Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 10 of 22
Found at i:1241799 original size:16 final size:17
Alignment explanation
Indices: 1241778--1241809 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1241768 CATTCATGTT
1241778 TTTTTAT-TCATATTAC
1 TTTTTATGTCATATTAC
1241794 TTTTTATGTCATATTA
1 TTTTTATGTCATATTA
1241810 TATTTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.25, C:0.09, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTTATGTCATATTAC
Found at i:1241815 original size:16 final size:16
Alignment explanation
Indices: 1241780--1241817 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1241770 TTCATGTTTT
*
1241780 TTTATTCATATTACTT
1 TTTATTCATATTACTA
1241796 TTTATGTCATATTA-TA
1 TTTAT-TCATATTACTA
1241812 TTTATT
1 TTTATT
1241818 TATCATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 11 0.55
17 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTATTCATATTACTA
Found at i:1241836 original size:24 final size:25
Alignment explanation
Indices: 1241805--1241863 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
1241795 TTTTATGTCA
1241805 TATTATATTTATTTAT-CAT-ATTT
1 TATTATATTTATTTATACATAATTT
1241828 TAATTATA-TT-TTTATCACATAATTT
1 T-ATTATATTTATTTAT-ACATAATTT
1241853 TATTATATTTA
1 TATTATATTTA
1241864 AAATTATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
22 5 0.17
23 3 0.10
24 15 0.50
25 7 0.23
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTATATTTATTTATACATAATTT
Found at i:1242320 original size:29 final size:28
Alignment explanation
Indices: 1242247--1242322 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 28
1242237 TTGTTATTTG
* *
1242247 ATATTTCATGAATTTAT-ATCATATTTAT
1 ATATTTTAT-AATTTATAATCATATTTAA
*
1242275 ATATTTTATTATATTATAATCATATTTAAA
1 ATATTTTATAAT-TTATAATCATATTT-AA
1242305 ATATTTTATAATTTATAA
1 ATATTTTATAATTTATAA
1242323 AATTTTTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.05
28 12 0.29
29 15 0.37
30 12 0.29
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (28 bp):
ATATTTTATAATTTATAATCATATTTAA
Found at i:1242325 original size:19 final size:20
Alignment explanation
Indices: 1242301--1242354 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1242291 TAATCATATT
*
1242301 TAAAATATTTTATA-ATTTA
1 TAAAATATTTTATATATTAA
1242320 TAAAAT-TTTTATATATTAA
1 TAAAATATTTTATATATTAA
**
1242339 TAATTTATTTTATATA
1 TAAAATATTTTATATA
1242355 AATTTAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.23
19 14 0.47
20 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAAATATTTTATATATTAA
Found at i:1242964 original size:6 final size:6
Alignment explanation
Indices: 1242935--1242990 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
1242925 ACTCAATATT
* *
1242935 TTTAAA TATTAAA -TAAATA TTTAAA TTTAAA -TAAATA TTTAAA TTTAAA
1 TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
1242984 TTTAAA T
1 TTTAAA T
1242991 AAATAATTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 6 0.15
6 24 0.59
7 11 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:1242966 original size:18 final size:18
Alignment explanation
Indices: 1242935--1242984 Score: 91
Period size: 18 Copynumber: 2.7 Consensus size: 18
1242925 ACTCAATATT
1242935 TTTAAATATTAAATAAATA
1 TTTAAAT-TTAAATAAATA
1242954 TTTAAATTTAAATAAATA
1 TTTAAATTTAAATAAATA
1242972 TTTAAATTTAAAT
1 TTTAAATTTAAAT
1242985 TTAAATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 24 0.77
19 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAAATTTAAATAAATA
Found at i:1246243 original size:30 final size:30
Alignment explanation
Indices: 1246208--1246269 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1246198 TATATAGGTT
* *
1246208 TTAAACTTTTAATT-TTATTAAATTATATTA
1 TTAAACTTTT-ATTATTAATAAATTAAATTA
1246238 TTAAACTTTTATTATTAATAAATTAAATTA
1 TTAAACTTTTATTATTAATAAATTAAATTA
1246268 TT
1 TT
1246270 TATATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (30 bp):
TTAAACTTTTATTATTAATAAATTAAATTA
Found at i:1246252 original size:14 final size:14
Alignment explanation
Indices: 1246208--1246255 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
1246198 TATATAGGTT
1246208 TTAAACTTTTAATTTTA
1 TTAAACTTTT-A--TTA
*
1246225 TTAAA-TTATATTA
1 TTAAACTTTTATTA
1246238 TTAAACTTTTATTA
1 TTAAACTTTTATTA
1246252 TTAA
1 TTAA
1246256 TAAATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 8 0.29
14 11 0.39
15 1 0.04
16 3 0.11
17 5 0.18
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAAACTTTTATTA
Found at i:1246785 original size:22 final size:21
Alignment explanation
Indices: 1246757--1246797 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1246747 ATAAAAATAT
*
1246757 TATTTTTATATTAATATTTATA
1 TATTTTTAAATTAA-ATTTATA
1246779 TATTTTTAAATTAAATTTA
1 TATTTTTAAATTAAATTTA
1246798 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTTAAATTAAATTTATA
Found at i:1246808 original size:27 final size:27
Alignment explanation
Indices: 1246778--1246911 Score: 91
Period size: 27 Copynumber: 4.8 Consensus size: 27
1246768 TAATATTTAT
*
1246778 ATATTTTTAAATTAAATTTAAATAAAA
1 ATATTTTTAAATTTAATTTAAATAAAA
*
1246805 ATATTTTT--A-TT-ATTTAAATAATA
1 ATATTTTTAAATTTAATTTAAATAAAA
*
1246828 AT-TTAAATT-AATTTAATTTAAATAATTAA
1 ATATT--TTTAAATTTAATTTAAATAA--AA
1246857 ATATCATATTTAAATTTAATTTAATATAAAA
1 ATAT--T-TTTAAATTTAATTTAA-ATAAAA
* *
1246888 CAAATTTATTAAATTTATTTTAAA
1 -ATATTT-TTAAATTTAATTTAAA
1246912 GTATTAAAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
22 2 0.02
23 13 0.15
24 3 0.03
25 2 0.02
26 2 0.02
27 18 0.21
29 5 0.06
30 16 0.19
31 5 0.06
32 16 0.19
33 4 0.05
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (27 bp):
ATATTTTTAAATTTAATTTAAATAAAA
Found at i:1246819 original size:23 final size:23
Alignment explanation
Indices: 1246736--1246825 Score: 69
Period size: 27 Copynumber: 3.7 Consensus size: 23
1246726 AGTAAGTCTA
1246736 TTTTATTATTT--ATAAAAATAT
1 TTTTATTATTTAAATAAAAATAT
** *
1246757 TATTT-TTATATTAATATTTATATAT
1 T-TTTATTAT-TTAA-ATAAAAATAT
1246782 TTTTAAATTAAATTTAAATAAAAATAT
1 TTTT--ATT--ATTTAAATAAAAATAT
1246809 TTTTATTATTTAAATAA
1 TTTTATTATTTAAATAA
1246826 TAATTTAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
21 5 0.09
22 5 0.09
23 10 0.19
24 3 0.06
25 11 0.21
27 13 0.25
28 4 0.08
29 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTATTATTTAAATAAAAATAT
Found at i:1246831 original size:35 final size:35
Alignment explanation
Indices: 1246769--1246835 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
1246759 TTTTTATATT
*
1246769 AATATTTATATATTTTTAAATTAAATTTAAATAAA
1 AATATTTATATATTTTTAAATAAAATTTAAATAAA
1246804 AATATTT-T-TATTATTTAAATAATAATTTAAAT
1 AATATTTATATATT-TTTAAATAA-AATTTAAAT
1246836 TAATTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 4 0.14
34 9 0.31
35 16 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
AATATTTATATATTTTTAAATAAAATTTAAATAAA
Found at i:1246846 original size:15 final size:14
Alignment explanation
Indices: 1246816--1246854 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
1246806 TATTTTTATT
1246816 ATTTAAATAA--TA
1 ATTTAAATAATTTA
1246828 ATTTAAATTAATTTA
1 ATTTAAA-TAATTTA
1246843 ATTTAAATAATT
1 ATTTAAATAATT
1246855 AAATATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.29
13 3 0.12
14 5 0.21
15 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTAAATAATTTA
Found at i:1249432 original size:2 final size:2
Alignment explanation
Indices: 1249425--1249461 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1249415 TGATCTTCCC
1249425 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1249462 GATGGATCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1250261 original size:2 final size:2
Alignment explanation
Indices: 1250256--1250280 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1250246 AAAAAAAATG
1250256 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
1250281 ACGAAATTCA
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:1253509 original size:16 final size:16
Alignment explanation
Indices: 1253487--1253529 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
1253477 TCATGTAAAA
1253487 TTAATTAATTTTATA-
1 TTAATTAATTTTATAC
1253502 TATAATTATAATTTTATAC
1 T-TAA-T-TAATTTTATAC
1253521 TTAATTAAT
1 TTAATTAAT
1253530 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 1 0.04
16 7 0.29
17 2 0.08
18 13 0.54
19 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATTAATTTTATAC
Found at i:1253609 original size:18 final size:18
Alignment explanation
Indices: 1253494--1253640 Score: 72
Period size: 18 Copynumber: 7.9 Consensus size: 18
1253484 AAATTAATTA
*
1253494 ATTTTATATATAATT-AT
1 ATTTTATATTTAATTAAT
*
1253511 AATTTTATACTTAATTAAT
1 -ATTTTATATTTAATTAAT
* *
1253530 ATTTTAAAATTTTAATTATTT
1 ATTTT-ATA-TTTAATTA-AT
* *
1253551 AATTTAATAATATAATT-AT
1 -ATTTTAT-ATTTAATTAAT
** *
1253570 A-TTTATTATTTACGTAAA
1 ATTTTA-TATTTAATTAAT
1253588 ATTTTATATTTAATTAAT
1 ATTTTATATTTAATTAAT
1253606 ATTTTA-A-TT-ATTAAAT
1 ATTTTATATTTAATT-AAT
*
1253622 ATATTTTTATTTATATTAA
1 AT-TTTATATTTA-ATTAA
1253641 AAAATTAAAA
Statistics
Matches: 96, Mismatches: 18, Indels: 28
0.68 0.13 0.20
Matches are distributed among these distances:
15 3 0.03
16 7 0.07
17 12 0.12
18 38 0.40
19 11 0.11
20 9 0.09
21 11 0.11
22 5 0.05
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (18 bp):
ATTTTATATTTAATTAAT
Found at i:1254597 original size:17 final size:18
Alignment explanation
Indices: 1254577--1254613 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1254567 TTGATTTGTA
*
1254577 TTTAAATAA-AATTTTAT
1 TTTAAATAATAAATTTAT
1254594 TTTAAATAATAAATTTAT
1 TTTAAATAATAAATTTAT
1254612 TT
1 TT
1254614 ATGTTTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAATAATAAATTTAT
Found at i:1256116 original size:17 final size:15
Alignment explanation
Indices: 1256094--1256132 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1256084 TACTGCATAA
1256094 TTTATAAATAAATAATT
1 TTTATAAAT--ATAATT
*
1256111 TTTATAAATTTAATT
1 TTTATAAATATAATT
1256126 TTTATAA
1 TTTATAA
1256133 TTTAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
17 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTATAAATATAATT
Found at i:1256134 original size:14 final size:15
Alignment explanation
Indices: 1256106--1256137 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1256096 TATAAATAAA
1256106 TAATTTTTATAAATT
1 TAATTTTTATAAATT
1256121 TAATTTTTAT-AATT
1 TAATTTTTATAAATT
1256135 TAA
1 TAA
1256138 AATAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATTTTTATAAATT
Found at i:1256151 original size:21 final size:20
Alignment explanation
Indices: 1256127--1256179 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1256117 AATTTAATTT
*
1256127 TTATAATTTAAAATAATTATA
1 TTATAATTTAAAATAA-TAAA
*
1256148 TTATTATTTAAAAATAATAAA
1 TTATAATTT-AAAATAATAAA
*
1256169 TAATAATTTAA
1 TTATAATTTAA
1256180 TAAAATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.07
21 18 0.67
22 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATAATTTAAAATAATAAA
Found at i:1256190 original size:10 final size:11
Alignment explanation
Indices: 1256129--1256190 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 11
1256119 TTTAATTTTT
1256129 ATAATTTAA-A
1 ATAATTTAATA
*
1256139 ATAA-TTATATT
1 ATAATTTA-ATA
* *
1256150 ATTATTTAAAA
1 ATAATTTAATA
*
1256161 ATAA-TAAATA
1 ATAATTTAATA
1256171 ATAATTTAATA
1 ATAATTTAATA
1256182 A-AATTTAAT
1 ATAATTTAAT
1256191 TTTAAATTAC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
9 3 0.08
10 21 0.52
11 13 0.32
12 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATTTAATA
Found at i:1257628 original size:2 final size:2
Alignment explanation
Indices: 1257621--1257650 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1257611 TTTAAAACGA
1257621 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
1257651 CAAATATAAA
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:1261007 original size:2 final size:2
Alignment explanation
Indices: 1261002--1261029 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1260992 TAGATGAAGA
1261002 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
1261030 TTAAAATTTG
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:1270009 original size:14 final size:13
Alignment explanation
Indices: 1269981--1270019 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1269971 ATAATATTTA
1269981 TTAAATTTAATAT
1 TTAAATTTAATAT
*
1269994 TTAAATTTTATCAT
1 TTAAATTTAAT-AT
1270008 TTATAATTTAAT
1 TTA-AATTTAAT
1270020 CTTTTTATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 5 0.23
15 7 0.32
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATTTAATAT
Found at i:1270514 original size:3 final size:3
Alignment explanation
Indices: 1270508--1270534 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1270498 AACAAAAGCG
1270508 GCA GCA GCA GCA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA
1270535 ACTGCATAAA
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:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:1273303 original size:76 final size:76
Alignment explanation
Indices: 1273071--1273378 Score: 334
Period size: 76 Copynumber: 4.0 Consensus size: 76
1273061 GTTCATCTAC
* * * *
1273071 AAGCTATTGTCATG-GTTTGAAGCTCAAGTTTTAAGCTTGTGTGGAAGACCGACTCTCAGAGTTT
1 AAGCTATTGTCATGAG-TCGAAACTCAAGTTTTAAGCTTGTGCGGAAGATCGACTCTCAGA-TTT
*
1273135 AACGCTTATATAT
64 AACACTTATATAT
* * * * *
1273148 AAGCTCTTGTCATGAGTCGAAACTCTGAGTTTTAAGCTTGTGCGGAAGATCAACTCTCAAAGTTA
1 AAGCTATTGTCATGAGTCGAAACTC-AAGTTTTAAGCTTGTGCGGAAGATCGACTCTCAGATTTA
* *
1273213 ACGCTTATAAAT
65 ACACTTATATAT
* * *
1273225 AAGCTCTTGTCATGAGTCGAAACTCGAGTTTTAAGCTTGTGCGGAAGATCGACTCTCGGATTTAA
1 AAGCTATTGTCATGAGTCGAAACTCAAGTTTTAAGCTTGTGCGGAAGATCGACTCTCAGATTTAA
*
1273290 CACTTACATAT
66 CACTTATATAT
* * * * * **
1273301 AAGCTATTGTCA-CAGGCAGAAACTCAAGTTTTAAGCTTATGTGG-AGAACAGACTCTTGGATCT
1 AAGCTATTGTCATGAGTC-GAAACTCAAGTTTTAAGCTTGTGCGGAAGATC-GACTCTCAGAT-T
1273364 TAACACTTATATAT
63 TAACACTTATATAT
1273378 A
1 A
1273379 GGCAATTTAA
Statistics
Matches: 200, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
75 7 0.04
76 88 0.44
77 74 0.37
78 31 0.16
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (76 bp):
AAGCTATTGTCATGAGTCGAAACTCAAGTTTTAAGCTTGTGCGGAAGATCGACTCTCAGATTTAA
CACTTATATAT
Found at i:1278440 original size:4 final size:4
Alignment explanation
Indices: 1278431--1278459 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1278421 AATATCTTTT
1278431 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1278460 AGTAATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1279156 original size:18 final size:17
Alignment explanation
Indices: 1279135--1279183 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1279125 TAATTTTTTT
*
1279135 ATTTATTTTAATATAAAA
1 ATTTATATT-ATATAAAA
*
1279153 ATTTATATTATATAAAT
1 ATTTATATTATATAAAA
*
1279170 ATTAATATGTATAT
1 ATTTATAT-TATAT
1279184 GTATTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTTATATTATATAAAA
Found at i:1280601 original size:20 final size:18
Alignment explanation
Indices: 1280565--1280603 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1280555 TTTTCCATAT
*
1280565 ATTAAAAAATATTTTTAA
1 ATTAAAAAATATATTTAA
1280583 ATTAAAAAATAAATATTTAA
1 ATTAAAAAAT--ATATTTAA
1280603 A
1 A
1280604 ATTTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
20 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAAAAAATATATTTAA
Found at i:1281147 original size:6 final size:6
Alignment explanation
Indices: 1281124--1281159 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1281114 GGTTCTTTTT
* *
1281124 CTCTTT CTCTTC CTCTTC CTCTTC GTCTTC CTCTTC
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
1281160 TGCGAGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (6 bp):
CTCTTC
Found at i:1290447 original size:37 final size:35
Alignment explanation
Indices: 1290406--1290495 Score: 85
Period size: 35 Copynumber: 2.5 Consensus size: 35
1290396 TTAATTTTAT
*
1290406 TATTTAAAATTATA-TTAAAAAATTAATTTTATATTAA
1 TATTTAAAATTAAATTTAAAAAA--AATTTT-TATTAA
** * *
1290443 TATTTTTAATTAAATTTAAATAAAATTTTTATTAT
1 TATTTAAAATTAAATTTAAAAAAAATTTTTATTAA
*
1290478 TATTTAAAAAT-AATTTAA
1 TATTTAAAATTAAATTTAA
1290496 TTTAAATTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
34 7 0.16
35 13 0.30
36 6 0.14
37 11 0.25
38 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TATTTAAAATTAAATTTAAAAAAAATTTTTATTAA
Found at i:1290453 original size:24 final size:23
Alignment explanation
Indices: 1290426--1290473 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1290416 TATATTAAAA
* * *
1290426 AATTAATTTTATATTAATATTTTT
1 AATTAAATTTA-AATAAAATTTTT
1290450 AATTAAATTTAAATAAAATTTTT
1 AATTAAATTTAAATAAAATTTTT
1290473 A
1 A
1290474 TTATTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTAAATTTAAATAAAATTTTT
Found at i:1290455 original size:32 final size:33
Alignment explanation
Indices: 1290384--1290456 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
1290374 CAAGTTTAGA
*
1290384 TTAATTTAAAAATTAATTTTATTATTTAAAATT
1 TTAATTAAAAAATTAATTTTATTATTTAAAATT
* *
1290417 AT-ATTAAAAAATTAATTTTA-TA-TTAATATTT
1 TTAATTAAAAAATTAATTTTATTATTTAA-AATT
1290448 TTAATTAAA
1 TTAATTAAA
1290457 TTTAAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
30 4 0.12
31 6 0.18
32 23 0.68
33 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TTAATTAAAAAATTAATTTTATTATTTAAAATT
Found at i:1295883 original size:2 final size:2
Alignment explanation
Indices: 1295876--1295904 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1295866 TCCACCACCC
1295876 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1295905 CTAGTTCTGC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1299953 original size:16 final size:15
Alignment explanation
Indices: 1299928--1299958 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1299918 GATAATTTTG
1299928 TTTTTAAAAAATATA
1 TTTTTAAAAAATATA
1299943 TTTTTATAAAAATATA
1 TTTTTA-AAAAATATA
1299959 AAATCACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTTAAAAAATATA
Found at i:1300725 original size:2 final size:2
Alignment explanation
Indices: 1300718--1300753 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1300708 CATACGAATA
1300718 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
1300754 TATTACACCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1303429 original size:13 final size:14
Alignment explanation
Indices: 1303385--1303447 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 14
1303375 CCAACATGTC
*
1303385 AATATAAAAATAAA
1 AATATAAATATAAA
* *
1303399 TAAGATATATAATAAA
1 -AATATAAAT-ATAAA
1303415 AA-ATAAATTATAAA
1 AATATAAA-TATAAA
1303429 AATAATAAATATAAA
1 AAT-ATAAATATAAA
1303444 AATA
1 AATA
1303448 CAAAAATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 12 0.30
15 18 0.45
16 10 0.25
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
AATATAAATATAAA
Found at i:1303911 original size:13 final size:13
Alignment explanation
Indices: 1303893--1303917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1303883 TTTTATTTAA
1303893 TTTTAAATATATT
1 TTTTAAATATATT
1303906 TTTTAAATATAT
1 TTTTAAATATAT
1303918 AATGTTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATATT
Found at i:1305029 original size:20 final size:21
Alignment explanation
Indices: 1305006--1305044 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1304996 ACTTTACGTA
* *
1305006 TAAATTTAGATAA-ATTTTAG
1 TAAACTTAAATAATATTTTAG
1305026 TAAACTTAAATAATATTTT
1 TAAACTTAAATAATATTTT
1305045 TACATATAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (21 bp):
TAAACTTAAATAATATTTTAG
Found at i:1307033 original size:14 final size:15
Alignment explanation
Indices: 1307005--1307033 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1306995 AATTCAACTC
1307005 TTTATACATAAAATA
1 TTTATACATAAAATA
1307020 TTTATACA-AAAATA
1 TTTATACATAAAATA
1307034 CAACATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTATACATAAAATA
Found at i:1310405 original size:16 final size:17
Alignment explanation
Indices: 1310379--1310412 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1310369 ATTATTATAT
1310379 GAGTGTTTAAAAAAAAA
1 GAGTGTTTAAAAAAAAA
1310396 GAGT-TTTAAAAAAAAA
1 GAGTGTTTAAAAAAAAA
1310412 G
1 G
1310413 TTATTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.24
Consensus pattern (17 bp):
GAGTGTTTAAAAAAAAA
Found at i:1312361 original size:2 final size:2
Alignment explanation
Indices: 1312354--1312397 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1312344 ACATGCATAC
1312354 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
1312396 AT
1 AT
1312398 GTGTGTGTGT
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:1315773 original size:63 final size:64
Alignment explanation
Indices: 1315701--1315831 Score: 183
Period size: 64 Copynumber: 2.1 Consensus size: 64
1315691 CCTTAAATTA
* * * * *
1315701 TTTTATATTTCA-TTTTTATCTGTAACAGAAAATTAATTAATTTAATCGCTGACTTTTTATATT
1 TTTTATATTTCATTTTTTACCTATAACAGAAAATTAATTAACTTAATCACTGACTTTTTATACT
* * *
1315764 TTTTATATTTTATTTTTTACCTATAACAGAAAATTGATTAACTTAATCACTGGCTTTTTATACT
1 TTTTATATTTCATTTTTTACCTATAACAGAAAATTAATTAACTTAATCACTGACTTTTTATACT
1315828 TTTT
1 TTTT
1315832 GAATTTTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
63 11 0.19
64 48 0.81
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.53
Consensus pattern (64 bp):
TTTTATATTTCATTTTTTACCTATAACAGAAAATTAATTAACTTAATCACTGACTTTTTATACT
Found at i:1322864 original size:83 final size:84
Alignment explanation
Indices: 1322755--1322923 Score: 243
Period size: 86 Copynumber: 2.0 Consensus size: 84
1322745 TGCAATAAAT
* * * *
1322755 TATGGGATTATGAGGCTGGTATAAAGGTGCTATGTCT-G-AAAAAAATGTCAAATAATGTATGGT
1 TATGGGACTATGAGGCTGGGAAAAAGGTGCTATGTCTAGAAAAAAAATGTCAAATAATATATGGT
1322818 GTTCATTACCTTATCTGTAC
66 GTTCATTACCTTAT-TGTAC
* *
1322838 TATGGGACTATGAGGCTGGGAAAAAGGTGCTATGTTTAGAAAAAAAAATGTTAAATAATATATGG
1 TATGGGACTATGAGGCTGGGAAAAAGGTGCTATGTCTAG-AAAAAAAATGTCAAATAATATATGG
*
1322903 TGTTCATTACCTTGTTGTAC
65 TGTTCATTACCTTATTGTAC
1322923 T
1 T
1322924 GTATTCAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
83 33 0.43
84 1 0.01
85 6 0.08
86 36 0.47
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.34
Consensus pattern (84 bp):
TATGGGACTATGAGGCTGGGAAAAAGGTGCTATGTCTAGAAAAAAAATGTCAAATAATATATGGT
GTTCATTACCTTATTGTAC
Found at i:1324661 original size:22 final size:22
Alignment explanation
Indices: 1324614--1324667 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
1324604 AGGGGAATTT
* * *
1324614 TTTAAATTTATTTTTATTTAAT
1 TTTAAATATATTTTTATTAAAA
1324636 TTTAAATATATATTTT-TTAAAA
1 TTTAAATATAT-TTTTATTAAAA
1324658 TTTATAATAT
1 TTTA-AATAT
1324668 TATAAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTAAATATATTTTTATTAAAA
Found at i:1325452 original size:2 final size:2
Alignment explanation
Indices: 1325447--1325478 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1325437 CCGCACACAA
1325447 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
1325479 GTCGATGCTG
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:1325743 original size:41 final size:41
Alignment explanation
Indices: 1325697--1325802 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
1325687 ATTAATATAA
1325697 ATTTTTAACAGAAATCAATCTTTCACTAAGAATGAATGATTC
1 ATTTTTAACAGAAATCAATCTTTCACTAAGAATGAATGA-TC
* * *** *
1325739 TTTTTTAATA-ACAATCAAT-TTTTTTTAAGAATGATTGATC
1 ATTTTTAACAGA-AATCAATCTTTCACTAAGAATGAATGATC
* *
1325779 ATTTTTAAGAGATATCAATCTTTC
1 ATTTTTAACAGAAATCAATCTTTC
1325803 TACGTATAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
40 16 0.31
41 20 0.39
42 15 0.29
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.43
Consensus pattern (41 bp):
ATTTTTAACAGAAATCAATCTTTCACTAAGAATGAATGATC
Found at i:1325830 original size:10 final size:10
Alignment explanation
Indices: 1325808--1325846 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1325798 CTTTCTACGT
1325808 ATAAATTTAA
1 ATAAATTTAA
* *
1325818 ATAGATTTGA
1 ATAAATTTAA
1325828 ATAAATTTAA
1 ATAAATTTAA
1325838 ATAATATTT
1 ATAA-ATTT
1325847 TACACATTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (10 bp):
ATAAATTTAA
Found at i:1326088 original size:61 final size:61
Alignment explanation
Indices: 1326017--1326137 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 61
1326007 ATTATTCCAG
* * *
1326017 GACAATACAACCAACTTTTTTAGGTTCATTATTGATATATATCGAACA-ATATTTGGATTGA
1 GACAAAACAACCAACATTTTTAGGTTCATTATTGATATATATC-AAAATATATTTGGATTGA
1326078 GACAAAACAACCAACATTTTTAGGTTCATTATTGATATATATCAAAATTATATTTGGATT
1 GACAAAACAACCAACATTTTTAGGTTCATTATTGATATATATCAAAA-TATATTTGGATT
1326138 AGTCTCAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
60 3 0.05
61 41 0.75
62 11 0.20
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (61 bp):
GACAAAACAACCAACATTTTTAGGTTCATTATTGATATATATCAAAATATATTTGGATTGA
Found at i:1326897 original size:28 final size:28
Alignment explanation
Indices: 1326838--1326907 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
1326828 CCACTCATTT
*
1326838 ATTTGTCAAAAATAGTGGTTATTTTGTG
1 ATTTGTCAAAAATGGTGGTTATTTTGTG
1326866 -TTTGTCAAAAATGGTGGTT-TCCTTTG-G
1 ATTTGTCAAAAATGGTGGTTAT--TTTGTG
*
1326893 ATTTGTCAAATATGG
1 ATTTGTCAAAAATGG
1326908 AGGCTTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
26 1 0.03
27 19 0.51
28 17 0.46
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGGTTATTTTGTG
Found at i:1329511 original size:21 final size:22
Alignment explanation
Indices: 1329482--1329527 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1329472 TGTTCAGACA
** *
1329482 AGTAGTACTCCGTAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1329504 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1329525 AGT
1 AGT
1329528 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1334666 original size:17 final size:18
Alignment explanation
Indices: 1334633--1334666 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1334623 TAAAAAGAAA
1334633 AAAATGCTTAGAAAATTT
1 AAAATGCTTAGAAAATTT
*
1334651 AAAATG-TTATAAAATT
1 AAAATGCTTAGAAAATT
1334667 ATACGGAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (18 bp):
AAAATGCTTAGAAAATTT
Found at i:1335814 original size:21 final size:21
Alignment explanation
Indices: 1335789--1335830 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1335779 ACCATCATCT
1335789 GATAAAACCGTGTTCATCACC
1 GATAAAACCGTGTTCATCACC
1335810 GATAAAACCGTGTTCATCACC
1 GATAAAACCGTGTTCATCACC
1335831 ATGCTTGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (21 bp):
GATAAAACCGTGTTCATCACC
Found at i:1340955 original size:2 final size:2
Alignment explanation
Indices: 1340950--1341001 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1340940 AAAGTAAAAG
1340950 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
1340992 AT AT AT AT AT
1 AT AT AT AT AT
1341002 CCACACCTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1343808 original size:85 final size:84
Alignment explanation
Indices: 1343699--1343868 Score: 252
Period size: 85 Copynumber: 2.0 Consensus size: 84
1343689 CAATAAATTA
* * * *
1343699 TGGGATTATGAGGCTGGTATAAAGGTGCTCTGTTTA-AAAAAAAATTGTCAAATAATGTACGGTG
1 TGGGACTATGAGGCTGGTAAAAAGGTGCTATGTTTAGAAAAAAAAATGTCAAATAATGT-CGGTG
1343763 TTCATTACCTTATCTGTACTG
65 TTCATTACCTTAT-TGTACTG
* *
1343784 TGGGACTATGAGGCTGGTAAAAAGGTGCTATGTTTAGAAAAAAAAATGTTAAATAATGTTGGTGT
1 TGGGACTATGAGGCTGGTAAAAAGGTGCTATGTTTAGAAAAAAAAATGTCAAATAATGTCGGTGT
*
1343849 TCATTACCTTGTTGTACTG
66 TCATTACCTTATTGTACTG
1343868 T
1 T
1343869 ATTCGAATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
84 8 0.10
85 49 0.64
86 20 0.26
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (84 bp):
TGGGACTATGAGGCTGGTAAAAAGGTGCTATGTTTAGAAAAAAAAATGTCAAATAATGTCGGTGT
TCATTACCTTATTGTACTG
Found at i:1344371 original size:14 final size:15
Alignment explanation
Indices: 1344329--1344377 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 15
1344319 AATATTTAAA
1344329 ATTAAAA-TTTAATT
1 ATTAAAATTTTAATT
1344343 ATTAAATACTTTTAATT
1 ATTAAA-A-TTTTAATT
1344360 -TTAAAATTTTAATAT
1 ATTAAAATTTTAAT-T
1344375 ATT
1 ATT
1344378 TTAATTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 13 0.43
15 3 0.10
16 7 0.23
17 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTAAAATTTTAATT
Found at i:1346306 original size:2 final size:2
Alignment explanation
Indices: 1346301--1346348 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1346291 GCACACAAAC
1346301 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
1346343 AT AT AT
1 AT AT AT
1346349 GTGTGTGTGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1346353 original size:2 final size:2
Alignment explanation
Indices: 1346348--1346377 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1346338 TATATATATA
1346348 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1346378 GCGATGCCGG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1346663 original size:64 final size:61
Alignment explanation
Indices: 1346595--1346718 Score: 176
Period size: 64 Copynumber: 2.0 Consensus size: 61
1346585 AATTATTCCA
* * * *
1346595 AGACAACACAACCAACTTTTTTAGGTTCATTATTGATATATATCATCAAACAATATTTGGATTG
1 AGACAAAACAACCAACATTTTTAGGTACATAATTG--ATATAT-ATCAAACAATATTTGGATTG
*
1346659 AGACAAAACAACCAACATTTTTAGGTACATAATTGATATATGTCAAACAATATTTGGATT
1 AGACAAAACAACCAACATTTTTAGGTACATAATTGATATATATCAAACAATATTTGGATT
1346719 AGTCTCAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 18 0.33
62 6 0.11
64 31 0.56
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (61 bp):
AGACAAAACAACCAACATTTTTAGGTACATAATTGATATATATCAAACAATATTTGGATTG
Found at i:1347732 original size:14 final size:16
Alignment explanation
Indices: 1347703--1347734 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1347693 AATGAAAAAT
1347703 AAATCCATTGTTCCAA
1 AAATCCATTGTTCCAA
1347719 AAAT-CATT-TTCCAA
1 AAATCCATTGTTCCAA
1347733 AA
1 AA
1347735 CTTTTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (16 bp):
AAATCCATTGTTCCAA
Found at i:1351484 original size:5 final size:5
Alignment explanation
Indices: 1351471--1351501 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1351461 AGACAGCCAG
*
1351471 AGATG AGATT AGATT AGATT AGATT AGATT A
1 AGATT AGATT AGATT AGATT AGATT AGATT A
1351502 CCCACTTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (5 bp):
AGATT
Found at i:1356407 original size:14 final size:13
Alignment explanation
Indices: 1356384--1356417 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1356374 AATTTAATTT
1356384 AATTTAAATTTTA
1 AATTTAAATTTTA
1356397 AATTATAAATTTTA
1 AATT-TAAATTTTA
*
1356411 AAATTAA
1 AATTTAA
1356418 TTTGAGCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTAAATTTTA
Found at i:1357082 original size:22 final size:21
Alignment explanation
Indices: 1357033--1357082 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
1357023 TAAAAGAATC
1357033 ATTAAT-AATTTAATTTAAAA
1 ATTAATAAATTTAATTTAAAA
*
1357053 ATCT--TAAATTTAAATTTTAAA
1 AT-TAATAAATTT-AATTTAAAA
1357074 ATTAATAAA
1 ATTAATAAA
1357083 AAAAAAGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
19 1 0.04
20 8 0.33
21 11 0.46
22 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAATAAATTTAATTTAAAA
Found at i:1358681 original size:27 final size:26
Alignment explanation
Indices: 1358628--1358679 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
1358618 TTATAATTTA
*
1358628 ATTAATAAAAATATTTTTAATTAAAT
1 ATTAATAAAAATATTTTTAAATAAAT
1358654 ATTAATATAAAATATTTTTTAAATAA
1 ATTAATA-AAAATA-TTTTTAAATAA
1358680 TAAAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 6 0.26
28 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTAATAAAAATATTTTTAAATAAAT
Found at i:1358684 original size:19 final size:20
Alignment explanation
Indices: 1358660--1358697 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1358650 AAATATTAAT
1358660 ATAAAAT-ATTTTTTAAATA
1 ATAAAATAATTTTTTAAATA
1358679 ATAAAATAATTTTTTAAAT
1 ATAAAATAATTTTTTAAAT
1358698 TTATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAATAATTTTTTAAATA
Found at i:1358686 original size:26 final size:26
Alignment explanation
Indices: 1358631--1358687 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
1358621 TAATTTAATT
* *
1358631 AATAAAAATATTTTTAATTAAATATT
1 AATAAAAATATTTTTAAATAAATATA
1358657 AATATAAAATATTTTTTAAAT-AATA-A
1 AATA-AAAATA-TTTTTAAATAAATATA
1358683 AATAA
1 AATAA
1358688 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 1 0.04
26 8 0.30
27 10 0.37
28 8 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATAAAAATATTTTTAAATAAATATA
Found at i:1362933 original size:24 final size:23
Alignment explanation
Indices: 1362918--1362961 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
1362908 TATAATTTAT
1362918 AATATAT-ATTAATTTATATTTT
1 AATATATCATTAATTTATATTTT
* *
1362940 TATATATCATATAATTTTTATT
1 AATATATCAT-TAATTTATATT
1362962 ATACAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 2 0.11
24 10 0.56
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
AATATATCATTAATTTATATTTT
Found at i:1363049 original size:14 final size:13
Alignment explanation
Indices: 1363027--1363074 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 13
1363017 ATTTAATGAA
1363027 AAAATATTAAATATT
1 AAAA-ATTAAAT-TT
1363042 AAAAATTAAATTTTT
1 AAAAATTAAA--TTT
*
1363057 AAAAAATAAATTT
1 AAAAATTAAATTT
1363070 AAAAA
1 AAAAA
1363075 ATAATATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 8 0.27
14 6 0.20
15 15 0.50
16 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAAATTAAATTT
Found at i:1363058 original size:15 final size:15
Alignment explanation
Indices: 1363027--1363069 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1363017 ATTTAATGAA
*
1363027 AAAATATTAAA-TATT
1 AAAA-ATTAAATTTTT
1363042 AAAAATTAAATTTTT
1 AAAAATTAAATTTTT
*
1363057 AAAAAATAAATTT
1 AAAAATTAAATTT
1363070 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAATTAAATTTTT
Found at i:1365839 original size:6 final size:6
Alignment explanation
Indices: 1365824--1365888 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
1365814 TAATTCAAAA
* * *
1365824 AAATTC AAATAT AAATTT AAATTT AAATTT -AATTT -AATTT AACAATAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -A-AATTT
*
1365872 AAATTT ATTATTT AAAT
1 AAATTT A-AATTT AAAT
1365889 ATATTAAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
5 10 0.21
6 28 0.58
7 6 0.12
8 4 0.08
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:1365851 original size:18 final size:18
Alignment explanation
Indices: 1365824--1365891 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
1365814 TAATTCAAAA
*
1365824 AAATTCAAATATAAATTT
1 AAATTTAAATATAAATTT
*
1365842 AAATTTAAAT-TTAATTT
1 AAATTTAAATATAAATTT
1365859 -AATTTAACAATATAAATTT
1 AAATTT-A-AATATAAATTT
*
1365878 ATTATTTAAATATA
1 A-AATTTAAATATA
1365892 TTAAAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
16 5 0.12
17 7 0.17
18 12 0.29
19 12 0.29
20 1 0.02
21 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTTAAATATAAATTT
Found at i:1365964 original size:21 final size:20
Alignment explanation
Indices: 1365940--1365978 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1365930 ATATTTTATA
1365940 ATTTAATTTAAATAAAATATT
1 ATTTAATTT-AATAAAATATT
* *
1365961 ATTTTATTTTATAAAATA
1 ATTTAATTTAATAAAATA
1365979 ATAATTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAATTTAATAAAATATT
Found at i:1366737 original size:2 final size:2
Alignment explanation
Indices: 1366730--1366759 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1366720 AGATTAGAAA
1366730 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1366760 ATTCATCAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1369071 original size:13 final size:13
Alignment explanation
Indices: 1369020--1369076 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1369010 AGTTTAATTT
*
1369020 ATGAATTAA-TTT
1 ATGAATTAAGTTC
* *
1369032 ATGAGTTCAGTTC
1 ATGAATTAAGTTC
*
1369045 ATGAATT-CGATTC
1 ATGAATTAAG-TTC
1369058 ATGAATTAAGTTC
1 ATGAATTAAGTTC
1369071 ATGAAT
1 ATGAAT
1369077 ATAATTTATG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
12 8 0.22
13 27 0.75
14 1 0.03
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (13 bp):
ATGAATTAAGTTC
Found at i:1369160 original size:21 final size:21
Alignment explanation
Indices: 1369128--1369168 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1369118 ATGGATTTTT
1369128 GTTTAACGTTTATGA-TTTATG
1 GTTTAACGTTTA-GAGTTTATG
1369149 GTTTATAC-TTTAGAGTTTAT
1 GTTTA-ACGTTTAGAGTTTAT
1369169 TGTTATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.11
21 14 0.78
22 2 0.11
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (21 bp):
GTTTAACGTTTAGAGTTTATG
Found at i:1369200 original size:15 final size:17
Alignment explanation
Indices: 1369175--1369206 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1369165 TTATTGTTAT
1369175 TAAGTGTTTAG-GTTTC
1 TAAGTGTTTAGAGTTTC
1369191 TAAG-GTTTAGAGTTTC
1 TAAGTGTTTAGAGTTTC
1369207 ATGAGTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.22, C:0.06, G:0.25, T:0.47
Consensus pattern (17 bp):
TAAGTGTTTAGAGTTTC
Found at i:1369363 original size:13 final size:13
Alignment explanation
Indices: 1369345--1369397 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
1369335 AATCAAGTTT
1369345 ATAAATTTAATTC
1 ATAAATTTAATTC
*
1369358 ATAAATTTAATTT
1 ATAAATTTAATTC
* *
1369371 ATAAATTCAAATC
1 ATAAATTTAATTC
* *
1369384 ATATATTTATTTC
1 ATAAATTTAATTC
1369397 A
1 A
1369398 AATTTACAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAAATTTAATTC
Found at i:1369371 original size:26 final size:26
Alignment explanation
Indices: 1369342--1369392 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1369332 AAGAATCAAG
* *
1369342 TTTATAAATTTAATTCATAAATTTAA
1 TTTATAAATTCAAATCATAAATTTAA
*
1369368 TTTATAAATTCAAATCATATATTTA
1 TTTATAAATTCAAATCATAAATTTA
1369393 TTTCAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTATAAATTCAAATCATAAATTTAA
Found at i:1377027 original size:2 final size:2
Alignment explanation
Indices: 1377015--1377059 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
1377005 ACATAGGGTA
* * * *
1377015 AT AT AT TT AT AT AT TT AT AT AT AT AT AT AC AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1377057 AT A
1 AT A
1377060 AAAAAAGGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1378858 original size:13 final size:13
Alignment explanation
Indices: 1378840--1378866 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1378830 AGCAAGAATC
1378840 CTTCAAACTTCTT
1 CTTCAAACTTCTT
1378853 CTTCAAACTTCTT
1 CTTCAAACTTCTT
1378866 C
1 C
1378867 ATTCCTAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (13 bp):
CTTCAAACTTCTT
Found at i:1384715 original size:11 final size:11
Alignment explanation
Indices: 1384694--1384753 Score: 53
Period size: 11 Copynumber: 6.1 Consensus size: 11
1384684 TTTAAAATAT
1384694 TATAA-ATTTA
1 TATAATATTTA
1384704 TATAATATTTA
1 TATAATATTTA
*
1384715 TAAAATATTT-
1 TATAATATTTA
1384725 T-T-ATATTT-
1 TATAATATTTA
1384733 T-T-ATATTTA
1 TATAATATTTA
*
1384742 TATCATATTTA
1 TATAATATTTA
1384753 T
1 T
1384754 TTTTTGTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
8 14 0.32
9 1 0.02
10 7 0.16
11 22 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TATAATATTTA
Found at i:1384732 original size:8 final size:8
Alignment explanation
Indices: 1384719--1384765 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
1384709 TATTTATAAA
1384719 ATATTTTT
1 ATATTTTT
1384727 ATATTTTT
1 ATATTTTT
*
1384735 ATATTTAT
1 ATATTTTT
*
1384743 ATCATATTT
1 AT-ATTTTT
1384752 AT-TTTTT
1 ATATTTTT
*
1384759 GTATTTT
1 ATATTTT
1384766 ATTTTAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
7 5 0.16
8 21 0.66
9 6 0.19
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (8 bp):
ATATTTTT
Found at i:1384917 original size:21 final size:21
Alignment explanation
Indices: 1384877--1384940 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
1384867 TTTTGACATA
*
1384877 TTCATA-TATTTATT-TTATG
1 TTCATATTATTTTTTATTATG
1384896 TTCATATTATTTTTTATTATG
1 TTCATATTATTTTTTATTATG
*
1384917 TT-TTAATTATTTTTTATTTATG
1 TTCAT-ATTATTTTTTA-TTATG
1384939 TT
1 TT
1384941 GTGTTAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.15
20 8 0.21
21 18 0.46
22 7 0.18
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (21 bp):
TTCATATTATTTTTTATTATG
Found at i:1384937 original size:11 final size:10
Alignment explanation
Indices: 1384900--1384934 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1384890 TTTATGTTCA
1384900 TATTATTTTT
1 TATTATTTTT
1384910 TATTATGTTTT
1 TATTAT-TTTT
*
1384921 AATTATTTTT
1 TATTATTTTT
1384931 TATT
1 TATT
1384935 TATGTTGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (10 bp):
TATTATTTTT
Found at i:1385210 original size:18 final size:18
Alignment explanation
Indices: 1385187--1385225 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1385177 TAATATTATG
*
1385187 TATATTATGA-TATATTTA
1 TATATTAT-ATTATATTCA
1385205 TATATTATATTATATTCA
1 TATATTATATTATATTCA
1385223 TAT
1 TAT
1385226 TATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TATATTATATTATATTCA
Found at i:1385589 original size:11 final size:12
Alignment explanation
Indices: 1385570--1385627 Score: 61
Period size: 11 Copynumber: 5.2 Consensus size: 12
1385560 TTGTATCGTG
1385570 TTATATTTTA-A
1 TTATATTTTATA
*
1385581 TTATTTTTTATA
1 TTATATTTTATA
1385593 TTATA-TTTATA
1 TTATATTTTATA
* *
1385604 TTATATCTCA-A
1 TTATATTTTATA
1385615 TT-TATTTTATA
1 TTATATTTTATA
1385626 TT
1 TT
1385628 TTTATAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 5 0.13
11 26 0.68
12 7 0.18
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:1385924 original size:4 final size:4
Alignment explanation
Indices: 1385915--1385990 Score: 58
Period size: 4 Copynumber: 19.8 Consensus size: 4
1385905 ACTAAAAGAA
*
1385915 AAAG AAAG AAAAG AAAG AAAG -AA- AAAG AAAG AAAG AAA- AGAG ATAA-
1 AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A-AAG
1385961 AAATG -AA- AAAG AAAG AAAG -AAG AAGAG AAA
1 AAA-G AAAG AAAG AAAG AAAG AAAG AA-AG AAA
1385991 AAATTTTATG
Statistics
Matches: 59, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
3 13 0.22
4 37 0.63
5 9 0.15
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:1385939 original size:23 final size:23
Alignment explanation
Indices: 1385909--1385986 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
1385899 TCAGCAACTA
1385909 AAAGAAAAAGAAAGAAAAGAAAG
1 AAAGAAAAAGAAAGAAAAGAAAG
1385932 AAAGAAAAAGAAAG-AAAGAAA-
1 AAAGAAAAAGAAAGAAAAGAAAG
* * *
1385953 AGAGATAAA-AATGAAAAAGAAAG
1 AAAGAAAAAGAAAG-AAAAGAAAG
*
1385976 AAAGAAGAAGA
1 AAAGAAAAAGA
1385987 GAAAAAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.07
21 7 0.16
22 14 0.31
23 20 0.44
24 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03
Consensus pattern (23 bp):
AAAGAAAAAGAAAGAAAAGAAAG
Found at i:1385942 original size:14 final size:14
Alignment explanation
Indices: 1385915--1385986 Score: 94
Period size: 14 Copynumber: 5.1 Consensus size: 14
1385905 ACTAAAAGAA
1385915 AAAGAAAG-AAAAG
1 AAAGAAAGAAAAAG
1385928 AAAGAAAGAAAAAG
1 AAAGAAAGAAAAAG
1385942 AAAGAAAGAAAAGAG
1 AAAGAAAGAAAA-AG
1385957 ATAA-AAATGAAAAAG
1 A-AAGAAA-GAAAAAG
*
1385972 AAAGAAAGAAGAAG
1 AAAGAAAGAAAAAG
1385986 A
1 A
1385987 GAAAAAATTT
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
13 8 0.15
14 26 0.49
15 12 0.23
16 7 0.13
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (14 bp):
AAAGAAAGAAAAAG
Found at i:1386072 original size:5 final size:5
Alignment explanation
Indices: 1386062--1386094 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1386052 TACATATTAA
1386062 TATTT TATTT TATTT TATTT TATATT T-TTT TAT
1 TATTT TATTT TATTT TATTT TAT-TT TATTT TAT
1386095 ATGTATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 3 0.12
5 20 0.77
6 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:1386407 original size:15 final size:16
Alignment explanation
Indices: 1386371--1386410 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1386361 TTTAATATTT
*
1386371 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
1386388 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
1386403 ATAAAATT
1 ATAAAATT
1386411 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:1386636 original size:20 final size:21
Alignment explanation
Indices: 1386600--1386640 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1386590 AATCATATTT
*
1386600 ATATTATTTTTTGTATATAAA
1 ATATTATATTTTGTATATAAA
1386621 ATATTATATTTT-TATATAAA
1 ATATTATATTTTGTATATAAA
1386641 TTTTTTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATTATATTTTGTATATAAA
Found at i:1386768 original size:588 final size:585
Alignment explanation
Indices: 1385950--1387046 Score: 1627
Period size: 588 Copynumber: 1.9 Consensus size: 585
1385940 AGAAAGAAAG
* * * *
1385950 AAAAGAGATAAAAATGAAAAAGAAAGAAAGAAGAAGAGAAAAAATTTTATGTATTTATATTTATA
1 AAAAGAGAAAAAAAAGAAAAAGAAAGAAAGAAGAAAAGAAAAAATTTTATATATTTATATTTATA
* * * *
1386015 TTTTTTTATAAAATATTATATTTTTGTATAAATTTTTTACATATTAATATTTTATTTTATTTTAT
66 TTTTTTTATAAAATATTATATTTTTATATAAATTTTTTACATATTAATAATTCATTTTATTTCAT
* * * * *
1386080 TTTATATTTTTTTATATGTATGTATATTTGTGTTATATGCATACCATTTTCATGTTATATTTTAA
131 TGTATA-TTTTTTATATGTATATATATTCGTGTCATATACATACCATTTTCATGTTATATTTT-A
1386145 ATTTTTTTTATAAATATCGTGTTTATATTATTTTTATATTATTAAAATAAAATAAATTT-TATAA
194 ATTTTTTTTATAAATATCGTGTTTATATTATTTTTATATTATTAAAATAAAATAAATTTATATAA
* * *
1386209 ATTTTTA-TATATTAATTGTTAGTTTATTTATATTTTGATATATTCGTGTATTCGTGA-CATATT
259 ATTTTTACT-TATTAATTATTAGTTTATTTATATTTTAATATATTCGTGTATTCAT-ATCATATT
1386272 CATATTATTTTTCATGCTACGTATTAATTTTTATATATATTGAGTTCGTATCATATCTCAATTCA
322 CATATTATTTTTCATGCTACGTATTAATTTTTATATATATTGAGTTCGTATCATATCTCAATTCA
** * * **
1386337 TTTTTCTCCTATTTTGTTAGGGGTTTTAATATTTATAAAATTTTTAATTAAATAAAATTATAATT
387 TTTTT-TCCTACCTCGCTAGAAGTTTTAATATTTATAAAATTTTTAATTAAATAAAATTATAATT
*
1386402 AATAAAATTTAGTTAAAAATATTTAAGAAATAAATTTAAAGTTAAAATTTAATCATACATATATA
451 AATAAAATTTAGTTAAAAATATTTAACAAATAAATTTAAAGTTAAAATTTAATCATACATATATA
1386467 TAATTTTAACTATATAAATAAATTTGGTGCTGACACGTGGTACTTTTTTTTTACTTTCAGCAGCT
516 TAATTTTAACTATATAAATAAATTTGGTGCTGACACGTGGTACTTTTTTTTTACTTTCAGCAGCT
1386532 GAACA
581 GAACA
*
1386537 AAAAGAGAAAAAAAAAGAAAAAGGAAAGAAAGAATAAAAGAAAAAATTTATATAATCATATT-TA
1 AAAAGAG-AAAAAAAAGAAAAA-GAAAGAAAGAAGAAAAGAAAAAATTT-TAT-AT-AT-TTATA
1386601 TATTAT-TTTTTGTATATAAAATATTATATTTTTATATAAATTTTTTACATATTAATAATTCATT
60 T-TTATATTTTT-T-TATAAAATATTATATTTTTATATAAATTTTTTACATATTAATAATTCATT
* * * * *
1386665 TTGTTTCA-TGTATA-TTTTTATATGTATATGTATTCGTGTCATGTACATATCATTTTCCTGTTA
122 TTATTTCATTGTATATTTTTTATATGTATATATATTCGTGTCATATACATACCATTTTCATGTTA
* **
1386728 TATTTT-A-TTTTTTTATAAATATCGTGTTTATATTATTTTTATATTGTTAACGTAAAATAAATT
187 TATTTTAATTTTTTTTATAAATATCGTGTTTATATTATTTTTATATTATTAAAATAAAATAAATT
* *
1386791 TATATAAATTTTTACTTATTAATTATTAGTTTATTTATATTTTAATATTTTTGTGTATTCATATC
252 TATATAAATTTTTACTTATTAATTATTAGTTTATTTATATTTTAATATATTCGTGTATTCATATC
* * * * *
1386856 ATATTCATATTATTTTTTATGTTGCGTATTAATTTTTATATATATTGAGTTTGTATCATGTCTCA
317 ATATTCATATTATTTTTCATGCTACGTATTAATTTTTATATATATTGAGTTCGTATCATATCTCA
* *
1386921 ATTCATTTTTTCTTGCCTCGCTAGAAGTTTTAATATTTATAAAATTTTTAATTAAATAAAATTAT
382 ATTCATTTTTTCCTACCTCGCTAGAAGTTTTAATATTTATAAAATTTTTAATTAAATAAAATTAT
*
1386986 AATTAATAAAATTTATTTAAAAATATTTAACAAATAAATTTAAAGTTAAAATTTAATCATA
447 AATTAATAAAATTTAGTTAAAAATATTTAACAAATAAATTTAAAGTTAAAATTTAATCATA
1387047 TAAAAAATTA
Statistics
Matches: 456, Mismatches: 42, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
587 7 0.02
588 173 0.38
589 149 0.33
590 4 0.01
591 48 0.11
592 10 0.02
593 12 0.03
594 53 0.12
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (585 bp):
AAAAGAGAAAAAAAAGAAAAAGAAAGAAAGAAGAAAAGAAAAAATTTTATATATTTATATTTATA
TTTTTTTATAAAATATTATATTTTTATATAAATTTTTTACATATTAATAATTCATTTTATTTCAT
TGTATATTTTTTATATGTATATATATTCGTGTCATATACATACCATTTTCATGTTATATTTTAAT
TTTTTTTATAAATATCGTGTTTATATTATTTTTATATTATTAAAATAAAATAAATTTATATAAAT
TTTTACTTATTAATTATTAGTTTATTTATATTTTAATATATTCGTGTATTCATATCATATTCATA
TTATTTTTCATGCTACGTATTAATTTTTATATATATTGAGTTCGTATCATATCTCAATTCATTTT
TTCCTACCTCGCTAGAAGTTTTAATATTTATAAAATTTTTAATTAAATAAAATTATAATTAATAA
AATTTAGTTAAAAATATTTAACAAATAAATTTAAAGTTAAAATTTAATCATACATATATATAATT
TTAACTATATAAATAAATTTGGTGCTGACACGTGGTACTTTTTTTTTACTTTCAGCAGCTGAACA
Found at i:1386995 original size:15 final size:16
Alignment explanation
Indices: 1386959--1386998 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1386949 TTTAATATTT
*
1386959 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
1386976 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
1386991 ATAAAATT
1 ATAAAATT
1386999 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:1387001 original size:16 final size:17
Alignment explanation
Indices: 1386959--1387001 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1386949 TTTAATATTT
*
1386959 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
1386976 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
1386991 ATAAAATTTAT
1 ATAAAATTTAT
1387002 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:1387433 original size:6 final size:6
Alignment explanation
Indices: 1387424--1387466 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
1387414 AAAATAATTT
1387424 TTTTAA TTTTAAA TTTTAA TTTTAA CTTTTAA TTTT-A TTTTAA
1 TTTTAA TTTT-AA TTTTAA TTTTAA -TTTTAA TTTTAA TTTTAA
1387467 AATAATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.15
6 17 0.50
7 12 0.35
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:1387442 original size:13 final size:13
Alignment explanation
Indices: 1387424--1387460 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1387414 AAAATAATTT
1387424 TTTTAATTTTAAA
1 TTTTAATTTTAAA
*
1387437 TTTTAATTTTAAC
1 TTTTAATTTTAAA
1387450 TTTTAATTTTA
1 TTTTAATTTTA
1387461 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTAATTTTAAA
Found at i:1387890 original size:29 final size:29
Alignment explanation
Indices: 1387829--1387886 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1387819 AATAATTATG
1387829 ATTAAAGAAAAAAAGCAAAAAAAAATTAA
1 ATTAAAGAAAAAAAGCAAAAAAAAATTAA
1387858 ATTAAAGAAAAAAAGC-AAAAAAAATTAA
1 ATTAAAGAAAAAAAGCAAAAAAAAATTAA
1387886 A
1 A
1387887 ATTATTCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (29 bp):
ATTAAAGAAAAAAAGCAAAAAAAAATTAA
Found at i:1388132 original size:79 final size:77
Alignment explanation
Indices: 1387934--1389442 Score: 1528
Period size: 79 Copynumber: 20.0 Consensus size: 77
1387924 AATTATAATT
* * * * *
1387934 AAAAAAAGCAAAGAAAATATTAAAGTTATTCTCTCACAAATTTATTCTTGGATGAATGAATAATA
1 AAAAAAAGCAAA-AAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATT
*
1387999 ATTATTAAAG---
65 ATGATTAAAGAAA
* * *
1388009 -AAAAAAGCAAAAAAAATTTTAAAATTATTCTCCCATC-AATTTATTTTTGGACAAAAGAATAAT
1 AAAAAAAGC-AAAAAAATATTAAAGTTATTCTCCCA-CAAATTTATTTTTGGACGAAAGAATAAT
1388072 TATGATTAAAGAAA
64 TATGATTAAAGAAA
* * * * *
1388086 ATAAAGAAGCAAAGAAAATATTAAAGTTATTATCCTATAAACTTATTTTTGGACGAATA-AATAA
1 A-AAAAAAGCAAA-AAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAA-AGAATAA
1388150 TTATGATTAAAG---
63 TTATGATTAAAGAAA
* * * *
1388162 ---AAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAACTTATTTTTGAATGAATGAATAATTA
1 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATTA
1388224 TGATT------A
66 TGATTAAAGAAA
* * * *
1388230 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCTCACCAATTTATTTTTGAACAAAAGAATAATTA
1 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATTA
1388295 TGATT-------
66 TGATTAAAGAAA
* * *
1388300 AAAAAAAG--AAAAAATATTAAATTTATTCTCCCATC-AATTTATTTTTAGACAAAAGAATAATT
1 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCA-CAAATTTATTTTTGGACGAAAGAATAATT
*
1388362 ATGATTAAAAAAA
65 ATGATTAAAGAAA
* * *
1388375 ATAAAAAAGCAAAGAAAATATTAAAGTTATTCTCACACAAACTTATTTTTGGATGAATA-AATAA
1 A-AAAAAAGCAAA-AAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAA-AGAATAA
1388439 TTATGATTAAAGAAA
63 TTATGATTAAAGAAA
** * *
1388454 AAAAGTA--AAAAAAATATTAAAGTTATTCTCCCACCAATTTATTTTTGGACAAAAGAATAATTA
1 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATTA
1388517 TGATTAAA-AAA
66 TGATTAAAGAAA
* * *
1388528 ATAAAAAAGCAAAGAAAATATTAAAGTTATTCTCTCACAAATTTATTATTGGACGAATGAATAAT
1 A-AAAAAAGCAAA-AAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAAT
1388593 TATGATTAAAGAAA
64 TATGATTAAAGAAA
* *
1388607 ATAAAAAAGCAAAGAAAATATTAAAATTATTCTCCCACAAATTTATTATTGGAC-AAATGAATAA
1 A-AAAAAAGCAAA-AAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAA-GAATAA
1388671 TTATGATTAAAGAAA
63 TTATGATTAAAGAAA
* * * * *
1388686 ATAAAAAAGCAAAGAAAATATTAAAATTATTCTCCCACAGACTTATTTTTGGATGAATGAATAAT
1 A-AAAAAAGCAAA-AAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAAT
1388751 TATGATTAAAG---
64 TATGATTAAAGAAA
* * * * * *
1388762 AAAAAAAGCAAAAAAAAATTAAAATTATTCTCGCACCAATTTATTTTTGGACAAAAGAATAAATA
1 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATTA
1388827 TGATT-----AA
66 TGATTAAAGAAA
* * * * *
1388834 TAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTCTTAGACGAATGAATAATAA
1 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATTA
*
1388899 TTATTAAAG---
66 TGATTAAAGAAA
* * * * *
1388908 -GAAAAAGCAAAAAAAAATTAAAGTTATTCTCCCGCCAATTTATTTTTGGATGAAAGAATAA-TA
1 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATTA
**
1388971 --ATT-ATTAAA
66 TGATTAAAGAAA
* * * * *
1388980 AGAAAAAGTAAAAAAAAATTAAAGTTATTCTCCCACAAATTTATTTTTGGATGAATGAATAATTA
1 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATTA
1389045 TGATTAAAGAAA
66 TGATTAAAGAAA
* * * * * *
1389057 ATAAAAAAGAAAAAAAATATTAAGGTTATTCTCCTACAAATTTATTCTTGGACGAATGAATAATA
1 A-AAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATT
*
1389122 ATTATTAAAGAAA
65 ATGATTAAAGAAA
** * * *
1389135 AAAGCAA--AAAAAAA-ATTAAAATTATTCTCCCACCAATTTATTTTTGGATGAAAGAATAA-TA
1 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATTA
**
1389196 --ATT-ATTAAA
66 TGATTAAAGAAA
* * * * *
1389205 AGAAAAAGTAAAAAAAAATTAAAGTTATTCTCCCACCAATTTATTTTTGGACAAAAGAATAATTA
1 AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATTA
1389270 TGATTAAAGAAA
66 TGATTAAAGAAA
* * * * * *
1389282 ATAAAAAAGAAAAAAAAATATTAAGGTTATTCTCCCACAAATTTATTCTTGGATGAATGAATAAC
1 A-AAAAAAG-CAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAAT
1389347 TATGATTAAAGAATA
64 TATGATTAAAGAA-A
* * * * * * *
1389362 TAAAAAAGTAAAAAAAATATTAAAGTTATTCTTCCACAAATTTATTCTTAGACGAATGAATAATA
1 AAAAAAAG-CAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATT
*
1389427 ATTATTAAAGAAA
65 ATGATTAAAGAAA
1389440 AAA
1 AAA
1389443 GTAAAAATAA
Statistics
Matches: 1222, Mismatches: 150, Indels: 121
0.82 0.10 0.08
Matches are distributed among these distances:
68 54 0.04
69 2 0.00
70 19 0.02
71 115 0.09
72 74 0.06
73 153 0.13
74 155 0.13
75 81 0.07
76 17 0.01
77 17 0.01
78 145 0.12
79 385 0.32
80 5 0.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (77 bp):
AAAAAAAGCAAAAAAATATTAAAGTTATTCTCCCACAAATTTATTTTTGGACGAAAGAATAATTA
TGATTAAAGAAA
Found at i:1389271 original size:675 final size:669
Alignment explanation
Indices: 1387866--1389475 Score: 2060
Period size: 675 Copynumber: 2.4 Consensus size: 669
1387856 AAATTAAAGA
* *
1387866 AAAAAAGC-AAAAAAAATTAAAATTATTCTCCCACCAATTTATTTTTGGATAAAAGAATAATTAT
1 AAAAAAGCAAAAAAAAATTAAAGTTATTCTCCCACCAATTTATTTTTGGACAAAAGAATAATTAT
* *
1387930 AATT-------A-AAAAAAGCAAAGAAAATATTAAAGTTATTCTCTCACAAATTTATTCTTGGAT
66 GATTAAAGAAAATAAAAAAGCAAAGAAAATATTAAAGTTATTCTCCCACAAATTTATTCTTGGAT
* * *
1387987 GAATGAATAATAATTATTAAAG----AAAAAAGCAAAAAAAATTTTAAAATTATTCTCCCATCAA
131 GAATGAATAATTATGATTAAAGAAATAAAAAAGCAAAAAAAATATTAAAATTATTCTCCCA-CAA
* * * *
1388048 TTTATTTTTGGACAAAAGAATAATTATGATTAAAGAAAATAAAGAAGCAAAGAAAATATTAAAGT
195 TTTATTTTTGGACGAATGAATAATTATGATTAAAG--AA-AAA-AAGCAAA-AAAAAATTAAAAT
* ** * * *
1388113 TATTATCCTATAAACTTATTTTTGGACGAATAAATAATTATGATTAAAGAAAAGCAAAAAAATAT
255 TATTCTCC-ACCAACTTATTTTTGGACGAAAAAATAAATATGATTAAAAAAAAGCAAAAAAATAT
* * *
1388178 TAAAGTTATTCTCCCACAAACTTATTTTTGAATGAATGAATAATTATGATTAAAAAAAAGCAAAA
319 TAAAGTTATTCTCCCACAAACTTATTTTAGAACGAATGAATAATAATGATTAAAAAAAAGCAAAA
* * *
1388243 AAATATTAAAGTTATTCTCTCACCAATTTATTTTTGAACAAAAGAATAATTATGATTAAAAAAAG
384 AAAAATTAAAGTTATTCTCCCACCAATTTATTTTTGAACAAAAGAATAATAATGATTAAAAAAAG
* *
1388308 AAAAAATATTAAATTTATTCTCCCATCAATTTATTTTTAGACAAAAGAATAATTATGATTAAAAA
449 AAAAAAAATTAAAGTTATTCTCCCATCAATTTATTTTTAGACAAAAGAATAATTATGATTAAAAA
* * *
1388373 AAATAAAAAAGCAAAGAAAATATTAAAGTTATTCTCACACAAACTTATTTTTGGATGAATAAATA
514 AAATAAAAAAGCAAAAAAAATATTAAAGTTATTCTCACACAAACTTATTCTTGGACGAATAAATA
* * * *
1388438 ATTATGATTAAAGAAAAAAAGTAAAAAAAATATTAAAGTTATTCTCCCACCAATTTATTTTTGGA
579 ATAATGATTAAAGAAAAAAAGCAAAAAAAAAATTAAAATTATTCTCCCACCAATTTATTTTTGGA
1388503 CAAAAGAATAATTATGATTAAAAAAAT
644 CAAAAGAATAATTA-GATTAAAAAAAT
* * * * * *
1388530 AAAAAAGCAAAGAAAATATTAAAGTTATTCTCTCACAAATTTATTATTGGACGAATGAATAATTA
1 AAAAAAGCAAA-AAAAAATTAAAGTTATTCTCCCACCAATTTATTTTTGGACAAAAGAATAATTA
* *
1388595 TGATTAAAGAAAATAAAAAAGCAAAGAAAATATTAAAATTATTCTCCCACAAATTTATTATTGGA
65 TGATTAAAGAAAATAAAAAAGCAAAGAAAATATTAAAGTTATTCTCCCACAAATTTATTCTTGGA
** *
1388660 CAAATGAATAATTATGATTAAAGAAAATAAAAAAGCAAAGAAAATATTAAAATTATTCTCCCACA
130 TGAATGAATAATTATGATTAAAG-AAATAAAAAAGCAAAAAAAATATTAAAATTATTCTCCCACA
* *
1388725 GACTTATTTTTGGATGAATGAATAATTATGATTAAAGAAAAAAAGCAAAAAAAAATTAAAATTAT
194 -ATTTATTTTTGGACGAATGAATAATTATGATTAAAGAAAAAAAGCAAAAAAAAATTAAAATTAT
*
1388790 TCTCGCACCAATTTATTTTTGGAC-AAAAGAATAAATATGATTAATAAAAAAGCAAAAAAATATT
258 TCTC-CACCAACTTATTTTTGGACGAAAA-AATAAATATGATTAA-AAAAAAGCAAAAAAATATT
* *
1388854 AAAGTTATTCTCCCACAAATTTATTCTTAG-ACGAATGAATAATAATTATTAAAGGAAAAAGCAA
320 AAAGTTATTCTCCCACAAACTTATT-TTAGAACGAATGAATAATAATGATTAAA--AAAAAGCAA
* * ** *
1388918 AAAAAAATTAAAGTTATTCTCCCGCCAATTTATTTTTGGATGAAAGAATAATAATTATTAAAAGA
382 AAAAAAATTAAAGTTATTCTCCCACCAATTTATTTTTGAACAAAAGAATAATAATGATT--AA-A
* ** *
1388983 AAAAGTAAAAAAAAATTAAAGTTATTCTCCCA-CAAATTTATTTTTGGATGAATGAATAATTATG
444 AAAAG--AAAAAAAATTAAAGTTATTCTCCCATC-AATTTATTTTTAGACAAAAGAATAATTATG
* * *
1389047 ATTAAAGAAAATAAAAAAG-AAAAAAAATATTAAGGTTATTCTC-CTACAAATTTATTCTTGGAC
506 ATTAAAAAAAATAAAAAAGCAAAAAAAATATTAAAGTTATTCTCAC-ACAAACTTATTCTTGGAC
* *
1389110 GAATGAATAATAATTATTAAAG-AAAAAAGCAAAAAAAAAATTAAAATTATTCTCCCACCAATTT
570 GAATAAATAATAATGATTAAAGAAAAAAAGCAAAAAAAAAATTAAAATTATTCTCCCACCAATTT
** **
1389174 ATTTTTGGATGAAAGAATAA-TA-ATTATTAAAA-
635 ATTTTTGGACAAAAGAATAATTAGATTAAAAAAAT
* *
1389206 GAAAAAGTAAAAAAAAATTAAAGTTATTCTCCCACCAATTTATTTTTGGACAAAAGAATAATTAT
1 AAAAAAGCAAAAAAAAATTAAAGTTATTCTCCCACCAATTTATTTTTGGACAAAAGAATAATTAT
* * *
1389271 GATTAAAGAAAATAAAAAAGAAAAAAAAATATTAAGGTTATTCTCCCACAAATTTATTCTTGGAT
66 GATTAAAGAAAATAAAAAAGCAAAGAAAATATTAAAGTTATTCTCCCACAAATTTATTCTTGGAT
* * * *
1389336 GAATGAATAACTATGATTAAAGAATATAAAAAAGTAAAAAAAATATTAAAGTTATTCTTCCACAA
131 GAATGAATAATTATGATTAAAGAA-ATAAAAAAGCAAAAAAAATATTAAAATTATTCTCCCAC-A
* * * * * **
1389401 ATTTATTCTTAGACGAATGAATAATAATTATTAAAG-AAAAAAGTAAAAATAAAAGCAAAAGTTA
194 ATTTATTTTTGGACGAATGAATAATTATGATTAAAGAAAAAAAGCAAAAA-AAAATTAAAA-TTA
1389465 TTCTCCCACCA
257 TTCT-CCACCA
1389476 GGTTTAGTGG
Statistics
Matches: 817, Mismatches: 95, Indels: 56
0.84 0.10 0.06
Matches are distributed among these distances:
664 8 0.01
665 2 0.00
666 49 0.06
673 4 0.00
674 127 0.16
675 269 0.33
676 28 0.03
677 71 0.09
678 2 0.00
679 69 0.08
680 64 0.08
681 57 0.07
682 67 0.08
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (669 bp):
AAAAAAGCAAAAAAAAATTAAAGTTATTCTCCCACCAATTTATTTTTGGACAAAAGAATAATTAT
GATTAAAGAAAATAAAAAAGCAAAGAAAATATTAAAGTTATTCTCCCACAAATTTATTCTTGGAT
GAATGAATAATTATGATTAAAGAAATAAAAAAGCAAAAAAAATATTAAAATTATTCTCCCACAAT
TTATTTTTGGACGAATGAATAATTATGATTAAAGAAAAAAAGCAAAAAAAAATTAAAATTATTCT
CCACCAACTTATTTTTGGACGAAAAAATAAATATGATTAAAAAAAAGCAAAAAAATATTAAAGTT
ATTCTCCCACAAACTTATTTTAGAACGAATGAATAATAATGATTAAAAAAAAGCAAAAAAAAATT
AAAGTTATTCTCCCACCAATTTATTTTTGAACAAAAGAATAATAATGATTAAAAAAAGAAAAAAA
ATTAAAGTTATTCTCCCATCAATTTATTTTTAGACAAAAGAATAATTATGATTAAAAAAAATAAA
AAAGCAAAAAAAATATTAAAGTTATTCTCACACAAACTTATTCTTGGACGAATAAATAATAATGA
TTAAAGAAAAAAAGCAAAAAAAAAATTAAAATTATTCTCCCACCAATTTATTTTTGGACAAAAGA
ATAATTAGATTAAAAAAAT
Found at i:1389729 original size:24 final size:23
Alignment explanation
Indices: 1389683--1389733 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1389673 TATTTATTGA
* *
1389683 ATAAATTTTAATATATAATAATT
1 ATAAATTTTAATAAATAAAAATT
*
1389706 ATAAATTATTATTAAATAAAAATT
1 ATAAATT-TTAATAAATAAAAATT
1389730 -TAAA
1 ATAAA
1389734 ATATAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAAATTTTAATAAATAAAAATT
Found at i:1390324 original size:3 final size:3
Alignment explanation
Indices: 1390316--1390354 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1390306 ATTTTACATT
1390316 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1390355 CCATAGACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1390787 original size:20 final size:20
Alignment explanation
Indices: 1390762--1390801 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1390752 TTATAAATTA
*
1390762 AATTAAATTATAAATAAAAT
1 AATTAAATTAAAAATAAAAT
* *
1390782 AATTAATTTAAAAATTAAAT
1 AATTAAATTAAAAATAAAAT
1390802 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTAAATTAAAAATAAAAT
Found at i:1391433 original size:18 final size:18
Alignment explanation
Indices: 1391410--1391444 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1391400 TTCACAATAA
1391410 AAACT-CATAAAAATATTT
1 AAACTCCAT-AAAATATTT
1391428 AAACTCCATAAAATATT
1 AAACTCCATAAAATATT
1391445 CTTAAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (18 bp):
AAACTCCATAAAATATTT
Found at i:1392189 original size:18 final size:19
Alignment explanation
Indices: 1392166--1392202 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1392156 AATTTTTGTT
*
1392166 ATAAAAATTATATT-TTTC
1 ATAAAAAATATATTATTTC
1392184 ATAAAAAATATATTATTTC
1 ATAAAAAATATATTATTTC
1392203 GTCTAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAAAAAATATATTATTTC
Found at i:1392214 original size:21 final size:21
Alignment explanation
Indices: 1392190--1392232 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1392180 TTTCATAAAA
*
1392190 AATATATTATTTCGTCTAACT
1 AATATATTATTTCATCTAACT
* *
1392211 AATATATTTTTTCATTTAACT
1 AATATATTATTTCATCTAACT
1392232 A
1 A
1392233 TCTCTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (21 bp):
AATATATTATTTCATCTAACT
Found at i:1392330 original size:25 final size:27
Alignment explanation
Indices: 1392272--1392322 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1392262 CCTTTTGATA
1392272 AAATTATAATAATATTTTACTAAATTAC
1 AAATTATAATAATA-TTTACTAAATTAC
1392300 AAATTATAA-AATA-TTA-TAAATTA
1 AAATTATAATAATATTTACTAAATTA
1392323 TATAATTACG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
27 4 0.17
28 9 0.39
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (27 bp):
AAATTATAATAATATTTACTAAATTAC
Found at i:1392450 original size:18 final size:19
Alignment explanation
Indices: 1392429--1392468 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1392419 ATTTTAATTT
1392429 AAAATTA-AA-TAAATTATA
1 AAAATTATAATTAAATTA-A
1392447 AAAATTATAATTAAATTAA
1 AAAATTATAATTAAATTAA
1392466 AAA
1 AAA
1392469 TAAGATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTATAATTAAATTAA
Found at i:1392627 original size:50 final size:50
Alignment explanation
Indices: 1392567--1392726 Score: 245
Period size: 50 Copynumber: 3.2 Consensus size: 50
1392557 ATATACTTAG
1392567 AGTCAACAATTATGACCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGACCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
*
1392617 TGTCAACAATTAT-AGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGA-CCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
* *
1392667 CGTCAACAATTATGGCCACCT-CTCTCTATTGTCAAAGGTTGGTGAATG-AT
1 AGTCAACAATTATGACCACCTCCT-TCTATTGTCAAAGGTTGGTGAA-GAAT
1392717 AGTCAACAAT
1 AGTCAACAAT
1392727 GACAACAACT
Statistics
Matches: 102, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
49 3 0.03
50 98 0.96
51 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTATGACCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:1395710 original size:50 final size:50
Alignment explanation
Indices: 1395651--1395785 Score: 225
Period size: 50 Copynumber: 2.7 Consensus size: 50
1395641 TATACTTAGA
* *
1395651 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
*
1395701 GTCAACAATTATGGCCAACTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
* *
1395751 GTCAACAATTATTGCCACCTCTTTCTATTGTCAAA
1 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAA
1395786 AATTGATGAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1395805 original size:50 final size:50
Alignment explanation
Indices: 1395650--1395809 Score: 223
Period size: 50 Copynumber: 3.2 Consensus size: 50
1395640 ATATACTTAG
*
1395650 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
* *
1395700 TGTCAACAATTATGGCCAACTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
* * * ** *
1395750 CGTCAACAATTATTGCCACCTCTTTCTATTGTCAAAAATTGATGAATG-AT
1 AGTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAA-GAAT
1395800 AGTCAACAAT
1 AGTCAACAAT
1395810 GACAACAACT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 97 0.99
51 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:1402723 original size:38 final size:38
Alignment explanation
Indices: 1402681--1402765 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 38
1402671 AAATCCTAAA
* * *
1402681 TTTATTATTTATAATTT-ATAAATAATTAAAATATTATT
1 TTTATTATTAAT-ATTTAATAAATAAATAAAATATAATT
*
1402719 TTTA-TATTAATATTTAAATAATTAAATAAAATATAATT
1 TTTATTATTAATATTT-AATAAATAAATAAAATATAATT
1402757 TTT-TTATTA
1 TTTATTATTA
1402766 TTAAATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
36 4 0.10
37 6 0.15
38 30 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (38 bp):
TTTATTATTAATATTTAATAAATAAATAAAATATAATT
Found at i:1405667 original size:17 final size:17
Alignment explanation
Indices: 1405645--1405678 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1405635 CTCATTAATT
1405645 ATTGACACAAGAGTGAG
1 ATTGACACAAGAGTGAG
* *
1405662 ATTGACATAAGATTGAG
1 ATTGACACAAGAGTGAG
1405679 GTTGGTGGCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (17 bp):
ATTGACACAAGAGTGAG
Found at i:1409608 original size:52 final size:52
Alignment explanation
Indices: 1409546--1409654 Score: 218
Period size: 52 Copynumber: 2.1 Consensus size: 52
1409536 AAGGGACCAT
1409546 GATATTTACCCAAAGAGAGATGAGCTGCAAGCTCCAACTCAAATTAGATCCA
1 GATATTTACCCAAAGAGAGATGAGCTGCAAGCTCCAACTCAAATTAGATCCA
1409598 GATATTTACCCAAAGAGAGATGAGCTGCAAGCTCCAACTCAAATTAGATCCA
1 GATATTTACCCAAAGAGAGATGAGCTGCAAGCTCCAACTCAAATTAGATCCA
1409650 GATAT
1 GATAT
1409655 AAGAATTCAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (52 bp):
GATATTTACCCAAAGAGAGATGAGCTGCAAGCTCCAACTCAAATTAGATCCA
Found at i:1415121 original size:22 final size:21
Alignment explanation
Indices: 1415092--1415132 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1415082 AATAAATTTT
1415092 TAAATAATA-TAATTATAAATA
1 TAAATAATATTAA-TATAAATA
1415113 TAAATTAATATTAATATAAA
1 TAAA-TAATATTAATATAAA
1415133 ATTTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 11 0.61
23 3 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATAATATTAATATAAATA
Found at i:1415988 original size:29 final size:29
Alignment explanation
Indices: 1415945--1416000 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1415935 GAGGTTTCAA
1415945 TTGGAATTTGACGCATCGGAGTGCGACAT
1 TTGGAATTTGACGCATCGGAGTGCGACAT
* *
1415974 TTGGATTTTGGCGCATCGGAGTGCGAC
1 TTGGAATTTGACGCATCGGAGTGCGAC
1416001 CAGGTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.29
Consensus pattern (29 bp):
TTGGAATTTGACGCATCGGAGTGCGACAT
Found at i:1416189 original size:19 final size:21
Alignment explanation
Indices: 1416167--1416217 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1416157 TTTTAATATA
*
1416167 AATATAAAT-TTTAGTT-TTT
1 AATATAAATATTTAATTATTT
**
1416186 AATATATTTATTTAATTATTT
1 AATATAAATATTTAATTATTT
1416207 AATATAAATAT
1 AATATAAATAT
1416218 ATTTTTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 7 0.28
20 6 0.24
21 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
AATATAAATATTTAATTATTT
Found at i:1416225 original size:21 final size:21
Alignment explanation
Indices: 1416158--1416226 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 21
1416148 TTAAAATATT
*
1416158 TTTAATATAAATATAAATTTTAGTT
1 TTTAATATAAATAT--ATTTT--TA
*
1416183 TTTAATAT--ATTTATTTAATTA
1 TTTAATATAAATATATTT--TTA
1416204 TTTAATATAAATATATTTTTA
1 TTTAATATAAATATATTTTTA
1416225 TT
1 TT
1416227 ATTTATCTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
21 18 0.49
23 11 0.30
25 8 0.22
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (21 bp):
TTTAATATAAATATATTTTTA
Done.