Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014781.1 Kokia drynarioides strain JFW-HI SEQ_129823, whole genome shotgun sequence
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: 419268
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 528 characters in sequence are not A, C, G, or T
Found at i:501 original size:59 final size:60
Alignment explanation
Indices: 438--787 Score: 351
Period size: 59 Copynumber: 5.9 Consensus size: 60
428 TAATTTTGAG
* * * **
438 AGTTTTGAGGTCAAAAATGGAGATTTTT-AAAGTTCGAGGGCAAAAACGGAATTTTTATA
1 AGTTTCGAGGTCAAAAATGGAGATTTTTGGAAGTTCGAGGGTAAAAACGGAATTTTTGGA
* * * *
497 AGTTTCGAGATCAAAAAT-GAGATTTTTGGAAGATCGAGGGTAAAAATGGGATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAGATTTTTGGAAGTTCGAGGGTAAAAACGGAATTTTTGGA
* **
556 AGTTTCGAGGTTAAAAATGG-GATTTTTGGAAGTTC-AGGGGTAAAAACAAAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAGATTTTTGGAAGTTCGA-GGGTAAAAACGGAATTTTTGGA
* * * * **
615 AGTTTTGAGGTCAAAAGTGG-GATTTTTGGAAGTT-TAGGTGTGAAAATTGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAGATTTTTGGAAGTTCGAGG-GTAAAAACGGAATTTTTGGA
* ** *
674 AGTTTCGAGGTCAAAAAT-GAGATTTTTGGAAGTT-TAGGGGTAAAAATAGAAGTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAGATTTTTGGAAGTTCGA-GGGTAAAAACGGAATTTTTGGA
* * * * *
733 AGTTTTGGGGTCAAAAGTGG-GATTTTTGGAAGTT-TAGGGGTAAAAAAGGAATTTT
1 AGTTTCGAGGTCAAAAATGGAGATTTTTGGAAGTTCGA-GGGTAAAAACGGAATTTT
788 GGATAATTTA
Statistics
Matches: 249, Mismatches: 34, Indels: 16
0.83 0.11 0.05
Matches are distributed among these distances:
58 13 0.05
59 232 0.93
60 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (60 bp):
AGTTTCGAGGTCAAAAATGGAGATTTTTGGAAGTTCGAGGGTAAAAACGGAATTTTTGGA
Found at i:583 original size:30 final size:30
Alignment explanation
Indices: 438--767 Score: 282
Period size: 30 Copynumber: 11.2 Consensus size: 30
428 TAATTTTGAG
* *
438 AGTTTTGAGGTCAAAAATGGAGATTTTT-AA
1 AGTTTCGAGGTCAAAAATGG-GATTTTTGGA
* * * **
468 AG-TTCGAGGGCAAAAACGGAATTTTTATA
1 AGTTTCGAGGTCAAAAATGGGATTTTTGGA
* *
497 AGTTTCGAGATCAAAAATGAGATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGGATTTTTGGA
*
527 AG-ATCGAGGGT-AAAAATGGGATTTTTGGA
1 AGTTTCGA-GGTCAAAAATGGGATTTTTGGA
*
556 AGTTTCGAGGTTAAAAATGGGATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGGATTTTTGGA
* ****
586 AG-TTCAGGGGT-AAAAACAAAATTTTTGGA
1 AGTTTC-GAGGTCAAAAATGGGATTTTTGGA
* *
615 AGTTTTGAGGTCAAAAGTGGGATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGGATTTTTGGA
** * *
645 AGTTT--AGGTGTGAAAATTGAATTTTTGGA
1 AGTTTCGAGGT-CAAAAATGGGATTTTTGGA
*
674 AGTTTCGAGGTCAAAAATGAGATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGGATTTTTGGA
* * * * *
704 AGTTTAGGGGT-AAAAATAGAAGTTTTGGA
1 AGTTTCGAGGTCAAAAATGGGATTTTTGGA
* * *
733 AGTTTTGGGGTCAAAAGTGGGATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGGATTTTTGGA
763 AGTTT
1 AGTTT
768 AGGGGTAAAA
Statistics
Matches: 239, Mismatches: 49, Indels: 24
0.77 0.16 0.08
Matches are distributed among these distances:
28 10 0.04
29 109 0.46
30 116 0.49
31 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (30 bp):
AGTTTCGAGGTCAAAAATGGGATTTTTGGA
Found at i:1932 original size:3 final size:3
Alignment explanation
Indices: 1879--1914 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1869 TTATATTTAT
1879 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1915 AAGCATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2647 original size:6 final size:6
Alignment explanation
Indices: 2633--2717 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
2623 TTTTTTAATT
* * * *
2633 AATTAA AATTTA AATTCA AA-TTA ATTTTA AACTT- AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* *** *
2679 AACTTAA AAGAAA AATTTA AACTTTA AA-CTA AATTTA AA
1 AA-TTTA AATTTA AATTTA AA-TTTA AATTTA AATTTA AA
2718 CCCAAAATGA
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
5 11 0.19
6 37 0.63
7 11 0.19
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (6 bp):
AATTTA
Found at i:2653 original size:12 final size:12
Alignment explanation
Indices: 2633--2717 Score: 50
Period size: 11 Copynumber: 7.2 Consensus size: 12
2623 TTTTTTAATT
*
2633 AATTAAAATTTA
1 AATTTAAATTTA
*
2645 AATTCAAA-TTA
1 AATTTAAATTTA
* *
2656 ATTTTAAACTT-
1 AATTTAAATTTA
2667 AATTTAAATTTA
1 AATTTAAATTTA
* ***
2679 AACTTAAAAGAAA
1 AA-TTTAAATTTA
2692 AATTTAAACTTTA
1 AATTTAAA-TTTA
*
2705 AA-CTAAATTTA
1 AATTTAAATTTA
2716 AA
1 AA
2718 CCCAAAATGA
Statistics
Matches: 55, Mismatches: 14, Indels: 9
0.71 0.18 0.12
Matches are distributed among these distances:
11 24 0.44
12 20 0.36
13 11 0.20
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (12 bp):
AATTTAAATTTA
Found at i:2656 original size:18 final size:17
Alignment explanation
Indices: 2633--2718 Score: 75
Period size: 17 Copynumber: 4.8 Consensus size: 17
2623 TTTTTTAATT
2633 AATTAAAATTTAAA-TTCA
1 AATT-AAATTTAAACTT-A
*
2651 AATTAATTTTAAACTTA
1 AATTAAATTTAAACTTA
*
2668 ATTTAAATTTAAACTTAA
1 AATTAAATTTAAACTT-A
**
2686 AAGAAAAATTTAAACTTTA
1 AA-TTAAATTTAAAC-TTA
*
2705 AACTAAATTTAAAC
1 AATTAAATTTAAAC
2719 CCAAAATGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
17 23 0.41
18 18 0.32
19 13 0.23
20 2 0.04
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (17 bp):
AATTAAATTTAAACTTA
Found at i:15266 original size:61 final size:61
Alignment explanation
Indices: 15171--15354 Score: 368
Period size: 61 Copynumber: 3.0 Consensus size: 61
15161 TAATTGCATC
15171 AGCAATGTGCCAACACAAAATTGGTATGATACCATGGTGAGGGACCAACTTAAGAAAACAG
1 AGCAATGTGCCAACACAAAATTGGTATGATACCATGGTGAGGGACCAACTTAAGAAAACAG
15232 AGCAATGTGCCAACACAAAATTGGTATGATACCATGGTGAGGGACCAACTTAAGAAAACAG
1 AGCAATGTGCCAACACAAAATTGGTATGATACCATGGTGAGGGACCAACTTAAGAAAACAG
15293 AGCAATGTGCCAACACAAAATTGGTATGATACCATGGTGAGGGACCAACTTAAGAAAACAG
1 AGCAATGTGCCAACACAAAATTGGTATGATACCATGGTGAGGGACCAACTTAAGAAAACAG
15354 A
1 A
15355 TGCTAATATG
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 123 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (61 bp):
AGCAATGTGCCAACACAAAATTGGTATGATACCATGGTGAGGGACCAACTTAAGAAAACAG
Found at i:20566 original size:19 final size:19
Alignment explanation
Indices: 20522--20569 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
20512 ATTCGTTTAG
* *
20522 ATTTGAAAGTTGGTTCAAA
1 ATTTGAGAGATGGTTCAAA
20541 ATTTGAGAGATGGTTCAAA
1 ATTTGAGAGATGGTTCAAA
20560 ATTTGAGAGA
1 ATTTGAGAGA
20570 GTTTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (19 bp):
ATTTGAGAGATGGTTCAAA
Found at i:31654 original size:3 final size:3
Alignment explanation
Indices: 31648--31678 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
31638 TTTTTCATAC
31648 AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG
31679 GTACATGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:36859 original size:23 final size:23
Alignment explanation
Indices: 36833--36905 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
36823 NNNNNNNNNT
36833 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* *
36856 GAGCACACGAAGTGCTAAACAGA
1 GAGCACACAAAGTGCTAATCAGA
*
36879 GAGCACACACAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
36902 GAGC
1 GAGC
36906 GCGCTAGTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:37266 original size:27 final size:27
Alignment explanation
Indices: 37236--37292 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
37226 ACTAAATTAT
37236 TTATATCTTGGGCTACAGAATTCGAAA
1 TTATATCTTGGGCTACAGAATTCGAAA
37263 TTATATCTTGGGCTACAGAATTCGAAA
1 TTATATCTTGGGCTACAGAATTCGAAA
37290 TTA
1 TTA
37293 CAACTCTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (27 bp):
TTATATCTTGGGCTACAGAATTCGAAA
Found at i:47212 original size:19 final size:18
Alignment explanation
Indices: 47173--47215 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
47163 GATGGCTAAT
*
47173 TTTGAAGAAAATGTTAAA
1 TTTGAAGAAAATATTAAA
47191 TTTGAAGAAAA-ATTAGAGA
1 TTTGAAGAAAATATTA-A-A
47210 TTTGAA
1 TTTGAA
47216 TCGGTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.55
19 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.33
Consensus pattern (18 bp):
TTTGAAGAAAATATTAAA
Found at i:48653 original size:18 final size:18
Alignment explanation
Indices: 48615--48655 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
48605 ATTATTTATC
* * *
48615 TTATTTATTTTTTATTTT
1 TTATTTATTTTTAAATAT
48633 TTATTTATTTTTAAATAT
1 TTATTTATTTTTAAATAT
48651 TTATT
1 TTATT
48656 GATGTGACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTATTTTTAAATAT
Found at i:48655 original size:4 final size:4
Alignment explanation
Indices: 48606--48642 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
48596 ATTTGGACAA
48606 TTAT TTAT CTTAT TTAT TT-T TTAT TT-T TTAT TTAT TT
1 TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
48643 TTAAATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 6 0.20
4 20 0.67
5 4 0.13
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (4 bp):
TTAT
Found at i:50159 original size:18 final size:18
Alignment explanation
Indices: 50121--50159 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50111 AAACAGATTT
*
50121 TTTTTAATAAAAACTTTA
1 TTTTTAATAAAAACTTAA
50139 TTTTTATATAAAAA-TTAA
1 TTTTTA-ATAAAAACTTAA
50157 TTT
1 TTT
50160 GAATAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTTAATAAAAACTTAA
Found at i:50348 original size:19 final size:20
Alignment explanation
Indices: 50304--50367 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
50294 TTATGATTTT
50304 ATTTTAATAATAAATTTTAAC
1 ATTTTAATAAT-AATTTTAAC
*
50325 A--TTAATAATAGTTTTAA-
1 ATTTTAATAATAATTTTAAC
* *
50342 ATTTTAAGAATAATTCTTAAT
1 ATTTTAATAATAATT-TTAAC
50363 ATTTT
1 ATTTT
50368 GTTGGAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 18 0.50
20 4 0.11
21 6 0.17
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTTTAATAATAATTTTAAC
Found at i:51434 original size:24 final size:24
Alignment explanation
Indices: 51403--51456 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
51393 TAATGTAGTA
*
51403 AAATATTATAACAATTA-AAAATAT
1 AAATATTATAA-AATTATAAAAAAT
51427 AAATATTATAAAATTATAAAAAAT
1 AAATATTATAAAATTATAAAAAAT
51451 -AATATT
1 AAATATT
51457 TTAGTTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATATTATAAAATTATAAAAAAT
Found at i:51442 original size:8 final size:8
Alignment explanation
Indices: 51407--51447 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
51397 GTAGTAAAAT
51407 ATTATAACA
1 ATTATAA-A
51416 ATTA-AAA
1 ATTATAAA
51423 A-TATAAA
1 ATTATAAA
51430 TATTATAAA
1 -ATTATAAA
51439 ATTATAAA
1 ATTATAAA
51447 A
1 A
51448 AATAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
6 2 0.07
7 5 0.17
8 12 0.41
9 10 0.34
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (8 bp):
ATTATAAA
Found at i:65310 original size:2 final size:2
Alignment explanation
Indices: 65303--65336 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
65293 AAAACCCTAA
65303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65337 GTGTGTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66015 original size:14 final size:14
Alignment explanation
Indices: 65978--66006 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
65968 TATTGATAAA
65978 AAATAAAT-AATTT
1 AAATAAATCAATTT
65991 AAATAAATCAATTT
1 AAATAAATCAATTT
66005 AA
1 AA
66007 TTAACTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATAAATCAATTT
Found at i:73212 original size:14 final size:14
Alignment explanation
Indices: 73193--73221 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
73183 TGTTAATGGC
73193 TGTTAAACAGGCTT
1 TGTTAAACAGGCTT
73207 TGTTAAACAGGCTT
1 TGTTAAACAGGCTT
73221 T
1 T
73222 ATGCCTGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (14 bp):
TGTTAAACAGGCTT
Found at i:74470 original size:52 final size:52
Alignment explanation
Indices: 74377--74476 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 52
74367 CATTGAAATG
* * **
74377 ATTAATTACCTTTGTCTGACAAGCTAGTCACTGTTGGTGGTAGGATTAGCAT
1 ATTAATTACCTATGTCTGACAAGCCAGTCACTGTTAATGGTAGGATTAGCAT
* * * *
74429 ATTAATTACGTATGTCTGAGAAGCCAGTTACTTTTAATGGTAGGATTA
1 ATTAATTACCTATGTCTGACAAGCCAGTCACTGTTAATGGTAGGATTA
74477 ACACAAATCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (52 bp):
ATTAATTACCTATGTCTGACAAGCCAGTCACTGTTAATGGTAGGATTAGCAT
Found at i:77476 original size:2 final size:2
Alignment explanation
Indices: 77469--77493 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
77459 GGATGGATGC
77469 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
77494 CTTCATGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:81032 original size:24 final size:24
Alignment explanation
Indices: 80986--81032 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
80976 ACCACGACCA
*
80986 ATTGCACTCTAATCTTTCTCTTTC
1 ATTGCACTCTAATCATTCTCTTTC
*
81010 ATTGCTCTCTAA-CATTCTACTTT
1 ATTGCACTCTAATCATTCT-CTTT
81033 TTTTCTCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.19, C:0.28, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTGCACTCTAATCATTCTCTTTC
Found at i:81547 original size:24 final size:23
Alignment explanation
Indices: 81519--81566 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
81509 CTCATTTATA
*
81519 TAAATAAAATAATAAATATGTATT
1 TAAATAAAATAA-AAATATATATT
**
81543 TAAATAATTTAAAAATATATATT
1 TAAATAAAATAAAAATATATATT
81566 T
1 T
81567 TTTATATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATAAAATAAAAATATATATT
Found at i:82522 original size:15 final size:15
Alignment explanation
Indices: 82504--82532 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
82494 AACACCCTTG
82504 CACTATTAATAACTA
1 CACTATTAATAACTA
82519 CACTATTAATAACT
1 CACTATTAATAACT
82533 GTCTTCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (15 bp):
CACTATTAATAACTA
Found at i:83391 original size:23 final size:23
Alignment explanation
Indices: 83341--83421 Score: 101
Period size: 23 Copynumber: 3.5 Consensus size: 23
83331 ACATTATTCG
*
83341 TGAACATGTTCAATTATATGTTAA
1 TGAACATGTTCGATTA-ATGTTAA
* **
83365 TGAACATGTTCGTTTAATGTTTG
1 TGAACATGTTCGATTAATGTTAA
83388 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGATTAATGTT-AA
83411 TGAACATGTTC
1 TGAACATGTTC
83422 ATGAACAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.65
24 14 0.29
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGTTAA
Found at i:85920 original size:12 final size:12
Alignment explanation
Indices: 85903--85928 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
85893 GTACACTTAA
85903 AAATATTAAAAC
1 AAATATTAAAAC
85915 AAATATTAAAAC
1 AAATATTAAAAC
85927 AA
1 AA
85929 CAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:85952 original size:41 final size:41
Alignment explanation
Indices: 85905--85984 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
85895 ACACTTAAAA
*
85905 ATATTAAAACAAATATTAAAACAACAAACAAATTAAAAACG
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
* * * *
85946 ATATTAAAACAATTCGTAAAACAACAAATAAATTGAAAA
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAA
85985 TGCAATAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (41 bp):
ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
Found at i:94325 original size:22 final size:22
Alignment explanation
Indices: 94300--94342 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
94290 TTTCTTCTTA
* *
94300 ATTCTTTAATTAATCGAATTCT
1 ATTCTGTAATCAATCGAATTCT
*
94322 ATTCTGTAATCACTCGAATTC
1 ATTCTGTAATCAATCGAATTC
94343 ATAATTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTCTGTAATCAATCGAATTCT
Found at i:95854 original size:6 final size:6
Alignment explanation
Indices: 95843--95867 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
95833 AGATGGATTA
95843 GATGGG GATGGG GATGGG GATGGG G
1 GATGGG GATGGG GATGGG GATGGG G
95868 TGAAGGAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GATGGG
Found at i:114392 original size:9 final size:9
Alignment explanation
Indices: 114375--114407 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
114365 CTCTTAATAT
*
114375 TTATATTTA
1 TTATTTTTA
114384 TTATTTTTA
1 TTATTTTTA
114393 TTATTTTTA
1 TTATTTTTA
114402 TT-TTTT
1 TTATTTT
114408 AGTTAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTTTTA
Found at i:114402 original size:15 final size:15
Alignment explanation
Indices: 114374--114406 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
114364 ACTCTTAATA
114374 TTTATATTTATTATT
1 TTTATATTTATTATT
114389 TTTATTATTT-TTATT
1 TTTA-TATTTATTATT
114404 TTT
1 TTT
114407 TAGTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATATTTATTATT
Found at i:120506 original size:18 final size:18
Alignment explanation
Indices: 120466--120505 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
120456 AATAATTATT
120466 TAAAATTATTAGAAATTA
1 TAAAATTATTAGAAATTA
*
120484 TAAAATTATT-GCAATTA
1 TAAAATTATTAGAAATTA
120501 TAAAA
1 TAAAA
120506 AATTAATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
TAAAATTATTAGAAATTA
Found at i:120643 original size:3 final size:3
Alignment explanation
Indices: 120635--120664 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
120625 ATACTTTTTA
120635 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
120665 TTATTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:120839 original size:25 final size:26
Alignment explanation
Indices: 120809--120867 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
120799 GTTTTAATAG
120809 TTTTTTTTATAATTT-CTTATAATT-
1 TTTTTTTTATAATTTACTTATAATTA
* * *
120833 TTATTTTTATTATTTATTTATAATTA
1 TTTTTTTTATAATTTACTTATAATTA
120859 TTTTTTTTA
1 TTTTTTTTA
120868 AGTTTTTCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 13 0.45
25 8 0.28
26 8 0.28
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTTTTTATAATTTACTTATAATTA
Found at i:121021 original size:21 final size:20
Alignment explanation
Indices: 120945--121023 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 20
120935 ATAAAAATTG
*
120945 TAAAAATATAATTAAAAGTTA
1 TAAAAATAT-ATTAAAATTTA
120966 TTAAAAAT-TA-TAAAATATT-
1 -TAAAAATATATTAAAAT-TTA
* *
120985 TGAAAATTATTTTTAAAATTTA
1 T-AAAAATA-TATTAAAATTTA
121007 TAAAAATATCATTAAAA
1 TAAAAATAT-ATTAAAA
121024 ATTTTATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
18 1 0.02
19 10 0.22
20 4 0.09
21 16 0.36
22 14 0.31
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (20 bp):
TAAAAATATATTAAAATTTA
Found at i:121028 original size:31 final size:30
Alignment explanation
Indices: 120936--121028 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 30
120926 ATTTTTAAAA
* * *
120936 TAAAAATTGTAAAAATATAATTAAAAGTTAT
1 TAAAAATTATAAAAATAT-ATTAAAAATTTT
120967 TAAAAATTAT-AAAATAT-TTGAAAATTATTTT
1 TAAAAATTATAAAAATATATT-AAAA--ATTTT
*
120998 TAAAATTTATAAAAATATCATTAAAAATTTT
1 TAAAAATTATAAAAATAT-ATTAAAAATTTT
121029 ATAATTTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
28 2 0.04
29 4 0.08
30 7 0.13
31 26 0.50
32 7 0.13
33 4 0.08
34 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (30 bp):
TAAAAATTATAAAAATATATTAAAAATTTT
Found at i:121062 original size:18 final size:17
Alignment explanation
Indices: 121018--121053 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
121008 AAAAATATCA
121018 TTAAAAATTTTATAATT
1 TTAAAAATTTTATAATT
121035 TTAACAAATTTTAT-ATT
1 TTAA-AAATTTTATAATT
121052 TT
1 TT
121054 TTAATAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAAAATTTTATAATT
Found at i:122604 original size:21 final size:22
Alignment explanation
Indices: 122555--122604 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
122545 TAAAAGGAAG
122555 TATTTAATTATTTAAACATGTT
1 TATTTAATTATTTAAACATGTT
* *
122577 TA-ATAATTATATT-AA-ATTTT
1 TATTTAATTAT-TTAAACATGTT
122597 TATTTAAT
1 TATTTAAT
122605 ATAATGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTTAATTATTTAAACATGTT
Found at i:125766 original size:20 final size:20
Alignment explanation
Indices: 125741--125779 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
125731 TTTTAAATTC
*
125741 AAAAAATTATAAAAATTATT
1 AAAAAAGTATAAAAATTATT
*
125761 AAAAAAGTGTAAAAATTAT
1 AAAAAAGTATAAAAATTAT
125780 ATTTACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAAAAGTATAAAAATTATT
Found at i:126224 original size:20 final size:20
Alignment explanation
Indices: 126199--126236 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
126189 TTTAATGTGT
*
126199 TATAAATTACATAATATATA
1 TATAAATAACATAATATATA
*
126219 TATAAATAACATAGTATA
1 TATAAATAACATAATATA
126237 AAGTATTATA
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:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
TATAAATAACATAATATATA
Found at i:131137 original size:42 final size:42
Alignment explanation
Indices: 131104--131200 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
131094 GCAACTGTCC
* * *
131104 TGGCTGGAGAAGTTGGAACAGAGGCCGTAGTTGCCACGGACT
1 TGGCTGGAGAAGATGGAACAGAGGCAGTAGTTGCCACTGACT
* *
131146 TGGCTGGGGAAGATGGAACAGAGGCAGTAGTTGCCACTGGCT
1 TGGCTGGAGAAGATGGAACAGAGGCAGTAGTTGCCACTGACT
*
131188 TGGCTGAAGAAGA
1 TGGCTGGAGAAGA
131201 AGGCAATGAC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.26, C:0.16, G:0.39, T:0.19
Consensus pattern (42 bp):
TGGCTGGAGAAGATGGAACAGAGGCAGTAGTTGCCACTGACT
Found at i:134326 original size:66 final size:66
Alignment explanation
Indices: 134201--134328 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 66
134191 ATAGTTTAGT
** * * * *
134201 AAGTGAAAATGGCTTTGCGGAAGTTTGGAAGGATGGATCGGAGTTTAATCGAAGGGAAGATAATT
1 AAGTGAAAATGGCTTTGCGGAAGTTCAGAAGGATGGATCGAAGTTCAATCAAAGAGAAGATAATT
134266 C
66 C
* * * * * *
134267 AAGTGAAAATGGCTTTGCGGAGGTTCAGAAGGGTTGATTGAAGTTCGATCAAATAGAAGATA
1 AAGTGAAAATGGCTTTGCGGAAGTTCAGAAGGATGGATCGAAGTTCAATCAAAGAGAAGATA
134329 TGTTGAGTAA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 50 1.00
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (66 bp):
AAGTGAAAATGGCTTTGCGGAAGTTCAGAAGGATGGATCGAAGTTCAATCAAAGAGAAGATAATT
C
Found at i:137442 original size:7 final size:7
Alignment explanation
Indices: 137390--137442 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
137380 CCACAACCCT
137390 CTTGCCA
1 CTTGCCA
*
137397 CTTACCA
1 CTTGCCA
*
137404 CTTACCA
1 CTTGCCA
*
137411 CTTACCA
1 CTTGCCA
137418 CTTGCCA
1 CTTGCCA
137425 CTTGCCA
1 CTTGCCA
137432 CTTGCCA
1 CTTGCCA
137439 CTTG
1 CTTG
137443 GGCTGTATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.19, C:0.42, G:0.09, T:0.30
Consensus pattern (7 bp):
CTTGCCA
Found at i:157566 original size:3 final size:3
Alignment explanation
Indices: 157558--157583 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
157548 AAGCGCAAAT
157558 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
157584 CTTTCCTATA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:165169 original size:16 final size:17
Alignment explanation
Indices: 165148--165187 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
165138 CTAGAGTTTT
*
165148 AGAGAAA-AGAAGAATG
1 AGAGAAACAAAAGAATG
165164 AGAGAAACCAAAAGAATG
1 AGAGAAA-CAAAAGAATG
165182 AGAGAA
1 AGAGAA
165188 GCTTAGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
18 14 0.67
ACGTcount: A:0.62, C:0.05, G:0.28, T:0.05
Consensus pattern (17 bp):
AGAGAAACAAAAGAATG
Found at i:203013 original size:6 final size:6
Alignment explanation
Indices: 203002--203029 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
202992 GGAAGGACAT
203002 GGCAGG GGCAGG GGCAGG GGCAGG GGCA
1 GGCAGG GGCAGG GGCAGG GGCAGG GGCA
203030 ACTTCAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.64, T:0.00
Consensus pattern (6 bp):
GGCAGG
Found at i:208953 original size:5 final size:5
Alignment explanation
Indices: 208945--208971 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
208935 AGGGGAGGGG
208945 GTGGA GTGGA GTGGA GTGGA GTGGA GT
1 GTGGA GTGGA GTGGA GTGGA GTGGA GT
208972 AGGGCATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.59, T:0.22
Consensus pattern (5 bp):
GTGGA
Found at i:216383 original size:47 final size:47
Alignment explanation
Indices: 216329--216421 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
216319 ATTGCCAAAC
216329 TAGCAAAGTAGAAACCAATTAAATCAATGGGCGCTTCCATTGTTTAT
1 TAGCAAAGTAGAAACCAATTAAATCAATGGGCGCTTCCATTGTTTAT
216376 TAGCAAAGTAGAAACCAATTAAATCAATGGGCGCTTCCATTGTTTA
1 TAGCAAAGTAGAAACCAATTAAATCAATGGGCGCTTCCATTGTTTA
216422 CTTCAATAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (47 bp):
TAGCAAAGTAGAAACCAATTAAATCAATGGGCGCTTCCATTGTTTAT
Found at i:226245 original size:22 final size:23
Alignment explanation
Indices: 226220--226265 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
226210 AATTTTTGTT
226220 AGAT-TAATGAAAATTTTTTAAA
1 AGATATAATGAAAATTTTTTAAA
* * *
226242 AGATATTATTAAATTTTTTTAAA
1 AGATATAATGAAAATTTTTTAAA
226265 A
1 A
226266 AAGTTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (23 bp):
AGATATAATGAAAATTTTTTAAA
Found at i:239425 original size:59 final size:60
Alignment explanation
Indices: 239349--239573 Score: 196
Period size: 60 Copynumber: 3.8 Consensus size: 60
239339 AAAAAATTGG
239349 TGTTGGTCAT-TGCATGGCCGACA-CCCTTTTTAATCTGATAAAAAAATCAAATTTTTTTA
1 TGTTGGTCATATGCATGGCCGACACCCCTTTTT-ATCTGATAAAAAAATCAAATTTTTTTA
* * * *
239408 TGTTGGTCATAT-AATGGCCGACACCCCTTTTT-TCAGATAATAAAATTTCAAATTTTTTTG
1 TGTTGGTCATATGCATGGCCGACACCCCTTTTTATCTGATAA-AAAA-ATCAAATTTTTTTA
* * * * * *
239468 TGTTGG-C-TATTGCATAGTCGACATCCCTTTTTATCTGAATTAAAAAAT-AAAATTTTTGA
1 TGTTGGTCATA-TGCATGGCCGACACCCCTTTTTATCTG-ATAAAAAAATCAAATTTTTTTA
* * * *
239527 GTGTTGGTCATA-CCATGACTGACACTCCCTTTTTTATCTGGTAAAAA
1 -TGTTGGTCATATGCATGGCCGACAC-CCC-TTTTTATCTGATAAAAA
239574 TTTAATTTTT
Statistics
Matches: 131, Mismatches: 22, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
58 9 0.07
59 34 0.26
60 57 0.44
61 16 0.12
62 15 0.11
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (60 bp):
TGTTGGTCATATGCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTTTTTA
Found at i:239572 original size:120 final size:119
Alignment explanation
Indices: 239348--239587 Score: 265
Period size: 120 Copynumber: 2.0 Consensus size: 119
239338 AAAAAAATTG
* * *
239348 GTGTTGGTCATTGCATGGCCGACACCCTTTTTAATCTGATAAAAAAATCAAATTTTTTTATGTTG
1 GTGTTGGTCATTGCATAGCCGACACCCTTTTTAATCTGATAAAAAAATCAAAATTTTTGATGTTG
* *
239413 GTCATATAATGGCCGACACCCCTTTTTTCAGATAAT-AAAATTTCAAATTTTTTT
66 GTCATACAATGACCGACACCCCTTTTTTCAGATAATAAAAATTT-AAATTTTTTT
* *
239467 GTGTTGG-CTATTGCATAGTCGACATCCCTTTTT-ATCTGAATTAAAAAAT-AAAATTTTTGAGT
1 GTGTTGGTC-ATTGCATAGCCGACA-CCCTTTTTAATCTG-ATAAAAAAATCAAAATTTTTGA-T
* * ** ** *
239529 GTTGGTCATACCATGACTGACACTCCCTTTTTT-ATCTGGTAAAAATTTAATTTTTTTT
62 GTTGGTCATACAATGACCGACAC-CCCTTTTTTCAGATAATAAAAATTTAAATTTTTTT
239587 G
1 G
239588 CATGGCCAAC
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
118 1 0.01
119 34 0.34
120 50 0.50
121 16 0.16
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (119 bp):
GTGTTGGTCATTGCATAGCCGACACCCTTTTTAATCTGATAAAAAAATCAAAATTTTTGATGTTG
GTCATACAATGACCGACACCCCTTTTTTCAGATAATAAAAATTTAAATTTTTTT
Found at i:239831 original size:117 final size:119
Alignment explanation
Indices: 239598--239831 Score: 253
Period size: 117 Copynumber: 2.0 Consensus size: 119
239588 CATGGCCAAC
*
239598 AAAAAATTCGAATTTTTTATCTAACAAAAAGGAAGTGTCGACCATGGCATAACCAACACCCAAAA
1 AAAAAATTCGAATTTTTTATCTAACAAAAAGG-AGTGTCGACCATGGCATAACCAACACCAAAAA
* * * *
239663 ATTTAATTTTTTATTTAGATAAAAAGGGCTATCAGCCATGCAATGGTCAACATAA
65 ATTTAATTTTTTATTCAGATAAAAAGGACTATCAGCCATGCAACGGCCAACATAA
* * * * *
239718 AAAAAATT-GAAATTTTTTATCTGA-AGAAAGG-GTGTTGACCATTGCATGACCAACACCAAAAA
1 AAAAAATTCG-AATTTTTTATCTAACAAAAAGGAGTGTCGACCATGGCATAACCAACACCAAAAA
** * * * *
239780 ATTTGGTTTTTT-TATCAGATAAATAGGATTGTCTGCCATCGC-ACGGCCAACA
65 ATTTAATTTTTTAT-TCAGATAAAAAGGACTATCAGCCAT-GCAACGGCCAACA
239832 CCCAAAAATT
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
116 1 0.01
117 64 0.67
118 2 0.02
119 7 0.07
120 21 0.22
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (119 bp):
AAAAAATTCGAATTTTTTATCTAACAAAAAGGAGTGTCGACCATGGCATAACCAACACCAAAAAA
TTTAATTTTTTATTCAGATAAAAAGGACTATCAGCCATGCAACGGCCAACATAA
Found at i:239962 original size:58 final size:58
Alignment explanation
Indices: 239854--239966 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 58
239844 ATTTTTTTTA
* ** *
239854 TCAGATTAAAAAGGGGTGTCAACTATGCAATGGTCAATATCAAAACTTTTTTTTCCTG
1 TCAGATAAAAAAGGGGTGTCAACTATGCAATGCCCAACATCAAAACTTTTTTTTCCTG
*** **
239912 TCAGATAAAAAAGAGGGTGTTGGCTATGCAATGCCCAACATCAAATTTTTTTTTT
1 TCAGATAAAAAAG-GGGTGTCAACTATGCAATGCCCAACATCAAAACTTTTTTTT
239967 TCAAATTCTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
58 12 0.27
59 33 0.73
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (58 bp):
TCAGATAAAAAAGGGGTGTCAACTATGCAATGCCCAACATCAAAACTTTTTTTTCCTG
Found at i:249833 original size:21 final size:23
Alignment explanation
Indices: 249807--249851 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
249797 ATAAAATTTT
249807 ATAAAATTAT-TAAATA-TTAAA
1 ATAAAATTATATAAATATTTAAA
249828 ATAAAATTATATAAATATTTAAA
1 ATAAAATTATATAAATATTTAAA
249851 A
1 A
249852 AATAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 10 0.45
22 6 0.27
23 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATAAAATTATATAAATATTTAAA
Found at i:249862 original size:29 final size:30
Alignment explanation
Indices: 249792--249868 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
249782 AAAAAAATTC
* * *
249792 AATAAATAAAATTTTATAAAATTATTAAAT
1 AATAAAAAAAATTATATAAAATTATTAAAA
*
249822 ATTAAAATAAAATTATAT-AAA-TATTTAAAA
1 AATAAAA-AAAATTATATAAAATTA-TTAAAA
*
249852 AATAAAAAAAATAATAT
1 AATAAAAAAAATTATAT
249869 TGGCGAGTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 11 0.28
30 19 0.49
31 9 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (30 bp):
AATAAAAAAAATTATATAAAATTATTAAAA
Found at i:253551 original size:28 final size:29
Alignment explanation
Indices: 253506--253564 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
253496 GATAAAATTA
**
253506 TAGTATAAAAAATCAAATCATTATCAAAT
1 TAGTATAAAAAATCAAATCACCATCAAAT
253535 TAGTAT-AAAAATCAAATCACCATCAAAT
1 TAGTATAAAAAATCAAATCACCATCAAAT
253563 TA
1 TA
253565 ATAAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (29 bp):
TAGTATAAAAAATCAAATCACCATCAAAT
Found at i:278900 original size:14 final size:15
Alignment explanation
Indices: 278875--278906 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
278865 ATATTAAGTT
278875 AATTTTATTTTTCAA
1 AATTTTATTTTTCAA
278890 AATTTTATTTTT-AA
1 AATTTTATTTTTCAA
278904 AAT
1 AAT
278907 AAATTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTTATTTTTCAA
Found at i:291264 original size:60 final size:60
Alignment explanation
Indices: 291190--291308 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 60
291180 AATTAAATTA
* * *
291190 ACAAATTTTATAAATATTGATGGCTAAATTTGTTGAATGTTTTATATTTAAGATCAAATG
1 ACAAATTTTATAAATATTAAAGACTAAATTTGTTGAATGTTTTATATTTAAGATCAAATG
* * *
291250 ACAAATTTTGTAAATTTTAAAGATTAAATTTGTTGAATGTTTTATATTTAAGATCAAAT
1 ACAAATTTTATAAATATTAAAGACTAAATTTGTTGAATGTTTTATATTTAAGATCAAAT
291309 TGATAGAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (60 bp):
ACAAATTTTATAAATATTAAAGACTAAATTTGTTGAATGTTTTATATTTAAGATCAAATG
Found at i:291303 original size:30 final size:30
Alignment explanation
Indices: 291215--291309 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
291205 ATTGATGGCT
291215 AAATTTGTTGAATGTTTTATATTTAAGATC
1 AAATTTGTTGAATGTTTTATATTTAAGATC
*** * *
291245 AAA--TGACAAAT-TTTGTAAATTTTAAAGATT
1 AAATTTGTTGAATGTTT-TATA-TTT-AAGATC
291275 AAATTTGTTGAATGTTTTATATTTAAGATC
1 AAATTTGTTGAATGTTTTATATTTAAGATC
291305 AAATT
1 AAATT
291310 GATAGAATGT
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
27 3 0.06
28 8 0.16
29 3 0.06
30 21 0.43
31 3 0.06
32 8 0.16
33 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (30 bp):
AAATTTGTTGAATGTTTTATATTTAAGATC
Found at i:291318 original size:30 final size:30
Alignment explanation
Indices: 291224--291319 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
291214 TAAATTTGTT
*
291224 GAATGTTTTATATTTAAGATCAAA-TGACA
1 GAATGTTTTATATTTAAGATCAAATTGATA
* * *
291253 -AAT-TTTGTAAATTTTAAAGATTAAATTTG-TT
1 GAATGTTT-TATA-TTT-AAGATCAAA-TTGATA
291284 GAATGTTTTATATTTAAGATCAAATTGATA
1 GAATGTTTTATATTTAAGATCAAATTGATA
291314 GAATGT
1 GAATGT
291320 GTAAATATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
27 3 0.06
28 6 0.12
29 6 0.12
30 23 0.44
31 3 0.06
32 8 0.15
33 3 0.06
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.44
Consensus pattern (30 bp):
GAATGTTTTATATTTAAGATCAAATTGATA
Found at i:293154 original size:40 final size:40
Alignment explanation
Indices: 293085--293166 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
293075 GCCTGATAGT
* *
293085 ATACACCGGTACGAAACCTGCTAGACACTAAGCCCGATAA
1 ATACACCGGCACGAAACCTACTAGACACTAAGCCCGATAA
* * * *
293125 ATACACCGGCACTAAGCCTACTAGGCACTAAGCTCGATAA
1 ATACACCGGCACGAAACCTACTAGACACTAAGCCCGATAA
293165 AT
1 AT
293167 TCTGGGGAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (40 bp):
ATACACCGGCACGAAACCTACTAGACACTAAGCCCGATAA
Found at i:294962 original size:6 final size:7
Alignment explanation
Indices: 294942--294966 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
294932 TTATCAATAT
294942 AATAAAA
1 AATAAAA
294949 AATAAAA
1 AATAAAA
294956 AATAAAA
1 AATAAAA
294963 AATA
1 AATA
294967 TTTTCGGCAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AATAAAA
Found at i:301443 original size:16 final size:16
Alignment explanation
Indices: 301405--301447 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
301395 CCGACTCGAC
* *
301405 TTATTTTAATTTTATA
1 TTATTTTTATATTATA
*
301421 ATA-TTTTATATTATA
1 TTATTTTTATATTATA
301436 TTATTTTTATAT
1 TTATTTTTATAT
301448 ATTATGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTTTATATTATA
Found at i:301595 original size:16 final size:17
Alignment explanation
Indices: 301565--301606 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
301555 TAAAAATGTA
*
301565 TAAAATTAT-TAATA-T
1 TAAAATAATGTAATATT
301580 TAAAATAATGTAATATT
1 TAAAATAATGTAATATT
*
301597 TAAAAAAATG
1 TAAAATAATG
301607 AAAAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 8 0.35
16 5 0.22
17 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
TAAAATAATGTAATATT
Found at i:315235 original size:18 final size:16
Alignment explanation
Indices: 315198--315228 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
315188 AATTAATAGA
315198 AAAATTATAATTTTTT
1 AAAATTATAATTTTTT
315214 AAAATTATAATTTTT
1 AAAATTATAATTTTT
315229 ATTAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAAATTATAATTTTTT
Found at i:315384 original size:13 final size:12
Alignment explanation
Indices: 315353--315387 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
315343 TAATTTTAGA
315353 TTTTTTATAACT
1 TTTTTTATAACT
315365 TTTTTTATAACT
1 TTTTTTATAACT
315377 TTTGTTTATAA
1 TTT-TTTATAA
315388 TATTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (12 bp):
TTTTTTATAACT
Found at i:318294 original size:24 final size:24
Alignment explanation
Indices: 318262--318309 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
318252 GCCGCCGAAG
318262 AAGCCCAAGGCAATTATATCAATT
1 AAGCCCAAGGCAATTATATCAATT
318286 AAGCCCAAGGCAATTATATCAATT
1 AAGCCCAAGGCAATTATATCAATT
318310 GGGCCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (24 bp):
AAGCCCAAGGCAATTATATCAATT
Found at i:325232 original size:29 final size:28
Alignment explanation
Indices: 325157--325233 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 28
325147 AGTTGAATTG
* *
325157 AATTTTGAAATCTAAAAAGTAAATGGACTG
1 AATTTT-AAATCT-AAAAGTAAATAGACTA
**
325187 AATTCTTAAAAATAAAAGTACAA-AGACTA
1 AATT-TTAAATCTAAAAGTA-AATAGACTA
325216 AATTTTAAATCTCAAAAG
1 AATTTTAAATCT-AAAAG
325234 AGTACATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
28 6 0.16
29 20 0.53
30 10 0.26
31 2 0.05
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (28 bp):
AATTTTAAATCTAAAAGTAAATAGACTA
Found at i:328894 original size:2 final size:2
Alignment explanation
Indices: 328887--328911 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
328877 GATTGAGCAA
328887 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
328912 AGATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:334500 original size:27 final size:27
Alignment explanation
Indices: 334432--334501 Score: 106
Period size: 26 Copynumber: 2.6 Consensus size: 27
334422 TTTTTGTACT
*
334432 ATTAATATTCTTATCCATAAATAGACC
1 ATTAAAATTCTTATCCATAAATAGACC
* *
334459 GTT-AAATTCTTATCCATATATAGACC
1 ATTAAAATTCTTATCCATAAATAGACC
334485 ATTAAAATTCTTATCCA
1 ATTAAAATTCTTATCCA
334502 GATCTCAACC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 23 0.61
27 15 0.39
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (27 bp):
ATTAAAATTCTTATCCATAAATAGACC
Found at i:334516 original size:27 final size:27
Alignment explanation
Indices: 334433--334517 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
334423 TTTTGTACTA
* * *
334433 TTAATATTCTTATCCATAAATAGACCG
1 TTAAAATTCTTATCCAGATATAGACCG
* *
334460 TT-AAATTCTTATCCATATATAGACCA
1 TTAAAATTCTTATCCAGATATAGACCG
*
334486 TTAAAATTCTTATCCAGATCTCA-ACCG
1 TTAAAATTCTTATCCAGATAT-AGACCG
334513 TTAAA
1 TTAAA
334518 CCGTTAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.46
27 26 0.52
28 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (27 bp):
TTAAAATTCTTATCCAGATATAGACCG
Found at i:337371 original size:98 final size:99
Alignment explanation
Indices: 337262--337442 Score: 292
Period size: 99 Copynumber: 1.8 Consensus size: 99
337252 TTTTCAACTG
337262 ATTTATAACATCATAATTAACTATGAAT-AATAATTATAAAATTAATAAATGTTCACTCTTTCTT
1 ATTTATAACATCATAATTAACTATGAATGAATAATTATAAAATTAATAAATGTTCACTCTTTCTT
337326 ACAATAATGATTTATTATAATATGTTTTGAAGTA
66 ACAATAATGATTTATTATAATATGTTTTGAAGTA
* * ** *
337360 ATTTATAACATCATAATTAACTATGAATGTATAATTATAAAATTGATGGATGTTCACTCTTTTTT
1 ATTTATAACATCATAATTAACTATGAATGAATAATTATAAAATTAATAAATGTTCACTCTTTCTT
* *
337425 ACAATGATGGTTTATTAT
66 ACAATAATGATTTATTAT
337443 CATACAGATA
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
98 28 0.37
99 47 0.63
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (99 bp):
ATTTATAACATCATAATTAACTATGAATGAATAATTATAAAATTAATAAATGTTCACTCTTTCTT
ACAATAATGATTTATTATAATATGTTTTGAAGTA
Found at i:344875 original size:6 final size:6
Alignment explanation
Indices: 344861--344896 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
344851 GTATTTATAG
*
344861 AAAACT AAAATT AAAATT AAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
344897 CATAGCAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:350467 original size:58 final size:61
Alignment explanation
Indices: 350359--350594 Score: 192
Period size: 65 Copynumber: 3.8 Consensus size: 61
350349 NNNNNNAAAA
* * * * *
350359 AAAAAAAACACTTCTTTTAACTTCTAAATTTTAAAAATCTTCTAACCATAGTTTCAA-CCCC
1 AAAACAAACACTT-ATTTAACTTCTAAATTTCACAACTCTTCTAACCATAGTTTCAACCCCC
* * * * *
350420 AAAA-AAA-AGTTATTTATCTTCTCAATTTCACAACTCTTTTAATCATAGTTTCAACCCCC
1 AAAACAAACACTTATTTAACTTCTAAATTTCACAACTCTTCTAACCATAGTTTCAACCCCC
* * * * **
350479 AAAACAAACACTTCTTTAACTTCTAAATTTCATAAATCTTCTAACCATATTTTTACCCCTCCCCC
1 AAAACAAACACTTATTTAACTTCTAAATTTCACAACTCTTCTAACCATA-GTTT----CAACCCC
350544 C
61 C
* * ** * *
350545 AAAA-AAACACTTCTTTAGCTTCCCAATTTCACAAATCTTCTAACTATAGT
1 AAAACAAACACTTATTTAACTTCTAAATTTCACAACTCTTCTAACCATAGT
350595 AACAATAGTT
Statistics
Matches: 141, Mismatches: 26, Indels: 13
0.78 0.14 0.07
Matches are distributed among these distances:
58 35 0.25
59 11 0.08
60 6 0.04
61 36 0.26
62 3 0.02
64 1 0.01
65 39 0.28
66 10 0.07
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (61 bp):
AAAACAAACACTTATTTAACTTCTAAATTTCACAACTCTTCTAACCATAGTTTCAACCCCC
Found at i:351113 original size:20 final size:21
Alignment explanation
Indices: 351088--351129 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
351078 TATTTTTTTA
351088 GTTGA-TTTTCTGAATTTATT
1 GTTGATTTTTCTGAATTTATT
351108 GTTGATTTTTTCTGAATTTATT
1 GTTGA-TTTTTCTGAATTTATT
351130 ATTTTGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
22 15 0.75
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.62
Consensus pattern (21 bp):
GTTGATTTTTCTGAATTTATT
Found at i:361172 original size:13 final size:13
Alignment explanation
Indices: 361156--361186 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
361146 TTTTTATATA
361156 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
*
361169 TTTTCTTTTTTTT
1 TTTTCTCTTTTTT
361182 TTTTC
1 TTTTC
361187 ACACTTCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:361717 original size:21 final size:21
Alignment explanation
Indices: 361691--361732 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
361681 ATGGATGTTC
361691 ACTCTTTTTTACAATAATAGT
1 ACTCTTTTTTACAATAATAGT
*
361712 ACTCTTTTTTATAATAATAGT
1 ACTCTTTTTTACAATAATAGT
361733 TTGCTATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (21 bp):
ACTCTTTTTTACAATAATAGT
Found at i:364747 original size:31 final size:31
Alignment explanation
Indices: 364712--364773 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
364702 CCCAATAACT
*
364712 TAAATAAAAACTTTTGAATAG-TTCAGTGACC
1 TAAATAAAAACTTTCGAATAGCTTCA-TGACC
*
364743 TAAATGAAAACTTTCGAATAGCTTCATGACC
1 TAAATAAAAACTTTCGAATAGCTTCATGACC
364774 ATGTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (31 bp):
TAAATAAAAACTTTCGAATAGCTTCATGACC
Found at i:371838 original size:16 final size:16
Alignment explanation
Indices: 371817--371847 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
371807 ATTTAAATTT
*
371817 AATATTTATTTTTTAA
1 AATATTTAATTTTTAA
371833 AATATTTAATTTTTA
1 AATATTTAATTTTTA
371848 TATTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATATTTAATTTTTAA
Found at i:375122 original size:21 final size:21
Alignment explanation
Indices: 375098--375149 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
375088 TGAGACAATA
375098 CTACCGATACAAGT-ATAACTT
1 CTACCGATACAAGTAAT-ACTT
* * *
375119 CTACCGAAACATGTAATGCTT
1 CTACCGATACAAGTAATACTT
375140 CTACCGATAC
1 CTACCGATAC
375150 TAAAAACTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTAATACTT
Found at i:376273 original size:193 final size:195
Alignment explanation
Indices: 375983--376353 Score: 482
Period size: 201 Copynumber: 1.9 Consensus size: 195
375973 TTGTACTATA
* *
375983 AACTGTTCCCTAACGATACTGCTCACACGAGCTGTCGAGAGTATGCAATAAGCATAATCCCAACC
1 AACTGTTCCCTAACGATACTGCTCACACGAGCTGTCAAGAATATGCAATAAGCATAATCCCAACC
* * * *
376048 ATCGTAGGGTCTGTAATTCATTTAGGATCCATA-TC-TCT-TTT-CCAAGTCACGATGCTACTC-
66 ATCGTAGGGCCTGTAATCCATTTAGAATCCATATTCTTCTATTTCCCAACTCACGATGCTACTCG
* *
376108 ACACGAGCTGTCAAAGACTCGCAACATATGCGGTACCTCAGCCATTGATACGGTATCTGTGCATA
131 A-ACGAGCTGTCAAAGACTAGCAACATATGCGATACCTCAGCCATTGATACGGTATCTGTGCATA
376173 T
195 T
* * * * * *
376174 AACTGTTCCTTAACTATGCTGCTCACACGAGCTGTCAAGAATATGCACTTATGCATAAATCTCAA
1 AACTGTTCCCTAACGATACTGCTCACACGAGCTGTCAAGAATATGCA-ATAAGCAT-AATCCCAA
*
376239 CCATCGTAGGGCCTGTAATCCATTTAGAATCCATATTTCTTTTCTCATTTCCCGACTCACGATGC
64 CCATCGTAGGGCCTGTAATCCATTTAGAATCCATA-TTC--TTCT-ATTTCCCAACTCACGATGC
* * *
376304 TGCTCGAACGAGCTGTCGAGGACTAGCAACATATGCGATACCTCAGCCAT
125 TACTCGAACGAGCTGTCAAAGACTAGCAACATATGCGATACCTCAGCCAT
376354 CGCGTCGGTT
Statistics
Matches: 151, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
191 42 0.28
192 6 0.04
193 39 0.26
195 2 0.01
198 3 0.02
200 3 0.02
201 55 0.36
202 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (195 bp):
AACTGTTCCCTAACGATACTGCTCACACGAGCTGTCAAGAATATGCAATAAGCATAATCCCAACC
ATCGTAGGGCCTGTAATCCATTTAGAATCCATATTCTTCTATTTCCCAACTCACGATGCTACTCG
AACGAGCTGTCAAAGACTAGCAACATATGCGATACCTCAGCCATTGATACGGTATCTGTGCATAT
Found at i:378205 original size:17 final size:17
Alignment explanation
Indices: 378182--378226 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
378172 AAATATATTT
378182 AATATTTATTAAAA-AA
1 AATATTTATTAAAATAA
* *
378198 TTATATTTAATAAAATAA
1 -AATATTTATTAAAATAA
378216 AATATTTATTA
1 AATATTTATTA
378227 TATTTATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTTATTAAAATAA
Found at i:378283 original size:39 final size:39
Alignment explanation
Indices: 378203--378291 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
378193 AAAAATTATA
* * *
378203 TTTAATAAAATAAAATATTTATTATATTTATTTATATTT
1 TTTAATATAATAAAACATTTATTATATTTATATATATTT
*
378242 TTTAATATAATAGAACATTTATTATA-TTATGATAT-TGTT
1 TTTAATATAATAAAACATTTATTATATTTAT-ATATAT-TT
378281 TTTAAATATAA
1 TTT-AATATAA
378292 ATATTTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
38 5 0.12
39 31 0.72
40 7 0.16
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (39 bp):
TTTAATATAATAAAACATTTATTATATTTATATATATTT
Found at i:378378 original size:14 final size:13
Alignment explanation
Indices: 378358--378401 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
378348 TTAATATATT
378358 ATATTTTTAAAAA
1 ATATTTTTAAAAA
378371 ATATTTTTAAATAA
1 ATATTTTTAAA-AA
*
378385 AAATTATTCTAAAAA
1 ATATT-TT-TAAAAA
378400 AT
1 AT
378402 TAAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 11 0.42
14 6 0.23
15 5 0.19
16 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTTTAAAAA
Found at i:379628 original size:26 final size:27
Alignment explanation
Indices: 379599--379650 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
379589 TTAAATTCTA
*
379599 ACACTT-AACTTTTCAGTTTATCAAAT
1 ACACTTAAAATTTTCAGTTTATCAAAT
379625 ACACTTAAAATTTTCAGTTTATCAAA
1 ACACTTAAAATTTTCAGTTTATCAAA
379651 GAACATCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (27 bp):
ACACTTAAAATTTTCAGTTTATCAAAT
Found at i:384174 original size:58 final size:58
Alignment explanation
Indices: 384084--384199 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
384074 ATCACTGGAG
*
384084 GTGGGTGAGCAAAAATATGAAATCCGATTGCACTGCCCTTAACCCATGTAGTCATAGC
1 GTGGGTGAGCAAAAATATGAAATCCGATTGCACTGCCCTTAACCCATATAGTCATAGC
* *
384142 GTGGGTGAGCAAAAATATGAAATCTGGTTGCACTGCCCTTAACCCATATAGTCATAGC
1 GTGGGTGAGCAAAAATATGAAATCCGATTGCACTGCCCTTAACCCATATAGTCATAGC
384200 CTTAATAATC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (58 bp):
GTGGGTGAGCAAAAATATGAAATCCGATTGCACTGCCCTTAACCCATATAGTCATAGC
Found at i:389097 original size:27 final size:27
Alignment explanation
Indices: 389052--389125 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
389042 TGTCAAAGTG
* * *
389052 GAGAGTGAGGATTCTAAGCTCCA-GTTC
1 GAGAATGAGGATCCAAAGC-CCAGGTTC
* * *
389079 GAGACTGATGATCCAAAGCCCAGGTTG
1 GAGAATGAGGATCCAAAGCCCAGGTTC
*
389106 GAGAATGAGGGTCCAAAGCC
1 GAGAATGAGGATCCAAAGCC
389126 TGAGGGGGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 3 0.08
27 35 0.92
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.19
Consensus pattern (27 bp):
GAGAATGAGGATCCAAAGCCCAGGTTC
Found at i:393786 original size:30 final size:30
Alignment explanation
Indices: 393752--393816 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
393742 TCAAATTATG
393752 TAATTTATATTCGAGTTAAAT-CAAATAACT
1 TAATTTATATTCGAGTT-AATCCAAATAACT
* * *
393782 TAATTTTTTATTGGAGTTTATCCAAATAACT
1 TAA-TTTATATTCGAGTTAATCCAAATAACT
393813 TAAT
1 TAAT
393817 AATTCAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (30 bp):
TAATTTATATTCGAGTTAATCCAAATAACT
Found at i:397036 original size:105 final size:105
Alignment explanation
Indices: 396850--397041 Score: 339
Period size: 105 Copynumber: 1.8 Consensus size: 105
396840 AAACACTTAC
*
396850 ACAAACCATATACAACATTAATTTACTAAATTTCATTTAAATCCTTCAAGAATTATAATGTTTGT
1 ACAAACCAAATACAACATTAATTTACTAAATTTCATTTAAATCCTTCAAGAATTATAATGTTTGT
* * *
396915 AGCATGATCCACAATATTCAAAATCCTTAACTTAAAATAT
66 AGCATGACCCAAAATATACAAAATCCTTAACTTAAAATAT
*
396955 ACAAACCAAATACAGCATTAATTTACTAAATTTCATTTAAATCCTTCAAGAATTATAATGTTTGT
1 ACAAACCAAATACAACATTAATTTACTAAATTTCATTTAAATCCTTCAAGAATTATAATGTTTGT
397020 AGCATGACCCAAAATATACAAA
66 AGCATGACCCAAAATATACAAA
397042 CCATATTGAC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 82 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (105 bp):
ACAAACCAAATACAACATTAATTTACTAAATTTCATTTAAATCCTTCAAGAATTATAATGTTTGT
AGCATGACCCAAAATATACAAAATCCTTAACTTAAAATAT
Found at i:397324 original size:28 final size:27
Alignment explanation
Indices: 397289--397343 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
397279 ACTTTGAAAT
*
397289 TTGAAATTTA-GATTAGAAAATCGAGAA
1 TTGAAA-TTAGGAATAGAAAATCGAGAA
*
397316 TTGACAATTAGGAATAGGAAATCGAGAA
1 TTGA-AATTAGGAATAGAAAATCGAGAA
397344 CAAGAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.25
Consensus pattern (27 bp):
TTGAAATTAGGAATAGAAAATCGAGAA
Found at i:402540 original size:2 final size:2
Alignment explanation
Indices: 402533--402559 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
402523 CCAAGAGGGG
402533 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
402560 AAAGAGAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:402695 original size:10 final size:10
Alignment explanation
Indices: 402680--402712 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
402670 CATTTTGTAG
402680 AAAATTAAAT
1 AAAATTAAAT
402690 AAAATTAAA-
1 AAAATTAAAT
402699 ATAAATTAAAT
1 A-AAATTAAAT
402710 AAA
1 AAA
402713 CCAAACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.05
10 19 0.90
11 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATTAAAT
Found at i:403200 original size:75 final size:75
Alignment explanation
Indices: 403077--403216 Score: 262
Period size: 75 Copynumber: 1.9 Consensus size: 75
403067 AAAGTATGCT
403077 AGTGAGGTATGCAGCACCATTCTCGTTAATACTGACCAAATTCTTTAACATTTAATGAAAATAAT
1 AGTGAGGTATGCAGCACCATTCTCGTTAATACTGACCAAATTCTTTAACATTTAATGAAAATAAT
403142 CGTAGTATTA
66 CGTAGTATTA
* *
403152 AGTGAGGTATGCAGCACCATTCTCGTTAATAGTGCCCAAATTCTTTAACATTTAATGAAAATAAT
1 AGTGAGGTATGCAGCACCATTCTCGTTAATACTGACCAAATTCTTTAACATTTAATGAAAATAAT
403217 GTTGGTCGAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (75 bp):
AGTGAGGTATGCAGCACCATTCTCGTTAATACTGACCAAATTCTTTAACATTTAATGAAAATAAT
CGTAGTATTA
Found at i:406373 original size:2 final size:2
Alignment explanation
Indices: 406366--406395 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
406356 ATTAATAATC
406366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
406396 TACTACCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:407572 original size:26 final size:25
Alignment explanation
Indices: 407540--407591 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
407530 CTAGGGAAGA
*
407540 GACGGTGG-GGGGAGAAGGAG-GGG
1 GACGGGGGTGGGGAGAAGGAGAGGG
*
407563 GACGGGGGTGGGGAGAGGGAGAGGG
1 GACGGGGGTGGGGAGAAGGAGAGGG
407588 GACG
1 GACG
407592 ATGGGGAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 11 0.44
25 7 0.28
ACGTcount: A:0.21, C:0.06, G:0.69, T:0.04
Consensus pattern (25 bp):
GACGGGGGTGGGGAGAAGGAGAGGG
Found at i:407658 original size:26 final size:25
Alignment explanation
Indices: 407613--407662 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
407603 TTTTCTTTTT
* *
407613 TTTTTTTTAATAATATTATATAATTA
1 TTTTATTTAATAATAATATA-AATTA
*
407639 TTTTATTTAATATTAATATAAATT
1 TTTTATTTAATAATAATATAAATT
407663 TTATTAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTATTTAATAATAATATAAATTA
Found at i:409767 original size:21 final size:21
Alignment explanation
Indices: 409710--409761 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
409700 ATAATAAAAT
*
409710 AATAACAAAATGACAACAAAC
1 AATAACAAAATGACATCAAAC
* *
409731 AACATCAAAATGACATCAAAC
1 AATAACAAAATGACATCAAAC
409752 AATAACAAAA
1 AATAACAAAA
409762 CAACATTGAA
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:0.65, C:0.19, G:0.04, T:0.12
Consensus pattern (21 bp):
AATAACAAAATGACATCAAAC
Found at i:414863 original size:33 final size:33
Alignment explanation
Indices: 414820--414891 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
414810 TTATCTGTTG
* *
414820 AAATTCAAATATTA-TTCAAAATTTGTAATATAC-
1 AAATTTAAATATTAGTT-AAAAATTGTAATA-ACT
414853 AAATTTAAATATTAGTTAAAAATTGTAATAACT
1 AAATTTAAATATTAGTTAAAAATTGTAATAACT
414886 AAATTT
1 AAATTT
414892 GAAAAAGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 2 0.06
33 31 0.89
34 2 0.06
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (33 bp):
AAATTTAAATATTAGTTAAAAATTGTAATAACT
Found at i:415976 original size:61 final size:61
Alignment explanation
Indices: 415903--416027 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 61
415893 TGTAAAACGT
415903 TAATTATCATAATTACATGAGTTAATTATTTTGACAGAGCCTCAAGTGTCCTGTTAATGCC
1 TAATTATCATAATTACATGAGTTAATTATTTTGACAGAGCCTCAAGTGTCCTGTTAATGCC
*
415964 TAATTATCATAATTACATGAGTTAATTATTTTGACAGAGTCTCAAGTGTCCTGTTAATGCC
1 TAATTATCATAATTACATGAGTTAATTATTTTGACAGAGCCTCAAGTGTCCTGTTAATGCC
416025 TAA
1 TAA
416028 CTAATATTTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (61 bp):
TAATTATCATAATTACATGAGTTAATTATTTTGACAGAGCCTCAAGTGTCCTGTTAATGCC
Found at i:417779 original size:10 final size:10
Alignment explanation
Indices: 417750--417779 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
417740 AGTTAACCTC
*
417750 TATATATATA
1 TATATATATT
417760 TATATATATT
1 TATATATATT
417770 TATATATATT
1 TATATATATT
417780 AGTTGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATATATT
Done.