Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 7 of 18
Found at i:2706397 original size:2 final size:2
Alignment explanation
Indices: 2706390--2706428 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2706380 GCTTGGTTCA
*
2706390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2706429 ATGAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2714497 original size:23 final size:24
Alignment explanation
Indices: 2714471--2714516 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2714461 ATTTTCTTTA
*
2714471 TCTATAATTAT-TTTCTTAAATAT
1 TCTAAAATTATGTTTCTTAAATAT
*
2714494 TCTAAAATTATGTTTTTTAAATA
1 TCTAAAATTATGTTTCTTAAATA
2714517 CCAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (24 bp):
TCTAAAATTATGTTTCTTAAATAT
Found at i:2714526 original size:24 final size:24
Alignment explanation
Indices: 2714474--2714532 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
2714464 TTCTTTATCT
* *
2714474 ATAATTATTTTCTTAAATATTCTA
1 ATAATTATTTTCTTAAATATCCAA
*
2714498 A-AATTATGTTTTTTAAATA-CCAA
1 ATAATTAT-TTTCTTAAATATCCAA
*
2714521 ATAATTTTTTTC
1 ATAATTATTTTC
2714533 ATGAACTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (24 bp):
ATAATTATTTTCTTAAATATCCAA
Found at i:2715019 original size:34 final size:35
Alignment explanation
Indices: 2714981--2715058 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 35
2714971 TAAAAAAATA
* *
2714981 ATTAAAATTATCTCATATTGGATATAAATTTGA-T
1 ATTAAAATTATCTCATATCGGATATAAATGTGATT
2715015 ATTAAAATTATCTCATATCGGATATAAATGTGATT
1 ATTAAAATTATCTCATATCGGATATAAATGTGATT
2715050 ATTAAAATT
1 ATTAAAATT
2715059 TATACAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 31 0.76
35 10 0.24
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (35 bp):
ATTAAAATTATCTCATATCGGATATAAATGTGATT
Found at i:2726603 original size:18 final size:18
Alignment explanation
Indices: 2726580--2726627 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
2726570 AAATCTGTGT
2726580 GTGTGTGTGTGTGTGCGC
1 GTGTGTGTGTGTGTGCGC
2726598 GTGTGTGTGTGTGTGCGC
1 GTGTGTGTGTGTGTGCGC
2726616 GCATGTGTGTGT
1 G--TGTGTGTGT
2726628 ATAGAATAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 19 0.68
20 9 0.32
ACGTcount: A:0.02, C:0.10, G:0.48, T:0.40
Consensus pattern (18 bp):
GTGTGTGTGTGTGTGCGC
Found at i:2726603 original size:20 final size:20
Alignment explanation
Indices: 2726578--2726627 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2726568 AAAAATCTGT
*
2726578 GTGTGTGTGTGTGTGTGCGC
1 GTGTGTGTGTGTGTGCGCGC
2726598 GTGTGTGTGTGTGTGCGCGC
1 GTGTGTGTGTGTGTGCGCGC
*
2726618 ATGTGTGTGT
1 GTGTGTGTGT
2726628 ATAGAATAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.02, C:0.10, G:0.48, T:0.40
Consensus pattern (20 bp):
GTGTGTGTGTGTGTGCGCGC
Found at i:2726627 original size:2 final size:2
Alignment explanation
Indices: 2726575--2726612 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2726565 CAGAAAAATC
* *
2726575 TG TG TG TG TG TG TG TG TG TG CG CG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2726613 CGCGCATGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.05, G:0.50, T:0.45
Consensus pattern (2 bp):
TG
Found at i:2739988 original size:26 final size:27
Alignment explanation
Indices: 2739959--2740010 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
2739949 TTTTTGTGAA
*
2739959 AAAAAAATGTTATTA-ACATCATGTTG
1 AAAAAAATGGTATTACACATCATGTTG
* *
2739985 AAAAATATGGTATTACACATTATGTT
1 AAAAAAATGGTATTACACATCATGTT
2740011 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAAAAATGGTATTACACATCATGTTG
Found at i:2740193 original size:27 final size:26
Alignment explanation
Indices: 2740163--2740214 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2740153 TAATTATTAT
*
2740163 ACGTGATGTTGAAGATTTAGTTGTTAC
1 ACGTGATGTT-AAAATTTAGTTGTTAC
*
2740190 ACGTTATGTTAAAATTTAGTTGTTA
1 ACGTGATGTTAAAATTTAGTTGTTA
2740215 GATATAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (26 bp):
ACGTGATGTTAAAATTTAGTTGTTAC
Found at i:2740211 original size:26 final size:27
Alignment explanation
Indices: 2740059--2740214 Score: 91
Period size: 27 Copynumber: 5.8 Consensus size: 27
2740049 GTTACATACT
* * * *
2740059 ATGTTAAAAATATAGCTGTTATACGAT-
1 ATGTTGAAAATTTAGTTGTTACACG-TG
* * * *
2740086 ATGTTGAAAATTTAATTATTACACATC
1 ATGTTGAAAATTTAGTTGTTACACGTG
* * * * * *
2740113 ATATTGAAAAATGTAATTGTTATATGTC
1 ATGTTG-AAAATTTAGTTGTTACACGTG
* * * * *
2740141 ATGTTGAGAATATAATTATTATACGTG
1 ATGTTGAAAATTTAGTTGTTACACGTG
* *
2740168 ATGTTGAAGATTTAGTTGTTACACGTT
1 ATGTTGAAAATTTAGTTGTTACACGTG
2740195 ATGTT-AAAATTTAGTTGTTA
1 ATGTTGAAAATTTAGTTGTTA
2740215 GATATAGTTG
Statistics
Matches: 100, Mismatches: 27, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
26 15 0.15
27 64 0.64
28 21 0.21
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (27 bp):
ATGTTGAAAATTTAGTTGTTACACGTG
Found at i:2747747 original size:2 final size:2
Alignment explanation
Indices: 2747740--2747777 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2747730 AACGCTCGAC
* *
2747740 AG AG AG AG AG AG CG AG AG AG AG AG AG AG AG AG AC AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2747778 TGTAAATACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2748596 original size:24 final size:23
Alignment explanation
Indices: 2748556--2748601 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2748546 TTTAACATTA
2748556 AAAATTCAACACAACAAAGATAAT
1 AAAATTCAACACAACAAA-ATAAT
*
2748580 AAAATT-AACATCCACAAAATAA
1 AAAATTCAACA-CAACAAAATAA
2748602 GATCATCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.63, C:0.17, G:0.02, T:0.17
Consensus pattern (23 bp):
AAAATTCAACACAACAAAATAAT
Found at i:2748698 original size:12 final size:12
Alignment explanation
Indices: 2748681--2748706 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2748671 GTTTTAAAAA
2748681 TATATATAATAT
1 TATATATAATAT
2748693 TATATATAATAT
1 TATATATAATAT
2748705 TA
1 TA
2748707 ATTTAATTTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATATAATAT
Found at i:2748810 original size:17 final size:17
Alignment explanation
Indices: 2748784--2748817 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2748774 TCAAATTTTT
* *
2748784 TGAATTAATAGACTCAA
1 TGAATCAATAGAATCAA
2748801 TGAATCAATAGAATCAA
1 TGAATCAATAGAATCAA
2748818 ACCATTTTAT
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:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (17 bp):
TGAATCAATAGAATCAA
Found at i:2752222 original size:17 final size:16
Alignment explanation
Indices: 2752188--2752236 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 16
2752178 CAGTAAAATC
2752188 TTAATAAATTAATA--
1 TTAATAAATTAATATT
2752202 TTAATAAATTAATAATT
1 TTAATAAATTAAT-ATT
2752219 TTAATTAAA-TAATATT
1 TTAA-TAAATTAATATT
2752235 TT
1 TT
2752237 TGATTGATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 13 0.42
15 1 0.03
16 5 0.16
17 8 0.26
18 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAATAAATTAATATT
Found at i:2757013 original size:10 final size:10
Alignment explanation
Indices: 2756998--2757022 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2756988 TACATATTTA
2756998 ATATTTTAAT
1 ATATTTTAAT
2757008 ATATTTTAAT
1 ATATTTTAAT
2757018 ATATT
1 ATATT
2757023 AATATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATATTTTAAT
Found at i:2757039 original size:25 final size:25
Alignment explanation
Indices: 2756991--2757048 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
2756981 GTAAAAATAC
*
2756991 ATAT-TTAATATTTTAATATATTTT
1 ATATATTAATATTATAATATATTTT
*
2757015 AATATATTAATATTATATTAT-TTTT
1 -ATATATTAATATTATAATATATTTT
2757040 ATCATATTA
1 AT-ATATTA
2757049 TTTTAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 2 0.07
25 14 0.48
26 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
ATATATTAATATTATAATATATTTT
Found at i:2767372 original size:13 final size:15
Alignment explanation
Indices: 2767354--2767387 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
2767344 TCCCCTTTCT
2767354 TTTTCATTTT-T-AA
1 TTTTCATTTTCTAAA
2767367 TTTTCATTTTCTAAA
1 TTTTCATTTTCTAAA
2767382 TTTTCA
1 TTTTCA
2767388 GTCCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 1 0.05
15 8 0.42
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTCATTTTCTAAA
Found at i:2767687 original size:18 final size:18
Alignment explanation
Indices: 2767664--2767698 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2767654 AACAGTTTGT
2767664 ACAGTAAGCTAATATTCA
1 ACAGTAAGCTAATATTCA
*
2767682 ACAGTAAGCTTATATTC
1 ACAGTAAGCTAATATTC
2767699 CACTGTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (18 bp):
ACAGTAAGCTAATATTCA
Found at i:2768892 original size:2 final size:2
Alignment explanation
Indices: 2768873--2768929 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
2768863 GGAAAAGGAT
* * *
2768873 TA TA TG TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2768915 TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA T
2768930 CTATCCGTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2786452 original size:16 final size:16
Alignment explanation
Indices: 2786431--2786461 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2786421 GAATTGTTTG
*
2786431 ATAATACCAAGCATGA
1 ATAATAACAAGCATGA
2786447 ATAATAACAAGCATG
1 ATAATAACAAGCATG
2786462 TGTACAATGA
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:0.52, C:0.16, G:0.13, T:0.19
Consensus pattern (16 bp):
ATAATAACAAGCATGA
Found at i:2790314 original size:49 final size:49
Alignment explanation
Indices: 2790239--2790338 Score: 123
Period size: 49 Copynumber: 2.0 Consensus size: 49
2790229 ATCTATGAGC
* * *
2790239 TATTTATAATAGTGAATTAGACCTAAACTTATTTGATGTACA-AGTAAAG
1 TATTTATAATACTGAATTAGACCTAAACCTACTTGATGTACAGA-TAAAG
* *
2790288 TATTTATAATAACT-AATTAGATCTAAACCTACTTGGTGTACAGATAAAG
1 TATTTATAAT-ACTGAATTAGACCTAAACCTACTTGATGTACAGATAAAG
2790337 TA
1 TA
2790339 ATAGCAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
49 41 0.93
50 3 0.07
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (49 bp):
TATTTATAATACTGAATTAGACCTAAACCTACTTGATGTACAGATAAAG
Found at i:2794168 original size:22 final size:22
Alignment explanation
Indices: 2794142--2794185 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2794132 TCCAATGTGA
*
2794142 AAATATCTTGATTTGGATATTG
1 AAATAACTTGATTTGGATATTG
2794164 AAATAACTTGATTTGGATATTG
1 AAATAACTTGATTTGGATATTG
2794186 GTATTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (22 bp):
AAATAACTTGATTTGGATATTG
Found at i:2797901 original size:20 final size:20
Alignment explanation
Indices: 2797876--2797915 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2797866 TTGAAATAAC
*
2797876 ATTTAAAAAAATTTTAAATT
1 ATTTAAAAAAATTTAAAATT
2797896 ATTTAAAAAAATTTAAAATT
1 ATTTAAAAAAATTTAAAATT
2797916 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTAAAAAAATTTAAAATT
Found at i:2797981 original size:29 final size:29
Alignment explanation
Indices: 2797949--2798011 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
2797939 AATCAAGGTC
2797949 TTATATTTTATTTTAAATCAAATAAATTT
1 TTATATTTTATTTTAAATCAAATAAATTT
* * *
2797978 TTATTTTTTATTTTAAATTAAATAAGTTT
1 TTATATTTTATTTTAAATCAAATAAATTT
2798007 TTATA
1 TTATA
2798012 ACTATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (29 bp):
TTATATTTTATTTTAAATCAAATAAATTT
Found at i:2803775 original size:176 final size:176
Alignment explanation
Indices: 2803476--2803809 Score: 544
Period size: 176 Copynumber: 1.9 Consensus size: 176
2803466 CTATTTAAGG
* * * * *
2803476 TAATAACTTTAATATAGAATTGCTGTAATTGATTAAAGAGTGCCTTAACTAATTAATGGAAATCT
1 TAATAACTTTAACACAGAATTGCTCTAATTGATTAAAGAGAGCCTTAACTAATTAATGCAAATCT
* * *
2803541 TATCTTCCTTCTAAGGTCTTTTTAACTAATTAGAACATTTTCTAATCAATTGAAACACTAACTAA
66 TATCGTCCTTCTAAGGTCTCTTTAACTAATTAGAACATTTTCTAATCAATTAAAACACTAACTAA
2803606 ACT-CAACCATCATACTATATATCATTAACACCTCACTAACTTAGGC
131 A-TGCAACCATCATACTATATATCATTAACACCTCACTAACTTAGGC
*
2803652 TAATAACTTTAACACATAATTGCTCTAATTGATTAAAGAGAGCCTTAACTAATTAATGCAAATCT
1 TAATAACTTTAACACAGAATTGCTCTAATTGATTAAAGAGAGCCTTAACTAATTAATGCAAATCT
* **
2803717 TATCGTCCTTTTAAGGTCTCTTTAACTAATTAGAACATTTTCTAATTGATTAAAACACTAACTAA
66 TATCGTCCTTCTAAGGTCTCTTTAACTAATTAGAACATTTTCTAATCAATTAAAACACTAACTAA
2803782 ATGCAACCATCATACTATATATCATTAA
131 ATGCAACCATCATACTATATATCATTAA
2803810 AAACATATTC
Statistics
Matches: 145, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
175 1 0.01
176 144 0.99
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (176 bp):
TAATAACTTTAACACAGAATTGCTCTAATTGATTAAAGAGAGCCTTAACTAATTAATGCAAATCT
TATCGTCCTTCTAAGGTCTCTTTAACTAATTAGAACATTTTCTAATCAATTAAAACACTAACTAA
ATGCAACCATCATACTATATATCATTAACACCTCACTAACTTAGGC
Found at i:2804863 original size:2 final size:2
Alignment explanation
Indices: 2804856--2804883 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2804846 TAGGATAAAA
2804856 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
2804884 GCCACATAGC
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:2808780 original size:21 final size:20
Alignment explanation
Indices: 2808740--2808780 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2808730 AGCTTTAGTG
* *
2808740 CTAATAAAATTTATTTTTTT
1 CTAAAAAAATTTAATTTTTT
2808760 CTAAAAAAATTTAAATTTTTT
1 CTAAAAAAATTT-AATTTTTT
2808781 TTTATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
CTAAAAAAATTTAATTTTTT
Found at i:2809553 original size:18 final size:18
Alignment explanation
Indices: 2809530--2809567 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2809520 GAGCTTAATG
2809530 AATTGACACGTGTGGTGA
1 AATTGACACGTGTGGTGA
2809548 AATTGACACGTGTGGTGA
1 AATTGACACGTGTGGTGA
2809566 AA
1 AA
2809568 AAAAACCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.26
Consensus pattern (18 bp):
AATTGACACGTGTGGTGA
Found at i:2823298 original size:20 final size:20
Alignment explanation
Indices: 2823275--2823312 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2823265 GAAAGATTGT
2823275 TTAATTGATAAATTAATTTA
1 TTAATTGATAAATTAATTTA
* *
2823295 TTAATTTATATATTAATT
1 TTAATTGATAAATTAATT
2823313 AATAAAAAAC
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTAATTGATAAATTAATTTA
Found at i:2835845 original size:30 final size:30
Alignment explanation
Indices: 2835793--2835855 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2835783 TCAAATTTTA
* *
2835793 ATATTTTTATTTTGAGTTAAATAAGTCCTT
1 ATATTTTTATTTTGAATCAAATAAGTCCTT
*
2835823 ATATTTTTATTTT-ACATCAAATAAGTTCTT
1 ATATTTTTATTTTGA-ATCAAATAAGTCCTT
2835853 ATA
1 ATA
2835856 ACTAATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.52
Consensus pattern (30 bp):
ATATTTTTATTTTGAATCAAATAAGTCCTT
Found at i:2839346 original size:16 final size:16
Alignment explanation
Indices: 2839327--2839361 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2839317 ATAAAGGGGA
2839327 TATATAAAAAAGGAGG
1 TATATAAAAAAGGAGG
2839343 TATATAAAAAAGGAGG
1 TATATAAAAAAGGAGG
2839359 TAT
1 TAT
2839362 TTCGANNNNN
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (16 bp):
TATATAAAAAAGGAGG
Found at i:2840534 original size:42 final size:42
Alignment explanation
Indices: 2840487--2840614 Score: 115
Period size: 42 Copynumber: 3.1 Consensus size: 42
2840477 TAAAGATAAT
2840487 ATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCA
1 ATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCA
* * * * * * ** *
2840529 ATTTAT-CTCTAAACATATCAAA-A-TA-AT-TTAGAGAT-AA
1 ATTTATATTTTGACCA-ATCAAATATTAGCTATTGGTCATCCA
2840566 TATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCA
1 -ATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCA
2840609 ATTTAT
1 ATTTAT
2840615 TTCTAAATAA
Statistics
Matches: 60, Mismatches: 18, Indels: 16
0.64 0.19 0.17
Matches are distributed among these distances:
37 1 0.02
38 17 0.28
39 7 0.12
40 4 0.07
41 7 0.12
42 23 0.38
43 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (42 bp):
ATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCA
Found at i:2840594 original size:159 final size:160
Alignment explanation
Indices: 2840393--2840701 Score: 401
Period size: 159 Copynumber: 1.9 Consensus size: 160
2840383 ATCTCTTGAG
* * **
2840393 ATAATTTGAAGATAATATTTAAATTGGACTAATCAAAAATTAGTTATTGGTCATTTAATTTATCT
1 ATAATTTGAAGATAATATTTAAATTGGACCAATCAAAAATTAGCTATTGGTCATCCAATTTATCT
* *
2840458 CTAAACAAATCAAAATAA-TTAAAGATAATATTTATA-TTTTGACCAATC-AAATATTAGCTATT
66 CTAAACAAATCAAAATAATTTAAAGATAATATTCATATTTTTGACCAATCAAAAT-TTAACTATT
*
2840520 GGTCATCCAATTTATCTCTAAACATATCAAA
130 GGTCATCCAAATTATCTCTAAACATATCAAA
* * *
2840551 ATAATTT-AGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTAT
1 ATAATTTGA-AGATAATATTTA-AATTGGACCAATCAAAAATTAGCTATTGGTCATCCAATTTAT
* * ** * *
2840615 TTCTAAATAAATCAAAATAATTTGGAGATAATCTTCATATTTTTGACCAATCAAAATTTAATTAT
64 CTCTAAACAAATCAAAATAATTTAAAGATAATATTCATATTTTTGACCAATCAAAATTTAACTAT
**
2840680 TGGTCATTTAAATTATCTCTAA
129 TGGTCATCCAAATTATCTCTAA
2840702 TAATTATATT
Statistics
Matches: 128, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
157 1 0.01
158 19 0.15
159 53 0.41
160 14 0.11
161 37 0.29
162 4 0.03
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (160 bp):
ATAATTTGAAGATAATATTTAAATTGGACCAATCAAAAATTAGCTATTGGTCATCCAATTTATCT
CTAAACAAATCAAAATAATTTAAAGATAATATTCATATTTTTGACCAATCAAAATTTAACTATTG
GTCATCCAAATTATCTCTAAACATATCAAA
Found at i:2840597 original size:80 final size:80
Alignment explanation
Indices: 2840393--2840701 Score: 392
Period size: 80 Copynumber: 3.9 Consensus size: 80
2840383 ATCTCTTGAG
* * * * * **
2840393 ATAATTT-GAAGATAATATTTA-AATTGGACTAATCAAAAATTAGTTATTGGTCATTTAATTTAT
1 ATAATTTAG-AGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTAT
2840456 CTCTAAACAAATCAAA
65 CTCTAAACAAATCAAA
*
2840472 ATAA-TTAAAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTATC
1 ATAATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTATC
*
2840536 TCTAAACATATCAAA
66 TCTAAACAAATCAAA
*
2840551 ATAATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTATT
1 ATAATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTATC
*
2840616 TCTAAATAAATCAAA
66 TCTAAACAAATCAAA
* * * ** ** *
2840631 ATAATTTGGAGATAATCTTCATATTTTTGACCAATCAAA-ATTTAATTATTGGTCATTTAAATTA
1 ATAATTTAGAGATAATATTTATA-TTTTGACCAATCAAATA-TTAGCTATTGGTCATCCAATTTA
2840695 TCTCTAA
64 TCTCTAA
2840702 TAATTATATT
Statistics
Matches: 203, Mismatches: 22, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
78 14 0.07
79 58 0.29
80 92 0.45
81 39 0.19
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (80 bp):
ATAATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTATC
TCTAAACAAATCAAA
Found at i:2847236 original size:23 final size:23
Alignment explanation
Indices: 2847206--2847281 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
2847196 TGGACTTTGT
*
2847206 CTTGATCACAAACTTCGTAGTCG
1 CTTGATCACGAACTTCGTAGTCG
*
2847229 CTTGATCACGAACTTCGTCGTCG
1 CTTGATCACGAACTTCGTAGTCG
*
2847252 CTTGATCACGAACTTCGCCA-TCG
1 CTTGATCACGAACTTCG-TAGTCG
2847275 CTTGATC
1 CTTGATC
2847282 TTCACTTCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.30
Consensus pattern (23 bp):
CTTGATCACGAACTTCGTAGTCG
Found at i:2858270 original size:12 final size:12
Alignment explanation
Indices: 2858253--2858282 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2858243 TCTTCCACGT
2858253 CCACGATTATGA
1 CCACGATTATGA
2858265 CCACGATTATGA
1 CCACGATTATGA
2858277 CCACGA
1 CCACGA
2858283 CCACGACCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (12 bp):
CCACGATTATGA
Found at i:2886866 original size:27 final size:27
Alignment explanation
Indices: 2886800--2887082 Score: 196
Period size: 27 Copynumber: 10.4 Consensus size: 27
2886790 TGTAACAACT
*
2886800 TTTTCATCATGACATGTAACAACTAAA
1 TTTTCAACATGACATGTAACAACTAAA
*
2886827 TTTTTTAACATGACATGTAACAACTAAA
1 -TTTTCAACATGACATGTAACAACTAAA
* *
2886855 TTTTCAACATGACATATAACATA-TATAT
1 TTTTCAACATGACATGTAACA-ACTA-AA
* ** *
2886883 TTTTCAATATTTCATGTAACAACTATAT
1 TTTTCAACATGACATGTAACAACTA-AA
* ***
2886911 TTTTTAACATGACGCATAACAACTAAA
1 TTTTCAACATGACATGTAACAACTAAA
* *** *
2886938 CTTTCAACATGGTTTGTAATAACTAAA
1 TTTTCAACATGACATGTAACAACTAAA
* * * *
2886965 TTTTCAATATGACATCTAACAATTATA
1 TTTTCAACATGACATGTAACAACTAAA
* * *
2886992 TTTTCAACTTGACGTGTAACAA-T-TA
1 TTTTCAACATGACATGTAACAACTAAA
* **
2887017 TTTTTAACATGGTATGTAACAACTAAA
1 TTTTCAACATGACATGTAACAACTAAA
* * ** *
2887044 TTTTAGAATATGATGTGTAAC-ACTACAT
1 TTTT-CAACATGACATGTAACAACTA-AA
2887072 TTTTCAACATG
1 TTTTCAACATG
2887083 GCATTAATAA
Statistics
Matches: 197, Mismatches: 51, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
25 19 0.10
26 2 0.01
27 92 0.47
28 84 0.43
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (27 bp):
TTTTCAACATGACATGTAACAACTAAA
Found at i:2886866 original size:55 final size:55
Alignment explanation
Indices: 2886800--2887082 Score: 200
Period size: 55 Copynumber: 5.2 Consensus size: 55
2886790 TGTAACAACT
* * *
2886800 TTTTCATCATGACATGTAACAACTAAATTTTTTAACATGACATGTAACAACTAAA
1 TTTTCAACATGACATATAACAACTAAATTTTTCAACATGACATGTAACAACTAAA
* * ** *
2886855 TTTTCAACATGACATATAACATA-TATATTTTTCAATATTTCATGTAACAACTATAT
1 TTTTCAACATGACATATAACA-ACTAAATTTTTCAACATGACATGTAACAACTA-AA
* ** * *** *
2886911 TTTTTAACATGACGCATAACAACTAAA-CTTTCAACATGGTTTGTAATAACTAAA
1 TTTTCAACATGACATATAACAACTAAATTTTTCAACATGACATGTAACAACTAAA
* * * * * * *
2886965 TTTTCAATATGACATCTAACAATTATA-TTTTCAACTTGACGTGTAACAA-T-TA
1 TTTTCAACATGACATATAACAACTAAATTTTTCAACATGACATGTAACAACTAAA
* ** * ** * ** *
2887017 TTTTTAACATGGTATGTAACAACTAAATTTTAGAATATGATGTGTAAC-ACTACAT
1 TTTTCAACATGACATATAACAACTAAATTTTTCAACATGACATGTAACAACTA-AA
2887072 TTTTCAACATG
1 TTTTCAACATG
2887083 GCATTAATAA
Statistics
Matches: 172, Mismatches: 49, Indels: 14
0.73 0.21 0.06
Matches are distributed among these distances:
52 22 0.13
53 17 0.10
54 37 0.22
55 73 0.42
56 23 0.13
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (55 bp):
TTTTCAACATGACATATAACAACTAAATTTTTCAACATGACATGTAACAACTAAA
Found at i:2886968 original size:83 final size:83
Alignment explanation
Indices: 2886799--2887082 Score: 276
Period size: 83 Copynumber: 3.5 Consensus size: 83
2886789 GTGTAACAAC
* *
2886799 TTTTTC-ATCATGACATGTAACAACTAAATTTTTTAACATGACATGTAACAACTAAATTTTCAAC
1 TTTTTCAAT-ATGACATGTAACAACTATATTTTTTAACATGACGTGTAACAACTAAATTTTCAAC
** * *
2886863 ATGACATATAACATA-TATA
65 ATGGTATGTAACA-ACTAAA
** ** *
2886882 TTTTTCAATATTTCATGTAACAACTATATTTTTTAACATGACGCATAACAACTAAACTTTCAACA
1 TTTTTCAATATGACATGTAACAACTATATTTTTTAACATGACGTGTAACAACTAAATTTTCAACA
* *
2886947 TGGTTTGTAATAACTAAA
66 TGGTATGTAACAACTAAA
* * * * * *
2886965 -TTTTCAATATGACATCTAACAATTATA-TTTTCAACTTGACGTGTAACAA-T-TATTTTTAACA
1 TTTTTCAATATGACATGTAACAACTATATTTTTTAACATGACGTGTAACAACTAAATTTTCAACA
2887026 TGGTATGTAACAACTAAA
66 TGGTATGTAACAACTAAA
** ** * *
2887044 TTTTAGAATATGATGTGTAAC-ACTACATTTTTCAACATG
1 TTTTTCAATATGACATGTAACAACTATATTTTTTAACATG
2887083 GCATTAATAA
Statistics
Matches: 163, Mismatches: 34, Indels: 11
0.78 0.16 0.05
Matches are distributed among these distances:
79 28 0.17
80 26 0.16
81 18 0.11
82 24 0.15
83 65 0.40
84 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (83 bp):
TTTTTCAATATGACATGTAACAACTATATTTTTTAACATGACGTGTAACAACTAAATTTTCAACA
TGGTATGTAACAACTAAA
Found at i:2892558 original size:33 final size:33
Alignment explanation
Indices: 2892521--2892584 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
2892511 TATATAACTC
*
2892521 TTTGAATAGTTATATTATGAAAGGAAATAACAG
1 TTTGAATAGTTATATTATGAAAGAAAATAACAG
*
2892554 TTTGAATAGTTATATTTTGAAAGAAAATAAC
1 TTTGAATAGTTATATTATGAAAGAAAATAAC
2892585 TCTTTACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.36
Consensus pattern (33 bp):
TTTGAATAGTTATATTATGAAAGAAAATAACAG
Found at i:2894789 original size:1 final size:1
Alignment explanation
Indices: 2894783--2894811 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
2894773 GGCCAGTCCT
2894783 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2894812 TGATTTCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2904641 original size:15 final size:15
Alignment explanation
Indices: 2904621--2904650 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2904611 TAATAAAAAA
2904621 ATTATATATATAACT
1 ATTATATATATAACT
2904636 ATTATATATATAACT
1 ATTATATATATAACT
2904651 TATTTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATATATATAACT
Found at i:2908528 original size:18 final size:18
Alignment explanation
Indices: 2908501--2908535 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2908491 AGCCAAACAT
2908501 AATGAAGATGACGATGAC
1 AATGAAGATGACGATGAC
*
2908519 AATGATGATGACGATGA
1 AATGAAGATGACGATGA
2908536 AAGAGTTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.09, G:0.29, T:0.20
Consensus pattern (18 bp):
AATGAAGATGACGATGAC
Found at i:2917270 original size:22 final size:21
Alignment explanation
Indices: 2917240--2917287 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2917230 TATATCAATT
* *
2917240 ATAGATTATAAACTATATATAA
1 ATAGGTTATAAACTATAGAT-A
*
2917262 ATAGGTTATAAATTATAGATA
1 ATAGGTTATAAACTATAGATA
2917283 ATAGG
1 ATAGG
2917288 CGCATGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.35
Consensus pattern (21 bp):
ATAGGTTATAAACTATAGATA
Found at i:2918158 original size:20 final size:21
Alignment explanation
Indices: 2918130--2918169 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2918120 TTTTTTATAA
2918130 AAAATCTTATACAA-TTATGTG
1 AAAATCTTATA-AATTTATGTG
2918151 AAAA-CTTATAAATTTATGT
1 AAAATCTTATAAATTTATGT
2918170 ATAGGGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAATCTTATAAATTTATGTG
Found at i:2933967 original size:126 final size:124
Alignment explanation
Indices: 2933822--2934061 Score: 338
Period size: 126 Copynumber: 1.9 Consensus size: 124
2933812 ATTTTATTGA
* * ** *
2933822 AAAAAAAAATTATTACACACTATGTTTAAGGTGTTTAACTGTAAGAGTTTATAT-TCTAGTGAAA
1 AAAAAAAAATTATTACACACCATGTTTAACGTGTTTAACTCAAAGAGTTTATATCT-TAGTAAAA
* * *
2933886 TACAAAAGTAGAGACCAAGTTATACACCATGTTACAAAAAAATGTTGTTACACACCATGCTG
65 TACAAAAATAAAGACCAAGTTACACACCATGTTA-AAAAAAA-GTTGTTACACACCATGCTG
* *
2933948 AAAAAAAAATTATTGCACACCATGTTTAACGTGTTTAACTCAAAGAGTTTGTATCTTAGTAAAAT
1 AAAAAAAAATTATTACACACCATGTTTAACGTGTTTAACTCAAAGAGTTTATATCTTAGTAAAAT
* *
2934013 ACAAAAATAAAGACCAAGTTACATATCATGTTAAAAAAAAGTTGTTACA
66 ACAAAAATAAAGACCAAGTTACACACCATGTTAAAAAAAAGTTGTTACA
2934062 TGTAATGTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
124 9 0.09
125 7 0.07
126 84 0.83
127 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (124 bp):
AAAAAAAAATTATTACACACCATGTTTAACGTGTTTAACTCAAAGAGTTTATATCTTAGTAAAAT
ACAAAAATAAAGACCAAGTTACACACCATGTTAAAAAAAAGTTGTTACACACCATGCTG
Found at i:2934069 original size:26 final size:27
Alignment explanation
Indices: 2934030--2934081 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2934020 TAAAGACCAA
*
2934030 GTTACATATCATG-TTAAAAAAAAGTT
1 GTTACATATAATGTTTAAAAAAAAGTT
*
2934056 GTTACATGTAATGTTTTAAAAAAAAG
1 GTTACATATAATG-TTTAAAAAAAAG
2934082 GTTATTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
28 11 0.50
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (27 bp):
GTTACATATAATGTTTAAAAAAAAGTT
Found at i:2934209 original size:26 final size:27
Alignment explanation
Indices: 2934160--2934211 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
2934150 TGACATATTA
**
2934160 AAAAAAAATTTATTACACTTCATGTTG
1 AAAAAAAATTTATTACACACCATGTTG
*
2934187 AAAAAAAA-TTATTATACACCATGTT
1 AAAAAAAATTTATTACACACCATGTT
2934212 TAAGGTGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (27 bp):
AAAAAAAATTTATTACACACCATGTTG
Found at i:2936719 original size:144 final size:144
Alignment explanation
Indices: 2936526--2936813 Score: 452
Period size: 144 Copynumber: 2.0 Consensus size: 144
2936516 TGACGGTACA
*
2936526 GTCTGACCCTGGAAATCGTTCTACTCCTTTCCCATTTGACATGAAATTGCCATCTAATAAAAAAC
1 GTCTGACCCTGGAAATCGCTCTACTCCTTTCCCATTTGACATGAAATTGCCATCTAATAAAAAAC
*
2936591 AGTGAGGGAAAAGATGTATACTTGTATTCAGATATTTAAGTTATTAGCTAGGAAAAGATCAAC-T
66 AGTGAGGGAAAAGATGTATACTTGTATTCAGATATTTAAGTTACTAGCTAGGAAAAGATCAACAT
2936655 TTTTTTTTCTCAAT
131 TTTTTTTTCTCAAT
* * * *
2936669 GTCTGACCCTGGAAATCGCTGTATCTCCTTTCTCATTTGACATGAAATTGCCCTTTAATAAAAAA
1 GTCTGACCCTGGAAATCGCTCTA-CTCCTTTCCCATTTGACATGAAATTGCCATCTAATAAAAAA
* * ** *
2936734 TAGTGAGGGAAAAGATGTATACTTGTATTCATATATTTAAGTTACTAGCTCTGAAAAGTTCAACT
65 CAGTGAGGGAAAAGATGTATACTTGTATTCAGATATTTAAGTTACTAGCTAGGAAAAGATCAAC-
2936799 ATTTTTTTTTCTCAA
129 ATTTTTTTTTCTCAA
2936814 ACAATAGATT
Statistics
Matches: 131, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
143 21 0.16
144 96 0.73
146 14 0.11
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (144 bp):
GTCTGACCCTGGAAATCGCTCTACTCCTTTCCCATTTGACATGAAATTGCCATCTAATAAAAAAC
AGTGAGGGAAAAGATGTATACTTGTATTCAGATATTTAAGTTACTAGCTAGGAAAAGATCAACAT
TTTTTTTTCTCAAT
Found at i:2938131 original size:54 final size:53
Alignment explanation
Indices: 2938029--2938144 Score: 153
Period size: 54 Copynumber: 2.2 Consensus size: 53
2938019 ACCTCACTAA
* * *
2938029 TTCCCCCCTTCTGAGTCCCGACCTAAAACTCCTACCCATCGCCTACCTAACTCC
1 TTCCCCCCCTCTGAGTCCCGACCT-AAACTCCCACCCATCGCCGACCTAACTCC
* *
2938083 TTCCCTCCCCTCTCGAGTCCCGACCT-AATTCCCCCCCATCGCCGACCTAACTCC
1 TTCCC-CCCCTCT-GAGTCCCGACCTAAACTCCCACCCATCGCCGACCTAACTCC
2938137 TTCCCCCC
1 TTCCCCCC
2938145 TCCCGCGAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
53 3 0.05
54 34 0.62
55 6 0.11
56 12 0.22
ACGTcount: A:0.16, C:0.53, G:0.08, T:0.23
Consensus pattern (53 bp):
TTCCCCCCCTCTGAGTCCCGACCTAAACTCCCACCCATCGCCGACCTAACTCC
Found at i:2940460 original size:15 final size:15
Alignment explanation
Indices: 2940440--2940473 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2940430 GGAGCCTGTG
*
2940440 GATGATGAGGGGTTT
1 GATGATGAGGAGTTT
*
2940455 GATGATGATGAGTTT
1 GATGATGAGGAGTTT
2940470 GATG
1 GATG
2940474 TTCTTATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (15 bp):
GATGATGAGGAGTTT
Found at i:2942074 original size:30 final size:30
Alignment explanation
Indices: 2942038--2942101 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
2942028 ATCCTCTTCA
*
2942038 TCATGATTTCTATGATAATTTTGAAACTCT
1 TCATGATTTCTATGATAATGTTGAAACTCT
* * *
2942068 TCATGATTTCTATTATCATGTTGAATCTCT
1 TCATGATTTCTATGATAATGTTGAAACTCT
2942098 TCAT
1 TCAT
2942102 TAACTTCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (30 bp):
TCATGATTTCTATGATAATGTTGAAACTCT
Found at i:2955674 original size:18 final size:17
Alignment explanation
Indices: 2955622--2955667 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2955612 CTTAAATTCT
2955622 TTTTTTTTTAAGAAAAA-
1 TTTTTTTTTAA-AAAAAG
*
2955639 TTTGTTCTTTAAAAAAAG
1 TTT-TTTTTTAAAAAAAG
2955657 TTTTTTTTTAA
1 TTTTTTTTTAA
2955668 TTAAAAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (17 bp):
TTTTTTTTTAAAAAAAG
Found at i:2960300 original size:62 final size:62
Alignment explanation
Indices: 2960123--2961225 Score: 742
Period size: 62 Copynumber: 18.0 Consensus size: 62
2960113 GCATCCACTA
* ** * *
2960123 GACTTAAACATCTTGGATGCCAATTAAATT-AGGCATAAAGTCTTTTTATG-C--C--AA-TG
1 GACTTAAACATCTTGGATGCTAGCTAAATTGA-GCTTAAACTCTTTTTATGCCAACATAACTG
* * * * * **
2960179 GACTTAAACATTTTGGATG-TCAACTAAATTGAGCTTAAACTCTCTTCATTCCATTATAACTG
1 GACTTAAACATCTTGGATGCT-AGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* * * * *
2960241 GACTTGAACATCATGGATGCTAGTTAAATTGAGCTTAAACTTTTTTTGTGCCAACATAACTG
1 GACTTAAACATCTTGGATGCTAGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* * * * * ** * *
2960303 GACTTAAATATCTTAGATGCTAGCTATATTGGGCTTAAAATCTTTTCGTGCCAATATAATTG
1 GACTTAAACATCTTGGATGCTAGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* * * * * *
2960365 GACTCAAATATCTTGGATGCCAACTAAATT-AGGCTTAAATTCTTTTTGTGCCAACATAACTG
1 GACTTAAACATCTTGGATGCTAGCTAAATTGA-GCTTAAACTCTTTTTATGCCAACATAACTG
* * * * * * *
2960427 GACTTAAACATATTGGATGCCTA-TTAAATTGGGCTTAAACTCTTTTCATGCCAACGTAATTA
1 GACTTAAACATCTTGGATG-CTAGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* * * * * ** * * *
2960489 GACTTAAACATTTTGTAAG-TAAGCTAAATTGTGCTTAAAGTCTTTTTACACTAAGACAACTG
1 GACTTAAACATCTTGGATGCT-AGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* * * * *
2960551 GACTAAAACATCTTGGATGTTAGCTAAATTAAGCTTAAACTCTTTTTATGTCAACATAACTA
1 GACTTAAACATCTTGGATGCTAGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* ** * * * * * * *
2960613 GACTTAAACATTTTATATGCCAACTACATTGGGCTTAAAGTCTTTTTATGCAAACATAACTA
1 GACTTAAACATCTTGGATGCTAGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* * * * * * **
2960675 GACTTAAGCATCTTAGATGCCAACTAAA--G-GCTTAAAGTCTTTTTATGCTAACATAGTTG
1 GACTTAAACATCTTGGATGCTAGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* * * * * ** ** * *
2960734 GACTTAAATATTTTGGATGAC-AACTAAATAGGGCTTAAACTCTCTTCGA-GCCATTACAACTA
1 GACTTAAACATCTTGGATG-CTAGCTAAATTGAGCTTAAACTCT-TTTTATGCCAACATAACTG
* * * * * * * * *
2960796 GATTTGAACATCTTAGATG-TCAGTTAAATTGGGCTTAAATTCTTTTTGTGCAAACATAACTA
1 GACTTAAACATCTTGGATGCT-AGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* * * * * * * * **
2960858 GCCTCAAACAACTTAGATGCCAGC-AATATTGAGC-TACAAATCTCTTTATGCCAACCTAACCA
1 GACTTAAACATCTTGGATGCTAGCTAA-ATTGAGCTTA-AACTCTTTTTATGCCAACATAACTG
* ** * * * * * * *
2960920 GACTTAAACATCTTGAATGCCGGTTAAATT-AGGCATAAATTCTTTTTGTACCAATATAACTA
1 GACTTAAACATCTTGGATGCTAGCTAAATTGA-GCTTAAACTCTTTTTATGCCAACATAACTG
* * ** *
2960982 GACTTAAACATCTTGGATGCCAACTAAATT-AGGCTTAAACTCTTTTCGTGCCAACATAATTG
1 GACTTAAACATCTTGGATGCTAGCTAAATTGA-GCTTAAACTCTTTTTATGCCAACATAACTG
* * * * * *
2961044 GACTTAAACATATTGGATGCTAGCTAAATTGGGCTTCAACTCTTTTCATGCCAACATGATTG
1 GACTTAAACATCTTGGATGCTAGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* * *
2961106 GACTTAAATATCTTGGATGCTAGCTAAA-TGAGGCTTAAATTCTTTTCATGCCAACATAACTG
1 GACTTAAACATCTTGGATGCTAGCTAAATTGA-GCTTAAACTCTTTTTATGCCAACATAACTG
* * * *
2961168 GATTTAAATATCTTGGATGCCAGCTAAATTTGA--TTAAACTCTTTTCATGCCAACATAA
1 GACTTAAACATCTTGGATGCTAGCTAAA-TTGAGCTTAAACTCTTTTTATGCCAACATAA
2961226 TTGTAGAAAC
Statistics
Matches: 823, Mismatches: 191, Indels: 61
0.77 0.18 0.06
Matches are distributed among these distances:
56 39 0.05
57 2 0.00
59 48 0.06
60 3 0.00
61 37 0.04
62 680 0.83
63 11 0.01
64 3 0.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Consensus pattern (62 bp):
GACTTAAACATCTTGGATGCTAGCTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
Found at i:2960365 original size:31 final size:31
Alignment explanation
Indices: 2960330--2960434 Score: 83
Period size: 31 Copynumber: 3.4 Consensus size: 31
2960320 TGCTAGCTAT
*
2960330 ATTGGGCTTAAAATCTTTTCGTGCCAATATA
1 ATTGGACTTAAAATCTTTTCGTGCCAATATA
* *
2960361 ATTGGACTCAAATATC--TTGGATGCCAACTA-A
1 ATTGGACTTAAA-ATCTTTTCG-TGCCAA-TATA
* * *
2960392 ATTAGG-CTTAAATTCTTTTTGTGCCAACATA
1 ATT-GGACTTAAAATCTTTTCGTGCCAATATA
*
2960423 ACTGGACTTAAA
1 ATTGGACTTAAA
2960435 CATATTGGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
30 8 0.14
31 40 0.69
32 10 0.17
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (31 bp):
ATTGGACTTAAAATCTTTTCGTGCCAATATA
Found at i:2960382 original size:124 final size:124
Alignment explanation
Indices: 2960121--2961227 Score: 825
Period size: 124 Copynumber: 9.0 Consensus size: 124
2960111 TTGCATCCAC
* * *
2960121 TAGACTTAAACATCTTGGATGCCAATTAAATT-AGGCATAAAGTCTTTTTATG-C--C--AA-TG
1 TAGACTTAAACATCTTGGATGCCAACTAAATTGA-GCTTAAACTCTTTTTATGCCAACATAACTG
* * * * * ** *
2960179 GACTTAAACATTTTGGATG-TCAACTAAATTGAGCTTAAACTCTCTTCATTCCATTATAAC
65 GACTTAAACATCTTGGATGCT-AGCTAAATTGGGCTTAAACTCTTTTCATGCCAACATAAT
* * * * ** * *
2960239 TGGACTTGAACATCATGGATGCTAGTTAAATTGAGCTTAAACTTTTTTTGTGCCAACATAACTGG
1 TAGACTTAAACATCTTGGATGCCAACTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTGG
* * * * * *
2960304 ACTTAAATATCTTAGATGCTAGCTATATTGGGCTTAAAATCTTTTCGTGCCAATATAAT
66 ACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTCTTTTCATGCCAACATAAT
* * * * *
2960363 TGGACTCAAATATCTTGGATGCCAACTAAATT-AGGCTTAAATTCTTTTTGTGCCAACATAACTG
1 TAGACTTAAACATCTTGGATGCCAACTAAATTGA-GCTTAAACTCTTTTTATGCCAACATAACTG
* * *
2960427 GACTTAAACATATTGGATGCCTA-TTAAATTGGGCTTAAACTCTTTTCATGCCAACGTAAT
65 GACTTAAACATCTTGGATG-CTAGCTAAATTGGGCTTAAACTCTTTTCATGCCAACATAAT
* * * * * * ** * * *
2960487 TAGACTTAAACATTTTGTAAG-TAAGCTAAATTGTGCTTAAAGTCTTTTTACACTAAGACAACTG
1 TAGACTTAAACATCTTGGATGCCAA-CTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTG
* * ** * * *
2960551 GACTAAAACATCTTGGATGTTAGCTAAATTAAGCTTAAACTCTTTTTATGTCAACATAAC
65 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTCTTTTCATGCCAACATAAT
* ** * * * * *
2960611 TAGACTTAAACATTTTATATGCCAACTACATTGGGCTTAAAGTCTTTTTATGCAAACATAACTAG
1 TAGACTTAAACATCTTGGATGCCAACTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTGG
* * * * * * * *
2960676 ACTTAAGCATCTTAGATGCCAACTAAA---GGCTTAAAGTCTTTTTATGCTAACATAGT
66 ACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTCTTTTCATGCCAACATAAT
* * * * * * ** ** * *
2960732 TGGACTTAAATATTTTGGATGACAACTAAATAGGGCTTAAACTCTCTTCGA-GCCATTACAACTA
1 TAGACTTAAACATCTTGGATGCCAACTAAATTGAGCTTAAACTCT-TTTTATGCCAACATAACTG
* * * * * ** * *
2960796 GATTTGAACATCTTAGATG-TCAGTTAAATTGGGCTTAAATTCTTTTTGTGCAAACATAAC
65 GACTTAAACATCTTGGATGCT-AGCTAAATTGGGCTTAAACTCTTTTCATGCCAACATAAT
* * * * * * * * *
2960856 TAGCCTCAAACAACTTAGATGCCAGC-AATATTGAGC-TACAAATCTCTTTATGCCAACCTAACC
1 TAGACTTAAACATCTTGGATGCCAACTAA-ATTGAGCTTA-AACTCTTTTTATGCCAACATAACT
* * ** * * * * ** * * *
2960919 AGACTTAAACATCTTGAATGCCGGTTAAATTAGGCATAAATTCTTTTTGTACCAATATAAC
64 GGACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTCTTTTCATGCCAACATAAT
** *
2960980 TAGACTTAAACATCTTGGATGCCAACTAAATT-AGGCTTAAACTCTTTTCGTGCCAACATAATTG
1 TAGACTTAAACATCTTGGATGCCAACTAAATTGA-GCTTAAACTCTTTTTATGCCAACATAACTG
* * *
2961044 GACTTAAACATATTGGATGCTAGCTAAATTGGGCTTCAACTCTTTTCATGCCAACATGAT
65 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTCTTTTCATGCCAACATAAT
* * * * * *
2961104 TGGACTTAAATATCTTGGATGCTAGCTAAA-TGAGGCTTAAATTCTTTTCATGCCAACATAACTG
1 TAGACTTAAACATCTTGGATGCCAACTAAATTGA-GCTTAAACTCTTTTTATGCCAACATAACTG
* * * * *
2961168 GATTTAAATATCTTGGATGCCAGCTAAATT-TGATTAAACTCTTTTCATGCCAACATAAT
65 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTCTTTTCATGCCAACATAAT
2961227 T
1 T
2961228 GTAGAAACCT
Statistics
Matches: 776, Mismatches: 186, Indels: 49
0.77 0.18 0.05
Matches are distributed among these distances:
118 41 0.05
119 2 0.00
121 91 0.12
122 3 0.00
123 41 0.05
124 588 0.76
125 10 0.01
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (124 bp):
TAGACTTAAACATCTTGGATGCCAACTAAATTGAGCTTAAACTCTTTTTATGCCAACATAACTGG
ACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTCTTTTCATGCCAACATAAT
Found at i:2960446 original size:186 final size:185
Alignment explanation
Indices: 2960119--2961225 Score: 832
Period size: 186 Copynumber: 6.0 Consensus size: 185
2960109 ATTTGCATCC
* * ** * * *
2960119 ACTAGACTTAAACATCTTGGATGCCAATTAAATTAGGCATAAAGTCTTTTTATG-C--C--AA-T
1 ACTAGACTTAAACATCTTAGATGCTAGCTAAATTGGGCTTAAAATC-TTTTATGCCAACATAATT
* * * * * * ** * ** *
2960178 GGACTTAAACATTTTGGATGTCAACTAAATT-GAGCTTAAACTCTCTTCATTCCATTATAACTGG
65 GGACTTAAATATCTTGGATGCCAGCTAAATTAG-GCTTAAATTCTTTTTGTGCCAACATAACTAG
* * * * * **
2960242 ACTTGAACATCATGGATGCTAGTTAAATTGAGCTTAAACTTTTTTTGTGCCAACATA
129 ACTTAAACATCTTGGATGCCAGCTAAATTGAGCTTAAACTCTTTTCATGCCAACATA
* * * * *
2960299 ACTGGACTTAAATATCTTAGATGCTAGCTATATTGGGCTTAAAATCTTTTCGTGCCAATATAATT
1 ACTAGACTTAAACATCTTAGATGCTAGCTAAATTGGGCTTAAAATCTTTT-ATGCCAACATAATT
* * *
2960364 GGACTCAAATATCTTGGATGCCAACTAAATTAGGCTTAAATTCTTTTTGTGCCAACATAACTGGA
65 GGACTTAAATATCTTGGATGCCAGCTAAATTAGGCTTAAATTCTTTTTGTGCCAACATAACTAGA
* * * *
2960429 CTTAAACATATTGGATGCCTA-TTAAATTGGGCTTAAACTCTTTTCATGCCAACGTA
130 CTTAAACATCTTGGATGCC-AGCTAAATTGAGCTTAAACTCTTTTCATGCCAACATA
* * * * * * * *
2960485 ATTAGACTTAAACAT-TTTGTAAG-TAAGCTAAATTGTGCTTAAAGTCTTTT-TACACTAAGACA
1 ACTAGACTTAAACATCTTAG-ATGCT-AGCTAAATTGGGCTTAAAATCTTTTATGC-C-AACATA
* * * ** * * * *
2960547 ACTGGACTAAAACATCTTGGATGTTAGCTAAATTAAGCTTAAACTCTTTTTATGTCAACATAACT
62 ATTGGACTTAAATATCTTGGATGCCAGCTAAATTAGGCTTAAATTCTTTTTGTGCCAACATAACT
* ** * * * * * *
2960612 AGACTTAAACATTTTATATGCCAACTACATTGGGCTTAAAGTCTTTTTATGCAAACATA
127 AGACTTAAACATCTTGGATGCCAGCTAAATTGAGCTTAAACTCTTTTCATGCCAACATA
* * * * * *
2960671 ACTAGACTTAAGCATCTTAGATGCCAACTAAA---GGCTTAAAGTCTTTTTATGCTAACATAGTT
1 ACTAGACTTAAACATCTTAGATGCTAGCTAAATTGGGCTTAAAATC-TTTTATGCCAACATAATT
* * * * * * * ** *
2960733 GGACTTAAATATTTTGGATGACAACTAAA-TAGGGCTTAAACTCTCTTCGAGCCATTACAACTAG
65 GGACTTAAATATCTTGGATGCCAGCTAAATTA-GGCTTAAATTCTTTTTGTGCCAACATAACTAG
* * * * * * * ** *
2960797 ATTTGAACATCTTAGATGTCAGTTAAATTGGGCTTAAATTCTTTTTGTGCAAACATA
129 ACTTAAACATCTTGGATGCCAGCTAAATTGAGCTTAAACTCTTTTCATGCCAACATA
* * * * * *
2960854 ACTAGCCTCAAACAACTTAGATGCCAGC-AATATTGAGC-TACAAATCTCTTTATGCCAACCTAA
1 ACTAGACTTAAACATCTTAGATGCTAGCTAA-ATTGGGCTTA-AAATCT-TTTATGCCAACATAA
*** * * * * * * *
2960917 CCAGACTTAAACATCTTGAATGCCGGTTAAATTAGGCATAAATTCTTTTTGTACCAATATAACTA
63 TTGGACTTAAATATCTTGGATGCCAGCTAAATTAGGCTTAAATTCTTTTTGTGCCAACATAACTA
* *
2960982 GACTTAAACATCTTGGATGCCAACTAAATT-AGGCTTAAACTCTTTTCGTGCCAACATA
128 GACTTAAACATCTTGGATGCCAGCTAAATTGA-GCTTAAACTCTTTTCATGCCAACATA
* * * * * * *
2961040 ATTGGACTTAAACATATTGGATGCTAGCTAAATTGGGCTTCAACTCTTTTCATGCCAACATGATT
1 ACTAGACTTAAACATCTTAGATGCTAGCTAAATTGGGCTTAAAATCTTTT-ATGCCAACATAATT
* * ** *
2961105 GGACTTAAATATCTTGGATGCTAGCTAAATGAGGCTTAAATTCTTTTCATGCCAACATAACTGGA
65 GGACTTAAATATCTTGGATGCCAGCTAAATTAGGCTTAAATTCTTTTTGTGCCAACATAACTAGA
* *
2961170 TTTAAATATCTTGGATGCCAGCTAAATTTGA--TTAAACTCTTTTCATGCCAACATA
130 CTTAAACATCTTGGATGCCAGCTAAA-TTGAGCTTAAACTCTTTTCATGCCAACATA
2961225 A
1 A
2961226 TTGTAGAAAC
Statistics
Matches: 724, Mismatches: 171, Indels: 59
0.76 0.18 0.06
Matches are distributed among these distances:
179 4 0.01
180 38 0.05
181 1 0.00
182 4 0.01
183 132 0.18
184 6 0.01
185 40 0.06
186 486 0.67
187 12 0.02
188 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Consensus pattern (185 bp):
ACTAGACTTAAACATCTTAGATGCTAGCTAAATTGGGCTTAAAATCTTTTATGCCAACATAATTG
GACTTAAATATCTTGGATGCCAGCTAAATTAGGCTTAAATTCTTTTTGTGCCAACATAACTAGAC
TTAAACATCTTGGATGCCAGCTAAATTGAGCTTAAACTCTTTTCATGCCAACATA
Found at i:2960681 original size:31 final size:29
Alignment explanation
Indices: 2960584--2960681 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 29
2960574 CTAAATTAAG
2960584 CTTAAACTCTTTTTATGTCAACATAACTAGA
1 CTTAAA-TCTTTTTATG-CAACATAACTAGA
* * *
2960615 CTTAAA-CATTTTATATGCCAAC-TACATTGGG
1 CTTAAATC-TTTT-TATG-CAACATA-ACTAGA
2960646 CTTAAAGTCTTTTTATGCAAACATAACTAGA
1 CTTAAA-TCTTTTTATGC-AACATAACTAGA
2960677 CTTAA
1 CTTAA
2960682 GCATCTTAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
29 1 0.02
30 7 0.13
31 38 0.72
32 6 0.11
33 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (29 bp):
CTTAAATCTTTTTATGCAACATAACTAGA
Found at i:2961034 original size:31 final size:30
Alignment explanation
Indices: 2960999--2961098 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 30
2960989 ACATCTTGGA
2960999 TGCCAACTAAATTAGGCTTAAACTCTTTTCG
1 TGCCAACTAAATT-GGCTTAAACTCTTTTCG
* * *
2961030 TGCCAAC-ATAATTGGACTTAAAC-ATATTGG
1 TGCCAACTA-AATTGG-CTTAAACTCTTTTCG
* * * *
2961060 ATGCTAGCTAAATTGGGCTTCAACTCTTTTCA
1 -TGCCAACTAAATT-GGCTTAAACTCTTTTCG
2961092 TGCCAAC
1 TGCCAAC
2961099 ATGATTGGAC
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
30 7 0.14
31 38 0.75
32 6 0.12
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (30 bp):
TGCCAACTAAATTGGCTTAAACTCTTTTCG
Found at i:2961175 original size:31 final size:30
Alignment explanation
Indices: 2961140--2961225 Score: 77
Period size: 31 Copynumber: 2.8 Consensus size: 30
2961130 TAAATGAGGC
2961140 TTAAATTCTTTTCATGCCAACATAACTGGA
1 TTAAATTCTTTTCATGCCAACATAACTGGA
** * * *
2961170 TTTAAATATC-TTGGATGCCAGC-TAAATTTGA
1 -TTAAAT-TCTTTTCATGCCAACAT-AACTGGA
*
2961201 TTAAACTCTTTTCATGCCAACATAA
1 TTAAATTCTTTTCATGCCAACATAA
2961226 TTGTAGAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
29 2 0.05
30 17 0.40
31 21 0.50
32 2 0.05
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (30 bp):
TTAAATTCTTTTCATGCCAACATAACTGGA
Found at i:2974379 original size:19 final size:19
Alignment explanation
Indices: 2974355--2974398 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2974345 GATCCGAGTA
2974355 TCTTCATACCCTAATTCTT
1 TCTTCATACCCTAATTCTT
*
2974374 TCTTCATACTCTAATTCTT
1 TCTTCATACCCTAATTCTT
*
2974393 GCTTCA
1 TCTTCA
2974399 ATGACCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.20, C:0.30, G:0.02, T:0.48
Consensus pattern (19 bp):
TCTTCATACCCTAATTCTT
Found at i:2975950 original size:57 final size:58
Alignment explanation
Indices: 2975841--2975952 Score: 172
Period size: 57 Copynumber: 1.9 Consensus size: 58
2975831 CATCTTTACA
* ** *
2975841 TGCATAGCATTTATTAAATTACATAAAATAAATTTATCACATGCACACTACTTTGCAT
1 TGCATAACATTTATTAAATTACATAAAATAAATCCATCACATGCAAACTACTTTGCAT
*
2975899 TGCATAACATTTATTAAATTGCAT-AAATAAATCCATCACATGCAAACTACTTTG
1 TGCATAACATTTATTAAATTACATAAAATAAATCCATCACATGCAAACTACTTTG
2975953 GATGAGTATG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 27 0.55
58 22 0.45
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (58 bp):
TGCATAACATTTATTAAATTACATAAAATAAATCCATCACATGCAAACTACTTTGCAT
Found at i:2981382 original size:15 final size:15
Alignment explanation
Indices: 2981364--2981400 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2981354 NNNNNNNNNN
*
2981364 GTGATTGCAAGTAAT
1 GTGATTGCAAGCAAT
2981379 GTGATTGCAAGCAAT
1 GTGATTGCAAGCAAT
2981394 GTGATTG
1 GTGATTG
2981401 TAAAGAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.32
Consensus pattern (15 bp):
GTGATTGCAAGCAAT
Found at i:2984068 original size:2 final size:2
Alignment explanation
Indices: 2984061--2984102 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2984051 CTAGAATGAA
2984061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2984102 A
1 A
2984103 GGTTTACCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3004537 original size:35 final size:35
Alignment explanation
Indices: 3004498--3004565 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
3004488 CATTTTCATA
*
3004498 TATTTGACATTTGATACTTCATATTTAACTTTATG
1 TATTTGACATTTGATACGTCATATTTAACTTTATG
* *
3004533 TATTTGGCATTTGATACGTGATATTTAACTTTA
1 TATTTGACATTTGATACGTCATATTTAACTTTA
3004566 GATGCAAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (35 bp):
TATTTGACATTTGATACGTCATATTTAACTTTATG
Found at i:3016349 original size:28 final size:28
Alignment explanation
Indices: 3016317--3016377 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
3016307 TTTCTTCTAC
3016317 GGTTCTACTTTTTTAAATTGCTCACTTA
1 GGTTCTACTTTTTTAAATTGCTCACTTA
3016345 GGTTCTACTTTTTTAAATTGCTCACTTA
1 GGTTCTACTTTTTTAAATTGCTCACTTA
3016373 GGTTC
1 GGTTC
3016378 AAACTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (28 bp):
GGTTCTACTTTTTTAAATTGCTCACTTA
Found at i:3016385 original size:28 final size:28
Alignment explanation
Indices: 3016317--3016385 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 28
3016307 TTTCTTCTAC
*
3016317 GGTTCTACTTTTTTAAATTGCTCACTTA
1 GGTTCAACTTTTTTAAATTGCTCACTTA
*
3016345 GGTTCTACTTTTTTAAATTGCTCACTTA
1 GGTTCAACTTTTTTAAATTGCTCACTTA
3016373 GGTTCAAACTTTT
1 GGTTC-AACTTTT
3016386 GTAACTGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 33 0.85
29 6 0.15
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49
Consensus pattern (28 bp):
GGTTCAACTTTTTTAAATTGCTCACTTA
Found at i:3017360 original size:27 final size:27
Alignment explanation
Indices: 3017322--3017377 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3017312 CTGAGAGCTG
3017322 GGAGAACAAAATTGCTTTGTTCGATCA
1 GGAGAACAAAATTGCTTTGTTCGATCA
3017349 GGAGAACAAAATTGCTTTGTTCGATCA
1 GGAGAACAAAATTGCTTTGTTCGATCA
3017376 GG
1 GG
3017378 CATAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (27 bp):
GGAGAACAAAATTGCTTTGTTCGATCA
Found at i:3018868 original size:49 final size:49
Alignment explanation
Indices: 3018809--3018921 Score: 129
Period size: 49 Copynumber: 2.3 Consensus size: 49
3018799 ATCTTAAACA
* * *
3018809 GAACAATTTGGATA-TTCCGTTGCAAGGATTTTATGACTTGAACTTGAAC
1 GAACAATTTGGAGACTT-CGTTGCAAGGATCTTATAACTTGAACTTGAAC
* * * *
3018858 GAACAATTTGGAGACTTCGTTTCAAGGGTCTTATAACTTGATCTTGAGC
1 GAACAATTTGGAGACTTCGTTGCAAGGATCTTATAACTTGAACTTGAAC
* *
3018907 GAACGATTTGAAGAC
1 GAACAATTTGGAGAC
3018922 CTCACTTCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 52 0.96
50 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (49 bp):
GAACAATTTGGAGACTTCGTTGCAAGGATCTTATAACTTGAACTTGAAC
Found at i:3018946 original size:49 final size:49
Alignment explanation
Indices: 3018831--3018955 Score: 142
Period size: 49 Copynumber: 2.6 Consensus size: 49
3018821 TATTCCGTTG
* * * **
3018831 CAAGGATTTTATGACTTGAACTTGAACGAACAATTTGGAGACTTCGTTT
1 CAAGGATTTTATGACTTGATCTTGAACGAACAATTTGAAGACCTCACTT
* * * * *
3018880 CAAGGGTCTTATAACTTGATCTTGAGCGAACGATTTGAAGACCTCACTT
1 CAAGGATTTTATGACTTGATCTTGAACGAACAATTTGAAGACCTCACTT
* *
3018929 CAAGGATTTTGTGACTTGTTCTTGAAC
1 CAAGGATTTTATGACTTGATCTTGAAC
3018956 TTCTAACTTT
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (49 bp):
CAAGGATTTTATGACTTGATCTTGAACGAACAATTTGAAGACCTCACTT
Found at i:3019189 original size:49 final size:49
Alignment explanation
Indices: 3019111--3019218 Score: 117
Period size: 49 Copynumber: 2.2 Consensus size: 49
3019101 TGCATATTGA
* *
3019111 AATGATTTGGAGACTTCGCTCCAACGGTCTTGTGACTTGTTCTTTAACG
1 AATGATTTGGAGACTTCGCTCCAACGGTCTTGCGACTTGTTCTTAAACG
* * ** * * * *
3019160 AATGATTTGGATACTTTGCTTTAAGGGTCTTGCGATTTGTTGTTAAATG
1 AATGATTTGGAGACTTCGCTCCAACGGTCTTGCGACTTGTTCTTAAACG
*
3019209 AACGATTTGG
1 AATGATTTGG
3019219 TCTTATGACT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (49 bp):
AATGATTTGGAGACTTCGCTCCAACGGTCTTGCGACTTGTTCTTAAACG
Found at i:3019261 original size:34 final size:34
Alignment explanation
Indices: 3019205--3019285 Score: 123
Period size: 34 Copynumber: 2.5 Consensus size: 34
3019195 TTTGTTGTTA
3019205 AATGAACGATTTG--GTCTTATGACTTAATCTTG
1 AATGAACGATTTGAAGTCTTATGACTTAATCTTG
*
3019237 AATGAACGATTTGAAGTCTTATGACTTGATCTTG
1 AATGAACGATTTGAAGTCTTATGACTTAATCTTG
*
3019271 AACGAAC-ATTTGAAG
1 AATGAACGATTTGAAG
3019286 ATTTCGCTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 13 0.29
33 8 0.18
34 24 0.53
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (34 bp):
AATGAACGATTTGAAGTCTTATGACTTAATCTTG
Found at i:3019829 original size:19 final size:19
Alignment explanation
Indices: 3019805--3019841 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3019795 CTTTAATCTT
3019805 CAGAATCTTCATCTGGAGG
1 CAGAATCTTCATCTGGAGG
*
3019824 CAGAATCTTCTTCTGGAG
1 CAGAATCTTCATCTGGAG
3019842 CCCTTGGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (19 bp):
CAGAATCTTCATCTGGAGG
Found at i:3019846 original size:75 final size:76
Alignment explanation
Indices: 3019693--3019846 Score: 265
Period size: 76 Copynumber: 2.0 Consensus size: 76
3019683 CTTCCAAAGG
* * *
3019693 CTTTGATTTTTTCTTCTGTTTGGAGGCTTTAATCTTCAAAATCTTCATCTGGAGGCCTGAATCTT
1 CTTTGATTTTTTCTTCTGTCTGGAAGCTTTAATCTTCAAAATCTTCATCTGGAGGCCAGAATCTT
3019758 CTTCTGGAGCC
66 CTTCTGGAGCC
*
3019769 CTTTGATTTTTTCTTCTGTCTGGAAGCTTTAATCTTCAGAATCTTCATCTGGAGG-CAGAATCTT
1 CTTTGATTTTTTCTTCTGTCTGGAAGCTTTAATCTTCAAAATCTTCATCTGGAGGCCAGAATCTT
3019833 CTTCTGGAGCC
66 CTTCTGGAGCC
3019844 CTT
1 CTT
3019847 GGACTTGCTT
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
75 22 0.30
76 52 0.70
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (76 bp):
CTTTGATTTTTTCTTCTGTCTGGAAGCTTTAATCTTCAAAATCTTCATCTGGAGGCCAGAATCTT
CTTCTGGAGCC
Found at i:3019862 original size:24 final size:24
Alignment explanation
Indices: 3019830--3019877 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3019820 GAGGCAGAAT
3019830 CTTCTTCTGGAGCCCTTGGACTTG
1 CTTCTTCTGGAGCCCTTGGACTTG
3019854 CTTCTTCTGGAGCCCTTGGACTTG
1 CTTCTTCTGGAGCCCTTGGACTTG
3019878 TGAGAGTTCT
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:0.08, C:0.29, G:0.25, T:0.38
Consensus pattern (24 bp):
CTTCTTCTGGAGCCCTTGGACTTG
Found at i:3022596 original size:24 final size:24
Alignment explanation
Indices: 3022542--3022597 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
3022532 AACCATAACG
3022542 TGTAACATATTTTTATACATAGCA
1 TGTAACATATTTTTATACATAGCA
* * *
3022566 TGAAACATGTTTTTATATAT-GACA
1 TGTAACATATTTTTATACATAG-CA
3022590 TGTAACAT
1 TGTAACAT
3022598 CATTGTGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (24 bp):
TGTAACATATTTTTATACATAGCA
Found at i:3022723 original size:18 final size:18
Alignment explanation
Indices: 3022697--3022731 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3022687 CCTTTAAGGG
*
3022697 TTTTTTTAAAAAATATTC
1 TTTTGTTAAAAAATATTC
*
3022715 TTTTGTTAAAACATATT
1 TTTTGTTAAAAAATATT
3022732 TGAACCTATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTTGTTAAAAAATATTC
Found at i:3031913 original size:1 final size:1
Alignment explanation
Indices: 3031904--3031978 Score: 132
Period size: 1 Copynumber: 75.0 Consensus size: 1
3031894 CCTGCTCTCT
*
3031904 CCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
*
3031969 CCCCCACCCC
1 CCCCCCCCCC
3031979 AACAGCCCAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3038519 original size:37 final size:40
Alignment explanation
Indices: 3038455--3038529 Score: 111
Period size: 38 Copynumber: 1.9 Consensus size: 40
3038445 TAAATTTTTA
*
3038455 TTTTTTATAATAATGCCTATAACTATTA-AA-AATAATTT
1 TTTTTTATAATAATGCCTATAAATATTACAAGAATAATTT
*
3038493 TTTTTTGTAATAATGCCTA-AAATATTACAAGAATAAT
1 TTTTTTATAATAATGCCTATAAATATTACAAGAATAAT
3038530 AAAATATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 7 0.21
38 20 0.61
39 6 0.18
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (40 bp):
TTTTTTATAATAATGCCTATAAATATTACAAGAATAATTT
Found at i:3038800 original size:17 final size:19
Alignment explanation
Indices: 3038773--3038807 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3038763 TTCTTTAGCT
3038773 TTTTCTTTC-TTAATTTTC
1 TTTTCTTTCTTTAATTTTC
3038791 TTTT-TTTCTTTAATTTT
1 TTTTCTTTCTTTAATTTT
3038808 TCATGAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCTTTAATTTTC
Found at i:3043773 original size:22 final size:21
Alignment explanation
Indices: 3043740--3043784 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
3043730 ATTTATTTTG
* * *
3043740 TTTTTTAGAAAATATTTTAAT
1 TTTTTTAAAAAAAATTTAAAT
3043761 TTTTTTAAAAAAAAATTTAAAT
1 TTTTTT-AAAAAAAATTTAAAT
3043783 TT
1 TT
3043785 AATTTTATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTTTAAAAAAAATTTAAAT
Found at i:3043779 original size:21 final size:21
Alignment explanation
Indices: 3043740--3043780 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3043730 ATTTATTTTG
* * *
3043740 TTTTTTAGAAAATATTTTAAT
1 TTTTTTAAAAAAAAATTTAAT
3043761 TTTTTTAAAAAAAAATTTAA
1 TTTTTTAAAAAAAAATTTAA
3043781 ATTTAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTTTTAAAAAAAAATTTAAT
Found at i:3043867 original size:7 final size:7
Alignment explanation
Indices: 3043855--3043884 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
3043845 CGAAACTTTG
3043855 AATTTAA
1 AATTTAA
3043862 AATTTAA
1 AATTTAA
3043869 AATTTAA
1 AATTTAA
3043876 AATTCTAA
1 AATT-TAA
3043884 A
1 A
3043885 TTCTAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (7 bp):
AATTTAA
Found at i:3058663 original size:27 final size:29
Alignment explanation
Indices: 3058632--3058706 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
3058622 GTCACATGGA
*
3058632 AAAAAATATTATTATTACACATCATATTA
1 AAAAAATATTATTATTACACATCATATTT
* ** *
3058661 AAAAAATAATATTATTACATGTTATATTT
1 AAAAAATATTATTATTACACATCATATTT
*
3058690 -AAAAATATT-TTGTTACA
1 AAAAAATATTATTATTACA
3058707 TTTTAATGTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 7 0.18
28 8 0.21
29 24 0.62
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (29 bp):
AAAAAATATTATTATTACACATCATATTT
Found at i:3058692 original size:30 final size:30
Alignment explanation
Indices: 3058613--3058694 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 30
3058603 TTAAAAAAGG
* ** *
3058613 TTATTACATGTCACATGGAAAAAAATATTA
1 TTATTACATGTCATATTTAAAAAAATAATA
**
3058643 TTATTACACATCATA-TTAAAAAAATAATA
1 TTATTACATGTCATATTTAAAAAAATAATA
*
3058672 TTATTACATGTTATATTTAAAAA
1 TTATTACATGTCATATTTAAAAA
3058695 TATTTTGTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 23 0.55
30 19 0.45
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.38
Consensus pattern (30 bp):
TTATTACATGTCATATTTAAAAAAATAATA
Found at i:3060030 original size:21 final size:22
Alignment explanation
Indices: 3060001--3060046 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
3059991 TGAAAACTAC
* *
3060001 ATAATATATTATTTTAATAAAA
1 ATAATATATTAATATAATAAAA
3060023 ATAA-ATATTAATATAATAAAA
1 ATAATATATTAATATAATAAAA
3060044 ATA
1 ATA
3060047 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATATATTAATATAATAAAA
Found at i:3063290 original size:2 final size:2
Alignment explanation
Indices: 3063285--3063313 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3063275 TTTCTCTCTT
3063285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3063314 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3064879 original size:27 final size:27
Alignment explanation
Indices: 3064841--3064932 Score: 168
Period size: 27 Copynumber: 3.4 Consensus size: 27
3064831 GATTAACCAG
3064841 TGACCATTTTTTTTTTTGAAAAA-AAAA
1 TGACCA-TTTTTTTTTTGAAAAACAAAA
3064868 TGACCATTTTTTTTTTGAAAAACAAAA
1 TGACCATTTTTTTTTTGAAAAACAAAA
3064895 TGACCATTTTTTTTTTGAAAAACAAAA
1 TGACCATTTTTTTTTTGAAAAACAAAA
3064922 TGACCATTTTT
1 TGACCATTTTT
3064933 AATTCAATAC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
26 16 0.25
27 48 0.75
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (27 bp):
TGACCATTTTTTTTTTGAAAAACAAAA
Found at i:3067667 original size:20 final size:20
Alignment explanation
Indices: 3067644--3067681 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3067634 AGAGTATTCA
3067644 ATAAAATCTCAGAGAACTTG
1 ATAAAATCTCAGAGAACTTG
* *
3067664 ATAAAATTTTAGAGAACT
1 ATAAAATCTCAGAGAACT
3067682 ATGAGAGTCG
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:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (20 bp):
ATAAAATCTCAGAGAACTTG
Found at i:3068419 original size:41 final size:41
Alignment explanation
Indices: 3068374--3068457 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
3068364 TTTAACTTCA
3068374 TAATCCACCACGTAAACCAAGAAAGAGGAAGGAGGGTGGAT
1 TAATCCACCACGTAAACCAAGAAAGAGGAAGGAGGGTGGAT
* *
3068415 TAATCCACCAGGTAAACCAAGAAAGAGGAAGGAGGGTGTAT
1 TAATCCACCACGTAAACCAAGAAAGAGGAAGGAGGGTGGAT
3068456 TA
1 TA
3068458 GAGGCTTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.42, C:0.15, G:0.29, T:0.14
Consensus pattern (41 bp):
TAATCCACCACGTAAACCAAGAAAGAGGAAGGAGGGTGGAT
Found at i:3074730 original size:28 final size:28
Alignment explanation
Indices: 3074689--3074789 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
3074679 CTTAGAAGAT
* *
3074689 GTATATTGCCATAAAACTATTTGAACAA
1 GTATATTGCAATAAAACTATTTGAAAAA
* *
3074717 GTATATTGCAATAAGACTATAATCTAGGAAGAA
1 GTATATTGCAATAAAACTAT--T-T--GAAAAA
** * *
3074750 GTATATTATAAAAAAATTATTTGAAAAA
1 GTATATTGCAATAAAACTATTTGAAAAA
3074778 GTATATTGCAAT
1 GTATATTGCAAT
3074790 TAGTATTGCA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
28 32 0.57
30 2 0.04
31 2 0.04
33 20 0.36
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.33
Consensus pattern (28 bp):
GTATATTGCAATAAAACTATTTGAAAAA
Found at i:3101668 original size:90 final size:90
Alignment explanation
Indices: 3101490--3101676 Score: 216
Period size: 90 Copynumber: 2.1 Consensus size: 90
3101480 GAAATCATAG
* * * * * * *
3101490 AAGACTGCAGGGCATAATTGAATGGTTATATAAAAGGGATTCTCTCGAGTAACGAGACACGTTCG
1 AAGACTACAGGGCATAATTGAATGGTTATATAAAAGGGATCCTCCCGAGAAACAAGACACATCCG
*** * *
3101555 ATGTTGAAGCTATCGACGATAAAAC
66 ATGCCAAAGCCACCGACGATAAAAC
3101580 AAGACTACAGGGCA-AAGTTGAATGGTTATATAAAAGGGATCCTCCCGAGAAACAAGACACATCC
1 AAGACTACAGGGCATAA-TTGAATGGTTATATAAAAGGGATCCTCCCGAGAAACAAGACACATCC
* *
3101644 GGTGCCAAAGCCACCGAC-AGTAAAAT
65 GATGCCAAAGCCACCGACGA-TAAAAC
3101670 AAGACTA
1 AAGACTA
3101677 TGGGGTAAGA
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
89 3 0.04
90 78 0.96
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.20
Consensus pattern (90 bp):
AAGACTACAGGGCATAATTGAATGGTTATATAAAAGGGATCCTCCCGAGAAACAAGACACATCCG
ATGCCAAAGCCACCGACGATAAAAC
Found at i:3110433 original size:84 final size:84
Alignment explanation
Indices: 3110289--3110442 Score: 211
Period size: 84 Copynumber: 1.8 Consensus size: 84
3110279 GTAGTAGAAG
* * **
3110289 AAAGTACAGACAATTTGCATCAGTCTTCTTGGTCTACAACTTTGGAATCTGAAGATAAGTCAGAT
1 AAAGTACAGACAATTTGCATCAATCTTCTTGGTCCACAACTTCAGAATCTGAAGATAAGTCAGAT
3110354 CATCTACTTACTGTGGCAA
66 CATCTACTTACTGTGGCAA
* * ** *
3110373 AAAGTACTGGCAATTTGCATCAATCTTCTTGGTCCATGACTTCAGAATTTGAAGGA-AAGTCAGA
1 AAAGTACAGACAATTTGCATCAATCTTCTTGGTCCACAACTTCAGAATCTGAA-GATAAGTCAGA
3110437 TCATCT
65 TCATCT
3110443 TACTGTGGAG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
84 58 0.97
85 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (84 bp):
AAAGTACAGACAATTTGCATCAATCTTCTTGGTCCACAACTTCAGAATCTGAAGATAAGTCAGAT
CATCTACTTACTGTGGCAA
Found at i:3112686 original size:26 final size:26
Alignment explanation
Indices: 3112646--3112696 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3112636 GTGTGTGTGT
* *
3112646 ATATATATATATATGTATGTACACAC
1 ATATACATATATATGTATGAACACAC
*
3112672 ATATACATATGTATGTATGAACACA
1 ATATACATATATATGTATGAACACA
3112697 TAATTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (26 bp):
ATATACATATATATGTATGAACACAC
Found at i:3118448 original size:25 final size:24
Alignment explanation
Indices: 3118420--3118466 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
3118410 GTTTGATCTC
*
3118420 CAATACTTACTACCATGTCTATTTT
1 CAATACTCACTACCAT-TCTATTTT
* *
3118445 CAATTCTCACTACTATTCTATT
1 CAATACTCACTACCATTCTATT
3118467 ACCCCTTCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.28, C:0.26, G:0.02, T:0.45
Consensus pattern (24 bp):
CAATACTCACTACCATTCTATTTT
Found at i:3123300 original size:82 final size:82
Alignment explanation
Indices: 3123157--3123319 Score: 245
Period size: 82 Copynumber: 2.0 Consensus size: 82
3123147 CTTCTTGAAG
* *
3123157 TCCTGAATTTTGATTGTTATCTACAAGTTAAATACCAATTGACATTAGAATGCAGGCCATCACAA
1 TCCTGAATTATGATTGTTATCTACAAGTTAAATACCAATTGACACTAGAATGCAGGCCATCACAA
3123222 AAGAAACACTGCTAGAC
66 AAGAAACACTGCTAGAC
* * * * * * *
3123239 TCCTGAATTATGATTGTTATCTACAAGTTAACTAGCAGTTGATACTAGAATGCTGGTCATCACCA
1 TCCTGAATTATGATTGTTATCTACAAGTTAAATACCAATTGACACTAGAATGCAGGCCATCACAA
3123304 AAGAAACACTGCTAGA
66 AAGAAACACTGCTAGA
3123320 TGCCCCTGCC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (82 bp):
TCCTGAATTATGATTGTTATCTACAAGTTAAATACCAATTGACACTAGAATGCAGGCCATCACAA
AAGAAACACTGCTAGAC
Found at i:3129358 original size:6 final size:6
Alignment explanation
Indices: 3129347--3129385 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
3129337 CTACCCTATC
* *
3129347 TATACA TATACA TATACA TATACA TATATA TATATA TAT
1 TATACA TATACA TATACA TATACA TATACA TATACA TAT
3129386 TCATTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (6 bp):
TATACA
Found at i:3142548 original size:3 final size:3
Alignment explanation
Indices: 3142540--3142576 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3142530 ACAACGTTTC
3142540 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
3142577 TTTGACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3147845 original size:301 final size:301
Alignment explanation
Indices: 3147463--3148072 Score: 1175
Period size: 301 Copynumber: 2.0 Consensus size: 301
3147453 CCGCCAATGC
3147463 TACTTGAATACCCATTGAACCATCCCAAAATTCCATACAAAATTACCAAACTCACCATGTGACAA
1 TACTTGAATACCCATTGAACCATCCCAAAATTCCATACAAAATTACCAAACTCACCATGTGACAA
3147528 CCAAGCTGCCTAAAAATGGAAACTAGTGGTGTTGTTATTCACTATTCTTTCTCATAATTTAATCA
66 CCAAGCTGCCTAAAAATGGAAACTAGTGGTGTTGTTATTCACTATTCTTTCTCATAATTTAATCA
3147593 TCAAAGGCCAATGGTCTGACCTAATTCATGGTAGGTGTTGAACAAATGCATATAGAAATTAAAGA
131 TCAAAGGCCAATGGTCTGACCTAATTCATGGTAGGTGTTGAACAAATGCATATAGAAATTAAAGA
*
3147658 CGCTAGCTAGTGTTACAAATAGCTCTATCGAGTTTTTTTGAAACTAGATCGTGCTTTCAGATGAA
196 CGCTAGCTAGTGTTACAAATAGCCCTATCGAGTTTTTTTGAAACTAGATCGTGCTTTCAGATGAA
*
3147723 CCTTGAGCTCGGGAAACCTAAGTCCTAAAGATTATAATTAT
261 CCTTAAGCTCGGGAAACCTAAGTCCTAAAGATTATAATTAT
3147764 TACTTGAATACCCATTGAACCATCCCAAAATTCCATACAAAATTACCAAACTCACCATGTGACAA
1 TACTTGAATACCCATTGAACCATCCCAAAATTCCATACAAAATTACCAAACTCACCATGTGACAA
3147829 CCAAGCTGCCTAAAAATGGAAACTAGTGGTGTTGTTATTCACTATTCTTTCTCATAATTTAATCA
66 CCAAGCTGCCTAAAAATGGAAACTAGTGGTGTTGTTATTCACTATTCTTTCTCATAATTTAATCA
3147894 TCAAAGGCCAATGGTCTGACCTAATTCATGGTAGGTGTTGAACAAATGCATATAGAAATTAAAGA
131 TCAAAGGCCAATGGTCTGACCTAATTCATGGTAGGTGTTGAACAAATGCATATAGAAATTAAAGA
3147959 CGCTAGCTAGTGTTACAAATAGCCCTATCGAGTTTTTTTGAAACTAGATCGTGCTTTCAGATGAA
196 CGCTAGCTAGTGTTACAAATAGCCCTATCGAGTTTTTTTGAAACTAGATCGTGCTTTCAGATGAA
* *
3148024 CCTTAAGCTTGGGAAACCTAAGTCCTAAAGATTATAGTTAT
261 CCTTAAGCTCGGGAAACCTAAGTCCTAAAGATTATAATTAT
*
3148065 TACATGAA
1 TACTTGAA
3148073 ATGTTGAAAT
Statistics
Matches: 304, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
301 304 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (301 bp):
TACTTGAATACCCATTGAACCATCCCAAAATTCCATACAAAATTACCAAACTCACCATGTGACAA
CCAAGCTGCCTAAAAATGGAAACTAGTGGTGTTGTTATTCACTATTCTTTCTCATAATTTAATCA
TCAAAGGCCAATGGTCTGACCTAATTCATGGTAGGTGTTGAACAAATGCATATAGAAATTAAAGA
CGCTAGCTAGTGTTACAAATAGCCCTATCGAGTTTTTTTGAAACTAGATCGTGCTTTCAGATGAA
CCTTAAGCTCGGGAAACCTAAGTCCTAAAGATTATAATTAT
Found at i:3149878 original size:2 final size:2
Alignment explanation
Indices: 3149871--3149967 Score: 95
Period size: 2 Copynumber: 48.5 Consensus size: 2
3149861 TTGCTTTTGG
** *
3149871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GC AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** * ** * *
3149913 AC GC AC AT AT AT AT AT GC AT AT AT AT AT AT AT AT AT AC AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3149955 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
3149968 GCCTCTCACA
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (2 bp):
AT
Found at i:3150550 original size:16 final size:16
Alignment explanation
Indices: 3150529--3150563 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3150519 TTTCTATTTA
3150529 TCAAGGAATCATTTCT
1 TCAAGGAATCATTTCT
3150545 TCAAGGAATCATTTCT
1 TCAAGGAATCATTTCT
3150561 TCA
1 TCA
3150564 CTCCTAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (16 bp):
TCAAGGAATCATTTCT
Found at i:3153034 original size:2 final size:2
Alignment explanation
Indices: 3153029--3153063 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3153019 CAACTGAAAT
*
3153029 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3153064 TTCAGATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3154183 original size:2 final size:2
Alignment explanation
Indices: 3154157--3154197 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
3154147 CTTATATAAT
* *
3154157 TC TC TT TC TC T- TC -C TC TC TC AC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3154197 T
1 T
3154198 AACCCCCTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3174461 original size:2 final size:2
Alignment explanation
Indices: 3174454--3174498 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3174444 TCAATTTTCG
3174454 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3174495 TA TA
1 TA TA
3174499 GATTCATTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3177166 original size:22 final size:23
Alignment explanation
Indices: 3177124--3177166 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3177114 TTACTTCCTA
*
3177124 ATTTATTTGATATATAGTTACAT
1 ATTTATTTGATATATACTTACAT
*
3177147 ATTTATTT-ATATTTACTTAC
1 ATTTATTTGATATATACTTAC
3177167 TGTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (23 bp):
ATTTATTTGATATATACTTACAT
Found at i:3178258 original size:5 final size:5
Alignment explanation
Indices: 3178250--3178283 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
3178240 GAAAGATCAG
*
3178250 AAAGA AAAGCA AAAGA AAAGA AGAGA AAAGA AAA
1 AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AAA
3178284 TCTTGGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:3180134 original size:48 final size:49
Alignment explanation
Indices: 3180082--3180187 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 49
3180072 GTGGAGGACG
*
3180082 AGGGTTACAGA-GAATATCAAACTGGCAAGGATGATGCTGCAGAGAATA
1 AGGGTTACAGATGAATATCAAACTGGCAAGGATGATGCTGCAGAGAACA
** *
3180130 AGGGTTGTGGAGATGAATATCTAACTGGCAAGGATGATGCTGCAGAGAACA
1 AGGG-T-TACAGATGAATATCAAACTGGCAAGGATGATGCTGCAGAGAACA
3180181 AGGGTTA
1 AGGGTTA
3180188 TGGAGATGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
48 4 0.08
49 2 0.04
50 5 0.10
51 39 0.78
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.21
Consensus pattern (49 bp):
AGGGTTACAGATGAATATCAAACTGGCAAGGATGATGCTGCAGAGAACA
Found at i:3180156 original size:51 final size:51
Alignment explanation
Indices: 3180093--3180198 Score: 185
Period size: 51 Copynumber: 2.1 Consensus size: 51
3180083 GGGTTACAGA
* *
3180093 GAATATCAAACTGGCAAGGATGATGCTGCAGAGAATAAGGGTTGTGGAGAT
1 GAATATCAAACTGGCAAGGATGATGCTGCAGAGAACAAGGGTTATGGAGAT
*
3180144 GAATATCTAACTGGCAAGGATGATGCTGCAGAGAACAAGGGTTATGGAGAT
1 GAATATCAAACTGGCAAGGATGATGCTGCAGAGAACAAGGGTTATGGAGAT
3180195 GAAT
1 GAAT
3180199 CTGATCATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.36, C:0.10, G:0.32, T:0.22
Consensus pattern (51 bp):
GAATATCAAACTGGCAAGGATGATGCTGCAGAGAACAAGGGTTATGGAGAT
Found at i:3191554 original size:2 final size:2
Alignment explanation
Indices: 3191542--3191580 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3191532 CTAGAGATAG
*
3191542 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3191581 TCATGTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3213323 original size:2 final size:2
Alignment explanation
Indices: 3213316--3213340 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3213306 ATGTCCTAAC
3213316 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3213341 GTTCAGGTCG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3214420 original size:61 final size:62
Alignment explanation
Indices: 3214321--3214438 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 62
3214311 TATTTAAGCA
* * *
3214321 TTTTAAGCATTTTGAAGTAATTTTTAATACACAGAG-AAAACTTTTGAACGTTTTGAATTTT
1 TTTTAAACATTTTGAAGTAATTTTTAATACACAAAGAAAAACTTTTGAACATTTTGAATTTT
* * * * * *
3214382 TTTTAAACATTTTGGAGTGATTTTTGATATATAAAGAAAAACTTTTGAGCATTTTGA
1 TTTTAAACATTTTGAAGTAATTTTTAATACACAAAGAAAAACTTTTGAACATTTTGA
3214439 GCATTCTTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
61 29 0.62
62 18 0.38
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (62 bp):
TTTTAAACATTTTGAAGTAATTTTTAATACACAAAGAAAAACTTTTGAACATTTTGAATTTT
Found at i:3214778 original size:21 final size:21
Alignment explanation
Indices: 3214720--3214779 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3214710 TAAAAATCAG
* * *
3214720 TCACATAATATCTAAAAATTAG
1 TCACGTAAT-TCTTAAAATTAA
* * *
3214742 TCACGCAATGCCTAAAATTAA
1 TCACGTAATTCTTAAAATTAA
3214763 TCACGTAATTCTTAAAA
1 TCACGTAATTCTTAAAA
3214780 ACTAATCTTG
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (21 bp):
TCACGTAATTCTTAAAATTAA
Found at i:3214785 original size:22 final size:22
Alignment explanation
Indices: 3214732--3214827 Score: 77
Period size: 22 Copynumber: 4.4 Consensus size: 22
3214722 ACATAATATC
* * * *
3214732 TAAAAATTAGTCACGCAATGCC
1 TAAAAACTAATCACGCAATACT
* * *
3214754 T-AAAATTAATCACGTAATTCT
1 TAAAAACTAATCACGCAATACT
**
3214775 TAAAAACTAATCTTGCAATACT
1 TAAAAACTAATCACGCAATACT
* * *
3214797 TAAAAACTAGTGACACAATACT
1 TAAAAACTAATCACGCAATACT
3214819 TAAAAACTA
1 TAAAAACTA
3214828 GTAATGTAAT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
21 17 0.29
22 42 0.71
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (22 bp):
TAAAAACTAATCACGCAATACT
Found at i:3214838 original size:22 final size:22
Alignment explanation
Indices: 3214773--3214838 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
3214763 TCACGTAATT
* **
3214773 CTTAAAAACTAATCTTGCAATA
1 CTTAAAAACTAGTAATGCAATA
* **
3214795 CTTAAAAACTAGTGACACAATA
1 CTTAAAAACTAGTAATGCAATA
*
3214817 CTTAAAAACTAGTAATGTAATA
1 CTTAAAAACTAGTAATGCAATA
3214839 TCTAATAACT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (22 bp):
CTTAAAAACTAGTAATGCAATA
Found at i:3219763 original size:2 final size:2
Alignment explanation
Indices: 3219751--3219786 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
3219741 ATCAAATTGG
3219751 GA GA TGA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3219787 GGATCGCACC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:3222646 original size:38 final size:38
Alignment explanation
Indices: 3222590--3222665 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
3222580 GATGCGTTTT
*
3222590 GAGCCAAATGACCGGCCCTGATTTATAGAAATAAGGTA
1 GAGCAAAATGACCGGCCCTGATTTATAGAAATAAGGTA
3222628 GAGCAAAATGACCGGCCCTGATTTATAGAAATAAGGTA
1 GAGCAAAATGACCGGCCCTGATTTATAGAAATAAGGTA
3222666 ACAAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (38 bp):
GAGCAAAATGACCGGCCCTGATTTATAGAAATAAGGTA
Found at i:3233171 original size:32 final size:28
Alignment explanation
Indices: 3233107--3233161 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
3233097 ATATTACAAA
3233107 CAAATAAATTACATCAAAAATAAATAAG
1 CAAATAAATTACATCAAAAATAAATAAG
* *
3233135 CAAATACATTACATCAAATATAAATAA
1 CAAATAAATTACATCAAAAATAAATAA
3233162 AATTTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.24
Consensus pattern (28 bp):
CAAATAAATTACATCAAAAATAAATAAG
Found at i:3239065 original size:18 final size:18
Alignment explanation
Indices: 3239042--3239079 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3239032 GTTGTGCTAT
3239042 ATAAATTTTTTCTTGCAA
1 ATAAATTTTTTCTTGCAA
*
3239060 ATAAATTTTTTCTTGTAA
1 ATAAATTTTTTCTTGCAA
3239078 AT
1 AT
3239080 CACCATTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (18 bp):
ATAAATTTTTTCTTGCAA
Found at i:3241815 original size:57 final size:57
Alignment explanation
Indices: 3241765--3241869 Score: 146
Period size: 55 Copynumber: 1.9 Consensus size: 57
3241755 TTAAAATAAA
*
3241765 ATATATAATATAAG-AATAA-AAATTAAAATAAAATA-A-AATATAAAAAATTAACAT
1 ATATATAATATAAGTAA-AATAAATTAAAATAAAATATATAATATAAAAAATTAAAAT
* *
3241819 TTATATAATATAGGTAAAATAAATTAAAATAAAATATATAATATAAAAAAT
1 ATATATAATATAAGTAAAATAAATTAAAATAAAATATATAATATAAAAAAT
3241870 ATATTAAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
54 14 0.31
55 18 0.40
56 1 0.02
57 12 0.27
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (57 bp):
ATATATAATATAAGTAAAATAAATTAAAATAAAATATATAATATAAAAAATTAAAAT
Done.