Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 15 of 27
Found at i:2245776 original size:42 final size:40
Alignment explanation
Indices: 2245728--2245834 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 40
2245718 AATTTACATA
2245728 TTTATATAATATTTATAATATTTTTATATT-ATAATTATAT
1 TTTATATAATATTTATAATATTTTTATATTAATAATT-TAT
* * *
2245768 TTAATATATTATATAATAA-ATTTTAATATATTAATAATTTAT
1 TTTATATAATAT-TTATAATATTTT--TATATTAATAATTTAT
*
2245810 TTTATATAA-ATTT-TAATATATTTAT
1 TTTATATAATATTTATAATATTTTTAT
2245835 GTATTCATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
38 3 0.05
39 3 0.05
40 20 0.36
41 7 0.13
42 16 0.29
43 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (40 bp):
TTTATATAATATTTATAATATTTTTATATTAATAATTTAT
Found at i:2245782 original size:22 final size:22
Alignment explanation
Indices: 2245757--2245817 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
2245747 ATTTTTATAT
2245757 TATAATTATATTTAATATATTA
1 TATAATTATATTTAATATATTA
*
2245779 TATAA-TAAATTTTAATATATTA
1 TATAATTATA-TTTAATATATTA
*
2245801 -ATAATT-TATTTTATATA
1 TATAATTATATTTAATATA
2245818 AATTTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.24
21 8 0.24
22 18 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATAATTATATTTAATATATTA
Found at i:2245822 original size:32 final size:33
Alignment explanation
Indices: 2245769--2245831 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
2245759 TAATTATATT
2245769 TAATATATTATATAATAAATTTTAATATATTAA
1 TAATATATTATATAATAAATTTTAATATATTAA
* *
2245802 TAATTTATTTTAT-ATAAATTTTAATATATT
1 TAATATATTATATAATAAATTTTAATATATT
2245832 TATGTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TAATATATTATATAATAAATTTTAATATATTAA
Found at i:2245833 original size:20 final size:20
Alignment explanation
Indices: 2245725--2245834 Score: 65
Period size: 25 Copynumber: 5.4 Consensus size: 20
2245715 CAAAATTTAC
2245725 ATATTTATATAATATTTATAAT
1 ATATTTATATAA-ATTT-TAAT
*
2245747 ATTTTTATATTATAATTATATTTAAT
1 A-TATT-TA-TATAA--AT-TTTAAT
2245773 ATATTATATAATAAATTTTAAT
1 ATATT-TAT-ATAAATTTTAAT
2245795 ATA-TTA-AT-AA--TT--T
1 ATATTTATATAAATTTTAAT
2245808 AT-TTTATATAAATTTTAAT
1 ATATTTATATAAATTTTAAT
2245827 ATATTTAT
1 ATATTTAT
2245835 GTATTCATAT
Statistics
Matches: 72, Mismatches: 2, Indels: 30
0.69 0.02 0.29
Matches are distributed among these distances:
13 6 0.08
14 2 0.03
15 4 0.06
17 4 0.06
18 2 0.03
19 3 0.04
20 7 0.10
21 1 0.01
22 10 0.14
23 5 0.07
24 3 0.04
25 15 0.21
26 8 0.11
27 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTATATAAATTTTAAT
Found at i:2246136 original size:28 final size:28
Alignment explanation
Indices: 2246081--2246150 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
2246071 TATTTTATAT
*
2246081 ATATATTTTTATATTCGTATTATATTTA
1 ATATATTTTTATATTCATATTATATTTA
2246109 ATATATTTTTATA-TCAT-TTCATATTTTA
1 ATATATTTTTATATTCATATT-ATA-TTTA
2246137 AT-T-TTTTTCATATT
1 ATATATTTTT-ATATT
2246151 TTATTTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
26 7 0.19
27 10 0.27
28 20 0.54
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (28 bp):
ATATATTTTTATATTCATATTATATTTA
Found at i:2246468 original size:20 final size:20
Alignment explanation
Indices: 2246445--2246498 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 20
2246435 TTATTATTAT
2246445 TATTCTAAAATTAA-AAAATA
1 TATT-TAAAATTAATAAAATA
2246465 TATTTAAAAATGTAATAAAATA
1 TATTT-AAAAT-TAATAAAATA
2246487 TAATTTAAAATT
1 T-ATTTAAAATT
2246499 TTTAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.03
20 9 0.30
21 4 0.13
22 12 0.40
23 4 0.13
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TATTTAAAATTAATAAAATA
Found at i:2246487 original size:22 final size:21
Alignment explanation
Indices: 2246451--2246496 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
2246441 TTATTATTCT
2246451 AAAATTAAAAAATAT-ATTTA
1 AAAATTAAAAAATATAATTTA
2246471 AAAATGTAATAAAATATAATTTA
1 AAAAT-TAA-AAAATATAATTTA
2246494 AAA
1 AAA
2246497 TTTTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.22
21 3 0.13
22 7 0.30
23 8 0.35
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATTAAAAAATATAATTTA
Found at i:2247247 original size:19 final size:20
Alignment explanation
Indices: 2247215--2247255 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
2247205 ACTTTTGTTA
2247215 TTTTACAATCTAAAAATTATT
1 TTTTACAATCT-AAAATTATT
2247236 TTTTA-AAT-TAAAATTATT
1 TTTTACAATCTAAAATTATT
2247254 TT
1 TT
2247256 ATTATACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 3 0.15
21 5 0.25
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTACAATCTAAAATTATT
Found at i:2247977 original size:18 final size:19
Alignment explanation
Indices: 2247954--2247990 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
2247944 TGGTCATTCT
2247954 TTTTATAAAATTA-AAAAA
1 TTTTATAAAATTAGAAAAA
2247972 TTTTATAAAATTAGAAAAA
1 TTTTATAAAATTAGAAAAA
2247991 AGTCTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTTATAAAATTAGAAAAA
Found at i:2248349 original size:47 final size:47
Alignment explanation
Indices: 2248277--2248412 Score: 150
Period size: 47 Copynumber: 2.9 Consensus size: 47
2248267 TATAATCTTA
* *
2248277 AAAAGTATAAACTTTCCTCACCAAATAATTTGTAATTTTTACAAT-AAT
1 AAAATTATAAACTTT--TCAACAAATAATTTGTAATTTTTACAATGAAT
* * * *
2248325 AAAGTTATAAATTTTTCTAACAAATAATTTGTAAATTTTGC-ATGAAT
1 AAAATTATAAACTTTTC-AACAAATAATTTGTAATTTTTACAATGAAT
* **
2248372 AAAATTATAAACTTTTCAACAAACAATTCATAATTTTTACA
1 AAAATTATAAACTTTTCAACAAATAATTTGTAATTTTTACA
2248413 CATAGAAATT
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
46 22 0.31
47 38 0.53
48 12 0.17
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (47 bp):
AAAATTATAAACTTTTCAACAAATAATTTGTAATTTTTACAATGAAT
Found at i:2248359 original size:24 final size:24
Alignment explanation
Indices: 2248298--2248363 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
2248288 CTTTCCTCAC
2248298 CAAATAATTTGT-AATTTTTACAA
1 CAAATAATTTGTAAATTTTTACAA
* * *
2248321 -TAATAAAGTTATAAATTTTT-CTAA
1 CAAAT-AATTTGTAAATTTTTAC-AA
2248345 CAAATAATTTGTAAATTTT
1 CAAATAATTTGTAAATTTT
2248364 GCATGAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
22 3 0.09
23 6 0.18
24 21 0.64
25 3 0.09
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (24 bp):
CAAATAATTTGTAAATTTTTACAA
Found at i:2249249 original size:17 final size:17
Alignment explanation
Indices: 2249215--2249258 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2249205 AGATAAAAAT
* * *
2249215 ATTTATTAGATATTCAA
1 ATTTATTAAACATCCAA
2249232 ATTTATTAAACATCCAA
1 ATTTATTAAACATCCAA
*
2249249 ATATATTAAA
1 ATTTATTAAA
2249259 TGAATTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTTATTAAACATCCAA
Found at i:2251500 original size:11 final size:11
Alignment explanation
Indices: 2251484--2251521 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2251474 AAATTGAAAT
2251484 ATAATATAAAA
1 ATAATATAAAA
2251495 ATAATATAAAA
1 ATAATATAAAA
*
2251506 A-AA-ATTAAA
1 ATAATATAAAA
2251515 ATAATAT
1 ATAATAT
2251522 GATGTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 6 0.25
10 4 0.17
11 14 0.58
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:2251846 original size:12 final size:12
Alignment explanation
Indices: 2251816--2251876 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
2251806 CGAATACAAT
*
2251816 ATAAAAAATTAA
1 ATAAAAAATAAA
* *
2251828 ATTAAAAGTAAA
1 ATAAAAAATAAA
*
2251840 ATAAAAAATAAC
1 ATAAAAAATAAA
2251852 ATAAATATAATATAA
1 ATAAA-A-AATA-AA
*
2251867 ATACAAAATA
1 ATAAAAAATA
2251877 TATAAAAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
12 23 0.61
13 5 0.13
14 5 0.13
15 5 0.13
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:2251867 original size:28 final size:28
Alignment explanation
Indices: 2251836--2251899 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
2251826 AAATTAAAAG
2251836 TAAAATAAAAAATAACAT--AAATATA-A
1 TAAAATAAAAAAT-ACATAAAAATATACA
* *
2251862 TATAAATACAAAATATATAAAAATATACA
1 TA-AAATAAAAAATACATAAAAATATACA
2251891 TAAAATAAA
1 TAAAATAAA
2251900 TTATTAACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 5 0.16
27 10 0.32
28 13 0.42
29 3 0.10
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (28 bp):
TAAAATAAAAAATACATAAAAATATACA
Found at i:2251993 original size:15 final size:15
Alignment explanation
Indices: 2251973--2252023 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2251963 AAAAATTTCA
2251973 TTTTTTTCTTCTTTT
1 TTTTTTTCTTCTTTT
* *
2251988 TTTTTTTTTTCCTTT
1 TTTTTTTCTTCTTTT
* *
2252003 TTCTTTCCTTCTTTCT
1 TTTTTTTCTTCTTT-T
2252019 TTTTT
1 TTTTT
2252024 CTTTCCTTAC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 23 0.82
16 5 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTCTTCTTTT
Found at i:2252016 original size:30 final size:28
Alignment explanation
Indices: 2251973--2252031 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
2251963 AAAAATTTCA
* *
2251973 TTTTTTTCTTCTTTTTTTTTTTTTTCCT
1 TTTTTTTCTTCTTTCTTTTTTCTTTCCT
2252001 TTTTCTTTCCTTCTTTCTTTTTTCTTTCCT
1 TTTT-TTT-CTTCTTTCTTTTTTCTTTCCT
2252031 T
1 T
2252032 ACCCTTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 4 0.15
29 3 0.11
30 20 0.74
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTTTTCTTCTTTCTTTTTTCTTTCCT
Found at i:2252022 original size:19 final size:19
Alignment explanation
Indices: 2251995--2252031 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2251985 TTTTTTTTTT
2251995 TTTCCTTTTTCTTTCCTTC
1 TTTCCTTTTTCTTTCCTTC
*
2252014 TTTCTTTTTTCTTTCCTT
1 TTTCCTTTTTCTTTCCTT
2252032 ACCCTTTCTC
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:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTCCTTTTTCTTTCCTTC
Found at i:2252039 original size:30 final size:30
Alignment explanation
Indices: 2251980--2252039 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2251970 TCATTTTTTT
* * ***
2251980 CTTCTTTTTTTTTTTTTTCCTTTTTCTTTC
1 CTTCTTTCTTTTTTCTTTCCTTACCCTTTC
2252010 CTTCTTTCTTTTTTCTTTCCTTACCCTTTC
1 CTTCTTTCTTTTTTCTTTCCTTACCCTTTC
2252040 TCTTTTCGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.72
Consensus pattern (30 bp):
CTTCTTTCTTTTTTCTTTCCTTACCCTTTC
Found at i:2253393 original size:202 final size:202
Alignment explanation
Indices: 2253047--2253452 Score: 812
Period size: 202 Copynumber: 2.0 Consensus size: 202
2253037 TTTGCATAAA
2253047 ATCATCTTACTTTAGGACTTCACCTCACATTTCTCATTAGGTTAGTATTATTTCAGTCGTAAAAC
1 ATCATCTTACTTTAGGACTTCACCTCACATTTCTCATTAGGTTAGTATTATTTCAGTCGTAAAAC
2253112 GCTAGAAATTTCTTTCCCGTTTCGAAGATACATACAATCTAATTGATCCTTGACAGGTTCAAATC
66 GCTAGAAATTTCTTTCCCGTTTCGAAGATACATACAATCTAATTGATCCTTGACAGGTTCAAATC
2253177 AATGAAGACCTGACACTAATATTATATGATTCTATCCTCCTTAGATGATGTTTTATAACAGATGT
131 AATGAAGACCTGACACTAATATTATATGATTCTATCCTCCTTAGATGATGTTTTATAACAGATGT
2253242 TGCATGT
196 TGCATGT
2253249 ATCATCTTACTTTAGGACTTCACCTCACATTTCTCATTAGGTTAGTATTATTTCAGTCGTAAAAC
1 ATCATCTTACTTTAGGACTTCACCTCACATTTCTCATTAGGTTAGTATTATTTCAGTCGTAAAAC
2253314 GCTAGAAATTTCTTTCCCGTTTCGAAGATACATACAATCTAATTGATCCTTGACAGGTTCAAATC
66 GCTAGAAATTTCTTTCCCGTTTCGAAGATACATACAATCTAATTGATCCTTGACAGGTTCAAATC
2253379 AATGAAGACCTGACACTAATATTATATGATTCTATCCTCCTTAGATGATGTTTTATAACAGATGT
131 AATGAAGACCTGACACTAATATTATATGATTCTATCCTCCTTAGATGATGTTTTATAACAGATGT
2253444 TGCATGT
196 TGCATGT
2253451 AT
1 AT
2253453 GAACAATTCT
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 204 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (202 bp):
ATCATCTTACTTTAGGACTTCACCTCACATTTCTCATTAGGTTAGTATTATTTCAGTCGTAAAAC
GCTAGAAATTTCTTTCCCGTTTCGAAGATACATACAATCTAATTGATCCTTGACAGGTTCAAATC
AATGAAGACCTGACACTAATATTATATGATTCTATCCTCCTTAGATGATGTTTTATAACAGATGT
TGCATGT
Found at i:2256123 original size:12 final size:11
Alignment explanation
Indices: 2256057--2256128 Score: 62
Period size: 11 Copynumber: 6.7 Consensus size: 11
2256047 CGACTCTTAA
2256057 ATAATATTAAAT
1 ATAATA-TAAAT
*
2256069 ATGATAT-AAT
1 ATAATATAAAT
*
2256079 TTAAT-T--AT
1 ATAATATAAAT
*
2256087 ATAATATAAAA
1 ATAATATAAAT
2256098 ATAATATAAAT
1 ATAATATAAAT
*
2256109 ATATTATACAAT
1 ATAATATA-AAT
2256121 ATAATATA
1 ATAATATA
2256129 TTTTAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
8 6 0.12
9 2 0.04
10 6 0.12
11 19 0.40
12 15 0.31
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:2256185 original size:28 final size:26
Alignment explanation
Indices: 2256111--2256187 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 26
2256101 ATATAAATAT
*
2256111 ATTATACAATATAATATATTTTAAAAA
1 ATTATAAAATATAATAT-TTTTAAAAA
*
2256138 ATAATAAAAATATTAATATTTTTAAAAA
1 ATTAT-AAAATA-TAATATTTTTAAAAA
* *
2256166 ATTATATAATATAA-ATTATTAA
1 ATTATAAAATATAATATTTTTAA
2256188 TATATCAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.16
26 3 0.07
27 9 0.21
28 18 0.42
29 6 0.14
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
ATTATAAAATATAATATTTTTAAAAA
Found at i:2256252 original size:45 final size:49
Alignment explanation
Indices: 2256158--2256253 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 49
2256148 TATTAATATT
2256158 TTTAAAAAATTATATAATATAAATTATTAATATATCAAAATTTATATAAA
1 TTTAAAAAATTATATAATATAAATTATTAATATATCAAAA-TTATATAAA
* *
2256208 TTTAAAATATTTTA-AATAT-AATTATT-ATATAAT-AAAA-TATATAAA
1 TTTAAAAAATTATATAATATAAATTATTAATAT-ATCAAAATTATATAAA
2256253 T
1 T
2256254 ATGATATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
45 9 0.21
47 8 0.19
48 9 0.21
49 5 0.12
50 12 0.28
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (49 bp):
TTTAAAAAATTATATAATATAAATTATTAATATATCAAAATTATATAAA
Found at i:2257538 original size:24 final size:27
Alignment explanation
Indices: 2257489--2257540 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2257479 AAAAATTCAG
2257489 TTAAAATAATATATTTAATATAATTTT
1 TTAAAATAATATATTTAATATAATTTT
*
2257516 TTAAAATGATA-A-TTAA-ATAATTTT
1 TTAAAATAATATATTTAATATAATTTT
2257540 T
1 T
2257541 AATTAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 9 0.38
25 4 0.17
26 1 0.04
27 10 0.42
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TTAAAATAATATATTTAATATAATTTT
Found at i:2257548 original size:25 final size:26
Alignment explanation
Indices: 2257493--2257548 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
2257483 ATTCAGTTAA
*
2257493 AATAAT-ATATTTAATATAATTTTTT
1 AATAATGATAATTAATATAATTTTTT
2257518 AA-AATGATAATTAA-ATAA-TTTTT
1 AATAATGATAATTAATATAATTTTTT
2257541 AATTAATG
1 AA-TAATG
2257549 TATATGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 7 0.26
24 7 0.26
25 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
AATAATGATAATTAATATAATTTTTT
Found at i:2257927 original size:27 final size:27
Alignment explanation
Indices: 2257897--2257952 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
2257887 GGATTTAGTT
2257897 AATTATATTTATATTT-TAATAATTTTA
1 AATTATATTTATATTTAT-ATAATTTTA
* * *
2257924 AATTTTATTTTTATTTATATATTTTTA
1 AATTATATTTATATTTATATAATTTTA
2257951 AA
1 AA
2257953 ATTAAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
AATTATATTTATATTTATATAATTTTA
Found at i:2259753 original size:18 final size:18
Alignment explanation
Indices: 2259732--2259766 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2259722 TAAAACAACA
2259732 TATACATACATATATGTG
1 TATACATACATATATGTG
* *
2259750 TATATATATATATATGT
1 TATACATACATATATGT
2259767 ACCTGAACAA
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:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (18 bp):
TATACATACATATATGTG
Found at i:2260690 original size:14 final size:14
Alignment explanation
Indices: 2260654--2260704 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
2260644 TATTACAAGA
2260654 AAATAATATTAATTT
1 AAATAA-ATTAATTT
*
2260669 -AATTAATTAATTTT
1 AAATAAATTAA-TTT
2260683 AAA-AAATTAATTT
1 AAATAAATTAATTT
2260696 AAATAAATT
1 AAATAAATT
2260705 TATTATAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 11 0.35
14 18 0.58
15 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATAAATTAATTT
Found at i:2260721 original size:18 final size:20
Alignment explanation
Indices: 2260700--2260737 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2260690 TAATTTAAAT
2260700 AAATT-TAT-TATAGATATA
1 AAATTATATATATAGATATA
*
2260718 AAATTATATATATATATATA
1 AAATTATATATATAGATATA
2260738 TATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AAATTATATATATAGATATA
Found at i:2260729 original size:2 final size:2
Alignment explanation
Indices: 2260722--2260746 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2260712 GATATAAAAT
2260722 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 T
2260747 TCATATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2261700 original size:21 final size:21
Alignment explanation
Indices: 2261652--2261700 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2261642 TTTTTATTAT
*
2261652 ATTAATAGTTAATTATTTTTA
1 ATTAATAATTAATTATTTTTA
**
2261673 AAAAATAATTGAA-TATTTTTA
1 ATTAATAATT-AATTATTTTTA
2261694 ATTAATA
1 ATTAATA
2261701 TAAAAGTTGA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTAATAATTAATTATTTTTA
Found at i:2264914 original size:2 final size:2
Alignment explanation
Indices: 2264907--2264932 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2264897 TGATGGATCC
2264907 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
2264933 CCCGTTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2266349 original size:20 final size:20
Alignment explanation
Indices: 2266299--2266355 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2266289 TTATGTATTT
* * *
2266299 TTATATATATATTTTAAGTA
1 TTATATATTTATTTAAAATA
2266319 TTATA-ATTTTATTTAAAATA
1 TTATATA-TTTATTTAAAATA
*
2266339 TTATATATTTATATAAA
1 TTATATATTTATTTAAA
2266356 TTTTGATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATATATTTATTTAAAATA
Found at i:2266364 original size:20 final size:19
Alignment explanation
Indices: 2266334--2266440 Score: 63
Period size: 20 Copynumber: 5.9 Consensus size: 19
2266324 ATTTTATTTA
*
2266334 AAATATTATATATTTATAT
1 AAATTTTATATATTTATAT
2266353 AAATTTTGATATA-TTA-AT
1 AAATTTT-ATATATTTATAT
*
2266371 -AA--TTAT-T-GTTATAT
1 AAATTTTATATATTTATAT
2266385 AAATTTTAATATATTTATAT
1 AAATTTT-ATATATTTATAT
*
2266405 ATTAATATTATAT-TTGTAT-T
1 A--AATTTTATATATT-TATAT
*
2266425 AATTTTTATAT-TTTAT
1 AAATTTTATATATTTAT
2266441 TTTAATTATT
Statistics
Matches: 71, Mismatches: 5, Indels: 26
0.70 0.05 0.25
Matches are distributed among these distances:
13 4 0.06
14 4 0.06
15 4 0.06
17 7 0.10
18 14 0.20
19 10 0.14
20 16 0.23
21 7 0.10
22 5 0.07
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
AAATTTTATATATTTATAT
Found at i:2266384 original size:32 final size:33
Alignment explanation
Indices: 2266331--2266417 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 33
2266321 ATAATTTTAT
* *
2266331 TTAAAATATTATATATTTATATAAATTTTGATATA
1 TTAATATATTA-ATA-TTATATAAATTTTAATATA
* *
2266366 TTAATA-ATTATTGTTATATAAATTTTAATATA
1 TTAATATATTAATATTATATAAATTTTAATATA
*
2266398 TTTATATATTAATATTATAT
1 TTAATATATTAATATTATAT
2266418 TTGTATTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
32 23 0.52
33 12 0.27
34 4 0.09
35 5 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (33 bp):
TTAATATATTAATATTATATAAATTTTAATATA
Found at i:2266405 original size:40 final size:38
Alignment explanation
Indices: 2266355--2266440 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 38
2266345 ATTTATATAA
2266355 ATTTTGATATATTAATAATTAT-TGTTATATAAATTTTAAT
1 ATTTT-ATATATTAAT-ATTATAT-TTATATAAATTTTAAT
* * *
2266395 ATATTTATATATTAATATTATATTTGTATTAATTTTTAT
1 AT-TTTATATATTAATATTATATTTATATAAATTTTAAT
2266434 ATTTTAT
1 ATTTTAT
2266441 TTTAATTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 5 0.12
39 20 0.49
40 13 0.32
41 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (38 bp):
ATTTTATATATTAATATTATATTTATATAAATTTTAAT
Found at i:2266426 original size:17 final size:17
Alignment explanation
Indices: 2266404--2266441 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2266394 TATATTTATA
2266404 TATTAA-TATTATATTT
1 TATTAATTATTATATTT
*
2266420 GTATTAATTTTTATATTT
1 -TATTAATTATTATATTT
2266438 TATT
1 TATT
2266442 TTAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TATTAATTATTATATTT
Found at i:2266435 original size:23 final size:23
Alignment explanation
Indices: 2266409--2266456 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2266399 TTATATATTA
2266409 ATATTATATTTGT-ATTAATTTTT
1 ATATTATATTT-TAATTAATTTTT
* *
2266432 ATATTTTATTTTAATTATTTTTT
1 ATATTATATTTTAATTAATTTTT
2266455 AT
1 AT
2266457 TTTGTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
ATATTATATTTTAATTAATTTTT
Found at i:2266447 original size:19 final size:19
Alignment explanation
Indices: 2266394--2266450 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
2266384 TAAATTTTAA
2266394 TATATTTATATATTAA-TAT
1 TATATTTATAT-TTAATTAT
* *
2266413 TATATTTGTA-TTAATTTT
1 TATATTTATATTTAATTAT
2266431 TATATTT-TATTTTAATTAT
1 TATATTTATA-TTTAATTAT
2266450 T
1 T
2266451 TTTTATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 6 0.19
18 9 0.28
19 17 0.53
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATATTTATATTTAATTAT
Found at i:2266754 original size:13 final size:14
Alignment explanation
Indices: 2266738--2266787 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2266728 TTTGAATGTT
2266738 AATTTTTT-TAATA
1 AATTTTTTGTAATA
2266751 AATTTTTTGATAA-A
1 AATTTTTTG-TAATA
* *
2266765 ATTTTATTTGTAATT
1 AATTT-TTTGTAATA
2266780 AATTTTTT
1 AATTTTTT
2266788 TACAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 8 0.27
14 11 0.37
15 11 0.37
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (14 bp):
AATTTTTTGTAATA
Found at i:2267834 original size:22 final size:19
Alignment explanation
Indices: 2267803--2267844 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
2267793 TATTTTTATT
2267803 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
2267824 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
2267844 T
1 T
2267845 TTTTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:2271240 original size:38 final size:38
Alignment explanation
Indices: 2271186--2271270 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
2271176 AACTAAAAAT
* *
2271186 TTATA-TTAAATAAAATTTTAAATA-TTTATTTATTTATA
1 TTATATTTAAATAAAATTTT-AATAGTATATTTA-TTAAA
*
2271224 TTATATTTAAAT-AAATTTTTATAGTATATTTATTAAA
1 TTATATTTAAATAAAATTTTAATAGTATATTTATTAAA
2271261 TTATATTTAA
1 TTATATTTAA
2271271 TATTTGTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 17 0.40
38 19 0.45
39 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (38 bp):
TTATATTTAAATAAAATTTTAATAGTATATTTATTAAA
Found at i:2272827 original size:14 final size:12
Alignment explanation
Indices: 2272797--2272860 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
2272787 AATTTTTATT
*
2272797 TTATTTAAATTA
1 TTATTTAAAATA
2272809 TTATTTAAAAATA
1 TTATTT-AAAATA
*
2272822 TATATTTTAAAT-
1 T-TATTTAAAATA
2272834 TTAATTATAAAATA
1 TT-ATT-TAAAATA
*
2272848 TT-TTTAATATA
1 TTATTTAAAATA
2272859 TT
1 TT
2272861 TTAGATGATA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
11 9 0.21
12 12 0.28
13 15 0.35
14 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTATTTAAAATA
Found at i:2280294 original size:25 final size:25
Alignment explanation
Indices: 2280266--2280318 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2280256 TATGATTTTG
* *
2280266 ATTTTAAGAACTTGTTATGATAGTA
1 ATTTTAAGAACTTATTACGATAGTA
**
2280291 ATTTTAAGAGTTTATTACGATAGTA
1 ATTTTAAGAACTTATTACGATAGTA
2280316 ATT
1 ATT
2280319 ACAATATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTTTAAGAACTTATTACGATAGTA
Found at i:2282531 original size:2 final size:2
Alignment explanation
Indices: 2282524--2282552 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2282514 GCTTTTTATG
2282524 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2282553 TACATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2283330 original size:3 final size:3
Alignment explanation
Indices: 2283322--2283353 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2283312 GCTACCAAAA
2283322 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2283354 GGAATTATAA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2284772 original size:2 final size:2
Alignment explanation
Indices: 2284767--2284806 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2284757 TGTTTTTTAA
2284767 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
2284807 TAGCTAGTTA
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:2287092 original size:34 final size:31
Alignment explanation
Indices: 2287033--2287098 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 31
2287023 TCACATAATT
2287033 ATATGATATAAATATAAAAAAATAAT-TAAA
1 ATATGATATAAATATAAAAAAATAATATAAA
*
2287063 ATATGATATATATATATAACACAACATAATATAAA
1 ATATGATATA-A-ATATAA-A-AAAATAATATAAA
2287098 A
1 A
2287099 ATATTACAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 10 0.33
31 1 0.03
32 6 0.20
33 1 0.03
34 7 0.23
35 5 0.17
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (31 bp):
ATATGATATAAATATAAAAAAATAATATAAA
Found at i:2287128 original size:19 final size:18
Alignment explanation
Indices: 2287092--2287134 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
2287082 CACAACATAA
*
2287092 TATAAAAATATTACAA-T
1 TATAAAAATATTAAAATT
2287109 TATAAAAATATATCAAAATT
1 TATAAAAATAT-T-AAAATT
2287129 TATAAA
1 TATAAA
2287135 GTATAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
18 1 0.05
19 3 0.14
20 7 0.32
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
TATAAAAATATTAAAATT
Found at i:2292809 original size:2 final size:2
Alignment explanation
Indices: 2292804--2292836 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2292794 TATATAGCAA
2292804 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 A
2292837 ACAAATTATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2293087 original size:20 final size:21
Alignment explanation
Indices: 2293062--2293117 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
2293052 TTTTATATTT
2293062 ATAATTAAATTTAAATAAA-A
1 ATAATTAAATTTAAATAAACA
** *
2293082 ATAATT-TTTTTATATAAACA
1 ATAATTAAATTTAAATAAACA
2293102 ATAATTTAAA-TTAAAT
1 ATAA-TTAAATTTAAAT
2293118 TGAATTAGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
19 9 0.33
20 11 0.41
21 7 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATTAAATTTAAATAAACA
Found at i:2293098 original size:19 final size:20
Alignment explanation
Indices: 2293071--2293108 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2293061 TATAATTAAA
2293071 TTTAAATAAA-AATAATTTT
1 TTTAAATAAACAATAATTTT
*
2293090 TTTATATAAACAATAATTT
1 TTTAAATAAACAATAATTT
2293109 AAATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATAAACAATAATTTT
Found at i:2294656 original size:12 final size:12
Alignment explanation
Indices: 2294641--2294679 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2294631 AAATGTATAA
*
2294641 AAAAATTAATAT
1 AAAAAGTAATAT
*
2294653 AAAAAGTGATAT
1 AAAAAGTAATAT
2294665 AAATAAGTAATAT
1 AAA-AAGTAATAT
2294678 AA
1 AA
2294680 GATTTAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (12 bp):
AAAAAGTAATAT
Found at i:2294939 original size:23 final size:26
Alignment explanation
Indices: 2294886--2294936 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
2294876 AAGAATTTAT
*
2294886 ATTTA-AT-TTATTAATAATATATAA
1 ATTTATATATTATTAATAATATACAA
2294910 ATTTATATATTATTAATAA-AT-CAA
1 ATTTATATATTATTAATAATATACAA
2294934 ATT
1 ATT
2294937 ATAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 10 0.42
25 4 0.17
26 10 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTATATATTATTAATAATATACAA
Found at i:2297931 original size:16 final size:16
Alignment explanation
Indices: 2297910--2297940 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2297900 TAGATACCCT
2297910 TTTCTTTCTTTCTTTG
1 TTTCTTTCTTTCTTTG
*
2297926 TTTCTTTGTTTCTTT
1 TTTCTTTCTTTCTTT
2297941 CCTTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTCTTTCTTTCTTTG
Found at i:2300572 original size:30 final size:30
Alignment explanation
Indices: 2300536--2300597 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
2300526 ATCCCAACAC
*
2300536 TAATTAATTCAGACCAAAAATATTCTTAAT
1 TAATTAATTAAGACCAAAAATATTCTTAAT
*
2300566 TAATTAATTAAGACCAAAAATGTTCTTAAT
1 TAATTAATTAAGACCAAAAATATTCTTAAT
2300596 TA
1 TA
2300598 CTCAACTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (30 bp):
TAATTAATTAAGACCAAAAATATTCTTAAT
Found at i:2300663 original size:15 final size:15
Alignment explanation
Indices: 2300643--2300674 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2300633 ACTCTCTCCA
2300643 TTCTTTTCTTTTCCT
1 TTCTTTTCTTTTCCT
2300658 TTCTTTTCTTTTCCT
1 TTCTTTTCTTTTCCT
2300673 TT
1 TT
2300675 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTTTTCCT
Found at i:2300954 original size:2 final size:2
Alignment explanation
Indices: 2300947--2300984 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2300937 TCATGTTGGA
2300947 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
2300985 TTGGGTTTAT
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):
AT
Found at i:2302387 original size:2 final size:2
Alignment explanation
Indices: 2302382--2302410 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2302372 GTGTGTGTGT
2302382 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2302411 TTGAAAAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2304319 original size:3 final size:3
Alignment explanation
Indices: 2304311--2304340 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2304301 TTTTAGATGC
2304311 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2304341 TCATCATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2304565 original size:2 final size:2
Alignment explanation
Indices: 2304558--2304593 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2304548 TAGAAAACTC
2304558 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
2304594 GATCACTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2305222 original size:25 final size:25
Alignment explanation
Indices: 2305180--2305237 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
2305170 AATTATTTTA
2305180 AAATTTAAA--TTTATTTATTATCT
1 AAATTTAAATTTTTATTTATTATCT
*
2305203 ACA-TTAAATTTTTATGTTATTATCT
1 AAATTTAAATTTTTAT-TTATTATCT
2305228 AAATTTAAAT
1 AAATTTAAAT
2305238 CTAAATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 5 0.17
23 2 0.07
24 5 0.17
25 11 0.38
26 6 0.21
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (25 bp):
AAATTTAAATTTTTATTTATTATCT
Found at i:2310588 original size:2 final size:2
Alignment explanation
Indices: 2310581--2310608 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2310571 ATGAGTTTGT
2310581 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2310609 AAGGCAAAGG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2311440 original size:161 final size:161
Alignment explanation
Indices: 2311109--2311569 Score: 617
Period size: 161 Copynumber: 2.8 Consensus size: 161
2311099 CACCTTAACA
* * *
2311109 CGGATGTCACATCATGAAATGGAGAAGGGTATTCCTGTCATTCTATCAAAATGTAGGAAATTTCA
1 CGGATGTCACATCATGAAAT-GAGAAGGGTATTTCTGTCATTCTATTAAAATGTAGGAAATTTTA
2311174 CAATTAAAAAAAAA-TAAAGGAAAAAGACCTAATCCAACCACTAGATACAAATAAACGAACAAAA
65 CAATTAAAAAAAAACTAAAGGAAAAAGACCTAATCCAACCACTAGATACAAATAAACGAACAAAA
* * **
2311238 AGTCACTCTGAATTTTTTGGAAAAGGAGGAACC
130 AGCCACAC-GAATTTTTCCGAAAAGGAGGAACC
* * * *
2311271 CCGATGTCATATCATGAAATCAGATGGGTATTTCTGTCATTCTATTAAAATGTAGGAAATTTTAC
1 CGGATGTCACATCATGAAATGAGAAGGGTATTTCTGTCATTCTATTAAAATGTAGGAAATTTTAC
* * *
2311336 -ACTAAAACAAAACACTAAAGGAGAAAGACCTAATCCAACCACTAAATACAAATAAACGAACAAA
66 AATTAAAA-AAAA-ACTAAAGGAAAAAGACCTAATCCAACCACTAGATACAAATAAACGAACAAA
*
2311400 AAGCCACAC-AA-TTTTCCGAACAAGGAGGGACC
129 AAGCCACACGAATTTTTCCGAA-AAGGAGGAACC
* *
2311432 CGGATGTCACAGCATGAAATGAGAAGGGTATTTCTGTCATTCTATTAAAATGTATGAAATTTCT-
1 CGGATGTCACATCATGAAATGAGAAGGGTATTTCTGTCATTCTATTAAAATGTAGGAAATTT-TA
** * * *
2311496 CAATTAAAAAAAAAAACTAAAGGAAAAAGACCTAATCCAACTGCTAGAGATAAATAAGCGAACAA
65 CAATT--AAAAAAAAACTAAAGGAAAAAGACCTAATCCAACCACTAGATACAAATAAACGAACAA
2311561 AAAGCCACA
128 AAAGCCACA
2311570 GTTAATTTTT
Statistics
Matches: 262, Mismatches: 29, Indels: 16
0.85 0.09 0.05
Matches are distributed among these distances:
160 13 0.05
161 113 0.43
162 74 0.28
163 58 0.22
164 4 0.02
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (161 bp):
CGGATGTCACATCATGAAATGAGAAGGGTATTTCTGTCATTCTATTAAAATGTAGGAAATTTTAC
AATTAAAAAAAAACTAAAGGAAAAAGACCTAATCCAACCACTAGATACAAATAAACGAACAAAAA
GCCACACGAATTTTTCCGAAAAGGAGGAACC
Found at i:2312293 original size:22 final size:21
Alignment explanation
Indices: 2312260--2312309 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
2312250 AATAAAAATA
2312260 ATAATAATATTTAAA-ATTTAATT
1 ATAA-AATATTTAAATA-TTAA-T
2312283 ATAAAATATTTAAATATTAAT
1 ATAAAATATTTAAATATTAAT
2312304 ATAAAA
1 ATAAAA
2312310 ACAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.27
22 14 0.54
23 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAATATTTAAATATTAAT
Found at i:2312306 original size:21 final size:22
Alignment explanation
Indices: 2312260--2312309 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
2312250 AATAAAAATA
2312260 ATAATAATATTTAAAATTTAATT
1 ATAA-AATATTTAAAATTTAATT
2312283 ATAAAATATTT-AAATATTAA-T
1 ATAAAATATTTAAAAT-TTAATT
2312304 ATAAAA
1 ATAAAA
2312310 ACAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAAATATTTAAAATTTAATT
Found at i:2312992 original size:53 final size:53
Alignment explanation
Indices: 2312898--2313008 Score: 138
Period size: 52 Copynumber: 2.1 Consensus size: 53
2312888 AAATTCTTTC
* * * *
2312898 AATTAGATTTAATTTAGTATATTTTAAATTTAAATAAATTTTTTATTTAAA-TT
1 AATTAGATTTAAATTAGTATATTTAAAAATAAAATAAA-TTTTTATTTAAATTT
2312951 AATTAGATTTAAATTA-T-TATTTAAAAAATAAAATAATATTTTTATTTAAATTT
1 AATTAGATTTAAATTAGTATATTT-AAAAATAAAATAA-ATTTTTATTTAAATTT
2313004 AATTA
1 AATTA
2313009 TAAAATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
51 5 0.10
52 23 0.45
53 23 0.45
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (53 bp):
AATTAGATTTAAATTAGTATATTTAAAAATAAAATAAATTTTTATTTAAATTT
Found at i:2313275 original size:21 final size:20
Alignment explanation
Indices: 2313225--2313275 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 20
2313215 TAAAAAATTG
2313225 TTATAGATTAAATTGAACTGT
1 TTATA-ATTAAATTGAACTGT
2313246 TTATAAATTAAATTGAA-TGAT
1 TTAT-AATTAAATTGAACTG-T
2313267 ATTATAATT
1 -TTATAATT
2313276 TAAAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.07
21 20 0.74
22 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (20 bp):
TTATAATTAAATTGAACTGT
Found at i:2319310 original size:7 final size:7
Alignment explanation
Indices: 2319298--2319322 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2319288 TTAATGAAAC
2319298 TTTCCCT
1 TTTCCCT
2319305 TTTCCCT
1 TTTCCCT
2319312 TTTCCCT
1 TTTCCCT
2319319 TTTC
1 TTTC
2319323 TTTTGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTCCCT
Found at i:2321284 original size:42 final size:42
Alignment explanation
Indices: 2321232--2321313 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
2321222 CAGCTTCTAT
2321232 GCTGGTAATCTGCATTTTATTTAAGTAGTTCTTAATATGCAA
1 GCTGGTAATCTGCATTTTATTTAAGTAGTTCTTAATATGCAA
*
2321274 GCTGGTAATCTGCATTTTGTTTAAGTAGTTCTTAATATGC
1 GCTGGTAATCTGCATTTTATTTAAGTAGTTCTTAATATGC
2321314 TATCTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (42 bp):
GCTGGTAATCTGCATTTTATTTAAGTAGTTCTTAATATGCAA
Found at i:2324232 original size:12 final size:12
Alignment explanation
Indices: 2324209--2324242 Score: 50
Period size: 12 Copynumber: 2.7 Consensus size: 12
2324199 AAACATCAAC
2324209 AAAGCAAAAAAAA
1 AAAG-AAAAAAAA
2324222 TAAAGAAAAAAAA
1 -AAAGAAAAAAAA
2324235 AAAGAAAA
1 AAAGAAAA
2324243 GAAGGTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 8 0.40
14 4 0.20
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:2327508 original size:2 final size:2
Alignment explanation
Indices: 2327501--2327539 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2327491 TGTATCCTTG
2327501 TA TA TA 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 TA TA TA T
2327540 TTTAAAATGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2331309 original size:23 final size:23
Alignment explanation
Indices: 2331283--2331326 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2331273 GGTTTAATCA
2331283 AATTATTATTAAAGTATTTTCTC
1 AATTATTATTAAAGTATTTTCTC
2331306 AATTATTATTAAAGTATTTTC
1 AATTATTATTAAAGTATTTTC
2331327 ACAAAGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (23 bp):
AATTATTATTAAAGTATTTTCTC
Found at i:2331804 original size:3 final size:3
Alignment explanation
Indices: 2331796--2331830 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2331786 CACCCACCGC
2331796 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
2331831 ATGCCTGCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:2335864 original size:18 final size:18
Alignment explanation
Indices: 2335837--2335899 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
2335827 TAATTTAAGT
*
2335837 TATTTTAATTTAAATTAA
1 TATTTAAATTTAAATTAA
*
2335855 TATTTAAATTGTAAA-AAA
1 TATTTAAATT-TAAATTAA
*
2335873 TATTT--ATTTAAATTTA
1 TATTTAAATTTAAATTAA
2335889 TATATTAAATT
1 TAT-TTAAATT
2335900 ATATAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
15 4 0.11
16 7 0.19
17 2 0.06
18 16 0.44
19 7 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATTTAAATTTAAATTAA
Found at i:2335908 original size:34 final size:34
Alignment explanation
Indices: 2335844--2335910 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
2335834 AGTTATTTTA
*
2335844 ATTTAAATTAATATTTAAATTGTAAAAAATATTT
1 ATTTAAATTAATATTTAAATTATAAAAAATATTT
* *
2335878 ATTTAAATTTATATATTAAATTAT-ATAAATATT
1 ATTTAAATTAATAT-TTAAATTATAAAAAATATT
2335911 AATAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
ATTTAAATTAATATTTAAATTATAAAAAATATTT
Found at i:2336224 original size:18 final size:21
Alignment explanation
Indices: 2336171--2336215 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
2336161 TAAATTTTAT
*
2336171 ATATATTTAAATAATAATAATTA
1 ATATA-TT-AATAATAATAAATA
2336194 ATATATTAATAATAATAAATA
1 ATATATTAATAATAATAAATA
2336215 A
1 A
2336216 AATTATAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 2 0.10
23 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATATTAATAATAATAAATA
Found at i:2336693 original size:13 final size:13
Alignment explanation
Indices: 2336675--2336699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2336665 CGAAGAAAAC
2336675 ATGTATAAGACAT
1 ATGTATAAGACAT
2336688 ATGTATAAGACA
1 ATGTATAAGACA
2336700 AAGTATCAAA
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:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (13 bp):
ATGTATAAGACAT
Found at i:2337190 original size:25 final size:23
Alignment explanation
Indices: 2337161--2337213 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 23
2337151 TTTCAATATC
2337161 AAATTTAA-AAATATTCAAAGTTTTT
1 AAATTTAATAAATATT--AA-TTTTT
2337186 AAATTTAATAAATATTAATTTTT
1 AAATTTAATAAATATTAATTTTT
2337209 AAATT
1 AAATT
2337214 CAAATGACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.37
24 2 0.07
25 8 0.30
26 7 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AAATTTAATAAATATTAATTTTT
Found at i:2337373 original size:17 final size:18
Alignment explanation
Indices: 2337351--2337416 Score: 59
Period size: 20 Copynumber: 3.7 Consensus size: 18
2337341 ATTAATTTTA
2337351 ATATTAAATATAATAA-AT
1 ATATT-AATATAATAATAT
2337369 A-ATTAATA-AA-AATAT
1 ATATTAATATAATAATAT
*
2337384 ATATTTAATATAATAATAAA
1 ATA-TTAATATAATAAT-AT
2337404 ATATTTAATATAA
1 ATA-TTAATATAA
2337417 AATTATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
14 2 0.05
15 5 0.12
16 5 0.12
17 9 0.22
18 3 0.07
19 3 0.07
20 14 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTAATATAATAATAT
Found at i:2337383 original size:22 final size:22
Alignment explanation
Indices: 2337356--2337426 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
2337346 TTTTAATATT
2337356 AAATATAATAAATAATTAATAA
1 AAATATAATAAATAATTAATAA
2337378 AAATATATATTTAATATAA-TAATAA
1 AAATATA-A--TAA-ATAATTAATAA
*
2337403 AATATTTAATATAA-AATT-ATAA
1 AA-ATATAATA-AATAATTAATAA
2337425 AA
1 AA
2337427 TTAAAATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
22 15 0.37
23 5 0.12
24 1 0.02
25 12 0.29
26 8 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATATAATAAATAATTAATAA
Found at i:2337409 original size:20 final size:19
Alignment explanation
Indices: 2337360--2337416 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 19
2337350 AATATTAAAT
*
2337360 ATAATAAATAATTAATA-A
1 ATAATAAATATTTAATATA
*
2337378 A-AATATATATTTAATATA
1 ATAATAAATATTTAATATA
2337396 ATAATAAAATATTTAATATA
1 ATAAT-AAATATTTAATATA
2337416 A
1 A
2337417 AATTATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 13 0.39
18 3 0.09
19 3 0.09
20 14 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATAAATATTTAATATA
Found at i:2339626 original size:14 final size:13
Alignment explanation
Indices: 2339602--2339631 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
2339592 GATATGAATG
2339602 TAATTTAATATTT
1 TAATTTAATATTT
2339615 TAATTATAATATTT
1 TAATT-TAATATTT
2339629 TAA
1 TAA
2339632 AAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TAATTTAATATTT
Found at i:2339642 original size:19 final size:19
Alignment explanation
Indices: 2339616--2339667 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
2339606 TTAATATTTT
2339616 AATT-ATAATATT-TTAAAA
1 AATTAATAAT-TTATTAAAA
*
2339634 AATTAATAATTTATTAATA
1 AATTAATAATTTATTAAAA
* *
2339653 AATTACTCATTTATT
1 AATTAATAATTTATT
2339668 TTTAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (19 bp):
AATTAATAATTTATTAAAA
Found at i:2339677 original size:20 final size:20
Alignment explanation
Indices: 2339652--2339694 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2339642 ATTTATTAAT
*
2339652 AAATTACTCATTTATTTTTA
1 AAATTACTCATTTATATTTA
*
2339672 AAATTATTCATTTATATTTA
1 AAATTACTCATTTATATTTA
2339692 AAA
1 AAA
2339695 ATTTTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATTACTCATTTATATTTA
Found at i:2339697 original size:21 final size:20
Alignment explanation
Indices: 2339624--2339697 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 20
2339614 TTAATTATAA
* *
2339624 TATTTTAAAAAATTAATAATT
1 TATTTT-AAAAATTACTCATT
2339645 TA--TTAATAAATTACTCATT
1 TATTTTAA-AAATTACTCATT
* *
2339664 TATTTTTAAAATTATTCATT
1 TATTTTAAAAATTACTCATT
2339684 TATATTTAAAAATT
1 TAT-TTTAAAAATT
2339698 TTATATATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.05
19 14 0.32
20 14 0.32
21 14 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTTTAAAAATTACTCATT
Found at i:2340052 original size:17 final size:18
Alignment explanation
Indices: 2340025--2340060 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2340015 TTTTAAAATT
2340025 AAAATTAAAATTATATAA
1 AAAATTAAAATTATATAA
*
2340043 AAAATT-AAATTTTATAA
1 AAAATTAAAATTATATAA
2340060 A
1 A
2340061 TTATGTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTAAAATTATATAA
Found at i:2340188 original size:16 final size:16
Alignment explanation
Indices: 2340166--2340209 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2340156 CTTTTTTAAA
2340166 AATTAT-TTTTTAT-T
1 AATTATATTTTTATAT
*
2340180 AATTATATTTTAATAT
1 AATTATATTTTTATAT
2340196 AATTATAATTTTTA
1 AATTAT-ATTTTTA
2340210 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 6 0.24
16 7 0.28
17 6 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTATATTTTTATAT
Found at i:2340253 original size:37 final size:36
Alignment explanation
Indices: 2340212--2340318 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 36
2340202 AATTTTTAAT
*
2340212 TTTAAAAATATATT-TTCTTATTTAATATAAATATAAC
1 TTTAAAAAT-T-TTATTATTATTTAATATAAATATAAC
**
2340249 TTTAAAAATTTTAATTATTATTTAATATAAATATATT
1 TTTAAAAATTTT-ATTATTATTTAATATAAATATAAC
* **
2340286 TTTAATAAAATTTT-TAATTATTTACCATAAATA
1 TTT-A-AAAATTTTATTATTATTTAATATAAATA
2340319 AATTAATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
35 2 0.03
36 1 0.02
37 48 0.80
38 1 0.02
39 8 0.13
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (36 bp):
TTTAAAAATTTTATTATTATTTAATATAAATATAAC
Found at i:2340291 original size:17 final size:17
Alignment explanation
Indices: 2340264--2340296 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2340254 AAATTTTAAT
2340264 TATTATTTAATATAAATA
1 TATTATTTAATA-AAATA
2340282 TATT-TTTAATAAAAT
1 TATTATTTAATAAAAT
2340297 TTTTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTATTTAATAAAATA
Found at i:2340306 original size:40 final size:37
Alignment explanation
Indices: 2340229--2340307 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
2340219 ATATATTTTC
2340229 TTATTTAATATAAATATAACTTTAAAAATTTTAATTA
1 TTATTTAATATAAATATAACTTTAAAAATTTTAATTA
**
2340266 TTATTTAATATAAATATATTTTTAATAAAATTTTTAATTA
1 TTATTTAATATAAATATAACTTT-A-AAAA-TTTTAATTA
2340306 TT
1 TT
2340308 TACCATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 21 0.57
38 1 0.03
39 4 0.11
40 11 0.30
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (37 bp):
TTATTTAATATAAATATAACTTTAAAAATTTTAATTA
Found at i:2340428 original size:27 final size:27
Alignment explanation
Indices: 2340388--2340439 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
2340378 ATTAAACTAA
2340388 AATATATATTTTAT-TATTAATTTTAAT
1 AATATATATTTTATAT-TTAATTTTAAT
2340415 AATAT-TATTATTATATTTAATTTTA
1 AATATATATT-TTATATTTAATTTTA
2340440 TTATTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 4 0.17
27 18 0.78
28 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
AATATATATTTTATATTTAATTTTAAT
Found at i:2340457 original size:21 final size:21
Alignment explanation
Indices: 2340395--2340461 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
2340385 TAAAATATAT
2340395 ATTTTATTATTA--AT-TTTA
1 ATTTTATTATTATTATATTTA
**
2340413 ATAATATTATTATTATATTTA
1 ATTTTATTATTATTATATTTA
*
2340434 ATTTTATTATTATT-TTTTTAA
1 ATTTTATTATTATTATATTT-A
2340455 ATTTTAT
1 ATTTTAT
2340462 CAAAATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 10 0.25
20 6 0.15
21 24 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTATTATTATTATATTTA
Found at i:2340460 original size:27 final size:27
Alignment explanation
Indices: 2340404--2340458 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
2340394 TATTTTATTA
*
2340404 TTAATTTTAATAATATTATTATTATAT
1 TTAATTTTAATAATATTATTATTAAAT
* * *
2340431 TTAATTTTATTATTATT-TTTTTAAAT
1 TTAATTTTAATAATATTATTATTAAAT
2340457 TT
1 TT
2340459 TATCAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTAATTTTAATAATATTATTATTAAAT
Found at i:2340471 original size:36 final size:38
Alignment explanation
Indices: 2340386--2340491 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 38
2340376 ATATTAAACT
*
2340386 AAAATATATATTTTATTATTAATTTTAATAATATTATTATT
1 AAAAT-TA-ATTTTATTATT-ATTTTAATAATATTATTATC
* * **
2340427 ATATTTAATTTTATTATTATTTTTTTAA-ATT-TTATC
1 AAAATTAATTTTATTATTATTTTAATAATATTATTATC
*
2340463 AAAATTAATTTTATTATTTATTTAAATAA
1 AAAATTAATTTTATTA-TTATTTTAATAA
2340492 ACCTTTTAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
36 18 0.33
37 12 0.22
38 8 0.15
39 11 0.20
40 2 0.04
41 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (38 bp):
AAAATTAATTTTATTATTATTTTAATAATATTATTATC
Found at i:2341143 original size:2 final size:2
Alignment explanation
Indices: 2341138--2341166 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2341128 TGTGTGTGTG
2341138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2341167 GACTAGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2341488 original size:32 final size:32
Alignment explanation
Indices: 2341452--2341513 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
2341442 TAGATGTCAA
* * *
2341452 TATATTTATTTTTTATTTTTATATTTAAAAAT
1 TATATTTATTTTTAATATTAATATTTAAAAAT
2341484 TATATTTATTTTTAATATTAATATTTAAAA
1 TATATTTATTTTTAATATTAATATTTAAAA
2341514 TAAAATAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
TATATTTATTTTTAATATTAATATTTAAAAAT
Found at i:2342072 original size:2 final size:2
Alignment explanation
Indices: 2342065--2342101 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2342055 GAGTTTTGAA
2342065 AG 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 A
2342102 AGAAAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2342281 original size:17 final size:17
Alignment explanation
Indices: 2342254--2342314 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
2342244 AAATTCATTT
2342254 ATTTATAAATAAATATAA
1 ATTT-TAAATAAATATAA
*
2342272 ATTTTAAAT-ATTATAA
1 ATTTTAAATAAATATAA
*
2342288 ATATTTAAATATATA-AA
1 AT-TTTAAATAAATATAA
2342305 ATTTTTAAAT
1 A-TTTTAAAT
2342315 TTCAAAACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.22
17 22 0.59
18 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTTAAATAAATATAA
Found at i:2343365 original size:28 final size:28
Alignment explanation
Indices: 2343327--2343435 Score: 102
Period size: 27 Copynumber: 3.9 Consensus size: 28
2343317 AATTTAAATT
*
2343327 AAATAATTTATATATTTATATTTTATTTA
1 AAAT-ATTTATATATTTATATTATATTTA
2343356 TAAAT-TTTAT-TATATTATAATTATATTTA
1 -AAATATTTATATAT-TTAT-ATTATATTTA
*
2343385 AAATATTT-TATATTTATATCA-ATTTTA
1 AAATATTTATATATTTATATTATA-TTTA
* *
2343412 ATATATTAATA-ATTTATATTATAT
1 AAATATTTATATATTTATATTATAT
2343436 AAATTTTGAT
Statistics
Matches: 67, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
26 1 0.01
27 26 0.39
28 21 0.31
29 15 0.22
30 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (28 bp):
AAATATTTATATATTTATATTATATTTA
Found at i:2343370 original size:29 final size:28
Alignment explanation
Indices: 2343333--2343490 Score: 95
Period size: 27 Copynumber: 5.8 Consensus size: 28
2343323 AATTAAATAA
*
2343333 TTTA-TATATTTATATTTTATTTATAAAT
1 TTTATTATATTTATATTATATTTA-AAAT
2343361 TTTATTATA-TTATAATTATATTTAAAAT
1 TTTATTATATTTAT-ATTATATTTAAAAT
* * *
2343389 ATT-TTATATTTATATCA-ATTTTAATAT
1 TTTATTATATTTATATTATA-TTTAAAAT
* *
2343416 ATTAATA-ATTTATATTATA--T-AAAT
1 TTTATTATATTTATATTATATTTAAAAT
* * *
2343440 TTTGA-TA-ATATATATTATA-TTATATT
1 TTT-ATTATATTTATATTATATTTAAAAT
2343466 TTTATTATATTAAATATATTATATT
1 TTTATTATATT---TATATTATATT
2343491 CATATTATTC
Statistics
Matches: 103, Mismatches: 12, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
24 18 0.17
25 4 0.04
26 8 0.08
27 29 0.28
28 21 0.20
29 13 0.13
30 9 0.09
31 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTATTATATTTATATTATATTTAAAAT
Found at i:2343475 original size:25 final size:25
Alignment explanation
Indices: 2343420--2343490 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
2343410 TAATATATTA
* *
2343420 ATAATTTATATTATA-TAAATTTTG
1 ATAATATATATTATATTATATTTTG
*
2343444 ATAATATATATTATATTATATTTTT
1 ATAATATATATTATATTATATTTTG
* *
2343469 ATTATAT-TAAATATATTATATT
1 ATAATATAT-ATTATATTATATT
2343491 CATATTATTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
24 15 0.38
25 25 0.62
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (25 bp):
ATAATATATATTATATTATATTTTG
Found at i:2343495 original size:11 final size:10
Alignment explanation
Indices: 2343334--2343498 Score: 71
Period size: 9 Copynumber: 16.9 Consensus size: 10
2343324 ATTAAATAAT
2343334 TTATA-TAT-
1 TTATATTATA
*
2343342 TTATATTTTA
1 TTATATTATA
*
2343352 TT-TA-TAAA
1 TTATATTATA
*
2343360 TTTTATTATA
1 TTATATTATA
2343370 TTATAATTATA
1 TTAT-ATTATA
* * *
2343381 TTTAAAATATT
1 -TTATATTATA
2343392 TTATATTTATA
1 TTATA-TTATA
* *
2343403 TCA-ATTTTA
1 TTATATTATA
*
2343412 ATATATTA-A
1 TTATATTATA
*
2343421 TAAT-TTATA
1 TTATATTATA
*
2343430 TTATA-TAAA
1 TTATATTATA
* *
2343439 TTTTGATAATA
1 TTAT-ATTATA
2343450 -TATATTATA
1 TTATATTATA
*
2343459 TTATATTTTTA
1 TTATA-TTATA
2343470 TTATATTA-A
1 TTATATTATA
*
2343479 ATATATTATA
1 TTATATTATA
2343489 TTCATATTAT
1 TT-ATATTAT
2343499 TCTATTTAAT
Statistics
Matches: 112, Mismatches: 29, Indels: 29
0.66 0.17 0.17
Matches are distributed among these distances:
8 12 0.11
9 37 0.33
10 27 0.24
11 33 0.29
12 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (10 bp):
TTATATTATA
Found at i:2343499 original size:14 final size:13
Alignment explanation
Indices: 2343362--2343515 Score: 52
Period size: 14 Copynumber: 11.5 Consensus size: 13
2343352 TTTATAAATT
2343362 TTATTATATTATAA
1 TTATTATATTAT-A
* **
2343376 TTATATTTAAAATA
1 TTAT-TATATTATA
2343390 TT-TTATATTTATA
1 TTATTATA-TTATA
* * *
2343403 TCAATTTTAATATA
1 T-TATTATATTATA
*
2343417 TTAATA-ATT-TA
1 TTATTATATTATA
*
2343428 -TATTATA-TAAA
1 TTATTATATTATA
*
2343439 TT-TTGATAATATA
1 TTATT-ATATTATA
2343452 -TATTATATTATA
1 TTATTATATTATA
*
2343464 TTTTTATTATATTAAA
1 ---TTATTATATTATA
2343480 TATATTATATTCATA
1 T-TATTATATT-ATA
*
2343495 TTATTCTATTTAATA
1 TTATTATA-TT-ATA
2343510 TTATTA
1 TTATTA
2343516 AGTCCATCTA
Statistics
Matches: 101, Mismatches: 22, Indels: 33
0.65 0.14 0.21
Matches are distributed among these distances:
10 5 0.05
11 6 0.06
12 17 0.17
13 13 0.13
14 27 0.27
15 22 0.22
16 11 0.11
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (13 bp):
TTATTATATTATA
Found at i:2343673 original size:14 final size:15
Alignment explanation
Indices: 2343656--2343691 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2343646 TTAAATTTAA
*
2343656 TAAAAAT-AATAAAT
1 TAAAAATAAAAAAAT
2343670 TAAAAATAAAAAAAT
1 TAAAAATAAAAAAAT
2343685 TAAAAAT
1 TAAAAAT
2343692 TAAATAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAAAATAAAAAAAT
Found at i:2343904 original size:2 final size:2
Alignment explanation
Indices: 2343897--2343926 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2343887 TGAACCGAAT
*
2343897 TA TA TA TA TA TC 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
2343927 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2345640 original size:205 final size:207
Alignment explanation
Indices: 2345359--2345876 Score: 591
Period size: 208 Copynumber: 2.5 Consensus size: 207
2345349 TTTTATAAAT
* *
2345359 ATTTTTAATTTTGATTTGATGCATTAAATATTTTATTTTTAAATTTTTTTAAAAAA-TCAAATCT
1 ATTTTTAA-GTTGATTTGATGTATTAAATATTTTATTTTT-AATTTTTTTAAAAAATTCAAATCT
* * * * *
2345423 TGATCAATAAAGATAAAGAAATACTATTCTTATTATTATTTGTT-TGAATATTGTT-GCCTTTCT
64 TGATCGATAAAGATAAAGAAATACTACTCTTCTTATAATTT-TTATGAATATTGTTACCCTTT-T
* * *
2345486 CATTTTT-ATAATTGCATAGTCAAAAATATCATTTCAACTTTATTTAAACGCAATTC-ATTTTAT
127 CATTTTTGATAATTACATAGTCAAAAATATCAGTTCAACTTTATCTAAACGCAATTCGA-TTTAT
* *
2345549 AAATGA-TTAAAAAGAG
191 AAATAATTTAAAAAAAG
* *
2345565 ATTTTTAAGTTGATTTGACGTATTAAATATTTTATTTTTAATTTTTTTAAAAAATTCAAATTTTG
1 ATTTTTAAGTTGATTTGATGTATTAAATATTTTATTTTTAATTTTTTTAAAAAATTCAAATCTTG
* *** *
2345630 ATTGATAAAGATAAAGAAATACTACTCTTCTCCCCAATTTTTATGAATGTTGTTACCCTTTTCAT
66 ATCGATAAAGATAAAGAAATACTACTCTTCT-TATAATTTTTATGAATATTGTTACCCTTTTCAT
** * ** ** *
2345695 TTTTGATAATTATGTAGTTAAAAATATCAGTTGGACTTTATCTAAGTGTAATTCGATTTATAAAT
130 TTTTGATAATTACATAGTCAAAAATATCAGTTCAACTTTATCTAAACGCAATTCGATTTATAAAT
*
2345760 AATTTAAAAAAAT
195 AATTTAAAAAAAG
* * * * *
2345773 ATTTTTAAGTAGATTTAATGTATTAAATATTTTATTTTTATTTTTTTTTTAAAAATT-AAATCCT
1 ATTTTTAAGTTGATTTGATGTATTAAATATTTTATTTTTA-ATTTTTTTAAAAAATTCAAATCTT
* * *
2345837 AATCGATAAATATAAAAAAATACTACTCTTCTTATCAATT
65 GATCGATAAAGATAAAGAAATACTACTCTTCTTAT-AATT
2345877 GAATTAGATA
Statistics
Matches: 261, Mismatches: 42, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
204 15 0.06
205 66 0.25
206 30 0.11
207 53 0.20
208 83 0.32
209 14 0.05
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (207 bp):
ATTTTTAAGTTGATTTGATGTATTAAATATTTTATTTTTAATTTTTTTAAAAAATTCAAATCTTG
ATCGATAAAGATAAAGAAATACTACTCTTCTTATAATTTTTATGAATATTGTTACCCTTTTCATT
TTTGATAATTACATAGTCAAAAATATCAGTTCAACTTTATCTAAACGCAATTCGATTTATAAATA
ATTTAAAAAAAG
Found at i:2346270 original size:250 final size:251
Alignment explanation
Indices: 2345673--2346672 Score: 1552
Period size: 251 Copynumber: 4.0 Consensus size: 251
2345663 CCAATTTTTA
* *
2345673 TGAATGTTGTTACCCTTTTCATTTTTGATAATTATGTAGTTAAAAATATCAGTTGGACTTTATCT
1 TGAATGTTGTTACCCTTTTCATTTTTGATAATTATGTAGTCAAAAATATCAGTCGGACTTTATCT
*
2345738 AAGTGTAATTCGATTTATAAATAATTTAAAAAAATATTTTTAAGTAGATTTAATGTATTAAATAT
66 AAGTGTAATTCGATTTATAAATAATTTAAAAAAGTATTTTTAAGTAGATTTAATGTATTAAATAT
* ** * *
2345803 TTTATTTTT-ATTTTTTTTTTAAAAATTAAA-TCCTAATCGATAAATATAAAAAAATACTACTCT
131 TTTATTTTTAAATTTTTTTAAAAAAATCAAATTCC-AATCAATAAATATAAAAAAATACTACTCT
*
2345866 TCTTATCAATTGAATTAGATAATAAATATTTACACC--CCAAGTCTTATAATAATTT
195 TCTTATCAATTGAATTAGATAATAAATATTTACACCATTCAAGTCTTATAATAATTT
* *
2345921 TGAATATTGTTACCCTTTTCATTTTTGATAATTATGTAGTTAAAAATATCAGTCGGACTTTATCT
1 TGAATGTTGTTACCCTTTTCATTTTTGATAATTATGTAGTCAAAAATATCAGTCGGACTTTATCT
* *
2345986 AAGTGTAATTCGATTTATAAATGATTTTAAAAAGTATTTTTAAGTAGATTTAATGTATTAAATAT
66 AAGTGTAATTCGATTTATAAATAATTTAAAAAAGTATTTTTAAGTAGATTTAATGTATTAAATAT
* * * *
2346051 TTTAGTTTT-AATTTTTTTAAAAAAATCAAATTTCAATCGATAAATATAAAAAAATACTACCCTT
131 TTTATTTTTAAATTTTTTTAAAAAAATCAAATTCCAATCAATAAATATAAAAAAATACTACTCTT
2346115 CTTATCAATTGAATTAGATAATAAATATTTACACCATTCAAGTCTTATAATAATTT
196 CTTATCAATTGAATTAGATAATAAATATTTACACCATTCAAGTCTTATAATAATTT
*
2346171 TGAATGTTGTTACCCTTTTCATTTTTAATAATTATGTAGTCAAAAATATCAGTCGGACTTTATCT
1 TGAATGTTGTTACCCTTTTCATTTTTGATAATTATGTAGTCAAAAATATCAGTCGGACTTTATCT
* ** *
2346236 AAGTGTAATTCGACTTATAAATGGTTTAAAAAAGTATTTTTAAATAGATTTAATGTATTAAATAT
66 AAGTGTAATTCGATTTATAAATAATTTAAAAAAGTATTTTTAAGTAGATTTAATGTATTAAATAT
* *
2346301 TTTATTTTTAAAAATTTTTTT--AAAAATCAAA-TCTCGATCAATAAATATAAAAGAATACTACT
131 TTTATTTTT--AAATTTTTTTAAAAAAATCAAATTC-CAATCAATAAATATAAAAAAATACTACT
*
2346363 TTTCTTATCAATTGAATTAGATAATAAATATTTACACCATTCAAGTCTTATAATAATTT
193 CTTCTTATCAATTGAATTAGATAATAAATATTTACACCATTCAAGTCTTATAATAATTT
* *
2346422 TGAATGTTGTTACCCTTTTCATTTTTGATAATAATGTAGTCAAAAATATCAATCGGACTTTATCT
1 TGAATGTTGTTACCCTTTTCATTTTTGATAATTATGTAGTCAAAAATATCAGTCGGACTTTATCT
* * *
2346487 AAGTGTAATTTGATTTATAAATAATTTTAAAAAA-TATTTTTAAGTAAATTTAATGCATTAAATA
66 AAGTGTAATTCGATTTATAAATAA-TTTAAAAAAGTATTTTTAAGTAGATTTAATGTATTAAATA
* * *
2346551 TTTTATTTTTAAAATTTTTTAAAAAAATCAAATTCCAATCAATAAATAT-AAAAAATACTATTTT
130 TTTTATTTTTAAATTTTTTTAAAAAAATCAAATTCCAATCAATAAATATAAAAAAATACTACTCT
* * * *
2346615 TCTTATCAATTGAATTAGGTAATAAATATTTAAACAATTCAAGTCATATAATAATTT
195 TCTTATCAATTGAATTAGATAATAAATATTTACACCATTCAAGTCTTATAATAATTT
2346672 T
1 T
2346673 TTTTCCAAAT
Statistics
Matches: 696, Mismatches: 45, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
248 214 0.31
249 11 0.02
250 217 0.31
251 234 0.34
252 11 0.02
253 9 0.01
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (251 bp):
TGAATGTTGTTACCCTTTTCATTTTTGATAATTATGTAGTCAAAAATATCAGTCGGACTTTATCT
AAGTGTAATTCGATTTATAAATAATTTAAAAAAGTATTTTTAAGTAGATTTAATGTATTAAATAT
TTTATTTTTAAATTTTTTTAAAAAAATCAAATTCCAATCAATAAATATAAAAAAATACTACTCTT
CTTATCAATTGAATTAGATAATAAATATTTACACCATTCAAGTCTTATAATAATTT
Found at i:2346549 original size:501 final size:498
Alignment explanation
Indices: 2345673--2346672 Score: 1608
Period size: 501 Copynumber: 2.0 Consensus size: 498
2345663 CCAATTTTTA
* * *
2345673 TGAATGTTGTTACCCTTTTCATTTTTGATAATTATGTAGTTAAAAATATCAGTTGGACTTTATCT
1 TGAATGTTGTTACCCTTTTCATTTTTAATAATTATGTAGTCAAAAATATCAGTCGGACTTTATCT
* *
2345738 AAGTGTAATTCGATTTATAAATAATTTAAAAAAATATTTTTAAGTAGATTTAATGTATTAAATAT
66 AAGTGTAATTCGACTTATAAATAATTTAAAAAAATATTTTTAAATAGATTTAATGTATTAAATAT
*** * *
2345803 TTTATTTTTATTTTTTTTTTAAAAATTAAATCCTAATCGATAAATATAAAAAAATACTACTCTTC
131 TTTATTTTTAAAATTTTTTTAAAAATCAAATCCTAATCAATAAATATAAAAAAATACTACTCTTC
2345868 TTATCAATTGAATTAGATAATAAATATTTACACCCCAAGTCTTATAATAATTTTGAATATTGTTA
196 TTATCAATTGAATTAGATAATAAATATTTACACCCCAAGTCTTATAATAATTTTGAATATTGTTA
* * *
2345933 CCCTTTTCATTTTTGATAATTATGTAGTTAAAAATATCAGTCGGACTTTATCTAAGTGTAATTCG
261 CCCTTTTCATTTTTGATAATAATGTAGTCAAAAATATCAATCGGACTTTATCTAAGTGTAATTCG
* * * *
2345998 ATTTATAAATGATTTTAAAAAGTATTTTTAAGTAGATTTAATGTATTAAATATTTTAGTTTT-AA
326 ATTTATAAATAATTTTAAAAAATATTTTTAAGTAAATTTAATGCATTAAATATTTTAGTTTTAAA
* * *
2346062 TTTTTTTAAAAAAATCAAATTTCAATCGATAAATATAAAAAAATACTACCCTTCTTATCAATTGA
391 ATTTTTTAAAAAAATCAAATTCCAATCAATAAATAT-AAAAAATACTACCCTTCTTATCAATTGA
* * *
2346127 ATTAGATAATAAATATTTACACCATTCAAGTCTTATAATAATTT
455 ATTAGATAATAAATATTTAAACAATTCAAGTCATATAATAATTT
2346171 TGAATGTTGTTACCCTTTTCATTTTTAATAATTATGTAGTCAAAAATATCAGTCGGACTTTATCT
1 TGAATGTTGTTACCCTTTTCATTTTTAATAATTATGTAGTCAAAAATATCAGTCGGACTTTATCT
** *
2346236 AAGTGTAATTCGACTTATAAATGGTTTAAAAAAGTATTTTTAAATAGATTTAATGTATTAAATAT
66 AAGTGTAATTCGACTTATAAATAATTTAAAAAAATATTTTTAAATAGATTTAATGTATTAAATAT
* * *
2346301 TTTATTTTTAAAAATTTTTTTAAAAATCAAAT-CTCGATCAATAAATATAAAAGAATACTACTTT
131 TTTATTTTT-AAAATTTTTTTAAAAATCAAATCCT-AATCAATAAATATAAAAAAATACTACTCT
* *
2346365 TCTTATCAATTGAATTAGATAATAAATATTTACACCATTCAAGTCTTATAATAATTTTGAATGTT
194 TCTTATCAATTGAATTAGATAATAAATATTTACACC--CCAAGTCTTATAATAATTTTGAATATT
2346430 GTTACCCTTTTCATTTTTGATAATAATGTAGTCAAAAATATCAATCGGACTTTATCTAAGTGTAA
257 GTTACCCTTTTCATTTTTGATAATAATGTAGTCAAAAATATCAATCGGACTTTATCTAAGTGTAA
* *
2346495 TTTGATTTATAAATAATTTTAAAAAATATTTTTAAGTAAATTTAATGCATTAAATATTTTATTTT
322 TTCGATTTATAAATAATTTTAAAAAATATTTTTAAGTAAATTTAATGCATTAAATATTTTAGTTT
***
2346560 TAAAATTTTTTAAAAAAATCAAATTCCAATCAATAAATATAAAAAATACTATTTTTCTTATCAAT
387 TAAAATTTTTTAAAAAAATCAAATTCCAATCAATAAATATAAAAAATACTACCCTTCTTATCAAT
*
2346625 TGAATTAGGTAATAAATATTTAAACAATTCAAGTCATATAATAATTT
452 TGAATTAGATAATAAATATTTAAACAATTCAAGTCATATAATAATTT
2346672 T
1 T
2346673 TTTTCCAAAT
Statistics
Matches: 460, Mismatches: 37, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
498 133 0.29
499 79 0.17
501 213 0.46
502 35 0.08
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (498 bp):
TGAATGTTGTTACCCTTTTCATTTTTAATAATTATGTAGTCAAAAATATCAGTCGGACTTTATCT
AAGTGTAATTCGACTTATAAATAATTTAAAAAAATATTTTTAAATAGATTTAATGTATTAAATAT
TTTATTTTTAAAATTTTTTTAAAAATCAAATCCTAATCAATAAATATAAAAAAATACTACTCTTC
TTATCAATTGAATTAGATAATAAATATTTACACCCCAAGTCTTATAATAATTTTGAATATTGTTA
CCCTTTTCATTTTTGATAATAATGTAGTCAAAAATATCAATCGGACTTTATCTAAGTGTAATTCG
ATTTATAAATAATTTTAAAAAATATTTTTAAGTAAATTTAATGCATTAAATATTTTAGTTTTAAA
ATTTTTTAAAAAAATCAAATTCCAATCAATAAATATAAAAAATACTACCCTTCTTATCAATTGAA
TTAGATAATAAATATTTAAACAATTCAAGTCATATAATAATTT
Found at i:2347212 original size:24 final size:26
Alignment explanation
Indices: 2347176--2347223 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
2347166 AACGTAACTT
2347176 TATAATTACAATTAA-AATTTTTTTA
1 TATAATTACAATTAATAATTTTTTTA
* *
2347201 TATATTTA-AATTAATTATTTTTT
1 TATAATTACAATTAATAATTTTTT
2347224 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
TATAATTACAATTAATAATTTTTTTA
Found at i:2347383 original size:21 final size:19
Alignment explanation
Indices: 2347357--2347400 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
2347347 AAAATTATTA
*
2347357 ATTATTATATTAATATATCAT
1 ATTATTATATAAATA-AT-AT
*
2347378 ATTATTTTATAAATAATAT
1 ATTATTATATAAATAATAT
2347397 ATTA
1 ATTA
2347401 AATAATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTATTATATAAATAATAT
Found at i:2348853 original size:24 final size:27
Alignment explanation
Indices: 2348803--2348854 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
2348793 TACATATTTT
*
2348803 TAAATAAAATTGATTTTAAATAGTAAAA
1 TAAATAAAAATGATTTTAAATA-TAAAA
2348831 TAAATAAAAAT-A-TTTAAAT-TAAAA
1 TAAATAAAAATGATTTTAAATATAAAA
2348855 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 5 0.22
26 7 0.30
27 1 0.04
28 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
TAAATAAAAATGATTTTAAATATAAAA
Found at i:2348855 original size:16 final size:15
Alignment explanation
Indices: 2348836--2348865 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
2348826 TAAAATAAAT
2348836 AAAAATATTTAAATTA
1 AAAAAT-TTTAAATTA
2348852 AAAAATTTTAAATT
1 AAAAATTTTAAATT
2348866 TTCAACGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAATTTTAAATTA
Found at i:2348993 original size:18 final size:20
Alignment explanation
Indices: 2348950--2349001 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
2348940 CATTAATCAA
2348950 TAAAAA-AATTTATGTTATGC
1 TAAAAATAATTTATGTTAT-C
*
2348970 TGAAAATAA-TTATGTTAT-
1 TAAAAATAATTTATGTTATC
2348988 TAAAAATATATTTA
1 TAAAAATA-ATTTA
2349002 CAACAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 7 0.26
19 1 0.04
20 17 0.63
21 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (20 bp):
TAAAAATAATTTATGTTATC
Found at i:2350080 original size:3 final size:3
Alignment explanation
Indices: 2350072--2350103 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2350062 AAATTCCGAA
*
2350072 AAC AAC AAC AAC ACC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
2350104 TAATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2351935 original size:2 final size:2
Alignment explanation
Indices: 2351928--2351960 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2351918 AAATTTCTTT
2351928 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
2351961 GTGTGTGTGT
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:2351965 original size:2 final size:2
Alignment explanation
Indices: 2351960--2351994 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2351950 TATATATATA
2351960 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2351995 ACATAAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2356704 original size:15 final size:16
Alignment explanation
Indices: 2356679--2356708 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2356669 TTTTATTATT
2356679 TATTATATTATTAAAA
1 TATTATATTATTAAAA
2356695 TATTAT-TTATTAAA
1 TATTATATTATTAAA
2356709 CTATAGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATATTATTAAAA
Found at i:2356782 original size:16 final size:15
Alignment explanation
Indices: 2356745--2356774 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2356735 TTCTTAAACA
2356745 AATTTAATTTTTAAT
1 AATTTAATTTTTAAT
2356760 AATTTAATTTTTAAT
1 AATTTAATTTTTAAT
2356775 TATGTTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTAATTTTTAAT
Found at i:2357128 original size:16 final size:18
Alignment explanation
Indices: 2357087--2357129 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
2357077 ATATAAATTA
2357087 TTAATATATCAAATTTCAT
1 TTAA-ATATCAAATTTCAT
*
2357106 ATAAATATCAAA-TTC-T
1 TTAAATATCAAATTTCAT
2357122 TTAAATAT
1 TTAAATAT
2357130 AATTATGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 8 0.36
19 3 0.14
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATATCAAATTTCAT
Done.