Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 46 of 214
Found at i:12553159 original size:49 final size:50
Alignment explanation
Indices: 12553071--12553178 Score: 130
Period size: 49 Copynumber: 2.2 Consensus size: 50
12553061 TGGTCCCACA
* * ** *
12553071 TAAGACCATGTCTGGGACATGGAGTTGGCACCGAGATGAGAGGTCCCCTG
1 TAAGACCATGTCTAGGACATGGAGTGGGCACCGAGATGAGAACTCCCATG
* *
12553121 TAAGACCAT-TCTAGGACATGGCA-TGGGCACCGATATGAGAACTTCCATG
1 TAAGACCATGTCTAGGACATGG-AGTGGGCACCGAGATGAGAACTCCCATG
12553170 TAAGACCAT
1 TAAGACCAT
12553179 ATCTGGGATT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
49 40 0.80
50 10 0.20
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (50 bp):
TAAGACCATGTCTAGGACATGGAGTGGGCACCGAGATGAGAACTCCCATG
Found at i:12553465 original size:12 final size:12
Alignment explanation
Indices: 12553448--12553486 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12553438 ATGAGTTATT
12553448 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
12553460 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
12553472 TAAGAAAGTAAG
1 TAAGTAAGCAAG
12553484 TAA
1 TAA
12553487 AGAAGAAGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:12558994 original size:26 final size:27
Alignment explanation
Indices: 12558948--12559000 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
12558938 TTTTCTTCTA
* *
12558948 ATTTGGACTTATTTTTTTTTTA-TTTT
1 ATTTGGAATTATTTTTATTTTAGTTTT
12558974 ATTTGGAATT-TTTTTAATTTTAGTTTT
1 ATTTGGAATTATTTTT-ATTTTAGTTTT
12559001 TAAGTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 5 0.22
26 14 0.61
27 4 0.17
ACGTcount: A:0.19, C:0.02, G:0.09, T:0.70
Consensus pattern (27 bp):
ATTTGGAATTATTTTTATTTTAGTTTT
Found at i:12565406 original size:19 final size:18
Alignment explanation
Indices: 12565372--12565417 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
12565362 AAATGAACAC
*
12565372 AAATAATATTAATAAAAATA
1 AAATAA-ATGAAT-AAAATA
12565392 AAATAAATGAATAAAATA
1 AAATAAATGAATAAAATA
12565410 ATAATAAA
1 A-AATAAA
12565418 CTATGAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 11 0.46
20 6 0.25
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAATGAATAAAATA
Found at i:12570641 original size:41 final size:41
Alignment explanation
Indices: 12570596--12570678 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
12570586 ATTGGAATTG
12570596 TAGACGACATAATTATCCATCGAAGGATTTGAATTAAATGC
1 TAGACGACATAATTATCCATCGAAGGATTTGAATTAAATGC
12570637 TAGACGACATAATTATCCATCGAAGGATTTGAATTAAATGC
1 TAGACGACATAATTATCCATCGAAGGATTTGAATTAAATGC
12570678 T
1 T
12570679 CACTTTGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (41 bp):
TAGACGACATAATTATCCATCGAAGGATTTGAATTAAATGC
Found at i:12573735 original size:16 final size:17
Alignment explanation
Indices: 12573714--12573746 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12573704 TTACTTTTGA
*
12573714 CTTTTTC-TAGATTTTT
1 CTTTTTCGTACATTTTT
12573730 CTTTTTCGTACATTTTT
1 CTTTTTCGTACATTTTT
12573747 GCCTGGCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.15, G:0.06, T:0.67
Consensus pattern (17 bp):
CTTTTTCGTACATTTTT
Found at i:12577287 original size:13 final size:13
Alignment explanation
Indices: 12577269--12577293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12577259 GTGGATGACG
12577269 ATCCTCAAGAGGA
1 ATCCTCAAGAGGA
12577282 ATCCTCAAGAGG
1 ATCCTCAAGAGG
12577294 CTGAAGATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (13 bp):
ATCCTCAAGAGGA
Found at i:12579746 original size:18 final size:18
Alignment explanation
Indices: 12579723--12579757 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12579713 AGATCAGCCT
*
12579723 AAAAATGCAAAACGAAAG
1 AAAAATGCAAAAAGAAAG
*
12579741 AAAAATTCAAAAAGAAA
1 AAAAATGCAAAAAGAAA
12579758 AAGTAATACA
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:0.71, C:0.09, G:0.11, T:0.09
Consensus pattern (18 bp):
AAAAATGCAAAAAGAAAG
Found at i:12581082 original size:27 final size:27
Alignment explanation
Indices: 12581052--12581249 Score: 221
Period size: 27 Copynumber: 7.4 Consensus size: 27
12581042 GGTATAACAT
*
12581052 TCATTTTACCCAATAT-GGGTATTTCGG
1 TCATTTTACCC-ATATGGGGTATTTTGG
* * *
12581079 TCATTTTA-CCTTATGGGAGAATTTCGG
1 TCATTTTACCCATATGGG-GTATTTTGG
*
12581106 TCATTCTACCC-TATGGAGGTATTTTGG
1 TCATTTTACCCATATGG-GGTATTTTGG
*
12581133 TCATTTTA-CCTTATAGGGGTATTTTGG
1 TCATTTTACCCATAT-GGGGTATTTTGG
*
12581160 TCATTTTACCC-TATGGGGCATTTTGG
1 TCATTTTACCCATATGGGGTATTTTGG
*
12581186 TCATTTTACCC-TATGGGGGTATTTTGA
1 TCATTTTACCCATAT-GGGGTATTTTGG
12581213 TCATTTTA-CCATATGGGAGTATTTTGG
1 TCATTTTACCCATATGGG-GTATTTTGG
12581240 TCATTTTACC
1 TCATTTTACC
12581250 TATTTTAGGG
Statistics
Matches: 150, Mismatches: 10, Indels: 21
0.83 0.06 0.12
Matches are distributed among these distances:
25 3 0.02
26 36 0.24
27 103 0.69
28 8 0.05
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCATATGGGGTATTTTGG
Found at i:12581110 original size:54 final size:52
Alignment explanation
Indices: 12581052--12581250 Score: 256
Period size: 54 Copynumber: 3.7 Consensus size: 52
12581042 GGTATAACAT
* * *
12581052 TCATTTTACCCAATAT-GGGTATTTCGGTCATTTTACCTTATGGGAGAATTTCGG
1 TCATTTTACCC--TATGGGGTATTTTGGTCATTTTACCTTATGGG-GTATTTTGG
*
12581106 TCATTCTACCCTATGGAGGTATTTTGGTCATTTTACCTTATAGGGGTATTTTGG
1 TCATTTTACCCTATGG-GGTATTTTGGTCATTTTACCTTAT-GGGGTATTTTGG
* * *
12581160 TCATTTTACCCTATGGGGCATTTTGGTCATTTTACCCTATGGGGGTATTTTGA
1 TCATTTTACCCTATGGGGTATTTTGGTCATTTTACCTTAT-GGGGTATTTTGG
*
12581213 TCATTTTACCATATGGGAGTATTTTGGTCATTTTACCT
1 TCATTTTACCCTATGGG-GTATTTTGGTCATTTTACCT
12581251 ATTTTAGGGT
Statistics
Matches: 129, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
52 3 0.02
53 50 0.39
54 73 0.57
55 3 0.02
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.44
Consensus pattern (52 bp):
TCATTTTACCCTATGGGGTATTTTGGTCATTTTACCTTATGGGGTATTTTGG
Found at i:12581222 original size:80 final size:81
Alignment explanation
Indices: 12581052--12581249 Score: 276
Period size: 80 Copynumber: 2.5 Consensus size: 81
12581042 GGTATAACAT
* * *
12581052 TCATTTTACCCA-ATATGGGTATTTCGGTCATTTTACCTTATGGGAGAATTTCGGTCATTCTACC
1 TCATTTTA-CCATATAGGGGTATTTTGGTCATTTTACCCTATGGGAGAATTTCGGTCATTCTACC
*
12581116 CTATGGAGGTATTTTGG
65 CTATGGAGGTATTTTGA
* * * *
12581133 TCATTTTACCTTATAGGGGTATTTTGGTCATTTTACCCTATGGG-GCATTTTGGTCATTTTACCC
1 TCATTTTACCATATAGGGGTATTTTGGTCATTTTACCCTATGGGAGAATTTCGGTCATTCTACCC
*
12581197 TATGGGGGTATTTTGA
66 TATGGAGGTATTTTGA
12581213 TCATTTTACCATAT-GGGAGTATTTTGGTCATTTTACC
1 TCATTTTACCATATAGGG-GTATTTTGGTCATTTTACC
12581250 TATTTTAGGG
Statistics
Matches: 105, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
79 3 0.03
80 65 0.62
81 37 0.35
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (81 bp):
TCATTTTACCATATAGGGGTATTTTGGTCATTTTACCCTATGGGAGAATTTCGGTCATTCTACCC
TATGGAGGTATTTTGA
Found at i:12585681 original size:41 final size:41
Alignment explanation
Indices: 12585624--12585773 Score: 210
Period size: 41 Copynumber: 3.7 Consensus size: 41
12585614 TGTAGATAGC
** * ** *
12585624 GATTCATGCTTTGTGCCTAGCAATCTTAATGTTGGTGTGTT
1 GATTCATGCTTTGTGCCTAGCAGGCTTAGTGCCGGTGTATT
*
12585665 GATTCAAGCTTTGTGCCTAGCAGGCTTAGTGCCGGTGTATT
1 GATTCATGCTTTGTGCCTAGCAGGCTTAGTGCCGGTGTATT
* * *
12585706 GATTTAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGTATT
1 GATTCATGCTTTGTGCCTAGCAGGCTTAGTGCCGGTGTATT
12585747 GATTCATGCTTTGTGCCTAGCAGGCTT
1 GATTCATGCTTTGTGCCTAGCAGGCTT
12585774 TGTAACACCT
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 97 1.00
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.38
Consensus pattern (41 bp):
GATTCATGCTTTGTGCCTAGCAGGCTTAGTGCCGGTGTATT
Found at i:12586531 original size:34 final size:34
Alignment explanation
Indices: 12586488--12586563 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
12586478 TAGCAAAAAG
12586488 ACATAAAATTTACCACATTGCCTTTCATTCCCAA
1 ACATAAAATTTACCACATTGCCTTTCATTCCCAA
12586522 ACATAAAATTTACCACATTGCCTTTCATTCCCAA
1 ACATAAAATTTACCACATTGCCTTTCATTCCCAA
*
12586556 AAATAAAA
1 ACATAAAA
12586564 ATAAGCAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.30
Consensus pattern (34 bp):
ACATAAAATTTACCACATTGCCTTTCATTCCCAA
Found at i:12602170 original size:21 final size:21
Alignment explanation
Indices: 12602127--12602170 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
12602117 TTATAAAATT
* *
12602127 ATTTAAAAAATATTTCATAAA
1 ATTTAAAAAATATATAATAAA
* *
12602148 ATTTTAAAAATATATAATGAA
1 ATTTAAAAAATATATAATAAA
12602169 AT
1 AT
12602171 ACAGATTCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTTAAAAAATATATAATAAA
Found at i:12602537 original size:2 final size:2
Alignment explanation
Indices: 12602532--12602574 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
12602522 GCTTTTTTTC
* *
12602532 CT CT CT C- CT CC CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12602573 CT
1 CT
12602575 TAGGTGAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:12602816 original size:10 final size:11
Alignment explanation
Indices: 12602799--12602835 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
12602789 AAAGAGCAAC
12602799 AAAGAGGAAAG
1 AAAGAGGAAAG
*
12602810 AAA-AGGAGAG
1 AAAGAGGAAAG
12602820 AAAGAGG-AAG
1 AAAGAGGAAAG
12602830 AAAGAG
1 AAAGAG
12602836 ACGACACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (11 bp):
AAAGAGGAAAG
Found at i:12615596 original size:31 final size:31
Alignment explanation
Indices: 12615561--12615664 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
12615551 CAATCTCGAT
*
12615561 TAGTTGGGTGACCAAAAAAGAAAAGAGGCAC
1 TAGTTGGGTGACCAAAAAAGAAAAGAGGCAA
* * * **
12615592 TAGTTAGGTGACCAAACTAA-AATA-A-TTAA
1 TAGTTGGGTGACCAAA-AAAGAAAAGAGGCAA
12615621 TAGTTGGGTGACCAAAAAAGAAAAG-GGACAA
1 TAGTTGGGTGACCAAAAAAGAAAAGAGG-CAA
*
12615652 TAGTTGGATGACC
1 TAGTTGGGTGACC
12615665 TATGGTGTAG
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
28 2 0.04
29 19 0.34
30 1 0.02
31 32 0.57
32 2 0.04
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (31 bp):
TAGTTGGGTGACCAAAAAAGAAAAGAGGCAA
Found at i:12622271 original size:24 final size:24
Alignment explanation
Indices: 12622240--12622302 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
12622230 AATATAAAAA
*
12622240 AATAATACAGT-ATAACTTTTA-AGT
1 AATAATACA-TAATAA-TTTTAGAAT
12622264 AATAATACATAATAATTTTAGAAT
1 AATAATACATAATAATTTTAGAAT
* *
12622288 AATAATGCACAATAA
1 AATAATACATAATAA
12622303 GTTCAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.18
24 28 0.82
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.33
Consensus pattern (24 bp):
AATAATACATAATAATTTTAGAAT
Found at i:12622754 original size:25 final size:25
Alignment explanation
Indices: 12622706--12622754 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12622696 CAAATCGAAA
* **
12622706 CAAAAATGAAATAAAAGATTAAAAT
1 CAAAAAGGAAATAAAAGAAAAAAAT
*
12622731 CAAAAAGGAAATAAAATAAAAAAA
1 CAAAAAGGAAATAAAAGAAAAAAA
12622755 AGTATCGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (25 bp):
CAAAAAGGAAATAAAAGAAAAAAAT
Found at i:12625139 original size:25 final size:25
Alignment explanation
Indices: 12625105--12625154 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
12625095 TAGCACCCTC
12625105 ATAACGCCCAAAAATTGGTACCTAG
1 ATAACGCCCAAAAATTGGTACCTAG
12625130 ATAACGCCCAAAAATTGGTACCTAG
1 ATAACGCCCAAAAATTGGTACCTAG
12625155 TTAATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (25 bp):
ATAACGCCCAAAAATTGGTACCTAG
Found at i:12626146 original size:18 final size:19
Alignment explanation
Indices: 12626107--12626146 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
12626097 AGAATATTTT
* *
12626107 TTAAAAATATATATATAGA
1 TTAAAAATATATAAATACA
12626126 TTAAAAATA-ATAAATACA
1 TTAAAAATATATAAATACA
12626144 TTA
1 TTA
12626147 TCGAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
TTAAAAATATATAAATACA
Found at i:12630481 original size:25 final size:26
Alignment explanation
Indices: 12630430--12630491 Score: 99
Period size: 25 Copynumber: 2.4 Consensus size: 26
12630420 ATAAAAAATA
12630430 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAAC-TTTTTTATTT
*
12630457 ATCAAAATATTATAA-TTTTTTATTT
1 ACCAAAATATTATAACTTTTTTATTT
12630482 ACCAAAATAT
1 ACCAAAATAT
12630492 ACAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 19 0.58
27 14 0.42
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (26 bp):
ACCAAAATATTATAACTTTTTTATTT
Found at i:12630586 original size:27 final size:26
Alignment explanation
Indices: 12630556--12630631 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
12630546 CACCCTGGTC
12630556 GTGCCAAGGTGATTGGCGGCACCAAAG
1 GTGCCAA-GTGATTGGCGGCACCAAAG
* *
12630583 GTGCCAAAGTGATTGGCGGCATCAATG
1 GTGCC-AAGTGATTGGCGGCACCAAAG
*
12630610 GTGCCATACTGATTGGCGGCAC
1 GTGCCA-AGTGATTGGCGGCAC
12630632 TACTCGTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.02
27 40 0.93
28 2 0.05
ACGTcount: A:0.24, C:0.22, G:0.34, T:0.20
Consensus pattern (26 bp):
GTGCCAAGTGATTGGCGGCACCAAAG
Found at i:12630746 original size:11 final size:11
Alignment explanation
Indices: 12630714--12630754 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
12630704 AAGTGCTGCG
12630714 GAAAAA-AAGA
1 GAAAAAGAAGA
*
12630724 GAAAAAG-TGA
1 GAAAAAGAAGA
*
12630734 GAAAGAGAAGA
1 GAAAAAGAAGA
12630745 GAAAAAGAAG
1 GAAAAAGAAG
12630755 GTATTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.02
Consensus pattern (11 bp):
GAAAAAGAAGA
Found at i:12630802 original size:21 final size:21
Alignment explanation
Indices: 12630778--12630820 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12630768 AATAATTGAT
12630778 TATATTGT-TATTATTGTTTTG
1 TATATTGTGTATTATT-TTTTG
*
12630799 TATATTTTGTATTATTTTTTG
1 TATATTGTGTATTATTTTTTG
12630820 T
1 T
12630821 TTTAGTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.70
Consensus pattern (21 bp):
TATATTGTGTATTATTTTTTG
Found at i:12630880 original size:3 final size:3
Alignment explanation
Indices: 12630872--12630903 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12630862 TTTTAGTTAG
12630872 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12630904 AGGTATTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:12634021 original size:11 final size:11
Alignment explanation
Indices: 12634005--12634031 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12633995 GCTTATGCTT
12634005 AAATTGTATCC
1 AAATTGTATCC
12634016 AAATTGTATCC
1 AAATTGTATCC
12634027 AAATT
1 AAATT
12634032 AAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:12636818 original size:27 final size:27
Alignment explanation
Indices: 12636764--12636818 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
12636754 TTAGTCACAT
* **
12636764 ATTGGTGCCGTCTTTTTATTCCTTTCC
1 ATTGGTGCCGCCTTTTTATTCCCCTCC
12636791 ATTGGTGCCGCCTTTTTATTCCCCTCC
1 ATTGGTGCCGCCTTTTTATTCCCCTCC
12636818 A
1 A
12636819 CCCTCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.09, C:0.31, G:0.15, T:0.45
Consensus pattern (27 bp):
ATTGGTGCCGCCTTTTTATTCCCCTCC
Found at i:12637555 original size:3 final size:3
Alignment explanation
Indices: 12637549--12637640 Score: 54
Period size: 3 Copynumber: 32.3 Consensus size: 3
12637539 CTTCCTTCCC
* * *
12637549 TCT TCT TCT TCT TCT TCT T-T TTT TCT T-T TCT CCT T-T CCT T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
12637593 T-T CCT TCT TTT TCTT TCT T-T T-T TCT TCT CCTT TCC TCT TCT TCT
1 TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT
12637637 TCT T
1 TCT T
12637641 TCTTTTTTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
2 12 0.18
3 51 0.75
4 5 0.07
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:12637572 original size:36 final size:36
Alignment explanation
Indices: 12637525--12637730 Score: 167
Period size: 37 Copynumber: 5.6 Consensus size: 36
12637515 AATTACCTTT
*
12637525 TTTTCTTTTTTTTCCT-TCCTTCCCTCTTCTTCTTC
1 TTTTCTTTTTTTTCCTCTCCTTTCCTCTTCTTCTTC
** *
12637560 TTCTTCTTTTTTTCTTTTCTCCTTTCCTTTTCTTTCCTTC
1 TT-TTCTTTTTTT-TCCTCTCCTTTCCTCTTC-TT-CTTC
*
12637600 TTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTC
1 -TTTTC-TT-TTTTTTCCTCTCCTTTCCTCTTCTTCTTC
*
12637639 -TTTCTTTTTTTTCCCTTCTCCTTTCCTTTTCTTTCCTTC
1 TTTTCTTTTTTTT-CC-TCTCCTTTCCTCTTC-TT-CTTC
*
12637678 TTTT-TCTTTCTTTCCTCTCCTTT-CT-TTC-T-TTC
1 TTTTCT-TTTTTTTCCTCTCCTTTCCTCTTCTTCTTC
* *
12637710 -TTTCTTTCTTTCCCTCTCCTT
1 TTTTCTTTTTTTTCCTCTCCTT
12637731 CCCCCCCCAA
Statistics
Matches: 144, Mismatches: 12, Indels: 34
0.76 0.06 0.18
Matches are distributed among these distances:
31 16 0.11
32 4 0.03
34 1 0.01
35 8 0.06
36 16 0.11
37 22 0.15
38 21 0.15
39 13 0.09
40 18 0.12
41 20 0.14
42 5 0.03
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (36 bp):
TTTTCTTTTTTTTCCTCTCCTTTCCTCTTCTTCTTC
Found at i:12637587 original size:43 final size:42
Alignment explanation
Indices: 12637521--12637691 Score: 121
Period size: 40 Copynumber: 4.2 Consensus size: 42
12637511 TAAAAATTAC
*
12637521 CTTTTTTTCTTTTTTTTCC-TTCCTTCCCTCTTCTTCTTCTTCTT
1 CTTTTTTTC--TTTTCTCCTTTCCTT-CCTCTTCTTCTTCTTCTT
* * *
12637565 CTTTTTTTCTTTTCTCCTTTCCTT-TTCTT-TCCTTCTTTTT
1 CTTTTTTTCTTTTCTCCTTTCCTTCCTCTTCTTCTTCTTCTT
*
12637605 CTTTCTTTT-TTCTTCTCCTTTCC-TCTTCTTCTTC-T-TTC-T
1 CTTT-TTTTCTT-TTCTCCTTTCCTTCCTCTTCTTCTTCTTCTT
** * * *
12637644 -TTTTTTTCCCTTCTCCTTTCCTT-TTCTT-TCCTTCTTTTT
1 CTTTTTTTCTTTTCTCCTTTCCTTCCTCTTCTTCTTCTTCTT
*
12637683 CTTTCTTTC
1 CTTTTTTTC
12637692 CTCTCCTTTC
Statistics
Matches: 105, Mismatches: 11, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
36 2 0.02
37 21 0.20
38 6 0.06
39 2 0.02
40 25 0.24
41 25 0.24
42 9 0.09
43 6 0.06
44 9 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (42 bp):
CTTTTTTTCTTTTCTCCTTTCCTTCCTCTTCTTCTTCTTCTT
Found at i:12637596 original size:10 final size:10
Alignment explanation
Indices: 12637581--12637717 Score: 61
Period size: 10 Copynumber: 14.5 Consensus size: 10
12637571 TTCTTTTCTC
12637581 CTTTCCTTTT
1 CTTTCCTTTT
12637591 CTTTCCTTCTT
1 CTTTCCTT-TT
12637602 -TTT-C-TTT
1 CTTTCCTTTT
12637609 C-TT--TTTT
1 CTTTCCTTTT
*
12637616 CTTCTCCTTTC
1 CTT-TCCTTTT
12637627 CTCTT-CTTCTT
1 CT-TTCCTT-TT
12637638 CTTT-CTTTT
1 CTTTCCTTTT
* *
12637647 TTTTCCCTTCTC
1 CTTT-CCTT-TT
12637659 CTTTCCTTTT
1 CTTTCCTTTT
12637669 CTTTCCTTCTT
1 CTTTCCTT-TT
12637680 -TTT-C-TTT
1 CTTTCCTTTT
* *
12637687 CTTTCCTCTC
1 CTTTCCTTTT
12637697 CTTT-C-TTT
1 CTTTCCTTTT
12637705 CTTT-C-TTT
1 CTTTCCTTTT
12637713 CTTTC
1 CTTTC
12637718 TTTCCCTCTC
Statistics
Matches: 100, Mismatches: 10, Indels: 35
0.69 0.07 0.24
Matches are distributed among these distances:
7 10 0.10
8 19 0.19
9 10 0.10
10 36 0.36
11 20 0.20
12 5 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:12637609 original size:4 final size:4
Alignment explanation
Indices: 12637588--12637721 Score: 72
Period size: 4 Copynumber: 34.0 Consensus size: 4
12637578 CTCCTTTCCT
*
12637588 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
* * * *
12637633 -TTC -TTC TTTC TTT- TTT- TTCC CTTC -TCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C -TTTC TTTC TTTC
*
12637678 -TT- TTTC TTTC TTTCC TCTCC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC
12637722 CCTCTCCTTC
Statistics
Matches: 106, Mismatches: 9, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
3 24 0.23
4 61 0.58
5 12 0.11
6 9 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:12637660 original size:78 final size:80
Alignment explanation
Indices: 12637522--12637690 Score: 258
Period size: 78 Copynumber: 2.1 Consensus size: 80
12637512 AAAAATTACC
**
12637522 TTTT-TTTCTTTTTTTTCCTTCCTTCCCTCTTCTTCTTCTTCTTCTTTTTTTCTTTTCTCCTTTC
1 TTTTCTTTCTTTTTTTTCCTTCCTTCCCTCTTCTTCTTCTTCTTCTTTTTTTCCCTTCTCCTTTC
12637586 CTTTTCTTTCCTTCT
66 CTTTTCTTTCCTTCT
*
12637601 TTTTCTTTCTTTTTTCTT-C-TCCTTTCCTCTTCTTCTTC-T-TTCTTTTTTTTCCCTTCTCCTT
1 TTTTCTTTCTTTTTT-TTCCTTCCTTCCCTCTTCTTCTTCTTCTTC-TTTTTTTCCCTTCTCCTT
12637662 TCCTTTTCTTTCCTTCT
64 TCCTTTTCTTTCCTTCT
12637679 TTTTCTTTCTTT
1 TTTTCTTTCTTT
12637691 CCTCTCCTTT
Statistics
Matches: 84, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
77 3 0.04
78 46 0.55
79 22 0.26
80 11 0.13
81 2 0.02
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (80 bp):
TTTTCTTTCTTTTTTTTCCTTCCTTCCCTCTTCTTCTTCTTCTTCTTTTTTTCCCTTCTCCTTTC
CTTTTCTTTCCTTCT
Found at i:12637715 original size:78 final size:75
Alignment explanation
Indices: 12637520--12637720 Score: 234
Period size: 78 Copynumber: 2.7 Consensus size: 75
12637510 ATAAAAATTA
* * **
12637520 CCTT-TTTTTCTTTTTTTTCCT-TCCTTCCCTCTTCTTCTTCTTC-TTCTTTTTTTCTTTTCTCC
1 CCTTCTTTTTC-TTTCTTTCCTCTCCTT-TCT-TTCTTCTTCTTCTTTCTTTTTTTCCCTTCTCC
12637582 TTTCCTTTTCTTT
63 TTTCCTTTTCTTT
* *
12637595 CCTTCTTTTTCTTTCTTTTTTCTTCTCCTTTC-CTCTTCTTCTTCTTTCTTTTTTTTCCCTTCTC
1 CCTTCTTTTTCTTTC---TTTCCTCTCCTTTCTTTCTTCTTCTTCTTTC-TTTTTTTCCCTTCTC
12637659 CTTTCCTTTTCTTT
62 CTTTCCTTTTCTTT
12637673 CCTTCTTTTTCTTTCTTTCCTCTCCTTTCTTTC-T-TTCTTTCTTTCTTT
1 CCTTCTTTTTCTTTCTTTCCTCTCCTTTCTTTCTTCTTC-TTCTTTCTTT
12637721 CCCTCTCCTT
Statistics
Matches: 109, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
74 6 0.06
75 28 0.26
76 19 0.17
77 3 0.03
78 48 0.44
79 5 0.05
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (75 bp):
CCTTCTTTTTCTTTCTTTCCTCTCCTTTCTTTCTTCTTCTTCTTTCTTTTTTTCCCTTCTCCTTT
CCTTTTCTTT
Found at i:12637719 original size:40 final size:35
Alignment explanation
Indices: 12637563--12637730 Score: 127
Period size: 36 Copynumber: 4.7 Consensus size: 35
12637553 CTTCTTCTTC
* *
12637563 TTCTTT-TTTTCTTTTCTCCTT-TCCTTTTCTTTCCT
1 TTCTTTCTTTT-TTTTC-CCTTCTCCTTTCCTTTTCT
* * *
12637598 TCTTTTTCTTTCTTTTT-TCTTCTCCTTTCCTCTTCTT
1 T-TCTTTCTTT-TTTTTCCCTTCTCCTTTCCTTTTC-T
12637635 CTTCTTTCTTTTTTTTCCCTTCTCCTTTCCTTTTCT
1 -TTCTTTCTTTTTTTTCCCTTCTCCTTTCCTTTTCT
*
12637671 TTCCTTCTTTTTCTTTCTTTCC-TCTCCTTT-C-TTTCT
1 TTCTTTCTTTTT-TTTC---CCTTCTCCTTTCCTTTTCT
*
12637707 TTCTTTC-TTTCTTTCCC-TCTCCTT
1 TTCTTTCTTTTTTTTCCCTTCTCCTT
12637731 CCCCCCCCAA
Statistics
Matches: 111, Mismatches: 11, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
31 9 0.08
34 4 0.04
35 18 0.16
36 35 0.32
37 33 0.30
38 10 0.09
39 2 0.02
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (35 bp):
TTCTTTCTTTTTTTTCCCTTCTCCTTTCCTTTTCT
Found at i:12637805 original size:27 final size:27
Alignment explanation
Indices: 12637765--12637843 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
12637755 TATTATAACA
* **
12637765 TTGGTGCCGTCAATGTCTTTGGCACCT
1 TTGGTGCCGCCAATCACTTTGGCACCT
12637792 TTGGTGCCGCCAATCACTTTGGCACCT
1 TTGGTGCCGCCAATCACTTTGGCACCT
* *
12637819 TTGGTACCGCCAATCACATTGGCAC
1 TTGGTGCCGCCAATCACTTTGGCAC
12637844 GACCAGGGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.16, C:0.30, G:0.23, T:0.30
Consensus pattern (27 bp):
TTGGTGCCGCCAATCACTTTGGCACCT
Found at i:12637971 original size:27 final size:27
Alignment explanation
Indices: 12637900--12637990 Score: 166
Period size: 27 Copynumber: 3.4 Consensus size: 27
12637890 TTTTTTTGTT
12637900 ATATTTTGGTAAATAAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
12637926 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAAT-AAAAAAAGTTATA
12637954 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
12637981 ATATTTTGGT
1 ATATTTTGGT
12637991 TATTTTTTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
26 14 0.22
27 30 0.48
28 19 0.30
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:12639255 original size:15 final size:15
Alignment explanation
Indices: 12639235--12639264 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12639225 ATAAAGAGAG
12639235 CTATAGCAAGTCTAT
1 CTATAGCAAGTCTAT
12639250 CTATAGCAAGTCTAT
1 CTATAGCAAGTCTAT
12639265 TTTTTTAACT
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:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
CTATAGCAAGTCTAT
Found at i:12640457 original size:20 final size:19
Alignment explanation
Indices: 12640419--12640457 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12640409 TTATCCTAGA
*
12640419 CCACACGGCCTGGACCCTT
1 CCACACGACCTGGACCCTT
*
12640438 CCACACGACCATGTACCCTT
1 CCACACGACC-TGGACCCTT
12640458 GTAATGCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.46, G:0.15, T:0.18
Consensus pattern (19 bp):
CCACACGACCTGGACCCTT
Found at i:12641517 original size:103 final size:103
Alignment explanation
Indices: 12641338--12641544 Score: 378
Period size: 103 Copynumber: 2.0 Consensus size: 103
12641328 TTTTTTTACA
**
12641338 TTGTCTATTCGGCTGGTAATATTTCAGCCTATAAACAGTCTATCTTGTAAAAATTTGAAGGTTAC
1 TTGTCTATTCAACTGGTAATATTTCAGCCTATAAACAGTCTATCTTGTAAAAATTTGAAGGTTAC
12641403 ATTACTTTTGACATATATAAACTTTGTGAGTTATTCAC
66 ATTACTTTTGACATATATAAACTTTGTGAGTTATTCAC
* *
12641441 TTGTCTATTCAACTGGTAATATTTCAGCCTATAAATAGTTTATCTTGTAAAAATTTGAAGGTTAC
1 TTGTCTATTCAACTGGTAATATTTCAGCCTATAAACAGTCTATCTTGTAAAAATTTGAAGGTTAC
12641506 ATTACTTTTGACATATATAAACTTTGTGAGTTATTCAC
66 ATTACTTTTGACATATATAAACTTTGTGAGTTATTCAC
12641544 T
1 T
12641545 CTCGATTTTC
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (103 bp):
TTGTCTATTCAACTGGTAATATTTCAGCCTATAAACAGTCTATCTTGTAAAAATTTGAAGGTTAC
ATTACTTTTGACATATATAAACTTTGTGAGTTATTCAC
Found at i:12652969 original size:42 final size:42
Alignment explanation
Indices: 12652844--12652970 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 42
12652834 TTTCGCCTTC
* * *
12652844 TAAAAGGGATGAAAGGTTAAAAACACCTATACATACCCCTAG
1 TAAAAGGGATGAAAGGTTAAAAACACCTGTACATACACCAAG
** * *
12652886 TGTAAGGGATGAAAGGTTAAAAACACCAGTAAATACACCAAG
1 TAAAAGGGATGAAAGGTTAAAAACACCTGTACATACACCAAG
* * *
12652928 TAAAAAGGATGAAAGGTTAAAAACACCTGTGCATACTCCAAG
1 TAAAAGGGATGAAAGGTTAAAAACACCTGTACATACACCAAG
12652970 T
1 T
12652971 GGGCGATTTT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.19
Consensus pattern (42 bp):
TAAAAGGGATGAAAGGTTAAAAACACCTGTACATACACCAAG
Found at i:12662956 original size:43 final size:44
Alignment explanation
Indices: 12662878--12663064 Score: 213
Period size: 43 Copynumber: 4.3 Consensus size: 44
12662868 GTGTCGGTAA
** *
12662878 CTTTAGCGGCGCTT-TTTATAATAAACGCCGCTATAGACCATGGT
1 CTTTAGCGGCGCTTATCCAT-ACAAACGCCGCTATAGACCATGGT
*
12662922 CTTTAGCGGCGCTTATCCATA-AAACGCCGCTATAGACCATGAT
1 CTTTAGCGGCGCTTATCCATACAAACGCCGCTATAGACCATGGT
* * * *
12662965 CTTTCGCGGTGCTTACCCAT-CAAACGCCGCTATAGACCTTGGT
1 CTTTAGCGGCGCTTATCCATACAAACGCCGCTATAGACCATGGT
* * *
12663008 CTTTAGCGGCGCTTA-ACAAACAAACGTCGCTATAG-CTCATGGT
1 CTTTAGCGGCGCTTATCCATACAAACGCCGCTATAGAC-CATGGT
*
12663051 TTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
12663065 TTAGAAAAAC
Statistics
Matches: 124, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
42 3 0.02
43 103 0.83
44 15 0.12
45 3 0.02
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (44 bp):
CTTTAGCGGCGCTTATCCATACAAACGCCGCTATAGACCATGGT
Found at i:12663449 original size:21 final size:21
Alignment explanation
Indices: 12663383--12663452 Score: 97
Period size: 21 Copynumber: 3.3 Consensus size: 21
12663373 TTTAAGCTGT
12663383 TCTGCTTCCCTCGCTGCAGCA
1 TCTGCTTCCCTCGCTGCAGCA
* *
12663404 TCTACTTCCCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCA
*
12663425 TCTGCTTCTCTCGCTGTC-GCA
1 TCTGCTTCCCTCGCTG-CAGCA
12663446 TCTGCTT
1 TCTGCTT
12663453 TAAGTTACTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.07, C:0.41, G:0.17, T:0.34
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTGCAGCA
Found at i:12663536 original size:21 final size:21
Alignment explanation
Indices: 12663496--12663536 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12663486 GAACCTCAGC
** *
12663496 TTCTCTCGCTGTTGCCTCTGT
1 TTCTCTCGCTGCCGCATCTGT
12663517 TTCTCTCGCTGCCGCATCTG
1 TTCTCTCGCTGCCGCATCTG
12663537 CTTTAAGTTG
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:0.02, C:0.37, G:0.20, T:0.41
Consensus pattern (21 bp):
TTCTCTCGCTGCCGCATCTGT
Found at i:12663563 original size:87 final size:87
Alignment explanation
Indices: 12663408--12663602 Score: 277
Period size: 87 Copynumber: 2.2 Consensus size: 87
12663398 GCAGCATCTA
* ** * *
12663408 CTTCCCTCGCTGCAGCCTCTGCTTCTCTCGCTGTCGCATCTGCTTTAAGTTACTGCTGGAGTTGT
1 CTTCTCTCGCTGTTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTTACTGCTGGAGTTCT
12663473 TCATA-CTTTCGTTGAACCTCAG
66 TCATATCTTT-GTTGAACCTCAG
* *
12663495 CTTCTCTCGCTGTTGCCTCTGTTTCTCTCGCTGCCGCATCTGCTTTAAGTT-GTAGCTGGAGTTC
1 CTTCTCTCGCTGTTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTTACT-GCTGGAGTTC
*
12663559 TTCATATCTTTTTTGAACCTCAG
65 TTCATATCTTTGTTGAACCTCAG
*
12663582 CTTCTCTCGATGTTGCCTCTG
1 CTTCTCTCGCTGTTGCCTCTG
12663603 ATTTAAGTTG
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
86 1 0.01
87 92 0.95
88 4 0.04
ACGTcount: A:0.11, C:0.30, G:0.19, T:0.40
Consensus pattern (87 bp):
CTTCTCTCGCTGTTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTTACTGCTGGAGTTCT
TCATATCTTTGTTGAACCTCAG
Found at i:12666020 original size:16 final size:16
Alignment explanation
Indices: 12665999--12666029 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12665989 GTAAATGGAG
12665999 TTAGGGATTTCAGAAC
1 TTAGGGATTTCAGAAC
*
12666015 TTAGGGATTTTAGAA
1 TTAGGGATTTCAGAA
12666030 GAGGAAAAAT
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:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
TTAGGGATTTCAGAAC
Found at i:12667579 original size:23 final size:23
Alignment explanation
Indices: 12667536--12667580 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12667526 TGCTTTTGTA
*
12667536 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
12667559 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
12667581 AATTAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:12668921 original size:40 final size:42
Alignment explanation
Indices: 12668865--12668962 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 42
12668855 TAATAATTGG
* **
12668865 TTTTAGCGGCGTTTTTTTATGTAACGCCGCTAATGCTCGATA
1 TTTTAGCGGCGTTTTTTCATAAAACGCCGCTAATGCTCGATA
* *
12668907 TTTTA-CGGCG-TTTTTCGTAAAATGCCGCTAATGCTCGAT-
1 TTTTAGCGGCGTTTTTTCATAAAACGCCGCTAATGCTCGATA
* * *
12668946 TATTAGTGGTGTTTTTT
1 TTTTAGCGGCGTTTTTT
12668963 GTCCAAACGC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
39 4 0.09
40 27 0.59
41 10 0.22
42 5 0.11
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.44
Consensus pattern (42 bp):
TTTTAGCGGCGTTTTTTCATAAAACGCCGCTAATGCTCGATA
Found at i:12674802 original size:22 final size:20
Alignment explanation
Indices: 12674766--12674824 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
12674756 GGCTCGGCCT
12674766 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
12674788 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
12674809 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
12674825 TTTTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:12674826 original size:11 final size:11
Alignment explanation
Indices: 12674806--12674933 Score: 113
Period size: 11 Copynumber: 11.4 Consensus size: 11
12674796 TAAAAATTAA
12674806 AAAAAGTATTTT
1 AAAAA-TATTTT
12674818 AAAAATATTTT
1 AAAAATATTTT
12674829 AAAAATATTTT
1 AAAAATATTTT
12674840 AAAAATATTTT
1 AAAAATATTTT
*
12674851 AAAATTAATTTTTTTT
1 -AAA--AA--TATTTT
12674867 AAAAAGTATTTT
1 AAAAA-TATTTT
12674879 AAAAATATTTT
1 AAAAATATTTT
*
12674890 --AAA-A-TTA
1 AAAAATATTTT
* *
12674897 AAAAATA-ATA
1 AAAAATATTTT
12674907 AAAAAGTATTTT
1 AAAAA-TATTTT
12674919 AAAAATATTTT
1 AAAAATATTTT
12674930 AAAA
1 AAAA
12674934 TTAAAAAATT
Statistics
Matches: 99, Mismatches: 7, Indels: 21
0.78 0.06 0.17
Matches are distributed among these distances:
7 2 0.02
8 1 0.01
9 6 0.06
10 8 0.08
11 46 0.46
12 24 0.24
13 2 0.02
14 2 0.02
15 3 0.03
16 5 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:12674922 original size:40 final size:39
Alignment explanation
Indices: 12674816--12674950 Score: 182
Period size: 39 Copynumber: 3.4 Consensus size: 39
12674806 AAAAAGTATT
*
12674816 TTAAAAATATTTTAAAAA-TATTTTAAAAATATTTTAAAA
1 TTAAAAA-ATTTAAAAAAGTATTTTAAAAATATTTTAAAA
**** *
12674855 TTAATTTTTTTTAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAA
*
12674894 TTAAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAT-TTAAAAAAGTATTTTAAAAATATTTTAAAA
12674934 TTAAAAAATTTAAAAAA
1 TTAAAAAATTTAAAAAA
12674951 TAAATATATT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
38 9 0.11
39 37 0.45
40 37 0.45
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (39 bp):
TTAAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:12674944 original size:16 final size:17
Alignment explanation
Indices: 12674917--12674962 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
12674907 AAAAAGTATT
*
12674917 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
12674934 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
12674950 ATAAATATATTTA
1 TTAAAAATATTTA
12674963 TTATATCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:12675908 original size:30 final size:28
Alignment explanation
Indices: 12675869--12675950 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
12675859 TTTTTAAGAA
* *
12675869 TTTTAAAATATTTTTTATAAATTTTATATT
1 TTTTAAAATAATTTTAAT-AATTTTA-ATT
*
12675899 TTTTCAAATAATTTTAATAATTTTAATT
1 TTTTAAAATAATTTTAATAATTTTAATT
*
12675927 TTTAAAAATAAATTTT-ATAATTTT
1 TTTTAAAAT-AATTTTAATAATTTT
12675951 TTGAATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 18 0.39
29 13 0.28
30 15 0.33
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTAAAATAATTTTAATAATTTTAATT
Found at i:12675911 original size:20 final size:18
Alignment explanation
Indices: 12675876--12675914 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12675866 GAATTTTAAA
*
12675876 ATATTTTTTATAAATTTT
1 ATATTTTTTAAAAATTTT
12675894 ATATTTTTTCAAATAATTTT
1 ATATTTTTT-AAA-AATTTT
12675914 A
1 A
12675915 ATAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTTTTAAAAATTTT
Found at i:12675927 original size:28 final size:28
Alignment explanation
Indices: 12675869--12675965 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 28
12675859 TTTTTAAGAA
*
12675869 TTTTAAAATATTTTTTATAAATTTTATATT
1 TTTTAAAATA-ATTTTAT-AATTTTATATT
*
12675899 TTTTCAAATAATTTTAATAATTTTA-ATT
1 TTTTAAAATAATTTT-ATAATTTTATATT
* * *
12675927 TTTAAAAATAAATTTTATAATTTTTTGAAT
1 TTTTAAAAT-AATTTTATAATTTTAT-ATT
12675957 TTTTAAAAT
1 TTTTAAAAT
12675966 TTAAAATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
28 18 0.32
29 17 0.30
30 21 0.38
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTTAAAATAATTTTATAATTTTATATT
Found at i:12675961 original size:31 final size:28
Alignment explanation
Indices: 12675869--12675964 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 28
12675859 TTTTTAAGAA
* *
12675869 TTTT-AAAATATTTTTTATAAATTTTATAT
1 TTTTAAAAATAATTTTAAT-AATTTTA-AT
**
12675898 TTTTTCAAATAATTTTAATAATTTTAAT
1 TTTTAAAAATAATTTTAATAATTTTAAT
12675926 TTTTAAAAATAAATTTT-ATAATTTTTTGAAT
1 TTTTAAAAAT-AATTTTAATAA--TTTT-AAT
12675957 TTTTAAAA
1 TTTTAAAA
12675965 TTTAAAATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
28 14 0.25
29 17 0.30
30 15 0.26
31 11 0.19
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
TTTTAAAAATAATTTTAATAATTTTAAT
Found at i:12677752 original size:34 final size:35
Alignment explanation
Indices: 12677686--12677752 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
12677676 ATAAAACAAT
* * * **
12677686 TTATTTTTTAATTTAACATATAAAATTTAATTTAA
1 TTATTTTTTAATATAAAAAATAAAATACAATTTAA
12677721 TTATTTTTTAA-ATAAAAAATAAAATACAATTT
1 TTATTTTTTAATATAAAAAATAAAATACAATTT
12677753 TTCTCTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 16 0.59
35 11 0.41
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (35 bp):
TTATTTTTTAATATAAAAAATAAAATACAATTTAA
Found at i:12683071 original size:168 final size:166
Alignment explanation
Indices: 12682787--12683286 Score: 678
Period size: 168 Copynumber: 3.0 Consensus size: 166
12682777 ATCAGAGATT
* * *
12682787 GAATATCCATGCAAGAGCCATATTGAAGATCAGAAGAGTGATGATCAAATGTGTCTAAAACCTGT
1 GAATATCCATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATC-AGTGTGTCTAAAACCCGT
* * * *
12682852 CAAGGAAGAACCTAAAGATGATGTTTGTGATAAACCCTTGCATGGGACTCCTTCATGCAAGGAAA
65 CAAGGAAGAAGCTAAAGATGATGTTTGTGATAAA-CCTTGTATGAGACTCCTCCATGCAAGGAAA
* * * *
12682917 CTAAGAGGAAGAAATCACGATCACTATGTTCTAACACA
129 CTAGGAGGAAGAAATCACAATCACAATGTTCTAAAACA
* * *
12682955 GAATATCTATGCAAGAGCTATATTGAAGATCATAAGAGTGATGATCAGTTGTGTCTAAAACCCGT
1 GAATATCCATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAG-TGTGTCTAAAACCCGT
* *
12683020 CAAGGAAGAAGCTAAAGATGGTGTTTATGATGAAACCTTGTATGAGACTCCTCCATGCAA-GAAA
65 CAAGGAAGAAGCTAAAGATGATGTTTGTGAT-AAACCTTGTATGAGACTCCTCCATGCAAGGAAA
** **
12683084 GCTAGGAGGACTAAATCACAATCACAATGTTCTAAAATT
129 -CTAGGAGGAAGAAATCACAATCACAATGTTCTAAAACA
* * *
12683123 GAATATCCATGCAAGAGCCATATTGAAGATCACAAGAGTAAAGATCAAGTGAGTCTAAAACCCGT
1 GAATATCCATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATC-AGTGTGTCTAAAACCCGT
* *
12683188 CAAAGAAGAAGCTAAAGATGATGTTTGTCATAAAACCTTGTATGAGACTCCTCCATGCAAGGAAA
65 CAAGGAAGAAGCTAAAGATGATGTTTGTGAT-AAACCTTGTATGAGACTCCTCCATGCAAGGAAA
* * *
12683253 CTAGGAAGAAGAAACCGCAATCACAATGTTCTAA
129 CTAGGAGGAAGAAATCACAATCACAATGTTCTAA
12683287 GCCTCGAAAG
Statistics
Matches: 292, Mismatches: 35, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
167 5 0.02
168 278 0.95
169 9 0.03
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (166 bp):
GAATATCCATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAGTGTGTCTAAAACCCGTC
AAGGAAGAAGCTAAAGATGATGTTTGTGATAAACCTTGTATGAGACTCCTCCATGCAAGGAAACT
AGGAGGAAGAAATCACAATCACAATGTTCTAAAACA
Found at i:12686483 original size:16 final size:18
Alignment explanation
Indices: 12686464--12686503 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12686454 TATTATTTTT
*
12686464 TTAAAAATA-T-AATACA
1 TTAAAAATACTAAAAACA
12686480 TTAAAAATACTAAAAACA
1 TTAAAAATACTAAAAACA
12686498 TTAAAA
1 TTAAAA
12686504 TAAATGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 1 0.05
18 11 0.52
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (18 bp):
TTAAAAATACTAAAAACA
Found at i:12687533 original size:22 final size:22
Alignment explanation
Indices: 12687493--12687551 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
12687483 TCATAATAGT
* *
12687493 TCAGATA-AGGTGCAAAACAAA
1 TCAGATATAGATGCAGAACAAA
*
12687514 TCAGATATAGATGCAGAACATA
1 TCAGATATAGATGCAGAACAAA
*
12687536 TTAGA-ATCAGATGCAG
1 TCAGATAT-AGATGCAG
12687552 TTTCCTACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.28
22 23 0.72
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (22 bp):
TCAGATATAGATGCAGAACAAA
Found at i:12691744 original size:9 final size:9
Alignment explanation
Indices: 12691730--12691823 Score: 127
Period size: 9 Copynumber: 10.4 Consensus size: 9
12691720 GTAGTGATTC
12691730 AATTCGGTT
1 AATTCGGTT
12691739 AATTCGGTT
1 AATTCGGTT
12691748 AATTCGAG-T
1 AATTCG-GTT
**
12691757 AATTTAGTT
1 AATTCGGTT
*
12691766 AATTCGGGT
1 AATTCGGTT
*
12691775 AATCCGGTT
1 AATTCGGTT
12691784 AATTCGGTT
1 AATTCGGTT
*
12691793 AATTCGGGT
1 AATTCGGTT
12691802 AATTCGGTT
1 AATTCGGTT
12691811 AATTCGGTT
1 AATTCGGTT
12691820 AATT
1 AATT
12691824 TTTAACCAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
8 1 0.01
9 71 0.97
10 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:12703324 original size:22 final size:22
Alignment explanation
Indices: 12703296--12703339 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
12703286 GGGTAAGAAA
12703296 TTGCATCTGAT-TCTGATATGTT
1 TTGCATCT-ATATCTGATATGTT
12703318 TTGCATCTATATCTGATATGTT
1 TTGCATCTATATCTGATATGTT
12703340 CTACACCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (22 bp):
TTGCATCTATATCTGATATGTT
Found at i:12703353 original size:21 final size:22
Alignment explanation
Indices: 12703307--12703354 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12703297 TGCATCTGAT
* * *
12703307 TCTGATATGTTTTGCATCTATA
1 TCTGATATGTTCTACACCTATA
12703329 TCTGATATGTTCTACACCT-TA
1 TCTGATATGTTCTACACCTATA
12703350 TCTGA
1 TCTGA
12703355 ACTGGTACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (22 bp):
TCTGATATGTTCTACACCTATA
Found at i:12709028 original size:17 final size:17
Alignment explanation
Indices: 12709008--12709075 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 17
12708998 AAACGCACCA
12709008 TTTCATTTTCTTTTTAT
1 TTTCATTTTCTTTTTAT
*
12709025 TTTCATTTTATTTTTTAT
1 TTTCATTTT-CTTTTTAT
12709043 TTT--TCTTTCTTTTT-T
1 TTTCAT-TTTCTTTTTAT
*
12709058 CCCTTCATTTTCTTTTTA
1 --TTTCATTTTCTTTTTA
12709076 CATCCCCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
15 1 0.02
16 6 0.15
17 14 0.34
18 19 0.46
19 1 0.02
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTCATTTTCTTTTTAT
Found at i:12709192 original size:17 final size:17
Alignment explanation
Indices: 12709165--12709232 Score: 63
Period size: 16 Copynumber: 4.1 Consensus size: 17
12709155 ATTCTTCTCG
12709165 TTTTA-TTT-TTTATTT
1 TTTTATTTTCTTTATTT
12709180 TTTTATTTT-TTT-TGTT
1 TTTTATTTTCTTTAT-TT
*
12709196 TTTTCTTCTTCTTTATTT
1 TTTTATT-TTCTTTATTT
* *
12709214 TTCTATTTTCTTTCTTT
1 TTTTATTTTCTTTATTT
12709231 TT
1 TT
12709233 CTTTCCCCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.14
16 14 0.32
17 13 0.30
18 10 0.23
19 1 0.02
ACGTcount: A:0.07, C:0.09, G:0.01, T:0.82
Consensus pattern (17 bp):
TTTTATTTTCTTTATTT
Found at i:12709233 original size:17 final size:16
Alignment explanation
Indices: 12709195--12709235 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
12709185 TTTTTTTTGT
12709195 TTTTTCTTCTTCTTTA
1 TTTTTCTTCTTCTTTA
* *
12709211 TTTTTCTATTTTCTTTC
1 TTTTTCT-TCTTCTTTA
12709228 TTTTTCTT
1 TTTTTCTT
12709236 TCCCCTCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTCTTCTTTA
Found at i:12710223 original size:23 final size:24
Alignment explanation
Indices: 12710176--12710221 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
12710166 TTTCATTGTG
12710176 AAAAAAAATGAATGAAAAAAATTT
1 AAAAAAAATGAATGAAAAAAATTT
12710200 AAAAAAAA-GAA-GAAAAAAATTT
1 AAAAAAAATGAATGAAAAAAATTT
12710222 TAGTCTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 3 0.14
24 8 0.36
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (24 bp):
AAAAAAAATGAATGAAAAAAATTT
Found at i:12714656 original size:17 final size:18
Alignment explanation
Indices: 12714634--12714669 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
12714624 GGAATAAAAT
*
12714634 AAAAGAATAAA-AGAAAC
1 AAAAGAAGAAATAGAAAC
12714651 AAAAGAAGAAATAGAAAC
1 AAAAGAAGAAATAGAAAC
12714669 A
1 A
12714670 GAATAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAGAAGAAATAGAAAC
Found at i:12715589 original size:23 final size:22
Alignment explanation
Indices: 12715562--12715691 Score: 178
Period size: 21 Copynumber: 6.0 Consensus size: 22
12715552 GCTTTGTCGA
12715562 TCAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
12715584 CTCAGGCACTTTATGTGTCGTAT
1 -TCAGGCACTTTATGTGTCGTAT
*
12715607 T-AGGCACTTTATGTGTCATAT
1 TCAGGCACTTTATGTGTCGTAT
12715628 CTCAGGCACTTTATGTGTCGT-T
1 -TCAGGCACTTTATGTGTCGTAT
**
12715650 TCAGGCACTTCGTGTGTCGT-T
1 TCAGGCACTTTATGTGTCGTAT
*
12715671 GCAGGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
12715692 ACTGATCAGG
Statistics
Matches: 97, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
20 9 0.09
21 46 0.47
22 3 0.03
23 39 0.40
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (22 bp):
TCAGGCACTTTATGTGTCGTAT
Found at i:12715614 original size:44 final size:44
Alignment explanation
Indices: 12715556--12715691 Score: 183
Period size: 44 Copynumber: 3.2 Consensus size: 44
12715546 TTATCGGCTT
*
12715556 TGTCG-ATCAGGCACTTTATGTGTCGTATCTCAGGCACTTTATG
1 TGTCGTATTAGGCACTTTATGTGTCGTATCTCAGGCACTTTATG
*
12715599 TGTCGTATTAGGCACTTTATGTGTCATATCTCAGGCACTTTATG
1 TGTCGTATTAGGCACTTTATGTGTCGTATCTCAGGCACTTTATG
** *
12715643 TGTCGT-TTCAGGCACTTCGTGTGTCGT-T-GCAGGCAC-TTATG
1 TGTCGTATT-AGGCACTTTATGTGTCGTATCTCAGGCACTTTATG
12715684 TGTCGTAT
1 TGTCGTAT
12715692 ACTGATCAGG
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
41 11 0.13
42 8 0.10
43 8 0.10
44 57 0.68
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (44 bp):
TGTCGTATTAGGCACTTTATGTGTCGTATCTCAGGCACTTTATG
Found at i:12724168 original size:25 final size:25
Alignment explanation
Indices: 12724140--12724195 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
12724130 ATTCGAGAAT
*
12724140 GCTCATACGAGCACATA-AATGGGAA
1 GCTCATACGAGC-CATATAACGGGAA
* * *
12724165 GCTCTTTCGAGCGATATAACGGGAA
1 GCTCATACGAGCCATATAACGGGAA
12724190 GCTCAT
1 GCTCAT
12724196 TAAAGCCGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21
Consensus pattern (25 bp):
GCTCATACGAGCCATATAACGGGAA
Found at i:12724814 original size:21 final size:21
Alignment explanation
Indices: 12724789--12724831 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12724779 TTAAATTTAG
*
12724789 TTCAATTTAATAAAATTCATA
1 TTCAATTCAATAAAATTCATA
**
12724810 TTCAATTCAATCCAATTCATA
1 TTCAATTCAATAAAATTCATA
12724831 T
1 T
12724832 CTTAGGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (21 bp):
TTCAATTCAATAAAATTCATA
Found at i:12736483 original size:42 final size:42
Alignment explanation
Indices: 12736387--12736583 Score: 220
Period size: 42 Copynumber: 4.7 Consensus size: 42
12736377 CAATTCCATA
* * * *
12736387 TCCCAGATATGGTCTTACATGCTATCATATATCGATGCCAATAG
1 TCCCAGACATGGTCTTACACG-AATCACATATCGATGCCAAT-G
* * *
12736431 --CTAG-CTATGGTCTTACACGATTCCCATATCGATGCCAATG
1 TCCCAGAC-ATGGTCTTACACGAATCACATATCGATGCCAATG
* *
12736471 TCCCAGACATGGTCTTACACGAATCTCATATCAATGCCAATG
1 TCCCAGACATGGTCTTACACGAATCACATATCGATGCCAATG
* * *
12736513 TCCCAGACATGGTCTTACATGAATCACATAACGAAGCCAATG
1 TCCCAGACATGGTCTTACACGAATCACATATCGATGCCAATG
*
12736555 TCCTAGACATGGTCTTACACGTAATCACA
1 TCCCAGACATGGTCTTACACG-AATCACA
12736584 GTTCAGTATC
Statistics
Matches: 130, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.01
41 16 0.12
42 105 0.81
43 8 0.06
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAATCACATATCGATGCCAATG
Found at i:12738862 original size:24 final size:24
Alignment explanation
Indices: 12738821--12738889 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
12738811 GACAAATAAA
* **
12738821 AATAATAATATAGCATAACTTTTA-
1 AATAATAATACATAATAA-TTTTAG
*
12738845 AGTAATAATACATAATAATTTTAG
1 AATAATAATACATAATAATTTTAG
* *
12738869 AATAATAATACACAATGATTT
1 AATAATAATACATAATAATTT
12738890 CGAAAACATG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 5 0.14
24 32 0.86
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (24 bp):
AATAATAATACATAATAATTTTAG
Found at i:12740494 original size:50 final size:50
Alignment explanation
Indices: 12740394--12740500 Score: 128
Period size: 50 Copynumber: 2.1 Consensus size: 50
12740384 AAATTTTGGC
* * *
12740394 AAGTAAGATTCGCCATCGTGGCTTTAATCTTTTTAACCGCAATGTCAGGG
1 AAGTAAGATTCACCATCGTGGCTTTAATCTGTTCAACCGCAATGTCAGGG
* * *
12740444 AAGTAAGATTCACCGAT-GTGGCTTTAATCTGTTCCACTGCATTG-CTAGGG
1 AAGTAAGATTCACC-ATCGTGGCTTTAATCTGTTCAACCGCAATGTC-AGGG
12740494 AAGTAAG
1 AAGTAAG
12740501 GTCTATAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.02
50 46 0.94
51 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (50 bp):
AAGTAAGATTCACCATCGTGGCTTTAATCTGTTCAACCGCAATGTCAGGG
Found at i:12740648 original size:44 final size:45
Alignment explanation
Indices: 12740600--12741102 Score: 183
Period size: 44 Copynumber: 10.8 Consensus size: 45
12740590 CTTTATTTTA
* * *
12740600 ATCTGCTCC-ACTGTAATCTTAGAGAGATAGGATTACTAGCTTCC
1 ATCTGCTCCGACTGTAATCTCAGGGAGATAAGATTACTAGCTTCC
* * * *
12740644 ATCTGCTCCGA-TGTAACCTCAGGGAGATAAGATTTCTGGCTTCA
1 ATCTGCTCCGACTGTAATCTCAGGGAGATAAGATTACTAGCTTCC
* * * * **
12740688 ATCTGATGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTA
1 ATC---T--G--CT-C-CGACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTCC
* * *
12740742 ATCCGCTCC-ACTGTAATATCAGGGAGATAGGATTACTAGCTTCC
1 ATCTGCTCCGACTGTAATCTCAGGGAGATAAGATTACTAGCTTCC
* *
12740786 ATCTGCTCCGA-TGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATC
1 ATCTGCTCCGACTGTAATCTCAGGGAGATAAGATTACTAGCTTC---C
* * * * * * **
12740833 TGATGTGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCATTTA-TTTTA
1 --ATCTG--CT-C-CGACTGTAATC-TCAGGGAGATAAGATTA-CTAGCTTCC
* *
12740884 ATCCGCTCC-ACTGTAATCTCAGGGAGATAGGATTACTAGCTTCC
1 ATCTGCTCCGACTGTAATCTCAGGGAGATAAGATTACTAGCTTCC
* * * *
12740928 ATCTGCTCCG-CTGTAATCTCAAGGAGATAAGATTTCTGGCTTCA
1 ATCTGCTCCGACTGTAATCTCAGGGAGATAAGATTACTAGCTTCC
* * * * **
12740972 ATCTGATGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTA
1 ATC---T--G--CT-C-CGACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTCC
* * * *
12741026 ATCCGCTCC-ACTGTAATCTCAGGGAGATAGGATTACTAACTTCA
1 ATCTGCTCCGACTGTAATCTCAGGGAGATAAGATTACTAGCTTCC
* *
12741070 ATCTGCTCCG-CTGTAATCTCAGGAAGACAAGAT
1 ATCTGCTCCGACTGTAATCTCAGGGAGATAAGAT
12741103 CTGTAATTTC
Statistics
Matches: 341, Mismatches: 68, Indels: 100
0.67 0.13 0.20
Matches are distributed among these distances:
42 2 0.01
43 6 0.02
44 210 0.62
45 7 0.02
46 3 0.01
47 9 0.03
49 11 0.03
51 6 0.02
52 3 0.01
53 8 0.02
54 71 0.21
55 3 0.01
56 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (45 bp):
ATCTGCTCCGACTGTAATCTCAGGGAGATAAGATTACTAGCTTCC
Found at i:12740810 original size:142 final size:142
Alignment explanation
Indices: 12740551--12741102 Score: 946
Period size: 142 Copynumber: 3.9 Consensus size: 142
12740541 AGATAAGACT
* * *
12740551 TGATACGATCTGCTCTACTGTAACTTC--AGAGATAAGATCCTTTATTTTAATCTGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
* * *
12740614 AATCTTAGAGAGATAGGATTACTAGCTTCCATCTGCTCCGATGTAACCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGATGTAATCTCAGGGAGATAAGATTT
12740679 CTGGCTTCAATC
131 CTGGCTTCAATC
12740691 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
*
12740756 AATATCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGATGTAATCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGATGTAATCTCAGGGAGATAAGATTT
12740821 CTGGCTTCAATC
131 CTGGCTTCAATC
* *
12740833 TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
* *
12740898 AATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGATGTAATCTCAGGGAGATAAGATTT
12740963 CTGGCTTCAATC
131 CTGGCTTCAATC
12740975 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
* * * * *
12741040 AATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGAAGACAAGAT
66 AATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGATGTAATCTCAGGGAGATAAGAT
12741103 CTGTAATTTC
Statistics
Matches: 391, Mismatches: 19, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
140 25 0.06
142 366 0.94
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (142 bp):
TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
AATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGATGTAATCTCAGGGAGATAAGATTT
CTGGCTTCAATC
Found at i:12742397 original size:7 final size:7
Alignment explanation
Indices: 12742381--12742413 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
12742371 ATTTTTACTC
*
12742381 TTTCAAT
1 TTTCATT
12742388 TTTCATT
1 TTTCATT
12742395 TTTCA-T
1 TTTCATT
12742401 TTTCATT
1 TTTCATT
12742408 TTTCAT
1 TTTCAT
12742414 CTTCTCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTCATT
Found at i:12742404 original size:13 final size:13
Alignment explanation
Indices: 12742381--12742413 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12742371 ATTTTTACTC
12742381 TTTCAATTTTCATT
1 TTTC-ATTTTCATT
12742395 TTTCATTTTCATT
1 TTTCATTTTCATT
12742408 TTTCAT
1 TTTCAT
12742414 CTTCTCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTCATTTTCATT
Found at i:12747663 original size:24 final size:23
Alignment explanation
Indices: 12747622--12747690 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 23
12747612 AAATAAAAAT
*
12747622 AATAATAATATAGT-ATAACTTTT-
1 AATAATAATACA-TAATAA-TTTTG
12747645 AAGTAATAATACATAATAATTTTGG
1 AA-TAATAATACATAATAATTTT-G
* *
12747670 AATAATAATACACAATGATTT
1 AATAATAATACATAATAATTT
12747691 CGAAAACATG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 7 0.18
24 30 0.77
25 2 0.05
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.38
Consensus pattern (23 bp):
AATAATAATACATAATAATTTTG
Found at i:12747793 original size:3 final size:3
Alignment explanation
Indices: 12747785--12747815 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12747775 ATAGTACATA
12747785 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12747816 GTAAAAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12767107 original size:24 final size:24
Alignment explanation
Indices: 12767080--12767129 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
12767070 TGTTATAGGT
* *
12767080 CATGTGCACCACACGGTCGTATGC
1 CATGTGCACCACACAGTCATATGC
12767104 CATGTGCACCACACAGTCATATGC
1 CATGTGCACCACACAGTCATATGC
12767128 CA
1 CA
12767130 AGTCGTGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (24 bp):
CATGTGCACCACACAGTCATATGC
Found at i:12767315 original size:29 final size:30
Alignment explanation
Indices: 12767269--12767340 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
12767259 CTACACGGGC
* *
12767269 AGACGACACGAGCATGTGTCAGGCCATGT-G
1 AGAC-ACACGGGCATGTGCCAGGCCATGTGG
* *
12767299 AGACACACGGGCGTGTGCCAGGCTATGTGG
1 AGACACACGGGCATGTGCCAGGCCATGTGG
*
12767329 AGCCACACGGGC
1 AGACACACGGGC
12767341 TAGCCATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 20 0.56
30 16 0.44
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (30 bp):
AGACACACGGGCATGTGCCAGGCCATGTGG
Found at i:12768239 original size:18 final size:18
Alignment explanation
Indices: 12768216--12768252 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12768206 AATCTACTTT
*
12768216 TTATTTTAAAATGAAAAA
1 TTATTTCAAAATGAAAAA
12768234 TTATTTCAAAATGAAAAA
1 TTATTTCAAAATGAAAAA
12768252 T
1 T
12768253 GGGAGTCGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
TTATTTCAAAATGAAAAA
Found at i:12770246 original size:80 final size:80
Alignment explanation
Indices: 12770094--12770286 Score: 221
Period size: 80 Copynumber: 2.4 Consensus size: 80
12770084 CGGTTTTAGT
* * *
12770094 AACTCACACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTT
1 AACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTT
*
12770159 AACCCGGATTTA-AC
66 AACCCGGATATATAC
** *
12770173 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATC
1 AACTCGCAC-AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-C
** *
12770237 TTAGTCCGGATATATTC
64 TTAACCCGGATATATAC
* * *
12770254 -ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AAC-TCGCACAATGCCTTCGGGACTTAACCCGGA
12770287 CAGCATTCAA
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
79 11 0.11
80 80 0.82
81 6 0.06
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (80 bp):
AACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTT
AACCCGGATATATAC
Found at i:12770247 original size:40 final size:40
Alignment explanation
Indices: 12770064--12770233 Score: 234
Period size: 40 Copynumber: 4.3 Consensus size: 40
12770054 TCCTCGTTCA
* * * ** *
12770064 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
12770103 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
12770143 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
12770183 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
12770223 AAGGCCTTCGG
1 AATGCCTTCGG
12770234 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 33 0.28
40 86 0.72
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:12770286 original size:120 final size:119
Alignment explanation
Indices: 12770064--12770286 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 119
12770054 TCCTCGTTCA
* * * *
12770064 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGATA
* *
12770129 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
66 TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * **
12770183 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CTTAACCCGGA
* *
12770247 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
12770287 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
119 37 0.43
120 44 0.51
121 6 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGATA
TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:12770295 original size:41 final size:41
Alignment explanation
Indices: 12770218--12770295 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
12770208 TTAGTATCTC
* * *
12770218 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
12770259 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
12770296 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:12778197 original size:120 final size:119
Alignment explanation
Indices: 12777975--12778237 Score: 316
Period size: 120 Copynumber: 2.2 Consensus size: 119
12777965 TCCTCGTTCA
* * **
12777975 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
* * * *
12778040 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCAC
66 TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATAC-ACTTAGCAC
* *
12778093 GAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACAC-AATGCCTTCGGGACTTAACCCGGA
** * ** *
12778158 TTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
64 TTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATATACACTTAGCAC
*
12778214 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
12778238 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 36 0.30
120 80 0.66
121 6 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATACACTTAGCAC
Found at i:12778198 original size:40 final size:40
Alignment explanation
Indices: 12777975--12778184 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
12777965 TCCTCGTTCA
* * * ** *
12777975 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
12778014 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
12778054 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
12778094 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
12778134 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
12778174 AAGGCCTTCGG
1 AATGCCTTCGG
12778185 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.21
40 126 0.79
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:12778221 original size:80 final size:80
Alignment explanation
Indices: 12777978--12778237 Score: 267
Period size: 80 Copynumber: 3.3 Consensus size: 80
12777968 TCGTTCAAAT
* * * ** * * *
12777978 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
12778042 ACAACTCGCACGAAT
66 ACAACTAGCACGAAA
* * *
12778057 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
12778122 ACAACTCGCACGAAT
66 ACAACTAGCACGAAA
** * **
12778137 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
*
12778201 ATTC-ACTTAGCAC-AAA
65 A-ACAAC-TAGCACGAAA
*
12778217 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
12778238 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
79 33 0.21
80 120 0.75
81 6 0.04
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ACAACTAGCACGAAA
Found at i:12778246 original size:41 final size:41
Alignment explanation
Indices: 12778169--12778246 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
12778159 TTAGTATCTC
* * *
12778169 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
12778210 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
12778247 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:12781241 original size:43 final size:43
Alignment explanation
Indices: 12781109--12781247 Score: 113
Period size: 43 Copynumber: 3.2 Consensus size: 43
12781099 GTGATTACAC
* * * * * *
12781109 GTAAGACCATGTCTGGGTCATTGGCTTTGTATAGA--GATAACAC
1 GTAAGACCATGTCTGGGACAGTGGCATCG-ATA-ATTGATAGCAT
** * ** *
12781152 GTAAGACCATGTCTGGGACTTTGGCATCGTTAATTGATTTCGT
1 GTAAGACCATGTCTGGGACAGTGGCATCGATAATTGATAGCAT
*
12781195 GTAAGACCCTGTCTGGGACAGTGGCATCGAT-ATATGATAGCAT
1 GTAAGACCATGTCTGGGACAGTGGCATCGATAAT-TGATAGCAT
12781238 GTAAGACCAT
1 GTAAGACCAT
12781248 ATATGGGATA
Statistics
Matches: 76, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
41 1 0.01
42 4 0.05
43 71 0.93
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (43 bp):
GTAAGACCATGTCTGGGACAGTGGCATCGATAATTGATAGCAT
Found at i:12794543 original size:5 final size:5
Alignment explanation
Indices: 12794533--12794561 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12794523 AGAAAGATAA
12794533 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
12794562 ACACAAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:12803672 original size:27 final size:27
Alignment explanation
Indices: 12803642--12803701 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
12803632 TTAGTTTTTG
12803642 TTATATATATACATACATATATTTGAT
1 TTATATATATACATACATATATTTGAT
* * ** *
12803669 TTATACATGTACATATTTATATTTTAT
1 TTATATATATACATACATATATTTGAT
*
12803696 ATATAT
1 TTATAT
12803702 TTCTATAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (27 bp):
TTATATATATACATACATATATTTGAT
Found at i:12803713 original size:19 final size:19
Alignment explanation
Indices: 12803678--12803727 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
12803668 TTTATACATG
* *
12803678 TACATATTTATATTTTATA
1 TACATATCTATAATTTATA
* *
12803697 TATATTTCTATAATTTATA
1 TACATATCTATAATTTATA
12803716 TACATATCTATA
1 TACATATCTATA
12803728 TATATCTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
TACATATCTATAATTTATA
Found at i:12805851 original size:24 final size:25
Alignment explanation
Indices: 12805803--12805852 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
12805793 CGTCTCTTTT
* * *
12805803 TTGCATTCATCTGCATTACATTTCA
1 TTGCATTCATATGCATTAAACTTCA
12805828 TTGCA-TCATATGCATTAAACTTCA
1 TTGCATTCATATGCATTAAACTTCA
12805852 T
1 T
12805853 AAGAAGACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (25 bp):
TTGCATTCATATGCATTAAACTTCA
Found at i:12808943 original size:7 final size:7
Alignment explanation
Indices: 12808918--12808971 Score: 58
Period size: 7 Copynumber: 7.7 Consensus size: 7
12808908 AAGAATGTTC
*
12808918 AAAAAAC
1 AAAAAAG
*
12808925 AAACAAAA
1 AAA-AAAG
12808933 AAAAAAG
1 AAAAAAG
12808940 AAAAAAG
1 AAAAAAG
12808947 AAAAAAG
1 AAAAAAG
12808954 --AAAAG
1 AAAAAAG
12808959 AAAAGAAG
1 AAAA-AAG
12808967 AAAAA
1 AAAAA
12808972 TAAAGGAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 5 0.12
7 23 0.56
8 13 0.32
ACGTcount: A:0.85, C:0.04, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:12808950 original size:14 final size:14
Alignment explanation
Indices: 12808918--12808971 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
12808908 AAGAATGTTC
* *
12808918 AAAAAACAAACAAAA
1 AAAAAAGAAA-AAAG
12808933 AAAAAAGAAAAAAG
1 AAAAAAGAAAAAAG
12808947 AAAAAAG--AAAAG
1 AAAAAAGAAAAAAG
12808959 AAAAGAAGAAAAA
1 AAAA-AAGAAAAA
12808972 TAAAGGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 9 0.26
13 3 0.09
14 10 0.29
15 12 0.35
ACGTcount: A:0.85, C:0.04, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:12808957 original size:19 final size:19
Alignment explanation
Indices: 12808929--12808971 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
12808919 AAAAACAAAC
12808929 AAAAAAAAAAGAAAA-AAG
1 AAAAAAAAAAGAAAAGAAG
12808947 AAAAAAGAAAAGAAAAGAAG
1 AAAAAA-AAAAGAAAAGAAG
12808967 AAAAA
1 AAAAA
12808972 TAAAGGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.26
19 9 0.39
20 8 0.35
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAGAAG
Found at i:12808976 original size:13 final size:12
Alignment explanation
Indices: 12808931--12808976 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
12808921 AAACAAACAA
12808931 AAAAAAAAGAA-
1 AAAAAAAAGAAG
12808942 AAAAGAAAA-AAG
1 AAAA-AAAAGAAG
12808954 AAAAGAAAAGAAG
1 AAAA-AAAAGAAG
12808967 AAAAATAAAG
1 AAAAA-AAAG
12808977 GAGAGGCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 6 0.19
12 14 0.45
13 11 0.35
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:12810090 original size:49 final size:46
Alignment explanation
Indices: 12809985--12810390 Score: 168
Period size: 45 Copynumber: 8.8 Consensus size: 46
12809975 CTAGTCTGAC
* * *
12809985 CTCCTTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAATCTTAT
1 CTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATAAATCAATCTTAT
* * **
12810031 CTCCCTGAAGTTGCAATGGAGCAGATTGAAGATAGGTTACAAATCTTAT
1 CTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATA-AAT-C-AATCTTAT
* *
12810080 CTCCTTGAAGTTGCAGTGGAGTAGATGGAAGCCATAAA-C---CTTAT
1 CTCCTTGAAGTTGCAGTGGAGCAGATTGAAG--ATAAATCAATCTTAT
* * * * * *
12810124 CCCCCTGAAGTTGCAATGGGGCAGGTTCAA-AT-AA-CAAGTCTTAT
1 CTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATAAATCAA-TCTTAT
* * * * *
12810168 CTCCCTGAAGTTGTAGTGGAGCAGACTGAACAT--AGCGAATCTTAT
1 CTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATAAATC-AATCTTAT
* * * * * * *
12810213 TTCCCTAAAGTTGCAATGGAACAGATTAAAGCTGTAAATTACAGATCTTAT
1 CTCCTTGAAGTTGCAGTGGAGCAGATTGAAG--ATAAA-T-CA-ATCTTAT
*
12810264 CT-CTCTGAAGTTGCAGT--AG-AG--T--AGATCACATCAAATCTTAT
1 CTCCT-TGAAGTTGCAGTGGAGCAGATTGAAGAT-AAATC-AATCTTAT
* * * *
12810305 CTCCCTGAAATTGCAGTGGAGCAGACTGAATAT-AA-CAAATCTTAT
1 CTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATAAATC-AATCTTAT
* * * * *
12810350 C-ACTCTGAATTTGCAGTAGAACAGACTGAAGCTATAAATCA
1 CTCCT-TGAAGTTGCAGTGGAGCAGATTGAAG--ATAAATCA
12810391 CAAACATTAT
Statistics
Matches: 270, Mismatches: 55, Indels: 68
0.69 0.14 0.17
Matches are distributed among these distances:
40 3 0.01
41 23 0.09
42 4 0.01
43 4 0.01
44 61 0.23
45 65 0.24
46 34 0.13
47 4 0.01
48 10 0.04
49 38 0.14
50 2 0.01
51 22 0.08
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (46 bp):
CTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATAAATCAATCTTAT
Found at i:12810350 original size:182 final size:180
Alignment explanation
Indices: 12810023--12810379 Score: 405
Period size: 182 Copynumber: 2.0 Consensus size: 180
12810013 AAAATAAATC
* * * **
12810023 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGATAGGTTACAAATCTTATCTCCTTGA
1 AATCTTATCTCCCTAAAGTTGCAATGGAACAGATTAAAGATAAATTACAAATCTTATCTCCTTGA
* * * **
12810088 AGTTGCAGTGGAGTAGATGGAAGCCATAAACCTTATCCCCCTGAAGTTGCAATGGGGCAGGTTCA
66 AGTTGCAGTAGAGTAGAT-GAA-CCATAAACCTTATCCCCCTGAAATTGCAATGGAGCAGACTCA
* * * * *
12810153 AATAACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAACATAGCG
129 AATAACAAATCTTATCACCCTGAAGTTGCAGTAGAACAGACTGAACATAGCG
* * *
12810205 AATCTTATTTCCCTAAAGTTGCAATGGAACAGATTAAAGCTGTAAATTACAGATCTTATCT-CTC
1 AATCTTATCTCCCTAAAGTTGCAATGGAACAGATTAAAG--ATAAATTACAAATCTTATCTCCT-
* * * *
12810269 TGAAGTTGCAGTAGAGTAGAT-CA-CATCAAATCTTATCTCCCTGAAATTGCAGTGGAGCAGACT
63 TGAAGTTGCAGTAGAGTAGATGAACCAT-AAACCTTATCCCCCTGAAATTGCAATGGAGCAGACT
* * *
12810332 GAATATAACAAATCTTATCACTCTGAATTTGCAGTAGAACAGACTGAA
127 CAA-ATAACAAATCTTATCACCCTGAAGTTGCAGTAGAACAGACTGAA
12810380 GCTATAAATC
Statistics
Matches: 145, Mismatches: 25, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
180 3 0.02
181 31 0.21
182 73 0.50
183 2 0.01
184 36 0.25
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (180 bp):
AATCTTATCTCCCTAAAGTTGCAATGGAACAGATTAAAGATAAATTACAAATCTTATCTCCTTGA
AGTTGCAGTAGAGTAGATGAACCATAAACCTTATCCCCCTGAAATTGCAATGGAGCAGACTCAAA
TAACAAATCTTATCACCCTGAAGTTGCAGTAGAACAGACTGAACATAGCG
Found at i:12810372 original size:137 final size:137
Alignment explanation
Indices: 12810162--12810418 Score: 327
Period size: 137 Copynumber: 1.9 Consensus size: 137
12810152 AAATAACAAG
* * * * **
12810162 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAACATAGCGAATCTTATTTCCCTAAAGTTGC
1 TCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAACATAACAAATCTTATCACCCTAAAGTTGC
* * * * * *
12810227 AATGGAACAGATTAAAGCTGTAAATTACAGATC-TTATCTCTCTGAAGTTGCAGTAGAGTAGATC
66 AATAGAACAGACTAAAGCTATAAATCACA-AACATTATCTCTCTAAAGTTGCAGTAGAGTAGATC
12810291 ACATCAAA
130 ACATCAAA
* * * *
12810299 TCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAATATAACAAATCTTATCACTCTGAATTTGC
1 TCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAACATAACAAATCTTATCACCCTAAAGTTGC
* * *
12810364 AGTAGAACAGACTGAAGCTATAAATCACAAACATTATCTCTCTAAAGTTGTAGTA
66 AATAGAACAGACTAAAGCTATAAATCACAAACATTATCTCTCTAAAGTTGCAGTA
12810419 AAATAGGCTG
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
136 2 0.02
137 98 0.98
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (137 bp):
TCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAACATAACAAATCTTATCACCCTAAAGTTGC
AATAGAACAGACTAAAGCTATAAATCACAAACATTATCTCTCTAAAGTTGCAGTAGAGTAGATCA
CATCAAA
Found at i:12812358 original size:19 final size:19
Alignment explanation
Indices: 12812308--12812360 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
12812298 TGATTTATAC
* *
12812308 ATGTACATATTTATATTTT
1 ATGTACATATCTATAATTT
* * *
12812327 ATATATATTTCTATAATTT
1 ATGTACATATCTATAATTT
12812346 ATGTACATATCTATA
1 ATGTACATATCTATA
12812361 TATATCTATA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.53
Consensus pattern (19 bp):
ATGTACATATCTATAATTT
Found at i:12815919 original size:7 final size:7
Alignment explanation
Indices: 12815907--12815933 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12815897 ATTAGTTCCC
12815907 AATATTT
1 AATATTT
12815914 AATATTT
1 AATATTT
12815921 AATATTT
1 AATATTT
12815928 AATATT
1 AATATT
12815934 GTTATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATATTT
Found at i:12816697 original size:18 final size:17
Alignment explanation
Indices: 12816671--12816704 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12816661 CCAAAACGCG
12816671 AAACATTTCCTTATTTTA
1 AAACATTTCCTT-TTTTA
*
12816689 AAACTTTTCCTTTTTT
1 AAACATTTCCTTTTTT
12816705 GAATAATAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (17 bp):
AAACATTTCCTTTTTTA
Found at i:12821149 original size:66 final size:69
Alignment explanation
Indices: 12821055--12821181 Score: 181
Period size: 66 Copynumber: 1.9 Consensus size: 69
12821045 TGTATATACA
* * *
12821055 ATATAATTTATTAAAAATTAAAATTTAGATTATAAGTACATAT-T-TG-AAAATATTTAAATGTA
1 ATATAATTTATTAAAAACTAAAATTTAGACTATAAATACATATATATGAAAAATATTTAAATGTA
12821117 TAAT
66 TAAT
*
12821121 ATATAATTTATTAAGAAACTAAAA-TTAGACTATAAATATATATATATGAAAAATATTTAAA
1 ATATAATTTATTAA-AAACTAAAATTTAGACTATAAATACATATATATGAAAAATATTTAAA
12821182 AACATAGTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
66 30 0.57
67 9 0.17
68 2 0.04
69 12 0.23
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (69 bp):
ATATAATTTATTAAAAACTAAAATTTAGACTATAAATACATATATATGAAAAATATTTAAATGTA
TAAT
Found at i:12821417 original size:15 final size:15
Alignment explanation
Indices: 12821397--12821441 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
12821387 CCAGCACAAG
*
12821397 ACAGAGCAGAACATA
1 ACAGAGCAGAACAGA
*
12821412 ACAGAGCAGAATAGA
1 ACAGAGCAGAACAGA
*
12821427 ACAGAGCATAACAGA
1 ACAGAGCAGAACAGA
12821442 GTAGAACTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.53, C:0.18, G:0.22, T:0.07
Consensus pattern (15 bp):
ACAGAGCAGAACAGA
Found at i:12821441 original size:20 final size:20
Alignment explanation
Indices: 12821418--12821475 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
12821408 CATAACAGAG
*
12821418 CAGAATAGAACAGAGCATAA
1 CAGAGTAGAACAGAGCATAA
*
12821438 CAGAGTAGAACTA-AACATAA
1 CAGAGTAGAAC-AGAGCATAA
*
12821458 AAGAGTAGAACAGAGCAT
1 CAGAGTAGAACAGAGCAT
12821476 GTATGTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.53, C:0.14, G:0.21, T:0.12
Consensus pattern (20 bp):
CAGAGTAGAACAGAGCATAA
Found at i:12821442 original size:40 final size:40
Alignment explanation
Indices: 12821397--12821475 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
12821387 CCAGCACAAG
**
12821397 ACAGAGCAGAAC-ATAACAGAGCAGAATAGAACAGAGCATA
1 ACAGAGCAGAACTA-AACAGAAAAGAATAGAACAGAGCATA
* * *
12821437 ACAGAGTAGAACTAAACATAAAAGAGTAGAACAGAGCAT
1 ACAGAGCAGAACTAAACAGAAAAGAATAGAACAGAGCAT
12821476 GTATGTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.53, C:0.15, G:0.22, T:0.10
Consensus pattern (40 bp):
ACAGAGCAGAACTAAACAGAAAAGAATAGAACAGAGCATA
Found at i:12831326 original size:6 final size:7
Alignment explanation
Indices: 12831309--12831333 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12831299 CAGAAGCAAA
12831309 AAAAATC
1 AAAAATC
12831316 AAAAATC
1 AAAAATC
12831323 AAAAATC
1 AAAAATC
12831330 AAAA
1 AAAA
12831334 CAACAGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATC
Found at i:12831621 original size:11 final size:11
Alignment explanation
Indices: 12831607--12831654 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
12831597 AAGAGAGGAG
12831607 AAAGAAAGAAA
1 AAAGAAAGAAA
12831618 AAAGAAAGAAA
1 AAAGAAAGAAA
*
12831629 GGAGAGAAAGAAA
1 --AAAGAAAGAAA
12831642 AGAAGAAA-AAA
1 A-AAGAAAGAAA
12831653 AA
1 AA
12831655 GGGACAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 1 0.03
11 16 0.50
12 5 0.16
13 10 0.31
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:12831623 original size:26 final size:25
Alignment explanation
Indices: 12831594--12831675 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 25
12831584 GAAATAGAAG
*
12831594 AGAAAGAGAGGAGAAAGAAAGAAAA-A
1 AGAAAGAAAGGAG--AGAAAGAAAAGA
12831620 AGAAAGAAAGGAGAGAAAGAAAAGA
1 AGAAAGAAAGGAGAGAAAGAAAAGA
* *
12831645 AGAAAAAAAAGG-GACAAA-AAAAGA
1 AG-AAAGAAAGGAGAGAAAGAAAAGA
12831669 GAGAAAG
1 -AGAAAG
12831676 CTTTTCGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 19 0.39
25 10 0.20
26 20 0.41
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (25 bp):
AGAAAGAAAGGAGAGAAAGAAAAGA
Found at i:12831822 original size:7 final size:7
Alignment explanation
Indices: 12831807--12831842 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
12831797 TAGGGTTTTC
*
12831807 GAAAGAA
1 GAAAAAA
12831814 GAAAAAA
1 GAAAAAA
12831821 GAAAAAA
1 GAAAAAA
12831828 GAAAAAGA
1 GAAAAA-A
12831836 GAAAAAA
1 GAAAAAA
12831843 ATTTAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:12832178 original size:12 final size:12
Alignment explanation
Indices: 12832161--12832187 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12832151 AAGGGAAGGG
12832161 AAAAAAGAGAAA
1 AAAAAAGAGAAA
12832173 AAAAAAGAGAAA
1 AAAAAAGAGAAA
12832185 AAA
1 AAA
12832188 GAGGAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:12832186 original size:21 final size:21
Alignment explanation
Indices: 12832160--12832208 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
12832150 GAAGGGAAGG
12832160 GAAAAAAGA-GAAAAAAAAAGA
1 GAAAAAAGAGGAAAAAAAAA-A
* *
12832181 GAAAAAAGAGGAAAGAAGAAA
1 GAAAAAAGAGGAAAAAAAAAA
12832202 GAAAAAA
1 GAAAAAA
12832209 CCCAGTCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
GAAAAAAGAGGAAAAAAAAAA
Found at i:12832625 original size:17 final size:17
Alignment explanation
Indices: 12832603--12832658 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
12832593 GTAATTTACC
12832603 AAAATTTTCGTGTTTCA
1 AAAATTTTCGTGTTTCA
*
12832620 AAAATTTTCATGTTTTCAA
1 AAAATTTTCGTG-TTTC-A
* *
12832639 AAAATTCTCGTGTTTTA
1 AAAATTTTCGTGTTTCA
12832656 AAA
1 AAA
12832659 TAAAATGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 15 0.45
18 7 0.21
19 11 0.33
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (17 bp):
AAAATTTTCGTGTTTCA
Found at i:12832643 original size:19 final size:19
Alignment explanation
Indices: 12832603--12832658 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
12832593 GTAATTTACC
12832603 AAAATTTTCGTG-TTTC-A
1 AAAATTTTCGTGTTTTCAA
*
12832620 AAAATTTTCATGTTTTCAA
1 AAAATTTTCGTGTTTTCAA
*
12832639 AAAATTCTCGTGTTTT-AA
1 AAAATTTTCGTGTTTTCAA
12832657 AA
1 AA
12832659 TAAAATGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.32
18 8 0.24
19 15 0.44
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (19 bp):
AAAATTTTCGTGTTTTCAA
Done.