Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397271.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_89.0, 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: 4184555
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 83639 characters in sequence are not A, C, G, or T
File 8 of 11
Found at i:2746341 original size:232 final size:232
Alignment explanation
Indices: 2745935--2746399 Score: 930
Period size: 232 Copynumber: 2.0 Consensus size: 232
2745925 TACCATCGAC
2745935 ATTATAATTAGCTATGACCTTGTGCTTTCTATAGTGAGTTTGTAACCTCTACATGTGCACCATTG
1 ATTATAATTAGCTATGACCTTGTGCTTTCTATAGTGAGTTTGTAACCTCTACATGTGCACCATTG
2746000 GCCAAGCCATCTATCTCTCTATAATTCATTTTCCCCATTGAACTCAACTCTCAGGAGGAGATTCC
66 GCCAAGCCATCTATCTCTCTATAATTCATTTTCCCCATTGAACTCAACTCTCAGGAGGAGATTCC
2746065 CATTGAACTTAATTCCCCGTCACCCTTGATGTACTTGACATGTTTCCCCTAGCTATAACTTTTGT
131 CATTGAACTTAATTCCCCGTCACCCTTGATGTACTTGACATGTTTCCCCTAGCTATAACTTTTGT
2746130 TAAAGGATCAACAGTATTACTCATTTGTTTTAAGGTA
196 TAAAGGATCAACAGTATTACTCATTTGTTTTAAGGTA
2746167 ATTATAATTAGCTATGACCTTGTGCTTTCTATAGTGAGTTTGTAACCTCTACATGTGCACCATTG
1 ATTATAATTAGCTATGACCTTGTGCTTTCTATAGTGAGTTTGTAACCTCTACATGTGCACCATTG
2746232 GCCAAGCCATCTATCTCTCTATAATTCATTTTCCCCATTGAACTCAACTCTCAGGAGGAGATTCC
66 GCCAAGCCATCTATCTCTCTATAATTCATTTTCCCCATTGAACTCAACTCTCAGGAGGAGATTCC
2746297 CATTGAACTTAATTCCCCGTCACCCTTGATGTACTTGACATGTTTCCCCTAGCTATAACTTTTGT
131 CATTGAACTTAATTCCCCGTCACCCTTGATGTACTTGACATGTTTCCCCTAGCTATAACTTTTGT
2746362 TAAAGGATCAACAGTATTACTCATTTGTTTTAAGGTA
196 TAAAGGATCAACAGTATTACTCATTTGTTTTAAGGTA
2746399 A
1 A
2746400 AGAATCTTTA
Statistics
Matches: 233, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
232 233 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (232 bp):
ATTATAATTAGCTATGACCTTGTGCTTTCTATAGTGAGTTTGTAACCTCTACATGTGCACCATTG
GCCAAGCCATCTATCTCTCTATAATTCATTTTCCCCATTGAACTCAACTCTCAGGAGGAGATTCC
CATTGAACTTAATTCCCCGTCACCCTTGATGTACTTGACATGTTTCCCCTAGCTATAACTTTTGT
TAAAGGATCAACAGTATTACTCATTTGTTTTAAGGTA
Found at i:2749631 original size:19 final size:20
Alignment explanation
Indices: 2749590--2749634 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
2749580 CTCAAAAATA
2749590 AAAGGAAGAAGAAGAAAGAC
1 AAAGGAAGAAGAAGAAAGAC
*
2749610 AAAGGAA-AAGAA-AAGAGCC
1 AAAGGAAGAAGAAGAA-AGAC
2749629 AAAGGA
1 AAAGGA
2749635 CATTTCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
20 7 0.30
ACGTcount: A:0.64, C:0.07, G:0.29, T:0.00
Consensus pattern (20 bp):
AAAGGAAGAAGAAGAAAGAC
Found at i:2755013 original size:28 final size:26
Alignment explanation
Indices: 2754953--2755013 Score: 61
Period size: 28 Copynumber: 2.2 Consensus size: 26
2754943 ATATAAATAT
*
2754953 TTTTAAAAATATAAATAATTCAATTT
1 TTTTAAAAATATAAATAATTCAATTA
*
2754979 TTATTAAATATTATAAA-AATTACAAATTA
1 TT-TTAAA-AATATAAATAATT-C-AATTA
2755008 TTTTAA
1 TTTTAA
2755014 TAAACGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 2 0.07
27 9 0.31
28 12 0.41
29 6 0.21
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTTAAAAATATAAATAATTCAATTA
Found at i:2773534 original size:59 final size:59
Alignment explanation
Indices: 2773372--2773597 Score: 240
Period size: 60 Copynumber: 3.8 Consensus size: 59
2773362 AAGGGACTTG
* * * * *
2773372 AAGCTCTAATTTATATTTGTTGGCAG-GGGCAGTTCTCACAAGTAGGTAAAGGGGGACCTA
1 AAGCTCTAATTTATATTTGGTGG-TGTGGGCAATTCCCACGAGTAGGTAAA-GGGGACCTA
* *
2773432 AAGCCCTAATTTATATTTGGTGGTGTGGGCAATTCCCACGAGTAGGTACAGGGAGACCTA
1 AAGCTCTAATTTATATTTGGTGGTGTGGGCAATTCCCACGAGTAGGTAAAGGG-GACCTA
* * * * * *
2773492 AAGCTC-AATTTATATTTTGTGGTGTGGGTAGTTCCTATGAGTAGGTAAAAGGGGACCTG
1 AAGCTCTAATTTATATTTGGTGGTGTGGGCAATTCCCACGAGTAGGT-AAAGGGGACCTA
* ** **
2773551 AAGCTCTGATTTATATTTGGTGGCATGGGTGATTCCCACGAGTAGGT
1 AAGCTCTAATTTATATTTGGTGGTGTGGGCAATTCCCACGAGTAGGT
2773598 GATGATGTTA
Statistics
Matches: 139, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
59 50 0.36
60 89 0.64
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.31
Consensus pattern (59 bp):
AAGCTCTAATTTATATTTGGTGGTGTGGGCAATTCCCACGAGTAGGTAAAGGGGACCTA
Found at i:2782443 original size:60 final size:60
Alignment explanation
Indices: 2782326--2782454 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 60
2782316 CTAAAGTCCA
* * ** *
2782326 AATTTATATTTCGTGGAATGGGTAGTTCCCACGAGTACGTAAAGGGGAACCTCAAGCCTT
1 AATTTATATTTCGTGGAATGAGTAATTCCCACGAGTACGTAAAAAGGAACCTCAAGCCAT
* * * *
2782386 AATTTATATTT-GCTGGCATGAGTAATTCCCACGAGTAGGTAAAAAAGG-ACTTGAAGCCAT
1 AATTTATATTTCG-TGGAATGAGTAATTCCCACGAGTACGT-AAAAAGGAACCTCAAGCCAT
*
2782446 GATTTATAT
1 AATTTATAT
2782455 CTGGTGGCGT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 1 0.02
60 51 0.89
61 5 0.09
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (60 bp):
AATTTATATTTCGTGGAATGAGTAATTCCCACGAGTACGTAAAAAGGAACCTCAAGCCAT
Found at i:2785262 original size:20 final size:20
Alignment explanation
Indices: 2785237--2785281 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
2785227 AAAGAAAAAA
2785237 AATACATAATTCTTTCCAAG
1 AATACATAATTCTTTCCAAG
*
2785257 AATACATAATTCTTTTCAAG
1 AATACATAATTCTTTCCAAG
2785277 AATAC
1 AATAC
2785282 GCTTTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (20 bp):
AATACATAATTCTTTCCAAG
Found at i:2788198 original size:80 final size:80
Alignment explanation
Indices: 2788084--2788466 Score: 483
Period size: 80 Copynumber: 4.8 Consensus size: 80
2788074 TCATTATTCC
* *
2788084 TAGCCCATAGTGTATATGACTATCTTAACACATACATCTCAGGGCATACATTTCATAACCTCATA
1 TAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCATA
*
2788149 AATCATTTACATGCT
66 AATCACTTACATGCT
* * *
2788164 CAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGACATACATTTCATAACCCCAT-
1 TAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCATA
2788228 AATCACTTACATGCT
66 AATCACTTACATGCT
* * * *
2788243 TAGCCCATAATGTATGTGACTATCT-GA-AC--ACATCTCATGGCATATATTTCATAACCTCATA
1 TAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCATA
*
2788304 AATCACTTATATGCT
66 AATCACTTACATGCT
* * * * *
2788319 TAACCCATAGTGTATATGACTATCTCAACACATGCATCTTATGGCGTACATTTCATAACCCCATA
1 TAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCATA
*
2788384 AATCACTTACATGTT
66 AATCACTTACATGCT
* * ** * * *
2788399 TAACCCATAGTGTACATGA-TATACTTTACACATACATTTCATGGCATACATGTT-ACAATCTCA
1 TAGCCCATAGTGTATATGACTAT-CTCAACACATACATCTCATGGCATACAT-TTCATAACCTCA
2788462 TAAAT
64 TAAAT
2788467 GGAACTCATG
Statistics
Matches: 261, Mismatches: 35, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
75 28 0.11
76 36 0.14
77 3 0.01
78 3 0.01
79 39 0.15
80 150 0.57
81 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.32
Consensus pattern (80 bp):
TAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCATA
AATCACTTACATGCT
Found at i:2788357 original size:155 final size:159
Alignment explanation
Indices: 2788084--2788466 Score: 499
Period size: 155 Copynumber: 2.4 Consensus size: 159
2788074 TCATTATTCC
2788084 TAGCCCATAGTGTATATGACTATCTTAACACATACATCTCAGGGCATACATTTCATAACCTCATA
1 TAGCCCATAGTGTATATGACTATCTTAACACA-ACATCTCAGGGCATACATTTCATAACCTCATA
* *
2788149 AATCATTTACATGCTCAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGACATACA
65 AATCACTTACATGCTCAACCCATAGTGTATATGACTATCTCAACACATACATCTCATGACATACA
2788214 TTTCATAACCCCAT-AATCACTTACATGCT
130 TTTCATAACCCCATAAATCACTTACATGCT
* * * * *
2788243 TAGCCCATAATGTATGTGACTATC-TGA-AC-ACATCTCATGGCATATATTTCATAACCTCATAA
1 TAGCCCATAGTGTATATGACTATCTTAACACAACATCTCAGGGCATACATTTCATAACCTCATAA
* * * * * *
2788305 ATCACTTATATGCTTAACCCATAGTGTATATGACTATCTCAACACATGCATCTTATGGCGTACAT
66 ATCACTTACATGCTCAACCCATAGTGTATATGACTATCTCAACACATACATCTCATGACATACAT
*
2788370 TTCATAACCCCATAAATCACTTACATGTT
131 TTCATAACCCCATAAATCACTTACATGCT
* * * * * * *
2788399 TAACCCATAGTGTACATGA-TATACTTTACACATACATTTCATGGCATACATGTT-ACAATCTCA
1 TAGCCCATAGTGTATATGACTAT-CTTAACACA-ACATCTCAGGGCATACAT-TTCATAACCTCA
2788462 TAAAT
63 TAAAT
2788467 GGAACTCATG
Statistics
Matches: 194, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
155 104 0.54
156 30 0.15
157 4 0.02
158 4 0.02
159 22 0.11
160 28 0.14
161 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.32
Consensus pattern (159 bp):
TAGCCCATAGTGTATATGACTATCTTAACACAACATCTCAGGGCATACATTTCATAACCTCATAA
ATCACTTACATGCTCAACCCATAGTGTATATGACTATCTCAACACATACATCTCATGACATACAT
TTCATAACCCCATAAATCACTTACATGCT
Found at i:2794518 original size:74 final size:74
Alignment explanation
Indices: 2794379--2794518 Score: 235
Period size: 74 Copynumber: 1.9 Consensus size: 74
2794369 TTCTACTCCT
* * **
2794379 AGTTTTTAGCAGTGAGCACTTAGTCAACTAACCATGCTTCTTGGTTGACTAAGTCTTTTTTGTTT
1 AGTTTTTAGCAGTGAACACTTAGTCAACTAACCATGCTTCTTGGTCGACTAAGTCTTTTCCGTTT
2794444 TCTGATTGA
66 TCTGATTGA
*
2794453 AGTTTTTAGCAGTGAACACTTAGTCGACTAACCATGCTTCTTGGTCGACTAAGTCTTTTCCGTTT
1 AGTTTTTAGCAGTGAACACTTAGTCAACTAACCATGCTTCTTGGTCGACTAAGTCTTTTCCGTTT
2794518 T
66 T
2794519 TGGACTAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (74 bp):
AGTTTTTAGCAGTGAACACTTAGTCAACTAACCATGCTTCTTGGTCGACTAAGTCTTTTCCGTTT
TCTGATTGA
Found at i:2796224 original size:17 final size:18
Alignment explanation
Indices: 2796202--2796237 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2796192 AAACTTAATA
*
2796202 TTATATATATAT-TATTT
1 TTATATAAATATATATTT
2796219 TTATATAAATATATATTT
1 TTATATAAATATATATTT
2796237 T
1 T
2796238 CCTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATAAATATATATTT
Found at i:2796644 original size:27 final size:28
Alignment explanation
Indices: 2796614--2796669 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
2796604 ATAATTTGAT
*
2796614 ATTTGATCGATTTGGTC-ATTTTTTTAA
1 ATTTGATCGATTTGATCAATTTTTTTAA
* *
2796641 ATTTGGTCGGTTTGATCAATTTTTTTAA
1 ATTTGATCGATTTGATCAATTTTTTTAA
2796669 A
1 A
2796670 AAATTAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.54
Consensus pattern (28 bp):
ATTTGATCGATTTGATCAATTTTTTTAA
Found at i:2801236 original size:16 final size:16
Alignment explanation
Indices: 2801217--2801260 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2801207 TCAAAAATGG
2801217 CCTGAACCCAAAACGA
1 CCTGAACCCAAAACGA
* *
2801233 CCTGAACTCAAAATGA
1 CCTGAACCCAAAACGA
**
2801249 CCCAAACCCAAA
1 CCTGAACCCAAA
2801261 TTGATATGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.36, G:0.09, T:0.09
Consensus pattern (16 bp):
CCTGAACCCAAAACGA
Found at i:2806730 original size:71 final size:72
Alignment explanation
Indices: 2806584--2806749 Score: 219
Period size: 71 Copynumber: 2.3 Consensus size: 72
2806574 ATTATAGAGA
* * * * *
2806584 TGCCATGGTCAACTATGTCTTTGAAATATCCCATTTTTTACGCATCAAGCTCATTATGGTCAACT
1 TGCCAAGGTCTACTATGTCTTTGAAATATCCCATTTTCTACGCATCAAGCTCATCAAGGTCAACT
2806649 ACACATG
66 ACACATG
* * * *
2806656 TGCCAAGGTCTACTATGTCTTTGCAATGTCCCATTTTCT-CGTATCTAGCTCATCAAGGTCAACT
1 TGCCAAGGTCTACTATGTCTTTGAAATATCCCATTTTCTACGCATCAAGCTCATCAAGGTCAACT
2806720 ACACATG
66 ACACATG
*
2806727 TGCCAAGGT-TGACTATGGCTTTG
1 TGCCAAGGTCT-ACTATGTCTTTG
2806750 TATTCTTTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
70 1 0.01
71 48 0.58
72 34 0.41
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (72 bp):
TGCCAAGGTCTACTATGTCTTTGAAATATCCCATTTTCTACGCATCAAGCTCATCAAGGTCAACT
ACACATG
Found at i:2809285 original size:20 final size:20
Alignment explanation
Indices: 2809260--2809301 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2809250 TTATGTGACT
2809260 GATTAATTTAATTGAATTAA
1 GATTAATTTAATTGAATTAA
2809280 GATTAATTTAATTGAATTAA
1 GATTAATTTAATTGAATTAA
2809300 GA
1 GA
2809302 ATGAATGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (20 bp):
GATTAATTTAATTGAATTAA
Found at i:2814547 original size:15 final size:16
Alignment explanation
Indices: 2814505--2814557 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
2814495 AAAAAAATTC
*
2814505 TTTTTCATCTTTTCAT
1 TTTTTCATCTTTTCAA
*
2814521 TGTTTTCCTC-TTTCAA
1 T-TTTTCATCTTTTCAA
2814537 TTTTTCATCTTTTC-A
1 TTTTTCATCTTTTCAA
2814552 TTTTTC
1 TTTTTC
2814558 TATAAACTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 14 0.44
16 11 0.34
17 7 0.22
ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTTCATCTTTTCAA
Found at i:2815053 original size:15 final size:15
Alignment explanation
Indices: 2815033--2815072 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2815023 TATATTGCTT
2815033 GGAATGTGATTATTG
1 GGAATGTGATTATTG
*
2815048 GGAATGTGATTGTTG
1 GGAATGTGATTATTG
* *
2815063 AGAACGTGAT
1 GGAATGTGAT
2815073 GCTGGGTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.28, C:0.03, G:0.35, T:0.35
Consensus pattern (15 bp):
GGAATGTGATTATTG
Found at i:2817090 original size:20 final size:21
Alignment explanation
Indices: 2817050--2817100 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
2817040 ACAATATAAA
*
2817050 GATAGATGGTTCAAAATCTATG
1 GATAGAT-GTTCAAAATCTATC
*
2817072 GATAGATGTT-AATATCTATC
1 GATAGATGTTCAAAATCTATC
2817092 GATAGATGT
1 GATAGATGT
2817101 GTACACTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 17 0.63
21 3 0.11
22 7 0.26
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (21 bp):
GATAGATGTTCAAAATCTATC
Found at i:2819306 original size:21 final size:22
Alignment explanation
Indices: 2819277--2819322 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2819267 AGAGGGTAGC
* *
2819277 ATAGCACATCATTTATCTATTG
1 ATAGCACATCATTGATCTATCG
*
2819299 ATAG-ACATTATTGATCTATCG
1 ATAGCACATCATTGATCTATCG
2819320 ATA
1 ATA
2819323 AATGATCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (22 bp):
ATAGCACATCATTGATCTATCG
Found at i:2822989 original size:21 final size:21
Alignment explanation
Indices: 2822965--2823004 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2822955 ATATACCTCG
*
2822965 AAACACAATATAAATACTATA
1 AAACACAATATAAACACTATA
*
2822986 AAACACTATATAAACACTA
1 AAACACAATATAAACACTA
2823005 CCTAAACACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (21 bp):
AAACACAATATAAACACTATA
Found at i:2823002 original size:11 final size:11
Alignment explanation
Indices: 2822965--2823004 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
2822955 ATATACCTCG
*
2822965 AAACACAATAT
1 AAACACTATAT
*
2822976 AAATACTATA-
1 AAACACTATAT
2822986 AAACACTATAT
1 AAACACTATAT
2822997 AAACACTA
1 AAACACTA
2823005 CCTAAACACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (11 bp):
AAACACTATAT
Found at i:2834056 original size:35 final size:35
Alignment explanation
Indices: 2834009--2834223 Score: 193
Period size: 35 Copynumber: 6.1 Consensus size: 35
2833999 ATGTAATTAC
* * *
2834009 CAATTAA-TCTAATAATTTAATTAAACAATTTAAT
1 CAATTAAGCCTAATAACTTAATTAAATAATTTAAT
* * *** * *
2834043 CAAGTAAGCCTAATTGACTTAATTGTTTAAGTTAAA
1 CAATTAAGCCTAA-TAACTTAATTAAATAATTTAAT
*
2834079 CAATTAAGCCCAATAACTTAATTAAATAATTTAAT
1 CAATTAAGCCTAATAACTTAATTAAATAATTTAAT
* * *
2834114 TAATTAAG-CTCAACAACTTAATTAAATAATTTTAAA
1 CAATTAAGCCT-AATAACTTAATTAAATAA-TTTAAT
* *
2834150 CAATCAAGCCTAATGACTTAATTAAATAATTTAAT
1 CAATTAAGCCTAATAACTTAATTAAATAATTTAAT
* * *
2834185 TAATTAAGTCC-AACAACTTAATTAAACAATTTTAAT
1 CAATTAAG-CCTAATAACTTAATTAAATAA-TTTAAT
2834221 CAA
1 CAA
2834224 GTACTTGAAA
Statistics
Matches: 141, Mismatches: 33, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
34 7 0.05
35 70 0.50
36 62 0.44
37 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.36
Consensus pattern (35 bp):
CAATTAAGCCTAATAACTTAATTAAATAATTTAAT
Found at i:2834104 original size:71 final size:71
Alignment explanation
Indices: 2834019--2834219 Score: 201
Period size: 71 Copynumber: 2.8 Consensus size: 71
2834009 CAATTAATCT
* * ** ***
2834019 AATAATTTAATTAAACAATTTAATCAAGTAAGC-CTAATTGACTTAATTGTTTAA-GTTAAACAA
1 AATAACTTAATTAAATAATTTAATCAAGTAAGCTC-AA-CAACTTAATTAAATAATGTTAAACAA
*
2834082 TTAAGCCC
64 TCAAGCCC
* * *
2834090 AATAACTTAATTAAATAATTTAATTAATTAAGCTCAACAACTTAATTAAATAATTTTAAACAATC
1 AATAACTTAATTAAATAATTTAATCAAGTAAGCTCAACAACTTAATTAAATAATGTTAAACAATC
*
2834155 AAGCCT
66 AAGCCC
* * * * *
2834161 AATGACTTAATTAAATAATTTAATTAATTAAG-TCCAACAACTTAATTAAACAATTTTAA
1 AATAACTTAATTAAATAATTTAATCAAGTAAGCT-CAACAACTTAATTAAATAATGTTAA
2834220 TCAAGTACTT
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
70 12 0.11
71 100 0.88
72 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (71 bp):
AATAACTTAATTAAATAATTTAATCAAGTAAGCTCAACAACTTAATTAAATAATGTTAAACAATC
AAGCCC
Found at i:2834167 original size:106 final size:106
Alignment explanation
Indices: 2834025--2834216 Score: 253
Period size: 106 Copynumber: 1.8 Consensus size: 106
2834015 ATCTAATAAT
* ***
2834025 TTAATTAAACAATTTAATCAAGTAAGCCTAATTGACTTAATTGTTTAAGTTAAACAATTAAGCCC
1 TTAATTAAACAATTTAAACAAGTAAGCCTAATTGACTTAATTAAATAAGTTAAACAATTAAGCCC
* *
2834090 AATAACTTAATTAAATAATTTAATTAATTAAGCTCAACAAC
66 AACAACTTAATTAAACAATTTAATTAATTAAGCTCAACAAC
* * ** *
2834131 TTAATTAAATAATTTTAAACAA-TCAAGCCTAA-TGACTTAATTAAATAATTTAATTAATTAAGT
1 TTAATTAAACAA-TTTAAACAAGT-AAGCCTAATTGACTTAATTAAATAAGTTAAACAATTAAGC
2834194 CCAACAACTTAATTAAACAATTT
64 CCAACAACTTAATTAAACAATTT
2834217 TAATCAAGTA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
106 57 0.78
107 16 0.22
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.36
Consensus pattern (106 bp):
TTAATTAAACAATTTAAACAAGTAAGCCTAATTGACTTAATTAAATAAGTTAAACAATTAAGCCC
AACAACTTAATTAAACAATTTAATTAATTAAGCTCAACAAC
Found at i:2834522 original size:15 final size:15
Alignment explanation
Indices: 2834504--2834533 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2834494 AACGGTTTGA
2834504 CTCAACCTTTCAGTG
1 CTCAACCTTTCAGTG
*
2834519 CTCAACCTTTTAGTG
1 CTCAACCTTTCAGTG
2834534 TGATTCAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (15 bp):
CTCAACCTTTCAGTG
Found at i:2840742 original size:15 final size:16
Alignment explanation
Indices: 2840703--2840743 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2840693 TCAAGAAGTG
*
2840703 AACATGATTATCATAA
1 AACATGATCATCATAA
*
2840719 AGCAT-ATCATCA-AA
1 AACATGATCATCATAA
2840733 AACATGATCAT
1 AACATGATCAT
2840744 ATCATCATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 6 0.29
15 11 0.52
16 4 0.19
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (16 bp):
AACATGATCATCATAA
Found at i:2845047 original size:23 final size:23
Alignment explanation
Indices: 2845007--2845061 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
2844997 CTTTGATTTT
*
2845007 TAGCTTTTTGAGAAGCATCTAAG
1 TAGCTTTTTGAGAAGCATCTAAA
* * *
2845030 TAGCTTTTTGGGAGGCATGTAAA
1 TAGCTTTTTGAGAAGCATCTAAA
*
2845053 TACCTTTTT
1 TAGCTTTTT
2845062 TACTAACTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (23 bp):
TAGCTTTTTGAGAAGCATCTAAA
Found at i:2850921 original size:28 final size:29
Alignment explanation
Indices: 2850882--2850936 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
2850872 ATATGTATGG
*
2850882 TCTTAATTTAGACAAGAAAA-ATATTTTA
1 TCTTAATCTAGACAAGAAAACATATTTTA
2850910 TCTTAATCTAGACAAGAAAACATATTT
1 TCTTAATCTAGACAAGAAAACATATTT
2850937 GTCTCGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (29 bp):
TCTTAATCTAGACAAGAAAACATATTTTA
Found at i:2863184 original size:2 final size:2
Alignment explanation
Indices: 2863179--2863210 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2863169 CTACACACAC
*
2863179 AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2863211 TTAATTCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:2872281 original size:45 final size:44
Alignment explanation
Indices: 2872217--2872302 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 44
2872207 TAGCTTCATT
* *
2872217 ATAGTCGACTACCTTAGCCCAGATTTGCAAAAAAACATGTTTACC
1 ATAGTCGACTACATTAGCCCAAATTTGC-AAAAAACATGTTTACC
*
2872262 ATAGTTGACTACATTAGCCCAAATTTGCAAAAAACATGTTT
1 ATAGTCGACTACATTAGCCCAAATTTGCAAAAAACATGTTT
2872303 GTCGATCGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 13 0.34
45 25 0.66
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (44 bp):
ATAGTCGACTACATTAGCCCAAATTTGCAAAAAACATGTTTACC
Found at i:2880713 original size:9 final size:10
Alignment explanation
Indices: 2880690--2880717 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2880680 GATCCACTCA
2880690 AAAAAATTTT
1 AAAAAATTTT
2880700 AAAAAATTTT
1 AAAAAATTTT
2880710 AAAAAATT
1 AAAAAATT
2880718 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:2894321 original size:31 final size:31
Alignment explanation
Indices: 2894284--2894344 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2894274 CTAGAATCTC
* **
2894284 TATATAAAGAAATGCTAGAACTTCTAGACTA
1 TATATAAAGAAATACTAGAACCCCTAGACTA
2894315 TATATAAAGAAATACTAGAACCCCTAGACT
1 TATATAAAGAAATACTAGAACCCCTAGACT
2894345 CTTCTACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.26
Consensus pattern (31 bp):
TATATAAAGAAATACTAGAACCCCTAGACTA
Found at i:2901309 original size:26 final size:26
Alignment explanation
Indices: 2901257--2901309 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
2901247 AAGAGATTAT
* *
2901257 AAAAATTATCAACCGAAAATCTTAAA
1 AAAAATTATCAACCGAAAATATGAAA
*
2901283 AAAAATTTTCTAA-CGAAAATATGAAA
1 AAAAATTATC-AACCGAAAATATGAAA
2901309 A
1 A
2901310 GATATTGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.25
Consensus pattern (26 bp):
AAAAATTATCAACCGAAAATATGAAA
Found at i:2921558 original size:30 final size:26
Alignment explanation
Indices: 2921502--2921551 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2921492 AAAATGCTGG
2921502 AGAAATTTATTTATTTATTAACTTTT
1 AGAAATTTATTTATTTATTAACTTTT
2921528 AGAAATTTATTTATTTATTAACTT
1 AGAAATTTATTTATTTATTAACTT
2921552 ACTTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (26 bp):
AGAAATTTATTTATTTATTAACTTTT
Found at i:2927032 original size:28 final size:28
Alignment explanation
Indices: 2927000--2927068 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
2926990 GGTGTTTAAG
*
2927000 AAAATAAAAATTAATCAGGATGTGTAAC
1 AAAATAGAAATTAATCAGGATGTGTAAC
* * *
2927028 AAAATAGAAATTAGTCAGGGTGTGTGAC
1 AAAATAGAAATTAATCAGGATGTGTAAC
*
2927056 AACATAGAAATTA
1 AAAATAGAAATTA
2927069 TAAAGTGTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (28 bp):
AAAATAGAAATTAATCAGGATGTGTAAC
Found at i:2927078 original size:28 final size:27
Alignment explanation
Indices: 2927020--2927098 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 27
2927010 TTAATCAGGA
*
2927020 TGTGTAACAAAATAGAAATTAGT-CAGGG
1 TGTGTAAC-AAATAGAAATTA-TAAAGGG
* *
2927048 TGTGTGACAACATAGAAATTATAAAGTG
1 TGTGTAACAA-ATAGAAATTATAAAGGG
*
2927076 TGTGTAACGAAATAGAGATTATA
1 TGTGTAAC-AAATAGAAATTATA
2927099 CAGAGCATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 3 0.07
28 38 0.88
29 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.28
Consensus pattern (27 bp):
TGTGTAACAAATAGAAATTATAAAGGG
Found at i:2930193 original size:2 final size:2
Alignment explanation
Indices: 2930186--2930217 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2930176 TAAGGGTGGC
2930186 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
2930218 TTACAGAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2936517 original size:20 final size:20
Alignment explanation
Indices: 2936468--2936518 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2936458 AATTTGTTTG
*
2936468 TTATGGGAAAAGCACATTCA
1 TTATGGGAAGAGCACATTCA
2936488 TTATGGGAAGAGCACATTCA
1 TTATGGGAAGAGCACATTCA
*
2936508 TTATGAGAAGA
1 TTATGGGAAGA
2936519 ATGGCTTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (20 bp):
TTATGGGAAGAGCACATTCA
Found at i:2951121 original size:16 final size:16
Alignment explanation
Indices: 2951097--2951127 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2951087 TTTTTCTAAA
*
2951097 TTTATTTCTTTGTTTC
1 TTTAGTTCTTTGTTTC
2951113 TTTAGTTCTTTGTTT
1 TTTAGTTCTTTGTTT
2951128 AAAGATTTAA
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:0.06, C:0.10, G:0.10, T:0.74
Consensus pattern (16 bp):
TTTAGTTCTTTGTTTC
Found at i:2952453 original size:23 final size:22
Alignment explanation
Indices: 2952427--2952469 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2952417 TTAAATATTC
* *
2952427 TTAAATATATTTTTTAATTAAAA
1 TTAAATAAAATTTTT-ATTAAAA
2952450 TTAAATAAAATTTTTATTAA
1 TTAAATAAAATTTTTATTAA
2952470 TATAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAAATAAAATTTTTATTAAAA
Found at i:2961370 original size:2 final size:2
Alignment explanation
Indices: 2961363--2961389 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2961353 TTTTATATCC
2961363 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2961390 CACACACACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2968360 original size:63 final size:63
Alignment explanation
Indices: 2968253--2968377 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 63
2968243 TTAAAAAAGG
* * *
2968253 AATATTTGACCTTGTAGTTTTAATCAAATTTTGAACCTTTCAACTATTGAGTGAGAGTTTTCA
1 AATATTTGACCTTGTAGCTTTAATCAAATTTTGAACCTTTCAACTATTAAATGAGAGTTTTCA
* *
2968316 AATATTTGACCTTGTAGCTTTAATCAAGTTTTGAA-CTTTGCAACTATTAAATGGGAGTTTTC
1 AATATTTGACCTTGTAGCTTTAATCAAATTTTGAACCTTT-CAACTATTAAATGAGAGTTTTC
2968378 GAATCCTTCA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 4 0.07
63 52 0.93
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (63 bp):
AATATTTGACCTTGTAGCTTTAATCAAATTTTGAACCTTTCAACTATTAAATGAGAGTTTTCA
Found at i:2968628 original size:21 final size:21
Alignment explanation
Indices: 2968594--2968633 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2968584 TCAATAATCT
*
2968594 TTGAACTTATTTGAGTGATCC
1 TTGAACTTACTTGAGTGATCC
* *
2968615 TTGAACTTGCTTGATTGAT
1 TTGAACTTACTTGAGTGAT
2968634 TCTTAAAGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (21 bp):
TTGAACTTACTTGAGTGATCC
Found at i:2970905 original size:36 final size:36
Alignment explanation
Indices: 2970860--2970947 Score: 151
Period size: 36 Copynumber: 2.4 Consensus size: 36
2970850 GTTATGTCCG
*
2970860 AGATAGTGGGGACTGATCATTGTTTGGGAATGTCTA
1 AGATAGTGGGGACCGATCATTGTTTGGGAATGTCTA
2970896 AGAGT-GTGGGGACCGATCATTGTTTGGGAATGTCTA
1 AGA-TAGTGGGGACCGATCATTGTTTGGGAATGTCTA
2970932 AGATAGTGGGGACCGA
1 AGATAGTGGGGACCGA
2970948 ACTATTATCT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
35 1 0.02
36 47 0.96
37 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.36, T:0.28
Consensus pattern (36 bp):
AGATAGTGGGGACCGATCATTGTTTGGGAATGTCTA
Found at i:2970970 original size:37 final size:36
Alignment explanation
Indices: 2970860--2970973 Score: 104
Period size: 36 Copynumber: 3.1 Consensus size: 36
2970850 GTTATGTCCG
* * * * **
2970860 AGATAGTGGGGACTGATCATTGTTTGGGAATGTCTA
1 AGATAGTGGGGACCGAACATTATCTAAGAATGTCTA
* * * **
2970896 AGAGT-GTGGGGACCGATCATTGTTTGGGAATGTCTA
1 AGA-TAGTGGGGACCGAACATTATCTAAGAATGTCTA
2970932 AGATAGTGGGGACCGAACTATTATCTAAGAATGTCTA
1 AGATAGTGGGGACCGAAC-ATTATCTAAGAATGTCTA
2970969 AGATA
1 AGATA
2970974 ATGGAGACTG
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.01
36 48 0.70
37 20 0.29
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.30
Consensus pattern (36 bp):
AGATAGTGGGGACCGAACATTATCTAAGAATGTCTA
Found at i:2979179 original size:3 final size:3
Alignment explanation
Indices: 2979171--2979213 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2979161 ATGTGTCAAG
2979171 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2979214 GAGCAATTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2992707 original size:24 final size:24
Alignment explanation
Indices: 2992662--2992707 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2992652 ATATCTCAAA
*
2992662 TAAATTATAACAAATTAATATTTT
1 TAAATTATAACAAACTAATATTTT
*
2992686 TAAATTATTAA-AAACTATTATT
1 TAAATTA-TAACAAACTAATATT
2992708 AATATATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAATTATAACAAACTAATATTTT
Found at i:2992935 original size:14 final size:13
Alignment explanation
Indices: 2992916--2992946 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
2992906 ATAGAAATGA
2992916 ATTATTAATAAATT
1 ATTATTAA-AAATT
2992930 ATTATTAAAAATT
1 ATTATTAAAAATT
2992943 ATTA
1 ATTA
2992947 ACATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTATTAAAAATT
Found at i:2996777 original size:17 final size:17
Alignment explanation
Indices: 2996755--2996789 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2996745 TTTAGTTTAG
2996755 TGCAACTTCCTTTAACA
1 TGCAACTTCCTTTAACA
2996772 TGCAACTTCCTTTAACA
1 TGCAACTTCCTTTAACA
2996789 T
1 T
2996790 CTGTTTGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.37
Consensus pattern (17 bp):
TGCAACTTCCTTTAACA
Found at i:3002032 original size:38 final size:38
Alignment explanation
Indices: 3001990--3002062 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
3001980 GACTTGAAAC
* *
3001990 TAAATATTAAAAAAATTCTTTAAAAATGCATATAAAAT
1 TAAATATTAAAAAAATTCTTCAAAAATACATATAAAAT
* **
3002028 TAAATATTAATAATTTTCTTCAAAAATACATATAA
1 TAAATATTAAAAAAATTCTTCAAAAATACATATAA
3002063 GGACTTGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (38 bp):
TAAATATTAAAAAAATTCTTCAAAAATACATATAAAAT
Found at i:3003077 original size:52 final size:52
Alignment explanation
Indices: 3003016--3003114 Score: 153
Period size: 52 Copynumber: 1.9 Consensus size: 52
3003006 TGAAAAGAAC
* *
3003016 AAATAATAAATCAAGGTAAAATATTTTCCTAAGTTAAATGCAAGCAAAACAT
1 AAATAATAAATCAAGGTAAAATATTTTCCTAAGCTAAATACAAGCAAAACAT
* * *
3003068 AAATAATAAATCTAGGTAAAATATTTTCTTAAGCTATATACAAGCAA
1 AAATAATAAATCAAGGTAAAATATTTTCCTAAGCTAAATACAAGCAA
3003115 TAAATTACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (52 bp):
AAATAATAAATCAAGGTAAAATATTTTCCTAAGCTAAATACAAGCAAAACAT
Found at i:3003364 original size:36 final size:35
Alignment explanation
Indices: 3003273--3003386 Score: 133
Period size: 36 Copynumber: 3.2 Consensus size: 35
3003263 TCACAATAGT
* * * *
3003273 TTTTTCACAAGATCAACTGAAACTTT-TACAAAGC
1 TTTTTCACTAGATCAACTGAAACTTTCAACAATGA
*
3003307 TTTTTCACTAGATCAAGTGAAACCTTTCAACAATGA
1 TTTTTCACTAGATCAACTGAAA-CTTTCAACAATGA
*
3003343 TTTTTCA-TAGACTCAACTGAAATCTTTCAACAATGG
1 TTTTTCACTAGA-TCAACTGAAA-CTTTCAACAATGA
3003379 TTTTTCAC
1 TTTTTCAC
3003387 GAACTCAACC
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
34 20 0.29
35 8 0.12
36 40 0.59
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (35 bp):
TTTTTCACTAGATCAACTGAAACTTTCAACAATGA
Found at i:3009436 original size:71 final size:70
Alignment explanation
Indices: 3009311--3009442 Score: 185
Period size: 71 Copynumber: 1.9 Consensus size: 70
3009301 ATAAATTGAT
* * *
3009311 AACCTTGAAGGTATATTTTTACATATAAAAGTACATCTGATCAAGATACGTAAGGTAGATACAAC
1 AACCTTGAAGGTATATTTTTACACACAAAAGTACACCTGATCAAGATACGTAAGGTAGATACAAC
3009376 ACATA
66 ACATA
* * *
3009381 AACCTTG-AGTGTATATTTTTGACACACAAAGGTATACCTGATCAAGATAGGTAAGGTAGATA
1 AACCTTGAAG-GTATATTTTT-ACACACAAAAGTACACCTGATCAAGATACGTAAGGTAGATA
3009443 TACAAGTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
69 2 0.04
70 17 0.31
71 35 0.65
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (70 bp):
AACCTTGAAGGTATATTTTTACACACAAAAGTACACCTGATCAAGATACGTAAGGTAGATACAAC
ACATA
Found at i:3010249 original size:28 final size:29
Alignment explanation
Indices: 3010217--3010280 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 29
3010207 TATTATACTT
*
3010217 AAAATTTTC-AGTTGAAGCTTAAACAATG
1 AAAATTTTCGAGTTGAAACTTAAACAATG
*
3010245 AAAA-TTTCGAGTTGAAACTTAAACAGTG
1 AAAATTTTCGAGTTGAAACTTAAACAATG
3010273 AAAATTTT
1 AAAATTTT
3010281 AATGTTTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 4 0.12
28 25 0.78
29 3 0.09
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (29 bp):
AAAATTTTCGAGTTGAAACTTAAACAATG
Found at i:3010801 original size:16 final size:16
Alignment explanation
Indices: 3010780--3010831 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 16
3010770 GTTTGCCAGG
3010780 TAAAAT-TTAATGATTT
1 TAAAATATTAAT-ATTT
3010796 TAAAATGATATAATATTTT
1 TAAAAT-AT-TAATA-TTT
3010815 TAAAATATTAATATTT
1 TAAAATATTAATATTT
3010831 T
1 T
3010832 TATCATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 10 0.31
17 5 0.16
18 4 0.12
19 13 0.41
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:3010828 original size:17 final size:17
Alignment explanation
Indices: 3010780--3010844 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
3010770 GTTTGCCAGG
3010780 TAAAAT-TTAATGA-TTT
1 TAAAATATTAAT-ATTTT
3010796 TAAAATGATATAATATTTT
1 TAAAAT-AT-TAATATTTT
3010815 TAAAATATTAATATTTT
1 TAAAATATTAATATTTT
**
3010832 TATCATATTAATA
1 TAAAATATTAATA
3010845 ATATTTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.14
17 20 0.47
18 4 0.09
19 13 0.30
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (17 bp):
TAAAATATTAATATTTT
Found at i:3010856 original size:17 final size:17
Alignment explanation
Indices: 3010805--3010857 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
3010795 TTAAAATGAT
* *
3010805 ATAATATTTTTAAAATA
1 ATAATATTTTTATATTA
*
3010822 TTAATATTTTTATCATATTA
1 ATAATA-TTTT-T-ATATTA
3010842 ATAATATTTTTATATT
1 ATAATATTTTTATATT
3010858 TTTATTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 10 0.34
18 5 0.17
19 5 0.17
20 9 0.31
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAATATTTTTATATTA
Found at i:3011203 original size:15 final size:15
Alignment explanation
Indices: 3011169--3011239 Score: 106
Period size: 15 Copynumber: 4.7 Consensus size: 15
3011159 CTTTACAATA
* *
3011169 CAATGTGATTACAGG
1 CAATGTGATTGCAAG
* *
3011184 TAATGTGATTGTAAG
1 CAATGTGATTGCAAG
3011199 CAATGTGATTGCAAG
1 CAATGTGATTGCAAG
3011214 CAATGTGATTGCAAG
1 CAATGTGATTGCAAG
3011229 CAATGTGATTG
1 CAATGTGATTG
3011240 TAGGAAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (15 bp):
CAATGTGATTGCAAG
Found at i:3011418 original size:27 final size:26
Alignment explanation
Indices: 3011388--3011526 Score: 77
Period size: 27 Copynumber: 5.0 Consensus size: 26
3011378 TAATATATTT
3011388 ATATTTATTATTATTAATTTTTATATA
1 ATATTT-TTATTATTAATTTTTATATA
* * * * *
3011415 ATATCATTTCTTAAATATATTTTTAATTTC
1 ATAT-TTTTATT-ATTA-ATTTTT-ATATA
*
3011445 ATATATTTTATT-TTTATTTATTATTATA
1 ATAT-TTTTATTATTAATTT-TTA-TATA
* *
3011473 ATCTTTTATATT-TT-ATTTTAATATATT
1 ATATTTT-TATTATTAATTTT--TATATA
3011500 ATATTTTTTATTATTAATTTTTATATA
1 ATA-TTTTTATTATTAATTTTTATATA
3011527 TATCAATCTT
Statistics
Matches: 84, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
26 1 0.01
27 34 0.40
28 26 0.31
29 11 0.13
30 12 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (26 bp):
ATATTTTTATTATTAATTTTTATATA
Found at i:3011479 original size:20 final size:18
Alignment explanation
Indices: 3011454--3011523 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 18
3011444 CATATATTTT
3011454 ATTTTTATTTATTATTATA
1 ATTTTTATTT-TTATTATA
*
3011473 ATCTTTTATATTTTATTTTA
1 AT-TTTTAT-TTTTATTATA
3011493 ATATATTATATTTTTTATTATTA
1 AT-T-TT-TA-TTTTTATTA-TA
3011516 ATTTTTAT
1 ATTTTTAT
3011524 ATATATCAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
19 3 0.07
20 18 0.43
21 6 0.14
22 10 0.24
23 5 0.12
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTATTTTTATTATA
Found at i:3011579 original size:55 final size:55
Alignment explanation
Indices: 3011376--3011579 Score: 138
Period size: 56 Copynumber: 3.6 Consensus size: 55
3011366 AAAATTTAAG
* * * *
3011376 TTTAATAT-ATTTATATTTATTATTATTAATTTTTATATAATATCATTTCTTAAATATATT
1 TTTAATATCA-TTAT-TTTATTTTTATTTA-TATTATAT-ATATCA-ATCTT-AATATATT
* * *
3011436 TTTAATTTCATATATTTTATTTTTA-TT-TA-T-TAT-TAT-AATCTTTTATATTTTAT
1 TTTAATATCAT-TATTTTATTTTTATTTATATTATATATATCAATC-TTAATA-TAT-T
* *
3011489 TTTAATAT-ATTATATTT-TTTATTATTAATTTTTATATATATCAATCTTAATATATT
1 TTTAATATCATTAT-TTTATTT-TTATTTA-TATTATATATATCAATCTTAATATATT
*
3011545 TTTAATATCATTATTTTATTTTCATTTATATTATA
1 TTTAATATCATTATTTTATTTTTATTTATATTATA
3011580 ATCTTATATA
Statistics
Matches: 113, Mismatches: 15, Indels: 37
0.68 0.09 0.22
Matches are distributed among these distances:
51 11 0.10
52 13 0.12
53 12 0.11
55 10 0.09
56 19 0.17
57 14 0.12
58 8 0.07
59 5 0.04
60 17 0.15
61 4 0.04
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (55 bp):
TTTAATATCATTATTTTATTTTTATTTATATTATATATATCAATCTTAATATATT
Found at i:3011612 original size:70 final size:74
Alignment explanation
Indices: 3011538--3011733 Score: 196
Period size: 70 Copynumber: 2.7 Consensus size: 74
3011528 ATCAATCTTA
*
3011538 ATATATTTTTAATATCAT-TATTTTATTTTCATTTATATTAT-AATCTTATAT-ATTTT-ATTTT
1 ATATATTTTTAATATCATATATTTTATTTTCATTTATATTATCAATATTATATAATTTTAATTTT
3011599 TTAT-TTTT
66 TTATATTTT
* * * *
3011607 GATATATTTTT-ATATTATATATTTTATTTTTATTTATTTTATCTATATTATATAAATTTTAATT
1 -ATATATTTTTAATATCATATATTTTATTTTCATTTATATTATCAATATTATAT-AATTTTAATT
3011671 TTTTATATTTT
64 TTTTATATTTT
* * *
3011682 ATTTTATTTTTAAT-TCTTATATTATATATTTT-ATTT-TAATTAT-AACATTATA
1 A-TATATTTTTAATATCATATATT-T-TATTTTCATTTAT-ATTATCAATATTATA
3011734 AAATATTTTT
Statistics
Matches: 104, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
69 6 0.06
70 31 0.30
71 8 0.08
73 5 0.05
74 10 0.10
75 27 0.26
76 11 0.11
77 6 0.06
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (74 bp):
ATATATTTTTAATATCATATATTTTATTTTCATTTATATTATCAATATTATATAATTTTAATTTT
TTATATTTT
Found at i:3011615 original size:55 final size:53
Alignment explanation
Indices: 3011432--3011722 Score: 155
Period size: 53 Copynumber: 5.6 Consensus size: 53
3011422 TTCTTAAATA
* * * *
3011432 TATTTTTAATTTCATATATTTTATTTTTATTTATTATTATAATCTTTTATATTT
1 TATTTTTATTTTTATATATTTTATTTTAATTTA-TATTATAATCTTATATATTT
* * *
3011486 TATTTTAATATATTATATTTTTTATTATTAATTTTTATATATATCAATCTTA-ATA---
1 TATTTTTAT-TTTTATATATTTTATT-TTAA--TTTATAT-TAT-AATCTTATATATTT
* * * *
3011541 TATTTTTAATATCAT-TATTTTATTTTCATTTATATTATAATCTTATATATTT
1 TATTTTTATTTTTATATATTTTATTTTAATTTATATTATAATCTTATATATTT
* * * * *
3011593 TATTTTTTATTTTTGATATA-TTT-TTAT-ATTATATATTTTATTTTTATTTATTT
1 TA-TTTTTATTTTT-ATATATTTTATTTTAATT-TATATTATAATCTTATATATTT
* * * * * *
3011646 TATCTATA-TTATATAAATTTTAATTT--TTTATATT-TTAT-TT-TAT-TTT
1 TATTTTTATTTTTATATATTTTATTTTAATTTATATTATAATCTTATATATTT
* *
3011692 TAATTCTTA-TATTATATATTTTATTTTAATT
1 T-ATTTTTATTTTTATATATTTTATTTTAATT
3011723 ATAACATTAT
Statistics
Matches: 182, Mismatches: 36, Indels: 43
0.70 0.14 0.16
Matches are distributed among these distances:
46 4 0.02
47 20 0.11
48 9 0.05
49 10 0.05
50 17 0.09
51 8 0.04
52 14 0.08
53 39 0.21
54 17 0.09
55 22 0.12
56 3 0.02
57 3 0.02
58 10 0.05
59 6 0.03
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.66
Consensus pattern (53 bp):
TATTTTTATTTTTATATATTTTATTTTAATTTATATTATAATCTTATATATTT
Found at i:3011632 original size:31 final size:31
Alignment explanation
Indices: 3011586--3011681 Score: 97
Period size: 31 Copynumber: 3.0 Consensus size: 31
3011576 TATAATCTTA
* *
3011586 TATATTTTATTTTTTATTTTTGATATATTTT-
1 TATATTATATATTTTATTTTT-ATATATTTTC
*
3011617 TATATTATATATTTTATTTTTATTTATTTTATC
1 TATATTATATATTTTATTTTTATATA-TTT-TC
3011650 TATATTATATAAATTTTAATTTTT-TATATTTT
1 TATATTATAT--ATTTT-ATTTTTATATATTTT
3011682 ATTTTATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
30 4 0.07
31 22 0.40
32 1 0.02
33 11 0.20
34 3 0.05
35 8 0.15
36 6 0.11
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (31 bp):
TATATTATATATTTTATTTTTATATATTTTC
Found at i:3011658 original size:38 final size:37
Alignment explanation
Indices: 3011555--3011683 Score: 108
Period size: 38 Copynumber: 3.5 Consensus size: 37
3011545 TTTAATATCA
* *
3011555 TTATTTTATTTTCA-TTTATAT-TATAATCTTATATATT
1 TTATTTT-TTTT-ATTTTATATATATTATATTATATATT
* *
3011592 TTATTTTTTATT-TTTGATATATTTTTATATTATATATT
1 TTATTTTTT-TTATTTTATATA-TATTATATTATATATT
*
3011630 TTATTTTTATTTATTTTATCTATATTATA-TA-A-ATT
1 TTATTTTT-TTTATTTTATATATATTATATTATATATT
*
3011665 TTAATTTTTTATATTTTAT
1 TT-ATTTTTTTTATTTTAT
3011684 TTTATTTTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
35 14 0.18
36 15 0.19
37 11 0.14
38 29 0.38
39 8 0.10
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (37 bp):
TTATTTTTTTTATTTTATATATATTATATTATATATT
Found at i:3011680 original size:35 final size:31
Alignment explanation
Indices: 3011586--3011725 Score: 104
Period size: 32 Copynumber: 4.3 Consensus size: 31
3011576 TATAATCTTA
* * *
3011586 TATATTTTATTTTTTATTTTTGATATATTT-T
1 TATATTATATATTTTATTTTTTATAT-TTTAT
*
3011617 TATATTATATATTTTATTTTTATTTATTTTAT
1 TATATTATATATTTTATTTTT-TATATTTTAT
3011649 CTATATTATATAAATTTTAATTTTTTATATTTTAT
1 -TATATTATAT--ATTTT-ATTTTTTATATTTTAT
* * * *
3011684 TTTATT-TTTAATTCTTATATTATATATTTTAT
1 TATATTATAT-ATT-TTATTTTTTATATTTTAT
*
3011716 TTTAATTATA
1 TAT-ATTATA
3011726 ACATTATAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
31 22 0.24
32 25 0.28
33 17 0.19
34 6 0.07
35 14 0.16
36 6 0.07
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (31 bp):
TATATTATATATTTTATTTTTTATATTTTAT
Found at i:3011682 original size:15 final size:15
Alignment explanation
Indices: 3011430--3011686 Score: 70
Period size: 15 Copynumber: 16.9 Consensus size: 15
3011420 ATTTCTTAAA
**
3011430 TATATTTTTAATTTCA
1 TATA-TTTTAATTTTT
*
3011446 TATATTTTATTTTTATT
1 TATATTTTA-ATTT-TT
* *
3011463 TATTATTATAATCTTT
1 TA-TATTTTAATTTTT
3011479 TATATTTT-A-TTTT
1 TATATTTTAATTTTT
* *
3011492 AATATATTATATTTTT
1 TATATTTTA-ATTTTT
*
3011508 TAT-TATTAATTTTT
1 TATATTTTAATTTTT
* * **
3011522 ATATATATCAATCTTAA
1 -TATATTTTAAT-TTTT
* **
3011539 TATATTTTTAATATCA
1 TATA-TTTTAATTTTT
*
3011555 T-TATTTTATTTTCATT
1 TATATTTTAATTT--TT
* * *
3011571 TATATTATAATCTTA
1 TATATTTTAATTTTT
3011586 TATATTTT-ATTTTT
1 TATATTTTAATTTTT
3011600 TAT-TTTTGATATATTTT
1 TATATTTT-A-AT-TTTT
* *
3011617 TATATTAT-ATATTT
1 TATATTTTAATTTTT
3011631 TAT-TTTT-ATTTATT
1 TATATTTTAATTT-TT
* * *
3011645 T-TA-TCTATATTATA
1 TATATTTTA-ATTTTT
*
3011659 TAAATTTTAATTTTT
1 TATATTTTAATTTTT
3011674 TATATTTT-ATTTT
1 TATATTTTAATTTT
3011687 ATTTTTAATT
Statistics
Matches: 176, Mismatches: 41, Indels: 50
0.66 0.15 0.19
Matches are distributed among these distances:
13 22 0.12
14 37 0.21
15 46 0.26
16 36 0.20
17 26 0.15
18 9 0.05
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TATATTTTAATTTTT
Found at i:3011731 original size:26 final size:27
Alignment explanation
Indices: 3011681--3011733 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
3011671 TTTTATATTT
* * *
3011681 TATTTTATTTTTAATTCTTATATTATA
1 TATTTTATTTTTAATTATAACATTATA
3011708 TATTTTA-TTTTAATTATAACATTATA
1 TATTTTATTTTTAATTATAACATTATA
3011734 AAATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTTATTTTTAATTATAACATTATA
Found at i:3011850 original size:24 final size:24
Alignment explanation
Indices: 3011823--3011868 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3011813 ATTGATTTTA
3011823 GACTATAATCA-CATTACATTATTT
1 GACTATAAT-ATCATTACATTATTT
* *
3011847 GACTGTAATATGATTACATTAT
1 GACTATAATATCATTACATTAT
3011869 AATCTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (24 bp):
GACTATAATATCATTACATTATTT
Found at i:3014218 original size:15 final size:15
Alignment explanation
Indices: 3014193--3014235 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 15
3014183 GGCACTGGTA
3014193 CTGAT-CTTCTTATG
1 CTGATACTTCTTATG
3014207 CTGATACTTCTT-TG
1 CTGATACTTCTTATG
3014221 CT-A-ACTTC-TATG
1 CTGATACTTCTTATG
3014233 CTG
1 CTG
3014236 TCCTGCGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.04
12 9 0.35
13 1 0.04
14 9 0.35
15 6 0.23
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.47
Consensus pattern (15 bp):
CTGATACTTCTTATG
Found at i:3022714 original size:7 final size:7
Alignment explanation
Indices: 3022702--3022727 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3022692 GTTGGACAAG
3022702 GAAAGAA
1 GAAAGAA
3022709 GAAAGAA
1 GAAAGAA
3022716 GAAAGAA
1 GAAAGAA
3022723 GAAAG
1 GAAAG
3022728 CAAAACTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (7 bp):
GAAAGAA
Found at i:3023167 original size:34 final size:34
Alignment explanation
Indices: 3023118--3023207 Score: 164
Period size: 34 Copynumber: 2.7 Consensus size: 34
3023108 TCTAACCTCG
*
3023118 GCAAAAAT-ATTCAGAAAGAAAAGATAGAATGAT
1 GCAAAAATCATTCAGAAGGAAAAGATAGAATGAT
3023151 GCAAAAATCATTCAGAAGGAAAAGATAGAATGAT
1 GCAAAAATCATTCAGAAGGAAAAGATAGAATGAT
3023185 GCAAAAATCATTCAGAAGGAAAA
1 GCAAAAATCATTCAGAAGGAAAA
3023208 AGTTCATAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 8 0.15
34 47 0.85
ACGTcount: A:0.56, C:0.09, G:0.19, T:0.17
Consensus pattern (34 bp):
GCAAAAATCATTCAGAAGGAAAAGATAGAATGAT
Found at i:3026559 original size:2 final size:2
Alignment explanation
Indices: 3026554--3026580 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3026544 ACTATATATA
3026554 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3026581 ACGTACGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3033007 original size:23 final size:23
Alignment explanation
Indices: 3032957--3033008 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3032947 TAGTGTGATA
* *
3032957 AGAAAAATCGATGTCTTAGGAAT
1 AGAAAGATCGATGTCTTAGAAAT
*
3032980 GGAAAGATCGAT-TCTTAGAAAAT
1 AGAAAGATCGATGTCTTAG-AAAT
3033003 AGAAAG
1 AGAAAG
3033009 CTTCAAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (23 bp):
AGAAAGATCGATGTCTTAGAAAT
Found at i:3033007 original size:74 final size:74
Alignment explanation
Indices: 3032908--3033086 Score: 182
Period size: 74 Copynumber: 2.4 Consensus size: 74
3032898 CTGACAAAAC
* * * * * * **
3032908 AAAGATTGATTCTCA-AAAATCAGAAAGG-TCTAGACTTTGTAGTGTGATAAGAAAAATCGATGT
1 AAAGATCGATTCTCAGAAAAT-AGAAAGGTTC-AAACTTTGAAGTGCGACAAGAAAAATCAACAT
* * *
3032971 CTTAGGAATGG
64 ATCAAGAATGG
* * * *
3032982 AAAGATCGATTCTTAGAAAATAGAAAGCTTCAAACTTTGAAGTGCGACAGGAAGAATCAACATAT
1 AAAGATCGATTCTCAGAAAATAGAAAGGTTCAAACTTTGAAGTGCGACAAGAAAAATCAACATAT
3033047 CAAGAATGG
66 CAAGAATGG
*
3033056 AAAGATCGATTCTCAGAAAACAGAAAGGTTC
1 AAAGATCGATTCTCAGAAAATAGAAAGGTTC
3033087 TGATGTAGAA
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
74 78 0.92
75 7 0.08
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (74 bp):
AAAGATCGATTCTCAGAAAATAGAAAGGTTCAAACTTTGAAGTGCGACAAGAAAAATCAACATAT
CAAGAATGG
Found at i:3033592 original size:31 final size:31
Alignment explanation
Indices: 3033548--3033662 Score: 119
Period size: 31 Copynumber: 3.8 Consensus size: 31
3033538 AGTGTAAGGA
3033548 TATACCTCCATTGTAAAAGGTAGTATAAAGT
1 TATACCTCCATTGTAAAAGGTAGTATAAAGT
* * * * *
3033579 TATATCTCTATTGTAAAAAGTAGTGTAAGGT
1 TATACCTCCATTGTAAAAGGTAGTATAAAGT
**
3033610 TATACCTCCA-TAAAAAAGGTAG-ATAAAAGT
1 TATACCTCCATTGTAAAAGGTAGTAT-AAAGT
* *
3033640 TATACCTCTATAG-AAAAGGTAGT
1 TATACCTCCATTGTAAAAGGTAGT
3033663 GTGTTAAAGG
Statistics
Matches: 66, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
29 1 0.02
30 31 0.47
31 34 0.52
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (31 bp):
TATACCTCCATTGTAAAAGGTAGTATAAAGT
Found at i:3033614 original size:62 final size:60
Alignment explanation
Indices: 3033516--3033664 Score: 176
Period size: 61 Copynumber: 2.5 Consensus size: 60
3033506 CTGTTGGTTG
* * **
3033516 GTTATACCTCCACA-AAAAATGTAGTGTAAGGATATACCTCCATTGTAAAAGGTAG-TATAAA
1 GTTATACCTCTATAGAAAAA-GTAGTGTAAGGATATACCTCCA-TAAAAAAGGTAGATA-AAA
* * *
3033577 GTTATATCTCTATTGTAAAAAGTAGTGTAAGGTTATACCTCCATAAAAAAGGTAGATAAAA
1 GTTATACCTCTATAG-AAAAAGTAGTGTAAGGATATACCTCCATAAAAAAGGTAGATAAAA
*
3033638 GTTATACCTCTATAGAAAAGGTAGTGT
1 GTTATACCTCTATAGAAAAAGTAGTGT
3033665 GTTAAAGGTT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
60 11 0.15
61 36 0.48
62 23 0.31
63 5 0.07
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (60 bp):
GTTATACCTCTATAGAAAAAGTAGTGTAAGGATATACCTCCATAAAAAAGGTAGATAAAA
Found at i:3044159 original size:26 final size:26
Alignment explanation
Indices: 3044130--3044181 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3044120 ACTTAAAACT
3044130 GTTT-TAATTATTTAAAAATTTAAAAA
1 GTTTGTAATT-TTTAAAAATTTAAAAA
**
3044156 GTTTGTAATTTTTATTAATTTAAAAA
1 GTTTGTAATTTTTAAAAATTTAAAAA
3044182 TTAAACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (26 bp):
GTTTGTAATTTTTAAAAATTTAAAAA
Found at i:3045220 original size:40 final size:40
Alignment explanation
Indices: 3045169--3045251 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
3045159 ATGGCCTTTT
* *
3045169 TGTGGGTGGCCAAATCTATGCGAGGCTCTTCGATTTTGTG
1 TGTGAGTGGCCAAATCTATGCAAGGCTCTTCGATTTTGTG
*
3045209 TGTGAGTGGCCAAATCTATGCAAGGCTCTTTGATTTTGTG
1 TGTGAGTGGCCAAATCTATGCAAGGCTCTTCGATTTTGTG
3045249 TGT
1 TGT
3045252 TTGTAGCCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.17, C:0.16, G:0.30, T:0.37
Consensus pattern (40 bp):
TGTGAGTGGCCAAATCTATGCAAGGCTCTTCGATTTTGTG
Found at i:3049125 original size:9 final size:9
Alignment explanation
Indices: 3049111--3049140 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3049101 TTATACTTAA
*
3049111 TTAATTGTT
1 TTAATTTTT
3049120 TTAATTTTT
1 TTAATTTTT
3049129 TTAATTTTT
1 TTAATTTTT
3049138 TTA
1 TTA
3049141 TAATTATAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (9 bp):
TTAATTTTT
Found at i:3049219 original size:20 final size:21
Alignment explanation
Indices: 3049188--3049226 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3049178 ATAGGGGGAT
3049188 AATGCATCAACCAATAAACCA
1 AATGCATCAACCAATAAACCA
3049209 AATGC-TCAACCAATAAAC
1 AATGCATCAACCAATAAAC
3049227 ACATTGCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.28, G:0.05, T:0.15
Consensus pattern (21 bp):
AATGCATCAACCAATAAACCA
Found at i:3059317 original size:2 final size:2
Alignment explanation
Indices: 3059310--3059351 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3059300 ACATGAGTTT
3059310 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3059352 AATGGTACCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3060618 original size:21 final size:22
Alignment explanation
Indices: 3060589--3060641 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
3060579 GCCTTCCAAA
* *
3060589 TTTTATCTTTTACATT-CTTTT
1 TTTTTTCTTTTACATTACCTTT
**
3060610 TTTTTTC-TTTATTTTACCTTT
1 TTTTTTCTTTTACATTACCTTT
3060631 TTTTTTCTTTT
1 TTTTTTCTTTT
3060642 TGTTTGTGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 6 0.23
21 17 0.65
22 3 0.12
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTTCTTTTACATTACCTTT
Found at i:3060731 original size:16 final size:18
Alignment explanation
Indices: 3060700--3060741 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
3060690 TTTTTTTATT
*
3060700 TTTTTAATATGTTTTACA
1 TTTTTAATATGTTTTAAA
3060718 TTTTTAA-A-GTTTTAAA
1 TTTTTAATATGTTTTAAA
3060734 -TTTTAATA
1 TTTTTAATA
3060742 ACTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.27
16 8 0.36
17 1 0.05
18 7 0.32
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTTAATATGTTTTAAA
Found at i:3067159 original size:19 final size:19
Alignment explanation
Indices: 3067135--3067171 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3067125 GTTTGCATCA
3067135 TAGTTCAAATAATATAAAG
1 TAGTTCAAATAATATAAAG
*
3067154 TAGTTCAATTAATATAAA
1 TAGTTCAAATAATATAAA
3067172 AATTTTATAT
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:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (19 bp):
TAGTTCAAATAATATAAAG
Found at i:3067305 original size:86 final size:86
Alignment explanation
Indices: 3067155--3067646 Score: 694
Period size: 86 Copynumber: 5.8 Consensus size: 86
3067145 AATATAAAGT
* *
3067155 AGTTCAATTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
*
3067220 TTTTACATTTATTAGTTTACA
66 TTTTACATTTGTTAGTTTACA
* *
3067241 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGCAATATATATTAA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
* *
3067306 TTTTACATTTGCTAGTTTATA
66 TTTTACATTTGTTAGTTTACA
* * * **
3067327 AGTTCAACTAATATAAATATTTTATATATTTAAGATTGCATCATAGTTCATGCAATGCAAATTAA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
*
3067392 TCTTACATTTGTTAGTTTACA
66 TTTTACATTTGTTAGTTTACA
*
3067413 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTTCATCATAGTTCAAGTAATATAAATTAA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
** *
3067478 TTTTACATTTGTTAGCGTGCA
66 TTTTACATTTGTTAGTTTACA
* *
3067499 AGTTCAACTAATATAAAAA-TTTAGATATTT---A----ATCATAGTTCCAGTAATATAAATTAA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
* *
3067556 TTTTATATTGGTTAGTTTACA
66 TTTTACATTTGTTAGTTTACA
* * * *
3067577 AATTCAACTAATATAAAAATTTTATATATTTAAGTTTTCATCATAGTTCCAATTAATATAAATTA
1 AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTT-CAAGTAATATAAATTA
3067642 ATTTT
65 ATTTT
3067647 GCTTTTAGTA
Statistics
Matches: 360, Mismatches: 37, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
78 59 0.16
79 10 0.03
82 1 0.00
85 10 0.03
86 261 0.73
87 19 0.05
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (86 bp):
AGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCATCATAGTTCAAGTAATATAAATTAA
TTTTACATTTGTTAGTTTACA
Found at i:3067545 original size:78 final size:79
Alignment explanation
Indices: 3067447--3067609 Score: 238
Period size: 78 Copynumber: 2.1 Consensus size: 79
3067437 TATATTTAAG
* * * *
3067447 ATTTCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGCGTGCAAGTTCAACTAATA
1 ATTTAATCATAGTTCAAGTAATATAAATTAATTTTACATTGGTTAGCGTACAAATTCAACTAATA
3067512 TAAAAA-TTTAGAT
66 TAAAAATTTTAGAT
* * **
3067525 ATTTAATCATAGTTCCAGTAATATAAATTAATTTTATATTGGTTAGTTTACAAATTCAACTAATA
1 ATTTAATCATAGTTCAAGTAATATAAATTAATTTTACATTGGTTAGCGTACAAATTCAACTAATA
*
3067590 TAAAAATTTTATAT
66 TAAAAATTTTAGAT
3067604 ATTTAA
1 ATTTAA
3067610 GTTTTCATCA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
78 63 0.84
79 12 0.16
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (79 bp):
ATTTAATCATAGTTCAAGTAATATAAATTAATTTTACATTGGTTAGCGTACAAATTCAACTAATA
TAAAAATTTTAGAT
Found at i:3067765 original size:12 final size:12
Alignment explanation
Indices: 3067748--3067797 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
3067738 CAACATTTTG
3067748 TAATATTACATA
1 TAATATTACATA
3067760 TAATA-TA-ATTA
1 TAATATTACA-TA
3067771 TAATATTACATA
1 TAATATTACATA
*
3067783 TAATATAAC-TA
1 TAATATTACATA
3067794 TAAT
1 TAAT
3067798 CAGATCCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
10 1 0.03
11 15 0.44
12 17 0.50
13 1 0.03
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATTACATA
Found at i:3067778 original size:23 final size:23
Alignment explanation
Indices: 3067748--3067797 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
3067738 CAACATTTTG
*
3067748 TAATATTACATATAATATAATTA
1 TAATATTACATATAATATAACTA
3067771 TAATATTACATATAATATAACTA
1 TAATATTACATATAATATAACTA
3067794 TAAT
1 TAAT
3067798 CAGATCCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATATTACATATAATATAACTA
Found at i:3081367 original size:2 final size:2
Alignment explanation
Indices: 3081362--3081388 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3081352 GAGGTTTTAA
3081362 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3081389 AAAGAAACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3081774 original size:2 final size:2
Alignment explanation
Indices: 3081767--3081802 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3081757 CAGAGGAAAT
*
3081767 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GC GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3081803 TTAAGAAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3084524 original size:13 final size:15
Alignment explanation
Indices: 3084497--3084528 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3084487 CCTAGTTGAT
3084497 TCTTTCTTTTCTCTC
1 TCTTTCTTTTCTCTC
*
3084512 TCTTTTTTTTCTCTC
1 TCTTTCTTTTCTCTC
3084527 TC
1 TC
3084529 CCCACTCGCC
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TCTTTCTTTTCTCTC
Found at i:3085490 original size:57 final size:57
Alignment explanation
Indices: 3085382--3085513 Score: 160
Period size: 57 Copynumber: 2.3 Consensus size: 57
3085372 TTAACAAAGG
* * * * * *
3085382 TGATGATATGTTTGAGTTGATGATATTTCATTGATGATACTTGGAAGAAATTTGCAT
1 TGATAATATGCTTGAGTTGATGATATTACATTGATAATACTTGGAACAAATTTACAT
*
3085439 CT-ATAATATGCTTAAGTTGATGATATTACATTGATAATACTTAGG-ACAAATTTACAT
1 -TGATAATATGCTTGAGTTGATGATATTACATTGATAATACTT-GGAACAAATTTACAT
*
3085496 TGATGATATGCTTGAGTT
1 TGATAATATGCTTGAGTT
3085514 TTGTTATAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
56 1 0.02
57 59 0.94
58 3 0.05
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.41
Consensus pattern (57 bp):
TGATAATATGCTTGAGTTGATGATATTACATTGATAATACTTGGAACAAATTTACAT
Found at i:3086894 original size:25 final size:25
Alignment explanation
Indices: 3086866--3086914 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
3086856 TACATTTTAC
3086866 TGACGGAATTAGGTGTTGCATTATT
1 TGACGGAATTAGGTGTTGCATTATT
3086891 TGACGGAATTAGGTGTTGCATTAT
1 TGACGGAATTAGGTGTTGCATTAT
3086915 CTACTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (25 bp):
TGACGGAATTAGGTGTTGCATTATT
Found at i:3088585 original size:29 final size:28
Alignment explanation
Indices: 3088537--3088643 Score: 151
Period size: 29 Copynumber: 3.8 Consensus size: 28
3088527 GGTAACTTTG
3088537 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
* *
3088565 ACATGTTTAGTCTTAACTTAGATAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
*
3088594 ATATGTTTGTCTTAATTTAAGACAAGAAA
1 ACATGTTTGTCTTAATTT-AGACAAGAAA
* *
3088623 ACATATTTGTCTAAATTTAGA
1 ACATGTTTGTCTTAATTTAGA
3088644 TAACATAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 20 0.29
29 49 0.71
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:3088606 original size:57 final size:59
Alignment explanation
Indices: 3088539--3088678 Score: 180
Period size: 57 Copynumber: 2.4 Consensus size: 59
3088529 TAACTTTGAC
* *
3088539 ATGTTTGTCTTAATTT-AGACAAGAAAACATGTTTAGTCTTAACTTAGAT-A-AGAAAAT
1 ATGTTTGTCTTAATTTAAGACAAGAAAACATATTT-GTCTAAACTTAGATAACAGAAAAT
* *
3088596 ATGTTTGTCTTAATTTAAGACAAGAAAACATATTTGTCTAAATTTAGATAACATAAAAT
1 ATGTTTGTCTTAATTTAAGACAAGAAAACATATTTGTCTAAACTTAGATAACAGAAAAT
*
3088655 ATTTATTGTCTTAA-TTACAGACAA
1 ATGT-TTGTCTTAATTTA-AGACAA
3088679 AAATTATCTT
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
57 28 0.38
58 18 0.25
59 12 0.16
60 15 0.21
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.38
Consensus pattern (59 bp):
ATGTTTGTCTTAATTTAAGACAAGAAAACATATTTGTCTAAACTTAGATAACAGAAAAT
Found at i:3094696 original size:58 final size:55
Alignment explanation
Indices: 3094634--3094772 Score: 179
Period size: 55 Copynumber: 2.5 Consensus size: 55
3094624 GCTTTCTAAC
* *
3094634 GATGTTTTCAAGCGCTTAGAGTCAGTATGATGAATATAGTAACTGAATGCTTTTTAGT
1 GATGTTTTCAAGCGCTCAG-G-CAG-AAGATGAATATAGTAACTGAATGCTTTTTAGT
* * * *
3094692 GATGTTTTCAAGGGCTCAGGGAGAAGGTGAATATAGTAACTGAATGCTTTTTATT
1 GATGTTTTCAAGCGCTCAGGCAGAAGATGAATATAGTAACTGAATGCTTTTTAGT
* *
3094747 GATGTTTTCAAGGGCTCAGGGAGAAG
1 GATGTTTTCAAGCGCTCAGGCAGAAG
3094773 GGATAGCTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
55 55 0.73
56 2 0.03
57 1 0.01
58 17 0.23
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (55 bp):
GATGTTTTCAAGCGCTCAGGCAGAAGATGAATATAGTAACTGAATGCTTTTTAGT
Found at i:3094737 original size:55 final size:55
Alignment explanation
Indices: 3094664--3094773 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
3094654 GTCAGTATGA
3094664 TGAATATAGTAACTGAATGCTTTTTAGTGATGTTTTCAAGGGCTCAGGGAGAAGG
1 TGAATATAGTAACTGAATGCTTTTTAGTGATGTTTTCAAGGGCTCAGGGAGAAGG
*
3094719 TGAATATAGTAACTGAATGCTTTTTATTGATGTTTTCAAGGGCTCAGGGAGAAGG
1 TGAATATAGTAACTGAATGCTTTTTAGTGATGTTTTCAAGGGCTCAGGGAGAAGG
3094774 GATAGCTAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.34
Consensus pattern (55 bp):
TGAATATAGTAACTGAATGCTTTTTAGTGATGTTTTCAAGGGCTCAGGGAGAAGG
Found at i:3095146 original size:22 final size:22
Alignment explanation
Indices: 3095121--3095174 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
3095111 GAAATTGATT
*
3095121 AGACTGGATTTTAAGTATTGCG
1 AGACTGGATTTTAAATATTGCG
**
3095143 AGACTGTTTTTTAAATATTGCG
1 AGACTGGATTTTAAATATTGCG
* *
3095165 TGACTTGATT
1 AGACTGGATT
3095175 ACTGTGTGAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (22 bp):
AGACTGGATTTTAAATATTGCG
Found at i:3095248 original size:22 final size:21
Alignment explanation
Indices: 3095189--3095256 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
3095179 TGTGACTAGT
*
3095189 TTTTAGGCATTACGTGATTGG
1 TTTTAGGCATTGCGTGATTGG
* * *
3095210 TTATAAGCATTGTGTGATTGG
1 TTTTAGGCATTGCGTGATTGG
*
3095231 TTGTTAGGCATTGCGTGATTGA
1 TT-TTAGGCATTGCGTGATTGG
3095253 TTTT
1 TTTT
3095257 TAAGCAATGC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 21 0.55
22 17 0.45
ACGTcount: A:0.19, C:0.07, G:0.28, T:0.46
Consensus pattern (21 bp):
TTTTAGGCATTGCGTGATTGG
Found at i:3095296 original size:23 final size:23
Alignment explanation
Indices: 3095270--3095314 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3095260 GCAATGCCTA
3095270 AGTCACACAATGCCTTACTAACT
1 AGTCACACAATGCCTTACTAACT
* *
3095293 AGTCACATAATGGCTTACTAAC
1 AGTCACACAATGCCTTACTAAC
3095315 AAATCATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.27
Consensus pattern (23 bp):
AGTCACACAATGCCTTACTAACT
Found at i:3095348 original size:23 final size:23
Alignment explanation
Indices: 3095301--3095350 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
3095291 CTAGTCACAT
* *
3095301 AATGGCTTACTAACAAATCATGC
1 AATGGCTTACTAACAAACCACGC
* *
3095324 AATGGCTTACTAGCAAGCCACGC
1 AATGGCTTACTAACAAACCACGC
3095347 AATG
1 AATG
3095351 CTCACCAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (23 bp):
AATGGCTTACTAACAAACCACGC
Found at i:3095386 original size:22 final size:22
Alignment explanation
Indices: 3095361--3095466 Score: 92
Period size: 21 Copynumber: 4.9 Consensus size: 22
3095351 CTCACCAACT
3095361 AGTCACGTAATACCTAAAAATA
1 AGTCACGTAATACCTAAAAATA
* * *
3095383 AGTCACGTAATGCCT-AAAGTC
1 AGTCACGTAATACCTAAAAATA
* * *
3095404 AGCCACGTAAT-GC-ACAAAGTA
1 AGTCACGTAATACCTA-AAAATA
* *
3095425 AGTCACGTAATACTTAAAAATT
1 AGTCACGTAATACCTAAAAATA
*
3095447 AGTCACGTAATGTCCTAAAA
1 AGTCACGTAAT-ACCTAAAA
3095467 CTACCAAAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.02
21 29 0.44
22 29 0.44
23 7 0.11
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (22 bp):
AGTCACGTAATACCTAAAAATA
Found at i:3096913 original size:2 final size:2
Alignment explanation
Indices: 3096906--3096936 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3096896 CATGCTTGCT
3096906 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 T
3096937 TGTATGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3099293 original size:13 final size:13
Alignment explanation
Indices: 3099275--3099301 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3099265 ATTTACTTAC
3099275 TATTGAGTAATAT
1 TATTGAGTAATAT
3099288 TATTGAGTAATAT
1 TATTGAGTAATAT
3099301 T
1 T
3099302 TTACGTCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTGAGTAATAT
Found at i:3110364 original size:2 final size:2
Alignment explanation
Indices: 3110357--3110394 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3110347 GTTACTACCC
*
3110357 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3110395 TCTTGAGAAT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3112616 original size:19 final size:20
Alignment explanation
Indices: 3112592--3112629 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3112582 ATAACTTCTT
*
3112592 TTTC-TTTCACTTATTTTTG
1 TTTCTTTTCACCTATTTTTG
3112611 TTTCTTTTCACCTATTTTT
1 TTTCTTTTCACCTATTTTT
3112630 TTCCACTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTCTTTTCACCTATTTTTG
Found at i:3115906 original size:25 final size:24
Alignment explanation
Indices: 3115863--3115912 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
3115853 ACCATAAAAA
3115863 AAGTTAAGAACTTAAATGA-CCTT
1 AAGTTAAGAACTTAAATGATCCTT
3115886 AAGTTAGATGAAC-TAATATGATCCTT
1 AAGTTA-A-GAACTTAA-ATGATCCTT
3115912 A
1 A
3115913 CTCACTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.26
24 4 0.17
25 8 0.35
26 5 0.22
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (24 bp):
AAGTTAAGAACTTAAATGATCCTT
Found at i:3123477 original size:35 final size:35
Alignment explanation
Indices: 3123452--3123533 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 35
3123442 TTATCTCGAA
*
3123452 AAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTTG
1 AAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTCG
* *
3123487 AAAAACCATTGTTGTAGGTTGTGGTTGAG-CTTGTG
1 AAAAACCATTGTTGAAGGTTGTGGTTGAGCCTT-CG
*
3123522 AAAAGCCATTGT
1 AAAAACCATTGT
3123534 AAAAACTTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 3 0.07
35 41 0.93
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (35 bp):
AAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTCG
Found at i:3125134 original size:35 final size:35
Alignment explanation
Indices: 3125082--3125153 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
3125072 TACTTGTATC
* * *
3125082 AAACCATTGCTGGAGGTTGTGGTTGAGCTTTTGAA
1 AAACCATTGCTGAAGGTTGTGGCTGAGCTTGTGAA
*
3125117 AAACCATTGTTGAAGGTTGTGGCTGAGCTTGTGAA
1 AAACCATTGCTGAAGGTTGTGGCTGAGCTTGTGAA
3125152 AA
1 AA
3125154 GCTATTGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.32
Consensus pattern (35 bp):
AAACCATTGCTGAAGGTTGTGGCTGAGCTTGTGAA
Found at i:3134008 original size:64 final size:63
Alignment explanation
Indices: 3133935--3134096 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
3133925 AAACATAGAT
**
3133935 AAAAACAACAATTAATACTCTTGAGCAAATAACAACAAATCATTAACAAG-ATTCAACAATGGAC
1 AAAAACAACAACAAATACTCTTGAGCAAATAA-AACAAATCATTAAC-AGTATTCAACAATGGAC
* * * * *
3133999 AAAAACAACAACAAATACTCTTCAACAAATTAAAACAGATCATTAACAGTCTTCAACAATGGAT
1 AAAAACAACAACAAATACTCTTGAGCAAA-TAAAACAAATCATTAACAGTATTCAACAATGGAC
*
3134063 AAAAACAACAACAAATAGTCTTGAATGCAAATAA
1 AAAAACAACAACAAATACTCTTG-A-GCAAATAA
3134097 TCTTCAAAGA
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 2 0.02
64 71 0.85
65 7 0.08
66 4 0.05
ACGTcount: A:0.54, C:0.19, G:0.07, T:0.20
Consensus pattern (63 bp):
AAAAACAACAACAAATACTCTTGAGCAAATAAAACAAATCATTAACAGTATTCAACAATGGAC
Found at i:3134083 original size:33 final size:33
Alignment explanation
Indices: 3133986--3134084 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 33
3133976 ATTAACAAGA
* *
3133986 TTCAACAATGGACAAAAACAACAACAAATACTC
1 TTCAACAATGGATAAAAACAACAACAAATAGTC
* ** *
3134019 TTCAACAA---ATTAAAACAGATC-ATTAACAGTC
1 TTCAACAATGGATAAAAACA-A-CAACAAATAGTC
3134050 TTCAACAATGGATAAAAACAACAACAAATAGTC
1 TTCAACAATGGATAAAAACAACAACAAATAGTC
3134083 TT
1 TT
3134085 GAATGCAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
30 7 0.14
31 15 0.30
32 2 0.04
33 18 0.36
34 8 0.16
ACGTcount: A:0.52, C:0.20, G:0.07, T:0.21
Consensus pattern (33 bp):
TTCAACAATGGATAAAAACAACAACAAATAGTC
Found at i:3136420 original size:686 final size:685
Alignment explanation
Indices: 3135445--3136810 Score: 2428
Period size: 686 Copynumber: 2.0 Consensus size: 685
3135435 TAAACACAAC
* *
3135445 AAATTCTTTGATTGAATATTTGCAGACTCAACACATTCTTTGCATTTGCTAACCTAGCAGGTGAT
1 AAATTCTTTAATTGAATATTTGCAGACTCAACACATTCTTTGCATTTGCTAACCTAACAGGTGAT
3135510 TGTTTCATGTATCTAACTGCCCCTCTAATACAAGAAATTAAATCATTCATTTCCTTCAGTCCATC
66 TGTTTCATGTATCTAACTGCCCCTCTAATACAAGAAATTAAATCATTCATTTCCTTCAGTCCATC
*
3135575 AGTGAAAATGAGATTAATATATGTGCAATGCATTTCATATGTAGAAATTTGCTTTCTAAAAAACT
131 AGTGAAAATGAGATTAATATATGTGCAATGCATCTCATATGTAGAAATTTGCTTTCTAAAAAACT
* * * *
3135640 ATTTCCTGCTAAGTTCAATTTTTTCTTTATATGTGCTATTGCAACATCATTGGAACTAGCATTAT
196 ATTTCCTACTAAGTTCAATTTTTGCTTTATATGTGCTATTGCAACATCATTGGAACCAACATTAT
3135705 CAACAGTAATAATGAAAACCTTACTAATCCCCCAATCACACTGACATTTATCAATCATTTTCCCA
261 CAACAGTAATAATGAAAACCTTACTAATCCCCCAATCACACTGACATTTATCAATCATTTTCCCA
* *
3135770 ATGGCCTCACCTTTGTGACTATAAATGGGACAAAAGTTTAAAATTATTTTTTGTAATTTCCAATC
326 ATGGCCTCACCTTTGTGACTATAAATGAGACAAAAGTTTAAAATTATTTTGTGTAATTTCCAATC
* *
3135835 ATTGTTTATAAAGTGATCTGTAAGACACATAAAATTTTCTCTTTGAATTGATGTCCATGTGTCTG
391 ATTGTTTATAAAGTGATCCGTAAGACACATAAAATTTTCTCTTTGAATTGATGTCCATGTGTATG
* *
3135900 TCATCAAAGAAACTCTAAAAGAAGATGTTCTTAGTATATGCTTGAAGTGGTTCTTTCCATTAACA
456 TCATCAAAGAAACTCTAAAAGAAGATGTTCTTAGTATATACTTGAAATGGTTCTTTCCATTAACA
3135965 AAAAGGTTATAGCAATCTTTAGCAATAGTCCATCATGATGGTACAATAAATCTAGGATATGAAGT
521 AAAAGGTTATAGCAATCTTTAGCAATAGTCCATCATGATGGTACAATAAATCTAGGATATGAAGT
* *
3136030 TGATGTGAATTCCTTAAATCATTCCTCTTCTACAAATCTAAAAATCAACTCATCTTTGATGATCA
586 TGACGTGAATTCCTTAAATCATTCCTCTTCGACAAATCTAAAAATCAACTCATCTTTGATGATCA
*
3136095 TTTTAACTGGAGACTTTCTAAGAGG-TTCTTCAAAT
651 TCTTAACTGGAGACTTTCTAAG-GGCTTCTTCAAAT
3136130 AAATTCTTTAATTGAATATTTGCAGACTCAACACATTCTTTGCATTTGCTAACCTAACAGGTGAT
1 AAATTCTTTAATTGAATATTTGCAGACTCAACACATTCTTTGCATTTGCTAACCTAACAGGTGAT
*
3136195 TGTTTCATGTATCTAACTGCCCCTCTAATACAAGTAATTAAATCATTCATTTCCTTCAGTCCATC
66 TGTTTCATGTATCTAACTGCCCCTCTAATACAAGAAATTAAATCATTCATTTCCTTCAGTCCATC
3136260 AGTGAAAATGAGATTAATGATATGTGCAATGCATCTCATATGTAGAAATTTGCTTTCTAAAAAAC
131 AGTGAAAATGAGATTAAT-ATATGTGCAATGCATCTCATATGTAGAAATTTGCTTTCTAAAAAAC
3136325 TATTTCCTACTAAGTTCAATTTTTGCTTTATATGTGCTATTGCAACATCATTGGAACCAACATTA
195 TATTTCCTACTAAGTTCAATTTTTGCTTTATATGTGCTATTGCAACATCATTGGAACCAACATTA
* * * * *
3136390 TCAACAGTAATAGTGGAAACTTTACTAATCCCCCAATCACACTGACATTTATTAATCATTTTCTC
260 TCAACAGTAATAATGAAAACCTTACTAATCCCCCAATCACACTGACATTTATCAATCATTTTCCC
*
3136455 AATGGCCTCACCTTTGTGACTATAAATGAGACAAAAGTTTAAAATTATTTTGTGTAATTTTCAAT
325 AATGGCCTCACCTTTGTGACTATAAATGAGACAAAAGTTTAAAATTATTTTGTGTAATTTCCAAT
*
3136520 CATTGTTTATAAAGTGATCCGTAAGACACATATAATTTTCTCTTTGAATTGATGTCCATGTGTAT
390 CATTGTTTATAAAGTGATCCGTAAGACACATAAAATTTTCTCTTTGAATTGATGTCCATGTGTAT
* * * *
3136585 GTCGTTAGAGAAACTCTAAAAGAAGATGTTCTTAGTATATATTTGAAATGGTTCTTTCCATTAAC
455 GTCATCAAAGAAACTCTAAAAGAAGATGTTCTTAGTATATACTTGAAATGGTTCTTTCCATTAAC
*
3136650 AAAAAGGTTATAGCAATCTTTAGCAATAGTCCATCATGATGGTATAATAAATCTAGGATATGAAG
520 AAAAAGGTTATAGCAATCTTTAGCAATAGTCCATCATGATGGTACAATAAATCTAGGATATGAAG
* *
3136715 TTGACGTGAATTCCTTAAATCCTTCCTCTTCGACAAATCTAAAAGTCAACTCATCTTTGATGATC
585 TTGACGTGAATTCCTTAAATCATTCCTCTTCGACAAATCTAAAAATCAACTCATCTTTGATGATC
3136780 ATCTTAACTGGAGACTTTCTAAGGGCTTCTT
650 ATCTTAACTGGAGACTTTCTAAGGGCTTCTT
3136811 GACTAAATTT
Statistics
Matches: 648, Mismatches: 31, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
685 147 0.23
686 501 0.77
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.36
Consensus pattern (685 bp):
AAATTCTTTAATTGAATATTTGCAGACTCAACACATTCTTTGCATTTGCTAACCTAACAGGTGAT
TGTTTCATGTATCTAACTGCCCCTCTAATACAAGAAATTAAATCATTCATTTCCTTCAGTCCATC
AGTGAAAATGAGATTAATATATGTGCAATGCATCTCATATGTAGAAATTTGCTTTCTAAAAAACT
ATTTCCTACTAAGTTCAATTTTTGCTTTATATGTGCTATTGCAACATCATTGGAACCAACATTAT
CAACAGTAATAATGAAAACCTTACTAATCCCCCAATCACACTGACATTTATCAATCATTTTCCCA
ATGGCCTCACCTTTGTGACTATAAATGAGACAAAAGTTTAAAATTATTTTGTGTAATTTCCAATC
ATTGTTTATAAAGTGATCCGTAAGACACATAAAATTTTCTCTTTGAATTGATGTCCATGTGTATG
TCATCAAAGAAACTCTAAAAGAAGATGTTCTTAGTATATACTTGAAATGGTTCTTTCCATTAACA
AAAAGGTTATAGCAATCTTTAGCAATAGTCCATCATGATGGTACAATAAATCTAGGATATGAAGT
TGACGTGAATTCCTTAAATCATTCCTCTTCGACAAATCTAAAAATCAACTCATCTTTGATGATCA
TCTTAACTGGAGACTTTCTAAGGGCTTCTTCAAAT
Found at i:3140986 original size:33 final size:33
Alignment explanation
Indices: 3140918--3141046 Score: 114
Period size: 33 Copynumber: 3.8 Consensus size: 33
3140908 TATAGAAAGA
* * * *
3140918 GCTTTTTCACAAGCTCAAGCATAACCTTTACACTT
1 GCTTTTTCA-AAGATCAAGTAGAACCTAT-CACTT
* * * *
3140953 GCTTTGTCAAGGATTAAGTAGAACCTATTACTT
1 GCTTTTTCAAAGATCAAGTAGAACCTATCACTT
* * * * *
3140986 GTTTTTTGAAAGATGAAGCAAAACCTATCACTT
1 GCTTTTTCAAAGATCAAGTAGAACCTATCACTT
*
3141019 GGTTTTTCAAAGATCAAGTAGAACCTAT
1 GCTTTTTCAAAGATCAAGTAGAACCTAT
3141047 ACAACTACCC
Statistics
Matches: 73, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
33 52 0.71
34 13 0.18
35 8 0.11
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (33 bp):
GCTTTTTCAAAGATCAAGTAGAACCTATCACTT
Found at i:3142976 original size:23 final size:23
Alignment explanation
Indices: 3142950--3142995 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3142940 GTGAAAGATT
*
3142950 GAATAACAAATTCCTCAAGAATC
1 GAATAACAAATACCTCAAGAATC
*
3142973 GAATAGCAAATACCTCAAGAATC
1 GAATAACAAATACCTCAAGAATC
3142996 ACTTTAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.22, G:0.11, T:0.20
Consensus pattern (23 bp):
GAATAACAAATACCTCAAGAATC
Found at i:3143527 original size:46 final size:46
Alignment explanation
Indices: 3143474--3143565 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
3143464 ACTCTTGAAA
3143474 AAGGTTTTCTGCAAATTTAATTCATTGTGTTCAAGAACCTATTTGT
1 AAGGTTTTCTGCAAATTTAATTCATTGTGTTCAAGAACCTATTTGT
*
3143520 AAGGTTTTCTGCAATTTTAATTCATTGTGTTCAAGAACCTATTTGT
1 AAGGTTTTCTGCAAATTTAATTCATTGTGTTCAAGAACCTATTTGT
3143566 TCTTACTTAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (46 bp):
AAGGTTTTCTGCAAATTTAATTCATTGTGTTCAAGAACCTATTTGT
Found at i:3148103 original size:2 final size:2
Alignment explanation
Indices: 3148096--3148122 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3148086 TATAATAGGC
3148096 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 T
3148123 CGAAGAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3155782 original size:22 final size:24
Alignment explanation
Indices: 3155757--3155808 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
3155747 AAGAATTGCA
3155757 TGACTGA-TTT-TTAAGG-ATTACG
1 TGACTGAGTTTATT-AGGCATTACG
*
3155779 TGACT-AGTTTATTTGGCATTACG
1 TGACTGAGTTTATTAGGCATTACG
3155802 TGACTGA
1 TGACTGA
3155809 ATATTAGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
22 10 0.40
23 13 0.52
24 1 0.04
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (24 bp):
TGACTGAGTTTATTAGGCATTACG
Found at i:3158042 original size:45 final size:45
Alignment explanation
Indices: 3157931--3158043 Score: 102
Period size: 45 Copynumber: 2.5 Consensus size: 45
3157921 CCAGTCACTT
* * * * *
3157931 AATGCCCTATCAAGCAGTCACGCAATAACTTATACTCAATTACGC
1 AATGACCTATCAACCAGTCACGCAATAACTCAAACTCAATAACGC
* * ** * * *
3157976 AACGACTTATCAATAAATCACGCAATCACTACAAACT-AGTAACGC
1 AATGACCTATCAACCAGTCACGCAATAACT-CAAACTCAATAACGC
3158021 AATGACCTATCAACCAGTCACGC
1 AATGACCTATCAACCAGTCACGC
3158044 GATACCAAAA
Statistics
Matches: 51, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
45 47 0.92
46 4 0.08
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (45 bp):
AATGACCTATCAACCAGTCACGCAATAACTCAAACTCAATAACGC
Found at i:3161536 original size:7 final size:7
Alignment explanation
Indices: 3161503--3161537 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
3161493 CATGGCCATT
*
3161503 CCCTACG
1 CCCTATG
*
3161510 CCCTACG
1 CCCTATG
3161517 CCCTATG
1 CCCTATG
3161524 CCCTATG
1 CCCTATG
3161531 CCCTATG
1 CCCTATG
3161538 AGTAACCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.49, G:0.14, T:0.23
Consensus pattern (7 bp):
CCCTATG
Found at i:3165516 original size:86 final size:86
Alignment explanation
Indices: 3165315--3165912 Score: 795
Period size: 86 Copynumber: 7.0 Consensus size: 86
3165305 TTATATTACT
* *
3165315 TATAAAATTTTTCATAATAGTTGAA-TTCGTAAACTAACAATTGTAAAATTAATTTATATTAC-T
1 TATAAAATTTTT-ATATTAGTTGAACTT-GTAAACTAACAAATGTAAAATTAATTTATATTACTT
*
3165378 ----TATGATGCAAACTTGAATA
64 GAACTATGATGCAAACTTAAATA
* * *
3165397 TATAAACTTTTTATATTACTTAAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
*
3165462 ACTATAATGCAAACTTAAATA
66 ACTATGATGCAAACTTAAATA
* *
3165483 TGTAAAATTTTTATATTAGTTGAATTTGTAAACTAACAAATGTAAAATTAATTTATATTAC-T--
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
*
3165545 --TATGATACAAACTTAAATA
66 ACTATGATGCAAACTTAAATA
*
3165564 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGCAAAATTAATTTATATTACTTGA
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
* * *
3165629 ATTATGATACAAATTTAAATA
66 ACTATGATGCAAACTTAAATA
* *
3165650 TATAAACTTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTATTTTATATTACTTGA
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
*
3165715 ACTATGATGTAAACTTAAATA
66 ACTATGATGCAAACTTAAATA
* ** *
3165736 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAATACAAATTTAATTTATATTACTTGA
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
*
3165801 ACTGTATATGATGTAAACTTAAATA
66 AC----TATGATGCAAACTTAAATA
* * * *
3165826 TATAAATTAAAGTTTTATATTAGTTGAACTTGTAAATTAACAAATGTAAAATTAATATATATTAA
1 TAT--A--AAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTAC
3165891 TTGAACTATGATGCAAACTTAA
62 TTGAACTATGATGCAAACTTAA
3165913 TAACATATCA
Statistics
Matches: 457, Mismatches: 40, Indels: 30
0.87 0.08 0.06
Matches are distributed among these distances:
81 117 0.26
82 15 0.03
85 1 0.00
86 231 0.51
90 37 0.08
92 1 0.00
94 55 0.12
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (86 bp):
TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
ACTATGATGCAAACTTAAATA
Done.