Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 15 of 18
Found at i:2507446 original size:16 final size:16
Alignment explanation
Indices: 2507425--2507475 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2507415 TAAGTTTTTT
2507425 TTTAAAAATATTTAAA
1 TTTAAAAATATTTAAA
**
2507441 TTTAAATTTATTT-AA
1 TTTAAAAATATTTAAA
* **
2507456 TTTATAAATAAATAAA
1 TTTAAAAATATTTAAA
2507472 TTTA
1 TTTA
2507476 TTTTTTTATA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAAAATATTTAAA
Found at i:2507540 original size:17 final size:19
Alignment explanation
Indices: 2507504--2507550 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
2507494 ATTATTATTT
2507504 AAATTT-TATTTGATTCAA
1 AAATTTATATTTGATTCAA
2507522 AAATTTATATTTG-TT-AA
1 AAATTTATATTTGATTCAA
*
2507539 AAATTTAAATTT
1 AAATTTATATTT
2507551 ATAAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 13 0.48
18 8 0.30
19 6 0.22
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (19 bp):
AAATTTATATTTGATTCAA
Found at i:2513198 original size:42 final size:42
Alignment explanation
Indices: 2513111--2513197 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
2513101 TAAAAATATA
* *
2513111 TTTTAAAAAATAAATATAAAATATATATTTTTTAATTAGATT
1 TTTTAAAAAATAAATATAAAATAAATATTTTTTAAGTAGATT
** *
2513153 TTTTAAAAAATTTGATA-AAAATAAATA-TTTTTACGTAGATT
1 TTTTAAAAAA-TAAATATAAAATAAATATTTTTTAAGTAGATT
2513194 TTTT
1 TTTT
2513198 TTAAAAGTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 16 0.41
42 19 0.49
43 4 0.10
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (42 bp):
TTTTAAAAAATAAATATAAAATAAATATTTTTTAAGTAGATT
Found at i:2513663 original size:23 final size:19
Alignment explanation
Indices: 2513616--2513663 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 19
2513606 GTTTATCAAT
2513616 TTTATTTAAAATTTTTTTA
1 TTTATTTAAAATTTTTTTA
*
2513635 TATATTTATAATATATTTTTTA
1 TTTATTTA-AA-AT-TTTTTTA
2513657 GTTTATT
1 -TTTATT
2513664 AAATAGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
21 2 0.09
22 7 0.30
23 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATTTAAAATTTTTTTA
Found at i:2515042 original size:18 final size:18
Alignment explanation
Indices: 2515017--2515064 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2515007 AAAAATTTAA
*
2515017 AAATTTATTTTTATA-TT
1 AAATTTATTTTTAAATTT
**
2515034 AATATTTATAATTAAATTT
1 AA-ATTTATTTTTAAATTT
2515053 AAATTTATTTTT
1 AAATTTATTTTT
2515065 TTAATTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 2 0.08
18 18 0.75
19 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATTTATTTTTAAATTT
Found at i:2516049 original size:18 final size:19
Alignment explanation
Indices: 2516011--2516063 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
2516001 ATCTCATAAG
2516011 ATTTAAATAA-AAATATTAA
1 ATTTAAA-AATAAATATTAA
2516030 ATTTAAAAATAAAT-TTAA
1 ATTTAAAAATAAATATTAA
**
2516048 ATAAAAAAATAAATAT
1 ATTTAAAAATAAATAT
2516064 ATTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTTAAAAATAAATATTAA
Found at i:2516173 original size:17 final size:17
Alignment explanation
Indices: 2516129--2516179 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
2516119 TTTAAAATTT
* *
2516129 TATATTATATATATATA
1 TATATTATATATTTTTA
*
2516146 T-TAATTTTATATTTTTA
1 TAT-ATTATATATTTTTA
2516163 TATATTATATAATTTTT
1 TATATTATAT-ATTTTT
2516180 TGATATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 1 0.04
17 19 0.70
18 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATTATATATTTTTA
Found at i:2516175 original size:25 final size:24
Alignment explanation
Indices: 2516124--2516178 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
2516114 CTCATTTTAA
2516124 AATTTTATATTATATATATATATT
1 AATTTTATATTATATATATATATT
*
2516148 AATTTTATATT-TTTATATATTATAT
1 AATTTTATATTATATATATA-TAT-T
2516173 AATTTT
1 AATTTT
2516179 TTGATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 7 0.25
24 14 0.50
25 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
AATTTTATATTATATATATATATT
Found at i:2516770 original size:5 final size:5
Alignment explanation
Indices: 2516760--2516784 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2516750 GCCCTTCTTC
2516760 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
2516785 TTGCATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:2517220 original size:27 final size:25
Alignment explanation
Indices: 2517168--2517226 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 25
2517158 ATTTAAAAAA
*
2517168 TAAATTAAACTTTAAATAAAAATTT
1 TAAATTAAACTTAAAATAAAAATTT
*
2517193 TAAATTCAAACTTAAGAATAAAACTTT
1 TAAATT-AAACTTAA-AATAAAAATTT
*
2517220 TTAATTA
1 TAAATTA
2517227 TAAAATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 6 0.21
26 8 0.28
27 15 0.52
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.39
Consensus pattern (25 bp):
TAAATTAAACTTAAAATAAAAATTT
Found at i:2517259 original size:22 final size:25
Alignment explanation
Indices: 2517241--2517295 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
2517231 ATTTATATTT
2517241 TATAA-TATAATTA-AA-TATATTT
1 TATAATTATAATTATAATTATATTT
* *
2517263 TGTAATTATAATTATAATTTTATTT
1 TATAATTATAATTATAATTATATTT
2517288 TATTAATT
1 TA-TAATT
2517296 GTTACTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 8 0.31
24 2 0.08
25 7 0.27
26 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TATAATTATAATTATAATTATATTT
Found at i:2517276 original size:23 final size:22
Alignment explanation
Indices: 2517234--2517290 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
2517224 TTATAAAATT
2517234 TATATTTTATAATATAATTAAA
1 TATATTTTATAATATAATTAAA
*
2517256 TATATTTTGTAATTATAATTATAA
1 TATATTTTATAA-TATAATTA-AA
*
2517280 TTTTATTTTAT
1 -TATATTTTAT
2517291 TAATTGTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.38
23 8 0.28
24 2 0.07
25 8 0.28
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TATATTTTATAATATAATTAAA
Found at i:2517364 original size:24 final size:24
Alignment explanation
Indices: 2517319--2517364 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2517309 ATATTTTTAT
*
2517319 AATAAAAATTATATCATATATTTC
1 AATAAAAATTATATAATATATTTC
*
2517343 AATAAAAATATATTTAAT-TATT
1 AATAAAAAT-TATATAATATATT
2517365 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
AATAAAAATTATATAATATATTTC
Found at i:2517984 original size:18 final size:17
Alignment explanation
Indices: 2517958--2517992 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2517948 ACAAATATAA
*
2517958 AATATACTTAAATAAAAT
1 AATAAACTTAAA-AAAAT
2517976 AATAAACTTAAAAAAAT
1 AATAAACTTAAAAAAAT
2517993 TTATTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAACTTAAAAAAAT
Found at i:2518276 original size:17 final size:16
Alignment explanation
Indices: 2518247--2518281 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2518237 ATTATTTTAG
*
2518247 TTAAAAATGTATTTTT
1 TTAAAAATATATTTTT
2518263 TTAAAATATATATTTTT
1 TTAAAA-ATATATTTTT
2518280 TT
1 TT
2518282 TGAACCAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTAAAAATATATTTTT
Found at i:2518884 original size:2 final size:2
Alignment explanation
Indices: 2518877--2518912 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2518867 TATCATAACA
2518877 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
2518913 TTTAGTTTTC
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:2520740 original size:15 final size:15
Alignment explanation
Indices: 2520698--2520731 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2520688 CATTTGAAAG
2520698 ATTC-AAAATCCCAAA
1 ATTCAAAAAT-CCAAA
2520713 ATTCAAAAATCCAAA
1 ATTCAAAAATCCAAA
2520728 ATTC
1 ATTC
2520732 TGAAATCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (15 bp):
ATTCAAAAATCCAAA
Found at i:2522258 original size:5 final size:5
Alignment explanation
Indices: 2522248--2522309 Score: 58
Period size: 5 Copynumber: 12.6 Consensus size: 5
2522238 AGAATTTATT
* *
2522248 TAATA TAATA TAATA TAAATA TAATA TAA-A T-ATA TAAATA TATTA AAAT-
1 TAATA TAATA TAATA T-AATA TAATA TAATA TAATA T-AATA TAATA TAATA
*
2522297 TTATA TAATA TAA
1 TAATA TAATA TAA
2522310 ATTATTAACG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
3 1 0.02
4 6 0.13
5 30 0.65
6 9 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:2522270 original size:16 final size:16
Alignment explanation
Indices: 2522249--2522311 Score: 71
Period size: 14 Copynumber: 4.2 Consensus size: 16
2522239 GAATTTATTT
2522249 AATATAATATAATATA
1 AATATAATATAATATA
2522265 AATATAATATAA-ATA
1 AATATAATATAATATA
* *
2522280 TATA-AATATATTA-A
1 AATATAATATAATATA
*
2522294 AAT-TTATATAATATA
1 AATATAATATAATATA
2522309 AAT
1 AAT
2522312 TATTAACGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 16 0.41
15 11 0.28
16 12 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATAATATAATATA
Found at i:2522292 original size:54 final size:54
Alignment explanation
Indices: 2522203--2522309 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
2522193 ACACGTAAAA
* * * *
2522203 ATAAAATAAATATAATATAAATATATAAGTTTATTAGAATTTATTTAATATAAT
1 ATAAAATAAATATAATATAAATATATAAATATATTAAAATTTATATAATATAAT
*
2522257 ATAATATAAATATAATATAAATATATAAATATATTAAAATTTATATAATATAA
1 ATAAAATAAATATAATATAAATATATAAATATATTAAAATTTATATAATATAA
2522310 ATTATTAACG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (54 bp):
ATAAAATAAATATAATATAAATATATAAATATATTAAAATTTATATAATATAAT
Found at i:2522308 original size:33 final size:33
Alignment explanation
Indices: 2522266--2522362 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 33
2522256 TATAATATAA
2522266 ATATAATATAAATATATAAATATATTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
* ** *
2522299 ATATAATATAAAT-TATTAACGTGTTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
*
2522331 ATATAAATATATAATATTTTAAATATTATTAA
1 ATAT-AATATA-AATA-TATAAATA-TATTAA
2522363 GATATAATAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
32 19 0.38
33 19 0.38
34 3 0.06
36 4 0.08
37 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATATTAAAATTT
Found at i:2522655 original size:13 final size:12
Alignment explanation
Indices: 2522632--2522685 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
2522622 AATTATATAA
2522632 AAATATT-TTTT
1 AAATATTATTTT
2522643 AAAATATTATTTT
1 -AAATATTATTTT
* *
2522656 CAA-ATTAATTT
1 AAATATTATTTT
2522667 AAATATTATTTTT
1 AAATATTA-TTTT
2522680 AAATAT
1 AAATAT
2522686 AATTCGCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 9 0.26
12 13 0.37
13 13 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (12 bp):
AAATATTATTTT
Found at i:2522674 original size:23 final size:24
Alignment explanation
Indices: 2522644--2522689 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
2522634 ATATTTTTTA
2522644 AAATATTATTTTCAAAT-TAATTT
1 AAATATTATTTTCAAATATAATTT
*
2522667 AAATATTATTTTTAAATATAATT
1 AAATATTATTTTCAAATATAATT
2522690 CGCTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
AAATATTATTTTCAAATATAATTT
Found at i:2523920 original size:13 final size:13
Alignment explanation
Indices: 2523890--2523918 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2523880 TTATCAATTA
2523890 TTTTATTTTTATT
1 TTTTATTTTTATT
2523903 TTTTA-TTTTATT
1 TTTTATTTTTATT
2523915 TTTT
1 TTTT
2523919 TACTCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:2523931 original size:17 final size:18
Alignment explanation
Indices: 2523911--2523946 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2523901 TTTTTTATTT
*
2523911 TATTTTTTTACT-CAAAA
1 TATTTTTTAACTACAAAA
2523928 TATTTTTTAACTACAAAA
1 TATTTTTTAACTACAAAA
2523946 T
1 T
2523947 TATCTTTCAT
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:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTTTTAACTACAAAA
Found at i:2525710 original size:25 final size:25
Alignment explanation
Indices: 2525676--2525726 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2525666 TTGGTTGAGG
*
2525676 ACAGCCCATTAGTTTCAATTCCCAA
1 ACAGCCCATTAGATTCAATTCCCAA
2525701 ACAGCCCATTAGATTCAATTCCCAA
1 ACAGCCCATTAGATTCAATTCCCAA
2525726 A
1 A
2525727 ACATAGTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.25
Consensus pattern (25 bp):
ACAGCCCATTAGATTCAATTCCCAA
Found at i:2530232 original size:2 final size:2
Alignment explanation
Indices: 2530225--2530257 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2530215 ACCAAATCTA
2530225 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
2530258 AATGCAATTA
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:2530398 original size:2 final size:2
Alignment explanation
Indices: 2530391--2530419 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2530381 ACCAAATCTA
2530391 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 A
2530420 ATTAAAAATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2530425 original size:156 final size:155
Alignment explanation
Indices: 2530233--2530522 Score: 483
Period size: 156 Copynumber: 1.9 Consensus size: 155
2530223 TAATATATAT
*
2530233 ATATATATATATATATATATATATAAATGCAATTAAAAAAATTTATGTAATTTACTTTTATAAAA
1 ATATATATATATATATATATATATAAAT-CAATTAAAAAAATTTATGTAATTTACTTTTACAAAA
*
2530298 TATCTATCTTTACATGTGATATAACATTTTTTTTTATTTTATTCAAAAAATTATACAGGCAAGAT
65 TATCTATCTTTACATGTGATAT-A-ATATTTTTTTATTTTATTCAAAAAATTATACAGGCAAGAT
2530363 GATTTTGGTGTCATGAAAACCAAATCTA
128 GATTTTGGTGTCATGAAAACCAAATCTA
* **
2530391 ATATATATATATATATATATATATATAT-AATTAAAAATGTTTATGTAATTTACTTTTACAAAAT
1 ATATATATATATATATATATATATAAATCAATTAAAAAAATTTATGTAATTTACTTTTACAAAAT
* *
2530455 ATCTATCTTTACATGTGATATAATATTTTTTTATTTTATTCAAAAAATTATATAGGTAAGATGAT
66 ATCTATCTTTACATGTGATATAATATTTTTTTATTTTATTCAAAAAATTATACAGGCAAGATGAT
2530520 TTT
131 TTT
2530523 TTTTAAAAAA
Statistics
Matches: 125, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
154 43 0.34
155 1 0.01
156 54 0.43
158 27 0.22
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (155 bp):
ATATATATATATATATATATATATAAATCAATTAAAAAAATTTATGTAATTTACTTTTACAAAAT
ATCTATCTTTACATGTGATATAATATTTTTTTATTTTATTCAAAAAATTATACAGGCAAGATGAT
TTTGGTGTCATGAAAACCAAATCTA
Found at i:2542922 original size:54 final size:54
Alignment explanation
Indices: 2542862--2542967 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 54
2542852 TATATCTATA
* * *
2542862 TCTTTTTAAGGCAAGAGTCTATATATGGAAGATCTATTAGTGCCAAAATTAATG
1 TCTTTTTAAGGCAAGAATCCATATATGGAAGACCTATTAGTGCCAAAATTAATG
2542916 TCTTTTTAAGGCAAGAATCCATATATGGAAGACCTATTAGTGCCAAAATTAA
1 TCTTTTTAAGGCAAGAATCCATATATGGAAGACCTATTAGTGCCAAAATTAA
2542968 CTTCCTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (54 bp):
TCTTTTTAAGGCAAGAATCCATATATGGAAGACCTATTAGTGCCAAAATTAATG
Found at i:2544644 original size:34 final size:35
Alignment explanation
Indices: 2544567--2544647 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
2544557 AATATAAATA
* * *
2544567 TTAAAAAATATATTAAGTTATTTAAATTTATAA-T
1 TTAAAAAATATATTAAATTACTAAAATTTATAATT
*
2544601 TTAATAAAAAATATTAAATTACTAAAATTTA-AATTT
1 TTAA-AAAATATATTAAATTACTAAAATTTATAA-TT
2544637 TTAAAAAATAT
1 TTAAAAAATAT
2544648 CTTTTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 6 0.15
35 28 0.72
36 5 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (35 bp):
TTAAAAAATATATTAAATTACTAAAATTTATAATT
Found at i:2545919 original size:20 final size:21
Alignment explanation
Indices: 2545867--2545920 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
2545857 TATCTTTCAA
2545867 AAATTAATATATTTAAAAAATT
1 AAATTAATA-ATTTAAAAAATT
2545889 AAATTAA-AATTTAAAAAA-T
1 AAATTAATAATTTAAAAAATT
2545908 AAGA-TAATAATTT
1 AA-ATTAATAATTT
2545921 TTAAGTGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.20
20 16 0.53
21 1 0.03
22 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATTAATAATTTAAAAAATT
Found at i:2547140 original size:14 final size:15
Alignment explanation
Indices: 2547123--2547155 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2547113 TTATAATATA
2547123 TTAAAT-ATAAAAAT
1 TTAAATAATAAAAAT
*
2547137 TTAATTAATAAAAAT
1 TTAAATAATAAAAAT
2547152 TTAA
1 TTAA
2547156 TCTCTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAATAATAAAAAT
Found at i:2554101 original size:52 final size:52
Alignment explanation
Indices: 2554023--2554125 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
2554013 ATTAGTTTGT
2554023 TGTGTTAATATTAAGCACGTTTGCTTAGATCAATGTTGCTAATGTTTTCTCA
1 TGTGTTAATATTAAGCACGTTTGCTTAGATCAATGTTGCTAATGTTTTCTCA
2554075 TGTGTTAATATTAAGCACGTTTGCTTAGATCAATGTTGCTAATGTTTTCTC
1 TGTGTTAATATTAAGCACGTTTGCTTAGATCAATGTTGCTAATGTTTTCTC
2554126 TAATGCTTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (52 bp):
TGTGTTAATATTAAGCACGTTTGCTTAGATCAATGTTGCTAATGTTTTCTCA
Found at i:2555167 original size:95 final size:95
Alignment explanation
Indices: 2555056--2555244 Score: 308
Period size: 95 Copynumber: 2.0 Consensus size: 95
2555046 ATAATAATTT
*
2555056 TAGACATCAATATCAAGGTGT-TTTTATATCCAACAGAGAAACTTTAAAGCAATAAGATGCTTTC
1 TAGACATCAATATCAAGGTGTCTTTT-TATCCAACAGAGAAACTTTAAAGCAACAAGATGCTTTC
* *
2555120 AGGCAGCGGGGTGCAAAGTTGTATATATTCA
65 AGGCAGCAGGGTGCAAAATTGTATATATTCA
* *
2555151 TAGACATCAATGTCAAGTTGTCTTTTTATCCAACAGAGAAACTTTAAAGCAACAAGATGCTTTCA
1 TAGACATCAATATCAAGGTGTCTTTTTATCCAACAGAGAAACTTTAAAGCAACAAGATGCTTTCA
*
2555216 GGCAGCAGGGTGCAAAATTGTATCTATTC
66 GGCAGCAGGGTGCAAAATTGTATATATTC
2555245 CCTATATCCA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
95 83 0.95
96 4 0.05
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (95 bp):
TAGACATCAATATCAAGGTGTCTTTTTATCCAACAGAGAAACTTTAAAGCAACAAGATGCTTTCA
GGCAGCAGGGTGCAAAATTGTATATATTCA
Found at i:2556050 original size:1 final size:1
Alignment explanation
Indices: 2556044--2556074 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
2556034 TGCGAAGTAG
*
2556044 TTTTTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2556075 CTTTAGGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:2556075 original size:8 final size:8
Alignment explanation
Indices: 2556044--2556078 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2556034 TGCGAAGTAG
*
2556044 TTTTTTTT
1 TTTTTTTC
*
2556052 TTTTTTTT
1 TTTTTTTC
2556060 TTTTTTTC
1 TTTTTTTC
2556068 TTTTTTTC
1 TTTTTTTC
2556076 TTT
1 TTT
2556079 AGGCTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (8 bp):
TTTTTTTC
Found at i:2556432 original size:23 final size:24
Alignment explanation
Indices: 2556406--2556461 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
2556396 TTATTATATG
2556406 TAAATATTTAAAATAAAT-AAAAT
1 TAAATATTTAAAATAAATAAAAAT
* **
2556429 TAAATAATT-AGGTAAATAAAAAT
1 TAAATATTTAAAATAAATAAAAAT
*
2556452 TAAAAATTTA
1 TAAATATTTA
2556462 GTTTTATAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAATATTTAAAATAAATAAAAAT
Found at i:2558506 original size:22 final size:22
Alignment explanation
Indices: 2558475--2558529 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
2558465 ATATGATACA
*
2558475 AAAAATTAATTAAAACATGACAT
1 AAAAA-TAATTAAAACATAACAT
* *
2558498 AAAAATAATTAAAATATAATAT
1 AAAAATAATTAAAACATAACAT
2558520 AAAATATAAT
1 AAAA-ATAAT
2558530 ATAATATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATAATTAAAACATAACAT
Found at i:2558530 original size:17 final size:17
Alignment explanation
Indices: 2558510--2558566 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
2558500 AAATAATTAA
*
2558510 AATATAATATAAAATAT
1 AATATAATATAAAAAAT
2558527 AATATAATATAAAAAAT
1 AATATAATATAAAAAAT
2558544 -ATA-AATATAATACAAAT
1 AATATAATATAA-A-AAAT
2558561 AA-ATAA
1 AATATAA
2558567 ACGTATTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
15 7 0.20
16 4 0.11
17 21 0.60
18 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATAATATAAAAAAT
Found at i:2558555 original size:25 final size:25
Alignment explanation
Indices: 2558515--2558563 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2558505 ATTAAAATAT
*
2558515 AATATAAAATATAATATAATATAAAA
1 AATATAAAATATAATACAA-ATAAAA
2558541 AATAT-AAATATAATACAAATAAA
1 AATATAAAATATAATACAAATAAA
2558564 TAAACGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 12 0.55
26 5 0.23
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (25 bp):
AATATAAAATATAATACAAATAAAA
Found at i:2558566 original size:19 final size:18
Alignment explanation
Indices: 2558509--2558567 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 18
2558499 AAAATAATTA
*
2558509 AAATATAATATAAAATAT
1 AAATATAATATAAAAAAT
2558527 -AATATAATATAAAAAATAT
1 AAATATAATAT-AAAAA-AT
*
2558546 AAATATAATACAAATAAAT
1 AAATATAATATAAA-AAAT
2558565 AAA
1 AAA
2558568 CGTATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 10 0.29
18 4 0.11
19 10 0.29
20 11 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATAATATAAAAAAT
Found at i:2559355 original size:3 final size:3
Alignment explanation
Indices: 2559347--2559380 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2559337 AATTTTGTAA
2559347 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2559381 CGCGAAGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2559710 original size:25 final size:26
Alignment explanation
Indices: 2559665--2559720 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
2559655 TAAAATACTA
*
2559665 TTTAATTTAAAAGAATTTTTTA-AAT
1 TTTAATTTAAAAGAATATTTTACAAT
*
2559690 TTTAATTATAAAA-TATATTTTACAAT
1 TTTAATT-TAAAAGAATATTTTACAAT
*
2559716 ATTAA
1 TTTAA
2559721 ATAATTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTAATTTAAAAGAATATTTTACAAT
Found at i:2562238 original size:2 final size:2
Alignment explanation
Indices: 2562233--2562257 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2562223 TCAAAAAAAG
2562233 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2562258 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2563487 original size:22 final size:22
Alignment explanation
Indices: 2563457--2563500 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2563447 TCATTCAGTC
*
2563457 TAAAAATTTAT-TTTATTATTT
1 TAAAAATTTATATTTAATATTT
2563478 TAAAATATTTATATTTAATATTT
1 TAAAA-ATTTATATTTAATATTT
2563501 ATATTTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 6 0.30
23 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TAAAAATTTATATTTAATATTT
Found at i:2563497 original size:13 final size:13
Alignment explanation
Indices: 2563481--2563506 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2563471 ATTATTTTAA
2563481 AATATTTATATTT
1 AATATTTATATTT
2563494 AATATTTATATTT
1 AATATTTATATTT
2563507 GATACATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:2564421 original size:15 final size:14
Alignment explanation
Indices: 2564386--2564418 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2564376 ATGTAAATAA
*
2564386 TAAAATTAATTTTT
1 TAAAATAAATTTTT
2564400 TAAAATAAATTTTT
1 TAAAATAAATTTTT
2564414 TAAAA
1 TAAAA
2564419 ATATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAATAAATTTTT
Found at i:2565871 original size:24 final size:27
Alignment explanation
Indices: 2565798--2565868 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
2565788 AAACAAGCCT
* *
2565798 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
2565826 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
*
2565853 CCATTTTTGATAAACA
1 CCATTTTTGACAAACA
2565869 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:2569748 original size:21 final size:21
Alignment explanation
Indices: 2569722--2569769 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2569712 AGATAGACAG
2569722 GATCGAATTGTATCACATGCC
1 GATCGAATTGTATCACATGCC
2569743 GATCGAATTGTATCACATGCC
1 GATCGAATTGTATCACATGCC
*
2569764 AATCGA
1 GATCGA
2569770 TTTATAGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (21 bp):
GATCGAATTGTATCACATGCC
Found at i:2571796 original size:14 final size:14
Alignment explanation
Indices: 2571786--2571828 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 14
2571776 ATTTAAAAGT
2571786 AAATAAATAAAATA
1 AAATAAATAAAATA
2571800 AAATAAAATATAAATA
1 AAAT-AAATA-AAATA
2571816 TGAAATAAATAAA
1 --AAATAAATAAA
2571829 TATGTACTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.16
15 5 0.20
16 7 0.28
17 5 0.20
18 4 0.16
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:2571831 original size:21 final size:21
Alignment explanation
Indices: 2571788--2571828 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
2571778 TTAAAAGTAA
2571788 ATAAATAAAATAAAATAAAAT
1 ATAAATAAAATAAAATAAAAT
2571809 ATAAATATGAAAT-AAATAAA
1 ATAAATA--AAATAAAATAAA
2571829 TATGTACTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
ATAAATAAAATAAAATAAAAT
Found at i:2573211 original size:20 final size:20
Alignment explanation
Indices: 2573180--2573222 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
2573170 GAATTGAATA
*
2573180 TAAAAATCAAATACAAATATT
1 TAAAAATCAAATA-AAAAATT
2573201 TAAAAAT-AAATAAAAAATT
1 TAAAAATCAAATAAAAAATT
2573220 TAA
1 TAA
2573223 GTAACATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 5 0.24
21 7 0.33
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAATCAAATAAAAAATT
Found at i:2575282 original size:16 final size:14
Alignment explanation
Indices: 2575243--2575298 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 14
2575233 AATAATATAT
*
2575243 AAATAATATTATTA
1 AAATAATATTTTTA
2575257 AAAT-ATATTTTTA
1 AAATAATATTTTTA
2575270 ATATATAATATTTAATTA
1 A-A-ATAATATTT--TTA
2575288 AAAT-ATATTTT
1 AAATAATATTTT
2575299 AATTAGTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
13 10 0.28
14 5 0.14
15 8 0.22
16 8 0.22
17 1 0.03
18 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATAATATTTTTA
Found at i:2575288 original size:31 final size:33
Alignment explanation
Indices: 2575235--2575298 Score: 98
Period size: 31 Copynumber: 2.0 Consensus size: 33
2575225 TTAATTATAA
2575235 TAATATATAAATAATATTATTAAAATATATTTT
1 TAATATATAAATAATATTATTAAAATATATTTT
2575268 TAATATAT-AAT-AT-TTAATTAAAATATATTTT
1 TAATATATAAATAATATT-ATTAAAATATATTTT
2575299 AATTAGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 2 0.07
31 17 0.57
32 3 0.10
33 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
TAATATATAAATAATATTATTAAAATATATTTT
Found at i:2575299 original size:16 final size:16
Alignment explanation
Indices: 2575253--2575303 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
2575243 AAATAATATT
2575253 ATTAAAATATA-TTT-
1 ATTAAAATATATTTTA
*
2575267 -TTAATATATAATATTTA
1 ATTAAAATAT-AT-TTTA
2575284 ATTAAAATATATTTTA
1 ATTAAAATATATTTTA
2575300 ATTA
1 ATTA
2575304 GTAAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 8 0.27
14 1 0.03
16 11 0.37
17 2 0.07
18 8 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAAAATATATTTTA
Found at i:2577948 original size:22 final size:20
Alignment explanation
Indices: 2577923--2577977 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 20
2577913 TAAATAAATC
2577923 TTTAAAATAAATTAATTTTTTA
1 TTTAAAATAAATTAA--TTTTA
2577945 TTTAAAAT-AA--AATTTTA
1 TTTAAAATAAATTAATTTTA
2577962 TTTAAATATAAATTAA
1 TTTAAA-ATAAATTAA
2577978 AAGATAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 11 0.38
18 2 0.07
19 4 0.14
21 4 0.14
22 8 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAAATAAATTAATTTTA
Found at i:2578020 original size:29 final size:30
Alignment explanation
Indices: 2577951--2578020 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
2577941 TTTATTTAAA
* *
2577951 ATAAAATTTTATTTAAATATAAATTAAAAG
1 ATAAAAATTTATTTAAATATAAATAAAAAG
* * *
2577981 ATAAAACTTTATTTTAATAT-AATAAAAAT
1 ATAAAAATTTATTTAAATATAAATAAAAAG
2578010 ATAAAAATTTA
1 ATAAAAATTTA
2578021 CTTGGGAGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 17 0.49
30 18 0.51
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (30 bp):
ATAAAAATTTATTTAAATATAAATAAAAAG
Found at i:2578363 original size:16 final size:15
Alignment explanation
Indices: 2578321--2578371 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2578311 AAATATTGAC
*
2578321 ATAA-AAATAAAATA
1 ATAATAAATAAATTA
2578335 TATAATAATATAAATTA
1 -ATAATAA-ATAAATTA
*
2578352 ATCAATAAATAATTTA
1 AT-AATAAATAAATTA
2578368 ATAA
1 ATAA
2578372 ATTATCATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 6 0.19
16 13 0.42
17 12 0.39
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATAAATAAATTA
Found at i:2578363 original size:24 final size:23
Alignment explanation
Indices: 2578331--2578385 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
2578321 ATAAAAATAA
*
2578331 AATATATAATA-ATATAAATTAATC
1 AATAAATAATATA-ATAAATT-ATC
*
2578355 AATAAATAATTTAATAAATTATC
1 AATAAATAATATAATAAATTATC
*
2578378 ATTAAATA
1 AATAAATA
2578386 TATGATCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.37
24 16 0.59
25 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
AATAAATAATATAATAAATTATC
Found at i:2580178 original size:2 final size:2
Alignment explanation
Indices: 2580173--2580202 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2580163 AAATATATAT
2580173 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2580203 CACTTTCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2582564 original size:2 final size:2
Alignment explanation
Indices: 2582559--2582588 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2582549 ATATATAAGT
2582559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2582589 AGTTGCTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2584682 original size:19 final size:19
Alignment explanation
Indices: 2584626--2584683 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
2584616 TATAACATAA
* *
2584626 TTAAATATATTTAATAAAT
1 TTAAATATAATTAATATAT
* * *
2584645 ATAAAAATTAATATGATATAT
1 TTAAATA-TAAT-TAATATAT
2584666 TTAAATATAATTAATATA
1 TTAAATATAATTAATATA
2584684 ATATATTTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
19 11 0.38
20 7 0.24
21 11 0.38
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAAATATAATTAATATAT
Found at i:2584697 original size:14 final size:14
Alignment explanation
Indices: 2584614--2584688 Score: 56
Period size: 14 Copynumber: 5.8 Consensus size: 14
2584604 ACAATTTAAG
*
2584614 AATATAACATAATT
1 AATATAATATAATT
* *
2584628 AA-ATATATTTAATA
1 AATATA-ATATAATT
2584642 AATATAA-A-AATT
1 AATATAATATAATT
*
2584654 AATATGATAT-ATT
1 AATATAATATAATT
2584667 --TA-AATATAATT
1 AATATAATATAATT
2584678 AATATAATATA
1 AATATAATATA
2584689 TTTTATATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
10 4 0.09
11 5 0.11
12 9 0.20
13 9 0.20
14 16 0.35
15 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (14 bp):
AATATAATATAATT
Found at i:2584720 original size:18 final size:18
Alignment explanation
Indices: 2584697--2584748 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2584687 TATTTTATAT
2584697 ATTTTATTTATATTTACA
1 ATTTTATTTATATTTACA
*
2584715 ATTTTAATTTAT-TTTATA
1 ATTTT-ATTTATATTTACA
2584733 A-TTTATGTTATATTTA
1 ATTTTAT-TTATATTTA
2584749 ATTTTATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.07
17 7 0.23
18 15 0.50
19 6 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTATTTATATTTACA
Found at i:2584736 original size:12 final size:12
Alignment explanation
Indices: 2584680--2584757 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 12
2584670 ATATAATTAA
*
2584680 TATAATATATTT
1 TATAATTTATTT
2584692 TATATATTT-TATT
1 TATA-ATTTAT-TT
*
2584705 TAT-ATTTACAATT
1 TATAATTT--ATTT
2584718 T-TAATTTATTT
1 TATAATTTATTT
*
2584729 TATAATTTATGT
1 TATAATTTATTT
2584741 TAT-ATTTAATTT
1 TATAATTT-ATTT
2584753 TATAA
1 TATAA
2584758 AGTTAATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
11 12 0.23
12 24 0.46
13 16 0.31
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (12 bp):
TATAATTTATTT
Found at i:2585043 original size:4 final size:4
Alignment explanation
Indices: 2585034--2585065 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
2585024 TAAAAACAAC
*
2585034 ATTT ATTT ATTT ATTT ATTT ATTT GTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2585066 GTTTGATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:2585070 original size:12 final size:12
Alignment explanation
Indices: 2585035--2585070 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2585025 AAAAACAACA
*
2585035 TTTATTTATTTA
1 TTTATTTATTTG
2585047 TTTATTTATTTG
1 TTTATTTATTTG
*
2585059 TTTATTTGTTTG
1 TTTATTTATTTG
2585071 ATTCTATCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:2585181 original size:14 final size:15
Alignment explanation
Indices: 2585162--2585190 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2585152 TTGTTAATAA
2585162 AATTATT-TTTTTTT
1 AATTATTATTTTTTT
2585176 AATTATTATTTTTTT
1 AATTATTATTTTTTT
2585191 CATCAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
AATTATTATTTTTTT
Found at i:2587922 original size:19 final size:21
Alignment explanation
Indices: 2587890--2587934 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2587880 TGACAACCTC
2587890 TTAAAATCTATCCAC-TCTTT
1 TTAAAATCTATCCACTTCTTT
2587910 TTAAAAT-TATCCACTTTCTTT
1 TTAAAATCTATCCAC-TTCTTT
2587931 TTAA
1 TTAA
2587935 TTATTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.30
20 7 0.30
21 9 0.39
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAAATCTATCCACTTCTTT
Found at i:2588186 original size:21 final size:20
Alignment explanation
Indices: 2588168--2588210 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2588158 AATTATTTAC
2588168 TTAA-AAATTATTTTTATTT
1 TTAATAAATTATTTTTATTT
*
2588187 TTAATTTAATTATTTTTATTT
1 TTAA-TAAATTATTTTTATTT
2588208 TTA
1 TTA
2588211 CAAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
21 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTAATAAATTATTTTTATTT
Found at i:2589435 original size:18 final size:18
Alignment explanation
Indices: 2589406--2589451 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
2589396 TTAAATTTTG
2589406 AATATATTAAAATAATT-TA
1 AATAT-TTAAAA-AATTATA
2589425 AATATTTAAAAAATTATA
1 AATATTTAAAAAATTATA
2589443 AATATTTAA
1 AATATTTAA
2589452 TTTGATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.15
18 17 0.65
19 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATTTAAAAAATTATA
Found at i:2589440 original size:26 final size:26
Alignment explanation
Indices: 2589394--2589451 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
2589384 TAATAAACGG
* *
2589394 ATTTAAATTTTGAATATATTA-AAAT
1 ATTTAAATTTTGAAAAAATTATAAAT
2589419 AATTTAAATATTT-AAAAAATTATAAAT
1 -ATTTAAAT-TTTGAAAAAATTATAAAT
2589446 ATTTAA
1 ATTTAA
2589452 TTTGATATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTTAAATTTTGAAAAAATTATAAAT
Found at i:2597690 original size:31 final size:31
Alignment explanation
Indices: 2597654--2597730 Score: 84
Period size: 34 Copynumber: 2.4 Consensus size: 31
2597644 TTTTTACATA
* *
2597654 ATTTATTAATTTTA-TTAAATGTTTTAAAATT
1 ATTTATTAATTTTATTTAAAAG-CTTAAAATT
2597685 ATTTATTATTTATTTTATTTAAAAGCTTAAAATT
1 ATTTATTA---ATTTTATTTAAAAGCTTAAAATT
*
2597719 ATTTATTCATTT
1 ATTTATTAATTT
2597731 AATATAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
31 12 0.31
34 21 0.54
35 6 0.15
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (31 bp):
ATTTATTAATTTTATTTAAAAGCTTAAAATT
Found at i:2597803 original size:21 final size:21
Alignment explanation
Indices: 2597778--2597853 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
2597768 GTTAATTAAT
2597778 TAAAATATTTTAATAAATATA
1 TAAAATATTTTAATAAATATA
*
2597799 TAAAATAATATTT-ATAAA-ATT
1 TAAAAT-AT-TTTAATAAATATA
*
2597820 TTAAATATTATTAA-AATATATA
1 TAAAATATT-TTAATAA-ATATA
*
2597842 TAAAATAATTTA
1 TAAAATATTTTA
2597854 TCAATATGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 1 0.02
20 6 0.14
21 18 0.41
22 16 0.36
23 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAATATTTTAATAAATATA
Found at i:2598770 original size:13 final size:13
Alignment explanation
Indices: 2598754--2598800 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
2598744 TTTTATTATT
2598754 AATATTTATAATA
1 AATATTTATAATA
*
2598767 AATATTTATCATA
1 AATATTTATAATA
* *
2598780 ATTAATTATAAT-
1 AATATTTATAATA
2598792 AATATTTAT
1 AATATTTAT
2598801 TATATTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 7 0.25
13 21 0.75
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
AATATTTATAATA
Found at i:2598823 original size:53 final size:51
Alignment explanation
Indices: 2598759--2598889 Score: 151
Period size: 50 Copynumber: 2.6 Consensus size: 51
2598749 TTATTAATAT
* *
2598759 TTATAATAAATATTTATCATAA-TTAATTATAATAATATTTATTATATTTTTAA
1 TTATAATAAATATTGA-CATAATTTAA-AAT-ATAATATTTATTATATTTTTAA
* * *
2598812 TTATAATAAATA-TGAGATAATTTAAAATTTATTATTTATTATATTTTTAA
1 TTATAATAAATATTGACATAATTTAAAATATAATATTTATTATATTTTTAA
* *
2598862 TTATAATAAATA-TGAGATAATTCAAAAT
1 TTATAATAAATATTGACATAATTTAAAAT
2598890 TTAAATCCAG
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
50 47 0.66
51 6 0.08
52 6 0.08
53 12 0.17
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.49
Consensus pattern (51 bp):
TTATAATAAATATTGACATAATTTAAAATATAATATTTATTATATTTTTAA
Found at i:2598856 original size:50 final size:50
Alignment explanation
Indices: 2598794--2598892 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
2598784 ATTATAATAA
*
2598794 TATTTATTATATTTTTAATTATAATAAATATGAGATAATTTAAAATTTAT
1 TATTTATTATATTTTTAATTATAATAAATATGAGATAATTCAAAATTTAT
2598844 TATTTATTATATTTTTAATTATAATAAATATGAGATAATTCAAAATTTA
1 TATTTATTATATTTTTAATTATAATAAATATGAGATAATTCAAAATTTA
2598893 AATCCAGCTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (50 bp):
TATTTATTATATTTTTAATTATAATAAATATGAGATAATTCAAAATTTAT
Found at i:2604054 original size:19 final size:19
Alignment explanation
Indices: 2604027--2604068 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2604017 GGCCAAAATA
*
2604027 ATATTATTTATT-TTAGTAT
1 ATATAATTTATTATTAG-AT
2604046 ATATAATTTATTATTAGAT
1 ATATAATTTATTATTAGAT
2604065 ATAT
1 ATAT
2604069 TTTTTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
ATATAATTTATTATTAGAT
Found at i:2604156 original size:21 final size:21
Alignment explanation
Indices: 2604132--2604204 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
2604122 ACATGATTTC
*
2604132 AAAATTATTATCAACTTTATT
1 AAAATTATTATCAAATTTATT
* *
2604153 AAAATT-GTATCAAATGTTATC
1 AAAATTATTATCAAAT-TTATT
* *
2604174 AAAACTATTAT-AAAGATTATT
1 AAAATTATTATCAAA-TTTATT
2604195 AAAATTATTA
1 AAAATTATTA
2604205 AAAAATTATA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
20 7 0.17
21 31 0.76
22 3 0.07
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (21 bp):
AAAATTATTATCAAATTTATT
Found at i:2604164 original size:42 final size:42
Alignment explanation
Indices: 2604111--2604202 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
2604101 TTTTTTATAC
* * * *
2604111 AAAATTATATCACATGATT-TCAAAATTATTATCAACTTTATT
1 AAAATTATATCAAATG-TTATCAAAACTATTATAAACATTATT
* *
2604153 AAAATTGTATCAAATGTTATCAAAACTATTATAAAGATTATT
1 AAAATTATATCAAATGTTATCAAAACTATTATAAACATTATT
2604195 AAAATTAT
1 AAAATTAT
2604203 TAAAAAATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.05
42 40 0.95
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (42 bp):
AAAATTATATCAAATGTTATCAAAACTATTATAAACATTATT
Found at i:2604319 original size:11 final size:11
Alignment explanation
Indices: 2604305--2604343 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
2604295 TATCAAAAGT
2604305 TATTAAAGTCA
1 TATTAAAGTCA
*
2604316 TATTAAAG-CC
1 TATTAAAGTCA
2604326 TATTAAA-TCA
1 TATTAAAGTCA
2604336 TATTAAAG
1 TATTAAAG
2604344 ACTAGTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (11 bp):
TATTAAAGTCA
Found at i:2604336 original size:20 final size:20
Alignment explanation
Indices: 2604305--2604359 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
2604295 TATCAAAAGT
*
2604305 TATTAAAGTCATATTAAAGCC
1 TATTAAA-TCATATTAAAGAC
2604326 TATTAAATCATATTAAAGAC
1 TATTAAATCATATTAAAGAC
*
2604346 TAGTAATATCATAT
1 TATTAA-ATCATAT
2604360 GGCTAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (20 bp):
TATTAAATCATATTAAAGAC
Found at i:2604390 original size:17 final size:17
Alignment explanation
Indices: 2604370--2604423 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
2604360 GGCTAACAAA
2604370 ATTATATCAAAAGTTAT
1 ATTATATCAAAAGTTAT
2604387 ATTATAT-AATATA-TTAT
1 ATTATATCAA-A-AGTTAT
2604404 ATTATA-CAAAAGTTAT
1 ATTATATCAAAAGTTAT
2604420 -TTAT
1 ATTAT
2604424 TTATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
17 20 0.61
18 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (17 bp):
ATTATATCAAAAGTTAT
Found at i:2604774 original size:21 final size:20
Alignment explanation
Indices: 2604767--2604886 Score: 84
Period size: 21 Copynumber: 5.8 Consensus size: 20
2604757 ATTAAAATCA
2604767 TATTAAAA-ACTATT-AAAAT
1 TATTAAAATA-TATTAAAAAT
* * *
2604786 AATATAAAAAATTATTAAAAGT
1 TAT-TAAAATA-TATTAAAAAT
*
2604808 TATTAAAATTATTTTAAAAAT
1 TATTAAAA-TATATTAAAAAT
* *
2604829 TATCAAAATAATATTAAAAGT
1 TATTAAAAT-ATATTAAAAAT
*
2604850 TATT-AAATCATATTAAAATT
1 TATTAAAAT-ATATTAAAAAT
2604870 TATTAAATATTATATTA
1 TATTAAA-A-TATATTA
2604887 TATAAAAAGT
Statistics
Matches: 80, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.03
20 24 0.30
21 39 0.49
22 14 0.17
23 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
TATTAAAATATATTAAAAAT
Found at i:2604802 original size:31 final size:31
Alignment explanation
Indices: 2604767--2604847 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
2604757 ATTAAAATCA
*
2604767 TATTAAAAACTATTAAAATAATATAAAAAAT
1 TATTAAAAAATATTAAAATAATATAAAAAAT
** * * *
2604798 TATTAAAAGTTATTAAAATTATTTTAAAAAT
1 TATTAAAAAATATTAAAATAATATAAAAAAT
*
2604829 TATCAAAATAATATTAAAA
1 TATTAAAA-AATATTAAAA
2604848 GTTATTAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 33 0.80
32 8 0.20
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.37
Consensus pattern (31 bp):
TATTAAAAAATATTAAAATAATATAAAAAAT
Found at i:2604806 original size:52 final size:52
Alignment explanation
Indices: 2604750--2604856 Score: 160
Period size: 52 Copynumber: 2.1 Consensus size: 52
2604740 TAGCAATATC
*
2604750 AAAAGTTATTAAAATCATATTAAAAACTATTAAAATAATATAAAAAATTATT
1 AAAAGTTATTAAAATCATATTAAAAACTATCAAAATAATATAAAAAATTATT
* * * * *
2604802 AAAAGTTATTAAAATTATTTTAAAAATTATCAAAATAATATTAAAAGTTATT
1 AAAAGTTATTAAAATCATATTAAAAACTATCAAAATAATATAAAAAATTATT
2604854 AAA
1 AAA
2604857 TCATATTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (52 bp):
AAAAGTTATTAAAATCATATTAAAAACTATCAAAATAATATAAAAAATTATT
Found at i:2604853 original size:10 final size:9
Alignment explanation
Indices: 2604750--2604882 Score: 70
Period size: 10 Copynumber: 12.9 Consensus size: 9
2604740 TAGCAATATC
2604750 AAAAGTTATT
1 AAAA-TTATT
2604760 AAAATCATATT
1 AAAAT--TATT
*
2604771 AAAAACTATT
1 -AAAATTATT
*
2604781 AAAATAATATAA
1 AAAAT--TAT-T
2604793 AAAATTATT
1 AAAATTATT
2604802 AAAAGTTATT
1 AAAA-TTATT
2604812 AAAATTATTTT
1 AAAATTA--TT
*
2604823 AAAAATTATC
1 -AAAATTATT
2604833 AAAATAATATT
1 AAAAT--TATT
2604844 AAAAGTTATT
1 AAAA-TTATT
2604854 -AAATCATATT
1 AAAAT--TATT
2604864 AAAATTTATT
1 AAAA-TTATT
2604874 AAATATTAT
1 AAA-ATTAT
2604883 ATTATATAAA
Statistics
Matches: 99, Mismatches: 6, Indels: 36
0.70 0.04 0.26
Matches are distributed among these distances:
8 1 0.01
9 20 0.20
10 40 0.40
11 20 0.20
12 18 0.18
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (9 bp):
AAAATTATT
Found at i:2604864 original size:52 final size:52
Alignment explanation
Indices: 2604756--2604882 Score: 157
Period size: 52 Copynumber: 2.5 Consensus size: 52
2604746 TATCAAAAGT
* * * **
2604756 TATTAAAATCATATTAAAAACTATTAAAATAATATAAAAAATTATTAAAAGT
1 TATTAAAATTATATTAAAAATTATCAAAATAATATAAAAAATTATTAAAACA
* * * *
2604808 TATTAAAATTATTTTAAAAATTATCAAAATAATATTAAAAGTTATTAAATCA
1 TATTAAAATTATATTAAAAATTATCAAAATAATATAAAAAATTATTAAAACA
*
2604860 TATTAAAATT-TATTAAATATTAT
1 TATTAAAATTATATTAAAAATTAT
2604883 ATTATATAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
51 11 0.17
52 53 0.83
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (52 bp):
TATTAAAATTATATTAAAAATTATCAAAATAATATAAAAAATTATTAAAACA
Found at i:2604885 original size:42 final size:42
Alignment explanation
Indices: 2604767--2604886 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
2604757 ATTAAAATCA
* *
2604767 TATTAAAAAC-TATTAAAATAATAT-AAAA-AATTATTAAAAGT
1 TATTAAAATCATATTAAAA-ATTATCAAAATAA-TATTAAAAGT
* *
2604808 TATTAAAATTATTTTAAAAATTATCAAAATAATATTAAAAGT
1 TATTAAAATCATATTAAAAATTATCAAAATAATATTAAAAGT
* * *
2604850 TATT-AAATCATATTAAAATTTATTAAATATTATATTA
1 TATTAAAATCATATTAAAAATTATCAAA-ATAATATTA
2604887 TATAAAAAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 31 0.47
42 33 0.50
43 2 0.03
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (42 bp):
TATTAAAATCATATTAAAAATTATCAAAATAATATTAAAAGT
Found at i:2605194 original size:21 final size:20
Alignment explanation
Indices: 2605179--2605306 Score: 109
Period size: 21 Copynumber: 6.2 Consensus size: 20
2605169 TAAATTATAG
*
2605179 AAAATATTATCAAAATTATATT
1 AAAA-ATTATCAAAATCATA-T
** *
2605201 AAAGCTTATTAAAATCATATT
1 AAAAATTATCAAAATCATA-T
2605222 AAAAATT-TCAAAATCATAT
1 AAAAATTATCAAAATCATAT
* *
2605241 AAAAATAATTAAAATCATATT
1 AAAAATTATCAAAATCATA-T
*
2605262 AAATATTATCAAAATCATA-
1 AAAAATTATCAAAATCATAT
2605281 ACTAAAATTA-CTAAAATCATAT
1 A--AAAATTATC-AAAATCATAT
2605303 AAAA
1 AAAA
2605307 TGTTATATTA
Statistics
Matches: 87, Mismatches: 13, Indels: 14
0.76 0.11 0.12
Matches are distributed among these distances:
19 8 0.09
20 24 0.28
21 51 0.59
22 4 0.05
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.34
Consensus pattern (20 bp):
AAAAATTATCAAAATCATAT
Found at i:2605223 original size:11 final size:11
Alignment explanation
Indices: 2605207--2605307 Score: 69
Period size: 11 Copynumber: 9.8 Consensus size: 11
2605197 TATTAAAGCT
2605207 TATTAAAATCA
1 TATTAAAATCA
2605218 TATTAAAA--A
1 TATTAAAATCA
2605227 T-TTCAAAATCA
1 TATT-AAAATCA
*
2605238 TATAAAAAT-A
1 TATTAAAATCA
2605248 -ATTAAAATCA
1 TATTAAAATCA
2605258 TATT-AAAT-A
1 TATTAAAATCA
*
2605267 TTATCAAAATCA
1 -TATTAAAATCA
*
2605279 TAACTAAAAT--
1 T-ATTAAAATCA
*
2605289 TACTAAAATCA
1 TATTAAAATCA
2605300 TA-TAAAAT
1 TATTAAAAT
2605308 GTTATATTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 25
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.03
9 22 0.30
10 16 0.22
11 25 0.34
12 8 0.11
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (11 bp):
TATTAAAATCA
Found at i:2605276 original size:61 final size:62
Alignment explanation
Indices: 2605190--2605306 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 62
2605180 AAATATTATC
* * * * *
2605190 AAAATTATATTAAAGCTTATTAAAATCAT-ATTAAAAATTTC-AAAATCATATAAAAATAATT
1 AAAATCATATTAAAGATTATCAAAATCATAACT-AAAATTACTAAAATCATATAAAAATAATT
*
2605251 AAAATCATATTAAATATTATCAAAATCATAACTAAAATTACTAAAATCATATAAAA
1 AAAATCATATTAAAGATTATCAAAATCATAACTAAAATTACTAAAATCATATAAAA
2605307 TGTTATATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 32 0.67
62 16 0.33
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.33
Consensus pattern (62 bp):
AAAATCATATTAAAGATTATCAAAATCATAACTAAAATTACTAAAATCATATAAAAATAATT
Found at i:2607328 original size:21 final size:22
Alignment explanation
Indices: 2607304--2607346 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2607294 GTTTTTTTAA
*
2607304 TATTTTTATCAAAAAA-TTATT
1 TATTTTTAACAAAAAACTTATT
*
2607325 TATTTTTAAGAAAAAACTTATT
1 TATTTTTAACAAAAAACTTATT
2607347 CGTTTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTTTTAACAAAAAACTTATT
Found at i:2612145 original size:3 final size:3
Alignment explanation
Indices: 2612137--2612172 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2612127 TTTCGTAAAC
2612137 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2612173 GATGATGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2616418 original size:13 final size:13
Alignment explanation
Indices: 2616386--2616426 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
2616376 TATATTTTTT
*
2616386 TATACAAAATAT-
1 TATACAATATATA
2616398 TATA-AATATATA
1 TATACAATATATA
*
2616410 TATACAATATAAA
1 TATACAATATATA
2616423 TATA
1 TATA
2616427 TCAAAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.24
12 8 0.32
13 11 0.44
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (13 bp):
TATACAATATATA
Found at i:2617713 original size:50 final size:50
Alignment explanation
Indices: 2617654--2617950 Score: 420
Period size: 50 Copynumber: 6.2 Consensus size: 50
2617644 TATACTTAGA
* * *
2617654 GTCAACAATTACGGTCACCTTTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
2617704 GTCAACAATTATGG------------ATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* **
2617742 GTCAACAATTAAGGTTACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
2617792 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
2617842 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
2617892 GTCAACAATTACGGCCACCTCTCTCTATTGTTAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
2617942 GTCAACAAT
1 GTCAACAAT
2617951 GGCAACAACT
Statistics
Matches: 226, Mismatches: 9, Indels: 24
0.87 0.03 0.09
Matches are distributed among these distances:
38 37 0.16
50 189 0.84
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:2617731 original size:38 final size:38
Alignment explanation
Indices: 2617680--2617752 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
2617670 ACCTTTCTCT
2617680 ATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGG
1 ATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGG
2617718 ATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTA
1 ATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTA
2617753 AGGTTACCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.29
Consensus pattern (38 bp):
ATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGG
Found at i:2622394 original size:50 final size:50
Alignment explanation
Indices: 2622335--2622593 Score: 340
Period size: 50 Copynumber: 5.2 Consensus size: 50
2622325 TATACTTAGA
* ** *
2622335 GTCAACAATTACGGTTACATTTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACATCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
2622385 GTCAACAATTATGGCCACCA-CTCTCTATTATCAAATGTTGGTGAAGAATT
1 GTCAACAATTATGGCCA-CATCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
2622435 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACATCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
2622485 GTCAATAATTATGGCCACCTCTCTCTATTGTCAAAGCTTGGTGAAGAATC
1 GTCAACAATTATGGCCACATCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * * * * *
2622535 GTCAACAATTACGACCACTTATCTCTATTGTCAAAGGTTAGTGAAGGATA
1 GTCAACAATTATGGCCACATCTCTCTATTGTCAAAGGTTGGTGAAGAATC
2622585 GTCAACAAT
1 GTCAACAAT
2622594 GGCAACAACT
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 182 0.98
51 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACATCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:2624798 original size:203 final size:203
Alignment explanation
Indices: 2624449--2624853 Score: 792
Period size: 203 Copynumber: 2.0 Consensus size: 203
2624439 CCAATGTGCT
*
2624449 TTACCAGGACTTACCAAAAATCTGCTAACAACTCCAACAGCATGAGATATATCAGGGTGAGTACA
1 TTACCAGGACTTACCAAAAATCTGCTAACAACTCCAACAGCATGAGATATATCAGGGCGAGTACA
2624514 TACCATAGTGTGCATCAGACTTCTAACTGCTGACGAATATGGAATAACTGACATTTCAGCCTTTT
66 TACCATAGTGTGCATCAGACTTCTAACTGCTGACGAATATGGAATAACTGACATTTCAGCCTTTT
2624579 CTTTTTTAGTAGATGGACATAACCTTTTACTTAACTTGAAATGTCCGGCAAGTGGAGTAGAAACT
131 CTTTTTTAGTAGATGGACATAACCTTTTACTTAACTTGAAATGTCCGGCAAGTGGAGTAGAAACT
2624644 GACTTTGC
196 GACTTTGC
*
2624652 TTACCAGGACTTACCAAAAATCTGCTAACAACTCCAACAGCATGAGATATATTAGGGCGAGTACA
1 TTACCAGGACTTACCAAAAATCTGCTAACAACTCCAACAGCATGAGATATATCAGGGCGAGTACA
2624717 TACCATAGTGTGCATCAGACTTCTAACTGCTGACGAATATGGAATAACTGACATTTCAGCCTTTT
66 TACCATAGTGTGCATCAGACTTCTAACTGCTGACGAATATGGAATAACTGACATTTCAGCCTTTT
2624782 CTTTTTTAGTAGATGGACATAACCTTTTACTTAACTTGAAATGTCCGGCAAGTGGAGTAGAAACT
131 CTTTTTTAGTAGATGGACATAACCTTTTACTTAACTTGAAATGTCCGGCAAGTGGAGTAGAAACT
2624847 GACTTTG
196 GACTTTG
2624854 AGTTTTTCAT
Statistics
Matches: 200, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
203 200 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (203 bp):
TTACCAGGACTTACCAAAAATCTGCTAACAACTCCAACAGCATGAGATATATCAGGGCGAGTACA
TACCATAGTGTGCATCAGACTTCTAACTGCTGACGAATATGGAATAACTGACATTTCAGCCTTTT
CTTTTTTAGTAGATGGACATAACCTTTTACTTAACTTGAAATGTCCGGCAAGTGGAGTAGAAACT
GACTTTGC
Found at i:2634499 original size:2 final size:2
Alignment explanation
Indices: 2634492--2634527 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2634482 AAGCAAGTTA
2634492 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
2634528 GTTTGATTTG
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:2636614 original size:22 final size:22
Alignment explanation
Indices: 2636589--2636641 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
2636579 TAGTTAGTTT
** *
2636589 TATATATTTTAATATATTATAA
1 TATATATAATAATAAATTATAA
2636611 TATATATAATAATAAATTATAA
1 TATATATAATAATAAATTATAA
*
2636633 TATAAATAA
1 TATATATAA
2636642 ATAAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATATATAATAATAAATTATAA
Found at i:2636615 original size:12 final size:12
Alignment explanation
Indices: 2636600--2636636 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2636590 ATATATTTTA
2636600 ATATATTATAAT
1 ATATATTATAAT
*
2636612 ATATATAATAAT
1 ATATATTATAAT
2636624 A-A-ATTATAAT
1 ATATATTATAAT
2636634 ATA
1 ATA
2636637 AATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 12 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATTATAAT
Found at i:2636637 original size:12 final size:13
Alignment explanation
Indices: 2636600--2636650 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
2636590 ATATATTTTA
*
2636600 ATATATTATAATAT
1 ATATAATATAA-AT
2636614 ATATAATAATAAAT
1 ATATAAT-ATAAAT
2636628 -TATAATATAAAT
1 ATATAATATAAAT
*
2636640 AAATAAATATA
1 ATAT-AATATA
2636651 TCAAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 6 0.19
13 8 0.25
14 14 0.44
15 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAATATAAAT
Found at i:2638764 original size:33 final size:32
Alignment explanation
Indices: 2638708--2638772 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
2638698 AAGGTATGAC
*
2638708 TTATTTTTTAAATGAGTATTTTTTTACTTAAAT
1 TTATTTTTTAAATGAATA-TTTTTTACTTAAAT
* *
2638741 TTATTTTTTAAATTTAATA-TTTTTATTTAAAT
1 TTATTTTTTAAA-TGAATATTTTTTACTTAAAT
2638773 CTTTTCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 12 0.43
33 12 0.43
34 4 0.14
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (32 bp):
TTATTTTTTAAATGAATATTTTTTACTTAAAT
Found at i:2639816 original size:2 final size:2
Alignment explanation
Indices: 2639809--2639844 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2639799 TTGATGAGAA
2639809 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
2639845 CGAAAATTCG
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:2640323 original size:32 final size:33
Alignment explanation
Indices: 2640280--2640343 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2640270 ATGCGAATAC
* *
2640280 ATATTTTAAAATTCATAT-AATATAAATTATTA
1 ATATATTAAAATTCATATAAATATAAAATATTA
*
2640312 ATATATTAAAATTTATATAAATATAAAATATT
1 ATATATTAAAATTCATATAAATATAAAATATT
2640344 TTAAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (33 bp):
ATATATTAAAATTCATATAAATATAAAATATTA
Found at i:2640327 original size:18 final size:18
Alignment explanation
Indices: 2640305--2640353 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
2640295 TATAATATAA
2640305 ATTATTAATATATTAAAAT
1 ATTATTAA-ATATTAAAAT
2640324 -TTATATAAATA-TAAAAT
1 ATTAT-TAAATATTAAAAT
2640341 ATT-TTAAATATTA
1 ATTATTAAATATTA
2640354 TTACGACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 6 0.22
17 9 0.33
18 9 0.33
19 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATTAAATATTAAAAT
Found at i:2640354 original size:27 final size:27
Alignment explanation
Indices: 2640294--2640354 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
2640284 TTTAAAATTC
* *
2640294 ATATAATATAAATTATTAATATATTAA
1 ATATTATATAAATTATAAATATATTAA
*
2640321 A-ATTTATATAAA-TATAAAATATTTTAA
1 ATA-TTATATAAATTAT-AAATATATTAA
2640348 ATATTAT
1 ATATTAT
2640355 TACGACACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 4 0.14
27 23 0.82
28 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATTATATAAATTATAAATATATTAA
Found at i:2640445 original size:36 final size:36
Alignment explanation
Indices: 2640403--2640478 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2640393 ATTATTAGGC
2640403 CTAAGCCATAACTTTGCTAGACTGATCCAGCTTATT
1 CTAAGCCATAACTTTGCTAGACTGATCCAGCTTATT
*
2640439 CTAAGCCATAACTTTGCTAGATTGATCCAGCTTATT
1 CTAAGCCATAACTTTGCTAGACTGATCCAGCTTATT
2640475 CTAA
1 CTAA
2640479 AGACCTGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (36 bp):
CTAAGCCATAACTTTGCTAGACTGATCCAGCTTATT
Found at i:2641862 original size:20 final size:21
Alignment explanation
Indices: 2641839--2641880 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
2641829 GACATGAATA
2641839 TATTTAATTT-TTTAAAA-ATT
1 TATTT-ATTTATTTAAAACATT
2641859 TATTTATTTATTTAAAACATT
1 TATTTATTTATTTAAAACATT
2641880 T
1 T
2641881 TTATAGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTATTTATTTAAAACATT
Found at i:2643409 original size:21 final size:21
Alignment explanation
Indices: 2643358--2643411 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2643348 TTACAATTTT
* *
2643358 AATATTAA-A-AAATTATTTA
1 AATATTAATATAAAGTATATA
2643377 AAT-TTAATTATAAAGTATATA
1 AATATTAA-TATAAAGTATATA
2643398 AATATTAATATAAA
1 AATATTAATATAAA
2643412 AATAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 4 0.14
19 3 0.10
20 1 0.03
21 17 0.59
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATATTAATATAAAGTATATA
Found at i:2644006 original size:22 final size:22
Alignment explanation
Indices: 2643957--2644012 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2643947 AAATTGATCG
* **
2643957 AATTTAATTTATTTAATTTGAT
1 AATTTATTTTATTTAATTAAAT
**
2643979 TTTTTATTTTATTTAATTAAAT
1 AATTTATTTTATTTAATTAAAT
2644001 AATTTAATTTTA
1 AATTT-ATTTTA
2644013 ATATATTTAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
AATTTATTTTATTTAATTAAAT
Found at i:2644195 original size:2 final size:2
Alignment explanation
Indices: 2644188--2644226 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2644178 TGCAATTTAC
2644188 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
2644227 GTATGTGTGT
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:2644397 original size:13 final size:13
Alignment explanation
Indices: 2644378--2644408 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2644368 TTATTTTTTA
2644378 AATATTTATATTT
1 AATATTTATATTT
*
2644391 GATATTTATATTT
1 AATATTTATATTT
2644404 AATAT
1 AATAT
2644409 ATATTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:2645031 original size:19 final size:20
Alignment explanation
Indices: 2645007--2645048 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2644997 AGTCAACTTG
*
2645007 AAAATAGTAT-TTTTTATTT
1 AAAATAATATATTTTTATTT
2645026 AAAATAATATATTTTTATTT
1 AAAATAATATATTTTTATTT
2645046 AAA
1 AAA
2645049 TTTATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AAAATAATATATTTTTATTT
Found at i:2645587 original size:17 final size:17
Alignment explanation
Indices: 2645567--2645602 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2645557 AAACTAACAC
2645567 TTAATTA-AAAAAATGAA
1 TTAATTAGAAAAAAT-AA
2645584 TTAATTAGAAAAAATAA
1 TTAATTAGAAAAAATAA
2645601 TT
1 TT
2645603 CATTCATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
TTAATTAGAAAAAATAA
Found at i:2646083 original size:25 final size:24
Alignment explanation
Indices: 2646028--2646085 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
2646018 TAATTTAAAA
* * *
2646028 TTTTTAATAATAATAGTTTATCAT
1 TTTTTATTTATAATAGTTTATAAT
**
2646052 TAATTATTTATAATAGTTTTATAAT
1 TTTTTATTTATAATAG-TTTATAAT
2646077 TTTTTATTT
1 TTTTTATTT
2646086 GGGTGTCGTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (24 bp):
TTTTTATTTATAATAGTTTATAAT
Found at i:2646480 original size:31 final size:34
Alignment explanation
Indices: 2646436--2646499 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 34
2646426 TAAATGTATT
*
2646436 AAAATCTACATAAA-ATA-AA-ATATTAATTATC
1 AAAATCTACATAAAGATATAATACATTAATTATC
* *
2646467 AAAATTTATATAAAGATATAATACATTAATTAT
1 AAAATCTACATAAAGATATAATACATTAATTAT
2646500 GATTAGGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 12 0.44
32 3 0.11
33 2 0.07
34 10 0.37
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (34 bp):
AAAATCTACATAAAGATATAATACATTAATTATC
Found at i:2646676 original size:20 final size:20
Alignment explanation
Indices: 2646629--2646667 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2646619 AATATGAAAA
2646629 AAAATA-ATTAAAATATAAT
1 AAAATACATTAAAATATAAT
2646648 AAAATACATTAAAAATATAA
1 AAAATACATT-AAAATATAA
2646668 ACATAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATACATTAAAATATAAT
Done.