Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 4 of 20
Found at i:615673 original size:41 final size:39
Alignment explanation
Indices: 615628--615705 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 39
615618 AATTAAAAAA
* *
615628 AAATTATTTTATTAAAAATAAAATTATTTATATTTACTATT
1 AAATTATTTTAAT-AAAATAAAATTATCTA-ATTTACTATT
* * *
615669 AAATTTTTTTAATAAATTAATATTATCTAATTTACTA
1 AAATTATTTTAATAAAATAAAATTATCTAATTTACTA
615706 ATCACATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 8 0.25
40 13 0.41
41 11 0.34
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (39 bp):
AAATTATTTTAATAAAATAAAATTATCTAATTTACTATT
Found at i:615718 original size:2 final size:2
Alignment explanation
Indices: 615711--615759 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
615701 TACTAATCAC
615711 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
615753 AT AT AT A
1 AT AT AT A
615760 CAGTGCATCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:622320 original size:4 final size:4
Alignment explanation
Indices: 622311--622336 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
622301 ACAGATAATA
622311 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
622337 TTTGAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:622561 original size:21 final size:20
Alignment explanation
Indices: 622520--622596 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 20
622510 TATTATCACG
622520 TAATATAAATATAAAATAAAAAA
1 TAATATAAA-AT--AATAAAAAA
* *
622543 TAATTTAAATATTATAAAAAA
1 TAATATAAA-ATAATAAAAAA
622564 TAAATATAAAATAATAAAAAA
1 T-AATATAAAATAATAAAAAA
622585 TAAATATAAAAT
1 T-AATATAAAAT
622597 TTTAATATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 31 0.63
22 7 0.14
23 11 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAATATAAAATAATAAAAAA
Found at i:622596 original size:32 final size:32
Alignment explanation
Indices: 622520--622596 Score: 77
Period size: 34 Copynumber: 2.3 Consensus size: 32
622510 TATTATCACG
*
622520 TAATATAAATATAAAATAAAAAATAATTTAAATA
1 TAATATAAA-ATAAAATAAAAAATAA-TAAAATA
* *
622554 TTATAAAAAATAAATATAAAATAATAA-AAAATA
1 TAATATAAAATAAA-ATAAAA-AATAATAAAATA
622587 -AATATAAAAT
1 TAATATAAAAT
622597 TTTAATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
32 8 0.22
33 10 0.28
34 13 0.36
35 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (32 bp):
TAATATAAAATAAAATAAAAAATAATAAAATA
Found at i:623247 original size:15 final size:15
Alignment explanation
Indices: 623215--623257 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
623205 TACTCATATT
*
623215 TAAATACATATTATATA
1 TAAATATAT-TTA-ATA
*
623232 TTAATATATTTAATA
1 TAAATATATTTAATA
623247 TAAATATATTT
1 TAAATATATTT
623258 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 3 0.13
17 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAATATATTTAATA
Found at i:623285 original size:18 final size:18
Alignment explanation
Indices: 623258--623292 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
623248 AAATATATTT
*
623258 TATTTTTAAATTTTTATA
1 TATTTATAAATTTTTATA
623276 TATTTATAAATTTTTAT
1 TATTTATAAATTTTTAT
623293 TTTATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATAAATTTTTATA
Found at i:623289 original size:25 final size:25
Alignment explanation
Indices: 623261--623311 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
623251 TATATTTTAT
*
623261 TTTTAAATTTT-TATATATTTATAAA
1 TTTT-AATTTTATATATATATATAAA
* *
623286 TTTTTATTTTATATTTATATATAAA
1 TTTTAATTTTATATATATATATAAA
623311 T
1 T
623312 ATATATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTAATTTTATATATATATATAAA
Found at i:623306 original size:8 final size:8
Alignment explanation
Indices: 623225--623307 Score: 68
Period size: 8 Copynumber: 11.0 Consensus size: 8
623215 TAAATACATA
623225 TTATATAT
1 TTATATAT
*
623233 TAATATAT
1 TTATATAT
623241 TTA-ATAT
1 TTATATAT
**
623248 AAATATAT
1 TTATATAT
*
623256 TT-TATTT
1 TTATATAT
* *
623263 TTAAATTT
1 TTATATAT
623271 TTATATAT
1 TTATATAT
*
623279 TTATAAAT
1 TTATATAT
623287 TT-T-TAT
1 TTATATAT
623293 TT-TATAT
1 TTATATAT
623300 TTATATAT
1 TTATATAT
623308 AAATATATAT
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
6 5 0.08
7 17 0.29
8 37 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATAT
Found at i:623318 original size:25 final size:24
Alignment explanation
Indices: 623267--623318 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
623257 TTATTTTTAA
* * *
623267 ATTTTTATATATTTATAAATTTTT
1 ATTTTTATATATATATAAATATAT
*
623291 ATTTTATATTTATATATAAATATAT
1 ATTTT-TATATATATATAAATATAT
623316 ATT
1 ATT
623319 AAATATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTTATATATATATAAATATAT
Found at i:623624 original size:26 final size:26
Alignment explanation
Indices: 623590--623654 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
623580 ATATTATAAT
623590 TTTATTATTAAAAAATATATTAAATTA
1 TTTA-TATTAAAAAATATATTAAATTA
* * *
623617 TTTATATTTTAAAATTTTATTAAATTA
1 TTTATA-TTAAAAAATATATTAAATTA
* *
623644 TTAATGTTAAA
1 TTTATATTAAA
623655 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 6 0.19
27 25 0.81
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTATATTAAAAAATATATTAAATTA
Found at i:631156 original size:37 final size:37
Alignment explanation
Indices: 631106--631181 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
631096 TGAAAGAGAG
631106 TTGAAATTCATTAGCTTATTATTGTTCTTTCTTTATA
1 TTGAAATTCATTAGCTTATTATTGTTCTTTCTTTATA
*
631143 TTGAAATTCATTAGCTTATTATTGTTCTTTCTTTTTA
1 TTGAAATTCATTAGCTTATTATTGTTCTTTCTTTATA
631180 TT
1 TT
631182 AATATTGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.59
Consensus pattern (37 bp):
TTGAAATTCATTAGCTTATTATTGTTCTTTCTTTATA
Found at i:631165 original size:21 final size:21
Alignment explanation
Indices: 631106--631166 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
631096 TGAAAGAGAG
631106 TTGAAATTCATTAGCTTATTA
1 TTGAAATTCATTAGCTTATTA
*
631127 TTG---TTC-TT-TCTT-TATA
1 TTGAAATTCATTAGCTTAT-TA
631143 TTGAAATTCATTAGCTTATTA
1 TTGAAATTCATTAGCTTATTA
631164 TTG
1 TTG
631167 TTCTTTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
15 1 0.03
16 8 0.26
17 2 0.06
18 3 0.10
19 3 0.10
20 2 0.06
21 11 0.35
22 1 0.03
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (21 bp):
TTGAAATTCATTAGCTTATTA
Found at i:637340 original size:12 final size:12
Alignment explanation
Indices: 637323--637347 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
637313 TATATATTAC
637323 ATTACATTATAT
1 ATTACATTATAT
637335 ATTACATTATAT
1 ATTACATTATAT
637347 A
1 A
637348 GTGTAATCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTACATTATAT
Found at i:639778 original size:12 final size:12
Alignment explanation
Indices: 639758--639797 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
639748 TCCCAATGCC
*
639758 TTTTCTTTCTTT
1 TTTTTTTTCTTT
639770 TTTTTTTTCTTT
1 TTTTTTTTCTTT
639782 TTTTTTTT-TTT
1 TTTTTTTTCTTT
639793 TTTTT
1 TTTTT
639798 CATTTTTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:639779 original size:16 final size:16
Alignment explanation
Indices: 639758--639804 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
639748 TCCCAATGCC
639758 TTTTCTTTCTTTTTTT
1 TTTTCTTTCTTTTTTT
*
639774 TTTTCTTTTTTTTTTT
1 TTTTCTTTCTTTTTTT
*
639790 TTTTTTTTCATTTTT
1 TTTTCTTTC-TTTTT
639805 GGTATGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.02, C:0.09, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTCTTTCTTTTTTT
Found at i:639781 original size:21 final size:20
Alignment explanation
Indices: 639757--639804 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 20
639747 GTCCCAATGC
639757 CTTTTCTTTCTTTTTTTTTTT
1 CTTTT-TTTCTTTTTTTTTTT
*
639778 CTTTTTTTTTTTTTTTTTTT
1 CTTTTTTTCTTTTTTTTTTT
639798 CATTTTT
1 C-TTTTT
639805 GGTATGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (20 bp):
CTTTTTTTCTTTTTTTTTTT
Found at i:639782 original size:10 final size:10
Alignment explanation
Indices: 639769--639804 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
639759 TTTCTTTCTT
639769 TTTTTTTTTC
1 TTTTTTTTTC
*
639779 TTTTTTTTTT
1 TTTTTTTTTC
639789 TTTTTTTTTC
1 TTTTTTTTTC
639799 ATTTTT
1 -TTTTT
639805 GGTATGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:639804 original size:1 final size:1
Alignment explanation
Indices: 639767--639797 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
639757 CTTTTCTTTC
*
639767 TTTTTTTTTTTCTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
639798 CATTTTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:639804 original size:12 final size:11
Alignment explanation
Indices: 639758--639797 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
639748 TCCCAATGCC
*
639758 TTTTCTTTCTTT
1 TTTTTTTTC-TT
639770 TTTTTTTTCTT
1 TTTTTTTTCTT
639781 TTTTTTTT-TT
1 TTTTTTTTCTT
639791 TTTTTTT
1 TTTTTTT
639798 CATTTTTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 9 0.33
11 10 0.37
12 8 0.30
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:640187 original size:3 final size:3
Alignment explanation
Indices: 640179--640206 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
640169 TTTATTCCTC
640179 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
640207 AATACATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:648864 original size:3 final size:3
Alignment explanation
Indices: 648856--648887 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
648846 ACTTATTTGC
648856 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
648888 CAAAACTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:649095 original size:2 final size:2
Alignment explanation
Indices: 649088--649123 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
649078 AACTACATAC
*
649088 AT AT AT AT AT AT AT AT AT AT AT AT 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
649124 TTCACCATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:649243 original size:16 final size:16
Alignment explanation
Indices: 649199--649244 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
649189 TTAAAATTTT
649199 TATATTATATTATA--A
1 TATATT-TATTATATTA
**
649214 TATATTTAAAATATTA
1 TATATTTATTATATTA
649230 TATATTTATTATATT
1 TATATTTATTATATT
649245 TATTAGATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 5 0.20
15 6 0.24
16 14 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTTATTATATTA
Found at i:649358 original size:3 final size:3
Alignment explanation
Indices: 649352--649401 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
649342 ACCATCGACC
* * *
649352 CAT CAT CAC CAT CAT CAT TAT CAT CAT CAT CAT CAT CAT CAT CAA CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
649400 CA
1 CA
649402 ACATTTTTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.36, C:0.34, G:0.00, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:649365 original size:9 final size:9
Alignment explanation
Indices: 649337--649401 Score: 58
Period size: 9 Copynumber: 7.0 Consensus size: 9
649327 GGGGGACATG
*
649337 TCACCACCA
1 TCACCATCA
649346 TCGACCCATCA
1 TC-A-CCATCA
649357 TCACCATCA
1 TCACCATCA
**
649366 TCATTATCA
1 TCACCATCA
*
649375 TCATCATCA
1 TCACCATCA
*
649384 TCATCATCA
1 TCACCATCA
*
649393 TCAACATCA
1 TCACCATCA
649402 ACATTTTTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
9 40 0.82
10 2 0.04
11 7 0.14
ACGTcount: A:0.34, C:0.38, G:0.02, T:0.26
Consensus pattern (9 bp):
TCACCATCA
Found at i:651273 original size:12 final size:12
Alignment explanation
Indices: 651252--651283 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
651242 TCAGTTTTGG
*
651252 TTAAATTTAAAT
1 TTAAAATTAAAT
651264 TTAAAATTAAAT
1 TTAAAATTAAAT
651276 TTAAAATT
1 TTAAAATT
651284 TTTTTAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAAAATTAAAT
Found at i:651983 original size:16 final size:16
Alignment explanation
Indices: 651962--651995 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
651952 TTATGTTATA
651962 TAAATTATT-TTATGTT
1 TAAATTATTATTAT-TT
651978 TAAATTATTATTATTT
1 TAAATTATTATTATTT
651994 TA
1 TA
651996 TTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TAAATTATTATTATTT
Found at i:652657 original size:2 final size:2
Alignment explanation
Indices: 652650--652682 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
652640 CAAGCTTAAT
652650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
652683 CTCTTATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:653660 original size:17 final size:18
Alignment explanation
Indices: 653630--653683 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
653620 AAATTAGTAT
*
653630 AATATAATACATTAATAAA
1 AATAAAATA-ATTAATAAA
653649 AATAAAA-AATTAATTAAA
1 AATAAAATAATTAA-TAAA
*
653667 AATAAAATAAGTAATAA
1 AATAAAATAATTAATAA
653684 TTTTTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 5 0.16
18 15 0.48
19 11 0.35
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AATAAAATAATTAATAAA
Found at i:654843 original size:2 final size:2
Alignment explanation
Indices: 654836--654875 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
654826 GTGACCTCTA
654836 AT AT AT AT AT AT A- 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 AT AT A
654876 AAAGTGTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:658120 original size:6 final size:6
Alignment explanation
Indices: 658105--658135 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
658095 GAAAGGAAGG
658105 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
658136 TGGGTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:659871 original size:18 final size:18
Alignment explanation
Indices: 659850--659956 Score: 61
Period size: 18 Copynumber: 5.4 Consensus size: 18
659840 TCACCACCAC
659850 CGCCACCTTCTTTCTTCT
1 CGCCACCTTCTTTCTTCT
* *
659868 CGCCCCCTTCCTTTGTCTCT
1 CGCCACCTT-CTTTCT-TCT
* *
659888 CCGCCCCCTTCCTTCTTCTCTCCAC
1 -CGCCACCTT-C-T-TTCT-T-C-T
*
659913 CCCCACCTTCTTTCTTCT
1 CGCCACCTTCTTTCTTCT
* * *
659931 CCCCACCTACTTCCTTCT
1 CGCCACCTTCTTTCTTCT
659949 CGCCACCT
1 CGCCACCT
659957 CCCCCTTCCT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
18 31 0.43
19 6 0.08
20 4 0.06
21 15 0.21
22 2 0.03
23 6 0.08
24 8 0.11
ACGTcount: A:0.06, C:0.53, G:0.05, T:0.36
Consensus pattern (18 bp):
CGCCACCTTCTTTCTTCT
Found at i:659894 original size:21 final size:21
Alignment explanation
Indices: 659855--660066 Score: 98
Period size: 21 Copynumber: 9.8 Consensus size: 21
659845 ACCACCGCCA
659855 CCTTCTT-TCTTCTCGCCCCCTT
1 CCTTCTTCTC-TC-CGCCCCCTT
659877 CCTT-TGTCTCTCCGCCCCCTT
1 CCTTCT-TCTCTCCGCCCCCTT
* *
659898 CCTTCTTCTCTCCACCCCC-A
1 CCTTCTTCTCTCCGCCCCCTT
659918 CCTTCTTTCTTCTCC-CCACCTACTT
1 CCTTC-TTC-TCTCCGCC-CC--CTT
* * *
659943 CCTTC-TCGCCACCTCCCCCTT
1 CCTTCTTC-TCTCCGCCCCCTT
*
659964 CCTTC-TCTC-CACCCCCACCTT
1 CCTTCTTCTCTC-CGCCC-CCTT
* * * **
659985 CTTTCTTCTCCCCACCTACTT
1 CCTTCTTCTCTCCGCCCCCTT
* * *
660006 CCTTC-TCGCCACCTCCCCCTT
1 CCTTCTTC-TCTCCGCCCCCTT
660027 CCTTCTTCTCTCCACCGCCCCCTT
1 CCTTCTTCTCT---CCGCCCCCTT
*
660051 CCTTCTTCTCGCCGCC
1 CCTTCTTCTCTCCGCC
660067 TGCAGCAGCT
Statistics
Matches: 149, Mismatches: 22, Indels: 39
0.71 0.10 0.19
Matches are distributed among these distances:
19 1 0.01
20 12 0.08
21 75 0.50
22 24 0.16
23 10 0.07
24 22 0.15
25 5 0.03
ACGTcount: A:0.05, C:0.56, G:0.04, T:0.35
Consensus pattern (21 bp):
CCTTCTTCTCTCCGCCCCCTT
Found at i:659927 original size:24 final size:24
Alignment explanation
Indices: 659894--660060 Score: 100
Period size: 24 Copynumber: 7.6 Consensus size: 24
659884 CTCTCCGCCC
*
659894 CCTTCCTTCTTCTCTCCACCCCCA
1 CCTTCTTTCTTCTCTCCACCCCCA
659918 CCTTCTTTC-T-TCT----CCCCA
1 CCTTCTTTCTTCTCTCCACCCCCA
* * *
659936 CCTACTTCCTTCTCGCCACCTCCC-
1 CCTTCTTTCTTCTCTCCACC-CCCA
659960 CCTTC---CTTCTCTCCACCCCCA
1 CCTTCTTTCTTCTCTCCACCCCCA
659981 CCTTCTTTC-T-TCT----CCCCA
1 CCTTCTTTCTTCTCTCCACCCCCA
* * *
659999 CCTACTTCCTTCTCGCCACCTCCC-
1 CCTTCTTTCTTCTCTCCACC-CCCA
*
660023 CCTTCCTTCTTCTCTCCACCGCCC-
1 CCTTCTTTCTTCTCTCCACC-CCCA
*
660047 CCTTCCTTCTTCTC
1 CCTTCTTTCTTCTC
660061 GCCGCCTGCA
Statistics
Matches: 111, Mismatches: 14, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
18 24 0.22
19 2 0.02
20 7 0.06
21 16 0.14
22 6 0.05
23 2 0.02
24 48 0.43
25 6 0.05
ACGTcount: A:0.07, C:0.56, G:0.02, T:0.35
Consensus pattern (24 bp):
CCTTCTTTCTTCTCTCCACCCCCA
Found at i:659969 original size:63 final size:63
Alignment explanation
Indices: 659898--660060 Score: 267
Period size: 63 Copynumber: 2.6 Consensus size: 63
659888 CCGCCCCCTT
659898 CCTT-CTTCTCTCCACCCCCACCTTCTTTCTTCTCCCCACCTACTTCCTTCTCGCCACCTCCC
1 CCTTCCTTCTCTCCACCCCCACCTTCTTTCTTCTCCCCACCTACTTCCTTCTCGCCACCTCCC
659960 CCTTCCTTCTCTCCACCCCCACCTTCTTTCTTCTCCCCACCTACTTCCTTCTCGCCACCTCCC
1 CCTTCCTTCTCTCCACCCCCACCTTCTTTCTTCTCCCCACCTACTTCCTTCTCGCCACCTCCC
*
660023 CCTTCCTTCTTCTCTCCACCGCCC-CCTTCCTTCTTCTC
1 CCTT-C--CTTCTCTCCACC-CCCACCTTCTTTCTTCTC
660061 GCCGCCTGCA
Statistics
Matches: 95, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
62 4 0.04
63 62 0.65
64 1 0.01
66 25 0.26
67 3 0.03
ACGTcount: A:0.07, C:0.56, G:0.02, T:0.35
Consensus pattern (63 bp):
CCTTCCTTCTCTCCACCCCCACCTTCTTTCTTCTCCCCACCTACTTCCTTCTCGCCACCTCCC
Found at i:659997 original size:18 final size:18
Alignment explanation
Indices: 659976--660019 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
659966 TTCTCTCCAC
* *
659976 CCCCACCTTCTTTCTTCT
1 CCCCACCTACTTCCTTCT
659994 CCCCACCTACTTCCTTCT
1 CCCCACCTACTTCCTTCT
*
660012 CGCCACCT
1 CCCCACCT
660020 CCCCCTTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.55, G:0.02, T:0.34
Consensus pattern (18 bp):
CCCCACCTACTTCCTTCT
Found at i:660027 original size:42 final size:42
Alignment explanation
Indices: 659961--660042 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
659951 CCACCTCCCC
* *
659961 CTTCCTTCTCTCCACCCCCACCTTCTTTCTTCTCCCCACCTA
1 CTTCCTTCTCGCCACCCCCACCTTCCTTCTTCTCCCCACCTA
*
660003 CTTCCTTCTCGCCACCTCCC-CCTTCCTTCTTCTCTCCACC
1 CTTCCTTCTCGCCACC-CCCACCTTCCTTCTTCTCCCCACC
660043 GCCCCCTTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 33 0.92
43 3 0.08
ACGTcount: A:0.07, C:0.56, G:0.01, T:0.35
Consensus pattern (42 bp):
CTTCCTTCTCGCCACCCCCACCTTCCTTCTTCTCCCCACCTA
Found at i:661675 original size:19 final size:19
Alignment explanation
Indices: 661653--661690 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
661643 GTTGATGGGC
661653 ATGTATGATTATG-ATGATG
1 ATGTATG-TTATGTATGATG
661672 ATGTATGTTATGTATGATG
1 ATGTATGTTATGTATGATG
661691 GTTGAGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (19 bp):
ATGTATGTTATGTATGATG
Found at i:661684 original size:9 final size:10
Alignment explanation
Indices: 661653--661689 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
661643 GTTGATGGGC
661653 ATGTATGATT
1 ATGTATGATT
*
661663 ATG-ATGATG
1 ATGTATGATT
661672 ATGTATG-TT
1 ATGTATGATT
661681 ATGTATGAT
1 ATGTATGAT
661690 GGTTGAGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (10 bp):
ATGTATGATT
Found at i:663306 original size:5 final size:5
Alignment explanation
Indices: 663296--663373 Score: 62
Period size: 5 Copynumber: 16.0 Consensus size: 5
663286 TGTAATTTTA
663296 AATAT AATAT AAT-T -ATAT AATAT -ATAT AATAT AA-A- AATATTT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA--T AATAT
663343 -ATAAT AATAT AATA- ATATAAT AATAT AATAT
1 AAT-AT AATAT AATAT A-AT-AT AATAT AATAT
663374 TTTAAATATA
Statistics
Matches: 61, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
3 4 0.07
4 11 0.18
5 36 0.59
6 5 0.08
7 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:663372 original size:8 final size:8
Alignment explanation
Indices: 663299--663404 Score: 93
Period size: 8 Copynumber: 14.0 Consensus size: 8
663289 AATTTTAAAT
663299 ATAATATA
1 ATAATATA
*
663307 ATTATATA
1 ATAATATA
663315 AT-ATAT-
1 ATAATATA
663321 ATAATATA
1 ATAATATA
*
663329 AAAATATTTA
1 ATAATA--TA
663339 AT-ATATA
1 ATAATATA
663346 ATAATATA
1 ATAATATA
663354 ATAATATA
1 ATAATATA
663362 ATAATATA
1 ATAATATA
* *
663370 AT-ATTTT
1 ATAATATA
663377 A-AATATA
1 ATAATATA
663384 AT--TATA
1 ATAATATA
663390 A-AATATA
1 ATAATATA
*
663397 AAAATATA
1 ATAATATA
663405 TAAACACGCA
Statistics
Matches: 81, Mismatches: 7, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
6 7 0.09
7 25 0.31
8 43 0.53
9 3 0.04
10 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATAATATA
Found at i:665557 original size:22 final size:18
Alignment explanation
Indices: 665518--665566 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 18
665508 TTATATTTTT
665518 AAAATTATTAAAAATAAA
1 AAAATTATTAAAAATAAA
*
665536 AAAATTAATTAACAATATTAA
1 AAAATT-ATTAA-AA-ATAAA
665557 AAAATATATT
1 AAAAT-TATT
665567 TATATATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.23
19 5 0.19
20 2 0.08
21 12 0.46
22 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTATTAAAAATAAA
Found at i:665558 original size:19 final size:18
Alignment explanation
Indices: 665516--665558 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
665506 ATTTATATTT
665516 TTAAAATTATTAAAAATA
1 TTAAAATTATTAAAAATA
** *
665534 AAAAAATTAATTAACAATA
1 TTAAAATT-ATTAAAAATA
665553 TTAAAA
1 TTAAAA
665559 AATATATTTA
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAATTATTAAAAATA
Found at i:668122 original size:2 final size:2
Alignment explanation
Indices: 668115--668147 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
668105 CTTCAGCGTC
*
668115 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
668148 TCTGCCATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:676586 original size:15 final size:15
Alignment explanation
Indices: 676551--676584 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
676541 TTTTAAAATA
676551 TAAAATAATATAACT
1 TAAAATAATATAACT
*
676566 TAAAATAATCTAA-T
1 TAAAATAATATAACT
676580 TAAAA
1 TAAAA
676585 ATCAACCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAATAATATAACT
Found at i:693997 original size:19 final size:19
Alignment explanation
Indices: 693973--694009 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
693963 GAAAGTAAGA
*
693973 ATAAGAATTAGAATAGTTG
1 ATAAGAATTAGAAGAGTTG
693992 ATAAGAATTAGAAGAGTT
1 ATAAGAATTAGAAGAGTT
694010 TTAAAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.30
Consensus pattern (19 bp):
ATAAGAATTAGAAGAGTTG
Found at i:695256 original size:4 final size:4
Alignment explanation
Indices: 695247--695274 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
695237 CACCAGCTGT
695247 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
695275 ATGAGAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:698455 original size:30 final size:31
Alignment explanation
Indices: 698400--698458 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
698390 TAATATTATT
*
698400 AAAATATTATTTATATAATTAATTTAAATAA
1 AAAATATTATTTAAATAATTAATTTAAATAA
698431 AAAATTATTA-TTAAATAA-TAATTTAAAT
1 AAAA-TATTATTTAAATAATTAATTTAAAT
698459 TAATTAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.38
31 11 0.42
32 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AAAATATTATTTAAATAATTAATTTAAATAA
Found at i:702055 original size:24 final size:25
Alignment explanation
Indices: 701994--702060 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
701984 ATCATTTTTT
*
701994 TAAAAAATAAATATTAAATTATATAA
1 TAAAAAAT-AATATTAAATTATAAAA
* * *
702020 -AAATAATTATATTTAA-TATAAAA
1 TAAAAAATAATATTAAATTATAAAA
*
702043 TAAAAAATAATATAAAAT
1 TAAAAAATAATATTAAAT
702061 AAATTTAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
23 6 0.19
24 19 0.61
25 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
TAAAAAATAATATTAAATTATAAAA
Found at i:702120 original size:16 final size:16
Alignment explanation
Indices: 702097--702208 Score: 102
Period size: 16 Copynumber: 6.9 Consensus size: 16
702087 CTTAAAACTT
*
702097 AAAAAAATTTAAACTC
1 AAAAAAATTTAAATTC
* *
702113 AAATAAATTTAAATTT
1 AAAAAAATTTAAATTC
702129 ATAAAAAATTTAAATTC
1 A-AAAAAATTTAAATTC
* *
702146 AAATAAATTTAAATTT
1 AAAAAAATTTAAATTC
*
702162 AAAAAAAATTAAA-TC
1 AAAAAAATTTAAATTC
* *
702177 TAAATAAATATAAA-TC
1 -AAAAAAATTTAAATTC
*
702193 TAAACAAATTTAAATT
1 -AAAAAAATTTAAATT
702209 TACCCACACC
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
15 1 0.01
16 62 0.79
17 15 0.19
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAAAAATTTAAATTC
Found at i:702174 original size:32 final size:32
Alignment explanation
Indices: 702095--702208 Score: 158
Period size: 32 Copynumber: 3.5 Consensus size: 32
702085 AACTTAAAAC
*
702095 TTAAAAAAATTTAAACTCAAATAAATTTAAAT
1 TTAAAAAAATTTAAATTCAAATAAATTTAAAT
702127 TTATAAAAAATTTAAATTCAAATAAATTTAAAT
1 TTA-AAAAAATTTAAATTCAAATAAATTTAAAT
* *
702160 TTAAAAAAAATTAAA-TCTAAATAAATATAAAT
1 TTAAAAAAATTTAAATTC-AAATAAATTTAAAT
* *
702192 CTAAACAAATTTAAATT
1 TTAAAAAAATTTAAATT
702209 TACCCACACC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
31 2 0.03
32 39 0.53
33 32 0.44
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (32 bp):
TTAAAAAAATTTAAATTCAAATAAATTTAAAT
Found at i:702577 original size:13 final size:13
Alignment explanation
Indices: 702559--702677 Score: 63
Period size: 13 Copynumber: 9.1 Consensus size: 13
702549 ATAATTTTAA
702559 ATATAATATAAAT
1 ATATAATATAAAT
702572 ATATAA-ATAAAT
1 ATATAATATAAAT
*
702584 TTAATAAATATAAA-
1 AT-AT-AATATAAAT
702598 A-ATAATATATAA-
1 ATATAATATA-AAT
702610 ATATAATAT-AAT
1 ATATAATATAAAT
* * *
702622 ACAATACATTTAAAC
1 A-TATA-ATATAAAT
*
702637 ACAATTAATAT-AAT
1 A-TA-TAATATAAAT
*
702651 ATATTAATATATAT
1 ATA-TAATATAAAT
702665 ATATAA-ATAAAT
1 ATATAATATAAAT
702677 A
1 A
702678 ATACATACAT
Statistics
Matches: 85, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
11 8 0.09
12 19 0.22
13 29 0.34
14 13 0.15
15 14 0.16
16 2 0.02
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATAATATAAAT
Found at i:702580 original size:19 final size:19
Alignment explanation
Indices: 702556--702691 Score: 70
Period size: 19 Copynumber: 7.3 Consensus size: 19
702546 TTAATAATTT
702556 TAAATATAATATAAATATA
1 TAAATATAATATAAATATA
* *
702575 TAAATA-AATTTAATAAATA
1 TAAATATAATATAA-ATATA
*
702594 TAAAAATAATATATAA-ATA
1 TAAATATAATATA-AATATA
* * *
702613 T-AATATAATACAATACATT
1 TAAATATAATATAA-ATATA
* *
702632 TAAACACAAT-T-AATATA
1 TAAATATAATATAAATATA
* *
702649 -ATATATTAATATATATATA
1 TAAATA-TAATATAAATATA
* *
702668 TAAATA-AATAATACATACA
1 TAAATATAAT-ATAAATATA
702687 TAAAT
1 TAAAT
702692 CATCAAATTT
Statistics
Matches: 87, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
16 3 0.03
17 7 0.08
18 21 0.24
19 39 0.45
20 16 0.18
21 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATATAATATAAATATA
Found at i:702588 original size:38 final size:39
Alignment explanation
Indices: 702546--702620 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 39
702536 AAATCTTATC
* * *
702546 TTAATAATTTTAAATATAATATA-AATATATAA-ATAAAT
1 TTAATAAATATAAAAATAATATATAA-ATATAATATAAAT
702584 TTAATAAATATAAAAATAATATATAAATATAATATAA
1 TTAATAAATATAAAAATAATATATAAATATAATATAA
702621 TACAATACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 26 0.81
39 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (39 bp):
TTAATAAATATAAAAATAATATATAAATATAATATAAAT
Found at i:702592 original size:32 final size:33
Alignment explanation
Indices: 702556--702627 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
702546 TTAATAATTT
* *
702556 TAAATAT-AATATAAATATATAAATA-AATTTAA
1 TAAATATAAAAAT-AATATATAAATATAATATAA
702588 TAAATATAAAAATAATATATAAATATAATATAA
1 TAAATATAAAAATAATATATAAATATAATATAA
702621 TACAATA
1 TA-AATA
702628 CATTTAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 19 0.54
33 12 0.34
34 4 0.11
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (33 bp):
TAAATATAAAAATAATATATAAATATAATATAA
Found at i:710163 original size:18 final size:18
Alignment explanation
Indices: 710140--710198 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
710130 TTTTATTCAT
710140 TATAAAATATAAATATAA
1 TATAAAATATAAATATAA
*
710158 TATAAATTATTAAATAT-A
1 TATAAAATA-TAAATATAA
*
710176 T-TAAAATTTTAAATATAA
1 TATAAAA-TATAAATATAA
710194 TATAA
1 TATAA
710199 TAAATATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 11 0.32
18 13 0.38
19 10 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAAATATAAATATAA
Found at i:710180 original size:17 final size:18
Alignment explanation
Indices: 710140--710198 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
710130 TTTTATTCAT
*
710140 TATAAAA-TATAAATATA
1 TATAAAATTTTAAATATA
710157 -ATATAAATTATTAAATATA
1 TATA-AAATT-TTAAATATA
710176 T-TAAAATTTTAAATATAA
1 TATAAAATTTTAAATAT-A
710194 TATAA
1 TATAA
710199 TAAATATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 3 0.09
17 11 0.31
18 8 0.23
19 13 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAAATTTTAAATATA
Found at i:714201 original size:2 final size:2
Alignment explanation
Indices: 714196--714225 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
714186 GGGGGACCTT
714196 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
714226 CAGGAGAAAG
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):
TA
Found at i:716388 original size:163 final size:166
Alignment explanation
Indices: 716175--716512 Score: 497
Period size: 163 Copynumber: 2.1 Consensus size: 166
716165 TTAAATTTAA
*
716175 ATTA-TATGTAACTATCTTAAAAATTAACTTCATAAATTAATTAAATTTAATTTCAAATTTACAT
1 ATTATTATATAACTATCTTAAAAATTAACTTCATAAATTAATTAAATTTAATTTCAAATTTACAT
* *
716239 GCATAAATTACTTATACTTTACTTGAAAAATCTTTTAACATTTTT-AA-TTTTTTATATAAGATG
66 ACATAAATTACTTATACTTTACTTAAAAAATCTTTTAACATTTTTAAATTTTTTTATATAAGATG
* *
716302 GATATTAATACGTGGGAGGTAATCACATACTAGTAG
131 AATATTAATACGTGAGAGGTAATCACATACTAGTAG
* **
716338 ATTATTATATAAC-ATCTTAGAAAA-TAACTTCATCAATTAATTAAATTTAATTTTGAATTTACA
1 ATTATTATATAACTATCTTA-AAAATTAACTTCATAAATTAATTAAATTTAATTTCAAATTTACA
** * *
716401 TATGTGAATTACTTATACTTTACTTAAAAAATCTTTTAATATTTTTAAATTTTTTTATATAAGAT
65 TACATAAATTACTTATACTTTACTTAAAAAATCTTTTAACATTTTTAAATTTTTTTATATAAGAT
* * *
716466 GAATATTAATACGTGAGAGGTGATCACTTGCTAGTAG
130 GAATATTAATACGTGAGAGGTAATCACATACTAGTAG
716503 ATTATTATAT
1 ATTATTATAT
716513 GACACAATTG
Statistics
Matches: 156, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
163 86 0.55
164 13 0.08
165 57 0.37
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (166 bp):
ATTATTATATAACTATCTTAAAAATTAACTTCATAAATTAATTAAATTTAATTTCAAATTTACAT
ACATAAATTACTTATACTTTACTTAAAAAATCTTTTAACATTTTTAAATTTTTTTATATAAGATG
AATATTAATACGTGAGAGGTAATCACATACTAGTAG
Found at i:717693 original size:13 final size:14
Alignment explanation
Indices: 717677--717707 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
717667 AAAAGAAGAA
717677 AGGAGAGAGAGA-G
1 AGGAGAGAGAGAGG
717690 AGGAGAGAGAGAGG
1 AGGAGAGAGAGAGG
717704 AGGA
1 AGGA
717708 AAGCGGGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (14 bp):
AGGAGAGAGAGAGG
Found at i:717697 original size:11 final size:11
Alignment explanation
Indices: 717681--717705 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
717671 GAAGAAAGGA
717681 GAGAGAGAGAG
1 GAGAGAGAGAG
717692 GAGAGAGAGAG
1 GAGAGAGAGAG
717703 GAG
1 GAG
717706 GAAAGCGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (11 bp):
GAGAGAGAGAG
Found at i:718651 original size:15 final size:15
Alignment explanation
Indices: 718631--718663 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
718621 AGCCATGACT
*
718631 AACAGCAACAACATC
1 AACAGCAACAACAAC
718646 AACAGCAACAACAAC
1 AACAGCAACAACAAC
718661 AAC
1 AAC
718664 GACAACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.33, G:0.06, T:0.03
Consensus pattern (15 bp):
AACAGCAACAACAAC
Found at i:719137 original size:14 final size:15
Alignment explanation
Indices: 719112--719142 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
719102 AATTTAACAA
719112 AAAAATATATTAAAT
1 AAAAATATATTAAAT
719127 AAAAATA-ATTAAAT
1 AAAAATATATTAAAT
719141 AA
1 AA
719143 TTTTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATATATTAAAT
Found at i:719402 original size:15 final size:14
Alignment explanation
Indices: 719382--719436 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 14
719372 CATATCGTAA
719382 TTATATTTAATATAT
1 TTATATTTAATA-AT
719397 TTATATTTATATAAATT
1 TTATATTTA-AT-AA-T
719414 TTAATATATTAATAAT
1 TT-ATAT-TTAATAAT
719430 TTATATT
1 TTATATT
719437 ATATAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.03
15 13 0.37
16 6 0.17
17 6 0.17
18 6 0.17
19 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATATTTAATAAT
Found at i:719428 original size:18 final size:19
Alignment explanation
Indices: 719398--719500 Score: 60
Period size: 21 Copynumber: 5.5 Consensus size: 19
719388 TTAATATATT
719398 TATATTTATATAAATTTTAA
1 TATA-TTATATAAATTTTAA
719418 TATATTA-AT-AA--TT--
1 TATATTATATAAATTTTAA
719431 TATATTATATAAATTTTAA
1 TATATTATATAAATTTTAA
* *
719450 AATATT-TATATATTCATATAA
1 TATATTATATAAATT--T-TAA
* *
719471 TAT-TTATATTATTTTTATA
1 TATATTATATAAATTTTA-A
719490 TCATATTATAT
1 T-ATATTATAT
719501 TATAATTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 25
0.67 0.06 0.26
Matches are distributed among these distances:
13 7 0.11
14 2 0.03
15 4 0.06
17 4 0.06
18 11 0.17
19 11 0.17
20 9 0.14
21 16 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATTATATAAATTTTAA
Found at i:719443 original size:32 final size:33
Alignment explanation
Indices: 719383--719473 Score: 121
Period size: 32 Copynumber: 2.7 Consensus size: 33
719373 ATATCGTAAT
719383 TATATTTAATATATTTATATTTATATAAATTTTAA
1 TATA-TTAATATATTTATA-TTATATAAATTTTAA
719418 TATATTAATA-ATTTATATTATATAAATTTTAA
1 TATATTAATATATTTATATTATATAAATTTTAA
* * * *
719450 AATATTTATATATTCATATAATAT
1 TATATTAATATATTTATATTATAT
719474 TTATATTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 23 0.45
33 18 0.35
34 6 0.12
35 4 0.08
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
TATATTAATATATTTATATTATATAAATTTTAA
Found at i:719445 original size:15 final size:15
Alignment explanation
Indices: 719382--719446 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 15
719372 CATATCGTAA
*
719382 TTATATT-TAATATAT
1 TTATATTAT-ATAAAT
719397 TTATATTTATATAAAT
1 TTATA-TTATATAAAT
*
719413 TT-TAATATATTAATAAT
1 TTATATTATA-T-A-AAT
719430 TTATATTATATAAAT
1 TTATATTATATAAAT
719445 TT
1 TT
719447 TAAAATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 4 0.10
15 13 0.32
16 11 0.27
17 7 0.17
18 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTATATAAAT
Found at i:719490 original size:30 final size:27
Alignment explanation
Indices: 719429--719513 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
719419 ATATTAATAA
* * *
719429 TTTATATTATATAA-ATTTTAAAATATT
1 TTTATATCATATAATATTAT-AATTATT
*
719456 TATATATTCATATAATATT-TATATTATT
1 TTTATA-TCATATAATATTATA-ATTATT
*
719484 TTTATATCATATTATATTATAATTATT
1 TTTATATCATATAATATTATAATTATT
719511 TTT
1 TTT
719514 TCATAATATT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 26 0.53
28 20 0.41
29 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTATATCATATAATATTATAATTATT
Found at i:719535 original size:13 final size:13
Alignment explanation
Indices: 719480--719537 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 13
719470 ATATTTATAT
*
719480 TATTTTTATATCA
1 TATTTTTATATTA
719493 TATTATATTATAATTA
1 TATT-T-TTAT-ATTA
719509 T-TTTTTCATA--A
1 TATTTTT-ATATTA
719520 TATTTTTATATTA
1 TATTTTTATATTA
719533 TATTT
1 TATTT
719538 AATATTATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
11 5 0.14
12 5 0.14
13 13 0.35
14 4 0.11
15 6 0.16
16 4 0.11
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTTATATTA
Found at i:720290 original size:23 final size:22
Alignment explanation
Indices: 720245--720307 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 22
720235 AAAATAAATT
720245 AAATTAAAAAATTATTATAT-AA
1 AAATTAAAAAATT-TTATATAAA
720267 AAATTAAAAAATTTTATATGTAAA
1 AAATTAAAAAATTTTATA--TAAA
*
720291 AAATTAATAAAAATTTA
1 AAATTAA-AAAATTTTA
720308 AAATTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 5 0.14
22 13 0.36
23 1 0.03
24 9 0.25
25 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATTAAAAAATTTTATATAAA
Found at i:720291 original size:22 final size:22
Alignment explanation
Indices: 720245--720285 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
720235 AAAATAAATT
720245 AAATTAAAAAATTATTATATAA
1 AAATTAAAAAATTATTATATAA
720267 AAATTAAAAAATT-TTATAT
1 AAATTAAAAAATTATTATAT
720286 GTAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATTAAAAAATTATTATATAA
Found at i:720310 original size:17 final size:17
Alignment explanation
Indices: 720290--720322 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
720280 TTATATGTAA
720290 AAAATTAATAAAAATTT
1 AAAATTAATAAAAATTT
*
720307 AAAATTATTAAAAATT
1 AAAATTAATAAAAATT
720323 ATATAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTAATAAAAATTT
Found at i:720421 original size:14 final size:14
Alignment explanation
Indices: 720404--720466 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
720394 AATAAAAATT
720404 AATAATTTAATTTA
1 AATAATTTAATTTA
720418 AATAA---AATTT-
1 AATAATTTAATTTA
720428 AAT-ATTTATATTTTA
1 AATAATTTA-A-TTTA
*
720443 AATAATTAAATTTA
1 AATAATTTAATTTA
720457 AATAAATTTA
1 AAT-AATTTA
720467 TAAATTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
9 1 0.03
10 3 0.08
11 5 0.13
12 1 0.03
13 1 0.03
14 15 0.38
15 9 0.23
16 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAATTTAATTTA
Found at i:720424 original size:24 final size:23
Alignment explanation
Indices: 720382--720447 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 23
720372 AGACTTAAAT
*
720382 TATTTATTTATAAATAAAAATTAA
1 TATTTAATT-TAAATAAAAATTAA
*
720406 TAATTTAATTTAAATAAAATTTAA
1 T-ATTTAATTTAAATAAAAATTAA
720430 TATTTATATTTTAAATAA
1 TATTTA-A-TTTAAATAA
720448 TTAAATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.14
24 16 0.43
25 16 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTTAATTTAAATAAAAATTAA
Found at i:721841 original size:2 final size:2
Alignment explanation
Indices: 721828--721883 Score: 67
Period size: 2 Copynumber: 28.0 Consensus size: 2
721818 AAAGACTTGA
* * *
721828 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT AT CT GT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
721870 AT CT GT CT CT CT CT
1 CT CT CT CT CT CT CT
721884 TTGCTTTGCT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.04, C:0.45, G:0.04, T:0.48
Consensus pattern (2 bp):
CT
Found at i:722064 original size:3 final size:3
Alignment explanation
Indices: 722056--722082 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
722046 TTCAAGCTTT
722056 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
722083 TAAAGATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:726853 original size:29 final size:29
Alignment explanation
Indices: 726821--726876 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
726811 TTTATTTTTA
726821 TTAATTGAG-TTGAGTTTTATTAAATAATG
1 TTAATTGAGTTTGAGTTTT-TTAAATAATG
726850 TTAATTGAGTTTGAGTTTTTTAAATAA
1 TTAATTGAGTTTGAGTTTTTTAAATAA
726877 AAATAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (29 bp):
TTAATTGAGTTTGAGTTTTTTAAATAATG
Found at i:727325 original size:24 final size:24
Alignment explanation
Indices: 727276--727325 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
727266 ATAATACCAT
* *
727276 CCATTGATGAATGCTGGAAGTCTA
1 CCATTGATGAATGCTGGAAATATA
727300 CCATTGATGAATGCTGGAAATATA
1 CCATTGATGAATGCTGGAAATATA
727324 CC
1 CC
727326 TCGAAATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (24 bp):
CCATTGATGAATGCTGGAAATATA
Found at i:728239 original size:13 final size:13
Alignment explanation
Indices: 728223--728247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
728213 TAAAAAATTA
728223 TAAATAAATAAAT
1 TAAATAAATAAAT
728236 TAAATAAATAAA
1 TAAATAAATAAA
728248 ATATATATTA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAATAAATAAAT
Found at i:728989 original size:2 final size:2
Alignment explanation
Indices: 728982--729021 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
728972 AAGATCAAAG
728982 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
729022 TTGTAAGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:730447 original size:17 final size:17
Alignment explanation
Indices: 730425--730492 Score: 61
Period size: 16 Copynumber: 4.0 Consensus size: 17
730415 TATGATATAA
730425 ATATATTATTAAAATTT
1 ATATATTATTAAAATTT
*
730442 ATATATTA-TAAATTATT
1 ATATATTATTAAAAT-TT
*
730459 A-AT-TTATTAAAATTA
1 ATATATTATTAAAATTT
*
730474 ATATAAATATTAAATATTT
1 ATAT-ATTATTAAA-ATTT
730493 TAAATATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.12
16 14 0.35
17 11 0.28
18 7 0.17
19 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATTATTAAAATTT
Found at i:730478 original size:27 final size:28
Alignment explanation
Indices: 730442--730529 Score: 78
Period size: 27 Copynumber: 3.2 Consensus size: 28
730432 ATTAAAATTT
*
730442 ATATATTATAAATTATTAATTTATTAAA
1 ATATAATATAAATTATTAATTTATTAAA
730470 AT-TAATATAAA-TATTAAATATT-TT-AA
1 ATATAATATAAATTATT-AAT-TTATTAAA
* *
730496 ATATAATA-AAATATATTAATATAATAAAA
1 ATATAATATAAAT-TATTAAT-TTATTAAA
730525 ATATA
1 ATATA
730530 CGAATAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
26 11 0.22
27 23 0.46
28 9 0.18
29 7 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATATAATATAAATTATTAATTTATTAAA
Found at i:730509 original size:19 final size:18
Alignment explanation
Indices: 730470--730528 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 18
730460 ATTTATTAAA
730470 ATTAATATAAATATTAAATAT
1 ATTAATAT-AATA--AAATAT
*
730491 TTTAAATATAATAAAATAT
1 ATT-AATATAATAAAATAT
730510 ATTAATATAATAAAA-AT
1 ATTAATATAATAAAATAT
730527 AT
1 AT
730529 ACGAATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.11
18 12 0.34
19 8 0.23
21 6 0.17
22 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAATATAATAAAATAT
Found at i:730529 original size:19 final size:19
Alignment explanation
Indices: 730470--730529 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
730460 ATTTATTAAA
*
730470 ATTAATATAAATATTAAATAT
1 ATTAATAT-AATA-AAAATAT
*
730491 TTTAAATATAAT-AAAATAT
1 ATT-AATATAATAAAAATAT
730510 ATTAATATAATAAAAATAT
1 ATTAATATAATAAAAATAT
730529 A
1 A
730530 CGAATAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.24
19 16 0.47
21 5 0.15
22 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAATATAATAAAAATAT
Found at i:730535 original size:19 final size:19
Alignment explanation
Indices: 730495--730540 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
730485 AAATATTTTA
**
730495 AATATAAT-AAAATATATT
1 AATATAATAAAAATATACG
730513 AATATAATAAAAATATACG
1 AATATAATAAAAATATACG
*
730532 AATAAAATA
1 AATATAATA
730541 GACAAAGGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AATATAATAAAAATATACG
Found at i:730751 original size:344 final size:342
Alignment explanation
Indices: 730202--730826 Score: 991
Period size: 343 Copynumber: 1.8 Consensus size: 342
730192 GGAGTATATG
* * * * * *
730202 AAGGCTTTGATATGCTTAATTGTTCTATGTCTTCTTCACTAGTTGAGTCTTTTGCCTATTCAAGG
1 AAGGCTTTGATATGCTGAACTGTTATATGTCTTCTTCACTAATTGAGTCTTTTACCTACTCAAGG
* * *
730267 TGTAAGCATTTAAAAATTAATTGACACTGCTTCTTTGTCCTTTGTTATCATTGACCATAAAATAT
66 TGTAAGCATTTAAAAATTAATTGACACTGCTTCTTCGTCCTTTGCTATCATTGACCAGAAAATAT
* * *
730332 CTCATTTGACCTGAATACCTCCCATTTAATAATATATAACATGATTATATAAATAAAATATATAT
131 CTCACTTGACCTGAATACCTCCCATTAAATAATATATAACATGATTATATAAATAAAATATAAAT
730397 AAAATTTTAAAAATATAATATGATATAAATATATTATTAAAATTTATATATTATAAATTATTAAT
196 AAAATTTT-AAAATATAATATGATATAAATATATTATTAAAATTTATATATTATAAATTATTAAT
*
730462 TTATTAAAATTAATATAAATATTAAATATTTTAAATATAATAAAATATATTAATATAATAAAAAT
260 ATATTAAAATTAATATAAATATTAAATATTTTAAATATAATAAAATATATTAATATAATAAAAAT
730527 ATACGAATAAAATAGACA
325 ATACGAATAAAATAGACA
730545 AAGGCTTTGATATGCTGAACTGTTATATGTCTTCTTCACTAATTGAGTCTTTTACCTACCTCAAG
1 AAGGCTTTGATATGCTGAACTGTTATATGTCTTCTTCACTAATTGAGTCTTTTACCTA-CTCAAG
* * *
730610 GTGTAAGCATTTAAAAATTAATTGAGACTGCTTCTTCGTCCTTTGCTATGATTGACCAGGAAATA
65 GTGTAAGCATTTAAAAATTAATTGACACTGCTTCTTCGTCCTTTGCTATCATTGACCAGAAAATA
** * * * *
730675 TCTCACTTGACCTGAATACCTCTTACTTAAATAATGTATTATATGATTATATAAATATAATATAA
130 TCTCACTTGACCTGAATACCTCCCA-TTAAATAATATATAACATGATTATATAAATAAAATATAA
*
730740 AT-AATTTTTAAAATATAATATGATATAAATATATTATTAAAATTTATATATTATAAATTATTAA
194 ATAAAATTTTAAAATATAATATGATATAAATATATTATTAAAATTTATATATTATAAATTATTAA
* *
730804 TATATTAAAATTCATATATATAT
259 TATATTAAAATTAATATAAATAT
730827 ATATATGTAT
Statistics
Matches: 255, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
343 128 0.50
344 92 0.36
345 35 0.14
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (342 bp):
AAGGCTTTGATATGCTGAACTGTTATATGTCTTCTTCACTAATTGAGTCTTTTACCTACTCAAGG
TGTAAGCATTTAAAAATTAATTGACACTGCTTCTTCGTCCTTTGCTATCATTGACCAGAAAATAT
CTCACTTGACCTGAATACCTCCCATTAAATAATATATAACATGATTATATAAATAAAATATAAAT
AAAATTTTAAAATATAATATGATATAAATATATTATTAAAATTTATATATTATAAATTATTAATA
TATTAAAATTAATATAAATATTAAATATTTTAAATATAATAAAATATATTAATATAATAAAAATA
TACGAATAAAATAGACA
Found at i:730765 original size:28 final size:30
Alignment explanation
Indices: 730747--730802 Score: 57
Period size: 28 Copynumber: 2.0 Consensus size: 30
730737 TAAATAATTT
*
730747 TTAAAATAT-AATATGATATAAATATATTA
1 TTAAAATATAAATATAATATAAATATATTA
* *
730776 TTAAAAT-T-TATATATTATAAAT-TATTA
1 TTAAAATATAAATATAATATAAATATATTA
730803 ATATATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 12 0.50
29 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (30 bp):
TTAAAATATAAATATAATATAAATATATTA
Found at i:730790 original size:17 final size:17
Alignment explanation
Indices: 730768--730822 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
730758 TATGATATAA
730768 ATATATTATTAAAATTT
1 ATATATTATTAAAATTT
*
730785 ATATATTA-TAAATTATT
1 ATATATTATTAAAAT-TT
*
730802 A-ATA-TATTAAAATTC
1 ATATATTATTAAAATTT
730817 ATATAT
1 ATATAT
730823 ATATATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 4 0.13
16 16 0.52
17 11 0.35
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATTATTAAAATTT
Found at i:730826 original size:18 final size:16
Alignment explanation
Indices: 730768--730822 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
730758 TATGATATAA
730768 ATATATTATTAAAATT
1 ATATATTATTAAAATT
730784 -TATA-TATTATAAATT
1 ATATATTATTA-AAATT
730799 AT-TAATATATTAAAATT
1 ATAT-AT-TATTAAAATT
730816 CATATAT
1 -ATATAT
730823 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 5 0.16
15 10 0.31
16 2 0.06
17 5 0.16
18 9 0.28
19 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATTATTAAAATT
Found at i:730826 original size:20 final size:19
Alignment explanation
Indices: 730768--730828 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 19
730758 TATGATATAA
730768 ATATATTATTAAA--ATT-T
1 ATATATTA-TAAATTATTAT
730785 ATATATTATAAATTATTA-
1 ATATATTATAAATTATTAT
730803 ATATATTA-AAATTCATATAT
1 ATATATTATAAATT-AT-TAT
730823 ATATAT
1 ATATAT
730829 ATATGTATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.11
17 13 0.34
18 13 0.34
19 2 0.05
20 6 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATTATAAATTATTAT
Found at i:731642 original size:20 final size:18
Alignment explanation
Indices: 731614--731703 Score: 81
Period size: 20 Copynumber: 4.6 Consensus size: 18
731604 CACAATTTTA
731614 AATACAATATAAAATATAT
1 AATA-AATATAAAATATAT
* *
731633 AGTATAAATATCAAATATTT
1 A--ATAAATATAAAATATAT
731653 AATAAATATATAAATAATAT
1 AATAAATATA-AAAT-ATAT
*
731673 AATAAATTTAAATATAATAT
1 AATAAATATAAA-AT-ATAT
731693 AATAATATATA
1 AATAA-ATATA
731704 TAATTTTATG
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
18 8 0.14
19 7 0.12
20 37 0.63
21 7 0.12
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (18 bp):
AATAAATATAAAATATAT
Found at i:731681 original size:29 final size:29
Alignment explanation
Indices: 731649--731711 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
731639 AATATCAAAT
731649 ATTTAATAAAT-ATATAAATAATATA-ATAA
1 ATTTAA-AAATAATAT-AATAATATATATAA
*
731678 ATTTAAATATAATATAATAATATATATAA
1 ATTTAAAAATAATATAATAATATATATAA
*
731707 TTTTA
1 ATTTA
731712 TGATTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTTAAAAATAATATAATAATATATATAA
Found at i:731708 original size:28 final size:26
Alignment explanation
Indices: 731655--731711 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 26
731645 AAATATTTAA
731655 TAAATATATAAATAATATAATAAATT
1 TAAATATATAAATAATATAATAAATT
*
731681 TAAATATAATATAATAATATATATAATTT
1 TAAATAT-ATA-AATAATATA-ATAAATT
731710 TA
1 TA
731712 TGATTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 7 0.26
27 3 0.11
28 9 0.33
29 8 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAATATATAAATAATATAATAAATT
Found at i:735458 original size:30 final size:30
Alignment explanation
Indices: 735422--735481 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
735412 ACTTATGTTC
735422 CATTCATTTTCTTGTCTAGTTGCTCATTGT
1 CATTCATTTTCTTGTCTAGTTGCTCATTGT
735452 CATTCATTTTCTTGTCTAGTTGCTCATTGT
1 CATTCATTTTCTTGTCTAGTTGCTCATTGT
735482 GACATAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (30 bp):
CATTCATTTTCTTGTCTAGTTGCTCATTGT
Found at i:735642 original size:23 final size:24
Alignment explanation
Indices: 735616--735678 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 24
735606 GATTCTATAC
735616 ATTATAATCTTCAGTCTC-CCTTG
1 ATTATAATCTTCAGTCTCACCTTG
* *
735639 ATTACTCA-C-T-ATTCCTCACCTTG
1 ATTA-TAATCTTCAGT-CTCACCTTG
735662 ATTATAATCTTCAGTCT
1 ATTATAATCTTCAGTCT
735679 GGTGATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 11
0.67 0.09 0.24
Matches are distributed among these distances:
21 2 0.07
22 6 0.20
23 15 0.50
24 5 0.17
25 2 0.07
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.43
Consensus pattern (24 bp):
ATTATAATCTTCAGTCTCACCTTG
Found at i:741355 original size:27 final size:30
Alignment explanation
Indices: 741315--741373 Score: 88
Period size: 27 Copynumber: 2.1 Consensus size: 30
741305 ATTATGTCCA
741315 TATCCAATGACAAAT-GAA-AGAG-TAACC
1 TATCCAATGACAAATGGAAGAGAGTTAACC
*
741342 TATCCAATGCCAAATGGAAGAGAGTTAACC
1 TATCCAATGACAAATGGAAGAGAGTTAACC
741372 TA
1 TA
741374 GTCGAAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 14 0.50
28 3 0.11
29 4 0.14
30 7 0.25
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (30 bp):
TATCCAATGACAAATGGAAGAGAGTTAACC
Found at i:741539 original size:16 final size:17
Alignment explanation
Indices: 741518--741550 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
741508 TATATTTTAA
*
741518 ATTTAATAAT-ATTATT
1 ATTTAAAAATGATTATT
741534 ATTTAAAAATGATTATT
1 ATTTAAAAATGATTATT
741551 TGAATTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
ATTTAAAAATGATTATT
Found at i:743328 original size:2 final size:2
Alignment explanation
Indices: 743321--743358 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
743311 TATAAGTATG
743321 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
743359 AACTGTAAAT
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:747671 original size:16 final size:17
Alignment explanation
Indices: 747642--747686 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 17
747632 TGATGATGTG
747642 ATATAAATATTAAA-TATT
1 ATATAAA-A-TAAATTATT
747660 ATATAAAATAAATTATT
1 ATATAAAATAAATTATT
747677 A-AT-AAATAAA
1 ATATAAAATAAA
747687 AATTTAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.27
16 6 0.23
17 6 0.23
18 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAAAATAAATTATT
Found at i:748459 original size:40 final size:40
Alignment explanation
Indices: 748404--748484 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
748394 TATTTCCGCC
*
748404 AGAAGTTGTTAAACAAAGTACTCAATTCCTATTATGGCAT
1 AGAAGTTGTTAAACAAAGTACTCAATTCCTATCATGGCAT
*
748444 AGAAGTTGTTAAACAAAGTACTCAATTCCTATCATGTCAT
1 AGAAGTTGTTAAACAAAGTACTCAATTCCTATCATGGCAT
748484 A
1 A
748485 TTATGGATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (40 bp):
AGAAGTTGTTAAACAAAGTACTCAATTCCTATCATGGCAT
Found at i:752120 original size:31 final size:33
Alignment explanation
Indices: 752085--752161 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 33
752075 TTTTTTATCG
752085 TTATTTAAATTATAATCATAAAT-A-TATATAA
1 TTATTTAAATTATAATCATAAATAATTATATAA
* *
752116 TTATTATAAA-TATTATCATATATAATTATATAA
1 TTATT-TAAATTATAATCATAAATAATTATATAA
752149 TT-TTT-AATTATAA
1 TTATTTAAATTATAA
752162 ATATTGACGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 2 0.05
31 21 0.54
32 7 0.18
33 9 0.23
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (33 bp):
TTATTTAAATTATAATCATAAATAATTATATAA
Found at i:752123 original size:13 final size:13
Alignment explanation
Indices: 752107--752144 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
752097 TAATCATAAA
752107 TATATATAATTAT
1 TATATATAATTAT
*
752120 TATAAAT-ATTAT
1 TATATATAATTAT
*
752132 CATATATAATTAT
1 TATATATAATTAT
752145 ATAATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATATAATTAT
Found at i:752123 original size:25 final size:26
Alignment explanation
Indices: 752093--752149 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
752083 CGTTATTTAA
752093 ATTATAATCATA-AAT-ATATATAATT
1 ATTATAAT-ATATAATCATATATAATT
*
752118 ATTATAA-ATATTATCATATATAATT
1 ATTATAATATATAATCATATATAATT
752143 A-TATAAT
1 ATTATAAT
752150 TTTTAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 3 0.11
24 7 0.25
25 18 0.64
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTATAATATATAATCATATATAATT
Found at i:753656 original size:20 final size:19
Alignment explanation
Indices: 753613--753688 Score: 61
Period size: 20 Copynumber: 4.1 Consensus size: 19
753603 TTAATATTTT
753613 ATTTTATTATTTAAAAATA
1 ATTTTATTATTTAAAAATA
* * *
753632 TTTTTATATATTTATAATTA
1 ATTTTAT-TATTTAAAAATA
*
753652 ATTTTA--A-ATAAAAAT-
1 ATTTTATTATTTAAAAATA
*
753667 ATTTTATTAATTAATAAATA
1 ATTTTATTATTTAA-AAATA
753687 AT
1 AT
753689 ATTTTTAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
15 6 0.14
16 5 0.12
17 2 0.05
18 3 0.07
19 10 0.23
20 17 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTATTATTTAAAAATA
Found at i:756881 original size:38 final size:37
Alignment explanation
Indices: 756801--756882 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
756791 TTATTATGCT
*
756801 ATTTTTAATTTATTAAATAAATAATATTTATATCATA
1 ATTTTTAATTTATTAAATAAATAATAATTATATCATA
* * * *
756838 TTTTTTTATTATATT-AATATATCATAATTATATCATA
1 ATTTTTAATT-TATTAAATAAATAATAATTATATCATA
756875 CATTTTTA
1 -ATTTTTA
756883 CCAAATTTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
37 27 0.75
38 9 0.25
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (37 bp):
ATTTTTAATTTATTAAATAAATAATAATTATATCATA
Found at i:762343 original size:9 final size:9
Alignment explanation
Indices: 762329--762406 Score: 52
Period size: 9 Copynumber: 8.6 Consensus size: 9
762319 TAAATCTATA
762329 TAATTAATT
1 TAATTAATT
762338 TAATTAATT
1 TAATTAATT
762347 TAATT--TT
1 TAATTAATT
* *
762354 AAATAAAATTT
1 TAAT-TAA-TT
*
762365 TAAATAATT
1 TAATTAATT
*
762374 TAATTAAAAT
1 TAATT-AATT
762384 TAATTAATT
1 TAATTAATT
* * *
762393 CAGTTAAAT
1 TAATTAATT
762402 TAATT
1 TAATT
762407 TTATCATTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
7 5 0.10
9 32 0.63
10 10 0.20
11 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (9 bp):
TAATTAATT
Found at i:762439 original size:20 final size:19
Alignment explanation
Indices: 762396--762445 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
762386 ATTAATTCAG
*
762396 TTAAATTAATTTTATCATT
1 TTAAATTAATTTTATAATT
762415 TTAAATTTAATTTTA-AATT
1 TTAAA-TTAATTTTATAATT
762434 TATAAAATTAAT
1 T-T-AAATTAAT
762446 AATATGAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAAATTAATTTTATAATT
Found at i:762716 original size:20 final size:19
Alignment explanation
Indices: 762687--762724 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
762677 TAATTAAATT
*
762687 TAATATAAATTATTATTTAA
1 TAATAAAAATTATT-TTTAA
762707 TAATAAAAATTATTTTTA
1 TAATAAAAATTATTTTTA
762725 TTTAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATAAAAATTATTTTTAA
Found at i:762718 original size:17 final size:17
Alignment explanation
Indices: 762684--762721 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
762674 ATTTAATTAA
*
762684 ATTTAATATAAATTATT
1 ATTTAATATAAATAATT
762701 ATTTAATAATAAA-AATT
1 ATTTAAT-ATAAATAATT
762718 ATTT
1 ATTT
762722 TTATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATATAAATAATT
Found at i:762744 original size:23 final size:23
Alignment explanation
Indices: 762675--762744 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 23
762665 AAATTTTTAA
* * *
762675 TTTAATTAAATTTAATATAAATT
1 TTTATTTAAATTTATTAAAAATT
* * *
762698 ATTATTT-AA-TAATAAAAATTATT
1 TTTATTTAAATTTATTAAAA--ATT
762721 TTTATTTAAATTTATTAAAAATT
1 TTTATTTAAATTTATTAAAAATT
762744 T
1 T
762745 AAAAAAGTTA
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
21 5 0.15
22 2 0.06
23 18 0.53
24 2 0.06
25 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTATTTAAATTTATTAAAAATT
Found at i:763072 original size:21 final size:21
Alignment explanation
Indices: 763046--763085 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
763036 TATTTTATTG
*
763046 AAAAATAAAATATTAATTAAA
1 AAAAATAAAAAATTAATTAAA
*
763067 AAAAATAAAAAATTTATTA
1 AAAAATAAAAAATTAATTA
763086 CCTAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATAAAAAATTAATTAAA
Found at i:767324 original size:20 final size:20
Alignment explanation
Indices: 767301--767346 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
767291 AAAAAACACG
767301 AATATAATATAAAA-AACTA-A
1 AATATAATA-AAAATAA-TATA
767321 AATATAATAAAAATAATATA
1 AATATAATAAAAATAATATA
767341 AATATA
1 AATATA
767347 CTATTAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
AATATAATAAAAATAATATA
Found at i:767863 original size:18 final size:18
Alignment explanation
Indices: 767840--767959 Score: 78
Period size: 18 Copynumber: 7.1 Consensus size: 18
767830 TTTAAATAAC
767840 AATTATAATATATATTAT
1 AATTATAATATATATTAT
* *
767858 AATTATTATATATTTTAT
1 AATTATAATATATATTAT
*
767876 AATTTTAAT-T-T-TTAT
1 AATTATAATATATATTAT
* * *
767891 TATTTTAATATTTATTAT
1 AATTATAATATATATTAT
* *
767909 AATTA-AAAATA-ATAAT
1 AATTATAATATATATTAT
767925 -ATTCAT--TATATA-TAT
1 AATT-ATAATATATATTAT
* *
767940 AATTATAATAAATATAAT
1 AATTATAATATATATTAT
767958 AA
1 AA
767960 GATAAAAAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
15 22 0.28
16 11 0.14
17 11 0.14
18 34 0.44
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTATAATATATATTAT
Found at i:767890 original size:15 final size:15
Alignment explanation
Indices: 767854--767905 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
767844 ATAATATATA
767854 TTATAATTATTATATATT
1 TTATAATT-TTA-AT-TT
767872 TTATAATTTTAATTT
1 TTATAATTTTAATTT
* *
767887 TTATTATTTTAATAT
1 TTATAATTTTAATTT
767902 TTAT
1 TTAT
767906 TATAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 19 0.59
16 2 0.06
17 3 0.09
18 8 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATAATTTTAATTT
Found at i:768997 original size:6 final size:6
Alignment explanation
Indices: 768986--769096 Score: 78
Period size: 6 Copynumber: 19.0 Consensus size: 6
768976 AAAAAAATTT
*
768986 ATTTAA ATTT-A ATTATAA ATATT-A ATTT-A ATTTAA ACTTAA ATTTAA
1 ATTTAA ATTTAA ATT-TAA AT-TTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
769033 ATTT-- ATTTAA ATTT-A ATTATAA ATATT-A ATATT-A ATTTAAA ATTTTA
1 ATTTAA ATTTAA ATTTAA ATT-TAA AT-TTAA AT-TTAA ATTT-AA ATTTAA
*
769080 ATTT-A ATTTAA ACTTAA
1 ATTTAA ATTTAA ATTTAA
769097 TTCAATTTAT
Statistics
Matches: 89, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.04
5 22 0.25
6 48 0.54
7 13 0.15
8 2 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:768998 original size:23 final size:23
Alignment explanation
Indices: 768972--769049 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 23
768962 AAATTTGATG
768972 TAATAAAAAAATTTATTTAAATT
1 TAATAAAAAAATTTATTTAAATT
*
768995 TAATTATAAATATTAATTTAATTTAAACT
1 TAA-TA-AAA-A--AATTT-ATTTAAATT
***
769024 TAA-ATTTAAATTTATTTAAATT
1 TAATAAAAAAATTTATTTAAATT
769046 TAAT
1 TAAT
769050 TATAAATATT
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
22 11 0.26
23 8 0.19
24 2 0.05
25 4 0.09
26 1 0.02
27 1 0.02
28 5 0.12
29 11 0.26
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATAAAAAAATTTATTTAAATT
Found at i:769014 original size:18 final size:16
Alignment explanation
Indices: 768986--769105 Score: 100
Period size: 18 Copynumber: 6.9 Consensus size: 16
768976 AAAAAAATTT
768986 ATTTAAATTTAATTATAA
1 ATTT-AATTTAATT-TAA
769004 ATATTAATTTAATTTAA
1 AT-TTAATTTAATTTAA
*
769021 ACTTAAATTTAAATTT--
1 A-TTTAATTT-AATTTAA
769037 ATTTAAATTTAATTATAA
1 ATTT-AATTTAATT-TAA
769055 ATATTAATATTAATTTAAA
1 AT-TTAAT-TTAATTT-AA
769074 ATTTTAATTTAATTTAA
1 A-TTTAATTTAATTTAA
* *
769091 ACTTAATTCAATTTA
1 ATTTAATTTAATTTA
769106 TACTTGAATA
Statistics
Matches: 87, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
15 6 0.07
16 19 0.22
17 13 0.15
18 30 0.34
19 18 0.21
20 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTTAATTTAA
Found at i:769018 original size:51 final size:52
Alignment explanation
Indices: 768976--769073 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 52
768966 TTGATGTAAT
768976 AAAAAAATTTATTTAAATTTAATTATAAATATTAAT-TTAATTTAAACTTAA
1 AAAAAAATTTATTTAAATTTAATTATAAATATTAATATTAATTTAAACTTAA
***
769027 ATTTAAATTTATTTAAATTTAATTATAAATATTAATATTAATTTAAA
1 AAAAAAATTTATTTAAATTTAATTATAAATATTAATATTAATTTAAA
769074 ATTTTAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
51 33 0.77
52 10 0.23
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (52 bp):
AAAAAAATTTATTTAAATTTAATTATAAATATTAATATTAATTTAAACTTAA
Found at i:769076 original size:41 final size:41
Alignment explanation
Indices: 768985--769090 Score: 55
Period size: 40 Copynumber: 2.6 Consensus size: 41
768975 TAAAAAAATT
* * *
768985 TATTTAAATTTAATTATAAATATTAATTT-AATTTAAACTTAAA
1 TATTAAAATTAAATT-TAAAT-TTAATTTAAATTT-AATTTAAA
*
769028 T-TT-AAATT-TATTTAAATTTAATTATAAATATTAATATT-AA
1 TATTAAAATTAAATTTAAATTTAATT-TAAAT-TTAAT-TTAAA
*
769068 T-TTAAAATTTTAATTT-AATTTAA
1 TATTAAAA-TTAAATTTAAATTTAA
769091 ACTTAATTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
38 6 0.11
39 6 0.11
40 13 0.25
41 12 0.23
42 11 0.21
43 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (41 bp):
TATTAAAATTAAATTTAAATTTAATTTAAATTTAATTTAAA
Done.