Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 8 of 362
Found at i:2631881 original size:24 final size:24
Alignment explanation
Indices: 2631851--2631900 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
2631841 TCCTACTTTG
*
2631851 ATTTTTTTTTCAACTTTTATTTTTA
1 ATTTTTTTTCCAAC-TTTATTTTTA
*
2631876 ATTTTTTTTCCAACTTTCTTTTTA
1 ATTTTTTTTCCAACTTTATTTTTA
2631900 A
1 A
2631901 GGTGATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTTTTTCCAACTTTATTTTTA
Found at i:2632479 original size:101 final size:101
Alignment explanation
Indices: 2632298--2632505 Score: 263
Period size: 101 Copynumber: 2.1 Consensus size: 101
2632288 TCCTTTGTGA
* * * * *
2632298 ATCTTGGGTAGTGTCCAATTGGTTGATTGTAATTAGTCATCAAAATAATCTGACAATAGCAATAC
1 ATCTTTGGTAATGTCCAATTAGTTGATCGGAATTAGTCATCAAAATAATCTGACAATAGCAATAC
* * * * * *
2632363 TAAGTTGTCAGTATTGATGATTGATCTAGGTGATGC
66 TAAGATGCCACTATTGATGATTCACCTAAGTGATGC
* * * * * *
2632399 ATCTTTGGTAATGTCTAATTAGTTGATCGGAATTTGTCGTTAAAATAATTTGACAATAGCAATGC
1 ATCTTTGGTAATGTCCAATTAGTTGATCGGAATTAGTCATCAAAATAATCTGACAATAGCAATAC
2632464 TAAGATGCCACTATTGATGATTCACCTAAGTGATGC
66 TAAGATGCCACTATTGATGATTCACCTAAGTGATGC
2632500 ATCTTT
1 ATCTTT
2632506 AATATAATAT
Statistics
Matches: 90, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 90 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.37
Consensus pattern (101 bp):
ATCTTTGGTAATGTCCAATTAGTTGATCGGAATTAGTCATCAAAATAATCTGACAATAGCAATAC
TAAGATGCCACTATTGATGATTCACCTAAGTGATGC
Found at i:2633144 original size:14 final size:14
Alignment explanation
Indices: 2633125--2633153 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2633115 CTTCTTTAGA
2633125 CAAAATGTTAGCAC
1 CAAAATGTTAGCAC
2633139 CAAAATGTTAGCAC
1 CAAAATGTTAGCAC
2633153 C
1 C
2633154 GTAAAACAAA
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:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (14 bp):
CAAAATGTTAGCAC
Found at i:2637851 original size:16 final size:16
Alignment explanation
Indices: 2637830--2637861 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2637820 TGAAGAACAC
2637830 TTATAAGAATTATCAA
1 TTATAAGAATTATCAA
2637846 TTATAAGAATTATCAA
1 TTATAAGAATTATCAA
2637862 ATACATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
TTATAAGAATTATCAA
Found at i:2641834 original size:88 final size:86
Alignment explanation
Indices: 2641742--2641905 Score: 202
Period size: 88 Copynumber: 1.9 Consensus size: 86
2641732 TTTTGTGCGC
* *
2641742 TCAATTGAATACTTAAACTTTCAAAATAAATAAAAAAGGCCCTCAAACTTCTTTAAAAAAAGTAA
1 TCAATTGAATACTTAAACTTTCAAAATAAATAAAAAAGACCCTCAAACTT-TTT-AAAAAAGCAA
*
2641807 TTAAGCCCCTGCTTTTTTTTCAA
64 TTAAGCCACTGCTTTTTTTTCAA
** * * * * * * *
2641830 TCAATTGGGTACTTGAACTTTCAAAATACATCAAAACGACCCTTAAAGTTTTTCAAAAAGCAATT
1 TCAATTGAATACTTAAACTTTCAAAATAAATAAAAAAGACCCTCAAACTTTTTAAAAAAGCAATT
2641895 AAGCCACTGCT
66 AAGCCACTGCT
2641906 CTTATTAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
86 20 0.31
87 3 0.05
88 41 0.64
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (86 bp):
TCAATTGAATACTTAAACTTTCAAAATAAATAAAAAAGACCCTCAAACTTTTTAAAAAAGCAATT
AAGCCACTGCTTTTTTTTCAA
Found at i:2642308 original size:25 final size:25
Alignment explanation
Indices: 2642274--2642321 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2642264 TAAAATTTTA
*
2642274 TAATTTTTTTCTAATTTTAAATATT
1 TAATATTTTTCTAATTTTAAATATT
*
2642299 TAATATTTTTCTAATTTTTAATA
1 TAATATTTTTCTAATTTTAAATA
2642322 AAAGCATGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TAATATTTTTCTAATTTTAAATATT
Found at i:2648022 original size:3 final size:3
Alignment explanation
Indices: 2648016--2648052 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
2648006 AAACATACAT
* *
2648016 TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAT TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2648053 GACGACGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2648132 original size:44 final size:45
Alignment explanation
Indices: 2648082--2648168 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 45
2648072 ATAACAATAC
* * *
2648082 TAATATATTAAGTTACAAAAGTAAAATAATAA-TAATGATAATGA
1 TAATATATCAAGTAACAAAAGTAAAATAATAAGTAATAATAATGA
* * *
2648126 TAATATATCAGGTAACTATAGTAAAATAATAAGTAATAATAAT
1 TAATATATCAAGTAACAAAAGTAAAATAATAAGTAATAATAAT
2648169 AACGTGTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 27 0.75
45 9 0.25
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.32
Consensus pattern (45 bp):
TAATATATCAAGTAACAAAAGTAAAATAATAAGTAATAATAATGA
Found at i:2651513 original size:4 final size:4
Alignment explanation
Indices: 2651499--2651530 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
2651489 TAAGTTATCA
2651499 AATT AATTT AATT AATT AATT AATT AATT AAT
1 AATT AA-TT AATT AATT AATT AATT AATT AAT
2651531 CATTGTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:2653442 original size:103 final size:104
Alignment explanation
Indices: 2653198--2653463 Score: 419
Period size: 103 Copynumber: 2.6 Consensus size: 104
2653188 GTTGTACATA
** *
2653198 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
2653263 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
2653302 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
2653366 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
2653405 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
2653464 AATAACGGTT
Statistics
Matches: 149, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:2660915 original size:103 final size:104
Alignment explanation
Indices: 2660671--2660936 Score: 419
Period size: 103 Copynumber: 2.6 Consensus size: 104
2660661 GTTGTACATA
** *
2660671 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
2660736 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
2660775 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
2660839 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
2660878 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
2660937 AATAACGGTT
Statistics
Matches: 149, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:2665539 original size:14 final size:15
Alignment explanation
Indices: 2665520--2665548 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2665510 TAGGGGTATA
2665520 AAATAAAATT-TGAT
1 AAATAAAATTGTGAT
2665534 AAATAAAATTGTGAT
1 AAATAAAATTGTGAT
2665549 TAACGGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (15 bp):
AAATAAAATTGTGAT
Found at i:2670073 original size:21 final size:19
Alignment explanation
Indices: 2670037--2670085 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
2670027 TCTTCTGTAC
2670037 TATTATATATATTTTCTAA
1 TATTATATATATTTTCTAA
2670056 TATTACTATATATATTTCTAA
1 TATTA-TATATAT-TTTCTAA
2670077 TA-TATATAT
1 TATTATATAT
2670086 TAAAATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.36
20 9 0.32
21 9 0.32
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTATATATATTTTCTAA
Found at i:2670182 original size:11 final size:11
Alignment explanation
Indices: 2670166--2670196 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2670156 TCTAAATGTA
2670166 TGTATATATTG
1 TGTATATATTG
*
2670177 TGTATATTTTG
1 TGTATATATTG
2670188 TGTATATAT
1 TGTATATAT
2670197 ATTATACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (11 bp):
TGTATATATTG
Found at i:2675449 original size:17 final size:17
Alignment explanation
Indices: 2675417--2675448 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2675407 CAAATATAAA
2675417 AACGATAAACCCAAAAG
1 AACGATAAACCCAAAAG
2675434 AACGA-AAACCCAAAA
1 AACGATAAACCCAAAA
2675449 AAAATAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.62, C:0.25, G:0.09, T:0.03
Consensus pattern (17 bp):
AACGATAAACCCAAAAG
Found at i:2677552 original size:25 final size:25
Alignment explanation
Indices: 2677516--2677563 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2677506 ATTGTTTGAT
2677516 AAATATAGATTTTAAATTATAAAAA
1 AAATATAGATTTTAAATTATAAAAA
* * *
2677541 AAATATATATTTTACATTTTAAA
1 AAATATAGATTTTAAATTATAAA
2677564 CCTTATTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATATAGATTTTAAATTATAAAAA
Found at i:2679440 original size:35 final size:35
Alignment explanation
Indices: 2679394--2679460 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
2679384 ATTAGATGAA
* *
2679394 CCAAAAACTTGAATATACGAAGCAAAGAAAGCGAG
1 CCAAAAACTTGAAGATACGAAGCAAAAAAAGCGAG
*
2679429 CCAAACACTTGAAGATACGAAGCAAAAAAAGC
1 CCAAAAACTTGAAGATACGAAGCAAAAAAAGC
2679461 AAACTAGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.52, C:0.19, G:0.18, T:0.10
Consensus pattern (35 bp):
CCAAAAACTTGAAGATACGAAGCAAAAAAAGCGAG
Found at i:2679744 original size:18 final size:18
Alignment explanation
Indices: 2679721--2679779 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 18
2679711 TATTTTACAT
2679721 TTTTGTAAGAATTGAGTA
1 TTTTGTAAGAATTGAGTA
* * *
2679739 TTTTGTTACAAAATTGCGTT
1 TTTTG-TA-AGAATTGAGTA
*
2679759 TTTTCTAAGAATTTGAGTA
1 TTTTGTAAGAA-TTGAGTA
2679778 TT
1 TT
2679780 GACAAAATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
18 8 0.26
19 11 0.35
20 12 0.39
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.49
Consensus pattern (18 bp):
TTTTGTAAGAATTGAGTA
Found at i:2690045 original size:21 final size:21
Alignment explanation
Indices: 2690011--2690051 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2690001 AATTAACTAC
*
2690011 TTTTAGATTATTTATTTTAAT
1 TTTTAGATTATTTAATTTAAT
2690032 TTTTA-ATTATTTTAATTTAA
1 TTTTAGATTA-TTTAATTTAA
2690052 AAATGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTAGATTATTTAATTTAAT
Found at i:2692117 original size:11 final size:11
Alignment explanation
Indices: 2692101--2692126 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2692091 ACCTTAAAAC
2692101 TATTGATGTTA
1 TATTGATGTTA
2692112 TATTGATGTTA
1 TATTGATGTTA
2692123 TATT
1 TATT
2692127 AATCAAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (11 bp):
TATTGATGTTA
Found at i:2693533 original size:36 final size:36
Alignment explanation
Indices: 2693486--2693585 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
2693476 ATCTATGCGC
2693486 CTAATTACTAAAATTATAACCACATATTTAGATGTA
1 CTAATTACTAAAATTATAACCACATATTTAGATGTA
* *
2693522 CTAATTACTAAAATTATAAGCACATATTTAGATGTT
1 CTAATTACTAAAATTATAACCACATATTTAGATGTA
*
2693558 CTAATTACTACAATTATAACCACATATT
1 CTAATTACTAAAATTATAACCACATATT
2693586 ATCCTTTGAC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.37
Consensus pattern (36 bp):
CTAATTACTAAAATTATAACCACATATTTAGATGTA
Found at i:2695121 original size:25 final size:25
Alignment explanation
Indices: 2695093--2695140 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2695083 CAATATGCAA
* *
2695093 TTCAATTCCACAATCCAATTTCACT
1 TTCAATTCAAAAATCCAATTTCACT
* *
2695118 TTCATTTCAAAAATCCACTTTCA
1 TTCAATTCAAAAATCCAATTTCA
2695141 AAATCAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.38
Consensus pattern (25 bp):
TTCAATTCAAAAATCCAATTTCACT
Found at i:2695625 original size:22 final size:24
Alignment explanation
Indices: 2695583--2695626 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
2695573 TAACTAAGTT
2695583 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
2695607 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
2695627 TCTTGCCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:2696091 original size:20 final size:22
Alignment explanation
Indices: 2696054--2696093 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
2696044 TCTTTATGAC
*
2696054 TTATATATATATATTTATTAGT
1 TTATATATATATAATTATTAGT
2696076 TTATA-ATA-ATAATTATTA
1 TTATATATATATAATTATTA
2696094 TAAAATCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
TTATATATATATAATTATTAGT
Found at i:2698188 original size:41 final size:41
Alignment explanation
Indices: 2698109--2698294 Score: 293
Period size: 41 Copynumber: 4.6 Consensus size: 41
2698099 CGATTTACCA
* * **
2698109 AAAACGCCGTTAAAA-ACTGAGCAATAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
*
2698149 AAAACGCCGCTAAAAGACAGAGCTTTAGCGACGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
* *
2698190 AAAACGCCGCTAAAAGAAAGAGCTTTAGTGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
*
2698231 AAAACGCCGATAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
2698272 AAAACGCCGCTAAAAGACAGAGC
1 AAAACGCCGCTAAAAGACAGAGC
2698295 AGTAGTTACA
Statistics
Matches: 133, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 14 0.11
41 119 0.89
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
Found at i:2698964 original size:46 final size:46
Alignment explanation
Indices: 2698897--2698988 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
2698887 ACTTAATAAT
* *
2698897 ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTTTTTA
1 ATTTGATTTATTCTAAATATTTATAATATTTAATGATAATTGTTTA
*
2698943 ATTTGATTTATTCTAAATATTTATAATATTTAATTATAATTGTTTA
1 ATTTGATTTATTCTAAATATTTATAATATTTAATGATAATTGTTTA
2698989 GTTCAATTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (46 bp):
ATTTGATTTATTCTAAATATTTATAATATTTAATGATAATTGTTTA
Found at i:2706431 original size:20 final size:20
Alignment explanation
Indices: 2706394--2706431 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2706384 ATGATGGGAG
*
2706394 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
2706414 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
2706432 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:2708319 original size:46 final size:46
Alignment explanation
Indices: 2708266--2708585 Score: 446
Period size: 46 Copynumber: 7.0 Consensus size: 46
2708256 AGTGTGCTCT
*
2708266 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
2708312 TTGATATGCAATGTGTAAGACCATGGTTGAAAGACACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2708358 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGA-
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA-AC
**
2708404 CTGATATGAAATGTGTAAGACCATTATTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
2708450 CTGATATGAAATATTTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
2708496 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
2708542 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
2708586 TCATGTCAAA
Statistics
Matches: 246, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
45 2 0.01
46 243 0.99
47 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:2712771 original size:57 final size:57
Alignment explanation
Indices: 2712702--2712815 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
2712692 TTCTCATTTA
2712702 TCTCTTATCTTGTTGGTTACCCACAAGCCTCTAAACAGCCTTTCTATACACATCTTG
1 TCTCTTATCTTGTTGGTTACCCACAAGCCTCTAAACAGCCTTTCTATACACATCTTG
2712759 TCTCTTATCTTGTTGGTTACCCACAAGCCTCTAAACAGCCTTTCTATACACATCTTG
1 TCTCTTATCTTGTTGGTTACCCACAAGCCTCTAAACAGCCTTTCTATACACATCTTG
2712816 ACTCCAACCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.37
Consensus pattern (57 bp):
TCTCTTATCTTGTTGGTTACCCACAAGCCTCTAAACAGCCTTTCTATACACATCTTG
Found at i:2714307 original size:20 final size:21
Alignment explanation
Indices: 2714272--2714318 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
2714262 TTTTAGGGTT
2714272 TTTTATAGAAAATTTT-AGAA
1 TTTTATAGAAAATTTTAAGAA
2714292 TTTTA-AGAAAAGTTTTAAGAA
1 TTTTATAGAAAA-TTTTAAGAA
2714313 TTTTAT
1 TTTTAT
2714319 GGTATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (21 bp):
TTTTATAGAAAATTTTAAGAA
Found at i:2714590 original size:10 final size:10
Alignment explanation
Indices: 2714575--2714633 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
2714565 TTATAATTTC
2714575 TATTTTTTAA
1 TATTTTTTAA
**
2714585 TATTTTTGGA
1 TATTTTTTAA
*
2714595 TGTTTTTTAA
1 TATTTTTTAA
2714605 -A-TTTTTAA
1 TATTTTTTAA
2714613 TTATTTTTTAA
1 -TATTTTTTAA
* *
2714624 AAATTTTTAA
1 TATTTTTTAA
2714634 GTTATTTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
8 7 0.18
10 24 0.63
11 7 0.18
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:2714621 original size:21 final size:22
Alignment explanation
Indices: 2714603--2714645 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2714593 GATGTTTTTT
2714603 AAATTTTTAA-TTATTTTTTAA
1 AAATTTTTAAGTTATTTTTTAA
2714624 AAATTTTTAAGTTATTTATTTA
1 AAATTTTTAAGTTATTT-TTTA
2714646 TTTATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
22 6 0.30
23 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
AAATTTTTAAGTTATTTTTTAA
Found at i:2715046 original size:27 final size:28
Alignment explanation
Indices: 2715016--2715069 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
2715006 AAGTAAGAGG
*
2715016 CCAAACCGATAAAAAAAGATAT-AAAGA
1 CCAAACCGATAAAAAAAAATATGAAAGA
*
2715043 CCAAACTGATAAAAAAAAATATGAAAG
1 CCAAACCGATAAAAAAAAATATGAAAG
2715070 TGATGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.63, C:0.13, G:0.11, T:0.13
Consensus pattern (28 bp):
CCAAACCGATAAAAAAAAATATGAAAGA
Found at i:2716377 original size:15 final size:15
Alignment explanation
Indices: 2716357--2716387 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2716347 AAGTAAAATA
2716357 AATAAGAATAATAAT
1 AATAAGAATAATAAT
2716372 AATAAGAATAATAAT
1 AATAAGAATAATAAT
2716387 A
1 A
2716388 GGGGCAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
AATAAGAATAATAAT
Found at i:2717504 original size:7 final size:7
Alignment explanation
Indices: 2717487--2717516 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2717477 GAGGTAAGGG
2717487 TTTTA-T
1 TTTTATT
2717493 TTTTATT
1 TTTTATT
2717500 TTTTATT
1 TTTTATT
2717507 TTTTATT
1 TTTTATT
2717514 TTT
1 TTT
2717517 CGAATCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:2720044 original size:15 final size:15
Alignment explanation
Indices: 2720024--2720131 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
2720014 TTTATGGAAA
*
2720024 ATCAAAGATATGGGT
1 ATCAAATATATGGGT
**
2720039 ATCAAATA-ATGGAA
1 ATCAAATATATGGGT
*
2720053 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
2720069 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
2720083 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
2720099 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
2720113 AGTCAAATATATGGGT
1 A-TCAAATATATGGGT
2720129 ATC
1 ATC
2720132 GAGATATTGG
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
14 13 0.19
15 44 0.63
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:2720053 original size:30 final size:30
Alignment explanation
Indices: 2720017--2720131 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
2720007 ATCCATATTT
*
2720017 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
2720047 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
2720077 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
2720107 TTGGAAAGTCAAATATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
2720132 GAGATATTGG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 82 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:2724734 original size:30 final size:30
Alignment explanation
Indices: 2724698--2724811 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
2724688 ATCCATATTT
*
2724698 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
2724728 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
2724758 TTGGAAAGTCAAAGATATGGGTATCAAAT-
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
2724787 ATTGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
2724812 GAGATATTGG
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 23 0.29
30 57 0.71
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:2728368 original size:11 final size:11
Alignment explanation
Indices: 2728354--2728393 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2728344 GTTTTCACCC
2728354 TATTTTGCTAT
1 TATTTTGCTAT
*
2728365 TATTTTACTAT
1 TATTTTGCTAT
* *
2728376 TATGTTGCTAC
1 TATTTTGCTAT
2728387 TATTTTG
1 TATTTTG
2728394 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:2733060 original size:17 final size:17
Alignment explanation
Indices: 2733040--2733082 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
2733030 AAATAATCTT
2733040 AAAGTAGTCAAA-ACCA
1 AAAGTAGTCAAAGACCA
2733056 GAAAGTA-TCAAAGACCA
1 -AAAGTAGTCAAAGACCA
2733073 AAGAGTAGTC
1 AA-AGTAGTC
2733083 TAGTCCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.30
17 14 0.61
18 2 0.09
ACGTcount: A:0.51, C:0.16, G:0.19, T:0.14
Consensus pattern (17 bp):
AAAGTAGTCAAAGACCA
Found at i:2735912 original size:63 final size:62
Alignment explanation
Indices: 2735803--2735927 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 62
2735793 TAAAGTTTTT
2735803 GATGTTGTTTGGTTAGATATGAAAAAGGACTAGTTTGTAAAGTAAAAATTGTTAATTTTGAC
1 GATGTTGTTTGGTTAGATATGAAAAAGGACTAGTTTGTAAAGTAAAAATTGTTAATTTTGAC
2735865 GATGTTGTTTGGTTAGATATGAAAAAAGGACTAGTTTGTAAAGTAAAAATTGTTAATTTTGAC
1 GATGTTGTTTGGTTAGATATG-AAAAAGGACTAGTTTGTAAAGTAAAAATTGTTAATTTTGAC
2735928 TATAGGAACT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 21 0.34
63 41 0.66
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.38
Consensus pattern (62 bp):
GATGTTGTTTGGTTAGATATGAAAAAGGACTAGTTTGTAAAGTAAAAATTGTTAATTTTGAC
Found at i:2738935 original size:40 final size:40
Alignment explanation
Indices: 2738884--2738961 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
2738874 CTTCGATAAT
* *
2738884 TTCACAGTTCAATGCAGTACACATAACAATATTCAGTAAC
1 TTCACAATTCAATGCAGTACACAAAACAATATTCAGTAAC
* **
2738924 TTCACAATTCAATTCAGTACTTAAAACAATATTCAGTA
1 TTCACAATTCAATGCAGTACACAAAACAATATTCAGTA
2738962 TTCTATAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (40 bp):
TTCACAATTCAATGCAGTACACAAAACAATATTCAGTAAC
Found at i:2739751 original size:46 final size:46
Alignment explanation
Indices: 2739691--2740010 Score: 433
Period size: 46 Copynumber: 7.0 Consensus size: 46
2739681 TTTGACATAA
* * * * ** * * *
2739691 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
** * *
2739737 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
** *** * *
2739783 TGCCATGGTATCTTTCAACCATGGTCTTACTTATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
2739829 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
2739875 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
2739921 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
2739967 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
2740011 AGAGCACACT
Statistics
Matches: 250, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 250 1.00
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:2742184 original size:18 final size:20
Alignment explanation
Indices: 2742169--2742205 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2742159 TAATAATAAA
*
2742169 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
2742189 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
2742206 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:2746373 original size:70 final size:70
Alignment explanation
Indices: 2746250--2746391 Score: 257
Period size: 70 Copynumber: 2.0 Consensus size: 70
2746240 ATTTTATCAT
* *
2746250 ATCCGTACAATTGGCATATTTTGATTTATTTAATAATATAATGTCATTATAATTTAATTATCATG
1 ATCCATACAATTGGCATATTTTGATTTATTTAATAATATAATGTCATTATAATTTAATTATCATA
2746315 AATTC
66 AATTC
*
2746320 ATCCATACAATTGGCATATTTTGATTTATTTAATAATATAATGTCATTGTAATTTAATTATCATA
1 ATCCATACAATTGGCATATTTTGATTTATTTAATAATATAATGTCATTATAATTTAATTATCATA
2746385 AATTC
66 AATTC
2746390 AT
1 AT
2746392 ATAATTTAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (70 bp):
ATCCATACAATTGGCATATTTTGATTTATTTAATAATATAATGTCATTATAATTTAATTATCATA
AATTC
Found at i:2746391 original size:25 final size:23
Alignment explanation
Indices: 2746347--2746407 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
2746337 ATTTTGATTT
* *
2746347 ATTTAATAATATAATGTCATTGTA
1 ATTTAATTATATAATGTCA-TATA
2746371 ATTTAATTATCATAAAT-TCATATA
1 ATTTAATTAT-AT-AATGTCATATA
2746395 ATTTAAATTATAT
1 ATTT-AATTATAT
2746408 TTGAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 11 0.34
26 3 0.09
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (23 bp):
ATTTAATTATATAATGTCATATA
Found at i:2748482 original size:18 final size:18
Alignment explanation
Indices: 2748461--2748497 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2748451 TGAGTTTTCG
2748461 AATTGGAATAACTCGAAT
1 AATTGGAATAACTCGAAT
* *
2748479 AATTTGAATAATTCGAAT
1 AATTGGAATAACTCGAAT
2748497 A
1 A
2748498 TCAAACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (18 bp):
AATTGGAATAACTCGAAT
Found at i:2760236 original size:30 final size:33
Alignment explanation
Indices: 2760200--2760265 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 33
2760190 ATAGTCTATA
*
2760200 TTTTTAT-AATTTTTAAAGAATT-AAAT-TAAT
1 TTTTTATCAATTTTAAAAGAATTAAAATGTAAT
*
2760230 TTTTTATCAATTTTAAAAGGATTAAAATGTAAT
1 TTTTTATCAATTTTAAAAGAATTAAAATGTAAT
2760263 TTT
1 TTT
2760266 ATCATTACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 7 0.23
31 13 0.42
32 4 0.13
33 7 0.23
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (33 bp):
TTTTTATCAATTTTAAAAGAATTAAAATGTAAT
Found at i:2769162 original size:2 final size:2
Alignment explanation
Indices: 2769155--2769182 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2769145 ATTTTTAAAA
2769155 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
2769183 GAAAAATAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2771058 original size:16 final size:17
Alignment explanation
Indices: 2771032--2771063 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2771022 TTTAATTAAC
2771032 TAAATTAATTTCTCAAT
1 TAAATTAATTTCTCAAT
2771049 TAAA-TAATTTCTCAA
1 TAAATTAATTTCTCAA
2771064 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTAATTTCTCAAT
Found at i:2776254 original size:30 final size:30
Alignment explanation
Indices: 2776218--2776275 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2776208 TGTACATTTT
*
2776218 TGGAAAGCTAATTGCCTAACAACCTAGTAG
1 TGGAAAGCTAATAGCCTAACAACCTAGTAG
**
2776248 TGGAAAGCTTGTAGCCTAACAACCTAGT
1 TGGAAAGCTAATAGCCTAACAACCTAGT
2776276 TTCCACATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (30 bp):
TGGAAAGCTAATAGCCTAACAACCTAGTAG
Found at i:2786648 original size:16 final size:18
Alignment explanation
Indices: 2786617--2786653 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
2786607 TAAAATATGA
*
2786617 ATACATAATCATAAATGT
1 ATACATAATCATAAATAT
2786635 ATACA-AAT-ATAAATAT
1 ATACATAATCATAAATAT
2786651 ATA
1 ATA
2786654 TATTACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (18 bp):
ATACATAATCATAAATAT
Found at i:2789775 original size:22 final size:21
Alignment explanation
Indices: 2789732--2789785 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
2789722 CATATATGTA
*
2789732 TAGTCTTGAGACAGTTGATCT
1 TAGTCTCGAGACAGTTGATCT
*
2789753 TAAGTCTCGAGACAAG-TGGTCT
1 T-AGTCTCGAGAC-AGTTGATCT
*
2789775 TTGTCTCGAGA
1 TAGTCTCGAGA
2789786 TAGAGGTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 10 0.36
22 16 0.57
23 2 0.07
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (21 bp):
TAGTCTCGAGACAGTTGATCT
Found at i:2797707 original size:23 final size:23
Alignment explanation
Indices: 2797680--2797744 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
2797670 TTTAATGTTC
**
2797680 ACGAACATGTTCATTTAAC-TTAA
1 ACGAACATGTTCA-CAAACATTAA
*
2797703 TCGAACATGTTCACAAACATTAA
1 ACGAACATGTTCACAAACATTAA
*
2797726 ACGAACATGTTCACGAACA
1 ACGAACATGTTCACAAACA
2797745 ATGTTAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 3 0.08
23 33 0.92
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.26
Consensus pattern (23 bp):
ACGAACATGTTCACAAACATTAA
Found at i:2798003 original size:12 final size:12
Alignment explanation
Indices: 2797988--2798022 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2797978 ATCGAGCCAA
*
2797988 TAAACAAGCTTT
1 TAAACGAGCTTT
*
2798000 TAAACGAGTTTT
1 TAAACGAGCTTT
2798012 TAAACGAGCTT
1 TAAACGAGCTT
2798023 GTTTGTAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (12 bp):
TAAACGAGCTTT
Found at i:2802821 original size:26 final size:26
Alignment explanation
Indices: 2802791--2802874 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 26
2802781 ATACATATTT
2802791 AATTATTTATATTTAGTCA-TATAATA
1 AATTATTTATATTTA-TCATTATAATA
* *
2802817 AATTATTAATATGATTTATTATTTTAATA
1 AATTATT--TAT-ATTTATCATTATAATA
*
2802846 AATTATTTAATATTT-TAATT-TAATA
1 AATTATTT-ATATTTATCATTATAATA
2802871 AATT
1 AATT
2802875 TTAAAAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
25 9 0.18
26 11 0.22
27 5 0.10
28 7 0.14
29 18 0.36
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (26 bp):
AATTATTTATATTTATCATTATAATA
Found at i:2802887 original size:16 final size:16
Alignment explanation
Indices: 2802866--2802899 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2802856 TATTTTAATT
2802866 TAATAAATTTTAAA-AA
1 TAAT-AATTTTAAATAA
2802882 TAATAATTTTAAATAA
1 TAATAATTTTAAATAA
2802898 TA
1 TA
2802900 TTCTTCGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATTTTAAATAA
Found at i:2802892 original size:25 final size:26
Alignment explanation
Indices: 2802837--2802893 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
2802827 ATGATTTATT
* * **
2802837 ATTTTAATAAATTATTTAATATTTTA
1 ATTTTAATAAATTATTAAAAATAATA
2802863 A-TTTAATAAATT-TTAAAAATAATA
1 ATTTTAATAAATTATTAAAAATAATA
2802887 ATTTTAA
1 ATTTTAA
2802894 ATAATATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 9 0.35
25 16 0.62
26 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTTAATAAATTATTAAAAATAATA
Found at i:2806118 original size:14 final size:15
Alignment explanation
Indices: 2806099--2806128 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2806089 AATTCAAAAG
2806099 AATGTTTTT-AATTA
1 AATGTTTTTAAATTA
2806113 AATGTTTTTAAATTA
1 AATGTTTTTAAATTA
2806128 A
1 A
2806129 TTTAAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
AATGTTTTTAAATTA
Found at i:2807068 original size:286 final size:286
Alignment explanation
Indices: 2806552--2807073 Score: 649
Period size: 286 Copynumber: 1.8 Consensus size: 286
2806542 ACATTAAGTG
* *
2806552 TGCATAATAAAATTAAAATGTATAAAAATGTTAAAATAAAACTTTAGATTAGTGGTAAATTAAAG
1 TGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAACTTTAGATTAGTGGTAAATTAAAA
* * * *** * *
2806617 GTTTTAGTATTGCAGTTGGTGTGGATTTAAATCCCACCATATGAATATTTTTATTTGGTTAAGTG
66 GTTTTACTAATGCAATTGGCCAGGATTCAAATCCCAACATATGAATATTTTTATTTGGTTAAGTG
* * **
2806682 AAAAAAATTAAAAGATCCTCAGAAAATATTACTTATTTTAATTACGAAAGGGTATTCTTGTAACT
131 AAAAAAATTAAAAGATCCTCAAAAAATATTACTTATTTTAATTACGAAAAGACATTCTTGTAACT
* * **
2806747 TTCTAGCCAAGTTAGTGACCCAATTGATTATGACACCAACTCAGTAAGGGATTTTATTAGTAGTA
196 TTCTAACCAAGTTAGTGACCCAATTAAAGATGACACCAACTCAGTAAGGGATTTTATTAGTAGTA
2806812 TAGATATATAACTGATGGAGGTAGTA
261 TAGATATATAACTGATGGAGGTAGTA
* *
2806838 TGCATAATAAAATTAAAATGTAT-AAAATATTAAAAT-AAAGTTATAGATTAGTGGTACATTAAA
1 TGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAACTT-TAGATTAGTGGTAAATTAAA
* * * * **
2806901 AGTTTTACTAATGTAATTGGCCAGGGTTCAAATTCCAACATATGTATATTTTTATTATTTTTTAA
65 AGTTTTACTAATGCAATTGGCCAGGATTCAAATCCCAACATATGAATATTTTTA-T-TTGGTTAA
* * * *
2806966 GTG-AAAAGATTAAAATATCCT-AAAATAATATTACTTATTTTAATTATGAAAATACATT-TTCG
128 GTGAAAAAAATTAAAAGATCCTCAAAA-AATATTACTTATTTTAATTACGAAAAGACATTCTT-G
* * * **
2807028 TGACTTTCTAACTAAGTTAGTGATCCGGTTAAAGATGACACCAACT
191 TAACTTTCTAACCAAGTTAGTGACCCAATTAAAGATGACACCAACT
2807074 TAACCAAGGT
Statistics
Matches: 196, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
284 5 0.03
285 77 0.39
286 105 0.54
287 9 0.05
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (286 bp):
TGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAACTTTAGATTAGTGGTAAATTAAAA
GTTTTACTAATGCAATTGGCCAGGATTCAAATCCCAACATATGAATATTTTTATTTGGTTAAGTG
AAAAAAATTAAAAGATCCTCAAAAAATATTACTTATTTTAATTACGAAAAGACATTCTTGTAACT
TTCTAACCAAGTTAGTGACCCAATTAAAGATGACACCAACTCAGTAAGGGATTTTATTAGTAGTA
TAGATATATAACTGATGGAGGTAGTA
Found at i:2818015 original size:16 final size:16
Alignment explanation
Indices: 2817994--2818064 Score: 60
Period size: 16 Copynumber: 4.5 Consensus size: 16
2817984 AATCTTTCTT
2817994 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
2818010 TTTATTTTT-TTTTT-
1 TTTATTTTTATTTTTA
* *
2818024 CTT-TTATTATTTATTA
1 TTTATTTTTATTT-TTA
*
2818040 TTT-TCTTTTCTTTTTA
1 TTTAT-TTTTATTTTTA
2818056 TTTTATTTT
1 -TTTATTTT
2818065 AGTTAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
13 4 0.09
14 5 0.11
15 7 0.16
16 15 0.34
17 12 0.27
18 1 0.02
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:2818028 original size:20 final size:20
Alignment explanation
Indices: 2818005--2818057 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2817995 TTATTTTTAT
*
2818005 TTTTATTTATTT-TTTTTTTC
1 TTTTA-TTATTTATTATTTTC
2818025 TTTTATTATTTATTATTTTC
1 TTTTATTATTTATTATTTTC
*
2818045 TTTTCTT-TTTATT
1 TTTTATTATTTATT
2818058 TTATTTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTATTATTTATTATTTTC
Found at i:2818028 original size:26 final size:25
Alignment explanation
Indices: 2817999--2818063 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
2817989 TTCTTTTTAT
*
2817999 TTTTATTTTTATTTATTTTTTTTTTC
1 TTTTATTTTTATTTA-TTTTCTTTTC
2818025 TTTTATTATTTA-TTATTTTCTTTTC
1 TTTTATT-TTTATTTATTTTCTTTTC
2818050 TTTT-TATTTTATTT
1 TTTTAT-TTTTATTT
2818064 TAGTTAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
24 5 0.14
25 16 0.46
26 10 0.29
27 4 0.11
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTATTTTTATTTATTTTCTTTTC
Found at i:2822202 original size:25 final size:24
Alignment explanation
Indices: 2822174--2822237 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 24
2822164 TATTAAAAGT
2822174 TATTTTTATTTAAATTTAATTACTA
1 TATTTTTATTTAAATTTAATTA-TA
* * * *
2822199 TATTTATA-TAAAATTTATTTATT
1 TATTTTTATTTAAATTTAATTATA
*
2822222 TATTTTAATATTAAAT
1 TATTTTTAT-TTAAAT
2822238 AAATAATTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
23 7 0.23
24 11 0.37
25 12 0.40
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTTTATTTAAATTTAATTATA
Found at i:2826236 original size:18 final size:20
Alignment explanation
Indices: 2826196--2826236 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2826186 TTATTTGTAT
*
2826196 AATATTTTAAACTTTTACAA
1 AATATTATAAACTTTTACAA
2826216 AATATTATAAA-TTTT-CAA
1 AATATTATAAACTTTTACAA
2826234 AAT
1 AAT
2826237 TTTTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 4 0.20
20 10 0.50
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTATAAACTTTTACAA
Found at i:2835529 original size:22 final size:24
Alignment explanation
Indices: 2835497--2835558 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 24
2835487 AATTTTAAAA
*
2835497 TTTTATAAAATTATTTGA-AAT-T
1 TTTTATTAAATTATTTGACAATGT
2835519 TTTTATTAAATTA-TTGATCAATGT
1 TTTTATTAAATTATTTGA-CAATGT
2835543 TTTTATTTAAATTATT
1 TTTTA-TTAAATTATT
2835559 GAGTTGTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 4 0.12
22 12 0.35
23 3 0.09
24 6 0.18
25 8 0.24
26 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (24 bp):
TTTTATTAAATTATTTGACAATGT
Found at i:2842624 original size:19 final size:22
Alignment explanation
Indices: 2842585--2842627 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
2842575 TACTCCGTAT
2842585 TTTTTATAATTTGTGAATTTAA
1 TTTTTATAATTTGTGAATTTAA
2842607 TTTTTAT-ATTT-T-AATTTAA
1 TTTTTATAATTTGTGAATTTAA
2842626 TT
1 TT
2842628 AATATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 1 0.05
21 4 0.19
22 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTTTATAATTTGTGAATTTAA
Found at i:2842703 original size:17 final size:17
Alignment explanation
Indices: 2842683--2842716 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2842673 TTAAATTAAT
*
2842683 AAATTTAAAAAATATAA
1 AAATCTAAAAAATATAA
*
2842700 AAATCTAAGAAATATAA
1 AAATCTAAAAAATATAA
2842717 GACTAAATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATCTAAAAAATATAA
Found at i:2842826 original size:44 final size:46
Alignment explanation
Indices: 2842746--2842840 Score: 151
Period size: 44 Copynumber: 2.1 Consensus size: 46
2842736 TAGTAAAATT
*
2842746 TAATTTTTTATTATATCTTATATATATTAATTG-TTTTTATCATAAA
1 TAATTTTTTATTATA-CTTATATATATTAATTGTTTTTTACCATAAA
2842792 TAATTTTTTATTATA-TTATATATATTAATTGTTTTTTACCATAAA
1 TAATTTTTTATTATACTTATATATATTAATTGTTTTTTACCATAAA
2842837 -AATT
1 TAATT
2842841 ATCGAATTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
44 20 0.43
45 12 0.26
46 15 0.32
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (46 bp):
TAATTTTTTATTATACTTATATATATTAATTGTTTTTTACCATAAA
Found at i:2843220 original size:30 final size:30
Alignment explanation
Indices: 2843186--2843242 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2843176 TTAATATATT
2843186 TTAAATTATAATTTTATTA-GTTTGAAGGAA
1 TTAAA-TATAATTTTATTATGTTTGAAGGAA
* *
2843216 TTAAATATATTTTTTTTATGTTTGAAG
1 TTAAATATAATTTTATTATGTTTGAAG
2843243 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (30 bp):
TTAAATATAATTTTATTATGTTTGAAGGAA
Found at i:2844979 original size:3 final size:3
Alignment explanation
Indices: 2844971--2845008 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
2844961 CCATGTCTCG
*
2844971 TTA TTA TTA TTA TTG TTA TTA TTA TTA TT- TTAA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT
2845009 GATTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2844988 original size:15 final size:15
Alignment explanation
Indices: 2844970--2845008 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
2844960 TCCATGTCTC
2844970 GTTATTATTATTATT
1 GTTATTATTATTATT
2844985 GTTATTATTATTATT
1 GTTATTATTATTATT
2845000 -TTAATTATT
1 GTT-ATTATT
2845009 GATTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (15 bp):
GTTATTATTATTATT
Found at i:2845280 original size:12 final size:12
Alignment explanation
Indices: 2845263--2845292 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2845253 AGCCCTTGGA
2845263 TTTTTTTTAAAT
1 TTTTTTTTAAAT
*
2845275 TTTTTTTTCAAT
1 TTTTTTTTAAAT
2845287 TTTTTT
1 TTTTTT
2845293 CAGGTGTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTAAAT
Found at i:2850293 original size:20 final size:20
Alignment explanation
Indices: 2850268--2850306 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2850258 TGTAATTGTC
2850268 CAATTACATAAAATATTATT
1 CAATTACATAAAATATTATT
* *
2850288 CAATTACATGAATTATTAT
1 CAATTACATAAAATATTAT
2850307 AACATTTATT
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:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (20 bp):
CAATTACATAAAATATTATT
Found at i:2851745 original size:25 final size:25
Alignment explanation
Indices: 2851716--2851764 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2851706 ATTAAACTAT
2851716 TTAAAAATATAATATTAATAAATAC
1 TTAAAAATATAATATTAATAAATAC
** * *
2851741 TTAAATCTATAATTTTATTAAATA
1 TTAAAAATATAATATTAATAAATA
2851765 TCTATTTCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAAAAATATAATATTAATAAATAC
Found at i:2852857 original size:24 final size:25
Alignment explanation
Indices: 2852818--2852865 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2852808 TTAATTTAAT
*
2852818 CTATTAAAAATTATAAAAATATATA
1 CTATTAAAAATAATAAAAATATATA
*
2852843 CTATT-AAAATAATAAAATTATAT
1 CTATTAAAAATAATAAAAATATAT
2852866 TTTTATTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
CTATTAAAAATAATAAAAATATATA
Found at i:2856840 original size:15 final size:15
Alignment explanation
Indices: 2856820--2856851 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2856810 ATACAAACGC
2856820 ACAACTAGAAACAGT
1 ACAACTAGAAACAGT
*
2856835 ACAACTGGAAACAGT
1 ACAACTAGAAACAGT
2856850 AC
1 AC
2856852 TTTCACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (15 bp):
ACAACTAGAAACAGT
Found at i:2859285 original size:25 final size:27
Alignment explanation
Indices: 2859239--2859294 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
2859229 TTTTATTTTA
* *
2859239 TTTTAATTTTGTTTGTA-GTTTTAAGG
1 TTTTAATTTTGTCTATATGTTTTAAGG
* *
2859265 TTTT-ATTTTGTCTATATTTTTTGAGG
1 TTTTAATTTTGTCTATATGTTTTAAGG
2859291 TTTT
1 TTTT
2859295 TGTTTTACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.16, C:0.02, G:0.16, T:0.66
Consensus pattern (27 bp):
TTTTAATTTTGTCTATATGTTTTAAGG
Found at i:2859358 original size:2 final size:2
Alignment explanation
Indices: 2859351--2859386 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2859341 TCAAGGCCTA
2859351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2859387 GAGATTTGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2860985 original size:27 final size:28
Alignment explanation
Indices: 2860955--2861007 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2860945 TAAAAAATAT
* *
2860955 TTTTTTA-ATATTTAATAATTTTATACA
1 TTTTTTACATATTAAAAAATTTTATACA
*
2860982 TTTTTTACTTATTAAAAAATTTTATA
1 TTTTTTACATATTAAAAAATTTTATA
2861008 TAATCATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTTTACATATTAAAAAATTTTATACA
Found at i:2862357 original size:22 final size:21
Alignment explanation
Indices: 2862332--2862372 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2862322 ATTGCTGAGA
2862332 CTAAGAAAAATCCAATAAAACT
1 CTAA-AAAAATCCAATAAAACT
* *
2862354 CTAAAGAAATTCAATAAAA
1 CTAAAAAAATCCAATAAAA
2862373 ATTTCCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.61, C:0.15, G:0.05, T:0.20
Consensus pattern (21 bp):
CTAAAAAAATCCAATAAAACT
Found at i:2862807 original size:25 final size:25
Alignment explanation
Indices: 2862779--2862835 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
2862769 TTCCTTAATG
*
2862779 ATTTTTAATGAATATAAT-T-TTTTT
1 ATTTTTAATAAATA-AATATATTTTT
*
2862803 CATTTTAAATAAATAAATATATTTTT
1 -ATTTTTAATAAATAAATATATTTTT
2862829 ATTTTTA
1 ATTTTTA
2862836 TAATTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 3 0.11
25 19 0.70
26 5 0.19
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTTTAATAAATAAATATATTTTT
Found at i:2867607 original size:15 final size:16
Alignment explanation
Indices: 2867575--2867615 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2867565 GTCTTTGTAC
*
2867575 TTTA-ATTTTGTTATT
1 TTTAGATTTTGTTAAT
2867590 TTTAGATTTTG-TAAT
1 TTTAGATTTTGTTAAT
2867605 TTTAGAATTTT
1 TTTAG-ATTTT
2867616 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (16 bp):
TTTAGATTTTGTTAAT
Found at i:2867614 original size:16 final size:17
Alignment explanation
Indices: 2867578--2867615 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2867568 TTTGTACTTT
*
2867578 AATTTTGTTATTTTTAG
1 AATTTTGTTAATTTTAG
2867595 -ATTTTG-TAATTTTAG
1 AATTTTGTTAATTTTAG
2867610 AATTTT
1 AATTTT
2867616 AAAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (17 bp):
AATTTTGTTAATTTTAG
Found at i:2873645 original size:50 final size:50
Alignment explanation
Indices: 2873590--2873690 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
2873580 ATGCTAACTA
2873590 AAACATTAATTTTTTTAACAATATTGGTGTTGTAATCTGTATAACAGTCC
1 AAACATTAATTTTTTTAACAATATTGGTGTTGTAATCTGTATAACAGTCC
2873640 AAACATTAATTTTTTTAACAATATTGGTGTTGTAATCTGTATAACAGTCC
1 AAACATTAATTTTTTTAACAATATTGGTGTTGTAATCTGTATAACAGTCC
2873690 A
1 A
2873691 CATGTACCTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (50 bp):
AAACATTAATTTTTTTAACAATATTGGTGTTGTAATCTGTATAACAGTCC
Found at i:2883061 original size:36 final size:36
Alignment explanation
Indices: 2883014--2883086 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
2883004 TCACATGTCC
2883014 ATTTTATTGCTCAATTAATAAAAATAGTATTAAAAA
1 ATTTTATTGCTCAATTAATAAAAATAGTATTAAAAA
2883050 ATTTTATTGCTCAATTAATAAAAATAGTATTAAAAA
1 ATTTTATTGCTCAATTAATAAAAATAGTATTAAAAA
2883086 A
1 A
2883087 CTGTCTTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (36 bp):
ATTTTATTGCTCAATTAATAAAAATAGTATTAAAAA
Found at i:2903316 original size:84 final size:86
Alignment explanation
Indices: 2903208--2903364 Score: 205
Period size: 84 Copynumber: 1.8 Consensus size: 86
2903198 ATAAAAAATA
* * * * *
2903208 TATATTTTTACTATTTTAATAATTT-ATATCTTAATAATTTAT-AGAAGATTAAATTAATTTTTT
1 TATAGTTTTACTATTTT-ATAATTTAAAATCTT-ATAAATTATAAAAAAATTAAA-TAATTTTTT
2903271 TA-TTATTTTTAATAAAATTAAAG
63 TATTTATTTTTAATAAAATTAAAG
*
2903294 TATAGTTTTATTATTTT-TAATTTAAAATCTTATAAATTATAAAAAAATTAAATAATTTTTTTAT
1 TATAGTTTTACTATTTTATAATTTAAAATCTTATAAATTATAAAAAAATTAAATAATTTTTTTAT
2903358 TTATTTT
66 TTATTTT
2903365 AGAACCGAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
84 25 0.40
85 22 0.35
86 15 0.24
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (86 bp):
TATAGTTTTACTATTTTATAATTTAAAATCTTATAAATTATAAAAAAATTAAATAATTTTTTTAT
TTATTTTTAATAAAATTAAAG
Found at i:2904008 original size:17 final size:19
Alignment explanation
Indices: 2903972--2904011 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2903962 TTTCCAAATT
*
2903972 ATAAAATTCAAAAATTTAA
1 ATAAAATTCAAAAATATAA
2903991 ATAAAATT-AAAAA-ATAA
1 ATAAAATTCAAAAATATAA
2904008 ATAA
1 ATAA
2904012 CTAAACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 5 0.25
19 8 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAAAATTCAAAAATATAA
Found at i:2904414 original size:23 final size:23
Alignment explanation
Indices: 2904370--2904421 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2904360 CTTGTATTTT
** *
2904370 TTTTTATTTATTTTGAATTTAATA
1 TTTTTATTTATTAAGAAATTAA-A
2904394 TTTTTATTT-TTAAGAAATTAAA
1 TTTTTATTTATTAAGAAATTAAA
2904416 TTTTTA
1 TTTTTA
2904422 CCTTTTGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.28
23 9 0.36
24 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTTATTTATTAAGAAATTAAA
Found at i:2909586 original size:22 final size:21
Alignment explanation
Indices: 2909560--2909602 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2909550 AAAAACTATC
2909560 TCAAAATTAT-ACATGAATTTTG
1 TCAAAATT-TGACAT-AATTTTG
2909582 TCAAAATTTGACATAATTTTG
1 TCAAAATTTGACATAATTTTG
2909603 ATTCAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (21 bp):
TCAAAATTTGACATAATTTTG
Found at i:2919524 original size:24 final size:21
Alignment explanation
Indices: 2919485--2919528 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
2919475 AGGTAATTAA
2919485 ATATTTTTAAAATAATATTTAT
1 ATATTTTTAAAATAAT-TTTAT
*
2919507 ATATATTTTATAATTAATTTTA
1 ATAT-TTTTA-AAATAATTTTA
2919529 AAAAATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTTTTAAAATAATTTTAT
Found at i:2932755 original size:15 final size:16
Alignment explanation
Indices: 2932735--2932770 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2932725 AATATAAATT
2932735 AAATAAAGTA-AAAAG
1 AAATAAAGTATAAAAG
*
2932750 AAATAAAGTATAAAAT
1 AAATAAAGTATAAAAG
2932766 AAATA
1 AAATA
2932771 GAAACAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (16 bp):
AAATAAAGTATAAAAG
Found at i:2932769 original size:16 final size:16
Alignment explanation
Indices: 2932718--2932770 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
2932708 ACTTATTAAT
*
2932718 TAAATATAA-TATAAAT
1 TAAATA-AAGTATAAAA
2932734 TAAATAAAGTA-AAAA
1 TAAATAAAGTATAAAA
*
2932749 GAAATAAAGTATAAAA
1 TAAATAAAGTATAAAA
2932765 TAAATA
1 TAAATA
2932771 GAAACAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 15 0.47
16 17 0.53
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
TAAATAAAGTATAAAA
Found at i:2933596 original size:40 final size:40
Alignment explanation
Indices: 2933551--2933637 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
2933541 AATTATAGAA
*
2933551 TACTGAATATTGTTTTGAGTACTAAATTGAATTGTAAAAT
1 TACTGAATATTGTTATGAGTACTAAATTGAATTGTAAAAT
* ** *
2933591 TACTGAATATTGTTATGTGTACTGCATTGAATTGTGAAAT
1 TACTGAATATTGTTATGAGTACTAAATTGAATTGTAAAAT
2933631 TACTGAA
1 TACTGAA
2933638 GTAATGAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (40 bp):
TACTGAATATTGTTATGAGTACTAAATTGAATTGTAAAAT
Found at i:2933909 original size:45 final size:45
Alignment explanation
Indices: 2933841--2933937 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
2933831 GATGACTACT
** *
2933841 GTTACTGTTACCGATTCGACACTTTGTGTGTCGAATATTGTTACC
1 GTTACTGTTACAAATTCGACACTTTGTGTGTCGAATACTGTTACC
* *
2933886 GTTACTGTTACAAATTC-AGCACTTTGTGTGTTGAATACTGTTACT
1 GTTACTGTTACAAATTCGA-CACTTTGTGTGTCGAATACTGTTACC
2933931 GTTACTG
1 GTTACTG
2933938 CTATCGTTGC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (45 bp):
GTTACTGTTACAAATTCGACACTTTGTGTGTCGAATACTGTTACC
Found at i:2938512 original size:29 final size:29
Alignment explanation
Indices: 2938470--2938530 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
2938460 CATTCCACTA
2938470 TAAGGAGACTATAATCACCTTGTCCTAAT
1 TAAGGAGACTATAATCACCTTGTCCTAAT
2938499 TAAGGAGACTATAATCACCTTGTCCTAAT
1 TAAGGAGACTATAATCACCTTGTCCTAAT
2938528 TAA
1 TAA
2938531 CATTCTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (29 bp):
TAAGGAGACTATAATCACCTTGTCCTAAT
Found at i:2944439 original size:48 final size:48
Alignment explanation
Indices: 2944348--2944440 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 48
2944338 TTGTTTCACT
* *
2944348 ATTTAAACTAATATTAAAAATTATTATTTATTTATTTTATTAATACAA
1 ATTTAAACTAATATTAAAAATTATTATTTATTAATTGTATTAATACAA
*
2944396 ATTTAAACTGAATA-TATACAATT-TTACTTTATTAATTGT-TTAATA
1 ATTTAAACT-AATATTA-AAAATTATTA-TTTATTAATTGTATTAATA
2944441 ATAAACCCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
48 20 0.51
49 19 0.49
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.49
Consensus pattern (48 bp):
ATTTAAACTAATATTAAAAATTATTATTTATTAATTGTATTAATACAA
Found at i:2951717 original size:43 final size:43
Alignment explanation
Indices: 2951655--2951976 Score: 259
Period size: 43 Copynumber: 7.5 Consensus size: 43
2951645 TAGCGGCATT
* *
2951655 TTTTTTCTAAAAAACGCCGCTAAAGACCAAGATCTTTAGCGGCG
1 TTTTTTAT-AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCG
*
2951699 TTTTTTATAAAAGCGCCGCTAAAGACCAAGACCTTTAGCGGCG
1 TTTTTTATAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCG
* *
2951742 CTTTTTTA-AAAAACGCCGCTAGAA-ACCAGGACCTTTAGCAGCG
1 -TTTTTTATAAAAACGCCGCTA-AAGACCAAGACCTTTAGCGGCG
* *
2951785 CTTTTTTA-AAAAACGCCGCTAGAA-ACCAGGACCTTTAGCAGCG
1 -TTTTTTATAAAAACGCCGCTA-AAGACCAAGACCTTTAGCGGCG
* * * * * * *
2951828 -CTTATA-AAAAACGCCGCTATAGACCTATACTTTTAACGGCG
1 TTTTTTATAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCG
* * * ** *
2951869 -CTTTTATAAAAAACGCCGCTAAAGGTCC-TGGTCTTTGGCGGCG
1 TTTTTTAT-AAAAACGCCGCTAAA-GACCAAGACCTTTAGCGGCG
* * * *
2951912 -CTTTTATAAAAACGCCGCTATAGACC-TGTACTTTTAGCGGCG
1 TTTTTTATAAAAACGCCGCTAAAGACCAAG-ACCTTTAGCGGCG
* *
2951954 CTTTTATAAAAAAACGCCGCTAA
1 -TTTTTTATAAAAACGCCGCTAA
2951977 TTTGCCCAGT
Statistics
Matches: 234, Mismatches: 35, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.00
41 40 0.17
42 23 0.10
43 134 0.57
44 36 0.15
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (43 bp):
TTTTTTATAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCG
Found at i:2951888 original size:170 final size:170
Alignment explanation
Indices: 2951662--2951975 Score: 393
Period size: 170 Copynumber: 1.8 Consensus size: 170
2951652 ATTTTTTTTC
* * *
2951662 TAAAAAACGCCGCTAAAGACCAAGATCTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAAA-GACC
1 TAAAAAACGCCGCTAAAGACCAAGATCTTTAACGGCGTTTTATATAAAAACGCCGCTAAAGGACC
*
2951726 AAGACCTTTAGCGGCGCTTTTTTAAAAAACGCCGCTAGAAACCAGGACCTTTAGCAGCGCTTTT-
66 -AGACCTTTAGCGGCGCTTTTAT-AAAAACGCCGCTAGAAACCAGGACCTTTAGCAGCGCTTTTA
*
2951790 TTAAAAAACGCCGCTAGAAACCAGGACCTTTAGCAGCGCTTA
129 TAAAAAAACGCCGCTAGAAACCAGGACCTTTAGCAGCGCTTA
* * * *
2951832 TAAAAAACGCCGCTATAGACCTATA-CTTTTAACGGCGCTTTTATA-AAAAACGCCGCTAAAGGT
1 TAAAAAACGCCGCTAAAGACCAAGATC-TTTAACGGCG-TTTTATATAAAAACGCCGCTAAAGGA
* ** * * * * * * *
2951895 CCTGGTCTTTGGCGGCGCTTTTATAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTA
64 CCAGACCTTTAGCGGCGCTTTTATAAAAACGCCGCTAGAAACCAGGACCTTTAGCAGCGCTTTTA
2951960 TAAAAAAACGCCGCTA
129 TAAAAAAACGCCGCTA
2951976 ATTTGCCCAG
Statistics
Matches: 121, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
169 35 0.29
170 77 0.64
171 9 0.07
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (170 bp):
TAAAAAACGCCGCTAAAGACCAAGATCTTTAACGGCGTTTTATATAAAAACGCCGCTAAAGGACC
AGACCTTTAGCGGCGCTTTTATAAAAACGCCGCTAGAAACCAGGACCTTTAGCAGCGCTTTTATA
AAAAAACGCCGCTAGAAACCAGGACCTTTAGCAGCGCTTA
Found at i:2951944 original size:85 final size:84
Alignment explanation
Indices: 2951664--2951976 Score: 321
Period size: 86 Copynumber: 3.7 Consensus size: 84
2951654 TTTTTTTCTA
* * * *
2951664 AAAAACGCCGCTAAAGACCAAG-A-TCTTTAGCGGCG-TTTTTTATAAAAGCGCCGCTAAAGACC
1 AAAAACGCCGCTATAGACC-TGTACT-TTTAGCGGCGCTTTTATA-AAAAACGCCGCTAAA-ACC
* *
2951726 AAGACCTTTAGCGGCGCTTTTTT
62 AGGACCTTTAGCGGCGCTTTTAT
* * * * * * *
2951749 AAAAAACGCCGCTAGAAACCAGGACCTTTAGCAGCGCTTTTTTAAAAAACGCCGCTAGAAACCAG
1 -AAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTATAAAAAACGCCGCTA-AAACCAG
* *
2951814 GACCTTTAGCAGCGCTTATA-
64 GACCTTTAGCGGCGCTTTTAT
* * * *
2951834 AAAAACGCCGCTATAGACCTATACTTTTAACGGCGCTTTTATAAAAAACGCCGCTAAAGGTCCTG
1 AAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAA--ACCAG
* *
2951899 G-TCTTTGGCGGCGCTTTTAT
64 GACCTTTAGCGGCGCTTTTAT
2951919 AAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTATAAAAAAACGCCGCTAA
1 AAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTAT-AAAAAACGCCGCTAA
2951977 TTTGCCCAGT
Statistics
Matches: 193, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
83 2 0.01
84 61 0.32
85 46 0.24
86 75 0.39
87 9 0.05
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (84 bp):
AAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAACCAGGA
CCTTTAGCGGCGCTTTTAT
Found at i:2952299 original size:21 final size:21
Alignment explanation
Indices: 2952275--2952322 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2952265 TCCTGTTCTG
*
2952275 CTCCGCCTCCCTTGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
2952296 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
2952317 CTCCGC
1 CTCCGC
2952323 TCTAAGTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.00, C:0.56, G:0.19, T:0.25
Consensus pattern (21 bp):
CTCCGCCTCCCTCGCTGCTGC
Found at i:2952910 original size:18 final size:18
Alignment explanation
Indices: 2952878--2952915 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2952868 TACAATATAG
2952878 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
2952897 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
2952914 TA
1 TA
2952916 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:2953244 original size:14 final size:15
Alignment explanation
Indices: 2953216--2953248 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2953206 GGCTTATGGG
2953216 TTTTTTAAAATATTC
1 TTTTTTAAAATATTC
*
2953231 TTTTTTCAAA-ATTC
1 TTTTTTAAAATATTC
2953245 TTTT
1 TTTT
2953249 ATTGTCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTTAAAATATTC
Found at i:2960878 original size:23 final size:23
Alignment explanation
Indices: 2960851--2960897 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
2960841 CAGCAATTTG
2960851 GTATAACATTAACAGGAGAAATA
1 GTATAACATTAACAGGAGAAATA
*
2960874 GTATACCATTAACAGGAGAAATA
1 GTATAACATTAACAGGAGAAATA
2960897 G
1 G
2960898 GACCAAGCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (23 bp):
GTATAACATTAACAGGAGAAATA
Found at i:2965344 original size:18 final size:17
Alignment explanation
Indices: 2965312--2965349 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2965302 TACAATATAG
2965312 ATAGTAAAATATTATTTA
1 ATAGTAAAATATTA-TTA
2965330 ATAGTAAAA-AGTTATTA
1 ATAGTAAAATA-TTATTA
2965347 ATA
1 ATA
2965350 CTTGATAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (17 bp):
ATAGTAAAATATTATTA
Found at i:2965677 original size:14 final size:15
Alignment explanation
Indices: 2965649--2965681 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2965639 AGGCTATGGG
2965649 TTTTTTAAAATATTC
1 TTTTTTAAAATATTC
*
2965664 TTTTTTCAAA-ATTC
1 TTTTTTAAAATATTC
2965678 TTTT
1 TTTT
2965682 ATTGTCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTTAAAATATTC
Found at i:2973297 original size:23 final size:23
Alignment explanation
Indices: 2973270--2973316 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
2973260 CAGCAATTTG
2973270 GTATAACATTAACAGGAGAAATA
1 GTATAACATTAACAGGAGAAATA
*
2973293 GTATACCATTAACAGGAGAAATA
1 GTATAACATTAACAGGAGAAATA
2973316 G
1 G
2973317 GACCAAGCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (23 bp):
GTATAACATTAACAGGAGAAATA
Found at i:2975889 original size:24 final size:24
Alignment explanation
Indices: 2975845--2975908 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
2975835 ACACTAAACC
* *
2975845 ATTTTCATATATATATTTATATAT
1 ATTTTCAAATATATATATATATAT
2975869 ATTTTCAAATA-ATA-ATATATAT
1 ATTTTCAAATATATATATATATAT
**
2975891 ATTTATCTTATATATATA
1 ATTT-TCAAATATATATA
2975909 CATTTATCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 11 0.33
23 8 0.24
24 13 0.39
25 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTTCAAATATATATATATATAT
Found at i:2976315 original size:25 final size:25
Alignment explanation
Indices: 2976281--2976328 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
2976271 TAGCTAATAA
2976281 TTCAACAAATGCTAATTCCACATAG
1 TTCAACAAATGCTAATTCCACATAG
2976306 TTCAACAAATGCTAATTCCACAT
1 TTCAACAAATGCTAATTCCACAT
2976329 TCAAAATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.25, G:0.06, T:0.29
Consensus pattern (25 bp):
TTCAACAAATGCTAATTCCACATAG
Found at i:2976527 original size:36 final size:38
Alignment explanation
Indices: 2976486--2976561 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
2976476 CTTCAAATAC
* * *
2976486 TAGTTAACTCCTAAACC-G-TAAATCTTAAACCATATA
1 TAGTTAACTCATAAACCTGCTAAACCCTAAACCATATA
2976522 TAGTTAACTCATAAACCTGCTTAAACCCTAAACCATATA
1 TAGTTAACTCATAAACCTGC-TAAACCCTAAACCATATA
2976561 T
1 T
2976562 CTTAAACTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 16 0.47
37 1 0.03
39 17 0.50
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (38 bp):
TAGTTAACTCATAAACCTGCTAAACCCTAAACCATATA
Found at i:2976798 original size:41 final size:41
Alignment explanation
Indices: 2976741--2977001 Score: 371
Period size: 41 Copynumber: 6.4 Consensus size: 41
2976731 GTTCTATGAC
* *
2976741 TTTTAGCAGCGTTTTACTGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
2976782 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAACGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
2976823 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAACGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
2976864 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGATCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
* *
2976905 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGATCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
* *** * **
2976946 TTTTAGCGGCATTTTAGTAAAAAACGCCGCTGTTGCTCT-GT
1 TTTTAGCGGCGTTTTA-CCGAAAGCGCCGCTAATGCTCTGGT
*
2976987 TTTTAGCTGCGTTTT
1 TTTTAGCGGCGTTTT
2977002 TCTTAAAACG
Statistics
Matches: 203, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 188 0.93
42 15 0.07
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
Found at i:2977621 original size:15 final size:15
Alignment explanation
Indices: 2977601--2977641 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
2977591 GGTGAGCAAA
*
2977601 ATTCAATTTAATTCG
1 ATTCAATTCAATTCG
*
2977616 ATTCAATTCGATTCG
1 ATTCAATTCAATTCG
2977631 ATTCAATTCAA
1 ATTCAATTCAA
2977642 AAAACTCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (15 bp):
ATTCAATTCAATTCG
Found at i:2981904 original size:9 final size:9
Alignment explanation
Indices: 2981890--2981919 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2981880 TTGTTTTGTC
2981890 ATTGTTATT
1 ATTGTTATT
*
2981899 ATTGTTATC
1 ATTGTTATT
2981908 ATTGTTATT
1 ATTGTTATT
2981917 ATT
1 ATT
2981920 TATTTCGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.63
Consensus pattern (9 bp):
ATTGTTATT
Found at i:2991099 original size:39 final size:39
Alignment explanation
Indices: 2991045--2991136 Score: 130
Period size: 39 Copynumber: 2.4 Consensus size: 39
2991035 ACAACGTTAA
* *
2991045 CAACATCTTCAACATCACCGACAGTGTCAGCAATACCGG
1 CAACATCTTCAACATCACCGACAATGTCAGCAACACCGG
* * *
2991084 CAACATCTTCAACATCACTGCCAATGTCAGCAACGCCGG
1 CAACATCTTCAACATCACCGACAATGTCAGCAACACCGG
*
2991123 CAACATCTCCAACA
1 CAACATCTTCAACA
2991137 CCAGCAACAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.34, C:0.36, G:0.13, T:0.17
Consensus pattern (39 bp):
CAACATCTTCAACATCACCGACAATGTCAGCAACACCGG
Found at i:2997666 original size:26 final size:27
Alignment explanation
Indices: 2997607--2997668 Score: 72
Period size: 31 Copynumber: 2.2 Consensus size: 27
2997597 ACTTATGACA
*
2997607 ATCTTCTAAGTATAATATAATAAACCAATTC
1 ATCTTCTAAGTATAATATAAT--A--AATCC
2997638 ATCTTCTAAGTATAATATAAT-AATCC
1 ATCTTCTAAGTATAATATAATAAATCC
2997664 ATCTT
1 ATCTT
2997669 TTTAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 9 0.30
31 21 0.70
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (27 bp):
ATCTTCTAAGTATAATATAATAAATCC
Found at i:3004237 original size:7 final size:7
Alignment explanation
Indices: 3004225--3004269 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
3004215 TTGCTTTCTT
3004225 TTTTTTC
1 TTTTTTC
3004232 TTTTTTC
1 TTTTTTC
3004239 TTTTTTC
1 TTTTTTC
3004246 -TTTTTC
1 TTTTTTC
3004252 -TTTTTC
1 TTTTTTC
3004258 -TTTTTC
1 TTTTTTC
3004264 TTTTTT
1 TTTTTT
3004270 TGACTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 18 0.49
7 19 0.51
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTC
Found at i:3004242 original size:6 final size:6
Alignment explanation
Indices: 3004226--3004268 Score: 68
Period size: 6 Copynumber: 6.8 Consensus size: 6
3004216 TGCTTTCTTT
3004226 TTTTTC TTTTTTC TTTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC -TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
3004269 TTGACTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.64
7 13 0.36
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:3004249 original size:12 final size:11
Alignment explanation
Indices: 3004219--3004268 Score: 57
Period size: 12 Copynumber: 4.3 Consensus size: 11
3004209 TAGACTTTGC
3004219 TTTCTTTTTTT
1 TTTCTTTTTTT
3004230 TCTT-TTTTCTTT
1 T-TTCTTTT-TTT
3004242 TTTCTTTTTCTT
1 TTTCTTTTT-TT
3004254 TTTCTTTTTCTT
1 TTTCTTTTT-TT
3004266 TTT
1 TTT
3004269 TTGACTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 8 0.23
12 27 0.77
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:3004882 original size:23 final size:24
Alignment explanation
Indices: 3004856--3004912 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
3004846 GAAATATCTT
* *
3004856 TAAAATAATAGCAAAAT-TAACAA
1 TAAAATAACAACAAAATATAACAA
3004879 TAAAATAACAACAAAATAGTAACAA
1 TAAAATAACAACAAAATA-TAACAA
*
3004904 TATAATAAC
1 TAAAATAAC
3004913 GAAATGACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.52
25 14 0.48
ACGTcount: A:0.65, C:0.11, G:0.04, T:0.21
Consensus pattern (24 bp):
TAAAATAACAACAAAATATAACAA
Found at i:3004902 original size:11 final size:11
Alignment explanation
Indices: 3004857--3004917 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
3004847 AAATATCTTT
*
3004857 AAAATAATAGC
1 AAAATAATAAC
* *
3004868 AAAATTAACAAT
1 AAAA-TAATAAC
*
3004880 AAAATAACAAC
1 AAAATAATAAC
*
3004891 AAAATAGTAAC
1 AAAATAATAAC
*
3004902 AATATAATAAC
1 AAAATAATAAC
*
3004913 GAAAT
1 AAAAT
3004918 GACAGCAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 31 0.79
12 8 0.21
ACGTcount: A:0.66, C:0.10, G:0.05, T:0.20
Consensus pattern (11 bp):
AAAATAATAAC
Done.