT
1287123 TTTCATTAAT
Statistics
Matches: 259, Mismatches: 11, Indels: 16
0.91 0.04 0.06
Matches are distributed among these distances:
269 9 0.03
270 180 0.69
271 4 0.02
272 1 0.00
275 2 0.01
276 3 0.01
277 60 0.23
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (267 bp):
ATAAATTTAGGCATGACCCCTGGTAGTTTACTTGTTCCTATATTAAAATTTGGTTACATTGTTTT
TAATTAAATTTATTGCTTTTAAATTGTAATAAAAATATATGCTTTCAAAATTTATAATAACTTCT
AAATTTTATTTATTATTTATTTATTTAAAGTACTAACATCACATTCAATTATGACACGATATTAT
ATTAATAGTGATAAAAATTTTTTAAAAAAATAGAAAATCAGTATGGTATAATATCACAATAAAAA
AAGAAAT
Found at i:1287220 original size:14 final size:14
Alignment explanation
Indices: 1287203--1287230 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1287193 TTTATCTTGG
1287203 TTTCTTTTTCTTTC
1 TTTCTTTTTCTTTC
1287217 TTTCTTTTTCTTTC
1 TTTCTTTTTCTTTC
1287231 AATGCCCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTTTCTTTC
Found at i:1287640 original size:4 final size:4
Alignment explanation
Indices: 1287631--1287661 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1287621 CTTAAAATGA
1287631 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1287662 ACCTGAGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1287801 original size:34 final size:33
Alignment explanation
Indices: 1287746--1287964 Score: 276
Period size: 34 Copynumber: 6.5 Consensus size: 33
1287736 ACCATCAATG
*
1287746 TGTTGATTAAATGGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCAT
* * *
1287779 TGTTGATTAAATAGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
* *
1287813 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
**
1287847 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATG-GTGATTTGGTAGCTTACCAT
* *
1287881 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
* * *
1287915 TGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGT-GATTTGGTAGCTTACCAT
1287949 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
1287965 GTTTTTACCA
Statistics
Matches: 162, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
33 17 0.10
34 144 0.89
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (33 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCAT
Found at i:1287887 original size:102 final size:101
Alignment explanation
Indices: 1287746--1287962 Score: 335
Period size: 102 Copynumber: 2.1 Consensus size: 101
1287736 ACCATCAATG
** * * * *
1287746 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATAGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTACC
1287811 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
*
1287847 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTAC
* * *
1287912 CATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1287949 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1287963 TGGTTTTTAC
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
101 14 0.13
102 91 0.87
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1292431 original size:34 final size:33
Alignment explanation
Indices: 1292374--1292594 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 33
1292364 AAGTGGGAGA
*
1292374 ATTGTTGATTAAATGGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACC
* * *
1292407 ATTGTTGATTAAATAGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
* *
1292441 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
**
1292475 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATG-GTGATTTGGTAGCTTACC
* *
1292509 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
* * *
1292543 ATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGT-GATTTGGTAGCTTACC
1292577 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1292595 GTTTTTACCA
Statistics
Matches: 164, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
33 19 0.12
34 144 0.88
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (33 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACC
Found at i:1292517 original size:102 final size:101
Alignment explanation
Indices: 1292374--1292592 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
1292364 AAGTGGGAGA
** * * * *
1292374 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATAGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTA
1292439 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
1292475 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTT
* * *
1292540 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1292577 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1292593 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1293331 original size:29 final size:28
Alignment explanation
Indices: 1293262--1293333 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
1293252 GAATCAGATG
* *
1293262 ATAATTTAAAATTTTATTTTTATTTAAT
1 ATAATATAAAAATTTATTTTTATTTAAT
* *
1293290 ATCAATCTGAAAATTTATTTTATTATTTAA-
1 AT-AATATAAAAATTTA-TTT-TTATTTAAT
1293320 ATAATATAAAAATT
1 ATAATATAAAAATT
1293334 ACTTATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.06
29 21 0.58
30 5 0.14
31 8 0.22
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (28 bp):
ATAATATAAAAATTTATTTTTATTTAAT
Found at i:1293779 original size:13 final size:12
Alignment explanation
Indices: 1293744--1293785 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 12
1293734 AACTTTAAAA
1293744 TTTATTTAAATT
1 TTTATTTAAATT
1293756 TTTAAATTTAATATT
1 TTT--ATTTAA-ATT
1293771 TTTATTTAAATT
1 TTTATTTAAATT
1293783 TTT
1 TTT
1293786 TTAAATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
14 6 0.22
15 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATTTAAATT
Found at i:1293786 original size:13 final size:13
Alignment explanation
Indices: 1293744--1293786 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1293734 AACTTTAAAA
1293744 TTTATTTAAATTT
1 TTTATTTAAATTT
*
1293757 TTAAATTT-AATATT
1 TT-TATTTAAAT-TT
1293771 TTTATTTAAATTT
1 TTTATTTAAATTT
1293784 TTT
1 TTT
1293787 TAAATGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATTTAAATTT
Found at i:1293786 original size:14 final size:14
Alignment explanation
Indices: 1293744--1293788 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1293734 AACTTTAAAA
1293744 TTTATTTAAATTTT
1 TTTATTTAAATTTT
** *
1293758 TAAATTT-AATATT
1 TTTATTTAAATTTT
1293771 TTTATTTAAATTTT
1 TTTATTTAAATTTT
1293785 TTTA
1 TTTA
1293789 AATGTAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTAAATTTT
Found at i:1296837 original size:2 final size:2
Alignment explanation
Indices: 1296794--1296823 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1296784 CACCTTTTTA
1296794 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
1296824 GCGTGTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1298665 original size:21 final size:20
Alignment explanation
Indices: 1298628--1298670 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1298618 ATTTAGATAA
*
1298628 AATGATGCATTGGTTGAGTG
1 AATGATGCATTGGTTGAATG
**
1298648 AATGAATGCATTTTTTGAATG
1 AATG-ATGCATTGGTTGAATG
1298669 AA
1 AA
1298671 AAAAATGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.37
Consensus pattern (20 bp):
AATGATGCATTGGTTGAATG
Found at i:1303001 original size:20 final size:20
Alignment explanation
Indices: 1302976--1303050 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1302966 TTTTCACAAT
1302976 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
1302996 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
1303016 TTGTATCGATACATT-TTGCA
1 TTGTATCGATACATTGTT-CA
* *
1303036 ATATATCGATACATT
1 TTGTATCGATACATT
1303051 CAGACATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 2 0.04
20 50 0.96
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1305471 original size:79 final size:79
Alignment explanation
Indices: 1305339--1305707 Score: 350
Period size: 79 Copynumber: 4.7 Consensus size: 79
1305329 GAGGATATTT
* * * * *
1305339 CAACCCCGATTTTATTT-TCAAAACATCAATTTTTCATAATCGAGGATACTCCAATCCTGTTATT
1 CAACCCCGACTTTATTTCT-AAAACATCGATTTTTCATAATCGGGGATACTCCAACCCCGTTATT
*
1305403 TTCGAGGGAATACTC
65 TTCGAGGGGATACTC
* * * * *
1305418 AAACCCCGGCTTTATTTCTAAAATATTGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTT
1 CAACCCCGACTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAACCCCGTTATTT
* *
1305483 TGGCGGGGATACTC
66 TCGAGGGGATACTC
* * * *** * * * * *
1305497 CAACCTCGGCCTTATTTCTAAAGTTTCGATTTTTCACAATCGGTGATACTCTAATCCCGTTATCT
1 CAACCCCGACTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAACCCCGTTATTT
1305562 TCGAGGGGATACT-
66 TCGAGGGGATACTC
* * * * ** * *
1305575 CAACCTCAATTTTATTT-TCAAAACGTCGA-TTTTCTATAATCAAGGATGCTCCAACCCTGTTAT
1 CAACCCCGACTTTATTTCT-AAAACATCGATTTTTC-ATAATCGGGGATACTCCAACCCCGTTAT
*
1305638 TTTTGAGGGGATACTC
64 TTTCGAGGGGATACTC
* * *
1305654 CAACCCCGATTTTATTTCTAGAACATCGATTTTTCATAATCAGGAGATACTCCA
1 CAACCCCGACTTTATTTCTAAAACATCGATTTTTCATAATC-GGGGATACTCCA
1305708 GCCTCATTGT
Statistics
Matches: 233, Mismatches: 50, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
77 6 0.03
78 53 0.23
79 159 0.68
80 15 0.06
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (79 bp):
CAACCCCGACTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAACCCCGTTATTT
TCGAGGGGATACTC
Found at i:1305671 original size:157 final size:156
Alignment explanation
Indices: 1305339--1305707 Score: 393
Period size: 157 Copynumber: 2.3 Consensus size: 156
1305329 GAGGATATTT
* * * *
1305339 CAACCCCGATTTTATTTTCAAAACATCAATTTTTCATAATCGAGGATACTCCAATCCTGTTATTT
1 CAACCCCGATTTTA-TTTCTAAACATCGATTTTTCATAATCG-GGATACTCCAATCCCGTTATCT
** * * **
1305404 TCGAGGGAATACTCAAACCCCGGCTTTATTTCTAAAATATTGATTTTTCACAATCGGGGATACTC
64 TCGAGGGAATACTCAAACCCCAACTTTATTTCTAAAACATCGATTTTTCACAATCAAGGATACTC
*
1305469 CAACCCCGTTATTTTGGCGGGGATACTC
129 CAACCCCGTTATTTTGGAGGGGATACTC
* *** ** * *
1305497 CAACCTCGGCCTTATTTCTAAAGTTTCGATTTTTCACAATCGGTGATACTCTAATCCCGTTATCT
1 CAACCCCGATTTTATTTCTAAA-CATCGATTTTTCATAATCGG-GATACTCCAATCCCGTTATCT
* * * * * *
1305562 TCGAGGGGATACTC-AACCTCAATTTTATTT-TCAAAACGTCGA-TTTTCTATAATCAAGGATGC
64 TCGAGGGAATACTCAAACCCCAACTTTATTTCT-AAAACATCGATTTTTC-ACAATCAAGGATAC
* *
1305624 TCCAACCCTGTTATTTTTGAGGGGATACTC
127 TCCAACCCCGTTATTTTGGAGGGGATACTC
1305654 CAACCCCGATTTTATTTCTAGAACATCGATTTTTCATAATCAGGAGATACTCCA
1 CAACCCCGATTTTATTTCTA-AACATCGATTTTTCATAATC-GG-GATACTCCA
1305708 GCCTCATTGT
Statistics
Matches: 169, Mismatches: 36, Indels: 12
0.78 0.17 0.06
Matches are distributed among these distances:
156 6 0.04
157 95 0.56
158 68 0.40
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (156 bp):
CAACCCCGATTTTATTTCTAAACATCGATTTTTCATAATCGGGATACTCCAATCCCGTTATCTTC
GAGGGAATACTCAAACCCCAACTTTATTTCTAAAACATCGATTTTTCACAATCAAGGATACTCCA
ACCCCGTTATTTTGGAGGGGATACTC
Found at i:1307565 original size:18 final size:18
Alignment explanation
Indices: 1307542--1307597 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1307532 TTGGGACTGT
*
1307542 AAAAAGAGACAAAGAAAA
1 AAAAAGAGAAAAAGAAAA
*
1307560 AAAAAGATAAAAAGAAAA
1 AAAAAGAGAAAAAGAAAA
**
1307578 AAGAAA-AGAGTAAGAAAA
1 AA-AAAGAGAAAAAGAAAA
1307596 AA
1 AA
1307598 CTAGATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 29 0.91
19 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (18 bp):
AAAAAGAGAAAAAGAAAA
Found at i:1308258 original size:16 final size:16
Alignment explanation
Indices: 1308237--1308274 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1308227 TGCTCTAATC
1308237 TTTCTTTAACATGTAT
1 TTTCTTTAACATGTAT
1308253 TTTCTTTAACATGTAT
1 TTTCTTTAACATGTAT
1308269 TTTCTT
1 TTTCTT
1308275 CTGCATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTCTTTAACATGTAT
Found at i:1309214 original size:17 final size:19
Alignment explanation
Indices: 1309166--1309222 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 19
1309156 TTTAATTATG
*
1309166 AATATAAAAATATAATTTTTA
1 AATATATAAA-AT-ATTTTTA
1309187 AATATATAAAATATTTTTA
1 AATATATAAAATATTTTTA
*
1309206 AA-A-ATAAAATATATTTA
1 AATATATAAAATATTTTTA
1309223 TTTTAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 13 0.38
18 1 0.03
19 9 0.26
20 2 0.06
21 9 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATATAAAATATTTTTA
Found at i:1309668 original size:16 final size:18
Alignment explanation
Indices: 1309642--1309674 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1309632 AATTTTATAT
1309642 ATTATTCAAAA-TAAATA
1 ATTATTCAAAATTAAATA
1309659 ATTA-TCAAAATTAAAT
1 ATTATTCAAAATTAAAT
1309675 TTATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTATTCAAAATTAAATA
Found at i:1309957 original size:26 final size:24
Alignment explanation
Indices: 1309910--1309957 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1309900 AATTTATAAT
1309910 TTATATAAAAAATAATAAATATTA
1 TTATATAAAAAATAATAAATATTA
*
1309934 TTATATTAATAAATAAATAAATAT
1 TTATA-TAAAAAAT-AATAAATAT
1309958 AAAAAAGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 7 0.33
26 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TTATATAAAAAATAATAAATATTA
Found at i:1310809 original size:3 final size:3
Alignment explanation
Indices: 1310796--1310839 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1310786 TTTCCCCTAA
* * *
1310796 ATT ATTT ATT ATT AAT ATT GTT ATT GTT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1310840 CGACCTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1311625 original size:2 final size:2
Alignment explanation
Indices: 1311618--1311647 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1311608 TGTAAATAAA
1311618 TC TC TC TC -C 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 T
1311648 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1311652 original size:2 final size:2
Alignment explanation
Indices: 1311647--1311675 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1311637 TCTCTCTCTC
1311647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1311676 CAGAAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1317427 original size:3 final size:3
Alignment explanation
Indices: 1317419--1317449 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1317409 GACCAAATGC
1317419 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1317450 CTACAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1318320 original size:18 final size:18
Alignment explanation
Indices: 1318297--1318400 Score: 61
Period size: 18 Copynumber: 5.6 Consensus size: 18
1318287 CCGATTTAAA
1318297 ATTTATATATTTTATTAT
1 ATTTATATATTTTATTAT
*
1318315 ATTTATAT-TATTTATAAT
1 ATTTATATAT-TTTATTAT
* * *
1318333 ATAATAAATTTTTTTATTAT
1 AT-TTATA-TATTTTATTAT
*
1318353 AATTTATATAAAATTTT-TAAT
1 -ATTTATAT---ATTTTATTAT
*
1318374 ATTTTTAT-TTTTATTAT
1 ATTTATATATTTTATTAT
*
1318391 ATATATATAT
1 ATTTATATAT
1318401 ATATTTTTAA
Statistics
Matches: 64, Mismatches: 12, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
16 4 0.06
17 10 0.16
18 18 0.28
19 4 0.06
20 18 0.28
21 6 0.09
22 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:1318355 original size:23 final size:24
Alignment explanation
Indices: 1318326--1318370 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1318316 TTTATATTAT
*
1318326 TTATAATATA-ATAAATTTTTTTA
1 TTATAATATATATAAAATTTTTTA
*
1318349 TTATAATTTATATAAAATTTTT
1 TTATAATATATATAAAATTTTT
1318371 AATATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATAATATATATAAAATTTTTTA
Found at i:1318371 original size:23 final size:23
Alignment explanation
Indices: 1318326--1318371 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1318316 TTTATATTAT
*
1318326 TTATAATATAATAAATTTTTTTA
1 TTATAATATAATAAATATTTTTA
*
1318349 TTATAATTTATATAAA-ATTTTTA
1 TTATAATATA-ATAAATATTTTTA
1318372 ATATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATAATATAATAAATATTTTTA
Found at i:1319087 original size:22 final size:22
Alignment explanation
Indices: 1319062--1319112 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
1319052 AACAAAAATA
1319062 AAAATAATTAATAATTA-ATTTT
1 AAAATAATTAA-AATTATATTTT
1319084 AAAAT-A-TAAAATTATATTTT
1 AAAATAATTAAAATTATATTTT
*
1319104 -TAATAATTA
1 AAAATAATTA
1319113 TTTTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 8 0.32
20 9 0.36
21 3 0.12
22 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATAATTAAAATTATATTTT
Found at i:1319123 original size:12 final size:13
Alignment explanation
Indices: 1319098--1319148 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
1319088 TATAAAATTA
1319098 TATTTTTAATAAT
1 TATTTTTAATAAT
1319111 TATTTTTAA-AAT
1 TATTTTTAATAAT
1319123 TA--TTT-ATAAT
1 TATTTTTAATAAT
1319133 T-TTTTTAATAA-
1 TATTTTTAATAAT
1319144 TATTT
1 TATTT
1319149 ATTCTCAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
9 1 0.03
10 7 0.21
11 4 0.12
12 12 0.36
13 9 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTTTAATAAT
Found at i:1319138 original size:34 final size:34
Alignment explanation
Indices: 1319069--1319148 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
1319059 ATAAAAATAA
* *
1319069 TTAATAATTAATTTTAAAATATAAAATTATATTT
1 TTAATAATTATTTTTAAAATATAAAATAATATTT
** *
1319103 TTAATAATTATTTTTAAAAT-TATTTATAATTTTT
1 TTAATAATTATTTTTAAAATATA-AAATAATATTT
1319137 TTAATAA-TATTT
1 TTAATAATTATTT
1319149 ATTCTCAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
33 7 0.17
34 33 0.82
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TTAATAATTATTTTTAAAATATAAAATAATATTT
Found at i:1319139 original size:21 final size:22
Alignment explanation
Indices: 1319106--1319150 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1319096 TATATTTTTA
1319106 ATAATTATTTTTAA-AATTATTT
1 ATAATTATTTTTAATAA-TATTT
1319128 ATAATT-TTTTTAATAATATTT
1 ATAATTATTTTTAATAATATTT
1319149 AT
1 AT
1319151 TCTCAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATAATTATTTTTAATAATATTT
Found at i:1319291 original size:14 final size:14
Alignment explanation
Indices: 1319255--1319307 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1319245 AAAATATGTT
* *
1319255 TAATAAATAAAAAA
1 TAATATATAATAAA
1319269 TAATATATAATAAA
1 TAATATATAATAAA
1319283 T-ATATTATAATAAA
1 TAATA-TATAATAAA
1319297 TTTAATATATA
1 --TAATATATA
1319308 TTATATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 3 0.09
14 22 0.67
16 5 0.15
17 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATATATAATAAA
Found at i:1319292 original size:21 final size:21
Alignment explanation
Indices: 1319267--1319312 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 21
1319257 ATAAATAAAA
1319267 AATAATATATAATAAATATATTAT
1 AATAA-ATATAAT--ATATATTAT
*
1319291 AATAAATTTAATATATATTAT
1 AATAAATATAATATATATTAT
1319312 A
1 A
1319313 TTTATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
23 6 0.29
24 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAAATATAATATATATTAT
Found at i:1319358 original size:19 final size:19
Alignment explanation
Indices: 1319314--1319361 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
1319304 TATATTATAT
1319314 TTATATTTAA-AATTTTGA
1 TTATATTTAATAATTTTGA
*
1319332 -TACT-TTTAATAATTTTTA
1 TTA-TATTTAATAATTTTGA
1319350 TTATATTTAATA
1 TTATATTTAATA
1319362 TAACATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 7 0.28
18 9 0.36
19 9 0.36
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATATTTAATAATTTTGA
Found at i:1319724 original size:7 final size:7
Alignment explanation
Indices: 1319714--1319743 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1319704 TTGTTACCAT
*
1319714 TTGGTAG
1 TTGGTGG
1319721 TTGGTGG
1 TTGGTGG
1319728 TTGGTGG
1 TTGGTGG
1319735 TTGGTGG
1 TTGGTGG
1319742 TT
1 TT
1319744 TGAACTTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (7 bp):
TTGGTGG
Found at i:1319919 original size:26 final size:25
Alignment explanation
Indices: 1319889--1319937 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
1319879 TTTTTTTATT
*
1319889 AATTAATATAA-AAATATATTATTTAA
1 AATTAAT-TAATAAA-ATAATATTTAA
1319915 AATTAATTAATAAAATAATATTT
1 AATTAATTAATAAAATAATATTT
1319938 TTTTAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATTAATTAATAAAATAATATTTAA
Found at i:1319920 original size:30 final size:29
Alignment explanation
Indices: 1319886--1319943 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1319876 TAATTTTTTT
1319886 ATTAATTAATATAAA-AATATATTATTTAAA
1 ATTAATTAATA-AAATAATAT-TTATTTAAA
*
1319916 ATTAATTAATAAAATAATATTTTTTTAA
1 ATTAATTAATAAAATAATATTTATTTAA
1319944 TTGACTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTAATTAATAAAATAATATTTATTTAAA
Found at i:1320413 original size:18 final size:19
Alignment explanation
Indices: 1320382--1320419 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1320372 AATATATTAT
1320382 TTAAAAAAATTTAA-AAAA
1 TTAAAAAAATTTAATAAAA
1320400 TTAAAAATAA-TTAATAAAA
1 TTAAAAA-AATTTAATAAAA
1320419 T
1 T
1320420 AATTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAAAAATTTAATAAAA
Found at i:1320630 original size:21 final size:20
Alignment explanation
Indices: 1320596--1320636 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1320586 TAAAATAAAT
1320596 TATTAATATATAATAATTTA
1 TATTAATATATAATAATTTA
* *
1320616 TATTCAATTTATAATATTTTA
1 TATT-AATATATAATAATTTA
1320637 AATAATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTAATATATAATAATTTA
Found at i:1320822 original size:2 final size:2
Alignment explanation
Indices: 1320815--1320852 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1320805 TTTAGTAGCC
1320815 TA TA 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 TA TA
1320853 GCACAGAGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1321388 original size:19 final size:19
Alignment explanation
Indices: 1321343--1321413 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
1321333 ATGTTTAACT
* * *
1321343 ATTATTTAACATAAATATA
1 ATTATTTAATATATATGTA
* *
1321362 A-T-TTTAATATATATTTT
1 ATTATTTAATATATATGTA
*
1321379 ATTATTTAATATAAATGTA
1 ATTATTTAATATATATGTA
*
1321398 ATTATTTATTATATAT
1 ATTATTTAATATATAT
1321414 ATACATATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
17 12 0.29
18 2 0.05
19 27 0.66
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (19 bp):
ATTATTTAATATATATGTA
Found at i:1321800 original size:15 final size:15
Alignment explanation
Indices: 1321780--1321822 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1321770 TTTATATAAA
1321780 ATATATTAAAATATT
1 ATATATTAAAATATT
*
1321795 ATATATTAATATATT
1 ATATATTAAAATATT
*
1321810 TTATAATTAAAAT
1 ATAT-ATTAAAAT
1321823 TAAATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATTAAAATATT
Found at i:1326297 original size:2 final size:2
Alignment explanation
Indices: 1326285--1326326 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1326275 CATAATTAAG
1326285 AT AT A- 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
1326326 A
1 A
1326327 GTTATGCTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1328959 original size:2 final size:2
Alignment explanation
Indices: 1328952--1328979 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1328942 ATCTAAATGA
1328952 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
1328980 TAACTGCCTA
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:1333540 original size:28 final size:28
Alignment explanation
Indices: 1333484--1333542 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1333474 ATTTTATATT
**
1333484 AATATTTTTATATTTTATAATTAAATAA
1 AATATTTTTATATTAAATAATTAAATAA
*
1333512 AATATTTTTATTATTAAATAA-TAATTAA
1 AATATTTTTA-TATTAAATAATTAAATAA
1333540 AAT
1 AAT
1333543 CATATCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AATATTTTTATATTAAATAATTAAATAA
Found at i:1335784 original size:13 final size:12
Alignment explanation
Indices: 1335751--1335791 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
1335741 AAATAACATT
*
1335751 AAATCAATTAAA
1 AAATTAATTAAA
1335763 AAATTAATTAAA
1 AAATTAATTAAA
1335775 AAATTAAATTATAA
1 AAATT-AATTA-AA
1335789 AAA
1 AAA
1335792 ATATAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 16 0.62
13 5 0.19
14 5 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATTAATTAAA
Found at i:1335791 original size:15 final size:15
Alignment explanation
Indices: 1335759--1335803 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1335749 TTAAATCAAT
1335759 TAAAAAATT-AA-T-
1 TAAAAAATTAAATTA
1335771 TAAAAAATTAAATTA
1 TAAAAAATTAAATTA
1335786 TAAAAAA-TATAATTA
1 TAAAAAATTA-AATTA
1335801 TAA
1 TAA
1335804 GATTACATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.31
13 2 0.07
14 3 0.10
15 15 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAAAATTAAATTA
Found at i:1336683 original size:16 final size:16
Alignment explanation
Indices: 1336638--1336690 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1336628 AAATTTTATC
1336638 AATCTAATTCAATTATA
1 AATCTAATTCAATT-TA
* *
1336655 AA---AATTTATTTTA
1 AATCTAATTCAATTTA
1336668 AATCTAATTCAATTTA
1 AATCTAATTCAATTTA
1336684 AATCTAA
1 AATCTAA
1336691 ATTAAATGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 4 0.14
14 7 0.24
16 16 0.55
17 2 0.07
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AATCTAATTCAATTTA
Found at i:1337601 original size:4 final size:4
Alignment explanation
Indices: 1337589--1337618 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
1337579 ATATACATAG
1337589 TATT ATATT TATT TATT TATT TATT TATT T
1 TATT -TATT TATT TATT TATT TATT TATT T
1337619 CAGTAATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1340108 original size:19 final size:19
Alignment explanation
Indices: 1340084--1340121 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1340074 AATTGTAACC
1340084 AAGAATATGATTTTAATGT
1 AAGAATATGATTTTAATGT
1340103 AAGAATATGATTTTAATGT
1 AAGAATATGATTTTAATGT
1340122 CATTCAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
AAGAATATGATTTTAATGT
Found at i:1341413 original size:24 final size:22
Alignment explanation
Indices: 1341361--1341413 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
1341351 TTATTAGTAA
* *
1341361 AATATTTAAATTATATTCTTTT
1 AATATTTAAATCATAATCTTTT
1341383 AATTATTTAAAATCATAATCTTTTT
1 AA-TATTT-AAATCATAATC-TTTT
1341408 AATATT
1 AATATT
1341414 AACAACACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 2 0.08
23 5 0.19
24 13 0.50
25 6 0.23
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATTTAAATCATAATCTTTT
Found at i:1349453 original size:20 final size:20
Alignment explanation
Indices: 1349422--1349467 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
1349412 TGAGTTTCAC
* *
1349422 ATATTTTAT-TTTGTTCAAT
1 ATATTTTATATTTTTTAAAT
1349441 -TATTTTATATTTTTTAAAT
1 ATATTTTATATTTTTTAAAT
1349460 ATATTTTA
1 ATATTTTA
1349468 ATAAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 8 0.35
20 7 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
ATATTTTATATTTTTTAAAT
Found at i:1351418 original size:32 final size:32
Alignment explanation
Indices: 1351377--1351437 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1351367 ATATTATGTG
*
1351377 TATAAATTTTGATATATTAATA-ATTTATAATA
1 TATAAATTTTAATA-ATTAATATATTTATAATA
*
1351409 TATAAATTTTAATAATTTATATATTTATA
1 TATAAATTTTAATAATTAATATATTTATA
1351438 TTTTATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (32 bp):
TATAAATTTTAATAATTAATATATTTATAATA
Found at i:1351421 original size:24 final size:23
Alignment explanation
Indices: 1351393--1351442 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1351383 TTTTGATATA
1351393 TTAATAATTTATAATATATAAATT
1 TTAATAATTTAT-ATATATAAATT
* *
1351417 TTAATAATTTATATATTTATATT
1 TTAATAATTTATATATATAAATT
1351440 TTA
1 TTA
1351443 TTATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATAATTTATATATATAAATT
Found at i:1351429 original size:17 final size:16
Alignment explanation
Indices: 1351377--1351443 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 16
1351367 ATATTATGTG
1351377 TATAAATTTTGATATATT
1 TATAAATTTT-ATA-ATT
* *
1351395 AAT-AA-TTTATAATA
1 TATAAATTTTATAATT
1351409 TATAAATTTTAATAATT
1 TATAAATTTT-ATAATT
* *
1351426 TATATA-TTTATATTT
1 TATAAATTTTATAATT
1351441 TAT
1 TAT
1351444 TATATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 4 0.10
15 13 0.32
16 9 0.22
17 12 0.30
18 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (16 bp):
TATAAATTTTATAATT
Found at i:1351435 original size:16 final size:16
Alignment explanation
Indices: 1351420--1351460 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1351410 ATAAATTTTA
1351420 ATAATTTA-TATATTT
1 ATAATTTATTATATTT
*
1351435 ATATTTTATTATATTT
1 ATAATTTATTATATTT
1351451 -TAA-TTATTAT
1 ATAATTTATTAT
1351461 TTATATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 9 0.39
16 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATAATTTATTATATTT
Found at i:1351448 original size:18 final size:19
Alignment explanation
Indices: 1351425--1351471 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
1351415 TTTTAATAAT
1351425 TTATATATTTATATT-TTA
1 TTATATATTTATATTATTA
1351443 TTATAT-TTTA-ATTATTA
1 TTATATATTTATATTATTA
1351460 TT-TATA-TTATAT
1 TTATATATTTATAT
1351472 GTACTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.35
17 11 0.42
18 6 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATATATTTATATTATTA
Found at i:1351750 original size:10 final size:9
Alignment explanation
Indices: 1351728--1351866 Score: 57
Period size: 8 Copynumber: 16.1 Consensus size: 9
1351718 TAACGATAAA
1351728 TTTA-ATAT
1 TTTATATAT
1351736 TTTATATAT
1 TTTATATAT
1351745 TTT-TATAT
1 TTTATATAT
1351753 TTT-TATAT
1 TTTATATAT
*
1351761 TATA-ATTAT
1 TTTATA-TAT
*
1351770 GTTTAAATAT
1 -TTTATATAT
1351780 TTTATAT-T
1 TTTATATAT
* * *
1351788 TATAAAAAT
1 TTTATATAT
1351797 TTTGATATA-
1 TTT-ATATAT
1351806 -TTA-ATA-
1 TTTATATAT
*
1351812 ATT-TATAT
1 TTTATATAT
* *
1351820 TATATAAAT
1 TTTATATAT
1351829 TTTA-ATAT
1 TTTATATAT
*
1351837 TATATATAT
1 TTTATATAT
*
1351846 ATATATATTAT
1 -TTTATA-TAT
*
1351857 TTTAAATAT
1 TTTATATAT
1351866 T
1 T
1351867 AAATTTTATT
Statistics
Matches: 100, Mismatches: 17, Indels: 27
0.69 0.12 0.19
Matches are distributed among these distances:
6 3 0.03
7 6 0.06
8 34 0.34
9 34 0.34
10 19 0.19
11 4 0.04
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (9 bp):
TTTATATAT
Found at i:1351754 original size:17 final size:17
Alignment explanation
Indices: 1351732--1351845 Score: 65
Period size: 17 Copynumber: 6.8 Consensus size: 17
1351722 GATAAATTTA
1351732 ATATTTTATATATTTTT
1 ATATTTTATATATTTTT
* *
1351749 ATATTTT-TATATTATA
1 ATATTTTATATATTTTT
*
1351765 ATTATGTTTAAATA-TTTT
1 A-TAT-TTTATATATTTTT
* * *
1351783 ATATTTATAAAAATTTTG
1 ATATTT-TATATATTTTT
* *
1351801 ATATATTA-ATA-ATTT
1 ATATTTTATATATTTTT
* * *
1351816 ATATTATATAAATTTTA
1 ATATTTTATATATTTTT
*
1351833 ATATTATATATAT
1 ATATTTTATATAT
1351846 ATATATATTA
Statistics
Matches: 73, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
15 8 0.11
16 14 0.19
17 34 0.47
18 14 0.19
19 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATATTTTATATATTTTT
Found at i:1351806 original size:27 final size:25
Alignment explanation
Indices: 1351745--1351807 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
1351735 TTTTATATAT
**
1351745 TTTTATAT-TTTTATATTATAATTA
1 TTTTATATATTTTATATTATAAAAA
*
1351769 TGTTTAAATATTTTATATTTATAAAAA
1 T-TTTATATATTTTATA-TTATAAAAA
1351796 TTTTGATATATT
1 TTTT-ATATATT
1351808 AATAATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 1 0.03
25 6 0.19
26 10 0.32
27 14 0.45
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
TTTTATATATTTTATATTATAAAAA
Found at i:1351829 original size:32 final size:33
Alignment explanation
Indices: 1351775--1351836 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
1351765 ATTATGTTTA
* *
1351775 AATATTTTATATTTATAAAAATTTTGATATATT
1 AATAATTTATATTTATAAAAATTTTAATATATT
*
1351808 AATAATTTATA-TTATATAAATTTTAATAT
1 AATAATTTATATTTATAAAAATTTTAATAT
1351837 TATATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (33 bp):
AATAATTTATATTTATAAAAATTTTAATATATT
Found at i:1351851 original size:32 final size:32
Alignment explanation
Indices: 1351782--1351851 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
1351772 TTAAATATTT
1351782 TATAT-TTATAAAAATTTTGATATATTAATAA
1 TATATATTATAAAAATTTTGATATATTAATAA
* *
1351813 TTTATATTATATAAATTTT-A-ATATTATATATA
1 TATATATTATAAAAATTTTGATATATTA-ATA-A
1351845 TATATAT
1 TATATAT
1351852 ATTATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 6 0.18
31 8 0.24
32 19 0.58
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (32 bp):
TATATATTATAAAAATTTTGATATATTAATAA
Found at i:1351853 original size:17 final size:16
Alignment explanation
Indices: 1351801--1351856 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
1351791 AAAAATTTTG
1351801 ATATATTA-AT-AATT
1 ATATATTATATAAATT
1351815 -TATATTATATAAATT
1 ATATATTATATAAATT
* *
1351830 TTAATATTATATATATAT
1 AT-ATATTATATAAAT-T
1351848 ATATATTAT
1 ATATATTAT
1351857 TTTAAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 7 0.20
14 2 0.06
15 4 0.11
16 1 0.03
17 19 0.54
18 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATATTATATAAATT
Found at i:1351881 original size:34 final size:34
Alignment explanation
Indices: 1351815--1351881 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
1351805 ATTAATAATT
*
1351815 TATATTATATAAATTTTAATATTATATATATATA
1 TATATTATATAAATATTAATATTATATATATATA
* * *
1351849 TATATTATTTTAAATATTAA-ATTTTATTTATAT
1 TATATTA-TATAAATATTAATATTATATATATAT
1351882 CGTACATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATTATATAAATATTAATATTATATATATATA
Found at i:1355018 original size:2 final size:2
Alignment explanation
Indices: 1355011--1355054 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1355001 GTCTGCACAG
1355011 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
1355053 AT
1 AT
1355055 CCAAACTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1361777 original size:2 final size:2
Alignment explanation
Indices: 1361770--1361797 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1361760 AAGAAGGGAA
1361770 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
1361798 TATTTCCAAC
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:1363559 original size:32 final size:32
Alignment explanation
Indices: 1363523--1363589 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
1363513 TAAGTTTACA
* *
1363523 TATTTATAATATTATTCATCGTTTTTAAATTT
1 TATTTATAAAATTATTCATCATTTTTAAATTT
*
1363555 TATTTATAAAATTATTTATCATTTTTAAATTT
1 TATTTATAAAATTATTCATCATTTTTAAATTT
1363587 TAT
1 TAT
1363590 CTTTTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (32 bp):
TATTTATAAAATTATTCATCATTTTTAAATTT
Found at i:1364182 original size:21 final size:21
Alignment explanation
Indices: 1364151--1364198 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
1364141 AAAATAATTA
1364151 AAAATAATAAATAATTATTCTT
1 AAAA-AATAAATAATTATTCTT
*
1364173 AAAAAATAAATAATTATTTTT
1 AAAAAATAAATAATTATTCTT
1364194 AAAAA
1 AAAAA
1364199 TTTTAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAATAAATAATTATTCTT
Found at i:1364710 original size:28 final size:29
Alignment explanation
Indices: 1364668--1364727 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
1364658 ACCTTACATC
*
1364668 TAATTTATATATTTTT-TTATTTAAAA-AT
1 TAATTTAAATATTTTTATT-TTTAAAATAT
*
1364696 TAATTTAAATTTTTTTATTTTTAAAATAT
1 TAATTTAAATATTTTTATTTTTAAAATAT
1364725 TAA
1 TAA
1364728 AATTGACCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TAATTTAAATATTTTTATTTTTAAAATAT
Found at i:1366909 original size:17 final size:16
Alignment explanation
Indices: 1366887--1366923 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1366877 TATTAAATTA
*
1366887 TATTAATAATATTTTAT
1 TATTAATAA-ATTTAAT
1366904 TATTAATAAATTTAAT
1 TATTAATAAATTTAAT
1366920 TATT
1 TATT
1366924 TAAATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTAATAAATTTAAT
Found at i:1366926 original size:17 final size:18
Alignment explanation
Indices: 1366877--1366926 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
1366867 TTTTTAATTT
*
1366877 TATTAAATTATATTAATAA
1 TATTTAATTAT-TTAATAA
*
1366896 TATTTTATTA-TTAATAA
1 TATTTAATTATTTAATAA
1366913 -ATTTAATTATTTAA
1 TATTTAATTATTTAA
1366927 ATTAATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.30
17 11 0.41
19 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTAATTATTTAATAA
Found at i:1366940 original size:14 final size:15
Alignment explanation
Indices: 1366869--1366940 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 15
1366859 GTTATAAATT
1366869 TTTAATTTTATTAAA
1 TTTAATTTTATTAAA
* *
1366884 -TT-ATATTAATAATA
1 TTTAATTTTATTAA-A
* *
1366898 TTTTATTATTAATAAA
1 TTTAATT-TTATTAAA
*
1366914 TTTAATTAT-TTAAA
1 TTTAATTTTATTAAA
1366928 -TTAATTTTATTAA
1 TTTAATTTTATTAA
1366941 GTAATATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
13 15 0.33
14 11 0.24
15 3 0.07
16 9 0.20
17 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAATTTTATTAAA
Found at i:1367090 original size:21 final size:21
Alignment explanation
Indices: 1367064--1367107 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1367054 ATTCAATAAA
*
1367064 ATTAAT-ATAAATATTTTATTT
1 ATTAATAATAAA-ATTTTAATT
1367085 ATTAATAATAAAATTTTAATT
1 ATTAATAATAAAATTTTAATT
1367106 AT
1 AT
1367108 ATTATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAATAATAAAATTTTAATT
Found at i:1367135 original size:23 final size:24
Alignment explanation
Indices: 1367070--1367124 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1367060 TAAAATTAAT
*
1367070 ATAAATATTTT-ATT-TATTA-ATA
1 ATAAA-ATTTTAATTATATTATTTA
1367092 ATAAAATTTTAATTATATTATTTA
1 ATAAAATTTTAATTATATTATTTA
1367116 ATAAAATTT
1 ATAAAATTT
1367125 ACATATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.17
22 8 0.28
23 5 0.17
24 11 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATAAAATTTTAATTATATTATTTA
Found at i:1367684 original size:10 final size:10
Alignment explanation
Indices: 1367660--1367698 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
1367650 ATTTTATCTC
1367660 TTTA-ATATA
1 TTTATATATA
1367669 -TTATATATA
1 TTTATATATA
1367678 TTTATATATA
1 TTTATATATA
*
1367688 TATATATATA
1 TTTATATATA
1367698 T
1 T
1367699 ATATCCGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 3 0.11
9 5 0.19
10 19 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTATATATA
Found at i:1367716 original size:2 final size:2
Alignment explanation
Indices: 1367664--1367702 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1367654 TATCTCTTTA
*
1367664 AT AT AT -T AT AT AT AT TT 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
1367703 CCGGTGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1367758 original size:23 final size:24
Alignment explanation
Indices: 1367722--1367767 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1367712 ATATAAATAT
1367722 ATAATAAATATTAA-AATTATTTTC
1 ATAATAAATATTAATAA-TATTTTC
*
1367746 ATAATTAA-ATTAATAATATTTT
1 ATAATAAATATTAATAATATTTT
1367768 TTCTACAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
ATAATAAATATTAATAATATTTTC
Found at i:1374283 original size:93 final size:93
Alignment explanation
Indices: 1374123--1374307 Score: 325
Period size: 93 Copynumber: 2.0 Consensus size: 93
1374113 CTTCTTTGTT
*
1374123 ATTCGAGTCAAGCCTAACAGCTCGCTGAACTGCCGCCAAGGCATCGTCAAATCTTCAGACAAACA
1 ATTCGAGTCAAGCCTAACAGCTCGCTGAACCGCCGCCAAGGCATCGTCAAATCTTCAGACAAACA
1374188 TCAAGAAAACATTATTAATTAGTTGGCC
66 TCAAGAAAACATTATTAATTAGTTGGCC
* **
1374216 ATTCGAGTCAAGCCTAACAGCTCGCTGAACCGCCGCTAAGGCATCGTCAAATCTTCAGACATTCA
1 ATTCGAGTCAAGCCTAACAGCTCGCTGAACCGCCGCCAAGGCATCGTCAAATCTTCAGACAAACA
*
1374281 TCAAGAAAACATTATTAATTGGTTGGC
66 TCAAGAAAACATTATTAATTAGTTGGC
1374308 TAACAGTTAT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (93 bp):
ATTCGAGTCAAGCCTAACAGCTCGCTGAACCGCCGCCAAGGCATCGTCAAATCTTCAGACAAACA
TCAAGAAAACATTATTAATTAGTTGGCC
Found at i:1379369 original size:17 final size:17
Alignment explanation
Indices: 1379349--1379385 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1379339 AAAATTTTTG
*
1379349 ATTTATTAAATTTAAAT
1 ATTTATAAAATTTAAAT
*
1379366 ATTTATAAAATTTATAT
1 ATTTATAAAATTTAAAT
1379383 ATT
1 ATT
1379386 CAATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATAAAATTTAAAT
Found at i:1381517 original size:9 final size:9
Alignment explanation
Indices: 1381505--1381548 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
1381495 CCCAGATTTC
1381505 ATTTTTTAA
1 ATTTTTTAA
1381514 ATTTTTT-A
1 ATTTTTTAA
1381522 ATTTTTATAA
1 ATTTTT-TAA
*
1381532 AATTTTTAA
1 ATTTTTTAA
1381541 ATATTTTT
1 AT-TTTTT
1381549 TATTTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 7 0.23
9 12 0.40
10 11 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:1382970 original size:5 final size:5
Alignment explanation
Indices: 1382960--1382991 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1382950 ACATAATGTA
*
1382960 AATAT AATAT AATAT AATAT AATAT AAAAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AA
1382992 AAATAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:1382978 original size:15 final size:15
Alignment explanation
Indices: 1382960--1383004 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1382950 ACATAATGTA
*
1382960 AATATAATATAATAT
1 AATATAATATAAAAT
1382975 AATATAATATAAAAT
1 AATATAATATAAAAT
*
1382990 AAAAATAATA-AAAAT
1 -AATATAATATAAAAT
1383005 TTGATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATATAATATAAAAT
Found at i:1383038 original size:27 final size:26
Alignment explanation
Indices: 1382998--1383055 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1382988 ATAAAAATAA
* *
1382998 TAAAAATTTGATATAAATATGTATATTT
1 TAAAAATATGATAT-AATATGTAT-TAT
*
1383026 TAAAAATAT-ATATTATATGTATTAT
1 TAAAAATATGATATAATATGTATTAT
1383051 TAAAA
1 TAAAA
1383056 TATTAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.26
26 8 0.30
27 4 0.15
28 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (26 bp):
TAAAAATATGATATAATATGTATTAT
Done.