Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 99 of 199
Found at i:27982806 original size:24 final size:24
Alignment explanation
Indices: 27982761--27982829 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
27982751 CCTCGAGGTT
* **
27982761 AAATGATTGATTTGTCCATGATGA
1 AAATGACTGATTTGTCTGTGATGA
* **
27982785 AAATGACTGATTTGACTGTGATTT
1 AAATGACTGATTTGTCTGTGATGA
*
27982809 AAATGACTGTTTTGTCTGTGA
1 AAATGACTGATTTGTCTGTGA
27982830 ATTGTATGAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (24 bp):
AAATGACTGATTTGTCTGTGATGA
Found at i:27982838 original size:24 final size:24
Alignment explanation
Indices: 27982785--27982844 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
27982775 TCCATGATGA
*
27982785 AAATGACTGATTTGACTGTGATTT
1 AAATGACTGATTTGACTGTGAATT
* *
27982809 AAATGACTGTTTTGTCTGTGAATT
1 AAATGACTGATTTGACTGTGAATT
**
27982833 GTATGACTGATT
1 AAATGACTGATT
27982845 CTGAGCATGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (24 bp):
AAATGACTGATTTGACTGTGAATT
Found at i:27983071 original size:32 final size:33
Alignment explanation
Indices: 27983020--27983173 Score: 156
Period size: 32 Copynumber: 4.8 Consensus size: 33
27983010 GCGATGATGT
*
27983020 TGATGGCTTTGTGCTGATCATATTACCGTC-AC
1 TGATGGCTTTGTGCCGATCATATTACCGTCTAC
* * * *
27983052 TGATGGCTGTGTACCGATCATATCACTG-CTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTCTAC
* *
27983084 TGATGGCTTTCTGCCTATCATATTACCGT-TAC
1 TGATGGCTTTGTGCCGATCATATTACCGTCTAC
* * * *
27983116 TGATGGATGTGTGCCGGTCATATCA-C-TACTAC
1 TGATGGCTTTGTGCCGATCATATTACCGT-CTAC
*
27983148 TGATGGCTTTGTGCCAATCATATTAC
1 TGATGGCTTTGTGCCGATCATATTAC
27983174 TATATTTATG
Statistics
Matches: 95, Mismatches: 22, Indels: 9
0.75 0.17 0.07
Matches are distributed among these distances:
30 1 0.01
31 2 0.02
32 92 0.97
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (33 bp):
TGATGGCTTTGTGCCGATCATATTACCGTCTAC
Found at i:27983121 original size:64 final size:64
Alignment explanation
Indices: 27983020--27983173 Score: 229
Period size: 64 Copynumber: 2.4 Consensus size: 64
27983010 GCGATGATGT
* *
27983020 TGATGGCTTTGTG-CTGATCATATTACCGTCACTGATGGCTGTGTACCGATCATATCACTGCTAC
1 TGATGGCTTTGTGCCT-ATCATATTACCGTCACTGATGGATGTGTACCGATCATATCACTACTAC
* * * *
27983084 TGATGGCTTTCTGCCTATCATATTACCGTTACTGATGGATGTGTGCCGGTCATATCACTACTAC
1 TGATGGCTTTGTGCCTATCATATTACCGTCACTGATGGATGTGTACCGATCATATCACTACTAC
*
27983148 TGATGGCTTTGTGCCAATCATATTAC
1 TGATGGCTTTGTGCCTATCATATTAC
27983174 TATATTTATG
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
64 79 0.98
65 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (64 bp):
TGATGGCTTTGTGCCTATCATATTACCGTCACTGATGGATGTGTACCGATCATATCACTACTAC
Found at i:27987509 original size:40 final size:40
Alignment explanation
Indices: 27987461--27987767 Score: 569
Period size: 40 Copynumber: 7.7 Consensus size: 40
27987451 GCAAACACAT
* *
27987461 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
27987501 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
27987541 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
27987581 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
27987621 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
27987661 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
27987701 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
27987741 TTGCCTTCGGGTCTTAGCCCGGGTATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
27987768 ATCCAATGCT
Statistics
Matches: 260, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 260 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:28009671 original size:15 final size:16
Alignment explanation
Indices: 28009645--28009674 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28009635 TAGAAAATGC
28009645 TTCTTCTTTTTTTCTT
1 TTCTTCTTTTTTTCTT
28009661 TTCTT-TTTTTTTCT
1 TTCTTCTTTTTTTCT
28009675 AAAGTAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTCTTCTTTTTTTCTT
Found at i:28012174 original size:30 final size:30
Alignment explanation
Indices: 28012138--28012228 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
28012128 GCTCGAACGG
* *
28012138 GTAACCTTGATATAATTTCATCTTGTGTGA
1 GTAACCTTGATATAATGTCAACTTGTGTGA
*
28012168 GTAACCTTGATATAATGTCAGCTTGTGTGA
1 GTAACCTTGATATAATGTCAACTTGTGTGA
* * *
28012198 GCAACCCTAATATAATGTCAACTTGTGTGA
1 GTAACCTTGATATAATGTCAACTTGTGTGA
28012228 G
1 G
28012229 CAACTTAGTC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (30 bp):
GTAACCTTGATATAATGTCAACTTGTGTGA
Found at i:28012361 original size:7 final size:7
Alignment explanation
Indices: 28012349--28012373 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28012339 GCTTATTACT
28012349 TGATATG
1 TGATATG
28012356 TGATATG
1 TGATATG
28012363 TGATATG
1 TGATATG
28012370 TGAT
1 TGAT
28012374 TACATTAATG
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:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (7 bp):
TGATATG
Found at i:28015159 original size:22 final size:22
Alignment explanation
Indices: 28015105--28015159 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
28015095 AATTTAAAAC
* * *
28015105 AATATCTTATATATGAAATAAT
1 AATATATTATAAATAAAATAAT
* *
28015127 AATGTACTATAAATAAAATAAT
1 AATATATTATAAATAAAATAAT
*
28015149 AATATTTTATA
1 AATATATTATA
28015160 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
AATATATTATAAATAAAATAAT
Found at i:28016638 original size:24 final size:22
Alignment explanation
Indices: 28016611--28016664 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
28016601 ATTAAAAATA
28016611 TTAAAAACATTT-TTTATAAACTTT
1 TTAAAAACATTTCTTT-T-AA-TTT
* *
28016635 TTAATAATATTTCTTTTAATTT
1 TTAAAAACATTTCTTTTAATTT
28016657 TTAAAAAC
1 TTAAAAAC
28016665 TAATTAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 9 0.36
23 2 0.08
24 11 0.44
25 3 0.12
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAAAACATTTCTTTTAATTT
Found at i:28020352 original size:14 final size:15
Alignment explanation
Indices: 28020335--28020368 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28020325 AAATATTATT
28020335 AAATTTTAAT-TAAA
1 AAATTTTAATATAAA
*
28020349 AAATTTTAATATTAA
1 AAATTTTAATATAAA
28020364 AAATT
1 AAATT
28020369 AGAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTTTAATATAAA
Found at i:28020403 original size:10 final size:9
Alignment explanation
Indices: 28020361--28020440 Score: 54
Period size: 10 Copynumber: 8.6 Consensus size: 9
28020351 ATTTTAATAT
28020361 TAAAAATTA
1 TAAAAATTA
* *
28020370 GAAAAAAATA
1 -TAAAAATTA
**
28020380 TAAAAATCG
1 TAAAAATTA
28020389 T-AAAATATA
1 TAAAAAT-TA
*
28020398 TAAAAATTT
1 TAAAAATTA
*
28020407 TAAAATTTTA
1 TAAAA-ATTA
*
28020417 TAAAAATCA
1 TAAAAATTA
28020426 TAAAAAATTA
1 T-AAAAATTA
28020436 TAAAA
1 TAAAA
28020441 CATACAGAAT
Statistics
Matches: 52, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
8 5 0.10
9 20 0.38
10 27 0.52
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:28020422 original size:46 final size:47
Alignment explanation
Indices: 28020372--28020466 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 47
28020362 AAAAATTAGA
* * *
28020372 AAAAAAT-AT-AAAAATCGTAAAATATATAAAAATTTTAAAATTTTAT
1 AAAAAATCATAAAAAATCATAAAACATA-AAAAATTATAAAATTTTAT
* * *
28020418 -AAAAATCATAAAAAATTATAAAACATACAGAATTATAAAATTTTAT
1 AAAAAATCATAAAAAATCATAAAACATAAAAAATTATAAAATTTTAT
28020464 AAA
1 AAA
28020467 GTCGTAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
45 6 0.15
46 18 0.45
47 16 0.40
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (47 bp):
AAAAAATCATAAAAAATCATAAAACATAAAAAATTATAAAATTTTAT
Found at i:28020429 original size:19 final size:18
Alignment explanation
Indices: 28020378--28020440 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
28020368 TAGAAAAAAA
* *
28020378 TATAAAAATCGTAAAATA
1 TATAAAAATCATAAAATT
**
28020396 TATAAAAATTTTAAAATTT
1 TATAAAAATCATAAAA-TT
*
28020415 TATAAAAATCATAAAAAAT
1 TATAAAAATCAT-AAAATT
28020434 TATAAAA
1 TATAAAA
28020441 CATACAGAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 14 0.38
19 19 0.51
20 4 0.11
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (18 bp):
TATAAAAATCATAAAATT
Found at i:28020733 original size:39 final size:38
Alignment explanation
Indices: 28020663--28020743 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 38
28020653 GGTCGTTAAA
** *
28020663 TTTTGTATGATTTTTATAAAATTTTACAATTTTTTTTAT
1 TTTTGTATGATTTTTATAAAAAATTACAA-TTTTTATAT
*
28020702 TTTTTTATGATTTTTATAAAAAATT-CTAATTTTTATAT
1 TTTTGTATGATTTTTATAAAAAATTAC-AATTTTTATAT
28020740 TTTT
1 TTTT
28020744 ATTAAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 13 0.35
39 24 0.65
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (38 bp):
TTTTGTATGATTTTTATAAAAAATTACAATTTTTATAT
Found at i:28020759 original size:28 final size:28
Alignment explanation
Indices: 28020703--28020763 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
28020693 TTTTTTTATT
*
28020703 TTTTTATGATTTTTATAAAAAATTCTAA
1 TTTTTATGATTTTTATAAAAAATTATAA
* *
28020731 TTTTTAT-ATTTTTATTAAAATTTAATAA
1 TTTTTATGATTTTTATAAAAAATT-ATAA
28020759 TTTTT
1 TTTTT
28020764 TCTTTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTTATGATTTTTATAAAAAATTATAA
Found at i:28029874 original size:74 final size:74
Alignment explanation
Indices: 28029753--28029906 Score: 263
Period size: 74 Copynumber: 2.1 Consensus size: 74
28029743 AATCAGATAA
* *
28029753 TGAAAGATGAACTTGATATGTTATGTCGTAAAAGGTTGTAGTTGTAATCGTTATGGTTTAGCTGA
1 TGAAAGATGAACTTGATATGCTATGTCATAAAAGGTTGTAGTTGTAATCGTTATGGTTTAGCTGA
28029818 ATAGCTTAG
66 ATAGCTTAG
* *
28029827 TGAAAGTTGAACTTGATATGCTATGTCATAAGAGGTTGTAGTTGTAATCGTTATGGTTTAGCTGA
1 TGAAAGATGAACTTGATATGCTATGTCATAAAAGGTTGTAGTTGTAATCGTTATGGTTTAGCTGA
*
28029892 GTAGCTTAG
66 ATAGCTTAG
28029901 TGAAAG
1 TGAAAG
28029907 GAAATTAAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (74 bp):
TGAAAGATGAACTTGATATGCTATGTCATAAAAGGTTGTAGTTGTAATCGTTATGGTTTAGCTGA
ATAGCTTAG
Found at i:28032197 original size:45 final size:45
Alignment explanation
Indices: 28032070--28032200 Score: 145
Period size: 45 Copynumber: 2.9 Consensus size: 45
28032060 CTATATGGCT
* * * * * *
28032070 AAAATTAGTCAGACCATAGCTAAAAGATGTTATGGCACCATGTTA
1 AAAATGAGTAAGACCATAGCTGAAAGATATTATGGCATCATGATA
* * * *
28032115 AAAATGATTAAAACAATAGCTGAAATATATTATGGCATCATGATA
1 AAAATGAGTAAGACCATAGCTGAAAGATATTATGGCATCATGATA
* * *
28032160 GAAATGAGTAAGACCATAGCTGAAAGACACTATGGCATCAT
1 AAAATGAGTAAGACCATAGCTGAAAGATATTATGGCATCAT
28032201 ATGAAAGCAC
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.25
Consensus pattern (45 bp):
AAAATGAGTAAGACCATAGCTGAAAGATATTATGGCATCATGATA
Found at i:28033519 original size:17 final size:17
Alignment explanation
Indices: 28033497--28033531 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28033487 CCTTATATAC
28033497 GTGTTATAGTAAGTTTG
1 GTGTTATAGTAAGTTTG
28033514 GTGTTATAGTAAGTTTG
1 GTGTTATAGTAAGTTTG
28033531 G
1 G
28033532 CATAGTCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (17 bp):
GTGTTATAGTAAGTTTG
Found at i:28045426 original size:23 final size:23
Alignment explanation
Indices: 28045378--28045429 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
28045368 CGCATACAGT
* * *
28045378 GTTCGCATGCTAAACACATGAGG
1 GTTCGCATACTAAACACATCAAG
28045401 GTTCGCATACTAAATCACA-CAAG
1 GTTCGCATACTAAA-CACATCAAG
28045424 GTTCGC
1 GTTCGC
28045430 TTAATAGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
GTTCGCATACTAAACACATCAAG
Found at i:28045451 original size:23 final size:23
Alignment explanation
Indices: 28045425--28045488 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
28045415 TCACACAAGG
*
28045425 TTCGCTTAATAGTTCATACAGGA
1 TTCGCATAATAGTTCATACAGGA
* * *
28045448 TTCGCATAATAGTTCACATAGGG
1 TTCGCATAATAGTTCATACAGGA
*
28045471 TTCACATAATAGTTCATA
1 TTCGCATAATAGTTCATA
28045489 TATGTTCACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (23 bp):
TTCGCATAATAGTTCATACAGGA
Found at i:28045485 original size:12 final size:12
Alignment explanation
Indices: 28045452--28045500 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
28045442 ACAGGATTCG
28045452 CATAATAGTTCA
1 CATAATAGTTCA
**
28045464 CAT-AGGGTTCA
1 CATAATAGTTCA
28045475 CATAATAGTTCA
1 CATAATAGTTCA
*
28045487 TAT-AT-GTTCA
1 CATAATAGTTCA
28045497 CATA
1 CATA
28045501 CTAATTCATA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
10 7 0.24
11 11 0.38
12 11 0.38
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (12 bp):
CATAATAGTTCA
Found at i:28045572 original size:36 final size:36
Alignment explanation
Indices: 28045525--28045594 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
28045515 ATTCACACAT
* *
28045525 TAAATCACATACTAAATTTCATGAAGGTTCGCATAC
1 TAAATCACATACTAAAGTACATGAAGGTTCGCATAC
* * *
28045561 TAAATCTCATACTAACGTACATGAGGGTTCGCAT
1 TAAATCACATACTAAAGTACATGAAGGTTCGCAT
28045595 GCTCATATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (36 bp):
TAAATCACATACTAAAGTACATGAAGGTTCGCATAC
Found at i:28045771 original size:24 final size:24
Alignment explanation
Indices: 28045742--28045798 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
28045732 ATTTATTAAG
28045742 GGGTTCGCACAACAATT-CACATAA
1 GGGTTCGCACAACAATTAC-CATAA
**
28045766 GGGTTCGCAGTACAATTACCATAA
1 GGGTTCGCACAACAATTACCATAA
*
28045790 GAGTTCGCA
1 GGGTTCGCA
28045799 TAATAGCTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (24 bp):
GGGTTCGCACAACAATTACCATAA
Found at i:28049180 original size:10 final size:11
Alignment explanation
Indices: 28049149--28049179 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
28049139 TTAAAAAAGA
28049149 ATTTTAAAAAT
1 ATTTTAAAAAT
28049160 ATTTTAAAAAT
1 ATTTTAAAAAT
28049171 ATTTTAAAA
1 ATTTTAAAA
28049180 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:28049213 original size:39 final size:40
Alignment explanation
Indices: 28049135--28049238 Score: 140
Period size: 39 Copynumber: 2.6 Consensus size: 40
28049125 AATTAAAACA
* *
28049135 AAAATTAAAAAAGAATTTTAAAA-ATATTTTAAAAATATTTT
1 AAAATTAAAAAATAA--TAAAAATATATTTTAAAAATATTTT
* *
28049176 AAAATTAAAAAATTA-AAAAATATATTTTAAAAGTATTTT
1 AAAATTAAAAAATAATAAAAATATATTTTAAAAATATTTT
28049215 AAAATTAAAAAATAATAAAAATAT
1 AAAATTAAAAAATAATAAAAATAT
28049239 TTATTATTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
38 4 0.07
39 31 0.55
40 8 0.14
41 13 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (40 bp):
AAAATTAAAAAATAATAAAAATATATTTTAAAAATATTTT
Found at i:28050281 original size:32 final size:31
Alignment explanation
Indices: 28050223--28050282 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
28050213 TATATCATAA
*
28050223 TTTTTACTATATTAATAATTATTATATAATT
1 TTTTTACTATATTAATAAATATTATATAATT
*
28050254 TTTTTACTGATATT-ATAAATGTGTATATA
1 TTTTTACT-ATATTAATAAATAT-TATATA
28050283 TGTAGATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (31 bp):
TTTTTACTATATTAATAAATATTATATAATT
Found at i:28060247 original size:16 final size:16
Alignment explanation
Indices: 28060222--28060264 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
28060212 AATCATGCAC
28060222 TAGA-AATTTTAAG-A
1 TAGAGAATTTTAAGTA
28060236 GTAGAGAATTTTAAGTTA
1 -TAGAGAATTTTAAG-TA
28060254 TAGAGAATTTT
1 TAGAGAATTTT
28060265 GGTTACGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.16
16 9 0.36
17 11 0.44
18 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (16 bp):
TAGAGAATTTTAAGTA
Found at i:28060806 original size:15 final size:15
Alignment explanation
Indices: 28060786--28060815 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28060776 AGGAGACAAC
*
28060786 CTAAAAAAATAATTT
1 CTAAAAAAAAAATTT
28060801 CTAAAAAAAAAATTT
1 CTAAAAAAAAAATTT
28060816 ATCATGCTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
CTAAAAAAAAAATTT
Found at i:28061226 original size:21 final size:20
Alignment explanation
Indices: 28061201--28061248 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 20
28061191 AGACAAAAAT
28061201 AACTAAGATAAAAAGATAACA
1 AACTAAGATAAAAAGA-AACA
28061222 AACT-AG--AAAAAGAAACA
1 AACTAAGATAAAAAGAAACA
28061239 AACTAA-ATAA
1 AACTAAGATAA
28061249 TAAAAAGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 2 0.08
20 2 0.08
21 4 0.17
ACGTcount: A:0.69, C:0.10, G:0.08, T:0.12
Consensus pattern (20 bp):
AACTAAGATAAAAAGAAACA
Found at i:28068612 original size:17 final size:17
Alignment explanation
Indices: 28068581--28068613 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28068571 ATATCTTTAA
28068581 TTTTTAAAAGTGGATTG
1 TTTTTAAAAGTGGATTG
28068598 TTTTTCAAAAG-GGATT
1 TTTTT-AAAAGTGGATT
28068614 AAATTAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.45
Consensus pattern (17 bp):
TTTTTAAAAGTGGATTG
Found at i:28071392 original size:26 final size:26
Alignment explanation
Indices: 28071339--28071397 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
28071329 TATTTTCTTG
* *
28071339 AAATTTTAACATGGGCAAAATCATCA
1 AAATTTTAACAAGGGCAAAATCACCA
*
28071365 AAATTTTAACAAGGGTAAAAT-AGCCA
1 AAATTTTAACAAGGGCAAAATCA-CCA
28071391 AAATTTT
1 AAATTTT
28071398 GCTACAGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (26 bp):
AAATTTTAACAAGGGCAAAATCACCA
Found at i:28090172 original size:13 final size:13
Alignment explanation
Indices: 28090154--28090186 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
28090144 CAATATTAGA
28090154 CACCATAATTCAT
1 CACCATAATTCAT
28090167 CACCATAATTCAT
1 CACCATAATTCAT
28090180 CACCATA
1 CACCATA
28090187 TAGCCCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.27
Consensus pattern (13 bp):
CACCATAATTCAT
Found at i:28092133 original size:44 final size:43
Alignment explanation
Indices: 28092069--28092180 Score: 136
Period size: 44 Copynumber: 2.6 Consensus size: 43
28092059 GAAGATGGCG
28092069 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAG-ATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG-AGAATTAAAG-CAAT
* * * **
28092113 AATCCTATCTCCCTGAAGTTGCGGTGGAGCGAATTAAAGTGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAGAATTAAAGCAAT
*
28092156 AGATCTTATCTCTCTGAAGTTGCAG
1 A-ATCTTATCTCCCTGAAGTTGCAG
28092181 AGAACAGATC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 4 0.07
44 54 0.93
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGAGAATTAAAGCAAT
Found at i:28092308 original size:45 final size:45
Alignment explanation
Indices: 28091987--28092621 Score: 358
Period size: 45 Copynumber: 14.5 Consensus size: 45
28091977 CAAATCCTGA
* ** * * *
28091987 CTCCCTGAAGTTACAGTGGAGTGGA-TTAGAGTAAGTAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCA-AGAAAGCAAGTCTTAT
* **
28092032 C-CTCCTGAAGTTGCAGTGG-GACAGACTGAAGATGGCGAA-TCTTAT
1 CTC-CCTGAAGTTGCAGTGGAG-CAGACTCAAGAAAGC-AAGTCTTAT
* * * * * *
28092077 CTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAA-TAA-TCCTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAAGCAAGTCTTAT
* * * **
28092121 CTCCCTGAAGTTGCGGTGGAGC-GAATTAA-AGTG-ATAGATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA-AG-TCTTAT
* * * * * * *
28092165 CTCTCTGAAGTTGCAG-AGAACAGA-TC--G-CATCTATTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTAT
* * * *
28092205 CTCCTTGAAGTTGCAGTGAAGCAGACT-GAGTAAGC-AGATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAG-TCTTAT
* *
28092249 C-CCCTGAGGTTGCAGTGGGGCAGACTCAAGAAAGCAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTAT
*
28092293 CTCCCTGAGGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTAT
* *
28092338 TTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTAT
* * * * *
28092383 C-CCCTTGAAATTGCAGTTGG-GCAGACTGAATAAA-CAAATCCTAT
1 CTCCC-TGAAGTTGCAG-TGGAGCAGACTCAAGAAAGCAAGTCTTAT
* * ** * * *
28092427 CTCCCTAAAGTTGTAGTGGAGTGGA-T-TAGAATG-ATGGATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA-AG-TCTTAT
* * ** * * * *
28092471 CTCTCTGAAGTTGTAGTAAAGCAGA-TC---ATATCAAATCGTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTAT
*
28092512 CTCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTAT
* * * * * *
28092557 C-CCCTTGAAATTGCAATGGGGCAGACTGAATAAA--AATATCTTAT
1 CTCCC-TGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAA-GTCTTAT
*
28092601 CTCCCTAAAGTTGCAGTGGAG
1 CTCCCTGAAGTTGCAGTGGAG
28092622 TAGATTGAGA
Statistics
Matches: 451, Mismatches: 100, Indels: 79
0.72 0.16 0.13
Matches are distributed among these distances:
40 20 0.04
41 32 0.07
42 9 0.02
43 39 0.09
44 143 0.32
45 199 0.44
46 9 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (45 bp):
CTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTAT
Found at i:28092445 original size:134 final size:133
Alignment explanation
Indices: 28092199--28092618 Score: 340
Period size: 133 Copynumber: 3.2 Consensus size: 133
28092189 TCGCATCTAT
* * * * **
28092199 TCTTATCTCCTTGAAGTTGCAGTGAAGCAGACTGAGTAAGCAGATCTTATCCCCTGAGGTTGCAG
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGAAAGCAAATCTTATCCCCTGAAATTGCAG
* * * *
28092264 TGGGGCAGACTCAAGAAAGCAAGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTCAAGAAAGC
66 TGGGGCAGACTCAAGAAAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGACTCAAGAAAGC
28092329 AAG
131 AAG
* *
28092332 TCTTATTTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAATCTTATCCCCTTGAAATTGC
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACT-AAGAAAGCAAATCTTATCCCC-TGAAATTGC
* * * * ** * *
28092397 AGTTGGGCAGACTGAATAAA-CAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGA-T-TAGAAT
64 AGTGGGGCAGACTCAAGAAAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGACTCAAGAAA
*
28092459 G-ATGG
129 GCA-AG
* * * * * * * * *
28092464 ATCTTATCTCTCTGAAGTTGTAGTAAAGCAGA-T--CATATCAAATCGTATCTCCCTGAAGTTAC
1 -TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGAAAGCAAATCTTATC-CCCTGAAATTGC
* * * * * * *
28092526 AGTGGAGCAGACTCAAGAAAGCAAGTCTTATC-CCCTTGAAA-TTGCAATGGGGCAGACTGAATA
64 AGTGGGGCAGACTCAAGAAAGCAAATCCTATCTCCC-T-AAAGTTGCAGTGGAGCAGACTCAAGA
*
28092589 AA--AATA
127 AAGCAA-G
*
28092595 TCTTATCTCCCTAAAGTTGCAGTG
1 TCTTATCTCCCTGAAGTTGCAGTG
28092619 GAGTAGATTG
Statistics
Matches: 224, Mismatches: 52, Indels: 25
0.74 0.17 0.08
Matches are distributed among these distances:
129 38 0.17
130 43 0.19
131 6 0.03
132 10 0.04
133 57 0.25
134 46 0.21
135 24 0.11
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (133 bp):
TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGAAAGCAAATCTTATCCCCTGAAATTGCAG
TGGGGCAGACTCAAGAAAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGACTCAAGAAAGC
AAG
Found at i:28092656 original size:174 final size:174
Alignment explanation
Indices: 28092339--28092656 Score: 480
Period size: 174 Copynumber: 1.8 Consensus size: 174
28092329 AAGTCTTATT
* * *
28092339 TCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAATCTTATCCCCTTGAAATTGCAGTTGGG
1 TCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAATCTTATCCCCTTGAAATTGCAATGGGG
* * * *** *
28092404 CAGACTGAATAAACAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAGAATGATGGATCTT
66 CAGACTGAATAAACAAATCCTATCTCCCTAAAGTTGCAGTGGAGTAGATTAGAATAACCAATCTA
28092469 ATCTCTCTGAAGTTGTAGTAAAGCAGATCATATCAAATCGTATC
131 ATCTCTCTGAAGTTGTAGTAAAGCAGATCATATCAAATCGTATC
*
28092513 TCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCCCCTTGAAATTGCAATGGGG
1 TCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAATCTTATCCCCTTGAAATTGCAATGGGG
*
28092578 CAGACTGAATAAA-AATATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTGAGAA-AACCAATC
66 CAGACTGAATAAACAA-ATCCTATCTCCCTAAAGTTGCAGTGGAGTAGATT-AGAATAACCAATC
28092641 TAATCTC-CTTGAAGTT
129 TAATCTCTC-TGAAGTT
28092657 ACAATGGAGT
Statistics
Matches: 129, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
173 3 0.02
174 122 0.95
175 4 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (174 bp):
TCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAATCTTATCCCCTTGAAATTGCAATGGGG
CAGACTGAATAAACAAATCCTATCTCCCTAAAGTTGCAGTGGAGTAGATTAGAATAACCAATCTA
ATCTCTCTGAAGTTGTAGTAAAGCAGATCATATCAAATCGTATC
Found at i:28092671 original size:88 final size:89
Alignment explanation
Indices: 28092224--28092671 Score: 195
Period size: 89 Copynumber: 5.1 Consensus size: 89
28092214 GTTGCAGTGA
* ** * * * * * *
28092224 AGCAGACTGAGTAAGCAGATCTTATC-CCCTGAGGTTGCAGTGGGGCAGACTCAAGAAAGCAAGT
1 AGCAGACTGAATAAAAATATCTTATCTCCCTAAAGTTACAGTGGAGCAGACTCAAGAAACCAAGT
* ** * *
28092288 CTTATCTCCC-TGAGGTTGCAGTGG
66 CTAATC-CCCTTGAAATTACAATGG
* * * * * * *
28092312 AGCAGACTCAAGAAAGCAA-GTCTTATTTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAA
1 AGCAGACTGAATAAA--AATATCTTATCTCCCTAAAGTTACAGTGGAGCAGACTCAAGAAACCAA
* * * *
28092376 ATCTTATCCCCTTGAAATTGCAGTTGG
64 GTCTAATCCCCTTGAAATTACA-ATGG
* ** ** * ** *
28092403 -GCAGACTGAATAAACAA-ATCCTATCTCCCTAAAGTTGTAGTGGAGTGGA-T-TAG-AATGATG
1 AGCAGACTGAATAAA-AATATCTTATCTCCCTAAAGTTACAGTGGAGCAGACTCAAGAAACCA-A
* * * ** * **
28092463 GATCTTAT-CTCTCTGAAGTTGTAGTAA
64 G-TCTAATCCCCT-TGAAATTACAATGG
* ** * * *
28092490 AGCAGA-T-CATATCAA-ATCGTATCTCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAGT
1 AGCAGACTGAATAAAAATATCTTATCTCCCTAAAGTTACAGTGGAGCAGACTCAAGAAACCAAGT
* *
28092552 CTTATCCCCTTGAAATTGCAATGG
66 CTAATCCCCTTGAAATTACAATGG
* * * **
28092576 GGCAGACTGAATAAAAATATCTTATCTCCCTAAAGTTGCAGTGGAGTAGA-TTGAGAAAACCAA-
1 AGCAGACTGAATAAAAATATCTTATCTCCCTAAAGTTACAGTGGAGCAGACTCAAG-AAACCAAG
* *
28092639 TCTAATCTCCTTGAAGTTACAATGG
65 TCTAATCCCCTTGAAATTACAATGG
*
28092664 AGTAGACT
1 AGCAGACT
28092672 AGAGCATTAC
Statistics
Matches: 274, Mismatches: 69, Indels: 34
0.73 0.18 0.09
Matches are distributed among these distances:
85 28 0.10
86 27 0.10
87 14 0.05
88 69 0.25
89 71 0.26
90 62 0.23
91 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (89 bp):
AGCAGACTGAATAAAAATATCTTATCTCCCTAAAGTTACAGTGGAGCAGACTCAAGAAACCAAGT
CTAATCCCCTTGAAATTACAATGG
Found at i:28094150 original size:26 final size:24
Alignment explanation
Indices: 28094121--28094189 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
28094111 TTATTATTTC
28094121 TATTTTTAACTTATATATGTAATCAT
1 TATTTTTAACTTATATATGTAAT--T
* * *
28094147 TA-TTTTCA-TAATATATAT-ATT
1 TATTTTTAACTTATATATGTAATT
28094168 TATTTTATAACTTATATATGTA
1 TATTTT-TAACTTATATATGTA
28094190 CATATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
21 3 0.09
22 3 0.09
23 4 0.12
24 16 0.48
25 5 0.15
26 2 0.06
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (24 bp):
TATTTTTAACTTATATATGTAATT
Found at i:28094183 original size:20 final size:21
Alignment explanation
Indices: 28094146--28094186 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
28094136 TATGTAATCA
28094146 TTATTTTCATAATATATATAT
1 TTATTTTCATAATATATATAT
28094167 TTATTTT-ATAACT-TATATAT
1 TTATTTTCATAA-TATATATAT
28094187 GTACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTCATAATATATATAT
Found at i:28098669 original size:92 final size:92
Alignment explanation
Indices: 28098519--28098869 Score: 333
Period size: 92 Copynumber: 3.8 Consensus size: 92
28098509 AGTCACTAGA
* * * * * *
28098519 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
1 CTTATCTCTCTGAAGTTGCAGTAGAGTAGA-T---CATAGCAAACCTTATCTCCCTGAAGTTGCA
28098584 GTGGAACAGATTAAAGCTATAAATTACAGAT
62 GTGGAACAGATTAAAGCTATAAATTACAGAT
* * * *
28098615 CTTATCTCTCTAAAGTTGCAGTAAAATAGATTATAGCAAACCTTATCTCCCTGAAGTTGCAGTGG
1 CTTATCTCTCTGAAGTTGCAGTAGAGTAGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGG
* *
28098680 AGCAGGTTCAAAG-T-T--A-TA-AG-T
66 AACAGATT-AAAGCTATAAATTACAGAT
* * * ** * *
28098701 CTTATCTC-CTTGAAGTTGCAGTGGAGTAGACTGAAGATAGCGAATATTATTTCCCTGAAATTGC
1 CTTATCTCTC-TGAAGTTGCAGTAGAGTAGA-T---CATAGCAAACCTTATCTCCCTGAAGTTGC
**
28098765 AGTAAAACAGATTAAAGCTATAAATTACAGAT
61 AGTGGAACAGATTAAAGCTATAAATTACAGAT
* *
28098797 CTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCTTGAAGTTGCAGT-G
1 CTTATCTCTCTGAAGTTGCAGTAGAGTAGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGG
28098861 AAGCAGATT
66 AA-CAGATT
28098870 GAAGATACCA
Statistics
Matches: 205, Mismatches: 35, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
85 1 0.00
86 25 0.12
87 3 0.01
88 2 0.01
89 5 0.02
90 33 0.16
91 4 0.02
92 69 0.34
93 5 0.02
94 2 0.01
95 4 0.02
96 51 0.25
97 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (92 bp):
CTTATCTCTCTGAAGTTGCAGTAGAGTAGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGG
AACAGATTAAAGCTATAAATTACAGAT
Found at i:28098781 original size:182 final size:182
Alignment explanation
Indices: 28098475--28098917 Score: 649
Period size: 182 Copynumber: 2.4 Consensus size: 182
28098465 CATGGTGAAT
* * * *
28098475 CTTATCTCCTTAAAGTTGCAATGGAGCAGATTGAAGTCACT-AGACTTATCTCCCTGAAGTTGCA
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAAGTCTTATCTCCCTGAAGTTGCA
* * **
28098539 GTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTAT
66 GTGGAGCAGACTGAAGATAGCAAATATTATTTCCCTGAAATTGCAGTAAAACAGATTAAAGCTAT
* *
28098604 AAATTACAGATCTTATCTCTCTAAAGTTGCAGTAAAATAGATTATAGCAAAC
131 AAATTACAGATCTTATCTCTCTAAAGTTGCAGTAAAACAGATCATAGCAAAC
* * * *
28098656 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTCAAAGTTA-TAAGTCTTATCTCCTTGAAGTTGC
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATT-GAAGTTACTAAGTCTTATCTCCCTGAAGTTGC
* *
28098720 AGTGGAGTAGACTGAAGATAGCGAATATTATTTCCCTGAAATTGCAGTAAAACAGATTAAAGCTA
65 AGTGGAGCAGACTGAAGATAGCAAATATTATTTCCCTGAAATTGCAGTAAAACAGATTAAAGCTA
* * *
28098785 TAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAAC
130 TAAATTACAGATCTTATCTCTCTAAAGTTGCAGTAAAACAGATCATAGCAAAC
* * *
28098838 CTTATCTCCTTGAAGTTGCAGTGAAGCAGATTGAAGATACCAA-TCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAAGTCTTATCTCCCTGAAGTTGCA
*
28098902 GTGGAGCAGATTGAAG
66 GTGGAGCAGACTGAAG
28098918 CTATTAATCC
Statistics
Matches: 231, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
181 68 0.29
182 163 0.71
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (182 bp):
CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAGACTGAAGATAGCAAATATTATTTCCCTGAAATTGCAGTAAAACAGATTAAAGCTAT
AAATTACAGATCTTATCTCTCTAAAGTTGCAGTAAAACAGATCATAGCAAAC
Found at i:28098854 original size:41 final size:41
Alignment explanation
Indices: 28098797--28098957 Score: 157
Period size: 44 Copynumber: 3.8 Consensus size: 41
28098787 AATTACAGAT
* *
28098797 CTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCATAGCAAAC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGA-AGCAAAC
* * *
28098838 CTTATCTCCTTGAAGTTGCAGT-GAAGCAGATTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTAG-AGCAGATTGAAG---CAAAC
*
28098882 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAATC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGC-A--AA-C
*
28098927 C-TATCTCCCTGAAGTTGTAGTAGAGCAGATT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATT
28098958 AAAACGATAA
Statistics
Matches: 100, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
40 1 0.01
41 29 0.29
42 2 0.02
44 66 0.66
45 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (41 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGCAAAC
Found at i:28098900 original size:44 final size:44
Alignment explanation
Indices: 28098838--28099267 Score: 193
Period size: 44 Copynumber: 9.5 Consensus size: 44
28098828 CATAGCAAAC
*
28098838 CTTATCTCCTTGAAGTTGCAGTGAAGCAGATTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATACCAAT
* * **
28098882 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAAT
1 CTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATACCAAT
* * *
28098926 CCTATCTCCCTGAAGTTGTAGT-AGAGCAGATTAAAACGATA--AAT
1 CTTATCTCCCTGAAGTTGCAGTGA-AGCAGATT-GAA-GATACCAAT
** * * * * * * *
28098970 CCAATAC-CTCT-AAGGTTGCAGT-AGGTCGGATTAAATCTATATAGCAAAC
1 CTTAT-CTCCCTGAA-GTTGCAGTGAAG-CAGATT-GA---AGATA-CCAAT
* **
28099019 CTTATCTCCCTGAAGTTGCAGTGGAA-CAGACTGAAGATAGTGAAT
1 CTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTGAAGATA-CCAAT
* * * *
28099064 CTTATTTCCCTGAAGTTGTAGTGGAA-CAGATTAAAGCTATAAATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTGAAG--AT--A--CCA-AT
* * * * * *
28099115 CTTATCTCTCTGAAGTTGCAAT-AGAGCAGA-T-CATAT-CTAAC
1 CTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTGAAGATACCAAT
* * * * *
28099156 CTTATCTCCTTGAAGTTGTAGTGGAGCAGGTTGAAGTTA-CAAGT
1 CTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATACCAA-T
* * *
28099200 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATA-CCAAT
* *
28099245 CTTATTTCCCTAAAGTTGCAGTG
1 CTTATCTCCCTGAAGTTGCAGTG
28099268 GAATAGATTA
Statistics
Matches: 292, Mismatches: 63, Indels: 61
0.70 0.15 0.15
Matches are distributed among these distances:
41 24 0.08
42 2 0.01
43 7 0.02
44 127 0.43
45 64 0.22
46 8 0.03
47 5 0.02
48 2 0.01
49 23 0.08
50 5 0.02
51 25 0.09
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATACCAAT
Found at i:28099179 original size:92 final size:92
Alignment explanation
Indices: 28099064--28099361 Score: 306
Period size: 92 Copynumber: 3.3 Consensus size: 92
28099054 GATAGTGAAT
* *
28099064 CTTATTTCCCTGAAGTTGTAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAA
* *
28099129 GTTGCAATAGAGCAGATCATATCTAAC
66 GTTGCAGTAGAGCAGATCATATCAAAC
* * * * * * *
28099156 CTTATCTCCTTGAAGTTGTAGTGGAGCAGGTTGAAG-T-T--A-CA-AG-TCTTATCTCCCTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAA
* * * * *
28099214 GTTGCAGTGGAGCAGACTGAAGATAGCGAAT
66 GTTGCAGTAGAGCAGA-T---CATATCAAAC
* * * *
28099245 CTTATTTCCCTAAAGTTGCAGTGGAATAGATTAAAGCTATAAATTACAAATCTTAT-TCCTCTGA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCT-CTCTGA
28099309 AGTTGCAGTAGAGCAGATCATATCAAAC
65 AGTTGCAGTAGAGCAGATCATATCAAAC
*
28099337 CTTATCTCTCTGAAGTTGCAGTGGA
1 CTTATCTCCCTGAAGTTGCAGTGGA
28099362 GCAGTTGTAG
Statistics
Matches: 162, Mismatches: 32, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
85 28 0.17
86 3 0.02
87 1 0.01
88 1 0.01
89 34 0.21
90 2 0.01
91 2 0.01
92 59 0.36
93 1 0.01
94 1 0.01
95 3 0.02
96 27 0.17
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (92 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAA
GTTGCAGTAGAGCAGATCATATCAAAC
Found at i:28099206 original size:181 final size:181
Alignment explanation
Indices: 28099019--28099365 Score: 581
Period size: 181 Copynumber: 1.9 Consensus size: 181
28099009 TATAGCAAAC
* * *
28099019 CTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGTGAATCTTATTTCCCTGAAGTTGTA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCGAATCTTATTTCCCTAAAGTTGCA
*
28099084 GTGGAACAGATTAAAGCTATAAATTACAGATCTTA-TCTCTCTGAAGTTGCAATAGAGCAGATCA
66 GTGGAACAGATTAAAGCTATAAATTACAAATCTTATTC-CTCTGAAGTTGCAATAGAGCAGATCA
* *
28099148 TATCTAACCTTATCTC-CTTGAAGTTGTAGTGGAGCAGGTTGAAGTTACAAGT
130 TATCAAACCTTATCTCTC-TGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
*
28099200 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTAAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCGAATCTTATTTCCCTAAAGTTGCA
* *
28099265 GTGGAATAGATTAAAGCTATAAATTACAAATCTTATTCCTCTGAAGTTGCAGTAGAGCAGATCAT
66 GTGGAACAGATTAAAGCTATAAATTACAAATCTTATTCCTCTGAAGTTGCAATAGAGCAGATCAT
28099330 ATCAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAG
131 ATCAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAG
28099366 TTGTAGTAGA
Statistics
Matches: 155, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
181 152 0.98
182 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (181 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCGAATCTTATTTCCCTAAAGTTGCA
GTGGAACAGATTAAAGCTATAAATTACAAATCTTATTCCTCTGAAGTTGCAATAGAGCAGATCAT
ATCAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
Found at i:28099313 original size:96 final size:96
Alignment explanation
Indices: 28098833--28099325 Score: 344
Period size: 96 Copynumber: 5.4 Consensus size: 96
28098823 CAGATCATAG
* * * * *
28098833 CAAACCTTATCTCCTTGAAGTTGCAGT-GAAGCAGATTGAAGATA-CCAATCTTATCTCCCTGAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTAG-AGCAGACTGAAGATAGCGAATCTTATTTCCCTGAA
* * *
28098896 GTTGCAGTGGAGCAGATTGAAGC--T--ATT-
65 GTTGTAGTGGAACAGATTAAAGCTATAAATTA
* * * * * * *
28098923 --AATCCTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAACGATA---AATC-CAATACCTCT-
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGACT-GAA-GATAGCGAATCTTATTTCC-CTG
* * * *
28098981 AAGGTTGCAGTAGG-TCGGATTAAATCTAT--A-TA
63 AA-GTTGTAGT-GGAACAGATTAAAGCTATAAATTA
* * * *
28099013 GCAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGTGAATCTTATTTCCCTGAA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAA
28099078 GTTGTAGTGGAACAGATTAAAGCTATAAATTA
65 GTTGTAGTGGAACAGATTAAAGCTATAAATTA
* * * * * * * * *
28099110 CAGATCTTATCTCTCTGAAGTTGCAATAGAGCAGA-T---CATATCTAACCTTATCTCCTTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAG
* * *
28099171 TTGTAGTGGAGCAGGTT---G----AAGTTA
66 TTGTAGTGGAACAGATTAAAGCTATAAATTA
* * *
28099195 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTAAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAG
* *
28099260 TTGCAGTGGAATAGATTAAAGCTATAAATTA
66 TTGTAGTGGAACAGATTAAAGCTATAAATTA
28099291 CAAATCTTAT-TCCTCTGAAGTTGCAGTAGAGCAGA
1 CAAATCTTATCTCC-CTGAAGTTGCAGTAGAGCAGA
28099326 TCATATCAAA
Statistics
Matches: 308, Mismatches: 62, Indels: 60
0.72 0.14 0.14
Matches are distributed among these distances:
85 35 0.11
86 1 0.00
87 5 0.02
88 51 0.17
89 38 0.12
90 6 0.02
91 4 0.01
92 36 0.12
93 31 0.10
94 25 0.08
95 10 0.03
96 64 0.21
97 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (96 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAG
TTGTAGTGGAACAGATTAAAGCTATAAATTA
Found at i:28099338 original size:318 final size:313
Alignment explanation
Indices: 28098701--28099361 Score: 848
Period size: 318 Copynumber: 2.1 Consensus size: 313
28098691 AGTTATAAGT
* **
28098701 CTTATCTCCTTGAAGTTGCAGTGGAGTAGACTGAAGATAGCGAATATTATTTCCCTGAAATTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCGAATATTATTTCCCTGAAATTGCA
*
28098766 GTAAAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAT
66 GTAAAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATCAT
28098831 AGCAAACCTTATCTCCTTGAAGTTGCAGTGAAGCAGATTGAAGATACCAATCTTATCTCCCTGAA
131 AGCAAACCTTATCTCCTTGAAGTTGCAGTGAAGCAGATTGAAGATACCAATCTTATCTCCCTGAA
* * ** * * *
28098896 GTTGCAGTGGAGCAGATTGAAGCTATTAATCCTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAA
196 GTTGCAGTGGAGCAGACTGAAGATACGAATCCTATCTCCCTAAAGTTGCAGTAGAACAGATTAAA
*
28098961 ACGATAAATCCAATACCTCTAAGGTTGCAGTAGGTCGGATTAAATCTATATAGCAAAC
261 ACGATAAATCAAATACCTCTAAGGTTGCAGTAGGTC-G---AAATCTATATA-CAAAC
* * * *
28099019 CTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGTGAATCTTATTTCCCTGAAGTTGTA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCGAATATTATTTCCCTGAAATTGCA
**
28099084 GTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATCAT
66 GTAAAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATCAT
* * * * * *
28099149 ATCTAACCTTATCTCCTTGAAGTTGTAGTGGAGCAGGTTGAAGTTA-CAAGTCTTATCTCCCTGA
131 AGCAAACCTTATCTCCTTGAAGTTGCAGTGAAGCAGATTGAAGATACCAA-TCTTATCTCCCTGA
* * * *
28099213 AGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAATAGATTA
195 AGTTGCAGTGGAGCAGACTGAAGATA-CGAATCCTATCTCCCTAAAGTTGCAGTAGAACAGATTA
* * *
28099278 AAGCTATAAATTACAAATCTTATTCCTCTGAA-GTTGCAGTAGAG-C-AGATC-ATAT-CAAAC
259 AAACGATAAA-T-CAAA---TA--CCTCT-AAGGTTGCAGTAG-GTCGAAATCTATATACAAAC
*
28099337 CTTATCTCTCTGAAGTTGCAGTGGA
1 CTTATCTCCCTGAAGTTGCAGTGGA
28099362 GCAGTTGTAG
Statistics
Matches: 300, Mismatches: 32, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
317 3 0.01
318 227 0.76
319 37 0.12
320 5 0.02
321 7 0.02
324 2 0.01
326 16 0.05
327 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (313 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCGAATATTATTTCCCTGAAATTGCA
GTAAAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATCAT
AGCAAACCTTATCTCCTTGAAGTTGCAGTGAAGCAGATTGAAGATACCAATCTTATCTCCCTGAA
GTTGCAGTGGAGCAGACTGAAGATACGAATCCTATCTCCCTAAAGTTGCAGTAGAACAGATTAAA
ACGATAAATCAAATACCTCTAAGGTTGCAGTAGGTCGAAATCTATATACAAAC
Found at i:28101024 original size:5 final size:5
Alignment explanation
Indices: 28101014--28101042 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28101004 TATTGTCGTT
28101014 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
28101043 TGGTTTGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:28112176 original size:3 final size:3
Alignment explanation
Indices: 28112170--28112203 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
28112160 GATAATAATG
* *
28112170 ACA ACA ACA ACA ACA ACA ACA ATA AAA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
28112204 AACTAAGCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.71, C:0.26, G:0.00, T:0.03
Consensus pattern (3 bp):
ACA
Found at i:28114493 original size:45 final size:45
Alignment explanation
Indices: 28114442--28114530 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
28114432 TAAAGATATT
*
28114442 TTATTAAGAGTTTAATTAAT-TTTTGACTTATCTTTATTTAGTTAG
1 TTATTAAGAGTTTAACTAATATTTT-ACTTATCTTTATTTAGTTAG
* *
28114487 TTATTAAGAGTTTAACTAATATTTTATTTATTTTTATTTAGTTA
1 TTATTAAGAGTTTAACTAATATTTTACTTATCTTTATTTAGTTA
28114531 AATAAATGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 36 0.90
46 4 0.10
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.57
Consensus pattern (45 bp):
TTATTAAGAGTTTAACTAATATTTTACTTATCTTTATTTAGTTAG
Found at i:28115016 original size:38 final size:41
Alignment explanation
Indices: 28114974--28115062 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 41
28114964 TAAACTCTGT
* *
28114974 TTTTAATT-TCT-C-ACTTAAACTCTTATTAGTGTAGGTTA
1 TTTTAATTATCTCCTACCTAAACTCTGATTAGTGTAGGTTA
*
28115012 TTTTAATATTAGTTTCCTACCTAAACTCTGATTAGTGTAGGTTA
1 TTTT-A-ATTA-TCTCCTACCTAAACTCTGATTAGTGTAGGTTA
28115056 TTTTAAT
1 TTTTAAT
28115063 ATTAGTTTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
38 4 0.10
39 1 0.02
40 3 0.07
42 4 0.10
43 2 0.05
44 28 0.67
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.49
Consensus pattern (41 bp):
TTTTAATTATCTCCTACCTAAACTCTGATTAGTGTAGGTTA
Found at i:28115039 original size:44 final size:44
Alignment explanation
Indices: 28114989--28115078 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
28114979 ATTTCTCACT
*
28114989 TAAACTCTTATTAGTGTAGGTTATTTTAATATTAGTTTCCTACC
1 TAAACTCTGATTAGTGTAGGTTATTTTAATATTAGTTTCCTACC
28115033 TAAACTCTGATTAGTGTAGGTTATTTTAATATTAGTTTCCTACC
1 TAAACTCTGATTAGTGTAGGTTATTTTAATATTAGTTTCCTACC
28115077 TA
1 TA
28115079 GTGTGTTTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (44 bp):
TAAACTCTGATTAGTGTAGGTTATTTTAATATTAGTTTCCTACC
Found at i:28120333 original size:26 final size:26
Alignment explanation
Indices: 28120258--28120333 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
28120248 ATTTTTTTCC
* *
28120258 CAATTTTACCCTTAGAAAAATTTTGA
1 CAATTTTACCCCTAGTAAAATTTTGA
* * *
28120284 CAATTTTATCCC-AATAAATTTTTTGA
1 CAATTTTACCCCTAGTAAA-ATTTTGA
**
28120310 TGATTTTACCCCTAGTAAAATTTT
1 CAATTTTACCCCTAGTAAAATTTT
28120334 AAGAAAATAT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
25 4 0.11
26 29 0.76
27 5 0.13
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (26 bp):
CAATTTTACCCCTAGTAAAATTTTGA
Found at i:28120503 original size:19 final size:18
Alignment explanation
Indices: 28120479--28120516 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
28120469 TGCAAATGTA
28120479 TCATTTCTC-TTTCTCATTT
1 TCATTT-TCATTTC-CATTT
28120498 TCATTTTCATTTCCATTT
1 TCATTTTCATTTCCATTT
28120516 T
1 T
28120517 GAGAAAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.63
Consensus pattern (18 bp):
TCATTTTCATTTCCATTT
Found at i:28123167 original size:13 final size:13
Alignment explanation
Indices: 28123134--28123168 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
28123124 TTTAGGCTTA
28123134 TTACTATTTAGAC
1 TTACTATTTAGAC
**
28123147 TTGTTATTTAGAC
1 TTACTATTTAGAC
28123160 TTACTATTT
1 TTACTATTT
28123169 TACATATTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (13 bp):
TTACTATTTAGAC
Found at i:28124915 original size:25 final size:24
Alignment explanation
Indices: 28124881--28124939 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
28124871 AGAAAGCAAC
* * *
28124881 AAAAATAAAATATATTCTAAAAAG
1 AAAAAGAAAACATAATCTAAAAAG
*
28124905 AAAAGAGAAAACCTAATCTAAAAAG
1 AAAA-AGAAAACATAATCTAAAAAG
28124930 AAAAAGAAAA
1 AAAAAGAAAA
28124940 GAAAATGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.69, C:0.07, G:0.08, T:0.15
Consensus pattern (24 bp):
AAAAAGAAAACATAATCTAAAAAG
Found at i:28127656 original size:9 final size:9
Alignment explanation
Indices: 28127642--28127666 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28127632 GATCAAGTAA
28127642 AATTAAATT
1 AATTAAATT
28127651 AATTAAATT
1 AATTAAATT
28127660 AATTAAA
1 AATTAAA
28127667 ATAAATATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:28128092 original size:17 final size:18
Alignment explanation
Indices: 28128072--28128115 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
28128062 CCAAAAATAA
28128072 TAATATTAT-AATAAATT
1 TAATATTATAAATAAATT
*
28128089 TAATATT-TAAATTAATT
1 TAATATTATAAATAAATT
28128106 TAATACTTAT
1 TAATA-TTAT
28128116 TCTAATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.04
17 19 0.83
18 2 0.09
19 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATTATAAATAAATT
Found at i:28132572 original size:29 final size:29
Alignment explanation
Indices: 28132540--28132598 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
28132530 CAAACAAAAT
28132540 TGAACCAGT-CATCAAAATACAAAC-ATCAA
1 TGAA-CAGTCCATCAAAATAC-AACTATCAA
**
28132569 TGAAGTGTCCATCAAAATACAACTATCAA
1 TGAACAGTCCATCAAAATACAACTATCAA
28132598 T
1 T
28132599 TAAATCGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.47, C:0.22, G:0.08, T:0.22
Consensus pattern (29 bp):
TGAACAGTCCATCAAAATACAACTATCAA
Found at i:28132611 original size:30 final size:29
Alignment explanation
Indices: 28132549--28132612 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
28132539 TTGAACCAGT
*
28132549 CATCAAAATACAAACATCAATGAAGTGTC
1 CATCAAAATACAAACATCAATGAAATGTC
*
28132578 CATCAAAATAC-AACTATCAATTAAATCGTC
1 CATCAAAATACAAAC-ATCAATGAAAT-GTC
28132608 CATCA
1 CATCA
28132613 TTGAAATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 3 0.10
29 20 0.65
30 8 0.26
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.23
Consensus pattern (29 bp):
CATCAAAATACAAACATCAATGAAATGTC
Found at i:28134178 original size:22 final size:22
Alignment explanation
Indices: 28134145--28134570 Score: 557
Period size: 22 Copynumber: 19.4 Consensus size: 22
28134135 AGCAATTATC
*
28134145 CAAC-ATTCGGACAACATTTAAT
1 CAACAATT-GGACAGCATTTAAT
* *
28134167 CAACAATTGGACAGCAATCAAT
1 CAACAATTGGACAGCATTTAAT
*
28134189 CAACATTTGGACAGCATTTAAT
1 CAACAATTGGACAGCATTTAAT
*
28134211 CAACAATTGGACAGCATTAAAT
1 CAACAATTGGACAGCATTTAAT
* * *
28134233 CAACATTTAGACAACATTTAAT
1 CAACAATTGGACAGCATTTAAT
* * *
28134255 CAATAATTGGACAACATTCAAT
1 CAACAATTGGACAGCATTTAAT
*
28134277 CAACAATTGGACAGCATTAAAT
1 CAACAATTGGACAGCATTTAAT
* * *
28134299 CAACATTTAGACAGAATTTAAT
1 CAACAATTGGACAGCATTTAAT
*
28134321 CAACAATTGGACAGCATTCAAT
1 CAACAATTGGACAGCATTTAAT
* *
28134343 CAATATTTGGACAGCATTTAAT
1 CAACAATTGGACAGCATTTAAT
*
28134365 CAACAATTGGACAGCATTCAAT
1 CAACAATTGGACAGCATTTAAT
* *
28134387 CAATATTTGGACAGCATTTAAT
1 CAACAATTGGACAGCATTTAAT
*
28134409 CAACAATTGGACAGCATTAAAT
1 CAACAATTGGACAGCATTTAAT
*
28134431 CAACAATTGGATAGCATTTAAT
1 CAACAATTGGACAGCATTTAAT
28134453 CAACAATTGGACAGCATTTAAT
1 CAACAATTGGACAGCATTTAAT
* * *
28134475 CAACAATTGAACAACATTAAAT
1 CAACAATTGGACAGCATTTAAT
*
28134497 CAACATTTGGACAGCATTTAAT
1 CAACAATTGGACAGCATTTAAT
* *
28134519 CAACAATTGGACAACATTCAAT
1 CAACAATTGGACAGCATTTAAT
* *
28134541 CAATATTTGGACAGCATTTAAT
1 CAACAATTGGACAGCATTTAAT
28134563 CAACAATT
1 CAACAATT
28134571 TTTACTTCAA
Statistics
Matches: 345, Mismatches: 58, Indels: 2
0.85 0.14 0.00
Matches are distributed among these distances:
22 342 0.99
23 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (22 bp):
CAACAATTGGACAGCATTTAAT
Found at i:28135527 original size:21 final size:18
Alignment explanation
Indices: 28135482--28135522 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
28135472 AATAATCTAA
28135482 CATCAAAAATTTATTTTT
1 CATCAAAAATTTATTTTT
28135500 CATCAAAAATTTATTTTT
1 CATCAAAAATTTATTTTT
28135518 CATCA
1 CATCA
28135523 TCAAACAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (18 bp):
CATCAAAAATTTATTTTT
Found at i:28141482 original size:13 final size:13
Alignment explanation
Indices: 28141464--28141500 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
28141454 ATAAACTACA
28141464 ATATACATACATG
1 ATATACATACATG
28141477 ATATACATACATG
1 ATATACATACATG
28141490 ATATACATACA
1 ATATACATACA
28141501 AATTTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (13 bp):
ATATACATACATG
Found at i:28145258 original size:34 final size:34
Alignment explanation
Indices: 28145211--28145338 Score: 134
Period size: 34 Copynumber: 3.8 Consensus size: 34
28145201 AGGAGAGGGA
* *
28145211 AAGAAGAAGAAAGAAAGAAAGAAAATAAAAGGAG
1 AAGAAGAAAAAAGAAAGAAAGAAAAGAAAAGGAG
* * *
28145245 AAGAAGAAAAAAGAATGAAAGACAAGGAAAGGAG
1 AAGAAGAAAAAAGAAAGAAAGAAAAGAAAAGGAG
* * *
28145279 AAG-AGAAAAAAAAGAAG-AAGAAGAAGAAGAGGGG
1 AAGAAGAAAAAAGA-AAGAAAGAA-AAGAAAAGGAG
* *
28145313 AGGAAGGAAAAAGAAAGAAAGAAAAG
1 AAGAAGAAAAAAGAAAGAAAGAAAAG
28145339 GTGATTTTTT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
33 13 0.17
34 50 0.66
35 13 0.17
ACGTcount: A:0.67, C:0.01, G:0.30, T:0.02
Consensus pattern (34 bp):
AAGAAGAAAAAAGAAAGAAAGAAAAGAAAAGGAG
Found at i:28145476 original size:28 final size:27
Alignment explanation
Indices: 28145424--28145477 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
28145414 TTTTATTATG
* * *
28145424 TTATTTAGTATATAAATTTTATGAAAT
1 TTATTTAGCATACAAAATTTATGAAAT
28145451 TTATTTAGCATGACAAAATTTATGAAA
1 TTATTTAGCAT-ACAAAATTTATGAAA
28145478 AAATTCATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (27 bp):
TTATTTAGCATACAAAATTTATGAAAT
Found at i:28148973 original size:16 final size:17
Alignment explanation
Indices: 28148944--28148977 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28148934 TCAAAATTAT
28148944 ACTAACTAAAAATAATA
1 ACTAACTAAAAATAATA
*
28148961 ACTAAC-AATAATAATA
1 ACTAACTAAAAATAATA
28148977 A
1 A
28148978 TACTAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (17 bp):
ACTAACTAAAAATAATA
Found at i:28149317 original size:27 final size:27
Alignment explanation
Indices: 28149278--28149342 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
28149268 AACACGACTA
* *
28149278 GTGCCACCAATGGGAATGGCACCATCG
1 GTGCCGCCAATGGGAATGACACCATCG
* * *
28149305 GTGCCGCCCATGGGAATGACACCTTTG
1 GTGCCGCCAATGGGAATGACACCATCG
28149332 GTGCCGCCAAT
1 GTGCCGCCAAT
28149343 TAGATACTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.18
Consensus pattern (27 bp):
GTGCCGCCAATGGGAATGACACCATCG
Found at i:28153954 original size:21 final size:21
Alignment explanation
Indices: 28153916--28153955 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28153906 CAAACTAATT
*
28153916 CTATTATTAATTTTAATCTAA
1 CTATTATTAATTTCAATCTAA
28153937 CTATTA-TAATATTCAATCT
1 CTATTATTAAT-TTCAATCT
28153956 CAGTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (21 bp):
CTATTATTAATTTCAATCTAA
Found at i:28154420 original size:27 final size:27
Alignment explanation
Indices: 28154382--28154472 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
28154372 GGAGGGTTTT
*
28154382 TGATTGGCGGCACCAAAGGTGCC-TAAC
1 TGATTGGCGGCACCAATGGTGCCAT-AC
*
28154409 TGATTGGCGGCACCGATGGTGCCATAC
1 TGATTGGCGGCACCAATGGTGCCATAC
* *
28154436 TGGTTGGCAGCACCAATGGTGCCATAC
1 TGATTGGCGGCACCAATGGTGCCATAC
28154463 TGATTGGCGG
1 TGATTGGCGG
28154473 GACTACTCGT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 55 0.98
28 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.22
Consensus pattern (27 bp):
TGATTGGCGGCACCAATGGTGCCATAC
Found at i:28154718 original size:3 final size:3
Alignment explanation
Indices: 28154710--28154735 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28154700 AGTTAGTTAG
28154710 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
28154736 AGGTATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:28157376 original size:27 final size:27
Alignment explanation
Indices: 28157287--28157377 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
28157277 ATGAGTAGTC
*
28157287 CCGCTAATCAGTATGGCACCATTGGTG
1 CCGCCAATCAGTATGGCACCATTGGTG
* *
28157314 CCGCCAACCAGTATGGCACCATCGGTG
1 CCGCCAATCAGTATGGCACCATTGGTG
* *
28157341 CCGCTAATCAGT-TAGGCACCTTTGGTG
1 CCGCCAATCAGTAT-GGCACCATTGGTG
*
28157368 CTGCCAATCA
1 CCGCCAATCA
28157378 AAAACCCTCC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 1 0.02
27 53 0.98
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.23
Consensus pattern (27 bp):
CCGCCAATCAGTATGGCACCATTGGTG
Found at i:28158247 original size:19 final size:21
Alignment explanation
Indices: 28158223--28158273 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
28158213 TGTTTGTTTT
28158223 ACAGAAAATAGA-TT-GGTCA
1 ACAGAAAATAGACTTAGGTCA
28158242 ACAGAAAAT-GACTTACAGGTCA
1 ACAGAAAATAGACTT--AGGTCA
28158264 ACAGAAAATA
1 ACAGAAAATA
28158274 AGCCTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
22 14 0.52
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.18
Consensus pattern (21 bp):
ACAGAAAATAGACTTAGGTCA
Found at i:28158442 original size:9 final size:9
Alignment explanation
Indices: 28158428--28158453 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28158418 TTTATTTTTA
28158428 AAAATATTT
1 AAAATATTT
28158437 AAAATATTT
1 AAAATATTT
28158446 AAAATATT
1 AAAATATT
28158454 AATATAAAAT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAATATTT
Found at i:28158581 original size:31 final size:30
Alignment explanation
Indices: 28158517--28158584 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
28158507 TATTTAGTCA
*
28158517 TTTAATAAATTATTAATATAATTTATTATT
1 TTTAATAAATTATTAATATAAATTATTATT
28158547 TTTAATAAATTATTTAATATTTAAATT-TTA-T
1 TTTAATAAATTA-TTAATA--TAAATTATTATT
28158578 TTTAATA
1 TTTAATA
28158585 GTAAATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 12 0.35
31 14 0.41
32 3 0.09
33 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTAATAAATTATTAATATAAATTATTATT
Found at i:28158666 original size:15 final size:15
Alignment explanation
Indices: 28158648--28158704 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
28158638 TATCAATATT
28158648 AATATTTTAATTATA
1 AATATTTTAATTATA
28158663 AATATTTATTGAAATTATA
1 AATA-TT-TT--AATTATA
* *
28158682 AATATATTAATAATA
1 AATATTTTAATTATA
28158697 AATATTTT
1 AATATTTT
28158705 GTAGTATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 17 0.49
16 2 0.06
17 4 0.11
18 1 0.03
19 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
AATATTTTAATTATA
Found at i:28158678 original size:19 final size:19
Alignment explanation
Indices: 28158628--28158686 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
28158618 TATTCACATA
* *
28158628 TTATTGAAAATATCAATAT
1 TTATTGAAATTATAAATAT
**
28158647 TAATATTTTAATTATAAATAT
1 T--TATTGAAATTATAAATAT
28158668 TTATTGAAATTATAAATAT
1 TTATTGAAATTATAAATAT
28158687 ATTAATAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (19 bp):
TTATTGAAATTATAAATAT
Found at i:28175291 original size:20 final size:20
Alignment explanation
Indices: 28175266--28175311 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
28175256 ATTTATTTTC
28175266 TAATTATTAAAAACTT-TAAA
1 TAATTATTAAAAA-TTGTAAA
28175286 TAATTATTAAAAATTGTAAA
1 TAATTATTAAAAATTGTAAA
28175306 TAATTA
1 TAATTA
28175312 ACAAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
TAATTATTAAAAATTGTAAA
Found at i:28175609 original size:21 final size:20
Alignment explanation
Indices: 28175575--28175631 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
28175565 AATTAATTAC
* *
28175575 TATTTATAATTTTTTGATAAT
1 TATTTTTAAATTTTT-ATAAT
28175596 TATTTTTAAATTTTTA-AAT
1 TATTTTTAAATTTTTATAAT
* *
28175615 AATTTTCTCAATTTTTA
1 TATTTT-TAAATTTTTA
28175632 ATAACTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 8 0.26
20 10 0.32
21 13 0.42
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTTTTAAATTTTTATAAT
Found at i:28175616 original size:22 final size:24
Alignment explanation
Indices: 28175556--28175618 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
28175546 AGTTTTAAAT
*
28175556 TAATTTTAAAATTAATTACTATTTA
1 TAATTTTTAAA-TAATTACTATTTA
** *
28175581 TAATTTTTTGATAATTA-TTTTTA
1 TAATTTTTAAATAATTACTATTTA
28175604 -AATTTTTAAATAATT
1 TAATTTTTAAATAATT
28175619 TTCTCAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 13 0.41
23 5 0.16
24 6 0.19
25 8 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TAATTTTTAAATAATTACTATTTA
Found at i:28175640 original size:20 final size:19
Alignment explanation
Indices: 28175598--28175677 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
28175588 TTGATAATTA
*
28175598 TTTTTAAATTTTTAAATAA-
1 TTTTTCAATTTTT-AATAAC
28175617 TTTTCTCAATTTTTAATAAC
1 TTTT-TCAATTTTTAATAAC
* *
28175637 TTTTACAAATTTTAAT---
1 TTTTTCAATTTTTAATAAC
*
28175653 TTTTTATAATTTTTAATAAC
1 TTTTT-CAATTTTTAATAAC
28175673 TTTTT
1 TTTTT
28175678 TACAATTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.08
17 9 0.18
19 19 0.39
20 17 0.35
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTCAATTTTTAATAAC
Found at i:28175676 original size:11 final size:10
Alignment explanation
Indices: 28175624--28175747 Score: 59
Period size: 9 Copynumber: 12.9 Consensus size: 10
28175614 TAATTTTCTC
28175624 AATTTTTAAT
1 AATTTTTAAT
*
28175634 AACTTTTACA-
1 AATTTTTA-AT
28175644 AA-TTTTAAT
1 AATTTTTAAT
28175653 --TTTTT-AT
1 AATTTTTAAT
28175660 AATTTTTAAT
1 AATTTTTAAT
* *
28175670 AACTTTTTTAC
1 AA-TTTTTAAT
*
28175681 AA-TTTTAAA
1 AATTTTTAAT
*
28175690 ATATTTTTAAC
1 A-ATTTTTAAT
**
28175701 AATACTTAAT
1 AATTTTTAAT
28175711 AATTATTTAA-
1 AATT-TTTAAT
* *
28175721 AATATCTAA-
1 AATTTTTAAT
*
28175730 AATTTTT-AC
1 AATTTTTAAT
28175739 AATTTTTAA
1 AATTTTTAA
28175748 ATATATATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
7 2 0.02
8 6 0.07
9 32 0.37
10 27 0.31
11 20 0.23
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:28175686 original size:10 final size:10
Alignment explanation
Indices: 28175577--28175686 Score: 52
Period size: 10 Copynumber: 11.1 Consensus size: 10
28175567 TTAATTACTA
28175577 TTTATAATTT
1 TTTATAATTT
28175587 TTTGATAATTAT
1 TTT-ATAATT-T
28175599 TTT-TAAATTT
1 TTTAT-AATTT
*
28175609 TTAAATAATTT
1 TT-TATAATTT
* *
28175620 TCT-CAATTT
1 TTTATAATTT
* *
28175629 TTAATAA-CT
1 TTTATAATTT
* *
28175638 TTTACAA--A
1 TTTATAATTT
28175646 TTT-TAATTT
1 TTTATAATTT
28175655 TTTATAATTT
1 TTTATAATTT
*
28175665 TTAATAACTTT
1 TTTATAA-TTT
*
28175676 TTTACAATTT
1 TTTATAATTT
28175686 T
1 T
28175687 AAAATATTTT
Statistics
Matches: 74, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
7 2 0.03
8 3 0.04
9 15 0.20
10 25 0.34
11 24 0.32
12 5 0.07
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (10 bp):
TTTATAATTT
Found at i:28175686 original size:20 final size:20
Alignment explanation
Indices: 28175598--28175747 Score: 104
Period size: 20 Copynumber: 7.8 Consensus size: 20
28175588 TTGATAATTA
28175598 TTTTTA-AATTTTTAAATAAT
1 TTTTTACAATTTTT-AATAAT
*
28175618 TTTCT-CAATTTTTAATAA-
1 TTTTTACAATTTTTAATAAT
* *
28175636 CTTTTACAA-ATTT--TAAT
1 TTTTTACAATTTTTAATAAT
*
28175653 TTTTTATAATTTTTAATAACT
1 TTTTTACAATTTTTAATAA-T
28175674 TTTTTACAA-TTTTAA-AAT
1 TTTTTACAATTTTTAATAAT
**
28175692 ATTTTTAACAATACTTAATAAT
1 -TTTTT-ACAATTTTTAATAAT
* * * *
28175714 TATTTAAAATATCTAA-AA-
1 TTTTTACAATTTTTAATAAT
28175732 TTTTTACAATTTTTAA
1 TTTTTACAATTTTTAA
28175748 ATATATATTT
Statistics
Matches: 101, Mismatches: 18, Indels: 24
0.71 0.13 0.17
Matches are distributed among these distances:
16 3 0.03
17 7 0.07
18 22 0.22
19 17 0.17
20 32 0.32
21 17 0.17
22 3 0.03
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTACAATTTTTAATAAT
Found at i:28175710 original size:77 final size:79
Alignment explanation
Indices: 28175577--28175747 Score: 179
Period size: 77 Copynumber: 2.2 Consensus size: 79
28175567 TTAATTACTA
* * * ** **
28175577 TTTATAATTTTTTGATAATTATTTTTAAATTTTTAAATAATTTTCTCAATTTTTAATAACT-TTT
1 TTTATAA-TTTTTAATAACTATTTTTAAATTTTAAAATAATTTTAACAATACTTAATAACTATTT
* *
28175641 ACAAAT-T-TTAATTT
65 A-AAATATCTAAAATT
* *
28175655 TTTATAATTTTTAATAACT-TTTTTACAATTTTAAAATATTTTTAACAATACTTAATAATTATTT
1 TTTATAATTTTTAATAACTATTTTTA-AATTTTAAAATAATTTTAACAATACTTAATAACTATTT
28175719 AAAATATCTAAAATT
65 AAAATATCTAAAATT
*
28175734 TTTACAATTTTTAA
1 TTTATAATTTTTAA
28175748 ATATATATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
76 6 0.08
77 41 0.53
78 12 0.16
79 18 0.23
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.55
Consensus pattern (79 bp):
TTTATAATTTTTAATAACTATTTTTAAATTTTAAAATAATTTTAACAATACTTAATAACTATTTA
AAATATCTAAAATT
Found at i:28195229 original size:3 final size:3
Alignment explanation
Indices: 28195221--28195255 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28195211 AGTAATTCTC
28195221 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28195256 AAGTCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28207350 original size:13 final size:13
Alignment explanation
Indices: 28207332--28207357 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28207322 TACAGCAAAA
28207332 CATAATTTAAAGG
1 CATAATTTAAAGG
28207345 CATAATTTAAAGG
1 CATAATTTAAAGG
28207358 TTAATTAAGA
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
CATAATTTAAAGG
Found at i:28208217 original size:20 final size:21
Alignment explanation
Indices: 28208192--28208230 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28208182 GGTGGTCTGG
*
28208192 AGTTGG-TGTTGTAACATCCA
1 AGTTGGATGTTGCAACATCCA
28208212 AGTTGGATGTTGCAACATC
1 AGTTGGATGTTGCAACATC
28208231 GAGGGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (21 bp):
AGTTGGATGTTGCAACATCCA
Found at i:28212239 original size:12 final size:13
Alignment explanation
Indices: 28212217--28212245 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28212207 ACTTCTTCTC
28212217 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
28212230 CTTTTC-TTCTTT
1 CTTTTCTTTCTTT
28212242 CTTT
1 CTTT
28212246 AACTTGCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:28212314 original size:3 final size:3
Alignment explanation
Indices: 28212306--28212360 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
28212296 TTTTACTTTC
28212306 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28212352 TAT TAT TAT
1 TAT TAT TAT
28212361 ATAATGCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:28212373 original size:28 final size:25
Alignment explanation
Indices: 28212318--28212371 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
28212308 TTATTATTAT
* *
28212318 TATTATTATTATTATTATATTATTA
1 TATTATTATTATTATTATATAATCA
28212343 TATTATTATTATTATTATATAATGCA
1 TATTATTATTATTATTATATAAT-CA
28212369 TAT
1 TAT
28212372 ATACATACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TATTATTATTATTATTATATAATCA
Found at i:28214552 original size:61 final size:57
Alignment explanation
Indices: 28214439--28214560 Score: 131
Period size: 61 Copynumber: 2.1 Consensus size: 57
28214429 TCATATATAA
** *
28214439 ATATATATATATGTATCTATATATATACTTTTTATATTTTATGATAGTTACATACGT
1 ATATATATATATGTATCTATATATATACTTTTTATATTTTAAAATAGTTACATACAT
* *
28214496 ATATATGTATATGTTTACTTATATATATA-TTTTATAATGATTTTAAAATA-TGTACATACAT
1 ATATATATATATGTAT-C-TATATATATACTTTT-T-AT-ATTTTAAAATAGT-TACATACAT
28214557 ATAT
1 ATAT
28214561 TTTTTTATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
57 14 0.26
58 5 0.09
59 11 0.20
60 3 0.06
61 21 0.39
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.50
Consensus pattern (57 bp):
ATATATATATATGTATCTATATATATACTTTTTATATTTTAAAATAGTTACATACAT
Found at i:28218477 original size:27 final size:27
Alignment explanation
Indices: 28218419--28218478 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
28218409 CATTGAAAGC
* * *
28218419 ACCTTTGTGGAGCAATATGAAAGGAAT
1 ACCTTTGTGGAGCAATATAAAAGAAAA
* * *
28218446 GCCTTTGTGGTGCCATATAAAAGAAAA
1 ACCTTTGTGGAGCAATATAAAAGAAAA
28218473 ACCTTT
1 ACCTTT
28218479 ATGGCAAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (27 bp):
ACCTTTGTGGAGCAATATAAAAGAAAA
Found at i:28219840 original size:18 final size:17
Alignment explanation
Indices: 28219813--28219846 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28219803 AAATATTATA
28219813 AATATATTTATATATTTC
1 AATATATTTATA-ATTTC
*
28219831 AATATTTTTATAATTT
1 AATATATTTATAATTT
28219847 TTAAGTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
AATATATTTATAATTTC
Found at i:28220029 original size:20 final size:20
Alignment explanation
Indices: 28220006--28220043 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28219996 ATAATATATG
*
28220006 ATAATTTATAATAAATATCT
1 ATAATCTATAATAAATATCT
*
28220026 ATAATCTATAATATATAT
1 ATAATCTATAATAAATAT
28220044 AAAAGCACGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATCTATAATAAATATCT
Found at i:28222764 original size:7 final size:7
Alignment explanation
Indices: 28222752--28222782 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28222742 AAAAAATTAA
*
28222752 ATCTTTT
1 ATCTTTC
28222759 ATCTTTC
1 ATCTTTC
28222766 ATCTTTC
1 ATCTTTC
28222773 ATCTTTC
1 ATCTTTC
28222780 ATC
1 ATC
28222783 CTTCTTCGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (7 bp):
ATCTTTC
Found at i:28233878 original size:40 final size:36
Alignment explanation
Indices: 28233818--28233903 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
28233808 AAACTAGTAT
* * *
28233818 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATTGTTAGTTATTATTTTGAGTATAAA-AC
28233854 TAATTATTATTGTTAGTTACTATTATTTTGAGTATAAAAC
1 T-ATTATTATTGTTAG-T--TATTATTTTGAGTATAAAAC
28233894 TATTATTATT
1 TATTATTATT
28233904 TTTATTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.31
38 1 0.02
39 9 0.21
40 15 0.36
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTATTATTGTTAGTTATTATTTTGAGTATAAAAC
Found at i:28235393 original size:16 final size:15
Alignment explanation
Indices: 28235372--28235401 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28235362 CAAATAAATA
28235372 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
28235388 TATTATTTTATATT
1 TATTATTTTATATT
28235402 ATTTTAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:28235622 original size:319 final size:318
Alignment explanation
Indices: 28235135--28235909 Score: 1308
Period size: 321 Copynumber: 2.4 Consensus size: 318
28235125 GCAAGTTGAA
* *
28235135 AAAAAAGTTAGTAAAACACTATTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACAATCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
*
28235200 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTTAGTGCATTATGTTTGA
66 ACTTT-AAAAAA-ATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGA
*
28235265 AATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAACCCTTATTCCTG-CCTT
129 AATTTATTAATTTAGTGCGTTTTTTAAATTAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCTT
*
28235329 TGCTCGTATTATTTTCCCGAATTTTATTACTTCCAA-ATAAATATATTATTTTCATATTTTATTA
194 TGCTCGTATTATTTTCCCGAATTTTATTACTTCCAATAAAAATATATTATTTTCATATTTTATTA
28235393 TTTTATATTATTTTAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAATTTTT
259 TTTTATATTATTTTAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAATTTTT
**
28235453 AAAAAAGTTAGTAAGCGTTCAATCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTT
1 AAAAAAGTTAGTAA---AACAATCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTT
28235518 ATTACTTTAAAAAAATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTG
63 ATTACTTTAAAAAAATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTG
*
28235583 AAATTTATTAATTTAGTGCGTTTTTTAAATTAATTTAGTGTAAAAAAAACCCTTATTCTTGCCCT
128 AAATTTATTAATTTAGTGCGTTTTTTAAATTAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCT
*
28235648 TTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAATAAAAATATATTATTTTCGTATTTTATT
193 TTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAATAAAAATATATTATTTTCATATTTTATT
28235713 ATTTTATATTATTTTAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAATTTTT
258 ATTTTATATTATTTTAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAATTTTT
* * * * * *
28235774 AAAAAAGTTAGTAAAACACTC-TTACTTCGACTATTTGTT--TGTTTTTTTCTCCGTATTTTATT
1 AAAAAAGTTAGTAAAACAATCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
* *
28235836 AATTTAAAAGATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAA
66 ACTTTAAAA-AAATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAA
28235901 ATTTATTAA
130 ATTTATTAA
28235910 ATATACCATT
Statistics
Matches: 432, Mismatches: 19, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
315 28 0.06
316 63 0.15
317 16 0.04
318 18 0.04
319 109 0.25
320 46 0.11
321 152 0.35
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.50
Consensus pattern (318 bp):
AAAAAAGTTAGTAAAACAATCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
ACTTTAAAAAAATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
TTTATTAATTTAGTGCGTTTTTTAAATTAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCTTTG
CTCGTATTATTTTCCCGAATTTTATTACTTCCAATAAAAATATATTATTTTCATATTTTATTATT
TTATATTATTTTAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAATTTTT
Found at i:28236311 original size:5 final size:5
Alignment explanation
Indices: 28236301--28236360 Score: 61
Period size: 5 Copynumber: 12.4 Consensus size: 5
28236291 TTTCTTCTTC
* * * *
28236301 TCCTT TCCTT TTCTT TCC-T TCTTT TCCTT T-CTT TCCTC TCCTC TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
*
28236349 TCCTT TTCTT TC
1 TCCTT TCCTT TC
28236361 TTCTTCTTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
4 7 0.16
5 38 0.84
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCCTT
Found at i:28236318 original size:10 final size:10
Alignment explanation
Indices: 28236303--28236371 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
28236293 TCTTCTTCTC
28236303 CTTTCCTTTT
1 CTTTCCTTTT
*
28236313 CTTTCCTTCT
1 CTTTCCTTTT
28236323 -TTTCC-TTT
1 CTTTCCTTTT
28236331 CTTTCCTCTCCTCT
1 CTTTCCT-T--T-T
28236345 CCTTTCCTTTT
1 -CTTTCCTTTT
28236356 CTTT-CTTCTT
1 CTTTCCTT-TT
28236366 CTTTCC
1 CTTTCC
28236372 CTCTCTTTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
8 2 0.04
9 13 0.27
10 19 0.40
11 3 0.06
12 1 0.02
13 1 0.02
14 2 0.04
15 7 0.15
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:28237646 original size:16 final size:19
Alignment explanation
Indices: 28237598--28237657 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
28237588 TTTAGTCATA
28237598 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT-AT
28237618 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTAATATAT
28237636 TAATAAATTATTTAATAT-T
1 TAATAAATTA-TTAATATAT
28237655 TAA
1 TAA
28237658 AATTTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.09
17 4 0.11
18 8 0.23
19 5 0.14
20 6 0.17
21 4 0.11
22 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAATATAT
Found at i:28239321 original size:21 final size:21
Alignment explanation
Indices: 28239297--28239348 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
28239287 AGAGCTTAGA
*
28239297 TCGTGTGGCTCAGGGAGATGG
1 TCGTGTGGCTCAGGGACATGG
**
28239318 TCGTGACGCTCAGGGACATGG
1 TCGTGTGGCTCAGGGACATGG
28239339 TCGTGTGGCT
1 TCGTGTGGCT
28239349 ACCCCACATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.13, C:0.19, G:0.42, T:0.25
Consensus pattern (21 bp):
TCGTGTGGCTCAGGGACATGG
Found at i:28242072 original size:21 final size:21
Alignment explanation
Indices: 28242048--28242183 Score: 107
Period size: 21 Copynumber: 6.5 Consensus size: 21
28242038 TGTGTTTGAT
*
28242048 TTCAGTTTAGCTCTTATGAGC
1 TTCAGTTTAACTCTTATGAGC
* *
28242069 TTCAG-TTAACTCATATGAGT
1 TTCAGTTTAACTCTTATGAGC
* * *
28242089 TTCAGTTTAACCCTTCT-AGGT
1 TTCAGTTTAACTCTTATGA-GC
* * *
28242110 TTCAGTTTAGCTCTTTTGAAC
1 TTCAGTTTAACTCTTATGAGC
* *
28242131 TTCAGTTTAACCCTTAT-AGGT
1 TTCAGTTTAACTCTTATGA-GC
* *
28242152 TTCCGTTCAACTCTTATGAGC
1 TTCAGTTTAACTCTTATGAGC
*
28242173 TTCCGTTTAAC
1 TTCAGTTTAAC
28242184 CTTTACGGGT
Statistics
Matches: 89, Mismatches: 21, Indels: 10
0.74 0.17 0.08
Matches are distributed among these distances:
20 19 0.21
21 68 0.76
22 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (21 bp):
TTCAGTTTAACTCTTATGAGC
Found at i:28242087 original size:20 final size:20
Alignment explanation
Indices: 28242048--28242095 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28242038 TGTGTTTGAT
* *
28242048 TTCAGTTTAGCTCTTATGAGC
1 TTCAG-TTAACTCATATGAGC
*
28242069 TTCAGTTAACTCATATGAGT
1 TTCAGTTAACTCATATGAGC
28242089 TTCAGTT
1 TTCAGTT
28242096 TAACCCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (20 bp):
TTCAGTTAACTCATATGAGC
Found at i:28242138 original size:42 final size:42
Alignment explanation
Indices: 28242069--28242184 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 42
28242059 TCTTATGAGC
* ** *
28242069 TTCAGTT-AACTCATATGAGTTTCAGTTTAACCCTTCTAGGT
1 TTCAGTTCAACTCTTATGAACTTCAGTTTAACCCTTATAGGT
* * *
28242110 TTCAGTTTAGCTCTTTTGAACTTCAGTTTAACCCTTATAGGT
1 TTCAGTTCAACTCTTATGAACTTCAGTTTAACCCTTATAGGT
* * *
28242152 TTCCGTTCAACTCTTATGAGCTTCCGTTTAACC
1 TTCAGTTCAACTCTTATGAACTTCAGTTTAACC
28242185 TTTACGGGTT
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 7 0.11
42 55 0.89
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (42 bp):
TTCAGTTCAACTCTTATGAACTTCAGTTTAACCCTTATAGGT
Found at i:28242195 original size:42 final size:40
Alignment explanation
Indices: 28242076--28242197 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 40
28242066 AGCTTCAGTT
* * * *
28242076 AACTCATATGAGTTTCAGTTTAACCCTTCTAGGTTTCAGTTT
1 AACTCTTATGAGCTTCAGTTTAA-CCTT-TAGGTTTCCGTTC
* * *
28242118 AGCTCTTTTGAACTTCAGTTTAACCCTTATAGGTTTCCGTTC
1 AACTCTTATGAGCTTCAGTTTAA-CCTT-TAGGTTTCCGTTC
*
28242160 AACTCTTATGAGCTTCCGTTTAACCTTTACGGGTTTCC
1 AACTCTTATGAGCTTCAGTTTAACCTTTA--GGTTTCC
28242198 ATTTAGCACT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
40 2 0.03
41 4 0.06
42 60 0.91
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (40 bp):
AACTCTTATGAGCTTCAGTTTAACCTTTAGGTTTCCGTTC
Found at i:28249325 original size:21 final size:21
Alignment explanation
Indices: 28249281--28249383 Score: 100
Period size: 21 Copynumber: 5.0 Consensus size: 21
28249271 TATATGCTGT
* *
28249281 GTTTCAG-TTAACTCATATGA
1 GTTTCAGTTTAACTCTTATGG
* *
28249301 GTTTCAGTTTAACCCTTCTGG
1 GTTTCAGTTTAACTCTTATGG
* * *
28249322 GTTTCAGTTTAGCTCTTTTGA
1 GTTTCAGTTTAACTCTTATGG
*
28249343 GCTTCAGTTTAACTCTTATGG
1 GTTTCAGTTTAACTCTTATGG
* * *
28249364 GTTTCCGTTCAGCTCTTATG
1 GTTTCAGTTTAACTCTTATG
28249384 AGCTTCTATT
Statistics
Matches: 66, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
20 7 0.11
21 59 0.89
ACGTcount: A:0.17, C:0.19, G:0.18, T:0.45
Consensus pattern (21 bp):
GTTTCAGTTTAACTCTTATGG
Found at i:28249353 original size:42 final size:42
Alignment explanation
Indices: 28249281--28249389 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
28249271 TATATGCTGT
* * * *
28249281 GTTTCAG-TTAACTCATATGAGTTTCAGTTTAACCCTTCTGG
1 GTTTCAGTTTAGCTCTTATGAGCTTCAGTTTAACCCTTATGG
* *
28249322 GTTTCAGTTTAGCTCTTTTGAGCTTCAGTTTAACTCTTATGG
1 GTTTCAGTTTAGCTCTTATGAGCTTCAGTTTAACCCTTATGG
* *
28249364 GTTTCCGTTCAGCTCTTATGAGCTTC
1 GTTTCAGTTTAGCTCTTATGAGCTTC
28249390 TATTCACTAC
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
41 7 0.12
42 51 0.88
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.44
Consensus pattern (42 bp):
GTTTCAGTTTAGCTCTTATGAGCTTCAGTTTAACCCTTATGG
Found at i:28249575 original size:43 final size:43
Alignment explanation
Indices: 28249512--28249780 Score: 387
Period size: 43 Copynumber: 6.3 Consensus size: 43
28249502 TTATAGAAAT
* *
28249512 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCTGC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
28249555 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
* * * *
28249598 AAACGCCGCTAATGGCCATGTTCTTTAGCGGTGCTTTTCTCGA
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
** * *
28249641 AAATACCGCTAAAGGCCATGTTCTTTAGCGGCTCTTTTCCCGA
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
* *
28249684 AAACGCCACTAAATGCCATGTTCTTTAGCGGCGCTTTT-CCGAC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCG-C
* * *
28249727 AAACGCCGTTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
28249770 AAACGCCGCTA
1 AAACGCCGCTA
28249781 TTGTTTGGTG
Statistics
Matches: 200, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
42 3 0.01
43 195 0.98
44 2 0.01
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
Found at i:28250336 original size:25 final size:26
Alignment explanation
Indices: 28250285--28250346 Score: 90
Period size: 25 Copynumber: 2.4 Consensus size: 26
28250275 TTTTACAATG
* *
28250285 ATTAAGTTATGTAAATAATATGAGTT
1 ATTAAGTTATGCAAATAATATAAGTT
*
28250311 ATTAAGTTATGCATAT-ATATAAGTT
1 ATTAAGTTATGCAAATAATATAAGTT
28250336 ATTAAGTTATG
1 ATTAAGTTATG
28250347 TAAGTTGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.44
Consensus pattern (26 bp):
ATTAAGTTATGCAAATAATATAAGTT
Found at i:28250350 original size:17 final size:17
Alignment explanation
Indices: 28250285--28250352 Score: 50
Period size: 17 Copynumber: 4.0 Consensus size: 17
28250275 TTTTACAATG
* *
28250285 ATTAAGTTATGTAAATA
1 ATTAAGTTATGTAAGTT
*
28250302 ATATGAGTTAT-TAAGTT
1 AT-TAAGTTATGTAAGTT
** *
28250319 ATGCA-TATATATAAGTT
1 ATTAAGT-TATGTAAGTT
28250336 ATTAAGTTATGTAAGTT
1 ATTAAGTTATGTAAGTT
28250353 GTTATGTGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
15 1 0.03
16 4 0.10
17 26 0.67
18 8 0.21
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (17 bp):
ATTAAGTTATGTAAGTT
Found at i:28250495 original size:9 final size:9
Alignment explanation
Indices: 28250443--28250506 Score: 71
Period size: 9 Copynumber: 7.4 Consensus size: 9
28250433 TATTTTAAAA
28250443 TTAT-TAAG
1 TTATGTAAG
*
28250451 TTATGTAAA
1 TTATGTAAG
* *
28250460 TTACGTGAG
1 TTATGTAAG
*
28250469 TTGT-TAAG
1 TTATGTAAG
28250477 TTAT-TAAG
1 TTATGTAAG
28250485 TTATGTAAG
1 TTATGTAAG
28250494 TTATGTAAG
1 TTATGTAAG
28250503 TTAT
1 TTAT
28250507 TATGTGAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
8 18 0.39
9 28 0.61
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28250502 original size:26 final size:25
Alignment explanation
Indices: 28250443--28250508 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
28250433 TATTTTAAAA
*
28250443 TTATTAAGTTATGTAAATTACGTGAG
1 TTATTAAGTTAT-TAAATTACGTAAG
* * *
28250469 TTGTTAAGTTATTAAGTTATGTAAG
1 TTATTAAGTTATTAAATTACGTAAG
28250494 TTATGTAAGTTATTA
1 TTAT-TAAGTTATTA
28250509 TGTGAATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 13 0.38
26 21 0.62
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (25 bp):
TTATTAAGTTATTAAATTACGTAAG
Found at i:28250511 original size:21 final size:21
Alignment explanation
Indices: 28250485--28250529 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
28250475 AGTTATTAAG
* *
28250485 TTATGT-AAGTTATGTAAGTTA
1 TTATGTGAA-TTATATAAGCTA
28250506 TTATGTGAATTATATAAGCTA
1 TTATGTGAATTATATAAGCTA
28250527 TTA
1 TTA
28250530 AGTTATATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (21 bp):
TTATGTGAATTATATAAGCTA
Found at i:28251265 original size:21 final size:21
Alignment explanation
Indices: 28251241--28251287 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28251231 TTAACTATTT
* *
28251241 AAATTAGTTAATGATATTGTA
1 AAATTAGATAATGAAATTGTA
* *
28251262 AAATTAGATGATTAAATTGTA
1 AAATTAGATAATGAAATTGTA
28251283 AAATT
1 AAATT
28251288 TCAAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (21 bp):
AAATTAGATAATGAAATTGTA
Found at i:28254855 original size:75 final size:74
Alignment explanation
Indices: 28254758--28255024 Score: 193
Period size: 75 Copynumber: 3.4 Consensus size: 74
28254748 TTAAGAATTT
* *
28254758 TTTGCGGCGTTTTTTTAGTAGCGCCACTAATGCTCAGACAAAACGACACCGTTTTACGAAAACTG
1 TTTGCGGCGTTTTTTCAGTAGCGCCACTAATGC-CAGCCAAAACGACACCGTTTTACGAAAACTG
28254823 AGAACAGAAC
65 AGAACAGAAC
** *
28254833 TTTGCGGCGTTTTTTCCTTAGCGCCGTAAAACCCATTAAATTCACAGCCAAAAACTG-CACCGTT
1 TTTGCGGCGTTTTTTCAGTAGCGCC-----A--C--T-AATGC-CAGCC-AAAAC-GACACCGTT
**** * ** *
28254897 TT--GTCTTCATTATTA-AGAATTT
53 TTACGAAAAC-TGAGAACAGAA--C
28254919 TTTGCGGCGTTTTTT-AGTAGCGCCACTAATGCCTAGCCAAAACGACACCGTTTTACGAAAACTG
1 TTTGCGGCGTTTTTTCAGTAGCGCCACTAATGCC-AGCCAAAACGACACCGTTTTACGAAAACTG
28254983 AGAACAGAAC
65 AGAACAGAAC
** *
28254993 TTTGCGGCGTTTTTTCCTTAGCGCCGCTAATG
1 TTTGCGGCGTTTTTTCAGTAGCGCCACTAATG
28255025 ACCACCTTTA
Statistics
Matches: 143, Mismatches: 28, Indels: 42
0.67 0.13 0.20
Matches are distributed among these distances:
73 1 0.01
74 30 0.21
75 46 0.32
76 7 0.05
78 1 0.01
80 2 0.01
82 1 0.01
84 7 0.05
85 18 0.13
86 29 0.20
87 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (74 bp):
TTTGCGGCGTTTTTTCAGTAGCGCCACTAATGCCAGCCAAAACGACACCGTTTTACGAAAACTGA
GAACAGAAC
Found at i:28255010 original size:160 final size:160
Alignment explanation
Indices: 28254510--28255019 Score: 878
Period size: 160 Copynumber: 3.2 Consensus size: 160
28254500 TAATGACCAC
* *
28254510 CTTTAGCGGCATTTTTCCCCTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAACTGCACCGT
1 CTTT-GCGGCGTTTTTCCCTTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAACTGCACCGT
* * *
28254575 TTTGTCTTCATTATTAAGAATTTTTTGCGGCATTTTTTAGTAGCGCCACTAATGCCCAGGCAAAA
65 TTTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCTAGACAAAA
28254640 CGACACCGTTTTACGAAAACTGAGAACAGAA
130 CGACACCGTTTTACGAAAACTGAGAACAGAA
* * *
28254671 CTTTGTGGCGTTTTTCCCTTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAATTGCACTGTT
1 CTTTGCGGCGTTTTTCCCTTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAACTGCACCGTT
28254736 TTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTTAGTAGCGCCACTAATG-CTCAGACAAA
66 TTGTCTTCATTATTAAGAATTTTTTGCGGCG-TTTTTTAGTAGCGCCACTAATGCCT-AGACAAA
28254800 ACGACACCGTTTTACGAAAACTGAGAACAGAA
129 ACGACACCGTTTTACGAAAACTGAGAACAGAA
* *
28254832 CTTTGCGGCGTTTTTTCCTTAGCGCCGTAAAACCCATTAAATTCACAGCCAAAAACTGCACCGTT
1 CTTTGCGGCGTTTTTCCCTTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAACTGCACCGTT
*
28254897 TTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCTAGCCAAAAC
66 TTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCTAGACAAAAC
28254962 GACACCGTTTTACGAAAACTGAGAACAGAA
131 GACACCGTTTTACGAAAACTGAGAACAGAA
*
28254992 CTTTGCGGCGTTTTTTCCTTAGCGCCGC
1 CTTTGCGGCGTTTTTCCCTTAGCGCCGC
28255020 TAATGACCAC
Statistics
Matches: 331, Mismatches: 15, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
160 174 0.53
161 157 0.47
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (160 bp):
CTTTGCGGCGTTTTTCCCTTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAACTGCACCGTT
TTGTCTTCATTATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCTAGACAAAAC
GACACCGTTTTACGAAAACTGAGAACAGAA
Found at i:28255318 original size:20 final size:21
Alignment explanation
Indices: 28255293--28255332 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
28255283 TTTTTATTTC
28255293 TTTTTAATTTTT-TAATTTTA
1 TTTTTAATTTTTATAATTTTA
28255313 TTTTTAATTTTTATAATTTT
1 TTTTTAATTTTTATAATTTT
28255333 TAAAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTAATTTTTATAATTTTA
Found at i:28255333 original size:28 final size:27
Alignment explanation
Indices: 28255293--28255370 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 27
28255283 TTTTTATTTC
* **
28255293 TTTTTAATTTTTTAATTTTATTTTTAA
1 TTTTTAAATTTTTAATTTTATTTACAA
*
28255320 TTTTTATAATTTTTAAAATTT-TTTACAA
1 TTTTTA-AATTTTT-AATTTTATTTACAA
*
28255348 TTTTTACAATTTTAAATTATTAT
1 TTTTTA-AATTTTTAATT-TTAT
28255371 ATTCAAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
27 9 0.22
28 25 0.62
29 6 0.15
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTAAATTTTTAATTTTATTTACAA
Done.