Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 21 of 171
Found at i:9653257 original size:21 final size:19
Alignment explanation
Indices: 9653203--9653267 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
9653193 ATAAATTTGT
9653203 TTTTTA-AACTTTTGTTAAA
1 TTTTTACAA-TTTTGTTAAA
*
9653222 TAGTTTTGCAATTTTGTTATAA
1 T--TTTTACAATTTTGTTA-AA
* *
9653244 TTTTTACAATTTTTTTACA
1 TTTTTACAATTTTGTTAAA
9653263 TTTTT
1 TTTTT
9653268 GTAATGGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.18
20 14 0.37
21 12 0.32
22 5 0.13
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (19 bp):
TTTTTACAATTTTGTTAAA
Found at i:9655269 original size:23 final size:23
Alignment explanation
Indices: 9655243--9655363 Score: 156
Period size: 23 Copynumber: 5.2 Consensus size: 23
9655233 ACACTAGCGC
9655243 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
9655266 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
9655289 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
9655314 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
9655337 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
9655360 GCTC
1 GCTC
9655364 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 62 0.72
24 1 0.01
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:9655312 original size:48 final size:46
Alignment explanation
Indices: 9655243--9655363 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
9655233 ACACTAGCGC
* *
9655243 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
9655289 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
*
9655337 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
9655364 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:9655392 original size:39 final size:39
Alignment explanation
Indices: 9655328--9655402 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
9655318 TCCGATTAGC
*
9655328 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
9655367 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
9655403 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:9655397 original size:23 final size:23
Alignment explanation
Indices: 9655362--9655455 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
9655352 CTTTGTGTGC
*
9655362 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
9655385 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
9655408 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
9655433 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
9655455 T
1 T
9655456 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:9658959 original size:6 final size:6
Alignment explanation
Indices: 9658948--9658986 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
9658938 TGATCAAAAT
* * *
9658948 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
9658987 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:9660645 original size:25 final size:24
Alignment explanation
Indices: 9660616--9660670 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
9660606 AGAAAAACTT
* * *
9660616 AATTTAAATTTTTAAAAATTATAAA
1 AATTTAAACTATT-AAAATAATAAA
*
9660641 GATTTAAACTATTAAAATAATAAA
1 AATTTAAACTATTAAAATAATAAA
9660665 AATTTA
1 AATTTA
9660671 TTTTTACTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTTAAACTATTAAAATAATAAA
Found at i:9665723 original size:6 final size:6
Alignment explanation
Indices: 9665712--9665742 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
9665702 GCTCGTGAGA
9665712 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
9665743 GAAGAGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:9675210 original size:20 final size:20
Alignment explanation
Indices: 9675185--9675222 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9675175 CATTGGAAAC
9675185 ACAGAGAGTGGAGAAAAAAA
1 ACAGAGAGTGGAGAAAAAAA
*
9675205 ACAGAGGGTGGAGAAAAA
1 ACAGAGAGTGGAGAAAAA
9675223 GGGGAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.34, T:0.05
Consensus pattern (20 bp):
ACAGAGAGTGGAGAAAAAAA
Found at i:9679724 original size:4 final size:4
Alignment explanation
Indices: 9679715--9679753 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
9679705 GTTCATTTCC
* *
9679715 CTCA CTCA CTCA CTCA CTCA CTCA CTCA CACA CACA CTC
1 CTCA CTCA CTCA CTCA CTCA CTCA CTCA CTCA CTCA CTC
9679754 TGTCTCTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.28, C:0.51, G:0.00, T:0.21
Consensus pattern (4 bp):
CTCA
Found at i:9681734 original size:17 final size:18
Alignment explanation
Indices: 9681701--9681735 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9681691 TCTCAAAAGC
9681701 ACTTTTGAGACATAAAAAT
1 ACTTTTGAGA-ATAAAAAT
9681720 ACTTTTGAG-ATAAAAA
1 ACTTTTGAGAATAAAAA
9681736 CATTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (18 bp):
ACTTTTGAGAATAAAAAT
Found at i:9684390 original size:25 final size:24
Alignment explanation
Indices: 9684362--9684411 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
9684352 AAATCAATCA
9684362 TTTA-ATAAATATTAATATATAATAT
1 TTTAGATAAATA-TAATATA-AATAT
**
9684387 TTTAGATCGATATAATATAAATAT
1 TTTAGATAAATATAATATAAATAT
9684411 T
1 T
9684412 AAATTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
25 11 0.50
26 5 0.23
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TTTAGATAAATATAATATAAATAT
Found at i:9686312 original size:31 final size:29
Alignment explanation
Indices: 9686277--9686339 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
9686267 AACTATATAA
* *
9686277 GAACTATGGTTTAATGTGTAATTGTATACAT
1 GAACTATGATTT--TGTGCAATTGTATACAT
*
9686308 GAACTTTGATTTTGTGCAATTGTATACAT
1 GAACTATGATTTTGTGCAATTGTATACAT
9686337 GAA
1 GAA
9686340 ATTTTGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.66
31 10 0.34
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (29 bp):
GAACTATGATTTTGTGCAATTGTATACAT
Found at i:9686323 original size:29 final size:30
Alignment explanation
Indices: 9686291--9686349 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
9686281 TATGGTTTAA
*
9686291 TGTGTAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
*
9686320 TGTGCAATTGTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
9686350 GATCAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:9689228 original size:58 final size:58
Alignment explanation
Indices: 9689164--9689283 Score: 195
Period size: 58 Copynumber: 2.1 Consensus size: 58
9689154 AAAAAGAATT
*
9689164 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
* * * *
9689222 GTTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
9689280 GTTT
1 GTTT
9689284 GTTGATGGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
Found at i:9689297 original size:58 final size:58
Alignment explanation
Indices: 9689188--9689298 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
9689178 TTTAGGAATA
**
9689188 AAATTATATTTGGATTTAAAAATATTTGGGTTTAGTTTATGAGTGTTTTTTAATAATG
1 AAATTATATTTGGATTTAAAAATATTTGGGTTTAGTTTATGAGTGGGTTTTAATAATG
* *
9689246 AAATTATATTTGGGTTTAAAAATATTTGGGTTTAGTTTGTTGA-TGGGTTTTAA
1 AAATTATATTTGGATTTAAAAATATTTGGGTTTAGTTT-ATGAGTGGGTTTTAA
9689299 ATATTAAGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 45 0.94
59 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.50
Consensus pattern (58 bp):
AAATTATATTTGGATTTAAAAATATTTGGGTTTAGTTTATGAGTGGGTTTTAATAATG
Found at i:9689434 original size:9 final size:9
Alignment explanation
Indices: 9689420--9689445 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9689410 ATAATATATT
9689420 TTTATTCGG
1 TTTATTCGG
9689429 TTTATTCGG
1 TTTATTCGG
9689438 TTTATTCG
1 TTTATTCG
9689446 AATTATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (9 bp):
TTTATTCGG
Found at i:9689451 original size:18 final size:18
Alignment explanation
Indices: 9689420--9689467 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
9689410 ATAATATATT
** *
9689420 TTTATTCGGTTTATTCGG
1 TTTATTCGAATTATTCGA
*
9689438 TTTATTCGAATTATTTGA
1 TTTATTCGAATTATTCGA
*
9689456 ATTATTCGAATT
1 TTTATTCGAATT
9689468 CGAAAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (18 bp):
TTTATTCGAATTATTCGA
Found at i:9689545 original size:23 final size:23
Alignment explanation
Indices: 9689501--9689546 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
9689491 AAAAAAAATT
**
9689501 TAACTCGATTCGTTTAACTCGAA
1 TAACTCGATTCGAATAACTCGAA
*
9689524 TAACTCGATTCGAATAATTCGAA
1 TAACTCGATTCGAATAACTCGAA
9689547 ATTCGAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (23 bp):
TAACTCGATTCGAATAACTCGAA
Found at i:9689563 original size:27 final size:28
Alignment explanation
Indices: 9689532--9689593 Score: 117
Period size: 27 Copynumber: 2.2 Consensus size: 28
9689522 AATAACTCGA
9689532 TTCGAATAATTCGAAATTCGAAA-TTTT
1 TTCGAATAATTCGAAATTCGAAATTTTT
9689559 TTCGAATAATTCGAAATTCGAAATTTTT
1 TTCGAATAATTCGAAATTCGAAATTTTT
9689587 TTCGAAT
1 TTCGAAT
9689594 TTTTCGATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (28 bp):
TTCGAATAATTCGAAATTCGAAATTTTT
Found at i:9689604 original size:26 final size:26
Alignment explanation
Indices: 9689532--9689606 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
9689522 AATAACTCGA
9689532 TTCGAATAATTCGAAATTCGAAATTTT
1 TTCGAATAATTCG-AATTCGAAATTTT
9689559 TTCGAATAATTCGAAATTCGAAATTTTT
1 TTCGAATAATTCG-AATTCGAAA-TTTT
**
9689587 TTCGAATTTTTCG-ATTCGAA
1 TTCGAATAATTCGAATTCGAA
9689607 TCGAATTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 7 0.16
27 23 0.51
28 15 0.33
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (26 bp):
TTCGAATAATTCGAATTCGAAATTTT
Found at i:9691853 original size:15 final size:14
Alignment explanation
Indices: 9691825--9691858 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
9691815 CAAAATAATT
*
9691825 AAATTTTATTTAAA
1 AAATTTTATATAAA
9691839 AAATATTTATATAAA
1 AAAT-TTTATATAAA
9691854 AAATT
1 AAATT
9691859 AAAAGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTTATATAAA
Found at i:9693351 original size:27 final size:29
Alignment explanation
Indices: 9693311--9693369 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
9693301 AAATACCTGA
*
9693311 CACCCTAATGGAGGGACACAAAGTGGCGG
1 CACCCTAATGGAGGAACACAAAGTGGCGG
***
9693340 CACCC-AA-GGAGGAACTTGAAGTGGCGG
1 CACCCTAATGGAGGAACACAAAGTGGCGG
9693367 CAC
1 CAC
9693370 TAAGGGGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 19 0.73
28 2 0.08
29 5 0.19
ACGTcount: A:0.31, C:0.25, G:0.34, T:0.10
Consensus pattern (29 bp):
CACCCTAATGGAGGAACACAAAGTGGCGG
Found at i:9693434 original size:19 final size:19
Alignment explanation
Indices: 9693410--9693448 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
9693400 TTTTGTGCCG
*
9693410 TGTGTGTGTTTATTTTATT
1 TGTGTGTGTTAATTTTATT
9693429 TGTGTGTGTTAATTTTATT
1 TGTGTGTGTTAATTTTATT
9693448 T
1 T
9693449 TGATTGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.21, T:0.67
Consensus pattern (19 bp):
TGTGTGTGTTAATTTTATT
Found at i:9693586 original size:20 final size:20
Alignment explanation
Indices: 9693535--9693597 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
9693525 CAAATAAACG
* *
9693535 GGAAAGAAAGAAAAAAAGAAA
1 GGAAAGAAAG-AAGAAGGAAA
* *
9693556 -G-AAGAAGGAAGAAGGAGA
1 GGAAAGAAAGAAGAAGGAAA
9693574 GGAAAGAAAGAAGAAGGAAA
1 GGAAAGAAAGAAGAAGGAAA
9693594 GGAA
1 GGAA
9693598 TGTAATGTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 7 0.21
19 7 0.21
20 20 0.59
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
GGAAAGAAAGAAGAAGGAAA
Found at i:9696723 original size:22 final size:21
Alignment explanation
Indices: 9696695--9696735 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
9696685 CGGTTTATGG
*
9696695 TTAGGGTTTAGTGTTTTAAATT
1 TTAGGGTTTAG-GATTTAAATT
9696717 TTAGGGTTTAGGATTTAAA
1 TTAGGGTTTAGGATTTAAA
9696736 GTTATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (21 bp):
TTAGGGTTTAGGATTTAAATT
Found at i:9697747 original size:21 final size:21
Alignment explanation
Indices: 9697723--9697769 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
9697713 CCATTTACCG
*
9697723 TTGACCTTTGA-TAGTTAACCA
1 TTGACCATTGACT-GTTAACCA
*
9697744 TTGACCATTGACTGTTAACCG
1 TTGACCATTGACTGTTAACCA
9697765 TTGAC
1 TTGAC
9697770 TTTTTGGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (21 bp):
TTGACCATTGACTGTTAACCA
Found at i:9700894 original size:23 final size:23
Alignment explanation
Indices: 9700827--9700976 Score: 101
Period size: 23 Copynumber: 6.4 Consensus size: 23
9700817 AGCACGTCTC
*
9700827 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTG--ATTAGCACTTTGT
* * *
9700852 GTGCTTTCTGATTGGCACTTTAT
1 GTGCTCTCTGATTAGCACTTTGT
*
9700875 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
** * **
9700898 GTATTCTCTGTTTAGCACCGTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
9700921 GTGCTCTCT-ATTGCCCAGCAC-TTAT
1 GTGCTCTCTGATT----AGCACTTTGT
*
9700946 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
9700967 GTACTCTCTG
1 GTGCTCTCTG
9700977 TTTGTTCCGT
Statistics
Matches: 97, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
21 13 0.13
22 4 0.04
23 53 0.55
25 22 0.23
26 5 0.05
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:9700924 original size:46 final size:48
Alignment explanation
Indices: 9700808--9700929 Score: 117
Period size: 46 Copynumber: 2.6 Consensus size: 48
9700798 ACTAGCGCGC
* *
9700808 TCTCTGTTTAGCA-CGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCT
1 TCTCTGTTTAGCACCGTAT-GTGCTCTCTG-TATTAGCACTGTGTGTGAT
* * ** * *
9700857 T-TCTGATTGGCACTTTATGTGCTCTCTG-ATTAGTACTTTGTGT-AT
1 TCTCTGTTTAGCACCGTATGTGCTCTCTGTATTAGCACTGTGTGTGAT
*
9700902 TCTCTGTTTAGCACCGTGTGTGCTCTCT
1 TCTCTGTTTAGCACCGTATGTGCTCTCT
9700930 ATTGCCCAGC
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
45 2 0.03
46 34 0.59
48 19 0.33
49 3 0.05
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (48 bp):
TCTCTGTTTAGCACCGTATGTGCTCTCTGTATTAGCACTGTGTGTGAT
Found at i:9701586 original size:21 final size:21
Alignment explanation
Indices: 9701560--9701603 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
9701550 TAAGGTCCAT
* *
9701560 TTGCCCCGGAGGAGTAGAGTA
1 TTGCCCAGGAGGAGCAGAGTA
9701581 TTGCCCAGGAGGAGCAGAGTA
1 TTGCCCAGGAGGAGCAGAGTA
9701602 TT
1 TT
9701604 ACGGTGGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.20
Consensus pattern (21 bp):
TTGCCCAGGAGGAGCAGAGTA
Found at i:9701661 original size:45 final size:45
Alignment explanation
Indices: 9701597--9701733 Score: 211
Period size: 45 Copynumber: 3.0 Consensus size: 45
9701587 AGGAGGAGCA
**
9701597 GAGTATTACGGTGGCTCGTCAAACTGAGCCTGATATCCTTGGCTT
1 GAGTATTGTGGTGGCTCGTCAAACTGAGCCTGATATCCTTGGCTT
*
9701642 GAGTATTGTGGTGGCTCGTCAACCTGAGCCTGATATCCTTGGCTT
1 GAGTATTGTGGTGGCTCGTCAAACTGAGCCTGATATCCTTGGCTT
* * * *
9701687 TAGTATTGTGGTGGCTCGTTAAACTGAGGCTGATATCTTTGGCTT
1 GAGTATTGTGGTGGCTCGTCAAACTGAGCCTGATATCCTTGGCTT
9701732 GA
1 GA
9701734 TGAGCTAGTG
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.34
Consensus pattern (45 bp):
GAGTATTGTGGTGGCTCGTCAAACTGAGCCTGATATCCTTGGCTT
Found at i:9703691 original size:16 final size:16
Alignment explanation
Indices: 9703670--9703719 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
9703660 TGATGGGGAT
9703670 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
*
9703686 ATTATTTT-TTATATT-
1 ATTATTTTGGTA-ATTA
*
9703701 A-TATTTTGGTTATTA
1 ATTATTTTGGTAATTA
9703716 ATTA
1 ATTA
9703720 ACTAGGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
14 9 0.33
15 5 0.19
16 13 0.48
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:9704686 original size:19 final size:18
Alignment explanation
Indices: 9704662--9704697 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9704652 AATTAAATTT
9704662 AAAATTAACCAAAACTTAA
1 AAAATTAACC-AAACTTAA
*
9704681 AAAATTAATCAAACTTA
1 AAAATTAACCAAACTTA
9704698 CCTGTCTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATTAACCAAACTTAA
Found at i:9710042 original size:2 final size:2
Alignment explanation
Indices: 9710035--9710080 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
9710025 CTTCACATCA
9710035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9710077 AT AT
1 AT AT
9710081 TGAATACTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9710497 original size:40 final size:40
Alignment explanation
Indices: 9710442--9710517 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
9710432 ATAGGACATG
9710442 TTTTAAAGGAATTTGACTTGGCATATTCCCCATATTACTT
1 TTTTAAAGGAATTTGACTTGGCATATTCCCCATATTACTT
9710482 TTTTAAAGGAATTTGACTTGGCATATTCCCCATATT
1 TTTTAAAGGAATTTGACTTGGCATATTCCCCATATT
9710518 CCTGCCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (40 bp):
TTTTAAAGGAATTTGACTTGGCATATTCCCCATATTACTT
Found at i:9714569 original size:17 final size:17
Alignment explanation
Indices: 9714538--9714570 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9714528 TAAACACTTA
9714538 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
9714555 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
9714571 AGTCTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:9714914 original size:20 final size:20
Alignment explanation
Indices: 9714863--9714915 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
9714853 TCCAAGTTTA
* *
9714863 TAATA-ATTTATTTATGTAT
1 TAATATATTTATATATATAT
*
9714882 TAATATATATATATATATAT
1 TAATATATTTATATATATAT
9714902 TAA-ATTATTTATAT
1 TAATA-TATTTATAT
9714916 TTAGAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TAATATATTTATATATATAT
Found at i:9747086 original size:41 final size:41
Alignment explanation
Indices: 9747041--9747124 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
9747031 TGGTGTCACG
* *
9747041 TGTCATTACAATATAGGAGTACAACAAATATATTGTTATAT
1 TGTCATCACAATATAAGAGTACAACAAATATATTGTTATAT
9747082 TGTCATCACAATATAAGAGTACAACAAATATATTGTTATAT
1 TGTCATCACAATATAAGAGTACAACAAATATATTGTTATAT
9747123 TG
1 TG
9747125 CTATATATAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.36
Consensus pattern (41 bp):
TGTCATCACAATATAAGAGTACAACAAATATATTGTTATAT
Found at i:9764101 original size:3 final size:3
Alignment explanation
Indices: 9764093--9764151 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
9764083 TTGATAAAAG
9764093 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
9764141 GAA GAA GAA GA
1 GAA GAA GAA GA
9764152 GTTGAAAGGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9769907 original size:26 final size:25
Alignment explanation
Indices: 9769878--9769935 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
9769868 ATTATTAATA
* *
9769878 ATATTAAA-AAAATTAATAAAAACAGT
1 ATATTAAATAAAA-TAA-AAAAAAACT
9769904 ATATTTAAATAAAATAAAAAAAAACT
1 ATA-TTAAATAAAATAAAAAAAAACT
9769930 ATATTA
1 ATATTA
9769936 TGTCACGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 3 0.11
26 13 0.46
27 8 0.29
28 4 0.14
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (25 bp):
ATATTAAATAAAATAAAAAAAAACT
Found at i:9787069 original size:26 final size:25
Alignment explanation
Indices: 9787039--9787088 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
9787029 TATCCTGATT
*
9787039 TGATGCAAAACGAAATATATAATAAA
1 TGATGCAAAAAGAAATAT-TAATAAA
* *
9787065 TGATGTAAAAATAAATATTAATAA
1 TGATGCAAAAAGAAATATTAATAA
9787089 TATAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.28
Consensus pattern (25 bp):
TGATGCAAAAAGAAATATTAATAAA
Found at i:9797330 original size:23 final size:24
Alignment explanation
Indices: 9797285--9797330 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
9797275 TTGGTTTTTT
*
9797285 TTTTTTTTGGTTTTTTGTCTTTGGA
1 TTTTTTTT-GTTTTTTGGCTTTGGA
*
9797310 TTTTTTTT-TTTTTTGGGTTTG
1 TTTTTTTTGTTTTTTGGCTTTG
9797331 TAAAAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.02, C:0.02, G:0.20, T:0.76
Consensus pattern (24 bp):
TTTTTTTTGTTTTTTGGCTTTGGA
Found at i:9798404 original size:2 final size:2
Alignment explanation
Indices: 9798397--9798429 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9798387 TTCACACCCT
9798397 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 A
9798430 ATGAACATTG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9803813 original size:19 final size:19
Alignment explanation
Indices: 9803791--9803828 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9803781 TTATGTTTTG
*
9803791 AAATATAATT-TATATAAAA
1 AAATACAATTATA-ATAAAA
9803810 AAATACAATTATAATAAAA
1 AAATACAATTATAATAAAA
9803829 CGTTACATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATACAATTATAATAAAA
Found at i:9803846 original size:2 final size:2
Alignment explanation
Indices: 9803839--9803866 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9803829 CGTTACATTC
9803839 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
9803867 TATTAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9812130 original size:15 final size:17
Alignment explanation
Indices: 9812105--9812142 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
9812095 TAAATTTGGA
9812105 ATGATCTTAAACCCA-G
1 ATGATCTTAAACCCATG
*
9812121 ATGA-CTTAAATCCATG
1 ATGATCTTAAACCCATG
9812137 ATGATC
1 ATGATC
9812143 CTAATTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 9 0.47
17 1 0.05
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (17 bp):
ATGATCTTAAACCCATG
Found at i:9813962 original size:26 final size:26
Alignment explanation
Indices: 9813926--9813976 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
9813916 CTCAAAGAAT
*
9813926 TTTGATCTCTGTTGACAAATAATTCA
1 TTTGATATCTGTTGACAAATAATTCA
*
9813952 TTTGATATCTGTTGACAAATGATTC
1 TTTGATATCTGTTGACAAATAATTC
9813977 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (26 bp):
TTTGATATCTGTTGACAAATAATTCA
Found at i:9831326 original size:21 final size:21
Alignment explanation
Indices: 9831268--9831327 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
9831258 TGTTTTACTT
*
9831268 TTAATCTGAATTAT-TTTAATTA
1 TTAATCT-AATTATATTT-TTTA
*
9831290 TTAATCTATTTATATTTTTTA
1 TTAATCTAATTATATTTTTTA
* *
9831311 TTAATTTAATTCTATTT
1 TTAATCTAATTATATTT
9831328 ATAATTAGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 22 0.69
22 10 0.31
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (21 bp):
TTAATCTAATTATATTTTTTA
Found at i:9831931 original size:18 final size:19
Alignment explanation
Indices: 9831897--9831932 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9831887 AAATGTCTCA
*
9831897 TAAATTTATGTATTTTTAC
1 TAAATTTATGTACTTTTAC
9831916 TAAATTT-TGTACTTTTA
1 TAAATTTATGTACTTTTA
9831933 TTTTTAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (19 bp):
TAAATTTATGTACTTTTAC
Found at i:9833153 original size:13 final size:14
Alignment explanation
Indices: 9833129--9833162 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
9833119 TTTATTTTTA
9833129 TAAATTATAATAAT
1 TAAATTATAATAAT
*
9833143 TAAATTA-AATATT
1 TAAATTATAATAAT
9833156 TAAATTA
1 TAAATTA
9833163 GCTTAGATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAATTATAATAAT
Found at i:9850142 original size:18 final size:18
Alignment explanation
Indices: 9850115--9850163 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
9850105 TTTCTTTTTC
*
9850115 AATTTGTAATTAATTTAA
1 AATTTTTAATTAATTTAA
9850133 AATTTTTAATT-ATTTAA
1 AATTTTTAATTAATTTAA
*
9850150 ATTTATTTAATTAA
1 AATT-TTTAATTAA
9850164 AATTTATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 9 0.33
18 17 0.63
19 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
AATTTTTAATTAATTTAA
Found at i:9855859 original size:50 final size:50
Alignment explanation
Indices: 9855800--9855901 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
9855790 TTTGCCAGCT
9855800 CAACATTAGCATCTGCAAAAACAATTAAAAAAATCCACATATATCCAGTC
1 CAACATTAGCATCTGCAAAAACAATTAAAAAAATCCACATATATCCAGTC
* *
9855850 CAACATTAGCATCTGCAAAAACAATTAAAATAATCCACATGTATCCAGTC
1 CAACATTAGCATCTGCAAAAACAATTAAAAAAATCCACATATATCCAGTC
9855900 CA
1 CA
9855902 CCTTGTTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.23
Consensus pattern (50 bp):
CAACATTAGCATCTGCAAAAACAATTAAAAAAATCCACATATATCCAGTC
Found at i:9860433 original size:137 final size:138
Alignment explanation
Indices: 9860186--9860461 Score: 430
Period size: 137 Copynumber: 2.0 Consensus size: 138
9860176 AAACAGCTAA
* *
9860186 AAAATGAAATCAATTATGAAATGCATTACATTCAAAACAACGATAAACAAAATATGGATATAACA
1 AAAATGAAATCAATTATGAAATGCATTACATTCAAAACAACAATAAACAAAAGATGGATATAACA
* *
9860251 CTAGCTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTG-AGATATGAA
66 CTAACTACAAAAGTAATTTAACAATATCATGTAGAAACAAGTTCACATGAAAGTGCA-ATATGAA
*
9860315 AGATATGCC
130 AGACATGCC
* ** ** *
9860324 AAAATGAAATCATTTATGGCATGTGTTACATTCAAAATAACAAT-AACAAAAGATGGATATAACA
1 AAAATGAAATCAATTATGAAATGCATTACATTCAAAACAACAATAAACAAAAGATGGATATAACA
9860388 CTAACTACAAAAGTAATTTAACAATATCATGTAGAAACAAGTTCACATGAAAGTGCAATATGAAA
66 CTAACTACAAAAGTAATTTAACAATATCATGTAGAAACAAGTTCACATGAAAGTGCAATATGAAA
9860453 GACATGCC
131 GACATGCC
9860461 A
1 A
9860462 TTTTCTGAAA
Statistics
Matches: 126, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
137 88 0.70
138 38 0.30
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (138 bp):
AAAATGAAATCAATTATGAAATGCATTACATTCAAAACAACAATAAACAAAAGATGGATATAACA
CTAACTACAAAAGTAATTTAACAATATCATGTAGAAACAAGTTCACATGAAAGTGCAATATGAAA
GACATGCC
Found at i:9863355 original size:16 final size:17
Alignment explanation
Indices: 9863334--9863370 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
9863324 TAAAACAAAT
9863334 ATTAAAAAATA-ATTAA
1 ATTAAAAAATACATTAA
*
9863350 ATT-AAAAATACATTAT
1 ATTAAAAAATACATTAA
9863366 ATTAA
1 ATTAA
9863371 GATAGTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 10 0.56
17 1 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTAAAAAATACATTAA
Found at i:9863553 original size:25 final size:22
Alignment explanation
Indices: 9863505--9863554 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 22
9863495 AAATAACAGC
*
9863505 AAAAATAATAGAAAAAATAGCA
1 AAAAATAATAGAAAAAATACCA
*
9863527 AAAAATAATAATAAAAACAGTACCA
1 AAAAATAAT-AGAAAAA-A-TACCA
9863552 AAA
1 AAA
9863555 TAGTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
23 6 0.26
24 1 0.04
25 7 0.30
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (22 bp):
AAAAATAATAGAAAAAATACCA
Found at i:9863591 original size:22 final size:22
Alignment explanation
Indices: 9863566--9863614 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
9863556 AGTAAAAAAC
9863566 AACAACAAAAAATAGC-A-ACCAA
1 AACAA-AAAAAATA-CAACACCAA
*
9863588 AACAATAAAAATACAACACCAA
1 AACAAAAAAAATACAACACCAA
9863610 AACAA
1 AACAA
9863615 TAATATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.04
21 8 0.33
22 15 0.62
ACGTcount: A:0.69, C:0.22, G:0.02, T:0.06
Consensus pattern (22 bp):
AACAAAAAAAATACAACACCAA
Found at i:9863597 original size:35 final size:37
Alignment explanation
Indices: 9863548--9863616 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 37
9863538 TAAAAACAGT
* *
9863548 ACCAAAATAGTAAAAA-ACAACAACAAAA-AATAGCA
1 ACCAAAACAATAAAAATACAACAACAAAACAATAGCA
*
9863583 ACCAAAACAATAAAAATACAACACCAAAACAATA
1 ACCAAAACAATAAAAATACAACAACAAAACAATA
9863617 ATATAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 14 0.48
36 11 0.38
37 4 0.14
ACGTcount: A:0.68, C:0.20, G:0.03, T:0.09
Consensus pattern (37 bp):
ACCAAAACAATAAAAATACAACAACAAAACAATAGCA
Found at i:9864351 original size:15 final size:15
Alignment explanation
Indices: 9864308--9864351 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
9864298 ATAATTATTT
*
9864308 TTTTAAAGTTAATTAA
1 TTTTAAA-TTAAATAA
9864324 TTTTAAA-TAAATAA
1 TTTTAAATTAAATAA
9864338 TTTTAAATTAAATA
1 TTTTAAATTAAATA
9864352 TTATAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.50
15 6 0.23
16 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
TTTTAAATTAAATAA
Found at i:9864755 original size:17 final size:19
Alignment explanation
Indices: 9864735--9864781 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
9864725 AATAATAGAT
*
9864735 ATTTAAAAAA-TCA-ACAA
1 ATTTAAAAAATTCATAAAA
9864752 ATTTAAAAAATTCATAAAA
1 ATTTAAAAAATTCATAAAA
9864771 ATTTTAAAAAA
1 A-TTTAAAAAA
9864782 ATTTATCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 10 0.38
18 3 0.12
19 4 0.15
20 9 0.35
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTTAAAAAATTCATAAAA
Found at i:9866435 original size:18 final size:19
Alignment explanation
Indices: 9866387--9866435 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
9866377 ATTAAATTCT
*
9866387 TTTAAAATTTA-AAAATAA
1 TTTAAAAATTATAAAATAA
*
9866405 TTTAAAAA-CATAAAA-AA
1 TTTAAAAATTATAAAATAA
9866422 TTTAAAAATTATAA
1 TTTAAAAATTATAA
9866436 CTTTTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTAAAAATTATAAAATAA
Found at i:9866836 original size:8 final size:8
Alignment explanation
Indices: 9866825--9866865 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
9866815 TAAATTTTTA
9866825 AAAATTAT
1 AAAATTAT
*
9866833 AAAAATAT
1 AAAATTAT
*
9866841 AAAAATAT
1 AAAATTAT
*
9866849 AAAATAAT
1 AAAATTAT
9866857 AAAATTAT
1 AAAATTAT
9866865 A
1 A
9866866 TTTTTACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAATTAT
Found at i:9867080 original size:30 final size:28
Alignment explanation
Indices: 9867046--9867176 Score: 81
Period size: 29 Copynumber: 4.6 Consensus size: 28
9867036 TTGAGTCTCC
9867046 TAAAAGTTGATAAAAATAAATTTGAGCCCT
1 TAAAAGTTGA-AAAAA-AAATTTGAGCCCT
* *
9867076 TAAAAATT-AAAAAAAAA-TTGAGGTCCT
1 TAAAAGTTGAAAAAAAAATTTGA-GCCCT
* * * *
9867103 TGAAAGTTGCTAAAAAAAATTTTA-ACCT
1 TAAAAGTTG-AAAAAAAAATTTGAGCCCT
* * *
9867131 ATAAAAGTTTAAAAAAAAAATTTAAACCCCT
1 -TAAAAG-TTGAAAAAAAAATTT-GAGCCCT
*
9867162 TAAAA-TTTAAAAAAA
1 TAAAAGTTGAAAAAAA
9867177 TAAAAATTTA
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
26 4 0.05
27 13 0.16
28 17 0.21
29 25 0.31
30 18 0.22
31 3 0.04
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.28
Consensus pattern (28 bp):
TAAAAGTTGAAAAAAAAATTTGAGCCCT
Found at i:9867149 original size:29 final size:28
Alignment explanation
Indices: 9867114--9867176 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
9867104 GAAAGTTGCT
*
9867114 AAAAAAAATTTTAA-CCTATAAAAGTTTAA
1 AAAAAAAATTTAAACCCT-TAAAA-TTTAA
9867143 AAAAAAAATTTAAACCCCTTAAAATTTAA
1 AAAAAAAATTTAAA-CCCTTAAAATTTAA
9867172 AAAAA
1 AAAAA
9867177 TAAAAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 23 0.74
30 5 0.16
31 3 0.10
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAAAAATTTAAACCCTTAAAATTTAA
Found at i:9873654 original size:2 final size:2
Alignment explanation
Indices: 9873647--9873689 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
9873637 AAAGTTTAAA
*
9873647 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9873689 A
1 A
9873690 AGAAAACATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9884304 original size:29 final size:28
Alignment explanation
Indices: 9884236--9884315 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
9884226 TTTTTTTTAA
*
9884236 TTTTATATTTTCTTAAAATTTTATAATTT
1 TTTTCTATTTT-TTAAAATTTTATAATTT
*
9884265 TTTTCTATTTTTTAATAATTTTGTAA-TT
1 TTTTCTATTTTTTAA-AATTTTATAATTT
*
9884293 TTTTGTACTTTTTTAAATATTTT
1 TTTTCTA-TTTTTTAAA-ATTTT
9884316 TTTAAATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 13 0.29
29 32 0.71
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.68
Consensus pattern (28 bp):
TTTTCTATTTTTTAAAATTTTATAATTT
Found at i:9884316 original size:39 final size:40
Alignment explanation
Indices: 9884273--9884373 Score: 109
Period size: 39 Copynumber: 2.6 Consensus size: 40
9884263 TTTTTTCTAT
* *
9884273 TTTTTAAT-AATTTTGTAATTTTTTGTA-CTTTTTTAAATA
1 TTTTTAATAAATTTTGTAATTTTTTCTATC-CTTTTAAATA
* * * *
9884312 TTTTT-TTAAATTTTATATTTTTTTCTATCCTTTTAAGTA
1 TTTTTAATAAATTTTGTAATTTTTTCTATCCTTTTAAATA
*
9884351 ATTTTAATAAATTTTGTAATTTT
1 TTTTTAATAAATTTTGTAATTTT
9884374 AAAAAAGAGT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
38 1 0.02
39 33 0.67
40 15 0.31
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (40 bp):
TTTTTAATAAATTTTGTAATTTTTTCTATCCTTTTAAATA
Found at i:9892580 original size:19 final size:20
Alignment explanation
Indices: 9892542--9892581 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
9892532 AATAGTGTTT
* *
9892542 TTATCTTTTATTAATTATAA
1 TTATCATTTATTAATAATAA
9892562 TTATCATTT-TTAATAATAA
1 TTATCATTTATTAATAATAA
9892581 T
1 T
9892582 CTCTAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATCATTTATTAATAATAA
Found at i:9895180 original size:18 final size:16
Alignment explanation
Indices: 9895145--9895191 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 16
9895135 AATTTCTATA
*
9895145 TTATTTTAAAT-TTTT
1 TTATTTTAAATATTCT
9895160 TTATTTATAAAATATTCT
1 TTATTT-T-AAATATTCT
9895178 TTATTTTAAATATT
1 TTATTTTAAATATT
9895192 ACTTGCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.21
16 8 0.29
17 5 0.18
18 9 0.32
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTTTAAATATTCT
Found at i:9898684 original size:18 final size:17
Alignment explanation
Indices: 9898661--9898712 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 17
9898651 ATAACTTTCA
9898661 AAAGTAAAAGTTAAAAAT
1 AAAGTAAAA-TTAAAAAT
*
9898679 AAAGTAAAATTGAAAAT
1 AAAGTAAAATTAAAAAT
*
9898696 -AA-TAAAATTGAAAAT
1 AAAGTAAAATTAAAAAT
9898711 AA
1 AA
9898713 GAGAGAGCGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 13 0.41
16 3 0.09
17 7 0.22
18 9 0.28
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (17 bp):
AAAGTAAAATTAAAAAT
Found at i:9919604 original size:28 final size:28
Alignment explanation
Indices: 9919561--9919641 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
9919551 AAATATTTTT
9919561 TTTATAT-TTTTATAATTTATTAAATAAA-
1 TTTATATATTTT-TAATTT-TTAAATAAAG
*
9919589 TTTA-ATTATTTTTAATTTTTAAAAAAAG
1 TTTATA-TATTTTTAATTTTTAAATAAAG
*
9919617 TTTTTATATTTTTGAATTTTTAAAT
1 TTTATATATTTTT-AATTTTTAAAT
9919642 TTTAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 9 0.20
28 21 0.47
29 15 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTATATATTTTTAATTTTTAAATAAAG
Found at i:9919635 original size:29 final size:27
Alignment explanation
Indices: 9919559--9919640 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 27
9919549 AAAAATATTT
*
9919559 TTTTTATATTTTTATAATTTATTAAATAAA
1 TTTTTATA-TTTT-TAATTT-TTAAAAAAA
*
9919589 -TTTAATTATTTTTAATTTTTAAAAAAA
1 TTTTTA-TATTTTTAATTTTTAAAAAAA
9919616 GTTTTTATATTTTTGAATTTTTAAA
1 -TTTTTATATTTTT-AATTTTTAAA
9919641 TTTTAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 8 0.18
28 13 0.29
29 22 0.49
30 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTTATATTTTTAATTTTTAAAAAAA
Found at i:9923731 original size:30 final size:30
Alignment explanation
Indices: 9923633--9923707 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
9923623 CAAATTTAAA
9923633 TTAAAAATAATAAAATTATATTTTATTCTC
1 TTAAAAATAATAAAATTATATTTTATTCTC
9923663 TTAAAAATAATAAAATTATATTTTATTCTC
1 TTAAAAATAATAAAATTATATTTTATTCTC
9923693 TTAAAAATAATAAAA
1 TTAAAAATAATAAAA
9923708 ATTTGATTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATATTTTATTCTC
Found at i:9923749 original size:60 final size:60
Alignment explanation
Indices: 9923633--9923749 Score: 141
Period size: 60 Copynumber: 1.9 Consensus size: 60
9923623 CAAATTTAAA
* * **
9923633 TTAAAAATAATAAAATTATATTTTATTCTCTTAAAAATAATAAAATTATATTTTATTCTC
1 TTAAAAATAATAAAATTATATTTAACTCTCTTAAAAATAATAAAATTATAAGTTATTCTC
*
9923693 TTAAAAATAATAAAAATT-TGATTTAACTCT-TTAAAAATAGTAAACA-TATAAGTTATT
1 TTAAAAATAAT-AAAATTAT-ATTTAACTCTCTTAAAAATAATAAA-ATTATAAGTTATT
9923750 AAAATAATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
60 34 0.69
61 15 0.31
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (60 bp):
TTAAAAATAATAAAATTATATTTAACTCTCTTAAAAATAATAAAATTATAAGTTATTCTC
Found at i:9924507 original size:41 final size:41
Alignment explanation
Indices: 9924458--9924535 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
9924448 TCAATTCTTT
*
9924458 AAAAGATGATTACTCAACTACCTTTTAAAAGATTTTGCATG
1 AAAAGATGATTACTCAAATACCTTTTAAAAGATTTTGCATG
9924499 AAAAGATGATTACTCAAATACCTTTTAAAAGATTTTG
1 AAAAGATGATTACTCAAATACCTTTTAAAAGATTTTG
9924536 TATGTTACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (41 bp):
AAAAGATGATTACTCAAATACCTTTTAAAAGATTTTGCATG
Found at i:9941245 original size:58 final size:58
Alignment explanation
Indices: 9941174--9941289 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
9941164 ATCAACAAAC
* * *
9941174 TAAACTCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAA-AACACTTATAAAT
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCT-AAATAACACTCATAAAT
* *
9941232 TAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCATAAAT
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAT
9941290 AACTCTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
57 3 0.06
58 49 0.94
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (58 bp):
TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAT
Found at i:9941720 original size:53 final size:52
Alignment explanation
Indices: 9941626--9941726 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 52
9941616 TGAATTTATG
9941626 TTGTTTACTTGAACTTTTACTTATTTTTTTATTATAATTTTATTGTATTGTCA
1 TTGTTTACTTGAACTTTTACTTATTTTTTTA-TATAATTTTATTGTATTGTCA
* *
9941679 TTGTTTACTTGAATTTTTTCACTTATTTATTTTA-AT-TTTTTATTGTAT
1 TTGTTTACTTGAA-CTTTT-ACTTATTT-TTTTATATAATTTTATTGTAT
9941727 AATCATGTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
53 24 0.56
54 6 0.14
55 8 0.19
56 5 0.12
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (52 bp):
TTGTTTACTTGAACTTTTACTTATTTTTTTATATAATTTTATTGTATTGTCA
Found at i:9942344 original size:2 final size:2
Alignment explanation
Indices: 9942337--9942369 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9942327 CTTCCCCCTG
9942337 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
9942370 AATCCTATGC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:9948980 original size:7 final size:7
Alignment explanation
Indices: 9948968--9948992 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9948958 CGATTCGAAT
9948968 AATTTGA
1 AATTTGA
9948975 AATTTGA
1 AATTTGA
9948982 AATTTGA
1 AATTTGA
9948989 AATT
1 AATT
9948993 CGAATTTTTT
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:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
AATTTGA
Found at i:9949825 original size:2 final size:2
Alignment explanation
Indices: 9949818--9949876 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
9949808 AGTACAAATA
9949818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9949860 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
9949877 AATTAAACAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9950127 original size:30 final size:29
Alignment explanation
Indices: 9950092--9950224 Score: 104
Period size: 30 Copynumber: 4.4 Consensus size: 29
9950082 CAAAAAAATT
*
9950092 TTTTAGAAAGTTTAGGGGCCAAAATGCCA
1 TTTTAGAAAGTTTAGGGGCCAAAATGCAA
* * *
9950121 TCTTTAGAAAATTTAGGAGCCAAAATGTAA
1 T-TTTAGAAAGTTTAGGGGCCAAAATGCAA
* * **
9950151 TTATTAGAAAGTTTAGTGGTCAAAATATAA
1 TT-TTAGAAAGTTTAGGGGCCAAAATGCAA
* * * **
9950181 TTTTTAGAAATTTTAAGGGTCAAAATATAA
1 -TTTTAGAAAGTTTAGGGGCCAAAATGCAA
*
9950211 TTTTGGAAAAGTTT
1 TTTTAG-AAAGTTT
9950225 GGGATTAAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
29 7 0.08
30 77 0.90
31 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (29 bp):
TTTTAGAAAGTTTAGGGGCCAAAATGCAA
Found at i:9950187 original size:60 final size:58
Alignment explanation
Indices: 9950092--9950244 Score: 148
Period size: 60 Copynumber: 2.6 Consensus size: 58
9950082 CAAAAAAATT
* *** * *
9950092 TTTTAGAAAGTTTAGGGGCCAAAATGCCATCTTTAGAAAATTT-AGGAGCCAAAATGTAA
1 TTTTAGAAAGTTTA-GGGTCAAAATATAATTTTTAGAAAATTTAAGG-GCCAAAATATAA
* *
9950151 TTATTAGAAAGTTTAGTGGTCAAAATATAATTTTTAGAAATTTTAAGGGTCAAAATATAA
1 TT-TTAGAAAGTTTAG-GGTCAAAATATAATTTTTAGAAAATTTAAGGGCCAAAATATAA
* *
9950211 TTTTGGAAAAGTTT-GGGATTAAAATATAATTTTT
1 TTTTAG-AAAGTTTAGGG-TCAAAATATAATTTTT
9950245 TAAACAAAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
58 2 0.03
59 22 0.28
60 52 0.66
61 3 0.04
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.37
Consensus pattern (58 bp):
TTTTAGAAAGTTTAGGGTCAAAATATAATTTTTAGAAAATTTAAGGGCCAAAATATAA
Found at i:9951279 original size:21 final size:20
Alignment explanation
Indices: 9951253--9951297 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
9951243 AATAATAGTA
9951253 TTTGCTT-GCTCTGTTCTTGCT
1 TTTGCTTCG-TCTGTTCTT-CT
9951274 TTTGCTTCTGTCTGTTCTTCT
1 TTTGCTTC-GTCTGTTCTTCT
9951295 TTT
1 TTT
9951298 TTGCAGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.55
22 9 0.41
23 1 0.05
ACGTcount: A:0.00, C:0.22, G:0.16, T:0.62
Consensus pattern (20 bp):
TTTGCTTCGTCTGTTCTTCT
Found at i:9951861 original size:11 final size:11
Alignment explanation
Indices: 9951847--9951889 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
9951837 AGTTAAATAT
9951847 TATTTTATTAA
1 TATTTTATTAA
9951858 TATTTTACTTAA
1 TATTTTA-TTAA
9951870 -ATATTTATTAA
1 TAT-TTTATTAA
9951881 TATTTTATT
1 TATTTTATT
9951890 TAGAAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:9961348 original size:23 final size:23
Alignment explanation
Indices: 9961322--9961442 Score: 156
Period size: 23 Copynumber: 5.2 Consensus size: 23
9961312 ACACTAGCGC
9961322 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
9961345 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
9961368 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
9961393 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
9961416 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
9961439 GCTC
1 GCTC
9961443 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 62 0.72
24 1 0.01
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:9961391 original size:48 final size:46
Alignment explanation
Indices: 9961322--9961442 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
9961312 ACACTAGCGC
* *
9961322 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
9961368 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
*
9961416 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
9961443 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:9961471 original size:39 final size:39
Alignment explanation
Indices: 9961407--9961481 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
9961397 TCCGATTAGC
*
9961407 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
9961446 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
9961482 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:9961526 original size:22 final size:22
Alignment explanation
Indices: 9961441--9961556 Score: 106
Period size: 22 Copynumber: 5.0 Consensus size: 22
9961431 CTTTGTGTGC
* *
9961441 TCAGTACTTTGTGTACTCTCTGT
1 TCAGTACTTCG-GTGCTCTCTGT
* * *
9961464 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGTACTTCG-GTGCTCTCTGT
* **
9961487 TGCCCAGCACTTATGTGCTCTCTGT
1 T---CAGTACTTCGGTGCTCTCTGT
9961512 TCAGTACTTCGGTGCTCTCTGT
1 TCAGTACTTCGGTGCTCTCTGT
*
9961534 TCAGTACTTCGGTACTCTCTGT
1 TCAGTACTTCGGTGCTCTCTGT
9961556 T
1 T
9961557 TGTTCCGTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
22 40 0.50
23 21 0.26
25 12 0.15
26 7 0.09
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (22 bp):
TCAGTACTTCGGTGCTCTCTGT
Found at i:9964470 original size:6 final size:6
Alignment explanation
Indices: 9964459--9964489 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
9964449 CCCCACAATC
9964459 CATTTG CATTTG CATTTG CATTTG CATTTG C
1 CATTTG CATTTG CATTTG CATTTG CATTTG C
9964490 TTAATTGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
CATTTG
Found at i:9966293 original size:20 final size:22
Alignment explanation
Indices: 9966268--9966309 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9966258 ATTATTTTTC
*
9966268 TAAAATT-TAT-TTCAAATATA
1 TAAAATTATATATTAAAATATA
9966288 TAAAATTATATATTAAAATATA
1 TAAAATTATATATTAAAATATA
9966310 GATTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 9 0.47
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAATTATATATTAAAATATA
Found at i:9966592 original size:13 final size:13
Alignment explanation
Indices: 9966544--9966592 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
9966534 TTTAGATTAA
*
9966544 ACTTTTCATAAGT
1 ACTTTTCAAAAGT
*
9966557 ACTTTTCAAAA-C
1 ACTTTTCAAAAGT
*
9966569 ATTTTTCAAAAGT
1 ACTTTTCAAAAGT
9966582 ACTTTTCAAAA
1 ACTTTTCAAAA
9966593 ACAATGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:9967967 original size:22 final size:22
Alignment explanation
Indices: 9967922--9967970 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
9967912 TTAGGATAGA
**
9967922 AAATTAAGAGAAAGAGAGTTTG
1 AAATTAAGAGAAAGAGAGGATG
9967944 AAATTAAGAGAAA-AGATGGATG
1 AAATTAAGAGAAAGAGA-GGATG
9967966 AAATT
1 AAATT
9967971 GAACGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.22
Consensus pattern (22 bp):
AAATTAAGAGAAAGAGAGGATG
Found at i:9970342 original size:162 final size:164
Alignment explanation
Indices: 9970075--9970403 Score: 635
Period size: 162 Copynumber: 2.0 Consensus size: 164
9970065 CGAGGTGGGC
9970075 GTCCATGTCCATGTCTGCAACAACAATGATCACTACTTACGAGTTCCTCAAACGGCTCTCAGCTA
1 GTCCATGTCCATGTCTGCAACAACAATGATCACTACTTACGAGTTCCTCAAACGGCTCTCAGCTA
*
9970140 AGAACCAAGAGAGCTTGGTGTAATTACATCCAGATG-AAAAAAAATTAGTGAAAACAGAGGTTTC
66 AGAACCAAGAGAGCTTGGTGTAATTACATCAAGATGAAAAAAAAATTAGTGAAAACAGAGGTTTC
9970204 -TTTTTCCCCTTCATTTTGGGTTCTTTGATATTT
131 TTTTTTCCCCTTCATTTTGGGTTCTTTGATATTT
9970237 GTCCATGTCCATGTCTGCAACAACAATGATCACTACTTACGAGTTCCTCAAACGGCTCTCAGCTA
1 GTCCATGTCCATGTCTGCAACAACAATGATCACTACTTACGAGTTCCTCAAACGGCTCTCAGCTA
9970302 AGAACCAAGAGAGCTTGGTGTAATTACATCAAGATGAAAAAAAAATTAGTGAAAACAGAGGTTTC
66 AGAACCAAGAGAGCTTGGTGTAATTACATCAAGATGAAAAAAAAATTAGTGAAAACAGAGGTTTC
9970367 TTTTTTCCCCTTCATTTTGGGTTCTTTGATATTT
131 TTTTTTCCCCTTCATTTTGGGTTCTTTGATATTT
9970401 GTC
1 GTC
9970404 TAAATCAAGC
Statistics
Matches: 164, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
162 100 0.61
163 28 0.17
164 36 0.22
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (164 bp):
GTCCATGTCCATGTCTGCAACAACAATGATCACTACTTACGAGTTCCTCAAACGGCTCTCAGCTA
AGAACCAAGAGAGCTTGGTGTAATTACATCAAGATGAAAAAAAAATTAGTGAAAACAGAGGTTTC
TTTTTTCCCCTTCATTTTGGGTTCTTTGATATTT
Found at i:9990732 original size:2 final size:2
Alignment explanation
Indices: 9990725--9990766 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
9990715 TGATTGCGTC
9990725 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9990767 TGTTCAAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9997524 original size:13 final size:13
Alignment explanation
Indices: 9997506--9997538 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
9997496 CCCAATTAAT
9997506 AAATAT-TAAACAA
1 AAATATGTAAA-AA
9997519 AAATATGTAAAAA
1 AAATATGTAAAAA
9997532 AAATATG
1 AAATATG
9997539 GACGATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (13 bp):
AAATATGTAAAAA
Found at i:10008181 original size:15 final size:16
Alignment explanation
Indices: 10008147--10008184 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
10008137 ACCAAATTAT
10008147 AAAATATTACAAAAAA
1 AAAATATTACAAAAAA
* *
10008163 AAAATATT-CAATAAC
1 AAAATATTACAAAAAA
10008178 AAAATAT
1 AAAATAT
10008185 AAAAATAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATATTACAAAAAA
Found at i:10008196 original size:22 final size:21
Alignment explanation
Indices: 10008155--10008196 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
10008145 ATAAAATATT
*
10008155 ACAAAAAAAAAATATTCAATA
1 ACAAAAAAAAAATATGCAATA
10008176 ACAAAATATAAAAATA-GCAAT
1 ACAAAA-A-AAAAATATGCAAT
10008197 GGTGCACGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (21 bp):
ACAAAAAAAAAATATGCAATA
Found at i:10022920 original size:3 final size:3
Alignment explanation
Indices: 10022912--10022938 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
10022902 CTCTAATTTC
10022912 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
10022939 TATTTAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:10037503 original size:46 final size:46
Alignment explanation
Indices: 10037447--10037560 Score: 183
Period size: 46 Copynumber: 2.5 Consensus size: 46
10037437 AGTGCTGGAG
* *
10037447 AAACAGTAAGCACACACAGTGCAAATCAGTAGGCACACATAGTGCA
1 AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACACATAGTACA
*
10037493 AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACATATAGTACA
1 AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACACATAGTACA
* *
10037539 AATCAATAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
10037561 TGAACAGTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.14
Consensus pattern (46 bp):
AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACACATAGTACA
Found at i:10037572 original size:23 final size:23
Alignment explanation
Indices: 10037450--10037560 Score: 159
Period size: 23 Copynumber: 4.8 Consensus size: 23
10037440 GCTGGAGAAA
10037450 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
10037473 CAGTAGGCACACATAGTGCAAAA
1 CAGTAAGCACACACAGTGCAAAT
10037496 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
10037519 CAGTAAGCACATATAGTACAAAT
1 CAGTAAGCACACACAGTGCAAAT
*
10037542 CAATAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
10037561 TGAACAGTAA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.14
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:10037864 original size:76 final size:76
Alignment explanation
Indices: 10037773--10037921 Score: 289
Period size: 76 Copynumber: 2.0 Consensus size: 76
10037763 ATTTTCAAAA
*
10037773 CTGTCCATTTGAGTCACAGTGACTAAATTATTTATATCTTGAGCTACAGAATTCAAAATTATTAT
1 CTGTCCATTTGAGTCACAGTCACTAAATTATTTATATCTTGAGCTACAGAATTCAAAATTATTAT
10037838 CCGCTTGAAAG
66 CCGCTTGAAAG
10037849 CTGTCCATTTGAGTCACAGTCACTAAATTATTTATATCTTGAGCTACAGAATTCAAAATTATTAT
1 CTGTCCATTTGAGTCACAGTCACTAAATTATTTATATCTTGAGCTACAGAATTCAAAATTATTAT
10037914 CCGCTTGA
66 CCGCTTGA
10037922 TGTTTCTAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.36
Consensus pattern (76 bp):
CTGTCCATTTGAGTCACAGTCACTAAATTATTTATATCTTGAGCTACAGAATTCAAAATTATTAT
CCGCTTGAAAG
Found at i:10041280 original size:12 final size:12
Alignment explanation
Indices: 10041247--10041288 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
10041237 TGGTTGAAGT
10041247 TAATAA-AATAA
1 TAATAACAATAA
10041258 -AATAA-AATAA
1 TAATAACAATAA
*
10041268 TGATAACAATAA
1 TAATAACAATAA
10041280 TAATAACAA
1 TAATAACAA
10041289 AATCTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 10 0.37
11 4 0.15
12 13 0.48
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (12 bp):
TAATAACAATAA
Found at i:10044806 original size:2 final size:2
Alignment explanation
Indices: 10044794--10044854 Score: 113
Period size: 2 Copynumber: 30.0 Consensus size: 2
10044784 AATTTTCATC
10044794 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10044837 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
10044855 GTATCTTATG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 56 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10047328 original size:5 final size:5
Alignment explanation
Indices: 10047318--10047355 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
10047308 GACTAAATTA
10047318 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT CCC
1 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT CCC
10047356 AAAACTACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.82, G:0.00, T:0.18
Consensus pattern (5 bp):
CCCCT
Found at i:10047643 original size:17 final size:17
Alignment explanation
Indices: 10047621--10047654 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
10047611 GTAATACTTT
10047621 TCAAAAATATTTTTGAG
1 TCAAAAATATTTTTGAG
10047638 TCAAAAATATTTTTGAG
1 TCAAAAATATTTTTGAG
10047655 AAAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TCAAAAATATTTTTGAG
Found at i:10047660 original size:17 final size:17
Alignment explanation
Indices: 10047623--10047660 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
10047613 AATACTTTTC
**
10047623 AAAAATATTTTTGAGTC
1 AAAAATATTTTTGAGAA
10047640 AAAAATATTTTTGAGAA
1 AAAAATATTTTTGAGAA
10047657 AAAA
1 AAAA
10047661 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (17 bp):
AAAAATATTTTTGAGAA
Found at i:10054589 original size:88 final size:88
Alignment explanation
Indices: 10054428--10054590 Score: 229
Period size: 88 Copynumber: 1.9 Consensus size: 88
10054418 CTTTTTGATG
* * * * **
10054428 CATTTTGAAAGTTTAAATATTCAATTAAGTGCAAAATAAAAGCAAGAGTTTAATTGTTTTTTTTT
1 CATTTTGAAAGTTCAAATATCCAATTAAGTGCAAAATAAAAACAAGAATTTAATTGTTTTTTTAA
*
10054493 TAAATTTGAGGGTCATTTCTATA
66 AAAATTTGAGGGTCATTTCTATA
* *
10054516 CATTTTGAAAGTTCAAATATCCAATTGAGTGCAAAATAAAAACAATAATTTAATTG-TTTTTTAA
1 CATTTTGAAAGTTCAAATATCCAATTAAGTGCAAAATAAAAACAAGAATTTAATTGTTTTTTTAA
10054580 AAAAGTTTGAG
66 AAAA-TTTGAG
10054591 ACTTTTTACG
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
87 9 0.14
88 56 0.86
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (88 bp):
CATTTTGAAAGTTCAAATATCCAATTAAGTGCAAAATAAAAACAAGAATTTAATTGTTTTTTTAA
AAAATTTGAGGGTCATTTCTATA
Found at i:10055947 original size:5 final size:5
Alignment explanation
Indices: 10055912--10055952 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
10055902 TTTAGTGATT
10055912 TAATA TAAATA TAAT- TACATA TAAT- TAATA TAATA TAATA T
1 TAATA T-AATA TAATA TA-ATA TAATA TAATA TAATA TAATA T
10055953 TCGGGTCGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 6 0.19
5 19 0.59
6 7 0.22
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:10057930 original size:44 final size:45
Alignment explanation
Indices: 10057873--10058015 Score: 134
Period size: 44 Copynumber: 3.2 Consensus size: 45
10057863 AAACAATAGT
* * * *
10057873 AAAAAC-GCA-TAAAAATAACATCCAAA-CAACTAAAATAACAAC
1 AAAAACAGCAGTAAAAATAACAACAAAATAAACAAAAATAACAAC
* *
10057915 CAAAACAGCAGT-AAAACAACAACAAAATAAACAAAAATAACAAC
1 AAAAACAGCAGTAAAAATAACAACAAAATAAACAAAAATAACAAC
* * * *
10057959 AAAAACAACAGAAAAAATGACAACAAAAATAGCAACAAAAATAATAAC
1 AAAAACAGCAGTAAAAATAACAAC-AAAATA--AACAAAAATAACAAC
10058007 -AAAACAGCA
1 AAAAACAGCA
10058016 CAAAAACAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
42 5 0.06
43 15 0.19
44 24 0.30
45 9 0.11
46 6 0.07
47 8 0.10
48 14 0.17
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.08
Consensus pattern (45 bp):
AAAAACAGCAGTAAAAATAACAACAAAATAAACAAAAATAACAAC
Found at i:10057959 original size:12 final size:12
Alignment explanation
Indices: 10057927--10058010 Score: 86
Period size: 12 Copynumber: 7.2 Consensus size: 12
10057917 AAACAGCAGT
*
10057927 AAAACAACAAC-
1 AAAATAACAACA
10057938 AAAAT-A-AACA
1 AAAATAACAACA
10057948 AAAATAACAACA
1 AAAATAACAACA
*
10057960 AAAACAACAGA-A
1 AAAATAACA-ACA
*
10057972 AAAATGACAACA
1 AAAATAACAACA
*
10057984 AAAATAGCAACA
1 AAAATAACAACA
*
10057996 AAAATAATAACA
1 AAAATAACAACA
10058008 AAA
1 AAA
10058011 CAGCACAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
9 3 0.05
10 6 0.10
11 6 0.10
12 44 0.73
13 1 0.02
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:10057968 original size:21 final size:21
Alignment explanation
Indices: 10057883--10058010 Score: 89
Period size: 21 Copynumber: 5.8 Consensus size: 21
10057873 AAAAACGCAT
* *
10057883 AAAAATAACATC-CAAACAAC
1 AAAAATAACAACAAAAACAAC
* * *
10057903 TAAAATAACAACCAAAACAGC
1 AAAAATAACAACAAAAACAAC
*
10057924 AGTAAAACAACAACAAAATA-AAC
1 A--AAAATAACAACAAAA-ACAAC
10057947 AAAAATAACAACAAAAACAAC
1 AAAAATAACAACAAAAACAAC
*
10057968 AGAAAAAATGACAACAAAAATAGCAAC
1 ---AAAAATAACAAC-AAAA-A-CAAC
*
10057995 AAAAATAATAACAAAA
1 AAAAATAACAACAAAA
10058011 CAGCACAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 19
0.73 0.10 0.16
Matches are distributed among these distances:
20 11 0.13
21 23 0.27
23 20 0.24
24 22 0.26
25 4 0.05
26 1 0.01
27 4 0.05
ACGTcount: A:0.70, C:0.18, G:0.04, T:0.09
Consensus pattern (21 bp):
AAAAATAACAACAAAAACAAC
Found at i:10058105 original size:21 final size:21
Alignment explanation
Indices: 10058033--10058107 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
10058023 AATTAAAAGT
*
10058033 ACCAAAACAGTAAAAAAAATAAC
1 ACCAAAACAGT--AAAAAATAGC
* * * *
10058056 ATCAAAATAATAAAAAATAGTA
1 ACCAAAACAGTAAAAAATAG-C
*
10058078 ACTAAAACAGTAAAAAATAGC
1 ACCAAAACAGTAAAAAATAGC
10058099 ACCAAAACA
1 ACCAAAACA
10058108 ATAATATAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
21 16 0.40
22 16 0.40
23 8 0.20
ACGTcount: A:0.67, C:0.15, G:0.05, T:0.13
Consensus pattern (21 bp):
ACCAAAACAGTAAAAAATAGC
Found at i:10058883 original size:25 final size:23
Alignment explanation
Indices: 10058837--10058883 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
10058827 ATTCGAAAAT
* *
10058837 AAATAATTAAATTTTATATATAC
1 AAATAATTAAAATTTACATATAC
10058860 AAATAATATAAAATTTACAGTATA
1 AAATAAT-TAAAATTTACA-TATA
10058884 TTTTAACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 9 0.45
25 4 0.20
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATAATTAAAATTTACATATAC
Found at i:10060400 original size:29 final size:29
Alignment explanation
Indices: 10060325--10060415 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 29
10060315 TCAAATTTGT
*
10060325 TTTAT-TTTAATAT-ATATATTTTGTATTA
1 TTTATGTTTAATATCATAT-TTTTATATTA
*
10060353 TTTAAAAGATTT-ATA-CATATTTTTATATTA
1 TTT--ATG-TTTAATATCATATTTTTATATTA
*
10060383 TTTATGTTTAATATCATATTTTCATAATTA
1 TTTATGTTTAATATCATATTTTTAT-ATTA
10060413 TTT
1 TTT
10060416 TTAACTCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
27 3 0.06
28 8 0.16
29 10 0.20
30 20 0.39
31 7 0.14
32 3 0.06
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (29 bp):
TTTATGTTTAATATCATATTTTTATATTA
Found at i:10061115 original size:4 final size:4
Alignment explanation
Indices: 10061102--10061135 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
10061092 TAAACTTCAA
10061102 AAAG -AAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
10061136 AAAAACCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:10070155 original size:2 final size:2
Alignment explanation
Indices: 10070148--10070182 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10070138 GTAAAAAGGA
10070148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10070183 ATGTAAAAGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10071131 original size:3 final size:3
Alignment explanation
Indices: 10071123--10071156 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
10071113 GTTGAAACAA
10071123 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
10071157 CAATTTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:10075045 original size:6 final size:6
Alignment explanation
Indices: 10075034--10075061 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
10075024 CTTGTAATGA
10075034 TCCATC TCCATC TCCATC TCCATC TCCA
1 TCCATC TCCATC TCCATC TCCATC TCCA
10075062 AGACAGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.50, G:0.00, T:0.32
Consensus pattern (6 bp):
TCCATC
Found at i:10076303 original size:30 final size:30
Alignment explanation
Indices: 10076267--10076323 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
10076257 AAGTTGTTTC
*
10076267 TTGCTGCTGCTG-TGGCTGCTGTTGTTGTAA
1 TTGCTGCTGCTGCT-GCAGCTGTTGTTGTAA
10076297 TTGCTGCTGCTGCTGCAGCTGTTGTTG
1 TTGCTGCTGCTGCTGCAGCTGTTGTTG
10076324 CTGATGATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.05, C:0.19, G:0.33, T:0.42
Consensus pattern (30 bp):
TTGCTGCTGCTGCTGCAGCTGTTGTTGTAA
Found at i:10076309 original size:6 final size:6
Alignment explanation
Indices: 10076298--10076455 Score: 64
Period size: 6 Copynumber: 26.3 Consensus size: 6
10076288 TTGTTGTAAT
* * * * * **
10076298 TGCTGC TGCTGC TGCAGC TGTTGT TGCTGA TGATGC AACTGC TGCTGC
1 TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC
** ** * * * *** **
10076346 AACTGC AACTGT TGCTGT TGTTGC TGCTGC TGCTGC AATTGC AACTGC
1 TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC
* * * *** ** *
10076394 TGCTGT TGTTGT TGCTGC TGCTGC TGCAAT TGCAAC TGCTGC TGTTGC
1 TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC
10076442 TGCTGC TGCTGC TG
1 TGCTGC TGCTGC TG
10076456 GTTCATGTAA
Statistics
Matches: 113, Mismatches: 39, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
6 113 1.00
ACGTcount: A:0.11, C:0.25, G:0.29, T:0.35
Consensus pattern (6 bp):
TGCTGC
Found at i:10076326 original size:39 final size:39
Alignment explanation
Indices: 10076268--10076368 Score: 103
Period size: 39 Copynumber: 2.6 Consensus size: 39
10076258 AGTTGTTTCT
* * * * *
10076268 TGCTGCTGCTGTGGCTGCTGTTGTTGTAATTGCTGCTGC
1 TGCTGCAGCTGTTGCTGCTGTTGATGCAACTGCTGCTGC
* *
10076307 TGCTGCAGCTGTTGTTGCTGATGATGCAACTGCTGCTGC
1 TGCTGCAGCTGTTGCTGCTGTTGATGCAACTGCTGCTGC
** * *
10076346 AACTGCAACTGTTGCTGTTGTTG
1 TGCTGCAGCTGTTGCTGCTGTTG
10076369 CTGCTGCTGC
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.11, C:0.21, G:0.31, T:0.38
Consensus pattern (39 bp):
TGCTGCAGCTGTTGCTGCTGTTGATGCAACTGCTGCTGC
Done.