Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold170
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: 1632119
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 57634 characters in sequence are not A, C, G, or T
File 7 of 11
Found at i:1048838 original size:16 final size:17
Alignment explanation
Indices: 1048808--1048858 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
1048798 GGATAAGGAA
**
1048808 TTTTAAAATGCTATTAT
1 TTTTAAAATATTATTAT
1048825 TTTTAAAAT-TTATTA-
1 TTTTAAAATATTATTAT
* *
1048840 ATTTAAAATATTAGTAT
1 TTTTAAAATATTATTAT
1048857 TT
1 TT
1048859 GTAATTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.29
16 10 0.36
17 10 0.36
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTTAAAATATTATTAT
Found at i:1053275 original size:44 final size:44
Alignment explanation
Indices: 1053205--1053290 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
1053195 AGAATGCGTG
* *
1053205 TAAGATACGAATACTTATTTATTACAGGCATTATCTAATATGAA
1 TAAGATACGAATACTTATTGACTACAGGCATTATCTAATATGAA
* * *
1053249 TAAGATACGGATACTTGTTGACTACAGGTATTATCTAATATG
1 TAAGATACGAATACTTATTGACTACAGGCATTATCTAATATG
1053291 GATATGTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (44 bp):
TAAGATACGAATACTTATTGACTACAGGCATTATCTAATATGAA
Found at i:1059007 original size:6 final size:6
Alignment explanation
Indices: 1058996--1059029 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1058986 CATGTACCAG
* *
1058996 CAGCAA CAGCAA CAGCAA CAACAA CAACAA CAGC
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGC
1059030 CATCATCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.35, G:0.12, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:1059595 original size:21 final size:23
Alignment explanation
Indices: 1059569--1059611 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1059559 TTAATATAGA
1059569 TTTAAATA-AAAT-ATAAAATCT
1 TTTAAATACAAATAATAAAATCT
*
1059590 TTTAAATACAATTAATAAAATC
1 TTTAAATACAAATAATAAAATC
1059612 AAACAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (23 bp):
TTTAAATACAAATAATAAAATCT
Found at i:1059713 original size:2 final size:2
Alignment explanation
Indices: 1059685--1059730 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
1059675 TATCTTTGTT
* *
1059685 TA TA TA TG T- TA T- TA TA TCA TT TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
1059726 TA TA T
1 TA TA T
1059731 CTTTATGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1060188 original size:20 final size:19
Alignment explanation
Indices: 1060152--1060189 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1060142 ATAAAATACA
1060152 TATATTTTTAATTATTTAT
1 TATATTTTTAATTATTTAT
*
1060171 TATATTTATTACTTATTTA
1 TATATTT-TTAATTATTTA
1060190 ATAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TATATTTTTAATTATTTAT
Found at i:1060302 original size:20 final size:18
Alignment explanation
Indices: 1060274--1060316 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1060264 TATTAATTTT
*
1060274 TAATATTA-T-TTTAAAG
1 TAATATTATTATTTAAAA
1060290 TACATATTATTATTTAAAA
1 TA-ATATTATTATTTAAAA
1060309 TAATATTA
1 TAATATTA
1060317 AAAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 6 0.26
18 7 0.30
19 8 0.35
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TAATATTATTATTTAAAA
Found at i:1063567 original size:18 final size:18
Alignment explanation
Indices: 1063544--1063578 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1063534 TTCACGGTAT
*
1063544 ATATATATATATATAAAA
1 ATATATACATATATAAAA
*
1063562 ATATATACATGTATAAA
1 ATATATACATATATAAA
1063579 TATTACAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
ATATATACATATATAAAA
Found at i:1065146 original size:15 final size:15
Alignment explanation
Indices: 1065126--1065158 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1065116 TCATTGGTGA
*
1065126 AATCTATGTTACTTG
1 AATCTATATTACTTG
1065141 AATCTATATTACTTG
1 AATCTATATTACTTG
1065156 AAT
1 AAT
1065159 TCGAGTATGT
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:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (15 bp):
AATCTATATTACTTG
Found at i:1065838 original size:2 final size:2
Alignment explanation
Indices: 1065825--1065865 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1065815 GACCAAACAA
*
1065825 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1065866 AACATAACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1071799 original size:6 final size:6
Alignment explanation
Indices: 1071788--1071812 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1071778 ATAATGATAT
1071788 GTTTGA GTTTGA GTTTGA GTTTGA G
1 GTTTGA GTTTGA GTTTGA GTTTGA G
1071813 AGAGAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GTTTGA
Found at i:1071829 original size:14 final size:14
Alignment explanation
Indices: 1071810--1071840 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1071800 GTTTGAGTTT
1071810 GAGAGAGAGAAAGA
1 GAGAGAGAGAAAGA
1071824 GAGAGAGAGAAAGA
1 GAGAGAGAGAAAGA
1071838 GAG
1 GAG
1071841 CTGAGTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (14 bp):
GAGAGAGAGAAAGA
Found at i:1072337 original size:25 final size:24
Alignment explanation
Indices: 1072318--1072366 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1072308 TTTTATTTTA
*
1072318 AAAAATTTAAATTTAATTTAAAAT
1 AAAAATTTAAATTTAATTTATAAT
*
1072342 AAAAATATTAAATTTAAATTATAAT
1 AAAAAT-TTAAATTTAATTTATAAT
1072367 TTTTTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAAATTTAAATTTAATTTATAAT
Found at i:1072405 original size:31 final size:29
Alignment explanation
Indices: 1072346--1072414 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
1072336 TAAAATAAAA
1072346 ATATTAAATTTAAATTATAATTTTTTAATAT
1 ATATTAAATTT-AATTATAATTTTTTAAT-T
*
1072377 ATATTAAATTT-TTTATTAATTTTATTAATT
1 ATATTAAATTTAATTA-TAATTTT-TTAATT
1072407 AT-TTAAAT
1 ATATTAAAT
1072415 AAAATATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 9 0.26
30 10 0.29
31 16 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
ATATTAAATTTAATTATAATTTTTTAATT
Found at i:1072851 original size:26 final size:27
Alignment explanation
Indices: 1072800--1072851 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1072790 TTATACAAAT
*
1072800 AATAAAAATTAATAAAAAAATCTGTGA
1 AATAAAAATTAATAAAAAAATATGTGA
1072827 AATAAAAATT-ATAACAAAAA-ATGTG
1 AATAAAAATTAATAA-AAAAATATGTG
1072852 TACTAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.25
Consensus pattern (27 bp):
AATAAAAATTAATAAAAAAATATGTGA
Found at i:1073882 original size:19 final size:20
Alignment explanation
Indices: 1073854--1073892 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1073844 ATTACGAGTT
*
1073854 ATTTATGAAA-AAATATGTA
1 ATTTACGAAACAAATATGTA
1073873 ATTTACGAAACAAATATGTA
1 ATTTACGAAACAAATATGTA
1073893 TCTAAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.33
Consensus pattern (20 bp):
ATTTACGAAACAAATATGTA
Found at i:1080575 original size:2 final size:2
Alignment explanation
Indices: 1080568--1080606 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1080558 ATAACCTGAA
1080568 AT 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 AT A
1080607 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1082153 original size:27 final size:26
Alignment explanation
Indices: 1082123--1082199 Score: 66
Period size: 28 Copynumber: 2.9 Consensus size: 26
1082113 ATTCGTATTA
*
1082123 TTTTAGATTTAAATTATATTATAAAAT
1 TTTTAAATTTAAATTATATT-TAAAAT
* **
1082150 TTTTAAATTTTAATATTTTATTTAATTT
1 TTTTAAA-TTTAA-ATTATATTTAAAAT
* *
1082178 TTTTACATTTAAA-TATTTTTAA
1 TTTTAAATTTAAATTATATTTAA
1082200 TTTGAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
25 7 0.17
26 1 0.02
27 11 0.27
28 15 0.37
29 7 0.17
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (26 bp):
TTTTAAATTTAAATTATATTTAAAAT
Found at i:1082170 original size:26 final size:27
Alignment explanation
Indices: 1082123--1082191 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
1082113 ATTCGTATTA
*
1082123 TTTTAGATTTAAATTATATTATAAAAT
1 TTTTAAATTTAAATTATATTATAAAAT
* **
1082150 TTTTAAATTTTAATATTTTATT-TAATTT
1 TTTTAAA-TTTAA-ATTATATTATAAAAT
*
1082178 TTTTACATTTAAAT
1 TTTTAAATTTAAAT
1082192 ATTTTTAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.06
27 11 0.31
28 15 0.43
29 7 0.20
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTTAAATTTAAATTATATTATAAAAT
Found at i:1082223 original size:45 final size:44
Alignment explanation
Indices: 1082144--1082236 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 44
1082134 AATTATATTA
* *
1082144 TAAA-ATTTTTAAATTTTAATATTTTATTTAATTTT-TTTACATT
1 TAAATATTTTTAAATTTGAATATTTTATTTAATTTTATTGA-ATT
*
1082187 TAAATATTTTT-AATTTGAATTTTTTATATTTAATTTTATTGAATT
1 TAAATATTTTTAAATTTGAA-TATTT-TATTTAATTTTATTGAATT
1082232 TAAAT
1 TAAAT
1082237 TTTATTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
43 11 0.26
44 10 0.23
45 19 0.44
46 3 0.07
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (44 bp):
TAAATATTTTTAAATTTGAATATTTTATTTAATTTTATTGAATT
Found at i:1082232 original size:30 final size:30
Alignment explanation
Indices: 1082144--1082248 Score: 92
Period size: 30 Copynumber: 3.5 Consensus size: 30
1082134 AATTATATTA
* * *
1082144 TAAAATTTTTAAATTTTAATA-TTTT-ATT
1 TAAATTTTTTATATTTAAATATTTTTAATT
* *
1082172 TAATTTTTTTACATTTAAATATTTTTAATT
1 TAAATTTTTTATATTTAAATATTTTTAATT
*
1082202 TGAATTTTTTATATTT-AAT-TTTATTGAATT
1 TAAATTTTTTATATTTAAATATTT-TT-AATT
*
1082232 TAAATTTTATTTTATTT
1 TAAATTTT-TTATATTT
1082249 TTTATCTTAC
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 20 0.32
29 9 0.14
30 27 0.43
31 7 0.11
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (30 bp):
TAAATTTTTTATATTTAAATATTTTTAATT
Found at i:1082242 original size:16 final size:14
Alignment explanation
Indices: 1082146--1082239 Score: 84
Period size: 15 Copynumber: 6.5 Consensus size: 14
1082136 TTATATTATA
*
1082146 AAATTTTTAAATTT
1 AAATTTTTTAATTT
* *
1082160 TAATATTTT-ATTT
1 AAATTTTTTAATTT
*
1082173 AATTTTTTTACATTT
1 AAATTTTTTA-ATTT
1082188 AAATATTTTTAATTT
1 AAAT-TTTTTAATTT
*
1082203 GAATTTTTTATATTT
1 AAATTTTTTA-ATTT
1082218 -AATTTTATTGAATTT
1 AAATTTT-TT-AATTT
1082233 AAATTTT
1 AAATTTT
1082240 ATTTTATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
13 10 0.15
14 18 0.28
15 24 0.37
16 13 0.20
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (14 bp):
AAATTTTTTAATTT
Found at i:1083048 original size:17 final size:17
Alignment explanation
Indices: 1083026--1083058 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1083016 AAACATTTTA
1083026 TATTTTAATT-TTTTATT
1 TATTTT-ATTATTTTATT
1083043 TATTTTATTATTTTAT
1 TATTTTATTATTTTAT
1083059 ATAAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTATTATTTTATT
Found at i:1083601 original size:20 final size:19
Alignment explanation
Indices: 1083556--1083610 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
1083546 ATATAAAAAT
*
1083556 TATAAATAATAAAATTTGTT
1 TATAAA-AATAAAATTTGTA
*
1083576 TAATAAAAATAATATATTGTA
1 T-ATAAAAATAAAAT-TTGTA
*
1083597 TATAAAAATTAAAT
1 TATAAAAATAAAAT
1083611 AATAATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
TATAAAAATAAAATTTGTA
Found at i:1083774 original size:21 final size:21
Alignment explanation
Indices: 1083748--1083787 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1083738 CTTTAGAAAA
1083748 AATAAATAAATTTT-CTTTGAC
1 AATAAA-AAATTTTCCTTTGAC
*
1083769 AATAAAACATTTTCCTTTG
1 AATAAAAAATTTTCCTTTG
1083788 GTTTCATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
AATAAAAAATTTTCCTTTGAC
Found at i:1084134 original size:18 final size:18
Alignment explanation
Indices: 1084113--1084148 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1084103 CTTTTAGTAG
* *
1084113 ATTTTTTTATTTTTATAT
1 ATTTATTTATATTTATAT
1084131 ATTTATTTATATTTATAT
1 ATTTATTTATATTTATAT
1084149 TTAAATATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTATTTATATTTATAT
Found at i:1084471 original size:26 final size:26
Alignment explanation
Indices: 1084441--1084490 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1084431 TTATTATTTT
*
1084441 TATAATTTAAT-TTTTTTATAATTATA
1 TATAA-TTAATATTTATTATAATTATA
1084467 TATAATTAATATTTATTATAATTA
1 TATAATTAATATTTATTATAATTA
1084491 ATTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TATAATTAATATTTATTATAATTATA
Found at i:1084505 original size:26 final size:27
Alignment explanation
Indices: 1084448--1084517 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 27
1084438 TTTTATAATT
*
1084448 TAATT-TTT-TTATAATTATATATAAT
1 TAATTATTTATTATAATTATATATAAA
1084473 TAA-TATTTATTATAATTA-AT-TAAAA
1 TAATTATTTATTATAATTATATAT-AAA
*
1084498 TAATTA-TTATTATATTTATA
1 TAATTATTTATTATAATTATA
1084518 ACCACAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 2 0.05
25 24 0.63
26 12 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TAATTATTTATTATAATTATATATAAA
Found at i:1084790 original size:11 final size:11
Alignment explanation
Indices: 1084770--1084818 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
1084760 ATAAAAATTA
1084770 AATT-AAATAT
1 AATTAAAATAT
*
1084780 AATCAAAATAT
1 AATTAAAATAT
*
1084791 GATTAAAATAT
1 AATTAAAATAT
1084802 AATTAAAA-AT
1 AATTAAAATAT
*
1084812 ATTTAAA
1 AATTAAA
1084819 CACATGAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
10 11 0.33
11 22 0.67
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (11 bp):
AATTAAAATAT
Found at i:1085377 original size:26 final size:25
Alignment explanation
Indices: 1085314--1085380 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
1085304 AAAAACTCGT
1085314 AATAAATATTAGTATATATGTAAAAA
1 AATAAATATTA-TATATATGTAAAAA
**
1085340 AAT-TGTATTTATATATTAT-TATAAAA
1 AATAAATA-TTATATA-TATGTA-AAAA
1085366 AATAAATATTATATA
1 AATAAATATTATATA
1085381 AATTCAATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
25 8 0.24
26 23 0.70
27 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
AATAAATATTATATATATGTAAAAA
Found at i:1085529 original size:60 final size:60
Alignment explanation
Indices: 1085402--1085518 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 60
1085392 TGAGATTGAG
* * * * * *
1085402 ATAACATTAATATCTTATATTATACACAATGAATGAAGATGAATGAGATAAAATTAATTA
1 ATAAAATTAATATATTATATTATACACAATAAATGAAGATAAATGAAAAAAAATTAATTA
* * *
1085462 ATCAAATTAATATATTATATTATACAGAATAAATGAGGATAAAT-AAAAAAAATTAAT
1 ATAAAATTAATATATTATATTATACACAATAAATGAAGATAAATGAAAAAAAATTAAT
1085519 ATATGAAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
59 11 0.23
60 37 0.77
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (60 bp):
ATAAAATTAATATATTATATTATACACAATAAATGAAGATAAATGAAAAAAAATTAATTA
Found at i:1085745 original size:36 final size:35
Alignment explanation
Indices: 1085700--1085815 Score: 99
Period size: 41 Copynumber: 3.0 Consensus size: 35
1085690 TTAATTTTTA
1085700 AAATTTTTATATTTATATTATATCGTATTTATATT
1 AAATTTTTATATTTATATTATATCGTATTTATATT
* *
1085735 AAATTATTTATTATTATATCTTATTATTTCATGT-TTTAATTTTT
1 AAATT-TTTA-TATT-TA---TATTATATC--GTATTT-A-TATT
*
1085779 AAAATTTTTATATTTATATTATATTGTATTTATATT
1 -AAATTTTTATATTTATATTATATCGTATTTATATT
1085815 A
1 A
1085816 CATGCCATGC
Statistics
Matches: 64, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
35 6 0.09
36 7 0.11
37 7 0.11
38 5 0.08
39 7 0.11
41 8 0.12
42 5 0.08
43 7 0.11
44 7 0.11
45 5 0.08
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (35 bp):
AAATTTTTATATTTATATTATATCGTATTTATATT
Found at i:1085755 original size:80 final size:80
Alignment explanation
Indices: 1085661--1085815 Score: 301
Period size: 80 Copynumber: 1.9 Consensus size: 80
1085651 AAAATATTTT
1085661 TTTATTATTATATCTTATTATTTCATGTTTTAATTTTTAAAATTTTTATATTTATATTATATCGT
1 TTTATTATTATATCTTATTATTTCATGTTTTAATTTTTAAAATTTTTATATTTATATTATATCGT
1085726 ATTTATATTAAATTA
66 ATTTATATTAAATTA
*
1085741 TTTATTATTATATCTTATTATTTCATGTTTTAATTTTTAAAATTTTTATATTTATATTATATTGT
1 TTTATTATTATATCTTATTATTTCATGTTTTAATTTTTAAAATTTTTATATTTATATTATATCGT
1085806 ATTTATATTA
66 ATTTATATTA
1085816 CATGCCATGC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (80 bp):
TTTATTATTATATCTTATTATTTCATGTTTTAATTTTTAAAATTTTTATATTTATATTATATCGT
ATTTATATTAAATTA
Found at i:1087612 original size:48 final size:48
Alignment explanation
Indices: 1087495--1087977 Score: 666
Period size: 48 Copynumber: 10.2 Consensus size: 48
1087485 CGAAACAAGT
1087495 ACCATCACCTGATCCACATACTACATCTCCGGTGACTCCTACTAGG--
1 ACCATCACCTGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
* *
1087541 -CCAT--CC-GATCCATATACTGCATCTCCGGTGACTCCTACTAGGCC
1 ACCATCACCTGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
1087585 ACCATCACCTGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
1 ACCATCACCTGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
*
1087633 ACCATCACCCGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
1 ACCATCACCTGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
*
1087681 ACCATCACCCGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
1 ACCATCACCTGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
*
1087729 ACCATCACCCGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
1 ACCATCACCTGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
* * * * * * *
1087777 ACCATCACCCGGTCCACATCCTCCATCTCCGATGAATCCTACAAGGCC
1 ACCATCACCTGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
*
1087825 ACCATCACCTGATCCACATACT-CAATCTCCAGTGACTCCTACTAGGCC
1 ACCATCACCTGATCCACATACTAC-ATCTCCGGTGACTCCTACTAGGCC
* * * *
1087873 ACCATCACCTGACCCAAATACT-CAATCTCCAGTGACTCCTACAAGGCC
1 ACCATCACCTGATCCACATACTAC-ATCTCCGGTGACTCCTACTAGGCC
* **
1087921 ACCATCACC---TCCACAAACT-CAATCTCCAATGACTCCTACTAGGCC
1 ACCATCACCTGATCCACATACTAC-ATCTCCGGTGACTCCTACTAGGCC
*
1087966 ACCAACACCTGA
1 ACCATCACCTGA
1087978 AATCCTAACT
Statistics
Matches: 400, Mismatches: 27, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
42 34 0.09
43 2 0.00
45 47 0.12
47 3 0.01
48 314 0.79
ACGTcount: A:0.27, C:0.41, G:0.12, T:0.21
Consensus pattern (48 bp):
ACCATCACCTGATCCACATACTACATCTCCGGTGACTCCTACTAGGCC
Found at i:1088036 original size:21 final size:21
Alignment explanation
Indices: 1088010--1088160 Score: 131
Period size: 21 Copynumber: 7.2 Consensus size: 21
1088000 GAACCAACAA
* * *
1088010 CACCAGTTCAATCTCCACCCC
1 CACCAGTTTACTCTCCACCAC
* * *
1088031 CACCAGTGTATTCCCCACCAC
1 CACCAGTTTACTCTCCACCAC
* *
1088052 CGCCGGTTTACTCTCCACCAC
1 CACCAGTTTACTCTCCACCAC
* * *
1088073 CACCAGTGTATTCCCCACCAC
1 CACCAGTTTACTCTCCACCAC
* *
1088094 CACCGGTTTACTCTCCACCTC
1 CACCAGTTTACTCTCCACCAC
** * *
1088115 CACCAGTGCATTTTCCACCAC
1 CACCAGTTTACTCTCCACCAC
* *
1088136 CACCGGTTTACTCTCCACCTC
1 CACCAGTTTACTCTCCACCAC
1088157 CACC
1 CACC
1088161 CATCCACTCA
Statistics
Matches: 98, Mismatches: 32, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 98 1.00
ACGTcount: A:0.20, C:0.48, G:0.09, T:0.23
Consensus pattern (21 bp):
CACCAGTTTACTCTCCACCAC
Found at i:1088080 original size:42 final size:42
Alignment explanation
Indices: 1088021--1088160 Score: 226
Period size: 42 Copynumber: 3.3 Consensus size: 42
1088011 ACCAGTTCAA
* *
1088021 TCTCCACCCCCACCAGTGTATTCCCCACCACCGCCGGTTTAC
1 TCTCCACCTCCACCAGTGTATTCCCCACCACCACCGGTTTAC
*
1088063 TCTCCACCACCACCAGTGTATTCCCCACCACCACCGGTTTAC
1 TCTCCACCTCCACCAGTGTATTCCCCACCACCACCGGTTTAC
* **
1088105 TCTCCACCTCCACCAGTGCATTTTCCACCACCACCGGTTTAC
1 TCTCCACCTCCACCAGTGTATTCCCCACCACCACCGGTTTAC
1088147 TCTCCACCTCCACC
1 TCTCCACCTCCACC
1088161 CATCCACTCA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.19, C:0.49, G:0.09, T:0.23
Consensus pattern (42 bp):
TCTCCACCTCCACCAGTGTATTCCCCACCACCACCGGTTTAC
Found at i:1088181 original size:42 final size:42
Alignment explanation
Indices: 1088021--1088229 Score: 161
Period size: 42 Copynumber: 4.8 Consensus size: 42
1088011 ACCAGTTCAA
* ** * * *
1088021 TCTCCACCCCCACCAGTGTATTCCCCACCACCGCCGGTTTAC
1 TCTCCACCTCCACCAGTCCACTCACCACCACCACCGGTTTAC
* ** * *
1088063 TCTCCACCACCACCAGTGTATTCCCCACCACCACCGGTTTAC
1 TCTCCACCTCCACCAGTCCACTCACCACCACCACCGGTTTAC
* * **
1088105 TCTCCACCTCCACCAGTGCATTTTCCACCACCACCGGTTTAC
1 TCTCCACCTCCACCAGTCCACTCACCACCACCACCGGTTTAC
* *
1088147 TCTCCACCTCCACCCA-TCCACTCACCTCCCCCACCGGTACATTCAC
1 TCTCCACCTCCA-CCAGTCCACTCACCACCACCACCGGT---TT-AC
* *
1088193 -CACCACCGCCTCCACCAGTCTACTCACCACCACCACC
1 TCTCCA---CCTCCACCAGTCCACTCACCACCACCACC
1088230 AGTCTCCTCT
Statistics
Matches: 142, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
42 106 0.75
43 3 0.02
45 6 0.04
46 2 0.01
47 3 0.02
48 22 0.15
ACGTcount: A:0.20, C:0.52, G:0.08, T:0.20
Consensus pattern (42 bp):
TCTCCACCTCCACCAGTCCACTCACCACCACCACCGGTTTAC
Found at i:1088181 original size:84 final size:84
Alignment explanation
Indices: 1088021--1088184 Score: 204
Period size: 84 Copynumber: 2.0 Consensus size: 84
1088011 ACCAGTTCAA
* * ** *
1088021 TCTCCACCCCCACCAGTGTATTCCCCACCACCGCCGGTTTACTCTCCACCACCACCAGTGTATTC
1 TCTCCACCCCCACCAGTGCATTCCCCACCACCACCGGTTTACTCTCCACCACCACCAGTCCACTC
*
1088086 CCCACCACCACCGGTTTAC
66 ACCACCACCACCGGTTTAC
* ** *
1088105 TCTCCACCTCCACCAGTGCATTTTCCACCACCACCGGTTTACTCTCCACCTCCACCCA-TCCACT
1 TCTCCACCCCCACCAGTGCATTCCCCACCACCACCGGTTTACTCTCCACCACCA-CCAGTCCACT
* *
1088169 CACCTCCCCCACCGGT
65 CACCACCACCACCGGT
1088185 ACATTCACCA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
84 64 0.96
85 3 0.04
ACGTcount: A:0.18, C:0.51, G:0.09, T:0.22
Consensus pattern (84 bp):
TCTCCACCCCCACCAGTGCATTCCCCACCACCACCGGTTTACTCTCCACCACCACCAGTCCACTC
ACCACCACCACCGGTTTAC
Found at i:1088345 original size:24 final size:24
Alignment explanation
Indices: 1088318--1088370 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1088308 ACCATCCCCA
*
1088318 CCACCACCAGTCTACTCTCCTCCT
1 CCACCACCAGTCTACTCTCCACCT
*
1088342 CCACCACCAGTCTCCTCTCCACCT
1 CCACCACCAGTCTACTCTCCACCT
1088366 CCACC
1 CCACC
1088371 CTCACCCCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.58, G:0.04, T:0.21
Consensus pattern (24 bp):
CCACCACCAGTCTACTCTCCACCT
Found at i:1088396 original size:108 final size:108
Alignment explanation
Indices: 1088259--1088479 Score: 397
Period size: 108 Copynumber: 2.0 Consensus size: 108
1088249 CCCTCACCCG
1088259 CACCCTCACCCACGCCACCAGTACAATCACCACCTCCACCTGTTCGTTCACCATCCCCACCACCA
1 CACCCTCACCCACGCCACCAGTACAATCACCACCTCCACCTGTTCGTTCACCATCCCCACCACCA
* * *
1088324 CCAGTCTACTCTCCTCCTCCACCACCAGTCTCCTCTCCACCTC
66 CCAGTCTACTCTCCTCCTCCACCACCAGTCTACTCACCACCAC
*
1088367 CACCCTCACCCCCGCCACCAGTACAATCACCACCTCCACCTGTTCGTTCACCATCCCCACCACCA
1 CACCCTCACCCACGCCACCAGTACAATCACCACCTCCACCTGTTCGTTCACCATCCCCACCACCA
*
1088432 CCAGTCTACTCTCCTCCTCCACCACCAGTTTACTCACCACCAC
66 CCAGTCTACTCTCCTCCTCCACCACCAGTCTACTCACCACCAC
1088475 CACCC
1 CACCC
1088480 GTTTACTCTC
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.21, C:0.55, G:0.05, T:0.19
Consensus pattern (108 bp):
CACCCTCACCCACGCCACCAGTACAATCACCACCTCCACCTGTTCGTTCACCATCCCCACCACCA
CCAGTCTACTCTCCTCCTCCACCACCAGTCTACTCACCACCAC
Found at i:1088453 original size:24 final size:24
Alignment explanation
Indices: 1088426--1088607 Score: 133
Period size: 21 Copynumber: 8.2 Consensus size: 24
1088416 ACCATCCCCA
* *
1088426 CCACCACCAGTCTACTCTCCTCCT
1 CCACCACCAGTTTACTCTCCACCT
*
1088450 CCACCACCAGTTTA--CT-CACCA
1 CCACCACCAGTTTACTCTCCACCT
*
1088471 CCACCACCCGTTTACTCTCCACCT
1 CCACCACCAGTTTACTCTCCACCT
*
1088495 ---CCACCAGTTTA-T-T-CACCA
1 CCACCACCAGTTTACTCTCCACCT
*
1088513 CCACCACCCGTTTACTCTCCACCT
1 CCACCACCAGTTTACTCTCCACCT
* *
1088537 ---CCACCAGTTTACTCACCACCA
1 CCACCACCAGTTTACTCTCCACCT
****
1088558 CCACCACCAGTCCGTTCTCCACCT
1 CCACCACCAGTTTACTCTCCACCT
* *
1088582 ---CCACCAGTTTACTCACCACCA
1 CCACCACCAGTTTACTCTCCACCT
1088603 CCACC
1 CCACC
1088608 GGTCTACTCA
Statistics
Matches: 119, Mismatches: 24, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
18 4 0.03
19 1 0.01
20 1 0.01
21 69 0.58
22 3 0.03
23 3 0.03
24 38 0.32
ACGTcount: A:0.22, C:0.51, G:0.05, T:0.22
Consensus pattern (24 bp):
CCACCACCAGTTTACTCTCCACCT
Found at i:1088455 original size:21 final size:21
Alignment explanation
Indices: 1088453--1088692 Score: 230
Period size: 21 Copynumber: 11.3 Consensus size: 21
1088443 TCCTCCTCCA
*
1088453 CCACCAGTTTACTCACCACCA
1 CCACCAGTTTACTCACCACCT
* *
1088474 CCACCCGTTTACTCTCCACCT
1 CCACCAGTTTACTCACCACCT
* *
1088495 CCACCAGTTTATTCACCACCA
1 CCACCAGTTTACTCACCACCT
* *
1088516 CCACCCGTTTACTCTCCACCT
1 CCACCAGTTTACTCACCACCT
*
1088537 CCACCAGTTTACTCACCACCACCA
1 CCACCAGTTTACT---CACCACCT
**** *
1088561 CCACCAGTCCGTTCTCCACCT
1 CCACCAGTTTACTCACCACCT
*
1088582 CCACCAGTTTACTCACCACCA
1 CCACCAGTTTACTCACCACCT
* * *
1088603 CCACCGGTCTACTCAACACCT
1 CCACCAGTTTACTCACCACCT
* * *
1088624 CCACCTGTCTACTCGCCACCT
1 CCACCAGTTTACTCACCACCT
* * *
1088645 CCACCAGTCTATTCGCCACCT
1 CCACCAGTTTACTCACCACCT
1088666 CCACCAGTTTACTCACCA-CT
1 CCACCAGTTTACTCACCACCT
1088686 ACCACCA
1 -CCACCA
1088693 TCACCATCAC
Statistics
Matches: 177, Mismatches: 38, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
20 2 0.01
21 160 0.90
24 15 0.08
ACGTcount: A:0.23, C:0.49, G:0.06, T:0.22
Consensus pattern (21 bp):
CCACCAGTTTACTCACCACCT
Found at i:1088516 original size:87 final size:84
Alignment explanation
Indices: 1088423--1088692 Score: 324
Period size: 87 Copynumber: 3.1 Consensus size: 84
1088413 TTCACCATCC
* * *
1088423 CCACCACCACCAGTCTACTCTCCTCCTCCACCACCAGTTTACTCACCACCACCACCCGTTTACTC
1 CCACCACCACCAGTCTACTCTCCACCT---CCACCAGTTTACTCACCACCACCACCCGTCTATTC
*
1088488 TCCACCTCCACCAGTTTATTCA
63 TCCACCTCCACCAGTTTACTCA
* * **
1088510 CCACCACCACCCGTTTACTCTCCACCTCCACCAGTTTACTCACCACCACCACCACCAGTCCGTTC
1 CCACCACCACCAGTCTACTCTCCACCTCCACCAGTTTACTCACCACCACCA-C-CC-GTCTATTC
1088575 TCCACCTCCACCAGTTTACTCA
63 TCCACCTCCACCAGTTTACTCA
* ** * * * * * *
1088597 CCACCACCACCGGTCTACTCAACACCTCCACCTGTCTACTCGCCACCTCCACCAGTCTATTCGCC
1 CCACCACCACCAGTCTACTCTCCACCTCCACCAGTTTACTCACCACCACCACCCGTCTATTCTCC
1088662 ACCTCCACCAGTTTACTCA
66 ACCTCCACCAGTTTACTCA
*
1088681 CCACTACCACCA
1 CCACCACCACCA
1088693 TCACCATCAC
Statistics
Matches: 158, Mismatches: 22, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
84 61 0.39
85 2 0.01
86 3 0.02
87 92 0.58
ACGTcount: A:0.22, C:0.50, G:0.06, T:0.22
Consensus pattern (84 bp):
CCACCACCACCAGTCTACTCTCCACCTCCACCAGTTTACTCACCACCACCACCCGTCTATTCTCC
ACCTCCACCAGTTTACTCA
Found at i:1088529 original size:63 final size:63
Alignment explanation
Indices: 1088423--1088692 Score: 245
Period size: 63 Copynumber: 4.2 Consensus size: 63
1088413 TTCACCATCC
* * * *
1088423 CCACCACCACCAGTCTACTCTCCTCCTCCACCACCAGTTTACTCACCACCACCACCCGTTTACTC
1 CCACCTCCACCAGTCTA-T-T-CACCACCACCACCAGTTTACTCACCACCACCACCAGTTTACTC
*
1088488 T
63 A
* * * *
1088489 CCACCTCCACCAGTTTATTCACCACCACCACCCGTTTACTCTCCACCTCCACCAGTTTACTCACC
1 CCACCTCCACCAGTCTATTCACCACCACCACCAGTTTACTCACCACCACCACCAGTTTACT---C
1088554 A
63 A
* ** * * * *
1088555 CCACCACCACCAGTCCGTTCTCCACCTCCACCAGTTTACTCACCACCACCACCGGTCTACTCA
1 CCACCTCCACCAGTCTATTCACCACCACCACCAGTTTACTCACCACCACCACCAGTTTACTCA
* * * * * * * * *
1088618 ACACCTCCACCTGTCTACTCGCCACCTCCACCAGTCTATTCGCCACCTCCACCAGTTTACTCA
1 CCACCTCCACCAGTCTATTCACCACCACCACCAGTTTACTCACCACCACCACCAGTTTACTCA
1088681 CCA-CTACCACCA
1 CCACCT-CCACCA
1088693 TCACCATCAC
Statistics
Matches: 165, Mismatches: 35, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
62 2 0.01
63 95 0.58
64 1 0.01
65 1 0.01
66 66 0.40
ACGTcount: A:0.22, C:0.50, G:0.06, T:0.22
Consensus pattern (63 bp):
CCACCTCCACCAGTCTATTCACCACCACCACCAGTTTACTCACCACCACCACCAGTTTACTCA
Found at i:1088535 original size:108 final size:107
Alignment explanation
Indices: 1088273--1088691 Score: 305
Period size: 108 Copynumber: 3.9 Consensus size: 107
1088263 CTCACCCACG
* *
1088273 CCACCAGTACAATCACCACCTCCACCTGTTCGTTCACCATCCCCACCACCACCAGTCTACTCTCC
1 CCACCAGTATAATCACCACCTCCACC----CGTTTA-C-TCCCCACCACCACCAGTCTACTCTCC
* * * * * *
1088338 TCCTCCACCACCAGTCTCCTCTCCACCTCCACCC---T-CACCC-CCG
60 TCCACCACCACCAGTCTACTCACCACCACCACCCGTTTACTCCCACCA
* *
1088381 CCACCAGTACAATCACCACCTCCACCTGTTCGTTCACCATCCCCACCACCACCAGTCTACTCTCC
1 CCACCAGTATAATCACCACCTCCACC----CGTTTA-C-TCCCCACCACCACCAGTCTACTCTCC
* * *
1088446 TCCTCCACCACCAGTTTACTCACCACCACCACCCGTTTACTCTCCACCT
60 TCCACCACCACCAGTCTACTCACCACCACCACCCGTTTACTC-CCACCA
* * * * * * * *
1088495 CCACCAGTTTATTCACCACCACCACCCGTTTACTCTCCACCTCCACCAGTTTACTCACCACCACC
1 CCACCAGTATAATCACCACCTCCACCCGTTTACTCCCCACCACCACCAGTCTACTCTCCTCCACC
*** * * *
1088560 ACCACCAGTCCGTTCTCCACCTCCACCAGTTTACTCACCACCA
66 ACCACCAGTCTACTCACCACCACCACCCGTTTACTC-CCACCA
* * * * * * * * *
1088603 CCACCGGTCTACTCAACACCTCCACCTGTCTACTCGCCACCTCCACCAGTCTA-T-T-CGCCACC
1 CCACCAGTATAATCACCACCTCCACCCGTTTACTCCCCACCACCACCAGTCTACTCTCCTCCACC
* * *
1088665 TCCACCAGTTTACTCACCACTACCACC
66 ACCACCAGTCTACTCACCACCACCACC
1088692 ATCACCATCA
Statistics
Matches: 260, Mismatches: 45, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
105 25 0.10
107 1 0.00
108 199 0.77
109 1 0.00
110 5 0.02
111 1 0.00
112 2 0.01
113 2 0.01
114 24 0.09
ACGTcount: A:0.21, C:0.51, G:0.06, T:0.21
Consensus pattern (107 bp):
CCACCAGTATAATCACCACCTCCACCCGTTTACTCCCCACCACCACCAGTCTACTCTCCTCCACC
ACCACCAGTCTACTCACCACCACCACCCGTTTACTCCCACCA
Found at i:1088692 original size:42 final size:42
Alignment explanation
Indices: 1088423--1088692 Score: 315
Period size: 42 Copynumber: 6.3 Consensus size: 42
1088413 TTCACCATCC
*
1088423 CCACCACCACCAGTCTACTCTCCTCCTCCACCACCAGTTTACTCA
1 CCACCACCACCAGTCTACTCTCCACCT---CCACCAGTTTACTCA
* * *
1088468 CCACCACCACCCGTTTACTCTCCACCTCCACCAGTTTATTCA
1 CCACCACCACCAGTCTACTCTCCACCTCCACCAGTTTACTCA
* *
1088510 CCACCACCACCCGTTTACTCTCCACCTCCACCAGTTTACTCACCA
1 CCACCACCACCAGTCTACTCTCCACCTCCACCAGTTTACT---CA
***
1088555 CCACCACCACCAGTCCGTTCTCCACCTCCACCAGTTTACTCA
1 CCACCACCACCAGTCTACTCTCCACCTCCACCAGTTTACTCA
* ** * * *
1088597 CCACCACCACCGGTCTACTCAACACCTCCACCTGTCTACTCG
1 CCACCACCACCAGTCTACTCTCCACCTCCACCAGTTTACTCA
* * *
1088639 CCACCTCCACCAGTCTATTCGCCACCTCCACCAGTTTACTCA
1 CCACCACCACCAGTCTACTCTCCACCTCCACCAGTTTACTCA
*
1088681 CCACTACCACCA
1 CCACCACCACCA
1088693 TCACCATCAC
Statistics
Matches: 193, Mismatches: 29, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
42 132 0.68
45 61 0.32
ACGTcount: A:0.22, C:0.50, G:0.06, T:0.22
Consensus pattern (42 bp):
CCACCACCACCAGTCTACTCTCCACCTCCACCAGTTTACTCA
Found at i:1091168 original size:26 final size:25
Alignment explanation
Indices: 1091109--1091174 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
1091099 TATAATCATT
**
1091109 ATATAAAATATGTTTAATTTTTTAAA
1 ATATAAAATATG-TTAAAATTTTAAA
*
1091135 A-ATTAAATATGTTAAAATTTTAAA
1 ATATAAAATATGTTAAAATTTTAAA
* *
1091159 CATATCAAATGTGTTA
1 -ATATAAAATATGTTA
1091175 GGTTAATCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 11 0.33
25 10 0.30
26 12 0.36
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (25 bp):
ATATAAAATATGTTAAAATTTTAAA
Found at i:1092015 original size:13 final size:14
Alignment explanation
Indices: 1091977--1092023 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1091967 TTTTAATTTT
*
1091977 AATAATATATTTAA
1 AATATTATATTTAA
*
1091991 AATATGATATTTAA
1 AATATTATATTTAA
*
1092005 TAT-TTATATTTAA
1 AATATTATATTTAA
1092018 ATATAT
1 A-ATAT
1092024 ATCAAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 9 0.35
14 16 0.62
15 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
AATATTATATTTAA
Found at i:1093991 original size:16 final size:15
Alignment explanation
Indices: 1093955--1094001 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
1093945 TTTTTATATT
1093955 TAAATATTAATAAAA
1 TAAATATTAATAAAA
*
1093970 TAAATATTAAATAAAG
1 TAAATATT-AATAAAA
*
1093986 TTAATAATTAATAAAA
1 TAAAT-ATTAATAAAA
1094002 ATATGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 8 0.30
16 16 0.59
17 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
TAAATATTAATAAAA
Found at i:1094064 original size:22 final size:19
Alignment explanation
Indices: 1094038--1094080 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 19
1094028 TTTAATATAA
1094038 AATTAAAAATTTAAATTTTATT
1 AATTAAAAA--TAAATTTT-TT
*
1094060 AATTATAAATAAATTTTTT
1 AATTAAAAATAAATTTTTT
1094079 AA
1 AA
1094081 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
22 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTAAAAATAAATTTTTT
Found at i:1095366 original size:23 final size:23
Alignment explanation
Indices: 1095333--1095382 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1095323 ATTAATAATA
*
1095333 AAAATTTAATAATA-TAATTTGAT
1 AAAATTAAATAATATTAATTT-AT
*
1095356 AAAATTAAATATTATTAATTTAT
1 AAAATTAAATAATATTAATTTAT
1095379 AAAA
1 AAAA
1095383 AAATTAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAATTAAATAATATTAATTTAT
Found at i:1095684 original size:14 final size:14
Alignment explanation
Indices: 1095667--1095815 Score: 57
Period size: 14 Copynumber: 10.9 Consensus size: 14
1095657 GTATAAACAT
1095667 TATATAATAAAATA
1 TATATAATAAAATA
*
1095681 TATAT-A-AACAT-
1 TATATAATAAAATA
1095692 TATATAATAAAATA
1 TATATAATAAAATA
* * * **
1095706 TACATAGTTAGGTA
1 TATATAATAAAATA
*
1095720 T-T-T--T-AAATT
1 TATATAATAAAATA
1095729 TATATAATAAAATTA
1 TATATAATAAAA-TA
* *
1095744 TTAATATATTAAAATT
1 -T-ATATAATAAAATA
1095760 TATATAA-AATATTATA
1 TATATAATAA-A--ATA
*
1095776 AATATAATAAAATA
1 TATATAATAAAATA
* *
1095790 TATA-AATTAATTA
1 TATATAATAAAATA
1095803 TAATATAATAAAA
1 T-ATATAATAAAA
1095816 AAATATATAT
Statistics
Matches: 96, Mismatches: 22, Indels: 33
0.64 0.15 0.22
Matches are distributed among these distances:
9 3 0.03
10 2 0.02
11 6 0.06
12 6 0.06
13 16 0.17
14 33 0.34
15 7 0.07
16 11 0.11
17 12 0.12
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (14 bp):
TATATAATAAAATA
Found at i:1095690 original size:25 final size:25
Alignment explanation
Indices: 1095658--1095707 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1095648 TTAGAATCGG
1095658 TATAAACATTATATAATAAAATATA
1 TATAAACATTATATAATAAAATATA
1095683 TATAAACATTATATAATAAAATATA
1 TATAAACATTATATAATAAAATATA
1095708 CATAGTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (25 bp):
TATAAACATTATATAATAAAATATA
Found at i:1095756 original size:17 final size:18
Alignment explanation
Indices: 1095730--1095829 Score: 62
Period size: 19 Copynumber: 5.3 Consensus size: 18
1095720 TTTTAAATTT
*
1095730 ATATAATAAAATTAT-TA
1 ATATATTAAAATTATATA
1095747 ATATATTAAAATTTATATA
1 ATATATTAAAA-TTATATA
*
1095766 AAATATTATAAA-TATAATA
1 ATATATTA-AAATTAT-ATA
*
1095785 AAATA-TATAAATTAATTATA
1 ATATATTA-AAATT-A-TATA
* **
1095805 ATATAATAAAAAAATATA
1 ATATATTAAAATTATATA
1095823 TATATAT
1 -ATATAT
1095830 ATACATAAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
17 10 0.15
18 17 0.25
19 24 0.35
20 14 0.21
21 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATTAAAATTATATA
Found at i:1095780 original size:28 final size:29
Alignment explanation
Indices: 1095724--1095815 Score: 98
Period size: 28 Copynumber: 3.1 Consensus size: 29
1095714 TAGGTATTTT
*
1095724 AAATTTATATAATAAAATTATTAATATATTA
1 AAATTTATATAA-AATATTA-TAATATATTA
*
1095755 AAATTTATATAAAATATTATAAATATAATA
1 AAATTTATATAAAATATTAT-AATATATTA
* *
1095785 AAA--TATATAAATTAATTATAATATAATA
1 AAATTTATATAAAAT-ATTATAATATATTA
1095813 AAA
1 AAA
1095816 AAATATATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
28 21 0.38
29 6 0.11
30 17 0.30
31 12 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
AAATTTATATAAAATATTATAATATATTA
Found at i:1095781 original size:18 final size:18
Alignment explanation
Indices: 1095763--1095830 Score: 65
Period size: 15 Copynumber: 4.0 Consensus size: 18
1095753 TAAAATTTAT
1095763 ATAAAATATTATAAATATA
1 ATAAAATA-TATAAATATA
1095782 ATAAAATATATAAAT-TA
1 ATAAAATATATAAATATA
* *
1095799 ATTATA-ATAT-AATA-A
1 ATAAAATATATAAATATA
*
1095814 A-AAAATATATATATATA
1 ATAAAATATATAAATATA
1095831 TACATAAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.05
15 9 0.22
16 7 0.17
17 7 0.17
18 7 0.17
19 8 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAATATATAAATATA
Found at i:1095828 original size:47 final size:47
Alignment explanation
Indices: 1095729--1095828 Score: 114
Period size: 47 Copynumber: 2.1 Consensus size: 47
1095719 ATTTTAAATT
* * * *
1095729 TATATAATAAAATTATTAATATATTAAAATTTATATAAAATATTATA
1 TATATAATAAAATTATAAATATATTAAAATATATATAAAAAAATATA
* *
1095776 AATATAATAAAATATATAAAT-TAATTATAATATA-ATAAAAAAATATA
1 TATATAATAAAAT-TATAAATAT-ATTAAAATATATATAAAAAAATATA
1095823 TATATA
1 TATATA
1095829 TATACATAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
47 29 0.66
48 15 0.34
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (47 bp):
TATATAATAAAATTATAAATATATTAAAATATATATAAAAAAATATA
Found at i:1095831 original size:23 final size:23
Alignment explanation
Indices: 1095765--1095837 Score: 58
Period size: 28 Copynumber: 3.0 Consensus size: 23
1095755 AAATTTATAT
*
1095765 AAAATAT-TATAAATATAATAAA
1 AAAATATATATATATATAATAAA
* *
1095787 ATATATAAATTAATTATAATATAATAAA
1 A-AAATATA-T-A-TAT-ATATAATAAA
1095815 AAAATATATATATATATACATAA
1 AAAATATATATATATATA-ATAA
1095838 GTTTAGAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
22 1 0.03
23 9 0.23
24 7 0.18
25 2 0.05
26 2 0.05
27 7 0.18
28 11 0.28
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATATATATATATATAATAAA
Found at i:1096146 original size:31 final size:29
Alignment explanation
Indices: 1096095--1096157 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
1096085 ATAAGTTTGA
*
1096095 TAATTTATAAATTTATATTTAATATTTATT
1 TAATTTATAAATTTATATTTAAT-TTTAAT
1096125 TAATATTA-AAATTATATATTTAATTTTAAT
1 TAAT-TTATAAATT-TATATTTAATTTTAAT
1096155 TAA
1 TAA
1096158 ATAATTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TAATTTATAAATTTATATTTAATTTTAAT
Found at i:1096418 original size:20 final size:20
Alignment explanation
Indices: 1096373--1096431 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
1096363 AAACATGTTT
* *
1096373 TATTATT-TAAAATATATTA
1 TATTATTATAAATTATTTTA
* *
1096392 AAATATTATAAATTATTTTA
1 TATTATTATAAATTATTTTA
*
1096412 TATTATTTATAAATTCTTTT
1 TATTA-TTATAAATTATTTT
1096432 CATTAAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
19 5 0.16
20 13 0.42
21 13 0.42
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATTATAAATTATTTTA
Found at i:1096436 original size:20 final size:21
Alignment explanation
Indices: 1096397--1096436 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1096387 TATTAAAATA
*
1096397 TTATAAATTATTTTATATTAT
1 TTATAAATTATTTTACATTAT
*
1096418 TTATAAATTCTTTT-CATTA
1 TTATAAATTATTTTACATTA
1096437 AATTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATAAATTATTTTACATTAT
Found at i:1096656 original size:24 final size:25
Alignment explanation
Indices: 1096629--1096691 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
1096619 GCGAAAAAAT
*
1096629 TAAAATATGATAAATAT-AT-TAATA
1 TAAAA-ATAATAAATATAATATAATA
1096653 TAAAAAATTAA-AAATATAATATAATA
1 T-AAAAA-TAATAAATATAATATAATA
1096679 TAAAAATAATAAA
1 TAAAAATAATAAA
1096692 ATTTTATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
24 11 0.33
25 16 0.48
26 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
TAAAAATAATAAATATAATATAATA
Found at i:1096693 original size:26 final size:24
Alignment explanation
Indices: 1096640--1096692 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
1096630 AAAATATGAT
*
1096640 AAATATATTAATATAAAAAATTAA
1 AAATATATTAATATAAAAAAATAA
1096664 AAATATAATATAATATAAAAATAATAA
1 AAATAT-AT-TAATATAAAAA-AATAA
1096691 AA
1 AA
1096693 TTTTATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 2 0.08
26 11 0.44
27 6 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATATATTAATATAAAAAAATAA
Found at i:1097712 original size:22 final size:24
Alignment explanation
Indices: 1097673--1097738 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 24
1097663 ATTTAGATTA
* *
1097673 ATTTAATTTAATT--TAAATTATT
1 ATTTAATTTAATTAAAAAATAATT
1097695 ATTT-ATTTAA-TAAAAAATAATT
1 ATTTAATTTAATTAAAAAATAATT
*
1097717 TTTTAAATTTAATTAAAAAATA
1 ATTT-AATTTAATTAAAAAATA
1097739 TATAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 1 0.03
21 6 0.17
22 14 0.39
24 6 0.17
25 9 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTAATTTAATTAAAAAATAATT
Found at i:1097771 original size:20 final size:22
Alignment explanation
Indices: 1097732--1097773 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
1097722 AATTTAATTA
1097732 AAAAATATATAATATTAATATT
1 AAAAATATATAATATTAATATT
*
1097754 AAAAATA-AT-ATTTTAATATT
1 AAAAATATATAATATTAATATT
1097774 TTTAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAATATATAATATTAATATT
Found at i:1099493 original size:7 final size:6
Alignment explanation
Indices: 1099456--1099489 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1099446 TTATTGAATC
*
1099456 AAATT- AAATAA AAATTA AAATTA AAATTA AAATT
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATT
1099490 TAAACTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:1099805 original size:6 final size:6
Alignment explanation
Indices: 1099796--1099846 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
1099786 ATATATATCG
* * *
1099796 TATTTA TATTTA AATATA TATATA TAATTTA TA-TTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA T-ATTTA TATTTA TATTTA TATTTA
1099844 TAT
1 TAT
1099847 GATTGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 5 0.13
6 29 0.74
7 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TATTTA
Found at i:1099825 original size:25 final size:26
Alignment explanation
Indices: 1099766--1099833 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 26
1099756 TTACTTTCAA
* *
1099766 ATATAATTAATATTATAATTATATAT
1 ATATAATTTATATTATAAATATATAT
*
1099792 ATCGT-ATTTATATT-TAAATATATAT
1 AT-ATAATTTATATTATAAATATATAT
1099817 ATATAATTTATATTATA
1 ATATAATTTATATTATA
1099834 TTTATATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 1 0.03
25 21 0.60
26 12 0.34
27 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
ATATAATTTATATTATAAATATATAT
Found at i:1099926 original size:14 final size:14
Alignment explanation
Indices: 1099909--1099939 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1099899 AACAAGAGTA
1099909 ATAATATAATTAAT
1 ATAATATAATTAAT
*
1099923 ATAATATATTTAAT
1 ATAATATAATTAAT
1099937 ATA
1 ATA
1099940 TGTAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAATATAATTAAT
Found at i:1099936 original size:9 final size:9
Alignment explanation
Indices: 1099924--1099993 Score: 62
Period size: 9 Copynumber: 8.2 Consensus size: 9
1099914 ATAATTAATA
1099924 TAATATATT
1 TAATATATT
*
1099933 TAATATATG
1 TAATATATT
1099942 TAA-ATATAT
1 TAATATAT-T
1099951 T--TATATT
1 TAATATATT
*
1099958 AAATAT-TT
1 TAATATATT
1099966 TAATATATT
1 TAATATATT
1099975 TAATAT-TT
1 TAATATATT
1099983 T-ATATTATT
1 TAATA-TATT
1099992 TA
1 TA
1099994 TTTCAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
7 4 0.08
8 19 0.39
9 26 0.53
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (9 bp):
TAATATATT
Found at i:1099974 original size:17 final size:17
Alignment explanation
Indices: 1099925--1099984 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
1099915 TAATTAATAT
1099925 AATATATTTAATATATGTA
1 AATAT-TTTAATATAT-TA
*
1099944 AATATATT--TATATTA
1 AATATTTTAATATATTA
*
1099959 AATATTTTAATATATTT
1 AATATTTTAATATATTA
1099976 AATATTTTA
1 AATATTTTA
1099985 TATTATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 9 0.25
16 5 0.14
17 15 0.42
18 2 0.06
19 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATATTTTAATATATTA
Found at i:1099991 original size:17 final size:17
Alignment explanation
Indices: 1099924--1099993 Score: 65
Period size: 17 Copynumber: 4.1 Consensus size: 17
1099914 ATAATTAATA
1099924 TAATATATTTAATATATGT
1 TAATAT-TTTAATATAT-T
* *
1099943 AAATATATT--TATATT
1 TAATATTTTAATATATT
*
1099958 AAATATTTTAATATATT
1 TAATATTTTAATATATT
1099975 TAATATTTT-ATATTATT
1 TAATATTTTAATA-TATT
1099992 TA
1 TA
1099994 TTTCAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.20
16 8 0.18
17 20 0.45
18 2 0.05
19 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (17 bp):
TAATATTTTAATATATT
Found at i:1099996 original size:31 final size:33
Alignment explanation
Indices: 1099925--1099989 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1099915 TAATTAATAT
1099925 AATATATTTAATATATGTAAATATATTTATATTA
1 AATAT-TTTAATATATGTAAATATATTTATATTA
*
1099959 AATATTTTAATATAT-TTAATAT-TTTATATTA
1 AATATTTTAATATATGTAAATATATTTATATTA
1099990 TTTATTTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.30
32 6 0.20
33 10 0.33
34 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (33 bp):
AATATTTTAATATATGTAAATATATTTATATTA
Found at i:1100111 original size:19 final size:17
Alignment explanation
Indices: 1100084--1100150 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 17
1100074 TTAAAATGTA
*
1100084 TTTAAAATAATTAATAAAT
1 TTTATAATAATTAAT--AT
1100103 TTTATAATAAATTAATAT
1 TTTATAAT-AATTAATAT
1100121 TTTAT-AT-A-TAA-AT
1 TTTATAATAATTAATAT
1100134 TTTATACAT-ATTAATAT
1 TTTATA-ATAATTAATAT
1100151 GGCAATTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 7 0.17
14 3 0.07
15 4 0.10
16 3 0.07
17 4 0.10
18 7 0.17
19 7 0.17
20 7 0.17
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTATAATAATTAATAT
Found at i:1106449 original size:25 final size:24
Alignment explanation
Indices: 1106407--1106454 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1106397 AGTTTACTAA
*
1106407 TTTATTTATTATTAAAATATTATT
1 TTTATTTAATATTAAAATATTATT
*
1106431 TTTATATTAATATTAAAATTTTAT
1 TTTAT-TTAATATTAAAATATTAT
1106455 AATAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATTTAATATTAAAATATTATT
Found at i:1106451 original size:20 final size:21
Alignment explanation
Indices: 1106428--1106484 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 21
1106418 TTAAAATATT
1106428 ATTTTTATATT-AATATT-AAA
1 ATTTTTATATTAAAT-TTAAAA
*
1106448 A-TTTTATAATAAATTTAAAA
1 ATTTTTATATTAAATTTAAAA
1106468 ATTTTTTATTATTAAAT
1 A-TTTTTA-TATTAAAT
1106485 AGTAATTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 10 0.33
20 8 0.27
22 5 0.17
23 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTATATTAAATTTAAAA
Found at i:1106452 original size:19 final size:20
Alignment explanation
Indices: 1106430--1106478 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1106420 AAAATATTAT
1106430 TTTTATATT-AATATT-AAAA
1 TTTTATATTAAAT-TTAAAAA
*
1106449 TTTTATAATAAATTTAAAAA
1 TTTTATATTAAATTTAAAAA
*
1106469 TTTTTTATTA
1 TTTTATATTA
1106479 TTAAATAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTATATTAAATTTAAAAA
Found at i:1107859 original size:15 final size:16
Alignment explanation
Indices: 1107839--1107868 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1107829 AAATAATAAA
1107839 TAAATT-AAATATATT
1 TAAATTAAAATATATT
1107854 TAAATTAAAATATAT
1 TAAATTAAAATATAT
1107869 AAAAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTAAAATATATT
Found at i:1107865 original size:25 final size:25
Alignment explanation
Indices: 1107799--1107884 Score: 66
Period size: 29 Copynumber: 3.2 Consensus size: 25
1107789 TATTATTTTT
*
1107799 TAAATTAAATATAAATTTAAAATGATTAA
1 TAAATTAAA-ATAAA-TAAAAAT-ATT-A
* * *
1107828 AAAATAATAAATAAATTAAATATATT-
1 TAAATTA-AAATAAA-TAAAAATATTA
*
1107854 TAAATTAAAATATATAAAAATATTA
1 TAAATTAAAATAAATAAAAATATTA
1107879 TAAATT
1 TAAATT
1107885 TCTAATTGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
24 9 0.19
25 12 0.26
26 5 0.11
28 3 0.06
29 16 0.34
30 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (25 bp):
TAAATTAAAATAAATAAAAATATTA
Found at i:1107883 original size:44 final size:40
Alignment explanation
Indices: 1107799--1107883 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 40
1107789 TATTATTTTT
*
1107799 TAAATTAAATATAAATTTAAAATGATTAAAAAATAATAAA
1 TAAATTAAATATAAAATTAAAATGATTAAAAAATAATAAA
*
1107839 TAAATTAAATATATTTAAATTAAAAT-ATATAAAAATATTATAAA
1 TAAATTAAATATA---AAATTAAAATGAT-TAAAAA-ATAATAAA
1107883 T
1 T
1107884 TTCTAATTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 13 0.34
42 2 0.05
43 15 0.39
44 8 0.21
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (40 bp):
TAAATTAAATATAAAATTAAAATGATTAAAAAATAATAAA
Found at i:1108165 original size:15 final size:15
Alignment explanation
Indices: 1108145--1108174 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1108135 TTTTTAAAAA
*
1108145 TAAATTGATTTAATT
1 TAAATTGAATTAATT
1108160 TAAATTGAATTAATT
1 TAAATTGAATTAATT
1108175 AAGATTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
TAAATTGAATTAATT
Found at i:1108386 original size:8 final size:8
Alignment explanation
Indices: 1108375--1108407 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1108365 CTTATAATAA
1108375 TTTTTAAT
1 TTTTTAAT
1108383 TTTTTAAT
1 TTTTTAAT
*
1108391 TTATT-AT
1 TTTTTAAT
1108398 TTTTTAAT
1 TTTTTAAT
1108406 TT
1 TT
1108408 AAAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTAAT
Found at i:1108392 original size:15 final size:15
Alignment explanation
Indices: 1108372--1108408 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1108362 AACCTTATAA
1108372 TAATTT-TTAATTTTT
1 TAATTTATT-ATTTTT
1108387 TAATTTATTATTTTT
1 TAATTTATTATTTTT
1108402 TAATTTA
1 TAATTTA
1108409 AAAATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TAATTTATTATTTTT
Found at i:1108859 original size:3 final size:3
Alignment explanation
Indices: 1108851--1108879 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1108841 GTATAAAGTA
1108851 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1108880 CATCGTCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1117688 original size:29 final size:30
Alignment explanation
Indices: 1117644--1117700 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
1117634 AATTTAAAAA
*
1117644 ATTTTAATAAATAAT-AATATATTAATTATT
1 ATTTTAATAAAAAATAAATAT-TTAATTATT
1117674 ATTTT-ATAAAAAATAAATATTTAATTA
1 ATTTTAATAAAAAATAAATATTTAATTA
1117701 AGTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTTTAATAAAAAATAAATATTTAATTATT
Found at i:1117994 original size:125 final size:124
Alignment explanation
Indices: 1117751--1118007 Score: 392
Period size: 126 Copynumber: 2.1 Consensus size: 124
1117741 TTTAAAATAA
* *
1117751 AAAAT-AAAAAAGTTTATTATTATTTTTTTAATAAAATTAAAAATAATAATTAATTAAGTTTAAA
1 AAAATAAAAAAAGTTTATTATTATATTTTTAATAAAATAAAAAATAATAATTAATTAAGTTTAAA
*
1117815 AAAATTATACTAACAAATTAAAATATTAATTATTATGTTTTTATAAAAATAAAAAATTTT
66 AAAATTATACTAACAAATTAAAATATTAATTATTATATTTTTAT-AAAATAAAAAATTTT
* * *
1117875 AAAATAAAAAAAGTTTTTTATTATAATTTTTAATAAAATAAAAAATAATATTTAATTAGGTTTAA
1 AAAATAAAAAAAGTTTATTATTAT-ATTTTTAATAAAATAAAAAATAATAATTAATTAAGTTTAA
* * *
1117940 AAAATTTATATTAACAAATTAAAATATT-ATTATTATATTTTTTTAAAATAAAAAATTTT
65 AAAAATTATACTAACAAATTAAAATATTAATTATTATATTTTTATAAAATAAAAAATTTT
*
1117999 AAATTAAAA
1 AAAATAAAA
1118008 TTTTATTAAT
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
124 28 0.23
125 31 0.26
126 62 0.51
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (124 bp):
AAAATAAAAAAAGTTTATTATTATATTTTTAATAAAATAAAAAATAATAATTAATTAAGTTTAAA
AAAATTATACTAACAAATTAAAATATTAATTATTATATTTTTATAAAATAAAAAATTTT
Found at i:1124080 original size:41 final size:41
Alignment explanation
Indices: 1124032--1124170 Score: 197
Period size: 41 Copynumber: 3.4 Consensus size: 41
1124022 TTTAATGGAG
1124032 CGTGCCCACGCCTTATCAAACGAGAGCTTCTGTTTTATTAA
1 CGTGCCCACGCCTTATCAAACGAGAGCTTCTGTTTTATTAA
* * * * * *
1124073 CATGCCCACTCCTTATTAAACGACAGTTTCTGTTTTTTTAA
1 CGTGCCCACGCCTTATCAAACGAGAGCTTCTGTTTTATTAA
* *
1124114 TGTGCCCACGCCTTATCAAATGAGAGCTTCTGTTTTATTAA
1 CGTGCCCACGCCTTATCAAACGAGAGCTTCTGTTTTATTAA
*
1124155 CGTGCCCACGTCTTAT
1 CGTGCCCACGCCTTAT
1124171 AAAAAAAAGA
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (41 bp):
CGTGCCCACGCCTTATCAAACGAGAGCTTCTGTTTTATTAA
Found at i:1125192 original size:20 final size:19
Alignment explanation
Indices: 1125157--1125208 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1125147 TATTTGCTTT
*
1125157 GAAAAAATAGAAGAAAAAATA
1 GAAAAAA-AAAAGAAAAAA-A
* *
1125178 TAAATAAAAAAGAAAAAAA
1 GAAAAAAAAAAGAAAAAAA
1125197 GAAAAAAAAAAG
1 GAAAAAAAAAAG
1125209 TGAAAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 11 0.42
20 10 0.38
21 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (19 bp):
GAAAAAAAAAAGAAAAAAA
Found at i:1125214 original size:20 final size:21
Alignment explanation
Indices: 1125169--1125214 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
1125159 AAAAATAGAA
*
1125169 GAAAAAATATAAATAAAAAAG
1 GAAAAAAGATAAATAAAAAAG
*
1125190 AAAAAAAGA-AAA-AAAAAAG
1 GAAAAAAGATAAATAAAAAAG
1125209 TGAAAA
1 -GAAAA
1125215 TTTTATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 7 0.33
20 7 0.33
21 7 0.33
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (21 bp):
GAAAAAAGATAAATAAAAAAG
Found at i:1130356 original size:6 final size:6
Alignment explanation
Indices: 1130345--1130399 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
1130335 ATTTATATCA
1130345 AAATAT AAATAT AAATAT AAA-A- AAAT-T AAATAT AATCATATT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AA--ATA-T AAATAT
*
1130393 ATATAT A
1 AAATAT A
1130400 TCCTACGTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
4 3 0.07
5 5 0.12
6 25 0.60
7 3 0.07
8 3 0.07
9 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (6 bp):
AAATAT
Found at i:1130400 original size:15 final size:15
Alignment explanation
Indices: 1130324--1130400 Score: 52
Period size: 15 Copynumber: 5.3 Consensus size: 15
1130314 TTTAACATTA
* * *
1130324 ATATTTAATTTATTT
1 ATATTAAATATATAT
* *
1130339 ATATCAAA-ATATAA
1 ATATTAAATATATAT
* *
1130353 ATA-TAAATATAAAA
1 ATATTAAATATATAT
*
1130367 AAATTAAATATA-AT
1 ATATTAAATATATAT
1130381 CATATTAAATATATAT
1 -ATATTAAATATATAT
1130397 ATAT
1 ATAT
1130401 CCTACGTTGA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
13 3 0.06
14 14 0.29
15 29 0.60
16 2 0.04
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATTAAATATATAT
Found at i:1131820 original size:21 final size:22
Alignment explanation
Indices: 1131783--1131832 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1131773 GAATAAGATT
*
1131783 TTTTTAATTACAAAA-TTTATA
1 TTTTTAATTAAAAAATTTTATA
1131804 TTTTTAA-TAAAATAATTTTATA
1 TTTTTAATTAAAA-AATTTTATA
1131826 TATTTTA
1 T-TTTTA
1131833 TACTAATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.16
21 9 0.36
22 7 0.28
23 5 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTAATTAAAAAATTTTATA
Found at i:1134032 original size:20 final size:18
Alignment explanation
Indices: 1133995--1134033 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
1133985 TTAATATATA
1133995 TTTTAATATAAATATAAT
1 TTTTAATATAAATATAAT
*
1134013 TTTTAAATATTAAATCTAAT
1 TTTT-AATA-TAAATATAAT
1134033 T
1 T
1134034 ATATCACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAATATAAATATAAT
Found at i:1145192 original size:22 final size:21
Alignment explanation
Indices: 1145150--1145192 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1145140 GACTTAACAT
*
1145150 GTTTGAATTTTTTTTATTTAA
1 GTTTGAATTTTTTTTAATTAA
1145171 GTTT-AATTTATTATTTAATTAA
1 GTTTGAATTT-TT-TTTAATTAA
1145193 TTACAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (21 bp):
GTTTGAATTTTTTTTAATTAA
Found at i:1145316 original size:17 final size:19
Alignment explanation
Indices: 1145270--1145322 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1145260 AATAAAATAA
* *
1145270 ATTATATTTAAATTTTTTT
1 ATTAAATTTAAATTTATTT
1145289 ATTAAAATTTAAATTTATTT
1 ATT-AAATTTAAATTTATTT
1145309 -TT-AATTTAAATTTA
1 ATTAAATTTAAATTTA
1145323 ATAAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 12 0.39
19 5 0.16
20 14 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTAAATTTAAATTTATTT
Found at i:1145421 original size:21 final size:20
Alignment explanation
Indices: 1145391--1145430 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1145381 ATTTTTATAA
* *
1145391 TAAAATTTAAATTATGTAATT
1 TAAAAATTAAACTAT-TAATT
1145412 TAAAAATTAAACTATTAAT
1 TAAAAATTAAACTATTAAT
1145431 AATATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
TAAAAATTAAACTATTAATT
Found at i:1146003 original size:20 final size:18
Alignment explanation
Indices: 1145969--1146015 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
1145959 GAATTTAAAT
1145969 TAATTTTAAAATAATTTTA
1 TAATTTTAAAATAA-TTTA
* *
1145988 TTATTTTACAAGTAATTTA
1 TAATTTTA-AAATAATTTA
1146007 TAATTTTAA
1 TAATTTTAA
1146016 TATTTTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 18 0.75
20 5 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTTTAAAATAATTTA
Found at i:1146954 original size:3 final size:3
Alignment explanation
Indices: 1146939--1146973 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1146929 TTTCATAAAA
*
1146939 AAT AAT AAA AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1146974 TAATTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1147825 original size:55 final size:55
Alignment explanation
Indices: 1147741--1147851 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
1147731 ATTGAACTCA
1147741 AGACTTGACGTTATACCAAGTGTTGAGTTGAGTTTCCATCTGTATAGACACAATT
1 AGACTTGACGTTATACCAAGTGTTGAGTTGAGTTTCCATCTGTATAGACACAATT
1147796 AGACTTGACGTTATACCAAGTGTTGAGTTGAGTTTCCATCTGTATAGACACAATT
1 AGACTTGACGTTATACCAAGTGTTGAGTTGAGTTTCCATCTGTATAGACACAATT
1147851 A
1 A
1147852 TTTGTTCAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (55 bp):
AGACTTGACGTTATACCAAGTGTTGAGTTGAGTTTCCATCTGTATAGACACAATT
Found at i:1147933 original size:15 final size:15
Alignment explanation
Indices: 1147895--1147925 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1147885 TCCTTTCATA
1147895 AAAAATAATAAAAAT
1 AAAAATAATAAAAAT
*
1147910 AAAAATAATAATAAT
1 AAAAATAATAAAAAT
1147925 A
1 A
1147926 TAATTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATAATAAAAAT
Found at i:1148363 original size:19 final size:21
Alignment explanation
Indices: 1148341--1148381 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
1148331 TAAATTTATT
*
1148341 AAATTTT-AATTTTAA-TAAA
1 AAATTTTGAATTGTAATTAAA
1148360 AAATTTTGAATTGTAATTAAA
1 AAATTTTGAATTGTAATTAAA
1148381 A
1 A
1148382 TTATAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
AAATTTTGAATTGTAATTAAA
Found at i:1148625 original size:2 final size:2
Alignment explanation
Indices: 1148618--1148645 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1148608 CAAAGAAATA
1148618 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
1148646 GAAGGAGAGG
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:1148662 original size:6 final size:6
Alignment explanation
Indices: 1148653--1148686 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1148643 TATGAAGGAG
*
1148653 AGGGAA AGGGAA AGGGAA AGAGAA AGGGAA AGGG
1 AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AGGG
1148687 GTTGTTAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGGAA
Found at i:1149497 original size:3 final size:3
Alignment explanation
Indices: 1149491--1149521 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1149481 AAAAAAAAGT
1149491 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1149522 GAATGGATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1150032 original size:6 final size:6
Alignment explanation
Indices: 1150021--1150045 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1150011 GTTAGTCACT
1150021 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
1150046 TTATTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:1150519 original size:2 final size:2
Alignment explanation
Indices: 1150512--1150538 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1150502 ACAATGATCA
1150512 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 A
1150539 AATGTGTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1150762 original size:19 final size:19
Alignment explanation
Indices: 1150740--1150783 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1150730 TATGATAAAA
*
1150740 TATAAATAAATTTAATATT
1 TATAAATAAATTTAACATT
* *
1150759 TAT-AATATATTTTACATT
1 TATAAATAAATTTAACATT
1150777 TATAAAT
1 TATAAAT
1150784 TTATTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TATAAATAAATTTAACATT
Found at i:1150882 original size:16 final size:16
Alignment explanation
Indices: 1150835--1150884 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1150825 TAATAAAATT
1150835 TAATATGAAATAA-AAAA
1 TAATAT-AAA-AATAAAA
*
1150852 TAAT-TAAAATTTAAAA
1 TAATATAAAA-ATAAAA
1150868 TAATATAAAAATAAAA
1 TAATATAAAAATAAAA
1150884 T
1 T
1150885 TTATATAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 1 0.04
15 3 0.11
16 15 0.54
17 9 0.32
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
TAATATAAAAATAAAA
Found at i:1153154 original size:20 final size:20
Alignment explanation
Indices: 1153117--1153154 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1153107 TAATTTTTAT
*
1153117 ATTTAATTTCAAACTCAAAA
1 ATTTAATTTCAAAATCAAAA
1153137 ATTTATATTT-AAAATCAA
1 ATTTA-ATTTCAAAATCAA
1153155 GTTTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTAATTTCAAAATCAAAA
Found at i:1157420 original size:26 final size:26
Alignment explanation
Indices: 1157391--1157440 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1157381 AAATTATTTT
*
1157391 ATTTAATATTTTTTAATAAATTTAAA
1 ATTTAATATATTTTAATAAATTTAAA
* * *
1157417 ATTTTATATATTTTATTATATTTA
1 ATTTAATATATTTTAATAAATTTA
1157441 TATAATTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTAATATATTTTAATAAATTTAAA
Found at i:1157719 original size:16 final size:17
Alignment explanation
Indices: 1157693--1157734 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1157683 TCAGTCATTC
*
1157693 TAAATTTAAAT-ATTT-
1 TAAACTTAAATGATTTA
1157708 TAATACTTAAATGATTTA
1 TAA-ACTTAAATGATTTA
1157726 TAAACTTAA
1 TAAACTTAA
1157735 TCAAGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 3 0.13
16 7 0.30
17 10 0.43
18 3 0.13
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAACTTAAATGATTTA
Found at i:1157962 original size:37 final size:36
Alignment explanation
Indices: 1157909--1157985 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 36
1157899 AAAATGAAAT
* ***
1157909 TCAATCAAACTTTGAGCTTTGGATTTTGAGTAAAAGC
1 TCAATCAAACTCTGAGCTTCAAATTTTGAGT-AAAGC
1157946 TCAATCAAACTCTGAGCTTCAAATTTTGAGTAAAGC
1 TCAATCAAACTCTGAGCTTCAAATTTTGAGTAAAGC
1157982 TCAA
1 TCAA
1157986 ACTTCTTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 9 0.25
37 27 0.75
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (36 bp):
TCAATCAAACTCTGAGCTTCAAATTTTGAGTAAAGC
Found at i:1160172 original size:20 final size:20
Alignment explanation
Indices: 1160123--1160172 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
1160113 ATTATTTTTA
*
1160123 TATATAATATAAATAAAATG
1 TATATAATACAAATAAAATG
*
1160143 TATA-AA-ACAATTTAAAAT-
1 TATATAATACAA-ATAAAATG
1160161 TATATAATACAA
1 TATATAATACAA
1160173 CATATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 7 0.28
19 10 0.40
20 8 0.32
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
TATATAATACAAATAAAATG
Found at i:1160191 original size:28 final size:29
Alignment explanation
Indices: 1160159--1160213 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
1160149 ACAATTTAAA
1160159 ATTATATAATACAACATAT-CATTTATAT
1 ATTATATAATACAACATATGCATTTATAT
* *
1160187 ATTATATAATATATCATATGCATTTAT
1 ATTATATAATACAACATATGCATTTAT
1160214 TTTTAGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (29 bp):
ATTATATAATACAACATATGCATTTATAT
Found at i:1163520 original size:49 final size:47
Alignment explanation
Indices: 1163425--1163523 Score: 119
Period size: 49 Copynumber: 2.1 Consensus size: 47
1163415 GAATTTAAAA
** *
1163425 TATATTATTTTATTATTTTATTTTTAAAAAATAATTAAAAATATTTT
1 TATATTATTTTATTATTTTATAATTAAAAAATAAATAAAAATATTTT
* *
1163472 TATATTAATATTTATATATTTTATAATT-AAATATAAATATAAATATTTT
1 TATATT-AT-TTTAT-TATTTTATAATTAAAAAATAAATAAAAATATTTT
1163521 TAT
1 TAT
1163524 TAGTTAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
47 6 0.14
48 2 0.05
49 26 0.59
50 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (47 bp):
TATATTATTTTATTATTTTATAATTAAAAAATAAATAAAAATATTTT
Found at i:1163752 original size:24 final size:23
Alignment explanation
Indices: 1163719--1163763 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1163709 ATTTATATTT
*
1163719 TTTTATATTATGTTTAAATTAAC
1 TTTTATATTATATTTAAATTAAC
*
1163742 TTTTATAATTATATTTATATTA
1 TTTTAT-ATTATATTTAAATTA
1163764 TGTATTACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTATATTATATTTAAATTAAC
Found at i:1166597 original size:11 final size:11
Alignment explanation
Indices: 1166581--1166606 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1166571 GCAGCGTTGA
1166581 TTTTTTCTTTT
1 TTTTTTCTTTT
1166592 TTTTTTCTTTT
1 TTTTTTCTTTT
1166603 TTTT
1 TTTT
1166607 CTGCTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:1166737 original size:35 final size:36
Alignment explanation
Indices: 1166687--1166771 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 36
1166677 AAATTTTTAC
**
1166687 AAATTTAATTTAATTTAATTGAAA-TTA-TTAAA-TT
1 AAATTTAATAAAATTT-ATTGAAATTTATTTAAATTT
*
1166721 AATATTTAATAAAATTTATTTAAATTTATTTAAATTT
1 AA-ATTTAATAAAATTTATTGAAATTTATTTAAATTT
1166758 AAATTTAAATAAAA
1 AAATTT-AATAAAA
1166772 GGTTTTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
34 8 0.19
35 15 0.35
36 9 0.21
37 11 0.26
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (36 bp):
AAATTTAATAAAATTTATTGAAATTTATTTAAATTT
Found at i:1166744 original size:11 final size:10
Alignment explanation
Indices: 1166732--1166758 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1166722 ATATTTAATA
1166732 AAATTTATTT
1 AAATTTATTT
1166742 AAATTTATTT
1 AAATTTATTT
1166752 AAATTTA
1 AAATTTA
1166759 AATTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
AAATTTATTT
Found at i:1167351 original size:14 final size:15
Alignment explanation
Indices: 1167328--1167357 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1167318 TCTTGTGAAA
1167328 AAAAATTCATAAAAT
1 AAAAATTCATAAAAT
1167343 AAAAA-TCATAAAAT
1 AAAAATTCATAAAAT
1167357 A
1 A
1167358 TTATAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATTCATAAAAT
Done.